Sungwook Woo and Paul W.K. Rothemund - Programmable Molecular Recognition Based On The Geometry of DNA Nanostructures

NATURE CHEMISTRY | www.nature.
com/naturechemistry 1
SUPPLEMENTARY INFORMATION
DOI: 10.1038/NCHEM.1070

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Sungwook Woo
1*
and Paul W. K. Rothemund
1,2,3*

Departments of
1
Bioengineering,
2
Computer Science, and
3
Computation & Neural Systems,
California Institute of Technology, 1200 E. California Blvd. Pasadena, CA 91125, USA
* Correspondence: woo@dna.caltech.edu and pwkr@dna.caltech.edu


Sungwook Woo
1*
1,2,3*

Departments of
1
Bioengineering,
2
3


Sungwook Woo
1*
1,2,3*

Departments of
1
Bioengineering,
2
3


Sungwook Woo
1*
1,2,3*

Departments of
1
Bioengineering,
2
3

!2011!Macmillan Publishers Limited. All rights reserved.!
NATURE CHEMISTRY | www.nature.com/naturechemistry 2
DOI: 10.1038/NCHEM.1070
Table of Contents

Supplementary Note S1: Materials and methods ............................................................................ 3
S1.1. Sample preparation ........................................................................................................... 3
S1.2. Atomic force microscopy .................................................................................................. 3
Supplementary Note S2: Design details .......................................................................................... 4
S2.1. Design of binary codes for stacking bonds ....................................................................... 4
S2.1.1. Design criteria for binary sequences ........................................................................... 4
S2.1.2. Example binary sequences .......................................................................................... 5
S2.1.3. Why use 7 active patches with a mismatch constraint of 4? ....................................... 6
S2.1.4. Error rates for binary sequences investigated in this study ......................................... 8
S2.2. Design of shape codes for stacking bonds. ....................................................................... 9
S2.2.1. Design criteria for shape sequences ............................................................................ 9
S2.2.2. Full list of candidate shape sequences for the (4,3,2) system ................................... 10
S2.2.3. Orthogonality graph for the (4,3,2) candidate shape sequences ................................ 11
S2.2.4. Size of shape sequence spaces with other parameters ............................................... 12
S2.3. Finding codes: searching for large orthogonal sets of sequences. .................................. 13
S2.4. Design of the origami structures ..................................................................................... 15
S2.5. Edge structure ................................................................................................................. 16
S2.6. Quencher strands ............................................................................................................. 18
S2.7. Warnings ......................................................................................................................... 19
S2.7.1. Length and width of a patch in shape design ............................................................ 19
S2.7.2. Potential interference from the remainder staples ..................................................... 21
S2.7.3. Possible collisions between edge staples .................................................................. 22
Supplementary Note S3: Thermodynamic measurements ............................................................ 23
S3.1. First energy model: assuming loop-loop interactions are neutral ................................... 25
S3.2. Second energy model: fitting with non-zero loop-loop interactions ............................... 28
Supplementary Note S4: Additional AFM Data ........................................................................... 30
S4.1. Stacking of rectangles ..................................................................................................... 30
S4.2. 5-origami chains with orthogonal binary-coded bonds ................................................... 32
S4.3. Origami dimers and chains with orthogonal shape-coded bonds ................................... 33
References ........................................................................................................................................ 34
Supplementary Note S5: Sequence lists and diagrams...35
DOI: 10.1038/NCHEM.1070
Supplementary Note S1: Materials and metbods
S1.1. Sample preparation
Individual origami structures that were not destined to be mixed with other structures were prepared
by a protocol similar to that presented in earlier work. Single-stranded M13mp18 DNA (scaffold strand)
was purchased from New England Biolabs (Catalog # N4040S) and staple strands were obtained
unpurified from Integrated DNA Technologies in water at 150 M each. Scaffold strand and staple
strands for each design were mixed together to target concentrations of ~2 nM and ~75 nM, respectively,
in 1 Tris-Acetate-EDTA (TAE) buffer with 12.5 mM magnesium acetate (TAE/Mg
2+
). The mixtures
were kept at 90C for 5 min and annealed from 90C to 20C with a constant rate of -1C/min.
To create origami chains with multiple bonds based on binary sequences (as shown in Fig. 2c of the
main text), constituent origami were first annealed separately from 90C to 20C. Next, corresponding
quencher strand mixtures for each origami (those that matched the edge staples used, see Section S2.6)
were added (at 10 the edge staple concentration) to each origami mixture. Each of the solutions was kept
at room temperature for 1 hr to ensure complete hybridization, and then they were mixed together, heated
to 50C, kept for 12 hr at 50C, and then cooled to 20C at a rate of -5C/hr.
For the origami chain (A-B-C-D) and dimers (A-B, B-C, C-D) with shape complementarity (as
shown in Fig. 3c,d), each origami mixture (scaffold + corresponding staples) was annealed separately
from 90C to 50C (with a rate of -1C/min), mixed together at 50C, and kept at 50C for 12 hr, then
cooled to 20C at a rate of -5C/hr. The mixing operation was performed inside a temperature-controlled
chamber (Coy Laboratory Products Inc.), to maintain the temperature at 50C while the samples were
transferred between test tubes.

S1.2. Atomic force microscopy
Samples for AFM imaging were prepared by depositing 5 l of the origami solution with 20 l of
TAE/Mg
2+
buffer onto freshly-cleaved mica (Ted Pella). In most cases, clean buffer solution was
deposited first and the origami solution was added on top of it. (For concentrated samples we felt this
procedure minimized spatial variation in the density of origami on the mica.) In cases wherein we were
concerned that this procedure might distort data (i.e. for thermodynamic data, section S3) we pre-diluted
the origami solution by 5-fold, and then deposit 25 l onto mica. AFM images were taken under
TAE/Mg
2+
buffer in Tapping Mode with a Nanoscope III Multimode AFM (Veeco Metrology Group,
now Bruker AXS). Typically, we used silicon nitride cantilevers with 2 nm radius silicon tips as AFM
probes (the short, fat A cantilever on SNL probes from Veeco, now Brucker AFM Probes).

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Supplementary Note S2: Design details
S2.1. Design of binary codes for stacking bonds
S2.1.1. exlgn crlterlu for blnury xequencex

The basic design criteria for binary sequences can be understood by analogy to criteria used for DNA
sequence design (Fig. S1a). Consider a DNA strand with the sequence 5-TAGCAGCAG-3; it is fully
complementary to (and hence would bind most strongly with) a strand bearing the sequence 5-
CTGCTGCTA-3 (Fig. S1a-left). However, the two strands also have a partially complementary
subsequence of length five, and could bind (albeit more weakly) via this partial interaction (Fig. S1a-
right). In general, when DNA sequences are designed, they are designed to minimize such undesired
interactionswith themselves, with their complements, and with any other strands that will be present in
solution at the same time. Simple algorithms for designing sequences use discrete criteria based on the
maximal number of base pairs that occur in any partially complementary species. For example, an
algorithm might be designed to find sequences that minimize this number. Partial bonds having the same
number of base pairs but different sequences are not equal in strength, and so more sophisticated
algorithms minimize the sequence-dependent binding energy of undesired interactions. Still more
sophisticated algorithms use such binding energies to maximize the probability that the desired
interactions form by considering the thermodynamic partition function.
Here, because we do not yet have a complete energy model for stacking bonds, we take a simple
approach based on counting (and minimizing) the number of active patches involved in the strongest
partial bonds. For example, consider an origami with the binary sequence 111111100000; with its
complementary partner it would form a stacking bond of strength 7 (Fig. S1b-left), but when rotated it can
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Figure S1. Issues in binary sequence design. (a) DNA sequence design must deal with the problem of
undesired partial complementarity. A desired bond is at left, an undesired partial bond at right. Binary sequence
design is analogous, as explained in the text. (b) A simple binary sequence that allows a full-strength, self-
complementary incorrect bond; this sequence, while nonpalindromic, is not uniquely-orienting. (c) A binary
sequence whose strongest partial bonds are only of strength 4; an example is shown at right.
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DOI: 10.1038/NCHEM.1070
also form a self-complementary, undesired interaction of strength 7 (Fig. S1b-right). In contrast, the
sequence 100100110111 binds its complement (Fig. S1c, left) with a strength-7 bond, but the strongest
possible partial bond that it can form has only strength 4 (Fig. S1c, right).
As for DNA, we are interested in minimizing such undesired interactions. For binary sequences of
length l and number of active patches p, we wrote a program that enumerates sequences which have a
maximum strength i for incorrect partial bonds (the mismatch constraint) with themselves and with their
complements. Conceptually, the program compares each sequence to itself (and its complementary
sequence) at all possible alignments, by sliding the sequences relative to each other; the number of
matches for each alignment is simply counted and the sequence is discarded if the number of matches
exceeds i for any alignment.
The set of sequences enumerated for a given (p,i) constituted a candidate set from which we later
attempted to construct maximal orthogonal subsets for use in making origami chains (see Section S2.3).
It turns out that for p=7, and l=12 or l=16 (the length of the sequence applicable to the regular and tall
rectangles used in our study, respectively), the candidate sets are empty for mismatch constraints i<3.
That is, however we design a binary sequence with 7 active patches (for l=12 or l=16), such a sequence
will have an undesired partial bond (with itself or its complement) involving at least 4 active patches.
More generally, for all p there exists at least i for which candidate sequences can be found. As i is made
larger, the size of the candidate set increases; this holds true for the size of the maximum orthogonal
subsets as well. Thus there is a tradeoff between the mismatch constraint i (our heuristic surrogate for the
experimental specificity) and the number of distinct sequences available as bond types. This can be seen
in Table S1 of section 2.1.3. Note that the minimum possible i is 2, since any pair of active patches in a
binary sequence belongs to a partially self-complementary subsequence with at least two active patches.
S2.1.2. Fxumple blnury xequencex
For the 12-patch system with 7 active patches, a total of 98 different binary sequences were found to
satisfy the mismatch constraint i=4; for the 16-patch system with (p,i) = (7,4), a total of 4614 sequences
were obtained. We give some examples from each candidate set below. Full candidate sets are available
upon request (woo@dna.caltech.edu); alternatively, one can generate the sets easily using the program
code (attached as a separate Supplementary file).

12-patch system (10 examples shown,
out of a total of 98):
0 1 0 0 1 0 1 1 0 1 1 1
0 1 0 0 1 1 0 0 1 1 1 1
0 1 0 1 0 1 0 0 1 1 1 1
1 1 0 0 0 1 0 1 1 0 1 1
1 1 0 0 0 1 1 1 1 0 1 0
1 1 0 0 1 0 0 0 1 1 1 1
1 1 0 0 0 0 1 1 1 1 0 1
1 1 0 0 0 1 1 0 1 1 0 1
1 1 0 0 1 0 0 0 1 1 1 1
1 1 0 0 1 0 1 1 0 1 0 1

16-patch system (10 examples shown,
out of a total of 4614):
0 0 0 0 1 0 0 0 1 1 1 0 1 1 0 1
0 0 0 0 1 0 0 1 0 0 1 0 1 1 1 1
0 0 0 0 1 0 0 1 0 1 0 0 1 1 1 1
0 0 0 0 1 0 0 1 0 1 1 0 0 1 1 1
0 0 0 0 1 0 0 1 0 1 1 0 1 1 1 0
1 0 0 1 1 0 0 0 1 1 0 1 0 0 0 1
1 0 0 1 1 0 0 0 1 1 0 1 0 1 0 0
1 0 0 1 1 0 0 1 0 0 0 0 0 1 1 1
1 0 0 1 1 0 0 1 0 0 0 0 1 1 0 1
1 0 0 1 1 0 0 1 0 0 0 0 1 1 1 0
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S2.1.S. Why uxe 7 uctlve putchex wlth u mlxmutch conxtrulnt of 4?
Our goal was to create the largest binary code that we could, with the largest number of distinct bond
types, subject to the constraint that the bonds would have high specificity (that is, the rate of incorrect
partial bond formation would be low.) We wrote a program to enumerate candidate sets for two different
sequence lengths, a variety of different numbers of active patches, and mismatch constraints. We further
used randomly seeded greedy search (see Section 2.3) to find the largest orthogonal subsets that we could
for each candidate set. Table S1 summarizes our results. We found that choosing the parameters (p, i) to
be (7,4), (8,5), or (9,6) with l=16 yielded orthogonal subsets with more than ten sequences, while still
maintaining a reasonably large energetic difference between full-strength correct bonds and partial
incorrect bonds.

1ota| # of ava||ab|e patches = 12
(regu|ar rectang|e)
1ota| # of ava||ab|e patches = 16
(ta|| rectang|e)
# of act|ve patches, # of act|ve patches,
S 6 7 8 9 S 6 7 8 9 10
# patches |n
part|a| bonds
2 4 (1) 320 (3) 0
3 214 (2) 0 0 1866 (27) 236 (6) 0 0
4 420 (13) 98 (2) 0 6320 (68) 4614 (12) 462 (2) 0
S 384 8 (1) 0 8322 2730 (13) 36 (2) 0
6 328 14 (1) 6400 3870 (13) 496 (3)

If one assumes the simplest model of binding energy for binary sequences (namely that the binding
energy is linear in the number of active patches involved in a bond) then the energy of a full correct bond
is pG
p
(where G
p
is the free energy of a bound active patch and is equal to 2 times G
st
, the free
energy of a stacked helix), the energy of the strongest partial bond is iG
p
and the equilibrium ratio
between the full correct bond and the strongest partial bond is: e
-(p-i)Gp/kT
. A full treatment of the total
error rate associated with a particular binary sequence would take into account not only the energy of the
strongest partial bond, but also the number (multiplicity) of the different partial bonds having this energy,
as well as the energies and multiplicities of all weaker partial bonds; such a treatment would calculate the
full partition function for the system. Instead, here we simply assume that the multiplicity of the strongest
partial bonds for different sequences is roughly the same. Given these assumptions then the equilibrium
error rates for sequences from the three different systems(7,4), (8,5), and (9,6)should be the same.
However, because the fraction of correct bonds versus unbound origami should increase with increasing p
it would make sense to choose sequences from the system with full bonds of higher strength, i.e. a (9,6)
system.
Table S1. Size of candidate sets and the largest orthogonal subsets found as a function of sequence length,
number of active patches, and mismatch constraint. Numbers in parentheses indicate the size of the largest
orthogonal subset found (See Note S2.3). Shaded areas indicate the systems with 3-patch difference between full-
strength and partial bonds (corresponding to an equilibrium ratio of e
-3Gp/kT
, where G
p
is the free energy of a
bound active patch and is equal to 2 times G
st
, the free energy of a stacked helix). Blank spaces indicate that the
search process was not performed for the corresponding parameters (because the result would either be
meaningless [i p] or not useful, since either no candidate sequences would be found, or i was too close to p for
bonds to be specific).
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To check our assumptions about error rates, we measured the error rates for sample sequences from
the (7,4), (8,5), and (9,6) candidate sets for length 12 sequences. Experiments analogous to those shown
in Fig. 2a in the main text were conducted; Fig. S2 shows representative AFM images for each sequence
tested. L-shaped labels on the origami made scoring correct head-to-tail bonds (L-L) easy; incorrect
bonds included both bonds with rotated orientation and bonds with head-to-tail orientation that were
misaligned. Surprisingly, the (7,4) sequence gave the best error rate, with the highest fraction of correct
bonds out of total bonds96.8% (N=344, for the sequence occurring in the bottom of Fig. S2a). The
other systems performed considerably less well, with the (8,5) sequence having 77.7% correct bonds
(N=358, Fig. S2b) and the (9,6) sequence having 52.7% correct bonds (N=277, Fig. S2c).

This surprising trend might not be a general phenomenon, since just a few sequences were examined,
or it could be the case that our assumption about the multiplicity of partial bonds is wrong and that, for
example, the (9,6) sequence observed just had many more partial bonds than the other systems, all of
them having the strongest possible strength (i). However, given our thermodynamic experiments (Section
S3) another possibility suggests itself: that G
p
is not constant as the number of active patches p increases
and thus the total stacking bond energy is not linear in the number of active patches. In particular, if G
p
decreases with increasing p then our results make sense. Then the energy difference between a full correct
bond and the strongest partial bond in the (9,6) system is not as large as the analogous energy difference
for the (8,5) system, which in turn is not as large as that for the (7,4) system. Such a sublinearity in
stacking bond energy might be explained by steric interference or electrostatic repulsion between active
patches, or it might be explained by a nonlinear bending energy term that increases as the use of more
active patches results in them being more spread out and requires them to overcome a large-scale
deformation of the origami. Because of the trends we observed in our experiments using sequences with
constant p and i (Section S3, G
p
seems to decrease as active patches are more spread-out along the
Figure S2. Comparison of sequence performance as a function of the number of active patches. A binary
sequence and its complement are placed on opposite edges of an origami such that it should form long chains; each
origami carries the label L. Full-strength correct bonds are measured by counting the bonds with head-to-tail
orientation (L-L). Partial bonds of all types are also counted; they usually involve origami bound in the rotated
orientation. (a) One (7,4) system, 100100110111 (top) and another 010111100011 (bottom). Error rate data
were taken for the bottom system; the top system is included to show a high-res image of a system of qualitatively
similar error rate. (b) An (8,5) system, 100101011111. (c) A (9,6) system, 110111001111. Scale bars: 500 nm.
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origami edge) we suspect the latter hypothesis is a more likely explanation. Clearly performance
measurements for many more sequences should be made, but based on these preliminary experiments, we
chose to explore (7,4) sequences in the context of a longer, 16-patch system.

S2.1.4. Frror rutex for blnury xequencex lnvextlguteJ ln thlx xtuJy
For edges of the tall rectangle system (which has 16 total available patches), there are 4614 different
binary sequences with (p, i) of (7,4), as shown in Table S1. Within the set of those binary sequences,
subsets (codes) can be found for which every pair of sequences from the subset is the mutually orthogonal
with the same matching criterion (no partial match between any pair of sequences involves more than 4
active patches). Our computer-aided search generated several codes of size 11 and 12; one code of size 12
and another code of size 11 were chosen for more detailed study. Each binary sequence from these codes
was tested in the same way as in Fig. 2a, i.e., the binary sequence and its complement were placed on
opposite edges of the tall rectangle, such that the rectangles form bonds in h2t orientation when the bonds
are full-strength and correct. For each case, AFM data were analyzed and bond orientations were
measured to obtain the ratio between the correct (h2t) bond orientation and the total number of bonds. The
error rate measured for each binary sequence and an example of annotated AFM data from which such
error rates are derived is shown in Table S2 below.

set sequence # sequence correct bonds N

seL1
1 0 0 0 0 0 1 0 1 1 1 1 0 0 0 1 1 90.07 423
2 1 1 1 0 0 0 0 0 1 1 0 0 0 1 0 1 84.39 338
3 0 0 1 0 0 0 0 0 1 0 1 1 0 1 1 1 79.73 301
4 1 1 0 0 0 0 0 0 1 0 1 1 1 0 0 1 86.30 941
3 0 1 1 0 1 0 1 0 0 0 1 0 0 1 0 1 87.96 191
6 0 1 0 0 0 1 0 1 0 0 0 1 1 0 1 1 97.33 243
7 1 0 0 0 1 0 0 0 1 1 0 1 0 0 1 1 82.23 324
8 0 1 1 1 1 0 0 1 0 0 0 0 1 0 1 0 96.33 346
9 1 0 0 1 0 0 1 0 0 1 1 0 0 1 0 1 72.34 142
10 1 1 1 0 1 0 1 0 0 1 0 0 0 0 1 0 87.64 239
11 1 0 0 0 0 1 0 1 1 0 0 1 0 1 0 1 83.68 337
12 1 1 0 1 0 0 0 1 0 0 0 0 1 1 0 1 83.36 339
seL2
1 0 0 0 1 0 1 1 1 1 0 0 0 1 1 0 0 94.39 639
2 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 0 78.07 436
3 1 0 1 0 0 1 0 0 0 0 1 1 0 1 1 0 93.24 210
4 1 0 0 0 1 0 0 0 1 0 1 0 1 1 0 1 74.29 210
3 0 1 1 1 0 0 0 0 1 0 1 1 0 0 1 0 93.41 827
6 1 1 0 0 0 0 0 0 1 0 0 1 1 1 1 0 93.34 112
7 1 1 0 1 0 1 0 0 1 0 0 0 0 0 1 1 94.20 448
8 1 0 0 1 1 0 0 1 0 1 0 0 0 1 0 1 91.67 168
9 1 1 0 1 0 0 0 0 0 0 1 1 0 1 0 1 81.68 473
10 0 1 1 0 0 1 0 1 1 0 0 0 1 0 0 1 78.33 300
11 1 0 0 1 1 0 1 0 0 0 1 0 0 0 1 1 93.81 113

Table S2. Error rates for stacking bonds made using binary sequences from two different sets (sequences
within each set are orthogonal) and an example of AFM image analysis. Each bond was labeled and counted
based on its orientation. The blue circles over the AFM image indicate bonds with the correct head-to-tail
orientation and the yellow circular arrow indicates a single bond with an incorrect rotated orientation. The
percentage of correct bonds (with h2t orientation) out of the total number of bonds analyzed (N) was recorded for
each binary sequence. The AFM image is for binary sequence #3 in set2. Scale bar: 200 nm.
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S2.2. Design of sbape codes for stacking bonds.
S2.2.1. exlgn crlterlu for xhupe xequencex

As in the design of binary sequences, the goal of minimizing undesired bonds dictates design criteria
for shape sequences. As before, fully self-complementary sequences (Fig. S3ab) or partially self-
complementary sequences (Fig. 3cd) must be avoided (unless a homodimer of origami is desired.)
Computer enumeration of candidate sets of sequences for shape codes is essentially similar to that for
binary codes, with two important differences. First, unlike the case for DNA or binary sequences, not all
shape sequences encode physically distinct bonds; we discuss this in the next section. Second, unlike the
case for DNA or binary sequences, the program must make an extra check for the self-complementarity of
the shape sequences complement. For DNA or binary codes, to evaluate whether a sequence should be a
candidate sequence, it is sufficient to check that sequences self-complementarity, and to check for any
partial complementarity that it might have with its complement. This is because for a DNA or binary
sequence, any self-complementary subsequence that occurs in the sequence implies the existence of a
corresponding self-complementary subsequence in the sequences complement, and vice versa. This is not
the case for shape sequences: the shape sequence 100001 has a strongest self-complementary partial
bond of strength 2, but its complement 011110 has a strongest self-complementary partial bond of
strength 4. We note also that the minimum possible mismatch constraint i for shape sequences is 2
patches (as it is for binary codes), but this limit holds for a different reason in the case of shape sequences
than for binary sequences. The reason is that, for an arbitrary shape sequence, the first two or last two
Figure S3. Examples of shape sequences and their partial bonds. (a) A 4-patch shape sequence could form a 4-
patch bond between distinct origami, but because it is fully self-complementary (b) it also allows full-strength
undesired bonds. (c) Another shape sequence and its complement could form a 4-patch bond, but (d) it also allows
partially self-complementary 3-patch bonds (3/4 the strength of a full bond). (e) A shape sequence and its
complement that we used between the A and B origami. (f) Examples of partially self-complementary
(homogeneous) bonds of strength 2 for the sequences in (e). (g) Examples of partial bonds of strength 1 between
the two distinct origami (heterogeneous) for the sequences in (e).
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Figure S4. Equivalences between shape sequences. (a), (b), (c),
and (d) are all equivalent with respect to the bond type they
encode. Vertical arrows denote stacking polarity. (a) and (b) are
related by a simple shift in depth, (b) and (c) are complementary,
(c) and (d) are related by a depth shift, and (a) and (d) are
complementary. (e) is, however, distinct from the others because it
is the reverse of (a), and has opposite stacking polarity.
patches both form self-complementary subsequences that can bind to themselves without steric hindrance
from any of the other patches (if the two origami carrying them are in a rotated orientation). The top two
and bottom two examples in Fig. S3f demonstrate this phenomenon.
Early on in the project we thought we might achieve a large number of specific bonds through the use
of a long (l=6 or l=9) shape sequences. Fitting these high complexity sequences into the relatively small
area of an origami necessitated using patches that were just 2 helices wide. These proved too flexible to
prevent bent-patch bonds (see S.2.7.1) so we decided to use 4-helix wide patches to implement shape
codes. This restricted the length of the shape sequences we could use to just 4 patches; similarly we
restricted ourselves to just three depths to avoid long, flexible patches. Fortunately, even with these
restrictions, the candidate set for the mismatch constrain i=2 had 16 elements, which we discuss next.
S2.2.2. Full llxt of cunJlJute xhupe xequencex for the (4,S,2) xyxtem
Given the number of patches (p) and number of depths (d), our program searches the entire sequence
space and examines the possible partial bonds for each shape sequence with itself, each sequence with its
complement, and each complement with itself to see if they exceed the mismatch constraint (i). For (p,d,i)
= (4,3,2) the program generated a candidate set of 16 unique shape sequences, listed at left below. Note
first, that if a sequence appears, its complement does not appear: our desire is to make a set of candidate
sequences for distinct bond types and a sequence and its complement are equivalent with respect to the
physical bond type that they encode. Similarly, sequences that are related by a simple shift in depth, such
as 0010 and 1121 (Fig. S4ab), encode the same bond type and are thus equivalent. Only a single
sequence from an equivalence class is included in the candidate set. Recall that due to stacking polarity, a
shape sequence (e.g. Fig. S4a) and its reverse (Fig. S4e) are inequivalent, unless they are palindromic.
(Shape sequences and their reverses are expected to be similar for some properties, e.g. flexibility.)

List of the 16 shape sequences:
1 0010 (= 1121 = 1011 = 2122)
2 0020
3 0021
4 0100
5 0102
6 0110 (B-C bond)
7 0200
8 0201
9 0211
10 0220
11 0221
12 1020 (C-D bond)
13 1120
14 1200 (= 2201, A-B bond)
15 1220
16 2010
(Equivalences are not exhaustively listed.)
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DOI: 10.1038/NCHEM.1070
S2.2.S. Orthogonullty gruph for the (4,S,2) cunJlJute xhupe xequencex
Using our computer program, one can check the orthogonality between any two sequences in the set
of 16 shapes listed in the previous section. By applying the same mismatch constraint for the strongest
partial bonds (i = 2) between different sequences, the orthogonality relations can be determined for each
pair of sequences (a total of 120 combinations). Fig. S5a shows the full orthogonality graph for all 16
shape sequences in the candidate set. Line segments between numbered circles indicate that the two shape
sequences corresponding to the numbers are orthogonal to each other. (For the identity of each shape
sequence, see list in the previous section.)
Sets of mutually orthogonal sequences correspond to complete subgraphs or cliques of the
orthogonality graph. That is, a set of vertices for which every pair of vertices is connected by a line
segment corresponds to a set of mutually orthogonal sequences. For example, one complete subgraph is
the red triangle in Fig. S5b which corresponds to an orthogonal subset with three sequences, {6,12,14}.
An exhaustive search confirmed that the size of the largest orthogonal subsets for the given system is 4
for example the subset indicated by the red subgraph in Fig. S5c: {3,6,7,16}. We attempted to construct
origami chains based on a subset of size 4. Unfortunately, the set we chose included sequence 5, which,
along with its reverse sequence 16, turned out to be susceptible to the formation of bent-patch bonds. In
the interest of saving time and money, and because we had demonstrated that sequence 6 worked well, we
ended up choosing the 3-sequence subset {6,12,14} to explore as a shape code. The four sequence
orthogonal subset {1,11,12,14} looks promising, but was not explored.

1
S
9
13
3
7 11
1S
2
4
6
8 10
12
14
16
1
S
9
13
3
7 11
1S
2
4
6
8 10
12
14
16
1
S
9
13
3
7 11
1S
2
4
6
8 10
12
14
16
Figure S5. Orthogonality graph for the candidate set of 16 shape sequences. (a) The full graph. Each line
connecting two numbered circles indicates that the two shape sequences are orthogonal. (b) Red triangle highlights
an orthogonal set of size three with sequences 6, 12, and 14. (c) Red subgraph highlights an orthogonal set of size
four with sequences 3, 6, 7, and 16.
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DOI: 10.1038/NCHEM.1070
S2.2.4. Slze of xhupe xequence xpucex wlth other purumeterx
In addition to the 4-patch system with d=3 and i=2, we explored other shape sequence spaces with
different parameters, a couple of which were tested experimentally (some results are shown in Note
S2.6.1). In the table below, we summarize the sizes of shape sequence spaces with various parameters
(different numbers of patches, different numbers of depths, different numbers of patches allowed in
incorrect bonds). In the right-hand column we report the size of the largest orthogonal subset discovered
over the course of multiple random searches, as described in Note S2.3.
For parameters not included in this table, one can easily obtain the shape sequence space not only
the size but the entire list of candidate shape sequences using the program code provided as a separate
Supplementary file.

# paLches
(p)
# depLhs
(d)
# paLches allowed
ln lncorrecL bonds
(i)
paLches ln
lncorrecL bonds
S|ze of shape
sequence
space
S|ze of |argest
orthogona| subsets
found
4
2 2 30 3 1
3 2 30 16 4
4 2 30 61 8
6
3
2 33 S 1
3 30 49 7
4
2 33 14S 6
3 30 423 22
9
3
2 22 2 1
3 33 14 S
4
2 22 233 6
3 33 1113 2S
S
2 22 6S10 1S
3 33 24791 60

Table S3. Sizes of shape sequence spaces and orthogonal subsets for different systems. The purple-shaded
parameters are those for the shape sequences most explored by this study.
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DOI: 10.1038/NCHEM.1070
S2.3. Finding codes: searcbing for large ortbogonal sets of sequences.
So far we have largely discussed, for both binary sequences and shape sequences, the symmetry and
mismatch constraints that are required of a sequence for it to be useful as an individual stacking bond in
isolation constraints such that, with high probability, the sequence will bind its complement by a full
correct bond rather than binding to itself or binding its complement by a partial bond. Given a set of
parameters including the length of the sequence, number of active patches, the number of depths (if
appropriate), and a mismatch constraint, we have shown that it is straightforward to enumerate all
sequences that individually satisfy the constraints. Our two most studied examples are the 4614 binary
sequences for (p,i) = (7,4) and the 16 shape sequences for (p,d,i) = (4,3,2). In order for such candidate
sequences to be used in a multiple-bond system, one must find a subset that is orthogonal that is, all
pairs of sequences must satisfy the mismatch constraint. A diagram of the orthogonality relation between
all 16 sequences in the (4,3,2) shape sequence candidate set, and example orthogonal subsets are
discussed and diagrammed in Section S2.2.3.
An important goal is to find the maximal orthogonal subset of a candidate set, to find a code of
sequences that can support the largest diversity of stacking bond types. For candidate sets containing
relatively few sequences, such as the (4,3,2) shape sequences, an exhaustive search through all possible
orthogonal subsets is possible. But for bigger candidate sets, the combinatorially large number of subsets
makes finding the maximal orthogonal subset by exhaustive search a computationally intractable task.
More specifically, the problem of finding the maximal orthogonal subset is a trivial rephrasing of the
well-known Max Clique problem in computer science. Max Clique is known to be NP-hard, and here two
facts about NP-hardness are relevant: (1) Most computer scientists believe that NP-hard problems can
only be solved exactly using an amount of time that is an exponential function of the size of the problem
this is what is meant by computationally intractable. (2) NP-hard problems can be approximated
thus while it might be computationally intractable to find the maximal orthogonal subset, it may be
possible to find large subsets, which are close in size to the maximal orthogonal subset, quickly.
There is a large literature on approximating NP-hard problems, but we did not take advantage of such
approximation techniques here. Instead, to quickly get large orthogonal subsets that we could use for
multiple stacking bonds, we implemented a simple, randomly seeded, greedy search procedure. For many
of the smaller candidate sets, the orthogonal sets we obtain are probably maximal; in the case of the (4,3,2)
shape code system we verified that this was the case. For larger candidate sets it is highly likely that the
orthogonal sets we have obtained are not maximal; it might be possible that there exist 13-sequence
orthogonal sets for the (7,4) binary code system. For the moment, the orthogonal sets that we have found
are satisfactory since we obtained orthogonal sets whose size roughly matches the maximum number of
origami that we can handle easily, or can afford in the lab. However, if the need should arise, e.g. for
much larger codes, many relatively fast algorithms for finding large cliques (and hence finding large
orthogonal subsets) are available. One example is Cliquer, a set of C routines that are available for
download from: http://users.tkk.fi/pat/cliquer.html
Our program for discovering large orthogonal subsets constructs them in a greedy fashion starting
from single sequences from the candidate set. Let the size of the candidate set be N. Each run of our
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DOI: 10.1038/NCHEM.1070
program constructs N different orthogonal subsets, by sequentially using each one of the elements of the
candidate set as a seed for a different orthogonal subset. The details of our program are as follows:
(1) The program first picks one candidate sequence as a seed; that candidate sequence becomes the first
element of the orthogonal set under construction.
(2) The program randomly picks another sequence from the candidate set and checks its orthogonality
with the existing element(s), with respect to the mismatch constraint i.
(3) If the newly picked sequence is orthogonal to the existing element(s), it is added to the set; otherwise
it is discarded.
(4) The program repeats steps (2) and (3) until all candidate sequences have been tested for the
orthogonality with the growing set. After all candidates have been tested, the orthogonal set is output.
(5) The program repeats steps (1) through (4) until all candidate sequences have been used as a seed for
an orthogonal set.
Since the construction of an orthogonal set is sensitive to the order of addition of candidate sequences
(a different order results in a different set), each run of the program results in N potentially distinct
orthogonal sets. Typically, we ran the program multiple times; we did not keep track of the number of
runs performed. The largest orthogonal subsets found are recorded in Table S1 (for binary sequences) and
Table S3 (for shape sequences).

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DOI: 10.1038/NCHEM.1070
S2.4. Design of tbe origami structures
Design of the rectangle systems (regular and tall) was performed based on the procedure described in
the original DNA origami paper, using MATLAB code. Origami with edge shapes (A, B, C, and D
origami) were designed using a modified version of the square lattice version of caDNAno. caDNAno
software was customized to allow (1) the creation of single stranded loopouts in the scaffold strand and (2)
the highlighting of the scaffold strand with a user-specified sequence (e.g. GC). Both features were
added to facilitate the process of shifting the scaffold strand and aligning GC on the edges. In our
modified version of caDNAno, the loop tool which is normally used to generate double-stranded loops
(loops involving both the scaffold and staple strands) has been changed to a tool that creates single-
stranded loops only in the scaffold strand. The highlighting feature has been integrated into caDNAnos
existing add sequence function, with which a user can select the scaffold sequence to use; now a user
can specify a sequence to highlight using the same dialog box (Fig. S6c). Color is fixed for each
highlighted base: G-Green, C-Cyan (light blue), A-Amber (roughly orange), T-Tomato (red). The length
limit for a highlighted sequence is set to be the same as caDNAnos existing length limit for the scaffold
sequence (20,000), so a user can highlight the entire scaffold sequence if desired. A few other minor
modifications include: (1) skipping the step of waiting for the user to click on the 5 end of the scaffold
during an add sequence operation if there is only one 5 scaffold end in the design, and (2) updating the
scaffold and staple sequences automatically after creating a new loopout (this automatic update works
only after the scaffold sequence has been defined). The modified version caDNAnoSQ_SW is available
as a separate Supplementary file (or by request to woo@dna.caltech.edu for latest version). For general
instructions and the original version of caDNAno, visit http://www.cadnano.org.

Figure S6. Screenshots of a version of caDNAno modified to allow placement of GC on origami edges. All
occurrences of the sequence GC are highlighted along the scaffold strand in the diagram by green and cyan for G
and C, respectively. (a) One can count the number of bases from a blunt-end on the edge to the next occurrence of
GC and (b) make a single-stranded loopout inside the structure to shift the scaffold sequences. In the example
design shown, the scaffold strand has been already aligned to have GC along the edge [as shown in the zoom-in
at (a)]. (c) Here we have shown highlighting of the sequence GC. One can enter any sequence to highlight at the
step where user selects the scaffold strand.
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DOI: 10.1038/NCHEM.1070
S2.5. Edge structure
Because accurate models (backed by high resolution structural data) of origami edges do not exist, it
is difficult to predict the exact structure and stacking configurations of the blunt-ends on the edges of
origami. Here we provide gross predictions based on the distance of the blunt-ends from the nearest
internal crossovers and the pattern of crossovers along the edge. We predict structures for three different
edge models: (1) a crossover-free edge (Fig. S7a), (2) a relaxed edge with only scaffold crossovers (Fig.
S7b), and (3) a stressed edge with both scaffold and staple crossovers (Fig. S7c). These predicted
structures in turn make predictions about the expected strength and behavior of the stacking bonds.
For all three models we are interested in the helical twist of the base pairs on the blunt-ends at the
edge, and for all three models we posit an internal crossover 16 base pairs interior to the edge. Here, we
draw bars, separated by the major/minor groove angles, on the face of the blunt ends to indicate the
helical twist of the base pair. To derive the orientation of these bars, we begin at the interior crossover and
consider the strand that is edgeward of the crossover (e.g. the orange 3D strand in Fig. S7a). We model
the two base pairs next to the crossover point as staggered up and down with respect to the midpoint of
the crossover, having a helical twist angle that is rotated from the midpoint by of the characteristic
rotation/bp of B-DNA (~34.6 given 10.4 bp/turn) that is approximately 17. (Similar modeling is
performed in Ref. 1.) From these first edgeward base pairs the base pairs at the blunt end are 15 base-
pairs away. Thus the blunt end base pairs have a helical twist angle that is rotated ~519 (15 34.6)
relative to the bases of the edgeward strand in the crossover (in a clockwise direction when viewed from
the blunt-ends towards the crossover) for a total of ~537 from the crossover midpoint. Given such a
model, which is crossover-free at the edge, the base pairs at the blunt-end would be oriented like those
depicted in Fig. S7a. We note that while we do not make such a structure in this work, origami with very
similar crossover-free edges have been made before (Ref. 10 of the main text) using tile adapters, and
so such structures can be experimentally synthesized.
Now consider a second origami with the same crossover-free edge structure, but with 15 base pairs
between the edge and the crossover. When such an origami binds via a stacking bond to the origami
described above, then the total number of base pairs between the first internal crossover points of the two
origami will be 15+16 = 31, or roughly 3 helical turns. This means that for such crossover-free origami,
the blunt-ends on opposite sides of the stacking bond are oriented with a relative twist angle of ~34.6 (as
depicted in Fig. S7d). Thus we would expect stacking of blunt ends between crossover free edges to be
native B-form stacking, and that it should be relatively strong.
Next consider our second edge structure, the relaxed edges (Fig. S7b), for which scaffold crossovers
connect every other pair of helices. This is the edge structure that we use in all our work on stacking
bonds, (except for structures pictured in Fig. 1e of the main text and Fig. S14j-o). Because the scaffold
crossovers act to pull the base pairs away from the helical twist angle that they would assume in a
crossover-free edge, whatever structure forms at relaxed edges cannot be B-form DNA. However,
because DNA can tolerate small deviations from B-form twist, we propose that the helices assume an
amount of twist strain (roughly 34.6, which is averaged over the 16 base pairs up to the crossover) and
maintain native major/minor groove angles between the bases at the blunt end (as depicted in Fig. S7b).
Given our model for relaxed edges, when two origami with relaxed edges bind via a stacking bond,
their blunt ends will not be able to stack via B-form stacking; rather, they should bind with slightly
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DOI: 10.1038/NCHEM.1070
different relative twist angles that are within approximately 34.6 of the natural twist angle in B-DNA
(Fig. S7e). We call such stacking between relaxed edges near-B-form stacking, which we predict would
be roughly as strong as B-form stacking. Since relaxed edges have a top-bottom asymmetry that is
defined by the major and minor grooves, near-B-form stacking can only occur when two origami bind in
either the head-to-tail or rotated orientations. This prediction agrees well with the distribution of observed
bond orientations, as discussed in the main text.
Finally, we consider the case of stressed edges. When staple crossovers are placed in opposition to
scaffold crossovers along an edge, we propose that the balancing of the stresses they induce results in a
near-flattening of the major and minor grooves (Fig. S7c). The resulting decrease in distinction between
the major and minor grooves should decrease the distinction between the top and bottom of the origami.
Therefore, we would predict that blunt-end stacking between such stressed edges (Fig. S7f) should allow
flipped bond orientations; this is indeed what is observed in experiments involving origami with stressed
edges, such as those shown in Fig. 1e of the main text and Fig. S14j-o.

No crossover
Only scaffold
crossovers
(relaxed edge)
Scaffold+staple
crossovers
(stressed edge)
(a)
(b)
(c)
(d)
(e)
(f)
16 bp
Figure S7. Comparative modeling of three different origami edge structures. (a) Crossover-free edges. (b)
Relaxed edges with only scaffold crossovers. (c) Stressed edges with both scaffold and staple crossovers. Each
circle indicates a blunt-end. In (a), both the black and colored bars (inside the circles) indicate the helical twist of
bases belonging to tile adapter strands. In general, tile adapter strands are strands that extend from the edge of an
origami to give it a geometry that is not possible using the canonical scaffold/staple geometry. Here, our intent is
that the tile adapter strands create a crossover-free edge; we do not show the details and did not use them in our
stacking experiments. He we use them as part of a thought experiment concerning the geometry of stacking
bonds, but we note that tile adapter strands have been used to create origami with a very similar crossover-free
edges (Ref. 10 in main text). In (b) and (c), black bars indicate the helical twist of bases from the scaffold strand,
and colored bars indicate the helical twist of bases from the staple strands. Bars of the same color indicate the same
strand, e.g., the orange staple in (a) runs for 1.5 helical turns in one helix, switches between helices at a 16-bp-deep
internal crossover, and runs back for a length of 1.5 helical turns in the adjacent helix, as depicted by the 3D
drawing. Black dotted arrows indicate crossovers at the edge. In all three models colored strands are intended to
make 16-bp-deep internal crossovers. The models in (a-c), predict that the blunt ends on the edge are either B-form
(a), near-B-form (b), or have disrupted base pairs that are incompatible with B-form geometry (c). (d-f) show
models of the juxtaposition that occurs when two different origami edges form a stacking bond; these bonding
models correspond to the edge structure models in (a), (b), and (c), respectively. Models (d) and (e) make
predictions for the relative helical twist between blunt-ends across the bond. Model (f) suggests that the disturbance
of the base pairs at the edge of the origami may decrease the distinction between the major and minor grooves
enough to create a top-bottom pseudosymmetry. This pseudosymmetry could allow bonding between origami in
one of the flipped orientations (not shown).
DOI: 10.1038/NCHEM.1070
S2.. Quencber strands
In a binary coded system in which multiple origami containing different binary sequences on their
edges are mixed together, interference can arise between the edge staples used to set the sequences on one
origami and the edges representing different sequences on another origami. This occurs because all
origami in the binary coded system share the same basic design, and their edges share the same staple
binding sites. For example, if one origami bears a sequence on its right edge that has a 1 in a particular
position, then the staple that creates that active patch can bind to the same location on a different origami
for which that location was intended to remain inactive, effectively flipping a 0 to a 1. In the worst
case, all of the origami would end up with exactly the same sequences, with the right edge of each
origami encoding a sequence that represents the bitwise OR of all the sequences on the right edges of the
original origami, and the left edge encoding an analogous bitwise OR of all the left-edge sequences.
Prevention of such interference could be achieved by purifying the origami to remove excess staples
before mixing the origami. But purification steps are usually accompanied by significant loss of the
origami themselves and may incompletely remove staples. In particular, simple and fast methods such as
spin filtration reduce excess staples only by a factor of 5- to 10- fold; more complete removal requires
more stringent methods such as gel purification. Complete removal is important because, as we observed
in tests of spin purification, relatively small and sporadic changes to edge sequences can significantly
increase error rate. As an alternative approach, we introduced strands complementary to the edge staples,
which we term quenchers.
Quenchers bind to the excess free edge staples in solution and effectively prevent them from binding
to the scaffold strand. Quenchers were designed so that they have complementary sequences to the
corresponding edge staples (thus quenchers have sequences derived from scaffold strand subsequences),
and extra two thymine bases were added to both the 5-end and the 3-end (so that the quencher sequence
becomes 5-TT-staple complement-TT-3). The thymine addition was done to minimize the potential
influence of (1) stacking interference from blunt ends that would be generated if simple complements
were used and (2) breathing of the resulting quencher-staple duplex that might allow the edge staple
strand to bind to a 0 location anyway, via a branch migration process.
The efficiency of the quenchers at blocking the free edge staples was not explicitly measured.
However, the high molar excess of the quenchers used (10 the concentration of edge staples) and the
high free energy of binding between the quenchers and the edge staples (on the order of ~40 kcal/mol,
calculated using Oligo Calc, http://www.basic.northwestern.edu/biotools/oligocalc.html) predicts the
concentration of free edge staples, in the presence of the quenchers, to be extremely small on the order
of 10
-21
nM. The experimental protocol for using quenchers is described in Supplementary Note S1, and
the detailed sequences are given in Supplementary Note S5.

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DOI: 10.1038/NCHEM.1070
S2.7. Warnings
In case one wants to repeat or adapt some of our experiments, we give warnings that describe some
difficulties which we have encountered and suggest some potential problems that we did not discuss in
the main text.
S2.7.1. Iength unJ wlJth of u putch ln xhupe Jexlgn
Besides the 4-patch design in the shape code system, we have tried other designs with higher
complexity (6-patch and 9-patch systems) that we expected to give higher specificity. But as the number
of patches increased, we had to design each patch with less material, yielding patches with a smaller
number of helices. The flexibility of DNA, coupled with the strength of the stacking interactions, caused
these narrow-patch systems to be more vulnerable to bent-patch bonds. Fig. S8 briefly summarizes the
two systems.
In the 6-patch design (Fig. S8a) we introduced physical gaps between each adjacent pair of 2-helix
patches, to minimize any effect of the electrostatic repulsion. (It seemed possible that electrostatic
repulsion between adjacent patches might decrease binding energy. This hypothesis has yet to be
adequately tested.) The introduction of physical gaps made the patches narrower and longer, allowing
various kinds of bent-patch bonds (~ 30% of all bonds) as shown in Fig. S8d,e. Because we used 3 helical
turns for each depth increment, the length of the longest protruding patch was 9 helical turns, which is
about 30% of the persistence length of double-crossover DNA tiles (~30 helical turns, ~100 nm) the
most similar structure to the 2-helix patch structure for which the persistence length is known
2
. We chose
to use a (6,4,3) shape code so that, in principle, the maximum-strength partial bond would have three
active patches (1/2 of the full strength). To our dismay, 5-patch bent-patch bonds formed; if the bending
energy were small, these bonds would have a binding energy comparable to that of full 6-patch correct
bond.
In the 9-patch system, (without physical gaps and with much shorter patches), a significant fraction of
the bonds (~20 %) were still bent-patch partial bonds (Fig. S8i,j). We had chosen to use a (9,5,2) shape
code so we had expected high binding specificity the strongest expected incorrect bonds would have a
binding energy 2/9 of a full correct bond. To decrease the flexibility of patches, we used a single helical
turn for each depth increment, so that the longest protruding patch was just 4 helical turns in length. Thus
it was to our further dismay that 8-patch bent-patch bonds formed, which were again potentially very
close in energy to full-strength bonds. As a point of interest we note that the 6- and 9-patch systems were
not twist-corrected, so the chains in Fig. S8g show the characteristic breaking pattern that is similar to that
shown in Fig. 1b of the main text. The global twist might be playing a role in encouraging bent-patch
bonds in these systems, but we have not done any experiments to test this possibility.
To decrease flexibility, our final successful shape code system employed only four of patches that
were 4-helices wide and protruded at most 6 helical turns. Many questions remain: How many patches are
optimal for this kind of study? How wide (in terms of number of helices) should each patch be? How long
can they be? What is the bending energy of the patches under the buffer condition used? We do not yet
have answers to these questions, but it is certain that there is a trade-off between the complexity (and
hence the potential specificity in ideal case without helix bending) and the bond reliability. Of course, this
problem is limited to soft systems like DNA, thus might be avoided in a system with sufficient rigidity.
!"
DOI: 10.1038/NCHEM.1070

50 nm
200 nm
50 nm

50 nm
200 nm
50 nm
30 nm
(a)
(b) (c) (d) (e)
(f)
(h) (l) ([) (g)
100 nm
Figure S8. Performance of 6-patch and 9-patch shape-coded systems. (a) Models of the 6-patch system. The
edge shapes of the A origami and B origami were designed such that the origami form continuous alternating AB
chains. Shape sequences were 132120 for A-B bonds and 011310 for B-A bonds. Stars indicate the locations of
dumbbell hairpins, which serve as topographic labels for AFM. (b) & (c) Typical AFM images of the system that
show full-strength correct bonds. (d) & (e) Typical bent-patch bonds which manage to bind via 5 active patches.
The red dotted lines on the models depict bent patches coming from the origami on the top, and the blue dotted
lines depict bent patches coming from the origami on the bottom. (f) Models of the 9-patch system. Shape
sequences were 034222043 for A-B bonds and 340224301 for B-A bonds. (g) & (h) Typical AFM images. Note
that the chains in (g) show the characteristic breaking pattern of the twisted origami chains described in Fig. 1 of
the main text. (i) & (j) Typical bent-patch bonds with 8-patch bond strength. The red and blue dotted lines in (i) are
used in the same way as in (d) or (e). The narrow blue dotted line in (j) roughly follows the blunt-ends and helical
sidewalls of the edge structures.
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DOI: 10.1038/NCHEM.1070
S2.7.2. Potentlul lnterference from the remulnJer xtuplex
Since the length of the scaffold strand is fixed to be 7249 bases, a DNA origami design that uses
fewer than 7249 bases will leave a remainder in the form of unfolded single-stranded scaffold in most
designs the remainder takes the form of a single loop. To avoid potential interactions of such a single-
stranded remainder on one origami with the remainder of another origami, it is usual to add a set of
remainder staple strands which have the function of hybridizing to the remainder and turning it into an
unreactive double-stranded loop.
When multiple origami which do not share the same underlying design are mixed together, e.g. as in
our A-B-C-D chains with shape complementarity, there is the possibility of interference between the
remainder staple strands of one origami and single-stranded regions of the other origami. In general, a
subset of staple strands from one origami may bind single-stranded loopouts on other origami via partial
complementarity. (Such loopouts are common in our system because they are used to enforce the GC
sequence constraint at the blunt ends of helices.) Binding of staple strands to loopouts does not, in general,
seem to affect the origami, but in certain cases remainder strands may have complementarity to
surrounding scaffold sequence outside of the loopout. In such cases the remainder strands can begin to
displace nearby staples. Because the remainder staples are designed to be continuous complements to
the remainder loop, each successive remainder staple that displaces a regular staple potentially opens up a
site for another remainder to bind. Remainder staples may thus sequentially unfold the local structure of
another origami. This process may be energetically favorable because the remainder strands make
continuous duplex which likely has a lower energy than origami structure (because of its crossovers and
twist strain). In some of our initial experiments on shape complementary origami, we experienced this
problem: individual origami folded well but when mixed together remainder staples from one origami
caused large structural disruptions in other origami. We do not show this data since none of our final
designs exhibit the problem.
Two potential solutions exist: (1) One can avoid the use of remainder staples in most cases single-
stranded remainder sections of the scaffold will cause no further problem. (2) One can design the
remainder loops of different origami to coincide (have almost the same sequence), so that the remainder
staples of one origami will not bind and invade loopouts of another origami. The latter approach was used
successfully in our A-B-C-D chain system.

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DOI: 10.1038/NCHEM.1070
S2.7.S. Poxxlble colllxlonx between eJge xtuplex
When designing an origami system with uniform edge sequences (e.g. GC) as in our system, if one
takes the same approach as ours generating loopouts to shift the scaffold sequences one should note
that doing so limits the number of possible edge staple strands. In the 7249-base sequence of the
M13mp18 scaffold strand, there are 393 occurrences of GC (occurring on average every 18.4 bases, see
schematic Fig. S9 below). Hence, ideally, there are 393 different positions at which edge staples can be
located. Given a particular geometric design for an origami, one has some choice in terms of which edge
staple positions to use; one can change the edge staple sequence at a particular geometric position in the
origami by changing the length of the loopouts and/or changing the position at which the scaffold
sequence starts in the design. However, when designing multiple origami that are large and use up all the
sequence, or further when the origami designs share a similar start position for the scaffold sequence
(as occurs in our shape-coded A, B, C, D system) there is a high probability that some of edge staples
from different designs will share subsequences or have identical sequence. For the shape code system we
explored this does not cause any difficulties since all edge staple positions are occupied by design.
However, in some potential systems (say a hybrid shape code/binary code system) it might be possible for
an edge staple present in one origami to fill in an empty edge staple position in another origami and give
unexpected results. For example, in some of our initial experiments (not shown) edge staple collisions
resulted in unintended aggregation. We note that taking an adapter strand approach to controlling edge
sequences (as suggested in the main text) would obviate this problem.

# of GC occurrences = 393
in total 7249 bases
Figure S9. The limited number of GC occurrences in the scaffold strand constrains the number of usable
edge staple strands. In case of the M13mp18 scaffold strand, with 7249 bases in total, there are 393 occurrences
of GC. The black circular strand represents the scaffold. The boxed area shows how an edge staple strand (blue)
binds to the scaffold and forms two GC blunt-ends (depicted by ellipses).
!!
DOI: 10.1038/NCHEM.1070
Supplementary Note S3: Tbermodynamic measurements
The free energy of the stacking bonds was measured by assuming that monomers and dimers of one-
sided rectangle origami (origami with edge staples on only one side, Fig. S10a) were at equilibrium. The
initial monomer concentration equals the total origami concentration, which was assumed to be the initial
scaffold concentration (assuming the yield of origami formation was ~100%). The equilibrium
concentrations of monomers and dimers were measured by depositing the samples on mica and counting
the numbers of each in AFM images (e.g. Fig. S10c). Here the relative ratio of monomers and dimers on
surface was assumed to be representative of the ratio in solution. At least two processes could invalidate
this assumption: (1) origami dimers might break upon deposition, artifactually elevating the monomers
count or (2) origami monomers might land so close to each other that they would be scored as a dimer,
artifactually elevating the dimer count. We did not try to estimate the frequency of these processes but we
did dilute the origami 5-fold from their formation concentration before depositing them; this decreased
the probability of a mismeasurement due to (2). In other experiments dilution was performed on the mica
surface, by pipetting a sample onto a 5 larger volume of buffer on the surface. Because origami stick so
quickly to mica, this protocol would run the risk of depositing dimers and monomers before they had the
chance to equilibrate at the new concentration. To decrease the potential for this effect, sample solutions
were pre-diluted, left to equilibrate for ~5 hours (a longer equilibration time, e.g. 10 hours, was tested for
the p=6 system and did not show a statistically significant difference, so we assumed that a 5 hour
equilibration time was long enough for the p=6 and weaker bonds), and then deposited without further
dilution. (To be completely free from the effects of surface deposition and dilution and to obtain more
detailed thermodynamic parameters, e.g. T
m
, H, and S, one could alternatively adopt solution-based
measurement techniques such as real-time FRET analysis.
3
)
The free energy of the stacking bonds was calculated as follows. From the counts of monomers M,
correct dimers, D, and incorrect dimers (misalignments or other orientations, other), and the concentration
of origami, [origami], we calculated the monomer concentration, [M], and dimer concentration, [D]:
M =
M origami
M+2D+2other
and D =
D origami
M+2D+2other
From [M] and [D] we calculated the equilibrium constant and the free energy of the bond
K=
[D]
[M]
2
and G=-RTlnK
where R is the gas constant (8.314 J/molK) and T is the temperature 295 K (22C).

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DOI: 10.1038/NCHEM.1070

2
300 nm
Figure S10. Thermodynamic measurements. (a) Schematic of the monomer/dimer equilibrium for one-sided
origami with six active stacking patches in the middle (binary sequence 000111111000). (b) The number of
active stacking patches and their locations were varied as shown and the free energy was measured in each case. (c)
A representative AFM image showing the distribution of the monomers and dimers as well as the distribution of
bond orientations.
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DOI: 10.1038/NCHEM.1070
S3.1. First energy model: assuming loop-loop interactions are neutral
We measured the free energy of stacking bonds for various systems with different numbers and
sequences of active patches (Fig. S10ab). Assuming that loop-loop interactions have a neutral effect on
the free energy of stacking bonds we calculated the free energy per helix for each system (Table S4 and
Fig. S11). The total binding energy was expected to be linear in the number of active patches which
would imply a constant free energy per helix, yet we observed free energies that varied between -2.67
kcal/mol and -1.42 kcal/mol depending on the system.
A few trends were observed. First, we observed that the magnitude of the binding energy per helix
decreased as the number of helices increases. We hypothesize that the resulting sublinearity of binding
energy is due to residual large-scale twist (or other deformation) of the origami structure; our picture is
that as the number of stacking patches increases and the patches become more spread out, the bending (or
twisting) penalty per patch increases. Such residual deformations seem likely to occur because, although
twist correction yields a better average twist and decreases global twist, local twist still differs greatly
from 10.4 bp/turn. This hypothesis is compatible with a second observed trend, one within the 4-patch
systems. The three 4-patch systems were designed such that one has all its active patches compactly
arranged in the middle (000011110000), another has its active patches highly spread-out
(100100001001) and the third has active patches with an intermediate spacing (001010010100).
Dimers in the system with compactly arranged active patches were most stable, while dimers in the
system with highly spread-out active patches were least stable; this again suggests a bending or twisting
penalty that increases as active patches spread out. Yet, the binding energies for the 2-patch systems did
not show a statistically significant difference between the system with most compactly arranged active
patches (000001100000) and the system with more spread-out active patches (000010010000). One
can imagine that 2-patch systems would be less affected by structural deformations because the bonds are
formed by 2-point connections no matter how much the edge is bent, 2-point connections could be made
by rotation of one origami with respect to the other.
Because we hypothesize that non-stacking factors are all destabilizing, we suggest that the average
energy obtained for the 2-patch systems, -2.63 kcal/mol (1 TAE with 12.5 mM Mg
2+
, 22C), is most
reflective of a pure stacking interaction. One literature value (Ref. 25 of the main text) for the energy of
GC/CG stacking is -2.17 kcal/mol (1M Na
+
solution at 37C). While buffer conditions between the two
experiments differ, we did our best to make the measurements comparable by correcting the literature
value using temperature-dependent data given in Ref. 25 of the main text. Fig. S12 shows a plot that we
reproduced based on experimental data given in Fig. 3a and Supplementary Table 2 of Ref. 25 of the main
text. Data were taken for five different temperatures (32C, 37C, 42C, 47C, and 52C). Assuming that
the temperature dependence of the enthalpy and the entropy of blunt-end stacking is negligible for the
given temperature range, it is appropriate to make a linear fit to G
st
as a function of temperature. A
regression line and its equation (R
2
= 0.8943) are shown in Fig. S12. Linear extrapolation to the y-axis
(T=22C) gives an energy of -2.42 kcal/mol at 22C, which is a very close value to the value we obtained.

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DOI: 10.1038/NCHEM.1070

System
&
b|nary code [or|gam|] (nM) G
(kca|]mo| hx) N (or|gam| count)

2paLch-(6,7) 000001100000 0.424 -2.3889 362
2paLch-(3,8) 000010010000 0.848* -2.6738 276
4paLch-(3,6,7,8) 000011110000 0.424 -1.7644 178
4paLch-(3,3,8,10) 001010010100 0.424 -1.6393 366
4paLch-(1,4,9,12) 100100001001 0.424 -1.3378 360
6paLch-(4,3,6,7,8,9) 000111111000 0.212
#
-1.4223 442

G
s
t
(
k
c
a
l
/
m
o
l
h
x
)
# patches
Table S4. Free energy of the stacking bond per helix for various systems.
&
Numbers in parentheses indicate the locations of active stacking patches (the 1s in the binary sequences).
*A higher concentration was used because it was hard to find dimers for this system.
#
A lower concentration was used because it was hard to find monomers for this system.
Figure S11. Free energy of the stacking bond per helix for various systems. Energy values per helix vary
depending on the number of patches, indicating a nonlinear relationship between the stacking energy and the number
of helices. The overall trend (decreasing |G
st
| as the number of patches increases) suggests that patches farther
away from the middle of the edge must bend more (to counter some remnant global deformation) to bind; this
hypothesis is consistent with the trend within the 4-patch systems. The binding energies for the 2-patch systems did
not show a statistically significant difference (the error bars partially overlap.) Error bars indicate standard error,
obtained by bootstrapping the count data and propagating errors through the equations.
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DOI: 10.1038/NCHEM.1070

y = 0.019x - 2.834
R = 0.8943
-3.2
-2.8
-2.4
-2.0
-1.6
-1.2
-0.8
-0.4
0.0
22 27 32 37 42 47 52
G
s
t
(
k
c
a
l
/
m
o
l
h
x
)
Temperature, C
Figure S12. Temperature dependence of the stacking free energy (data taken from Ref. 25 of the main text).
A linear fit and its extrapolation gives a stacking free energy of -2.42 kcal/mol at 22C, which is very close to the
value we obtained, -2.63 kcal/mol, at the same temperature.
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DOI: 10.1038/NCHEM.1070
S3.2. Second energy model: fitting witb non-zero loop-loop interactions
In the previous energy model, we assumed that loop-loop interactions are negligible. Here we take an
alternate approach and assume that loop-loop interactions are not necessarily neutral and further that they
may have some constant free energy value, G
ll
, either positive or negative. This assumption is somewhat
simplistic: if loop-loop interactions are attractive due to unintended base-pairing or base-stacking then the
attraction is likely to be highly sequence-dependent, and hence different between different pairs of loops.
We also assume that the stacking free energy is a linear function of both the number of active patches
(each contributing G
p
= 2G
st
) and the number of inactive patches (each contributing G
ll
). For
simplicity, for a given p, we averaged the measured free energies for different arrangements of active
patches. This resulted in a single free energy for each of three values of p (2, 4, and 6) which allowed us
to write the following three equations:
(1) 2G
p
+ 10G
ll
= -10.53
(2) 4G
p
+ 8G
ll
= -13.28
(3) 6G
p
+ 6G
ll
= -17.07
(all in kcal/mol)
Here we have more equations than unknowns. In principle, for this system of linear equations to be
consistent, the intersection of each pair of equations should coincide exactly. In practice, because of
experimental error and potential sequence-dependent effects, we expect that the intersections should lie in
close proximity to each other. Fig. S13 shows a plot of the three equations. The intersections occur at
(G
p
, G
ll
) = (-2.03, -0.65), (-2.24, -0.60), and (-2.37, -0.48), for equations (1) and (2), equations (1) and
(3), and equations (2) and (3), respectively. Least squares analysis gives a solution of (G
p
, G
ll
) = (-2.23,
-0.59) with a root mean square error of 0.24 (which can be roughly interpreted as the average distance of
the solution from each intersection in the plot of G
ll
vs. G
p
.
Thus we find that the average free energy of loop-loop interactions (G
ll
) is negative (suggesting that
loop-loop interactions contribute favorably to the binding) but smallless than half the average free
energy of a single base pair, -1.41 kcal/mol (nearest neighbor model Ref. 28 of the main text). It would
be interesting to ask whether the average loop-loop interaction is typical, or whether most loop-loop
interactions are neutral and just a few inactive patches contribute most of the binding energy. Answering
this question will require more experiments, in particular measurements of the binding energy for
stacking bonds that have the same stacking sequence, but loops of different base sequence. Another
observation is that G
ll
, the binding energy of a pair of inactive patches, is one-fourth the free energy for
an active patch G
p
Its effect on stacking bond strength will depend not just on this ratio, but the number
of inactive patches used. For a 16-patch stacking sequence with 7 active patches, the 9 inactive patches
will make a contribution to the binding energy that is roughly equivalent to two active patches, and about
one-fourth (coincidentally) of the total free energy of the bond. With respect to predicting the ratios of
correct vs. incorrect bonds, the contribution of loop-blunt end interactions (which occur frequently in
mismatch incorrect bonds) will likely have to be included; so far we have no quantitative data that address
such interactions. Finally, we observe that if this model is correct then we must reconcile the relatively
small |G
st
| observed (1.12 kcal/mol) with much higher literature values (2.42 kcal/mol). It may be
partially due to the difference in measurement methods, or it might suggest that the near-B-form stacks
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DOI: 10.1038/NCHEM.1070
(Note S2.5) which occur in 'relaxed' edges do, in fact, have a somewhat smaller free energy. Future
experiments using 'crossover-free' edges may address this question.

-4 -3 -2 -1 0 1
-4
-3
-2
-1
0
1
2
G
p
(kcal/mol)
G
l
l
(
k
c
a
l
/
m
o
l
)
-2.4 -2.2 -2
-0.7
-0.6
-0.5
-0.4

Eqn (1)
Eqn (2)
Eqn (3)
-2.4 -2.2 -2
-0.7
-0.6
-0.5
-0.4

Figure S13. Plots of the three equations given for G
p
and G
ll
in Note S3.2. Least squares analysis gives a
solution of (G
p
, G
ll
) = (-2.23, -0.59) with a root mean square error of 0.24. Inset shows a zoom-in view of the
plot near the intersections of the three lines.
!"
DOI: 10.1038/NCHEM.1070
Supplementary Note S4: Additional AFM Data
S4.1. Stacking of rectangles {figure caption on next page]

(a) (b) (c)
(d)
(e)
(f)
(g) (h) (l)
([) (k) (l)
(m)
(n)
(o)
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DOI: 10.1038/NCHEM.1070

Figure S14. Wide-field AFM images of rectangle origami systems. (a-c) Twist-corrected origami with relaxed
edges. Note that they form chains with lengths on the order of ~10 um. Chains formed by these origami break in a
way that suggests that the breakage occurs upon deposition since pieces lie close to each other. However, in
contrast to the twisted origami shown in (d-i), twist-corrected origami break into long pieces and show no
preferred direction for the shift between neighboring pieces. Note also that twist-corrected relaxed chains are
straight with very rare dislocations, as opposed to the twist-corrected origami with stressed edges shown in (j-o).
(d-i) Twisted origami (with relaxed edges). Chains break with a characteristic periodicity (2-6 origami) and
directional offset. Note that some parts of the chains seem to unwind while depositing, especially near the ends
(as suggested by the straight sections near the ends of twisted chains). (j-o) Origami with stressed edges (with
twist-correction). Bonds are promiscuous: many dislocations occur and the bond orientations are random. Orange
boxes and arrows show zoom-in areas. Scale bars in (a), (c), (j), (l), (m), (o) are 600 nm, and scale bars in (b),
(d-i), (k), (n) are 1 m.
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DOI: 10.1038/NCHEM.1070
S4.2. 5-origami cbains witb ortbogonal binary-coded bonds

Figure S15. Wide-field AFM images of 5-origami chains with orthogonal bonds based on a binary code.
Full correct bonds between each pair of origami resulted in chains with five distinct origami. Due to mismatched
bonds and small stoichiometric discrepancies, shorter chains, longer chains, and 5-origami chains containing
incorrect bonds were also found. 88% of total bonds analyzed (N=66) were correct bonds, and the fraction of
origami found in 5-origami chains was 31% (N=192). Scale bars, 500 nm.
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DOI: 10.1038/NCHEM.1070
S4.3. Urigami dimers and cbains witb ortbogonal sbape-coded bonds

Figure S16. Wide-field AFM images of dimers and 4-origami chains with orthogonal bonds based on a
shape code. (a-c) AFM of dimers of (a) A
r
+
l
B, (b) B
r
+
l
C, and (c) C
r
+
l
D, respectively, show high yields of
correct, full bonds. The fractions of correct bonds out of total bonds analyzed were 95% (N=191), 98% (N=203),
and 97% (N=179), respectively, and the fractions of origami found in correct dimers were 91% (N=397), 90%
(N=442), and 91% (N=384), respectively. (d) AFM of the A-B-C-D system show 4-origami chains with full,
correct bonds (some chains shown are folded), and some shorter chains that may result from stoichiometric
discrepancies or mismatched bonds. 81% of total bonds analyzed (N=279) were correct bonds, and the fraction of
origami found in 4-origami chains was 44% (N=430). Scale bars, 200 nm.
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DOI: 10.1038/NCHEM.1070
References
1. Sherman, W. B. & Seeman, N. C. Design of minimally strained nucleic acid nanotubes. Biophys. J. 90,
4546-4557, doi:10.1529/biophysj.105.080390 (2006).
2. Sa-Ardyen, P., Vologodskii, A. V. & Seeman, N. C. The flexibility of DNA double crossover
molecules. Biophys. J. 84, 3829-3837 (2003).
3. Sacc, B., Meyer, R., Feldkamp, U., Schroeder, H. & Niemeyer, C. M. High-throughput, real-time
monitoring of the self-assembly of DNA nanostructures by FRET spectroscopy. Angew. Chem., Int.
Ed. 47, 2135-2137 (2008).

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DOI: 10.1038/NCHEM.1070
Supplementary Note S5: Sequence lists and diagrams
S5.1. Rectangle witb 10.44 bpJturn

Core
Seq name Sequence
r0L11ml1 11ACA1AC1A1111CA111CCCCAA1CCC1
r0L11mr1 1AACAACCCACC1111CAACCC1AC1CACA
r0L11mr2 1AA1CCAC11CCACCCAC1AA1AAC1CACC1A
r0L11mr3 AAA1CACACC1A1111CCACCCACACAA1AAC
r0L11mr_fr A1AAC1CCA1A111AACAACCCCC1C1CA1
r0L11seam_l AA1A1CCC1AACACCAACCCCCAAACC1CCCC
r0L11seam_r CCACACCACCACAAAACC1AAAC1A1AACC1C
r0L13ml1 CAC1AA1CCCCACACAC1CAAA1AACC11A
r0L13mr1 1AAAC1ACCCACAA1AAACAACACC1A11C
r0L13mr2 AA111AA1AAA1CC1CA1CCAAA11111AA1C
r0L13mr3 CACCCA11AACCCCCC1C111A1C11CA1CC1
r0L13mr_fr AAA1AACACC11111AACC1CCC1CAC1CA
r0L13seam_l 111ACC1AA111CCCAAA1CC1CAAA11C1C1
r0L13seam_r 1A1A1111ACAACCCCACAAAAC1AAACCC1C
r0L13mr1 CAACACAAAC11AA111CA1C11CACAA1A
r0L13mr3 C1A1A1C1CC111CAAA1ACCCACCAACA1C1
r0L13mr_fr A1AACC1ACAA1AACCCA11CC11A1AC11
r0L13seam_l ACAAACCC1C1ACC1AAACA11CA1111CAAA
r0L17mr3 1CAA11ACACA1AAA1CAA1A1A1CCC11ACC
r0L17mr_fr C1CAA1ACC1A11AAA1CC111CCCAAA1C
r0L19ml1 CCACACAACCCC1CCC1AA1CACACCACCC
r0L19ml3 1CC1C1C1AA11CCC11CCCC1CAACACAC11
r0L19mr2 CCC1CAA11AACACCCCC1CCAACA11CACCA
r0L19mr_fr AACAC11CCACCACCACAACA1ACA11C1C
r0L19seam_r ACCA1CACCCCACCACCAAA1CAAA1AAAC1C
r0L1ml1 1CCAAAAC111CCACC1CAA111C1AA1CC
r0L1ml3 1111CACCCCCA1AC11CCCCCCAAC11111C
r0L1mr2 111AACCCCAA1CCAAACCCCAC1CCA1C111
r0L1mr_fr CCC1A1A1CCCC11CA1A11CACACCCACC
r0L1seam_r 11CA1CA11CCAC1AACCC1CA1ACCC111A1
r0L1L_seam CCCCACCC1CACAACCCCCACCC1CACAACCC
r0L1Ll1 CCACCC1CACACCCACCACCC1CAAAACCC
r0L1Ll2 CCA1ACCAACCCCAA1ACCAACCCCAACAC11
r0L1Ll3 1AACAC1CAC111CC1CACCAC11111C1C1
r0L1Lr1 CC1C1A1CACCC1AC1CACCACC11AA1AAC1
r0L21ml1 CAAAA1CCCC11A1AAA1CAAAACCCCCAA
r0L21ml3 AACCCC1CCC11CAC1C11C11CCCACCCCCC
r0L21ml_fl 111CCAC1CC1AA1CA1CC1CACCAAACCC
r0L21mr2 C1CACACC11CCAACACCAAAAAC1AAACCCA
r0L21mr3 C1CAC1A1CAA1A1C1CC1CAC11CCCCCAAC
r0L21mr_fr CCCAACA1CC1CC1AA1A1CCAAA1CC1CA
r0L21seam_r AAA1CCA11ACA1111CACCC1CACCAAA1CC
r0L23b_seam CC1CCCCACAAACCAACCCAACAAAA1CACAC
r0L23bl1 CA111ACACC11CACCCCCAAACCCAA1ACCC
r0L23br1 CCCCACC1AAACACCACCCCCA1CC1CA1C
r0L23br2 1111ACACACCAACCC1ACCCCACCAACAA1A
r0L23br3 CAAC1C11111A1AA1CAC1CACC1CAAAC1
r0L23ml2 CCACA1ACCACCC1CC111CCCCC1CACC1AA
r0L23ml_fl ACAACACCACCCCC1CCCCC1CC1CCCCCC
r0L23mr1 CAAA1ACC1A111ACA11CCCACAC1CCCA
r0L23mr3 CCCACCCAACCAC1AA1AAAACCCAAAACACA
r0L23seam_l CCAAAA1C1C111CA1CC1CC11CA1CC1C1C
r0L3ml1 CAC1ACCAA1ACAC1AAAACAC1A1C11CA
r0L3ml2 CC11CA1A11CAAAA1C1CCAAAAA1111CAC
r0L3ml3 C111CCA1CCA11A1ACCAACCCCCACCACCC
r0L3ml_fl ACAACCA11CC1AAACAAC111A1C1ACCC
r0L3mr1 111ACCC1ACACCAC1C1AC1CC11AC1AC
r0L3mr2 1CA1AA1CAA1CAAC111CCC111CAAAACCC
r0L3mr3 1AAACCCACC1CAC1CCC11CAC1CA1A1AAC
r0L3mr_fr ACCCCAA1CCA1ACCACCACCCCAACC1AA
r0L3seam_l CACC11CCCACCC111AA11C1A1CA1CCC11
r0L3seam_r CA1ACCCCCCCC1111CA1CCCCACCAAACAC
r0L3ml1 CAACAACCC1CC1CA11CAC1CAAA1CCAC
r0L3ml2 ACCCCCAC1AAACCCC1AAAA1ACC11AAACA
r0L3ml_fl C1ACAACC111CACCAC1AAACCAA1CACA
r0L3mr1 CAC1C1ACCC11A11ACCC111CC1C1CAA
r0L3mr2 CCACA11CCAAACCCAAACACACCA1AA1AAC
r0L3mr3 ACCCACACAAAA1CACCCCAACCACAAACAAA
r0L3mr_fr A1A11CACCAAACC1ACAAAA1ACC1A1C1
r0L3seam_l CCAAAACAACCCACCAACC1AAAA1111CCC1
r0L3seam_r A1A1CC11111C1CACAA1CAA1AAA1CAACC
r0L7ml1 A1ACA1AAAACAC1A1CA1AACC11CCA1C
r0L7mr1 AAC111A11ACCACCCCCAAACAACCC1CA
r0L7mr2 ACCAACAA1CAACACCC1CAACAA1AAA1CAA
r0L7mr3 A1A1AAAAAACCCA11CACCCACC1AA1CAC1
r0L7mr_fr 1ACCCAACCACCC111ACACACC1ACAA11
r0L7seam_l 1AACAAACCCA1A11CA11ACCCACAAAA11C
r0L7seam_r CCACAACACACCCC1AA1A1CACACACCCA1A
r0L9ml1 AAAAACA1C1111AA11CCACC111CACCA
r0L9mr1 CCC1AA11A11CAC11AACCCCAACCCAA1
r0L9mr2 CA11AC111A1ACAACCC11A1CC1C11CACC
r0L9mr3 CAA11AACACAA1CAAA1ACCAA1ACA1ACA1
r0L9mr_fr 11A1CC1CAACCCC11111A11AACAA1AC
r0L9seam_l C1AACACCCCCCAAAACCAA11ACCACA1AAC
r0L9seam_r AC11CCCCCCACCCC1111ACCCAACAC11CA
r1L0Lr2 CCA1AAC1CCCC1CCACACCC11AACAC1CC
r1L0Lr3 1ACCA11ACCCCCC1111CC1CAC1CCC1A11
r1L10fr1 ACAACAACCAA1C11ACCAACCC1C1CAAAAA
r1L10fr2 1C111CCA11AAACCAAC1ACCCCA1A1CCCA
r1L10fr3 AACCCC1ACACCC1AA111CCCAAA1CCAA
r1L12fr1 ACAA1CCCC1CAACAACAAAAA1AAC1CA1CC
r1L12fr2 1CC1AA11ACCC1CAACAC1ACCCAACACCCC

r1L12fr3 1AAACCCA1ACCACCA1C1ACAA11CCAAC
r1L14fr1 CACACAC1CCC11AAA1AACAA1AC11AA11C
r1L14fr2 AA1CA1AA1CAA111A1CAAAA1CCCC1A11A
r1L14fr3 C1CAA1AC11AC1ACAAAAACCCACCAC1A
r1L16fr1 CCCCACAA1CC11C1C1AAA1CC1A1ACC1C1
r1L16fr2 A11AA111A1ACAC1AACAC1ACCC1ACCA1A
r1L16fr3 ACA1CAA11CCC11ACAA1CC11CACAACA
r1L18fr1 CCACAAC1A1CCAACCC11ACAAC1111ACA1
r1L18fr2 1CAAAA11AAC1A11ACAC111ACCC11A1C1
r1L18fr3 CCA111ACA111CCACC1AAAAC1AACC1C
r1L20fr1 CCAACCAACAAACCAA11CACCAAAAACAA11
r1L20fr2 AAAA1A1CC1AAAACA1CCCCA11CACC1CAA
r1L20fr3 1CA1ACCC111ACCACCAC1AACCA111CA
r1L22fr1 A1CCCCC1CACA1ACAACCC11C1AAAAA1AC
r1L22fr2 ACCC1AAC1CCC1CAC1ACAACAACCCACCCA
r1L22fr3 ACA1CAC1AA1ACC1CCCACACACCCCAAC
r1L24br4 C1AAAACAC1C1C1CCA1CACCCAC1AA1A
r1L2fr1 CACACCA1AACAC11AA1CCCCCC1ACCACCC
r1L2fr2 1CCCAACCCA11CACACCACC11CCCCCACCC
r1L2fr3 CCCCCCAC1A11A11C1CAAACACAACCA1
r1L4fr1 1CAAACCACCCCC1CCC1CACACCACCCACC1
r1L4fr2 1CACAACC1ACCAACCCCCCAAACAACC1CAA
r1L4fr3 A11ACCA1CCCACCC1CACACCCCACACCC
r1L6fr1 C1A1C11ACCCAAA11A11CA11AC1CACCAA
r1L6fr2 11A1CACCA1CA11AACAC1CC11C1AACCAC
r1L6fr3 CAAC1CCCC1CACCCAC11CACC1ACCACC
r1L8fr1 1CAAAA1ACCCC11111AACAAAAA11ACCCA
r1L8fr2 A1ACCCCACCA111111C111AACAACCACCC
r1L8fr3 A1AACAAAACAAAC11ACCACAACCCAAAA
r-1L0Ll4 CAACCCC1C1ACCA11CCACACA111C1CC
r-1L10fl1 AAACCACACAC1ACC111AA11CC1ACCC1C1
r-1L10fl2 A1AACACCC1CAAA1CC111AAACACACCCCC
r-1L10fl3 CAA1CCCC1CA11111CCCCA1CACC1CAA
r-1L12fl1 C1CCAAC1ACA1CCAA1AAA1CA11111CCCC
r-1L12fl2 CCCAAACAAAA1A1CCAAC1AAAC1CC1111C
r-1L12fl3 CA1C1111A11ACCAAAA11AAC11C1ACC
r-1L14fl1 CACAACCCCACACCC1ACC1A111CA1A1C1A
r-1L14fl2 1C1ACAAA1A1CACCC1C1AA1ACACACCCAA
r-1L14fl3 AAAAACA1CCC1A1CACC1CA111CAACCC
r-1L16fl1 CCCCCC11CC111CA1CAACA11ACC1AACCC
r-1L16fl2 CCAC1AACAAAC1ACCA1C1CAA111CACACA
r-1L16fl3 1AA1CC1AAACCCC1CCCA11C1CCA1ACC
r-1L18fl1 1CCA1C1CC1CCAACCCCA11AACCC1ACCCA
r-1L18fl2 CCCCACCCC1C1ACA1CCCCCCA1AA1C1CAC
r-1L18fl3 1CACC11C1111CCCAC1CACCAA1CCC1C
r-1L20fl1 CC1CCAA11CCCCAAACC1C1CC1ACACC1CA
r-1L20fl2 CA11AA1CC1C1ACACCA1CCCCC11CCC1AA
r-1L20fl3 CACC1CCAAA1CCCCCAACCCCCC1CC111
r-1L22fl1 11CCCC111CCAC1A11AAACAACCCCC1AAA
r-1L22fl2 CAACC1CAACCAC1CACACCCCCACCCACC1C
r-1L22fl3 11C1111CAACCCCCAAAAACCC1CACCCA
r-1L24bl2 CCAC1AAA1CCCAACCC1AAACCAC111CCA
r-1L24bl3 AA1CAAC111111CCCC1CCACC1C1CCAC1C
r-1L2fl1 A1CCCA111CCCCCACCCA1AACCCCAACCCC
r-1L2fl2 CCC1CCC1CACC11AC1AAA1CAAACAAAC1A
r-1L2fl3 1C111CCACACCC11CCACCCACACCACCC
r-1L4fl1 1ACACACCCCACA111C1A1CA1CAC111CAA
r-1L4fl2 AA11C1C1CA1CCCAACCACCC1ACA1A1A11
r-1L4fl3 AAACACACCCAAA1CCCCCACC1ACCC1CA
r-1L6fl1 ACACCACAC11CACA1CC111AA1AACCAAC1
r-1L6fl2 1AA1CA11CCAACCCAAC1CACCACCC1CA1A
r-1L6fl3 A1CA1AACC1CAA11ACC11A1CCCACC11
r-1L8fl1 AACCCAACCAAAACAAC1111CCCAC11CACA
r-1L8fl2 1AA1AC1AAAA1C1ACC11AA1AA11CAAC11
r-1L8fl3 CCCAACAAAAA1C111ACAC1CCA11CA11
rL-rem1 ACCACC1A1AACC1CC111CC1CC11AC
rL-rem2 ACACCCCCCC1AC1A1CC11CC111CACC
rL-rem3 ACCACACCCCCCCCCC11AA1CCCCCCC1
rL-rem4 CAAC1C1ACCCC1CACCC1CCCCC1AACC
rL-rem3 ACCCAAACCACCCCCCCC1ACCCCCC1CC

Ldge stap|es that make re/oxed edqes
k|ght edge (from top to bottom)
r1L0_edge_r_2 C1CACAC1CC1CAACA1CAAAC1A11AACACC
r1L2_edge_r_2 CCACCACAACCACCACACCACCC1CACACCCC
r1L4_edge_r_2 CCACCAAAA1CACCACCA111CCCAA11ACAC
r1L6_edge_r_2 CAA1AA1AACCCAA1ACCAAACCCACCAAACC
r1L8_edge_r_2 CCA1A11A111A1CCCC11ACAAAA1AAACAC
r1L10_edge_r_2 C1C1C111CC11A1CAACCAA1CAA1AA1CCC
r1L12_edge_r_2 CC11A1ACAAA11C111C111AC1A1CA1A1C
r1L14_edge_r_2 C11ACA11AACACCC1CAAAACA1ACCCA1AC
r1L16_edge_r_2 CC1ACA1111CACC11ACAAA1AAACAAA11C
r1L18_edge_r_2 CCC1CAA1ACA1AA1AAAC1AA1ACA11ACAC
r1L20_edge_r_2 C1A11AC1C111AA1CCAA1A11111CAA1CC
r1L22_edge_r_2 CAA1AC11C111CA11AAA11AACCC11C1AC

Left edge (from top to bottom)
r-1L2_edge_l_2 CC1AACCA1C1AAAC1CACCCC1CA1AC11AC
r-1L4_edge_l_2 CCCCA1CC1CACCC1C11AAACCCCCC1111C
r-1L6_edge_l_2 CCCCAACCACCCCCACCC1CCA1C11AC11AC
r-1L8_edge_l_2 C1CA11A1ACCAC1CACCA1111AACAAC1CC
r-1L10_edge_l_2 CCCAA1CC1CA1AAA1A1ACCC1CCAA1AC1C
r-1L12_edge_l_2 C1CAA1A1AA1CC1C1CC11ACACC11AA11C
r-1L14_edge_l_2 CA1AAACC1AAA1CCCCAA1AAACCC1CACAC
r-1L16_edge_l_2 CAAACAACACAA1CCACCC1CACAC1C1CCAC
r-1L18_edge_l_2 CCCA11CACCC1AA1CCCC1CCCAACAAACCC
r-1L20_edge_l_2 CCAC1CCCAACC11CCCC11C1AAAACCACCC
r-1L22_edge_l_2 CC1A11CCCCCCCACCCCCCACACCCCC111C
r-1L24_edge_l_2 CCCAC1ACC1CAACCA1C1A1CACCCCCA1CC

Ldge stap|es that make stressed edqes
r1L0_edge_r C1CACAC1CC1CAACA1CAAAC1A
r1L2_edge_r 11AACACCCCACCACAACCACCACACCACCC1
r1L4_edge_r CACACCCCCCACCAAAA1CACCACCA111CCC
r1L6_edge_r AA11ACACCAA1AA1AACCCAA1ACCAAACCC
r1L8_edge_r ACCAAACCCCA1A11A111A1CCCC11ACAAA
r1L10_edge_r A1AAACACC1C1C111CC11A1CAACCAA1CA
r1L12_edge_r A1AA1CCCCC11A1ACAAA11C111C111AC1
r1L14_edge_r A1CA1A1CC11ACA11AACACCC1CAAAACA1
r1L16_edge_r ACCCA1ACCC1ACA1111CACC11ACAAA1AA
r1L18_edge_r ACAAA11CCCC1CAA1ACA1AA1AAAC1AA1A
r1L20_edge_r CA11ACACC1A11AC1C111AA1CCAA1A111
r1L22_edge_brc 11CAA1CCCAA1AC11C111CA11AAA11AACCC11C1AC

r-1L2_edge_Llc CCC1111CCC1AACCA1C1AAAC1CACCCC1CA1AC11AC
r-1L4_edge_l 11AC11ACCCCCA1CC1CACCC1C11AAACCC
r-1L6_edge_l ACAAC1CCCCCCAACCACCCCCACCC1CCA1C
r-1L8_edge_l CAA1AC1CC1CA11A1ACCAC1CACCA1111A
r-1L10_edge_l C11AA11CCCCAA1CC1CA1AAA1A1ACCC1C
r-1L12_edge_l CC1CACACC1CAA1A1AA1CC1C1CC11ACAC
r-1L14_edge_l C1C1CCACCA1AAACC1AAA1CCCCAA1AAAC
r-1L16_edge_l ACAAACCCCAAACAACACAA1CCACCC1CACA
r-1L18_edge_l AACCACCCCCCA11CACCC1AA1CCCC1CCCA
r-1L20_edge_l CCCC111CCCAC1CCCAACC11CCCC11C1AA
r-1L22_edge_l CCCCA1CCCC1A11CCCCCCCACCCCCCACAC
r-1L24_edge_l CCCAC1ACC1CAACCA1C1A1CAC

na|rp|n-|abe|ed stap|es (ha|rp|n sequence |n |owercase)
r0L3ml3_hp CC1CCC1CCCACAAACLccLcLLLLgaggaacaagLLLLcLLgLACCACAACACAAACA1
r0L7ml2_hp 1CCCC1CAACC11CA1LccLcLLLLgaggaacaagLLLLcLLgLCAACAC1ACA1C111C
r0L7ml3_hp CA111ACCCCA1AAAALccLcLLLLgaggaacaagLLLLcLLgLACCAAAA1AAA1CACC
r0L9ml2_hp CCACACCAAA1ACCACLccLcLLLLgaggaacaagLLLLcLLgLA11CAAC1A1AACCC1
r0L9ml3_hp 1A11A1ACCCCAACCALccLcLLLLgaggaacaagLLLLcLLgLAAC1CCAAAC11CA11
r0L11ml2_hp AACCACAC1CACAACCLccLcLLLLgaggaacaagLLLLcLLgLAAACCCCAC1CC111A
r0L11ml3_hp A11C1CCCCCCA1CAALccLcLLLLgaggaacaagLLLLcLLgL11C1AC1ACCA1AAAA
r0L13ml2_hp CAAAACC1AACCAC1ALccLcLLLLgaggaacaagLLLLcLLgLCA111AC11CAAACCC
r0L13ml3_hp ACAACCC111CAACCCLccLcLLLLgaggaacaagLLLLcLLgL11C1ACC1CCCAAAAA
r0L13ml2_hp A1A1CA1ACA1A1A11LccLcLLLLgaggaacaagLLLLcLLgL11AAA1CCCCCCACC1
r0L13ml3_hp C1A1AACCAAA1AA11LccLcLLLLgaggaacaagLLLLcLLgLCCCC1C1CCACCACAC
r0L13mr2_hp CAAACAC1C1CACCAALccLcLLLLgaggaacaagLLLLcLLgLAACAACA1CCAA11CA
r0L13seam_r_hp AACAA111AACAAAACLccLcLLLLgaggaacaagLLLLcLLgLAAAA11AAA11111C1
r0L17ml2_hp CCCA1CAAAAA1A111LccLcLLLLgaggaacaagLLLLcLLgLAAA11C1ACACCA1CA
r0L17ml3_hp CACC111CC1A11ACCLccLcLLLLgaggaacaagLLLLcLLgLCCACC1CC1ACC1C11
r0L17mr2_hp 1CAA1A1A1AACA11ALccLcLLLLgaggaacaagLLLLcLLgL1CA1111CA1A1CAAA
r0L17seam_l_hp 1AAA1CAC11AAAA11LccLcLLLLgaggaacaagLLLLcLLgLCCCA11AA11ACA111
r0L17seam_r_hp A1A11CC1ACCACAACLccLcLLLLgaggaacaagLLLLcLLgLCACCCCAA1CACCC1C
r0L19ml2_hp CC1C11CCCCCCACCCLccLcLLLLgaggaacaagLLLLcLLgLC11C1CC1A1ACCAAC
r0L19mr3_hp AC111CACA1CC1CA1LccLcLLLLgaggaacaagLLLLcLLgL1C111CCACC1CA11C
r0L19seam_l_hp CCCAAC1CAACCCCCALccLcLLLLgaggaacaagLLLLcLLgL11CCCCA111A1CA1C
r0L21ml2_hp C1CACA11CAAA11C1LccLcLLLLgaggaacaagLLLLcLLgL1A1CCCC1CC1CCCCC
r0L21seam_l_hp 1AAACCC1CA1ACCACLccLcLLLLgaggaacaagLLLLcLLgLCCCCAACCAAA1C1AA
r0L7ml_fl_hp AA11CCCCA1CAACCLccLcLLLLgaggaacaagLLLLcLLgLC1C1ACACAAACAAA
r0L9ml_fl_hp CC1111CAACA11A1LccLcLLLLgaggaacaagLLLLcLLgL1ACACC1CAC1AC1A
r0L11ml_fl_hp CA11ACAA1CACCA1LccLcLLLLgaggaacaagLLLLcLLgLAAA1CAAACCCACAC
r0L13ml_fl_hp ACCA11A11CA11CCLccLcLLLLgaggaacaagLLLLcLLgLA1A1AACCACC1CAC
r0L13ml1_hp A1A1111CC1CA111LccLcLLLLgaggaacaagLLLLcLLgL111AACCACCCCCAA
r0L13ml_fl_hp AA1CCCC111A111CLccLcLLLLgaggaacaagLLLLcLLgLAACCCAAA1AC1AC1
r0L17ml1_hp ACCACCCA11CCCAALccLcLLLLgaggaacaagLLLLcLLgLCCCCCA1CCACAA11
r0L17ml_fl_hp C1ACCCACA1AA1CALccLcLLLLgaggaacaagLLLLcLLgLCAAAACCCA1AAA11
r0L17mr1_hp CAAACA1CCA111CALccLcLLLLgaggaacaagLLLLcLLgLA11ACC11CCAA1CC
r0L19ml_fl_hp CCA1C1CCCAC111CLccLcLLLLgaggaacaagLLLLcLLgLACCCCACCCC11CC1
r0L19mr1_hp AACAAACCCA11A1CLccLcLLLLgaggaacaagLLLLcLLgLACA1CA1CCA1CAAA
r0L21mr1_hp CCC1CACAC11CC1CLccLcLLLLgaggaacaagLLLLcLLgLAACC1CAACCCAACA

!"
DOI: 10.1038/NCHEM.1070
D|agram for rectang|e w|th 10.44 bp]turn
wlLh poslLlons of dumbbells (orange clrcles) and poslLlons and lengLhs of loopouLs (black clrcles wlLh numbers) lndlcaLed

52
8
6
11
13
4
6
10
29
5
14
11
12
29
29
13
46
15
9
5
10
!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for rectang|e w|th 10.44 bp]turn - (1) w|th edge stap|es that create re/oxed edqes

-1 0 +1

< GATTGATACTCCCGACAGACACCTTACGATGTCCGCAACATCAAACATGACCACTGCTTTGAGTCACAA< <CTGCCGTGAATAGGCGGACCATGACTCGTTTTGGGGCGATTAGGATTAGGAAGAGAACTCCTCAGAGTC <
> CTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTT---ACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTG-------AGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCCTTATATCAACCCTCTC---GACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAG >
/ <TGCCATGTACCCAAGGATAACCCGAACGATAGGGACTTTTACTCCCACCACCGAGACTCCCACCGCCAAGAC-------TCCCACCGCCAAGACTCCCACCGCCATGATTTGGAGGACTCATGCCACTATGTGGGAATATAGTTGGGAGAG< \
| |
\ >AACAACTTTCAACAGTTTTTTCACGTTGAAAATCTCCAAAAAAAAGGCTCCAAAAGGAGCCTTTAATTGTAT-------CATGGCTTTTGATGATACAGGAGTGTACTGGTAATAAGTTTTAACGGGGTCAGTGCCTTGAGTAACAGTGCC> /
< GCATTGCTAGATTTCAAAACAGCAGAAAGGTCTGCAATCATTTACTTAAAAGACATACCCTAAAACGAT---TTGTTGAAAGTTGTCAAAAAAGTGCAACTTTTAGAGGTTTTTTTTCCGAGGTTTTCCTCGGAAATTAACATA< <GTACCGAAAACTACTATGTCCTCACATGACCATTATTCAAAATTGCCCCAGTCACGGAACTCATTGTCACGG---GCATATTTGTCAATTACGGGGGACGGATAAAGCCTTGGATAATAAGACTTTGTACTTTCATAATTCTCC <
CGTAACGATCTAAAGTTTTGTCGTCTTTCCAGACGTTAGTAAATGAATTTTCTGTATGGGATTTTGCTA> \ / >CGTATAAACAGTTAATGCCCCCTGCCTATTTCGGAACCTATTATTCTGAAACATGAAAGTATTAAGAGG
( | | )
GTTTTCGCCGGAAATTGAGGGACGTTCGGAGTCGCTGGCTTATATAGCCAATACGCACCCGCTACCAAC< / \ <TCCGGTTAGCAGACTGGACGGAGTTGGAGGACAGTTACGACCGCCGCCGAGACCACCACCAAGACCACC
> CAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTG---TTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCG> >TATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTATTTGTTTGTGAATATCA---AGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGG >
/ <AACAGTAACAGCCGCGTTGATAGCCATAGTTCGACAAATTCTTTAAGTGGAGCTTTCGTTCGACTATTTGGC-------ATACTGCGAATGACCTTGCCATTTAAGTCTCTGACGCGAAAGGTAAGACCGAAATAAACAAACACTTATAGT< \
| r0t3r0t3seam_r |
\ >GGACTAAAGACTTTTTCGTTTCCATTAAACGGGTAAAATACGTAATGCCACTACGAAGGCACCAACCTAAAA-------TTTTCGGTCATAGCCCCCTTATTAGCGTTTGCCATCTTTTCATAATCAAAATCACCGGAACCAGAGCCACCA> /
< GCCCTAGCAGTGGGAGTCGTCGCTTTCTGTCGTAGCCTTGCTCCCATCGTTGCCGATGTCTCCGAAACT---CCTGATTTCTGAAAAAGCAAAGGTAATTTGCCCATTTTATGCATTACGGTGATGCTTCCGTGGTTGGATTTT< <AAAAGCCAGTATCGGGGGAATAATCGCAAACGGTAGAAAAGTATTAGTTTTAGTGGCCTTGGTCTCGGTGGT---GGCCTTGGCGGAGGGAGTCTCGGCGGTGGGAGTCTTGGCGGTGGGAGTCTCGGTGGTGGGAGTCTCGGC <
CGGGATCGTCACCCTCAGCAGCGAAAGACAGCATCGGAACGAGGGTAGCAACGGCTACAGAGGCTTTGA> \ / >CCGGAACCGCCTCCCTCAGAGCCGCCACCCTCAGAACCGCCACCCTCAGAGCCACCACCCTCAGAGCCG
( | | )
GATTCATTGTACCTCGTCCAGCGCCTAAAGCTGTGTTAAATAGTCCGCTACTATGTTTAGAGGCAACAT< / \ <ATAGCTACCAAAGTAACCACTGCAAAGGCCGGAACGATTACCATTACCACGATGACCACTAAAACGACC
> CTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTA---CTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCG> >TGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGC---TATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGG >
/ <GAAACAAAGCGCGAACCATATTAGCGACCCCCAGTTTCTACTCACAAAATCACATAAGAAAACGGAGAAAGC-------ACGGCTACTTTTGCGCGATGTCAGACTGCGATTTCCGTTTGAACTAAGACAGCGATGACTAATGCCACGACG< \
| r0t5r0t5seam_r |
\ >CGGTGTACAGACCAGGCGCTGGCTGACCTTCATCAAGAGTAATCTTGACAAGAACCGGATATTCATTACCCA-------GAAAATTCATATGGTTTACCAGCGCCAAAGACAAAAGGGCGACATTCAACCGATTGAGGGAGGGAAGGTAAA> /
< GGCCTTGCTCCGCGTCTGCCAGTTAGTATTCCCTTGGCTTGACTGGTTGAAACTTTCTCCTGTCTACTT---GCCACATGTCTGGTCCGCGACCGACTGGAAGTAGTTCTCATTAGAACTGTTCTTGGCCTATAAGTAATGGGT< <CTTTTAAGTATACCAAATGGTCGCGGTTTCTGTTTTCCCGCTGTAAGTTGGCTAACTCCCTCCCTTCCATTT---ATAACTGCCTTTAATAAGTAATTTCCACTTAATAGTGGCAGTGGCTGAACTCGGTAAACCCTTAATCTC <
CCGGAACGAGGCGCAGACGGTCAATCATAAGGGAACCGAACTGACCAACTTTGAAAGAGGACAGATGAA> \ / >TATTGACGGAAATTATTCATTAAAGGTGAATTATCACCGTCACCGACTTGAGCCATTTGGGAATTAGAG
( | | )
GGTCAAGAATTTTAGCGTATTCCATTAAGTGTTACTAATTTCAACTTTAATTTGGTAGAGTTCGGGTTA< / \ <CAAACGATTGTATGACGCATTATTCCTCAGAATTAGTACGGTCAAGAAAACCCATAAGGCAATAATAAC
> CCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAAT---TTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATT> >TATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATATGTATGTATTTTCTAC---GTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTG >
/ <AATGATGAGCAAGACCACAAAGAGCAGTCCCGTTCGGAATAAGTGACTTACTCGTCGAAACAATGCAACTAA-------ATAACTAACACTGTTTTATTTGAATAAGGCACCACAGAAACGCAAAGAAAATATATACATACATAAAAGATG< \
| r0t7r0t7seam_r |
\ >ATTACAGGTAGAAAGATGATTTAGGAATACCACATTCAACTAATGCAGATACATAACGCCAAAAGGAATTAC-------GAGATAACCCACAAGAATTGAGTTAAGCCCAATAATAAGAGCAAGAAACAATGAAATAGCAATAGCTATCTT> /
< GAGTAATATGGTCAGTCCTGCAACCCTTCTTTTTAGATGCAATTATTTTGCTTGATTGCCTTGTTGTAA---TAATGTCCATCTTTCTACTAAATCCTTATGGTGTAAGTTGATTACGTCTATGTATTGCGGTTTTCCTTAATG< <CTCTATTGGGTGTTCTTAACTCAATTCGGGTTATTATTCTCGTTCTTTGTTACTTTATCGTTATCGATAGAA---TGGCTTCGGGAAAAATTCTTTTCATTCGTCTATCGGCTTGTTTCAATGGTCTTCCTTTGGCTCCTTTGC <
CTCATTATACCAGTCAGGACGTTGGGAAGAAAAATCTACGTTAATAAAACGAACTAACGGAACAACATT> \ / >ACCGAAGCCCTTTTTAAGAAAAGTAAGCAGATAGCCGAACAAAGTTACCAGAAGGAAACCGAGGAAACG
( | | )
GTCATAACCTGCGATAGGTCAGATTTGTAAAATGATAATGGGGGAGACCGTTTTGAAGAAAACGTTTTC< / \ <CCGACGATAAAAGTAAAAACTGCAATTTGTTTTTTAGCAAAGAATAAACCTAACCCTATTTATTATACC
> CAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAG---CCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTC> >TCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCGTTATTCTCTCTGTAAA---GGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGG >
/ <GGAGAGCGATAAAACCAAAAATAGCAGCAGACCATTTGCTCCCAATACTATCACAACGAGAATGATACGGAG-------AGACTATAATCGCGAGTTAATGGGAGACTGAAACAAGTCCCACAAGTCAATTAAGCAATAAGAGAGACATTT< \
| r0t9r0t9seam_r |
\ >ATAAATCAAAAATCAGGTATTATAGTCAGAAGCAAAGCGGATTGCATCAAAAAGATTAAGAGGAAGCCCGAA-------ACCTCCCGACTTGCGGGAGGTTTTGAAGCCTTAAATCAAGATTAGTTGCTATTTTGCACCCAGCTACAATTT> /
< GCCTTAGCAGTATTTATAAGTAACTTAGGGGGAGTTTACGAAATTTGTCAAGTCTTTTGCTCTTACTGG---TATTTAGTTTTTAGTCCATAATATCAGTCTTCGTTTCGCCTAACGTAGTTTTTCTAATTCTCCTTCGGGCTT< <TGGAGGGCTGAACGCCCTCCAAAACTTCGGAATTTAGTTCTAATCAACGATAAAACGTGGGTCGATGTTAAA---ATAGGACTTAGAATGGTTGCGATTGCTCGCAGAAAGGTCTCGGATTAAACGGTCAATGTTTTATTTGTC <
CGGAATCGTCATAAATATTCATTGAATCCCCCTCAAATGCTTTAAACAGTTCAGAAAACGAGAATGACC> \ / >TATCCTGAATCTTACCAACGCTAACGAGCGTCTTTCCAGAGCCTAATTTGCCAGTTACAAAATAAACAG
( | | )
GTTAATTCGAGATTCGGTAGGCGTTTTTACTGGAGAATAGTTTTCCTCGTTAATTTCCATGAGAGATTA< / \ <CCGAACGAACAAGAGCTACTCACGCCATGAACCAAATTATGGGCAAGAACCTTACTATTCCTTTCTGTC
> CAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAAT---CCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCT> >TCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTACGATGAAAATAAAAAC---GGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAG >
/ <GGACTGGACAACCTCAAACGAAGGCCAGACCAAGCGAAACTTCGAGCTTAATTTTGCGCTATAAACTTCAGA-------AGCGATTTTGCGGAGCGCAAGAATCTTATGGCCTATTCGGAAGATATAGACTAAATGCTACTTTTATTTTTG< \
| r0t1r0t11seam_r |
\ >CCATATAACAGTTGATTATTCTGCGAACGAGTAGATTTAGTTTGACCATTAGATACATTTCGCAAATGGTCA-------AATTCTGTCCAGACGACGACAATAAACAACATGTTCAGCTAATGCAGAACGCGCCTGTTTATCAACAATAGA> /
< GACTTATATTACGACATCGAGTTGTACAAAATTTATACGTTGATTTCATGCCACAGACCTTCAAAGTAA---GGTATATTGTCAACTAATAAGACGCTTGCTCATCTAAATCAAACTGGTAATCTATGTAAAGCGTTTACCAGT< <TTAAGACAGGTCTGCTGCTGTTATTTGTTGTACAAGTCGATTACGTCTTGCGCGGACAAATAGTTGTTATCT---ATTCAGGACTTGTTCTTTTTATTATAGGGTAGGATTAAATGCTCGTACATCTTTGGTTAGTTATTAGCC <
CTGAATATAATGCTGTAGCTCAACATGTTTTAAATATGCAACTAAAGTACGGTGTCTGGAAGTTTCATT> \ / >TAAGTCCTGAACAAGAAAAATAATATCCCATCCTAATTTACGAGCATGTAGAAACCAATCAATAATCGG
( | | )
GAGACTCCGAAATAACGAATTAAAACGATTAAGAAACGGAACGGACATACTAAATAACCTACAATTACG< / \ <TTATACCGCTAAGAGTTAATTCGGGATGACAACTCGCAACCGAAATATGACCATTCTTAAACATATTGC
> CTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGC---TACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTAT> >ACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCACATGTTGGCGTTGTTA---AATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACG >
/ <ATGATGATAATCATCTTAACTACGGTGGAAAAGTCGAGCGCGGGGTTTACTTTTATATCGATTTGTCCAATA-------TGAAATGGAAAACAGCCATGAAATATAAGAGAATAATGACCGAGCTTTTACGGAGTGTACAACCGCAACAAT< \
| r0t1r0t13seam_r |
\ >TCAACGCAAGGATAAAAAGAACCCTCATATATTTTAAATGCAATGCCTGAGTAATGTGTAGGTAAAGATTCA-------TTTTCAAATATATTTTAGTTAATTTCATCTTCTGACCTAAATTTAATGGTTTGAAATACCGACCGTGTGATA> /
< GTATTTCGATTTAGCCAACATGGTTTTTGTAATACTGGGACATTATGAAAACGCCCTCTTCGGAAATAA---AGTTGCGTTCCTATTTTTCTTGGGAGTATATAAAATTTACGTTACGGACTCATTACACATCCATTTCTAAGT< <AAAAGTTTATATAAAATCAATTAAAGTAGAAGACTGGATTTAAATTACCAAACTTTATGGCTGGCACACTAT---TTATTCCGCAATTTATTCTTATTTGTGGCCTTAGTATTAATGATCTTTTTCGGACAAATCATAGTATAC <
CATAAAGCTAAATCGGTTGTACCAAAAACATTATGACCCTGTAATACTTTTGCGGGAGAAGCCTTTATT> \ / >AATAAGGCGTTAAATAAGAATAAACACCGGAATCATAATTACTAGAAAAAGCCTGTTTAGTATCATATG
( | | )
GAGGTCTGAGAGTCCGTTACTGGACTATCGGAAACATCTAGAGAGTTTTTATCGATGGGAGAGGCCGTA< / \ <TTTCCATCAGAGAGTCTGGATACTAAAACTATTTAAGTGATAACTGAGAAGAGTCGCAGAATTAGATTC
> CTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCAT---TAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTT> >AGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGCCTAAGCCGGAGGTTAA---AAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAG >
/ <ATTAAATAGTCGATCTTGCCAACTTATAGTATAACTACCACTAAACTGACAGAGGCCGGAAAGAGTGGGAAA-------TCAAAAGAGCGCAAGAAACAGAACGCTAACCTAAACGTAGTCGTAAATGTATATCGGATTCGGCCTCCAATT< \
| r0t1r0t15seam_r |
\ >CAGAAAAGCCCCAAAAAGTATAAGCAAATATTTAAATTGTAAACGTTAATATTTTGTTAAAATTCGCATTAA-------TTACATTTAACAATTTCATTTGAATTACCTTTTTTAATGGAAACAGTACATAAATCAATATATGTGAGTGAA> /
< GTTTGTTCTCTTAGCTACTTGCCATTAGCATTTTGATCGTACAGTTAGTATACATGGGGCCAACTATTA---GTCTTTTCGGGGTTTTTCATATTCGTTTATAAATTTAACATTTGCAATTATAAAACAATTTTAAGCGTAATT< <AATGTAAATTGTTAAAGTAAACTTAATGGAAAAAATTACCTTTGTCATGTATTTAGTTATATACACTCACTT---ATTGGAACGAAGACATTTAGCAGCGATAATTAATTAAAAGGGAATCTTAGGAACTTTTGTATCGCTATC <
CAAACAAGAGAATCGATGAACGGTAATCGTAAAACTAGCATGTCAATCATATGTACCCCGGTTGATAAT> \ / >TAACCTTGCTTCTGTAAATCGTCGCTATTAATTAATTTTCCCTTAGAATCCTTGAAAACATAGCGATAG
( | | )
GGCAAACAAGGGTGCCTCTTAGGCTGCCCAACAATGAGCGAGTGTAAATTACAACTACTTTCGACCGAT< / \ <ATAACAAAGAGGGCTACATTTTCCATGACAATGACATATAAGTAGACTGCAATTTGGACTTTTAGATGC
> CCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTA---CAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAAT> >TTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGACAATCAGGCGAATCCGT---TATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACG >
/ <GTCCTTCCGGTCTGCGCTTAATAAAAACTACCGCAAGGATAACCAATTTTTTACTCGACTAAATTGTTTTTA-------AATTAAAACAAAAGAACTACAAACAAAGTAGTAGAAGAAAACGAGTCCATTAACTGTTAGTCCGCTTAGGCA< \
| r0t1r0t17seam_r |
\ >TGAGGGGACGACGACAGCAGCTTTCCGGCACCGCTTCTGGTGCCGGAAACCAGGCAAAGCGCCATTCGCCAT-------TTATCATCATATTCCTGATTATCAGATGATGGCAATTCATCAATATAATCCTGATTGTTTGGATTATACTTC> /
< GCCTAACTGGCATTACCCTATCCAGTGCAACCACATCTACCCGCGTAGCATTGGCACGTAGACGGTCAA---ACTCCCCTGCTGCTGTCGTCGAAAGGCCGTGGCGAAGACCACGGCCTTTGGTCCGTTTCGCGGTAAGCGGTA< <AATAGTAGTATAAGGACTAATAGTCTACTACCGTTAAGTAGTTATATTAGGACTAACAAACCTAATATGAAG---ACTTATTACCTTCCCAATCTTGGATGGTATAGTTTTAATAAACGTGCATTTTGTCTTTATTTCTTTAAC <
CGGATTGACCGTAATGGGATAGGTCACGTTGGTGTAGATGGGCGCATCGTAACCGTGCATCTGCCAGTT> \ / >TGAATAATGGAAGGGTTAGAACCTACCATATCAAAATTATTTGCACGTAAAACAGAAATAAAGAAATTG
( | | )
GGCAGCAAAATGTTGCAGCACTGACCCTTTTGGGACCGCAATGGGTTGAATTAGCGGAACGTCGTGTAG< / \ <TTATGCTCAACAGCTTAACAAACATTTCAGATTATGAAGATTTAGGAGTTTACATAATAGATAACTGCC
> CCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATC---CCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGA> >TTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTGTTCGGGCAAAGGATTT---AATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGG >
/ <GGGGAAAGCGGTCGACCGCATTATCGCTTCTCCGGGCGTGGCTAGCGGGAAGGGTTGTCAACGCGTCGGACT-------AAGGCGAGGAAGACCACCAAAGAAACAAGGCGTTTTACTATTACAATGAGTTTGACAAGCCCGTTTCCTAAA< \
| r0t1r0t19seam_r |
\ >TCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGC-------AAATCTAAAGCATCACCTTGCTGAACCTCAAATATCAAACCCTCAATCAATATCTGGTCAGTTGGCAAATCA> /
< GGTCACGGTTCGAACGTACGGACGTCCAGCTGAGATCTCCTAGGGGCCCATGGCTCGAGCTTAAGCATT---AGTACCAGTATCGACAAAGGACACACTTTAACAATAGGCGAGTGTTAAGGTGTGTTGTATGCTCGGCCTTCG< <TTTAGATTTCGTAGTGGAACGACTTGGAGTTTATAGTTTGGGAGTTAGTTATAGACCAGTCAACCGTTTAGT---TGTCAACTTTCCTTAACTCCTTCCAATAGATTTTATAGAAATCCTCGTGATTGTTGATTATCTAATCTC <
CCAGTGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCGTAA> \ / >ACAGTTGAAAGGAATTGAGGAAGGTTATCTAAAATATCTTTAGGAGCACTAACAACTAATAGATTAGAG
( | | )
GTTTGGCGGAGAGGGGCGCGCAACCGGCTAAGTAATTACGTCGACCGTGCTGTCCAAAGGGCTGACCTT< / \ <ACCACCAAGCAAGCCATAAAAATTACCGCTACAAAATCCCGATAGTCAAGCGCGTAATTTCTGATTATC
> CAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAA---AGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTAT> >TTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACTCTGTTTTATCTTCTGC---TGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAG >
/ <TCGCCCGTCACTCGCGTTGCGTTAATTACACTCAATCGAGTGAGTAATCCGTGGGGTCCGAAATGTGAAATA-------AAGTAAACGACGACCGAGAGTCGCACCGTGACAACGTCCGCCACAATTATGACTGAGACAAAATAGAAGACG< \
| r0t2r0t21seam_r |
\ >CTGGCCCTGAGAGAGTTAAGCGGTCCACGCTGGTTTGCCCCAGCAGGCGAAAATCCTGTTTGATGGTGGTTC-------ATCGTCTGAAATGGATTATTTACATTGGCAGATTCACCAGTCACACGACCAGTAATAAAAGGGACATTCTGG> /
< GCATAACCCGCGGTCCCACCAAAAAGAAAAGTGGTCACTCTGCCCGTTGTCGACTAACGGGAAGTGGCG---GACCGGGACTCTCTCAATTCGCCAGGTGCGACCAAACGGGGTCGTCCGCTTTTAGGACAAACTACCACCAAG< <TAGCAGACTTTACCTAATAAATGTAACCGTCTAAGTGGTCAGTGTGCTGGTCATTATTTTCCCTGTAAGACC---GGTTGTCTCTATCTTGGGAAGACTGGACTTTCGCATTCTTATGCACCGTGTCTGTTATAAAAACTTACC <
CGTATTGGGCGCCAGGGTGGTTTTTCTTTTCACCAGTGAGACGGGCAACAGCTGATTGCCCTTCACCGC> \ / >CCAACAGAGATAGAACCCTTCTGACCTGAAAGCGTAAGAATACGTGGCACAGACAATATTTTTGAATGG
( | | )
GGTAGCGGGACTATCTGCCAAAAAGCGGGAAACTGCAACCTCAGGTGCAAGAAATTATCACCTGAGAAC< / \ <GGTCGTTCCGGCTATCAAACTCAAGAAGATGAGTCCGTTCACTACAATAATGATTAGTTTCTTCATAAC
> CCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTG---TTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCG> >TGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCTATTGTTCTGGATATTA---CCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTG >
/ <AAGGTTTGACCTTGTTGTGAGTTGGGATAGAGCCCGATAAGAAAACTAAATATTCCCTAAAACGGCTAAAGC-------ACTCGCAGTTTTACATCCATAAAGGTACTCGCAAAAAGGACAACGTTACCGACCGATAACAAGACCTATAAT< \
| |
\ >CCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAAGAA-------AATCAGAGCGGGAGCTAAACAGGAGGCCGATTAAAGGGATTTTAGACAGGAACGGTACGCCAGAATCCTGAG> /
< GGGTGATGCACTTGGTAGTGGGTTTAGTTCAAAAAACCCCAGCTCCACGGCATTTCGTGATTTAGCCTT---GGGATTTCCCTCGGGGGCTAAATCTCGAACTGCCCCTTTCGGCCGCTTGCACCGCTCTTTCCTTCCCTTCTT< <TTAGTCTCGCCCTCGATTTGTCCTCCGGCTAATTTCCCTAAAATCTGTCCTTGCCATGCGGTCTTAGGACTC---TTCACAAAAATATTAGTCACTCCGGTGGCTCATTTTCTCAGACAGGTAGTGCGTTTAATTGGCAACATC <
> CCCACTACGTGAACCATCACCCAAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAA> >AAGTGTTTTTATAATCAGTGAGGCCACCGAGTAAAAGAGTCTGTCCATCACGCAAATTAACCGTTGTAG >

!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for rectang|e w|th 10.44 bp]turn - (2) w|th edge stap|es that create stressed edqes
(Cn|y the edge stap|es are d|fferent.)

-1 0 +1

< GATTGATACTCCCGACAGACACCTTACGATGTCCGCAACATCAAACATGACCACTGCTTTGAGTCACAA< <CTGCCGTGAATAGGCGGACCATGACTCGTTTTGGGGCGATTAGGATTAGGAAGAGAACTCCTCAGAGTC <
> CTAACTATGAGGGCTGTCTGTGGAATGCTACAGGCGTTGTAGTTTGTACTGGTGACGAAACTCAGTGTT---ACGGTACATGGGTTCCTATTGGGCTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTG-------AGGGTGGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCCTTATATCAACCCTCTC---GACGGCACTTATCCGCCTGGTACTGAGCAAAACCCCGCTAATCCTAATCCTTCTCTTGAGGAGTCTCAG >
/ <TGCCATGTACCCAAGGATAACCCGAACGATAGGGACTTTTACTCCCACCACCGAGACTCCCACCGCCAAGAC-------TCCCACCGCCAAGACTCCCACCGCCATGATTTGGAGGACTCATGCCACTATGTGGGAATATAGTTGGGAGAG< \
| r0t1r0t1tr0 |
\ >AACAACTTTCAACAGTTTTTTCACGTTGAAAATCTCCAAAAAAAAGGCTCCAAAAGGAGCCTTTAATTGTAT-------CATGGCTTTTGATGATACAGGAGTGTACTGGTAATAAGTTTTAACGGGGTCAGTGCCTTGAGTAACAGTGCC> /
< GCATTGCTAGATTTCAAAACAGCAGAAAGGTCTGCAATCATTTACTTAAAAGACATACCCTAAAACGAT---TTGTTGAAAGTTGTCAAAAAAGTGCAACTTTTAGAGGTTTTTTTTCCGAGGTTTTCCTCGGAAATTAACATA< <GTACCGAAAACTACTATGTCCTCACATGACCATTATTCAAAATTGCCCCAGTCACGGAACTCATTGTCACGG---GCATATTTGTCAATTACGGGGGACGGATAAAGCCTTGGATAATAAGACTTTGTACTTTCATAATTCTCC <
CGTAACGATCTAAAGTTTTGTCGTCTTTCCAGACGTTAGTAAATGAATTTTCTGTATGGGATTTTGCTA> \ / >CGTATAAACAGTTAATGCCCCCTGCCTATTTCGGAACCTATTATTCTGAAACATGAAAGTATTAAGAGG
( | | )
GTTTTCGCCGGAAATTGAGGGACGTTCGGAGTCGCTGGCTTATATAGCCAATACGCACCCGCTACCAAC< / \ <TCCGGTTAGCAGACTGGACGGAGTTGGAGGACAGTTACGACCGCCGCCGAGACCACCACCAAGACCACC
> CAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATCGGTTATGCGTGGGCGATGGTTG---TTGTCATTGTCGGCGCAACTATCGGTATCAAGCTGTTTAAGAAATTCACCTCGAAAGCAAGCTGATAAACCG> >TATGACGCTTACTGGAACGGTAAATTCAGAGACTGCGCTTTCCATTCTGGCTTTATTTGTTTGTGAATATCA---AGGCCAATCGTCTGACCTGCCTCAACCTCCTGTCAATGCTGGCGGCGGCTCTGGTGGTGGTTCTGGTGG >
/ <AACAGTAACAGCCGCGTTGATAGCCATAGTTCGACAAATTCTTTAAGTGGAGCTTTCGTTCGACTATTTGGC-------ATACTGCGAATGACCTTGCCATTTAAGTCTCTGACGCGAAAGGTAAGACCGAAATAAACAAACACTTATAGT< \
| r0t3r0t3seam_r |
\ >GGACTAAAGACTTTTTCGTTTCCATTAAACGGGTAAAATACGTAATGCCACTACGAAGGCACCAACCTAAAA-------TTTTCGGTCATAGCCCCCTTATTAGCGTTTGCCATCTTTTCATAATCAAAATCACCGGAACCAGAGCCACCA> /
< GCCCTAGCAGTGGGAGTCGTCGCTTTCTGTCGTAGCCTTGCTCCCATCGTTGCCGATGTCTCCGAAACT---CCTGATTTCTGAAAAAGCAAAGGTAATTTGCCCATTTTATGCATTACGGTGATGCTTCCGTGGTTGGATTTT< <AAAAGCCAGTATCGGGGGAATAATCGCAAACGGTAGAAAAGTATTAGTTTTAGTGGCCTTGGTCTCGGTGGT---GGCCTTGGCGGAGGGAGTCTCGGCGGTGGGAGTCTTGGCGGTGGGAGTCTCGGTGGTGGGAGTCTCGGC <
CGGGATCGTCACCCTCAGCAGCGAAAGACAGCATCGGAACGAGGGTAGCAACGGCTACAGAGGCTTTGA> \ / >CCGGAACCGCCTCCCTCAGAGCCGCCACCCTCAGAACCGCCACCCTCAGAGCCACCACCCTCAGAGCCG
( | | )
GATTCATTGTACCTCGTCCAGCGCCTAAAGCTGTGTTAAATAGTCCGCTACTATGTTTAGAGGCAACAT< / \ <ATAGCTACCAAAGTAACCACTGCAAAGGCCGGAACGATTACCATTACCACGATGACCACTAAAACGACC
> CTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTATCAGGCGATGATACAAATCTCCGTTGTA---CTTTGTTTCGCGCTTGGTATAATCGCTGGGGGTCAAAGATGAGTGTTTTAGTGTATTCTTTTGCCTCTTTCG> >TGCCGATGAAAACGCGCTACAGTCTGACGCTAAAGGCAAACTTGATTCTGTCGCTACTGATTACGGTGCTGC---TATCGATGGTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGTAATGGTGCTACTGGTGATTTTGCTGG >
/ <GAAACAAAGCGCGAACCATATTAGCGACCCCCAGTTTCTACTCACAAAATCACATAAGAAAACGGAGAAAGC-------ACGGCTACTTTTGCGCGATGTCAGACTGCGATTTCCGTTTGAACTAAGACAGCGATGACTAATGCCACGACG< \
| r0t5r0t5seam_r |
\ >CGGTGTACAGACCAGGCGCTGGCTGACCTTCATCAAGAGTAATCTTGACAAGAACCGGATATTCATTACCCA-------GAAAATTCATATGGTTTACCAGCGCCAAAGACAAAAGGGCGACATTCAACCGATTGAGGGAGGGAAGGTAAA> /
< GGCCTTGCTCCGCGTCTGCCAGTTAGTATTCCCTTGGCTTGACTGGTTGAAACTTTCTCCTGTCTACTT---GCCACATGTCTGGTCCGCGACCGACTGGAAGTAGTTCTCATTAGAACTGTTCTTGGCCTATAAGTAATGGGT< <CTTTTAAGTATACCAAATGGTCGCGGTTTCTGTTTTCCCGCTGTAAGTTGGCTAACTCCCTCCCTTCCATTT---ATAACTGCCTTTAATAAGTAATTTCCACTTAATAGTGGCAGTGGCTGAACTCGGTAAACCCTTAATCTC <
CCGGAACGAGGCGCAGACGGTCAATCATAAGGGAACCGAACTGACCAACTTTGAAAGAGGACAGATGAA> \ / >TATTGACGGAAATTATTCATTAAAGGTGAATTATCACCGTCACCGACTTGAGCCATTTGGGAATTAGAG
( | | )
GGTCAAGAATTTTAGCGTATTCCATTAAGTGTTACTAATTTCAACTTTAATTTGGTAGAGTTCGGGTTA< / \ <CAAACGATTGTATGACGCATTATTCCTCAGAATTAGTACGGTCAAGAAAACCCATAAGGCAATAATAAC
> CCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAACCATCTCAAGCCCAAT---TTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTATTCACTGAATGAGCAGCTTTGTTACGTTGATT> >TATTGATTGTGACAAAATAAACTTATTCCGTGGTGTCTTTGCGTTTCTTTTATATATGTATGTATTTTCTAC---GTTTGCTAACATACTGCGTAATAAGGAGTCTTAATCATGCCAGTTCTTTTGGGTATTCCGTTATTATTG >
/ <AATGATGAGCAAGACCACAAAGAGCAGTCCCGTTCGGAATAAGTGACTTACTCGTCGAAACAATGCAACTAA-------ATAACTAACACTGTTTTATTTGAATAAGGCACCACAGAAACGCAAAGAAAATATATACATACATAAAAGATG< \
| r0t7r0t7seam_r |
\ >ATTACAGGTAGAAAGATGATTTAGGAATACCACATTCAACTAATGCAGATACATAACGCCAAAAGGAATTAC-------GAGATAACCCACAAGAATTGAGTTAAGCCCAATAATAAGAGCAAGAAACAATGAAATAGCAATAGCTATCTT> /
< GAGTAATATGGTCAGTCCTGCAACCCTTCTTTTTAGATGCAATTATTTTGCTTGATTGCCTTGTTGTAA---TAATGTCCATCTTTCTACTAAATCCTTATGGTGTAAGTTGATTACGTCTATGTATTGCGGTTTTCCTTAATG< <CTCTATTGGGTGTTCTTAACTCAATTCGGGTTATTATTCTCGTTCTTTGTTACTTTATCGTTATCGATAGAA---TGGCTTCGGGAAAAATTCTTTTCATTCGTCTATCGGCTTGTTTCAATGGTCTTCCTTTGGCTCCTTTGC <
CTCATTATACCAGTCAGGACGTTGGGAAGAAAAATCTACGTTAATAAAACGAACTAACGGAACAACATT> \ / >ACCGAAGCCCTTTTTAAGAAAAGTAAGCAGATAGCCGAACAAAGTTACCAGAAGGAAACCGAGGAAACG
( | | )
GTCATAACCTGCGATAGGTCAGATTTGTAAAATGATAATGGGGGAGACCGTTTTGAAGAAAACGTTTTC< / \ <CCGACGATAAAAGTAAAAACTGCAATTTGTTTTTTAGCAAAGAATAAACCTAACCCTATTTATTATACC
> CAGTATTGGACGCTATCCAGTCTAAACATTTTACTATTACCCCCTCTGGCAAAACTTCTTTTGCAAAAG---CCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATGATAGTGTTGCTCTTACTATGCCTC> >TCTGATATTAGCGCTCAATTACCCTCTGACTTTGTTCAGGGTGTTCAGTTAATTCGTTATTCTCTCTGTAAA---GGCTGCTATTTTCATTTTTGACGTTAAACAAAAAATCGTTTCTTATTTGGATTGGGATAAATAATATGG >
/ <GGAGAGCGATAAAACCAAAAATAGCAGCAGACCATTTGCTCCCAATACTATCACAACGAGAATGATACGGAG-------AGACTATAATCGCGAGTTAATGGGAGACTGAAACAAGTCCCACAAGTCAATTAAGCAATAAGAGAGACATTT< \
| r0t9r0t9seam_r |
\ >ATAAATCAAAAATCAGGTATTATAGTCAGAAGCAAAGCGGATTGCATCAAAAAGATTAAGAGGAAGCCCGAA-------ACCTCCCGACTTGCGGGAGGTTTTGAAGCCTTAAATCAAGATTAGTTGCTATTTTGCACCCAGCTACAATTT> /
< GCCTTAGCAGTATTTATAAGTAACTTAGGGGGAGTTTACGAAATTTGTCAAGTCTTTTGCTCTTACTGG---TATTTAGTTTTTAGTCCATAATATCAGTCTTCGTTTCGCCTAACGTAGTTTTTCTAATTCTCCTTCGGGCTT< <TGGAGGGCTGAACGCCCTCCAAAACTTCGGAATTTAGTTCTAATCAACGATAAAACGTGGGTCGATGTTAAA---ATAGGACTTAGAATGGTTGCGATTGCTCGCAGAAAGGTCTCGGATTAAACGGTCAATGTTTTATTTGTC <
CGGAATCGTCATAAATATTCATTGAATCCCCCTCAAATGCTTTAAACAGTTCAGAAAACGAGAATGACC> \ / >TATCCTGAATCTTACCAACGCTAACGAGCGTCTTTCCAGAGCCTAATTTGCCAGTTACAAAATAAACAG
( | | )
GTTAATTCGAGATTCGGTAGGCGTTTTTACTGGAGAATAGTTTTCCTCGTTAATTTCCATGAGAGATTA< / \ <CCGAACGAACAAGAGCTACTCACGCCATGAACCAAATTATGGGCAAGAACCTTACTATTCCTTTCTGTC
> CAATTAAGCTCTAAGCCATCCGCAAAAATGACCTCTTATCAAAAGGAGCAATTAAAGGTACTCTCTAAT---CCTGACCTGTTGGAGTTTGCTTCCGGTCTGGTTCGCTTTGAAGCTCGAATTAAAACGCGATATTTGAAGTCT> >TCGCTAAAACGCCTCGCGTTCTTAGAATACCGGATAAGCCTTCTATATCTGATTTACGATGAAAATAAAAAC---GGCTTGCTTGTTCTCGATGAGTGCGGTACTTGGTTTAATACCCGTTCTTGGAATGATAAGGAAAGACAG >
/ <GGACTGGACAACCTCAAACGAAGGCCAGACCAAGCGAAACTTCGAGCTTAATTTTGCGCTATAAACTTCAGA-------AGCGATTTTGCGGAGCGCAAGAATCTTATGGCCTATTCGGAAGATATAGACTAAATGCTACTTTTATTTTTG< \
| r0t1r0t11seam_r |
\ >CCATATAACAGTTGATTATTCTGCGAACGAGTAGATTTAGTTTGACCATTAGATACATTTCGCAAATGGTCA-------AATTCTGTCCAGACGACGACAATAAACAACATGTTCAGCTAATGCAGAACGCGCCTGTTTATCAACAATAGA> /
< GACTTATATTACGACATCGAGTTGTACAAAATTTATACGTTGATTTCATGCCACAGACCTTCAAAGTAA---GGTATATTGTCAACTAATAAGACGCTTGCTCATCTAAATCAAACTGGTAATCTATGTAAAGCGTTTACCAGT< <TTAAGACAGGTCTGCTGCTGTTATTTGTTGTACAAGTCGATTACGTCTTGCGCGGACAAATAGTTGTTATCT---ATTCAGGACTTGTTCTTTTTATTATAGGGTAGGATTAAATGCTCGTACATCTTTGGTTAGTTATTAGCC <
CTGAATATAATGCTGTAGCTCAACATGTTTTAAATATGCAACTAAAGTACGGTGTCTGGAAGTTTCATT> \ / >TAAGTCCTGAACAAGAAAAATAATATCCCATCCTAATTTACGAGCATGTAGAAACCAATCAATAATCGG
( | | )
GAGACTCCGAAATAACGAATTAAAACGATTAAGAAACGGAACGGACATACTAAATAACCTACAATTACG< / \ <TTATACCGCTAAGAGTTAATTCGGGATGACAACTCGCAACCGAAATATGACCATTCTTAAACATATTGC
> CTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTATGATTTATTGGATGTTAATGC---TACTACTATTAGTAGAATTGATGCCACCTTTTCAGCTCGCGCCCCAAATGAAAATATAGCTAAACAGGTTAT> >ACTTTACCTTTTGTCGGTACTTTATATTCTCTTATTACTGGCTCGAAAATGCCTCACATGTTGGCGTTGTTA---AATATGGCGATTCTCAATTAAGCCCTACTGTTGAGCGTTGGCTTTATACTGGTAAGAATTTGTATAACG >
/ <ATGATGATAATCATCTTAACTACGGTGGAAAAGTCGAGCGCGGGGTTTACTTTTATATCGATTTGTCCAATA-------TGAAATGGAAAACAGCCATGAAATATAAGAGAATAATGACCGAGCTTTTACGGAGTGTACAACCGCAACAAT< \
| r0t1r0t13seam_r |
\ >TCAACGCAAGGATAAAAAGAACCCTCATATATTTTAAATGCAATGCCTGAGTAATGTGTAGGTAAAGATTCA-------TTTTCAAATATATTTTAGTTAATTTCATCTTCTGACCTAAATTTAATGGTTTGAAATACCGACCGTGTGATA> /
< GTATTTCGATTTAGCCAACATGGTTTTTGTAATACTGGGACATTATGAAAACGCCCTCTTCGGAAATAA---AGTTGCGTTCCTATTTTTCTTGGGAGTATATAAAATTTACGTTACGGACTCATTACACATCCATTTCTAAGT< <AAAAGTTTATATAAAATCAATTAAAGTAGAAGACTGGATTTAAATTACCAAACTTTATGGCTGGCACACTAT---TTATTCCGCAATTTATTCTTATTTGTGGCCTTAGTATTAATGATCTTTTTCGGACAAATCATAGTATAC <
CATAAAGCTAAATCGGTTGTACCAAAAACATTATGACCCTGTAATACTTTTGCGGGAGAAGCCTTTATT> \ / >AATAAGGCGTTAAATAAGAATAAACACCGGAATCATAATTACTAGAAAAAGCCTGTTTAGTATCATATG
( | | )
GAGGTCTGAGAGTCCGTTACTGGACTATCGGAAACATCTAGAGAGTTTTTATCGATGGGAGAGGCCGTA< / \ <TTTCCATCAGAGAGTCTGGATACTAAAACTATTTAAGTGATAACTGAGAAGAGTCGCAGAATTAGATTC
> CTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGCTACCCTCTCCGGCAT---TAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTGATTTGACTGTCTCCGGCCTTTCTCACCCTTT> >AGTTTTCTCGCGTTCTTTGTCTTGCGATTGGATTTGCATCAGCATTTACATATAGCCTAAGCCGGAGGTTAA---AAAGGTAGTCTCTCAGACCTATGATTTTGATAAATTCACTATTGACTCTTCTCAGCGTCTTAATCTAAG >
/ <ATTAAATAGTCGATCTTGCCAACTTATAGTATAACTACCACTAAACTGACAGAGGCCGGAAAGAGTGGGAAA-------TCAAAAGAGCGCAAGAAACAGAACGCTAACCTAAACGTAGTCGTAAATGTATATCGGATTCGGCCTCCAATT< \
| r0t1r0t15seam_r |
\ >CAGAAAAGCCCCAAAAAGTATAAGCAAATATTTAAATTGTAAACGTTAATATTTTGTTAAAATTCGCATTAA-------TTACATTTAACAATTTCATTTGAATTACCTTTTTTAATGGAAACAGTACATAAATCAATATATGTGAGTGAA> /
< GTTTGTTCTCTTAGCTACTTGCCATTAGCATTTTGATCGTACAGTTAGTATACATGGGGCCAACTATTA---GTCTTTTCGGGGTTTTTCATATTCGTTTATAAATTTAACATTTGCAATTATAAAACAATTTTAAGCGTAATT< <AATGTAAATTGTTAAAGTAAACTTAATGGAAAAAATTACCTTTGTCATGTATTTAGTTATATACACTCACTT---ATTGGAACGAAGACATTTAGCAGCGATAATTAATTAAAAGGGAATCTTAGGAACTTTTGTATCGCTATC <
CAAACAAGAGAATCGATGAACGGTAATCGTAAAACTAGCATGTCAATCATATGTACCCCGGTTGATAAT> \ / >TAACCTTGCTTCTGTAAATCGTCGCTATTAATTAATTTTCCCTTAGAATCCTTGAAAACATAGCGATAG
( | | )
GGCAAACAAGGGTGCCTCTTAGGCTGCCCAACAATGAGCGAGTGTAAATTACAACTACTTTCGACCGAT< / \ <ATAACAAAGAGGGCTACATTTTCCATGACAATGACATATAAGTAGACTGCAATTTGGACTTTTAGATGC
> CCGTTTGTTCCCACGGAGAATCCGACGGGTTGTTACTCGCTCACATTTAATGTTGATGAAAGCTGGCTA---CAGGAAGGCCAGACGCGAATTATTTTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAAT> >TTAATTTTGTTTTCTTGATGTTTGTTTCATCATCTTCTTTTGCTCAGGTAATTGACAATCAGGCGAATCCGT---TATTGTTTCTCCCGATGTAAAAGGTACTGTTACTGTATATTCATCTGACGTTAAACCTGAAAATCTACG >
/ <GTCCTTCCGGTCTGCGCTTAATAAAAACTACCGCAAGGATAACCAATTTTTTACTCGACTAAATTGTTTTTA-------AATTAAAACAAAAGAACTACAAACAAAGTAGTAGAAGAAAACGAGTCCATTAACTGTTAGTCCGCTTAGGCA< \
| r0t1r0t17seam_r |
\ >TGAGGGGACGACGACAGCAGCTTTCCGGCACCGCTTCTGGTGCCGGAAACCAGGCAAAGCGCCATTCGCCAT-------TTATCATCATATTCCTGATTATCAGATGATGGCAATTCATCAATATAATCCTGATTGTTTGGATTATACTTC> /
< GCCTAACTGGCATTACCCTATCCAGTGCAACCACATCTACCCGCGTAGCATTGGCACGTAGACGGTCAA---ACTCCCCTGCTGCTGTCGTCGAAAGGCCGTGGCGAAGACCACGGCCTTTGGTCCGTTTCGCGGTAAGCGGTA< <AATAGTAGTATAAGGACTAATAGTCTACTACCGTTAAGTAGTTATATTAGGACTAACAAACCTAATATGAAG---ACTTATTACCTTCCCAATCTTGGATGGTATAGTTTTAATAAACGTGCATTTTGTCTTTATTTCTTTAAC <
CGGATTGACCGTAATGGGATAGGTCACGTTGGTGTAGATGGGCGCATCGTAACCGTGCATCTGCCAGTT> \ / >TGAATAATGGAAGGGTTAGAACCTACCATATCAAAATTATTTGCACGTAAAACAGAAATAAAGAAATTG
( | | )
GGCAGCAAAATGTTGCAGCACTGACCCTTTTGGGACCGCAATGGGTTGAATTAGCGGAACGTCGTGTAG< / \ <TTATGCTCAACAGCTTAACAAACATTTCAGATTATGAAGATTTAGGAGTTTACATAATAGATAACTGCC
> CCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATC---CCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGA> >TTCCGCTCCTTCTGGTGGTTTCTTTGTTCCGCAAAATGATAATGTTACTCAAACTGTTCGGGCAAAGGATTT---AATACGAGTTGTCGAATTGTTTGTAAAGTCTAATACTTCTAAATCCTCAAATGTATTATCTATTGACGG >
/ <GGGGAAAGCGGTCGACCGCATTATCGCTTCTCCGGGCGTGGCTAGCGGGAAGGGTTGTCAACGCGTCGGACT-------AAGGCGAGGAAGACCACCAAAGAAACAAGGCGTTTTACTATTACAATGAGTTTGACAAGCCCGTTTCCTAAA< \
| r0t1r0t19seam_r |
\ >TCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGC-------AAATCTAAAGCATCACCTTGCTGAACCTCAAATATCAAACCCTCAATCAATATCTGGTCAGTTGGCAAATCA> /
< GGTCACGGTTCGAACGTACGGACGTCCAGCTGAGATCTCCTAGGGGCCCATGGCTCGAGCTTAAGCATT---AGTACCAGTATCGACAAAGGACACACTTTAACAATAGGCGAGTGTTAAGGTGTGTTGTATGCTCGGCCTTCG< <TTTAGATTTCGTAGTGGAACGACTTGGAGTTTATAGTTTGGGAGTTAGTTATAGACCAGTCAACCGTTTAGT---TGTCAACTTTCCTTAACTCCTTCCAATAGATTTTATAGAAATCCTCGTGATTGTTGATTATCTAATCTC <
CCAGTGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTCGTAA> \ / >ACAGTTGAAAGGAATTGAGGAAGGTTATCTAAAATATCTTTAGGAGCACTAACAACTAATAGATTAGAG
( | | )
GTTTGGCGGAGAGGGGCGCGCAACCGGCTAAGTAATTACGTCGACCGTGCTGTCCAAAGGGCTGACCTT< / \ <ACCACCAAGCAAGCCATAAAAATTACCGCTACAAAATCCCGATAGTCAAGCGCGTAATTTCTGATTATC
> CAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGACAGGTTTCCCGACTGGAA---AGCGGGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTAT> >TTCATTTGCTGCTGGCTCTCAGCGTGGCACTGTTGCAGGCGGTGTTAATACTGACTCTGTTTTATCTTCTGC---TGGTGGTTCGTTCGGTATTTTTAATGGCGATGTTTTAGGGCTATCAGTTCGCGCATTAAAGACTAATAG >
/ <TCGCCCGTCACTCGCGTTGCGTTAATTACACTCAATCGAGTGAGTAATCCGTGGGGTCCGAAATGTGAAATA-------AAGTAAACGACGACCGAGAGTCGCACCGTGACAACGTCCGCCACAATTATGACTGAGACAAAATAGAAGACG< \
| r0t2r0t21seam_r |
\ >CTGGCCCTGAGAGAGTTAAGCGGTCCACGCTGGTTTGCCCCAGCAGGCGAAAATCCTGTTTGATGGTGGTTC-------ATCGTCTGAAATGGATTATTTACATTGGCAGATTCACCAGTCACACGACCAGTAATAAAAGGGACATTCTGG> /
< GCATAACCCGCGGTCCCACCAAAAAGAAAAGTGGTCACTCTGCCCGTTGTCGACTAACGGGAAGTGGCG---GACCGGGACTCTCTCAATTCGCCAGGTGCGACCAAACGGGGTCGTCCGCTTTTAGGACAAACTACCACCAAG< <TAGCAGACTTTACCTAATAAATGTAACCGTCTAAGTGGTCAGTGTGCTGGTCATTATTTTCCCTGTAAGACC---GGTTGTCTCTATCTTGGGAAGACTGGACTTTCGCATTCTTATGCACCGTGTCTGTTATAAAAACTTACC <
CGTATTGGGCGCCAGGGTGGTTTTTCTTTTCACCAGTGAGACGGGCAACAGCTGATTGCCCTTCACCGC> \ / >CCAACAGAGATAGAACCCTTCTGACCTGAAAGCGTAAGAATACGTGGCACAGACAATATTTTTGAATGG
( | | )
GGTAGCGGGACTATCTGCCAAAAAGCGGGAAACTGCAACCTCAGGTGCAAGAAATTATCACCTGAGAAC< / \ <GGTCGTTCCGGCTATCAAACTCAAGAAGATGAGTCCGTTCACTACAATAATGATTAGTTTCTTCATAAC
> CCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGACTCTTG---TTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTCTTTTGATTTATAAGGGATTTTGCCGATTTCG> >TGAGCGTCAAAATGTAGGTATTTCCATGAGCGTTTTTCCTGTTGCAATGGCTGGCTATTGTTCTGGATATTA---CCAGCAAGGCCGATAGTTTGAGTTCTTCTACTCAGGCAAGTGATGTTATTACTAATCAAAGAAGTATTG >
/ <AAGGTTTGACCTTGTTGTGAGTTGGGATAGAGCCCGATAAGAAAACTAAATATTCCCTAAAACGGCTAAAGC-------ACTCGCAGTTTTACATCCATAAAGGTACTCGCAAAAAGGACAACGTTACCGACCGATAACAAGACCTATAAT< \
| r0t2r0t23r0t23br3 |
\ >CCCTAAAGGGAGCCCCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAAGAA-------AATCAGAGCGGGAGCTAAACAGGAGGCCGATTAAAGGGATTTTAGACAGGAACGGTACGCCAGAATCCTGAG> /
< GGGTGATGCACTTGGTAGTGGGTTTAGTTCAAAAAACCCCAGCTCCACGGCATTTCGTGATTTAGCCTT---GGGATTTCCCTCGGGGGCTAAATCTCGAACTGCCCCTTTCGGCCGCTTGCACCGCTCTTTCCTTCCCTTCTT< <TTAGTCTCGCCCTCGATTTGTCCTCCGGCTAATTTCCCTAAAATCTGTCCTTGCCATGCGGTCTTAGGACTC---TTCACAAAAATATTAGTCACTCCGGTGGCTCATTTTCTCAGACAGGTAGTGCGTTTAATTGGCAACATC <
> CCCACTACGTGAACCATCACCCAAATCAAGTTTTTTGGGGTCGAGGTGCCGTAAAGCACTAAATCGGAA> >AAGTGTTTTTATAATCAGTGAGGCCACCGAGTAAAAGAGTCTGTCCATCACGCAAATTAACCGTTGTAG >

!"
DOI: 10.1038/NCHEM.1070
SS.2. kectang|e w|th 10.67 bp]turn

Core
Seq name Sequence
r1L0g AAACAAACA1CAACAAAACAAAA11AA11ACA
r1L10e 1C11C11CC1CCAC1CCAACC1CACCCCC1AC
r1L10f 1AAACAACCAC111CCAACAACAC11A1111C
r1L12e 1AA11CCCCC1C1CC1CCCACC1CCCC11CAC
r1L12f 1CCCCAAA11CCCC1CAC1CCCCCCCA1111C
r1L14e 1CCC1CCCCCCCA1C1CC1CCAACAC1CACA1
r1L14f CCCCAAACCCCC1C11CCC1A11AA1ACA1CC
r1L20f CC1A1A11CCCAAA1CC1CAA1AAAAACCAAA
r1L22e A1CAAAAACCCC1111AA11CCACACCA11AC
r1L22f 1CAAA1A1CA11AACACCAACCCCCCAAA1CA
r1L24h A1AC1AACACCAACAC1A1CA1AACCCA11CC
r1L2e ACAAACAACC1CA11A1CACA1CAACA1CA1C
r1L2f A1CA1A11ACCACCACAACCACCCAC11111C
r1L4e CCACCC1CCACC11CC1CAACC1C111CCCCA
r1L4f 1AAACCA1ACACCCACCACCAAA1AC1AA11C
r1L6e A1CCAAA1CA11A111ACA11CCCCAACAC1C
r1L6f C1CAAA1CACC1ACA1111CACCCACAACCCC
r1L8e 1A1CC11C11ACAA1CACACCCCCAAACCC1C
r1L8f 111CC1CCC111CACCACCACC1A1CAACAAA
r3L0g CA111CAA11ACC1CACCAAAACA1CCCAA11
r3L10e AAA1CAAAC1A1CACCCCCA1CCCCCCCCC1C
r3L10f AAAACCC1ACAA1ACCCCCACA1ACA11AA1C
r3L12e C1CCCC1CAACCCCCCCCCACACCCCCAAAA1
r3L12f AA1CCCCCCC1AA1CAC1CACC1ACCCA11AA
r3L14e CA11CACCACCCCACCC1111CCCCAACCA1A
r3L14f C11CCC1AC1CCCCAAC1C11CCC1AAA1C1C
r3L16e 11C11AAAACAACCCC1CCCA11CCAAACCAC
r3L20e C1CCCAACCAA11C1AC1AA1AC111111ACA
r3L20f CC1CCCA1CAC1ACA111AC111CC11CAAAC
r3L22e 1CAC1A11ACCCCAACCAAAC1CC11CA11CC
r3L22f CCAACCACA1AC1CACAACCAAACCCC1CC11
r3L24h 1ACCACACCACCA1AAAAACCAAAA1CACC1C
r3L2e 1AAAAC111AA1CC1CA11C111C1CA11CC1
r3L2f CA1CAA1A1CAC1AACA11A1CA1AAA1A1CA
r3L4e CCCCC1CAA1CAA1A1C1CC1CACCCCAACC1
r3L4f AACCC1CAC1A11AACACCCCC1CACA11CAC
r3L6e 1ACCCCCACCACCAC1AA1AAAACAACACACC
r3L6f CAC1CACACCCA11CCAACACCAAACC1AAAC
r3L8e CCCCCC11CA11AAACCCA1111A1CC1CC1A
r3L8f ACCACCCCAA1CCCCCCC1ACACCAACCCCCA
r3L0g CCCACAAACAA1AACCCA11CCCCCA11A1AC
r3L10e C1C111CACACCCAAA1CAAC111CCAACCCA
r3L10f 1CAACCA11CC1CC11CCCAAA1CCCC111CC
r3L12e CAA11CCACCCCACCC1CC11111CCAAAA1C
r3L12f C1A11CCCCACAACA1ACCACCCCAC1CACCA
r3L14e 111CCCCCAACCACCCCCAC1CCC1CCCC1CA
r3L14f CC11C1AAACCCC11C1CC1CCCC1CCC1CCC
r3L16e 11C1A1AACCCCA11CACCC1AA1CACCCACC
r3L16f AACAAACCCCAAA1A111AAA11CACA1C1AC
r3L18e 111A111C1CACC1CA11CCC1CACACCAACA
r3L18f AAACCC1AAACCCAACCA1AAAAAAC1ACCA1
r3L20e 1CCAAC11AA1AAA1CA1ACACCCCACAACCC
r3L20f 1AACA1CC1CA11CCA1A1AACACAACACC1C
r3L22e AACCACAAACAC1ACC111AA11CACCC1C1C
r3L22f ACCA11AC1CACCA1AAA1CAAAAA1ACCCAC
r3L24h ACCC1111CCAAAACAAC1111CCC11CACAA
r3L2e CACAAC1CAA1CCAACCC11ACAA111ACA1C
r3L2f 11C1CAA1C1A11AAA1CC111CC11CCCAAA
r3L4e CAACCAAC1CAAACCAA11CACCAAACAA11C
r3L4f 1CAACAC1CACCACCACAACA1AACCACA11C
r3L6e 1ACAACAAACACA1ACAACCC11CAAAA1ACC
r3L6f 1CCCCAACC1CAAAC1A1CCCCC1CACACCAA
r3L8e ACAAACCCCACAA1CC1CACAAC11CCC1CAC
r3L8f CCC1ACCCAAACCACCCCCCCC1ACCAC1ACC
r7L0g CA1CAA1A1ACAC1AACAC1ACC1CC1ACCA1
r7L10e 1CCACCC1CC1AAACCAC1AAA1C1CACCCCC
r7L10f CCACC1CCCC111CCCCCACCACCC1111CAC
r7L12e CC1C111CCCCCCAACACC1CA11CCAACCCC
r7L12f CAC1CACAC1C1C1CAAA11C11AAACC11CC
r7L14e A1CCCCC1ACC1CCAC1C1ACACC1CC1CA1A
r7L14f A1CCC1CCCACCAACA1CCCAC1CCCCA1ACC
r7L16e 1CA1AA1CC1C1ACA1CCCCCCA1ACCACAC1
r7L16f 1CACC11CACAAAACCCCCAAAAACAC1C1CC
r7L18e 1A1CACCCACACAA1CCA1CAACCACCCCCC1
r7L18f ACCAAACA1C1AA1AC1111CCCCAACCCAAA
r7L20e A1C1111AAAAA11AACCAA1AAAAAAAACA1
r7L20f CAA11ACCAA1A1CCAAC1AAAC1C1CC1111
r7L22e AA1CCCCCC1CA11111CCCCA1CACC1CAAC
r7L22f CA1AACAC1CAAA1CC111AAACACACACCCC
r7L24h C1AA1AC1AAAA1C111ACAC1CCA11CA11C
r7L2e CA111ACA1A111CCACC1AAAAC1AACC1CA
r7L2f A1CAAAA1AC1A11ACAC111ACAACC11A1C
r7L4e CA1ACCCCC111ACCACCAC1AACCA111CAC
r7L4f 1AAAA1A11AAAACA1CCCCA11A1CACC1CA
r7L6e 1C111CA1CAA1ACC1CCCACACACCCCAAC1
r7L6f AACCC1AA1AC1AA1AACA1CAC1C11111A1
r7L8e AAACCCCCACCCCACCCAC1AAAACCAA1AC1
r7L8f AA1CAC1CCCAACC1CCCCACAAA111CCCC1
r-7L20f AACACACC1CCAAA1CCCCCACC1ACCC1CAA
r-7L22e 11AA1CA1CAACCCAAC1CACCAACCCC1CA1
r-7L22f 1CA1AACC1C1CAA11ACC11A1CCCACC11C
r-7L24h CCAACAAAAA1C1ACC11AA1AAA111CAAC1
r-7L2e CAA1CA1ACAA111A1CAAAA1CA1CCC1A11
r-7L2f 1CAA1AC1A11AC1ACAAAAACCCACCAC1A1

r-7L4e A1CC1AA1CCC1CAACAC1ACCCCAAACACCC
r-7L4f AAACCCAA11ACCACCA1C1ACAA11CCAACA
r-7L6e C11ACCAA1AAACCAAC1ACCCCAAA1A1CCC
r-7L6f ACCCC1A1CCC1AACCACCC1C11CACCCA1A
r-7L8e 1A1C11ACCCCAA1CCAAA1AACA1CC1CAA1
r-7L8f 11A111A1CCAACCCC11111AACCAACCAAA
r-1L0g 111AACAA111CA111CAA11ACCAAA1CCAA
r-1L10e 1CACAA1CACACCACCCAA1AAC11CCAC1A1
r-1L10f ACCCAAACAA1ACAAAA11CA1A1C111ACCC
r-1L12e CC1CA1AC1ACCCCC1111CA1CCC111CCAC
r-1L12f 1CACAC1CCCCCC11A11ACCC11CAC1C1C1
r-1L14e C1111CA1CC11CCAC1AACCC1CCCCCACC1
r-1L14f CAA111ACCA1ACACCAC1C1AC1ACC111AC
r-1L20f 1CCCAC1AACAA1ACAC1AAAACAAC1AA1C1
r-1L22e ACC1AACAACCCCA1A11CA11ACCAAACAC1
r-1L22f 1CACAACAAACC1CC1CA11CAC1AAC1AA1C
r-1L24h CACA1ACA1AACCCCAAAACCAA11ACCACCC
r-1L2e AAA1A1A1CAAACAACCCCACAAACAA11A1C
r-1L2f 1CCCAACA111AC11AA111CA1CA1AACACA
r-1L4e 1C1CCACA1ACCCACAAAACC1AACAAAAA1C
r-1L4f A1A1AAACCCACCACAA1AAACAAAA1CACA1
r-1L6e ACCCC111C11A1CCCC1A11C1A1CAA1CC1
r-1L6f A1ACAACC1ACCCAACC1CCCCACCCCCA11A
r-1L8e C1CACACCAA11AAC1CAACACCC1AACC1CC
r-1L8f CACCCCACC1AA11CACCCC1AA11AAAACAA
r-3L0g 1CCAAACAC1ACA1AAA1CAA1A1C11ACC11
r-3L20f CCAAC111ACCCA11A1ACCAACCCCACCCCC
r-3L22e C11CCCC1CC1CACC11CA1CAACC1CA1C11
r-3L22f A1ACCC1CCACCACAAACACCACAAAACA11C
r-3L24h 11CACA111ACCAA1ACCACA11CCAA1AACC
r-3L2e 1AAA111AA1C1AAA1CC1CA1CC111111AA
r-3L2f A1AAC1A1A1CC111CAAA1ACCCACA1C1AA
r-3L4e CC1AA1CCCA1111CCACCCAC1A11C1CACC
r-3L4f CCCACACCACAACCCCCC1C111ACA1CC1AC
r-3L0g CAA1AACC11CC11C1C1AAA1CC1ACC1C1C
r-3L10f AACAAC1CACCCAACC1AAA1A111ACCAACC
r-3L12f CCCCAAACACCCCC1CCC1CACACCCCACC1C
r-3L14f ACACCA11AAACAC11AA1CCCCCACCACCCC
r-3L16f CA1AAC1C1CAC111CC1CACCAC111C1C1A
r-3L18f 1CCCA111A1CCCCCACCCA1AACCAACCCC1
r-3L20e AAC1ACAA111CACCAC1AAACACCACAA1CA
r-3L20f ACACACCCCCCACA111C1A1CA1C111CAAA
r-3L22e 1AAA11CCA1CAACCC1C1ACACACCCAAACA
r-3L22f CACCACACCC11CACA1CC111AAACCAAC1A
r-3L24h ACCCAACAACA11A11ACACC1ACACCAC1AC
r-3L2e A1AAA1AACC11111AACC1CCCCA1C1CAC1
r-3L2f ACACAC1ACCCC11AAA1AACAA111AA11CA
r-3L4e ACA1AAC1A1A111AACAACCCCAACCC1C1C
r-3L4f CAA1CCCCCC1CAACAACAAAAA1C1CA1CCA
r-3L6f CAACAACCCCCACC1ACAA1111AAACCA111
r-3L8f 111C111AAACAAACAA1CAAA1AA1ACCCAA
r-7L0g AA11AA1111CCC11ACAA1CC11CACAACAC
r-7L10e 11A11CA1ACCCAA1AA1AACCCACCAA1ACC
r-7L10f CCCACCAA1AAACC1CAA11A1CACCCACCAA
r-7L12e C1CACAACC1ACCACCA11ACCA1CACCCAAA
r-7L12f AA1CACCACCCCACCC1CACACCCCACACCCC
r-7L14e 11CCCAACA11CACACCACC11CACCCCCACC
r-7L14f CCCCCACCC1A11A11C1CAAACACAACCA11
r-7L16e ACAACCCCCCCCC1111CC1CAC1C1CCC1A1
r-7L16f ACCA11AC1C1ACCA11CCACACA111C1CC1
r-7L18e 1CCC1CCCACC11AC1AAA1CAA11ACAAAC1
r-7L18f C111CCAC1CACCC11CCACCCACACCACCCA
r-7L20e AAA11C1CA1CCCAACCACCC1ACCCA1A1A1

r9L0y CC1ACA1111CACC11ACAAA1AAACAAA11C
r9L2y CCC1CAA1ACA1AA1AAAC1AA1ACA11ACAC
r9L4y C1A11AC1C111AA1CCAA1A11111CAA1CC
r9L6y CAAA11AACCC11C1ACAC1C1C1CCA1CACC
r9L8y CCCCCCA111ACACC1CCAACCC1AAACCCAC
r9L10y CCC1CACACAC11CCACCCC11CACCCCC1CC
r9L12y C1CCAA11CC1AA1CAA1CCCCCCC1ACCCAC
r9L14y CCAC111CACCCCACCCC1AACCC1CCA1C1C
r9L16y CA1C1CAA1CA1A1C1C1AA1CC1AAAAC1AC
r9L18y C1AAA1CCC11C1ACCCCC1CACACCA1AAAC
r9L20y C1CAA1A1AA1CC1C1CC11ACACC11AA11C
r9L22x CCCAA1CC1CA1AAA1A1ACCC1CCAA1AC1C

r-9L2L C11ACA11AACACCC1CAAAACA1ACCCA1AC
r-9L4L CC11A1ACAAA11C111C111AC1A1CA1A1C
r-9L6L C1C1C111CC11A1CAACCAA1CAA1AA1CCC
r-9L8L CCAC11ACAAAA1AAA1CCACACCC1AA111C
r-9L10L CCCAACAAAC11ACCAAAAAC1AACCACA1AC
r-9L12L CCA111CCCAA11ACACCC1CACCCAC11CAC
r-9L14L CCACCACAACCACCACACCACCC1CACACCCC
r-9L16L C1CACAC1CC1CAACA1CAAAC1A11AACACC
r-9L18L CC1AACCA1C1AAAC1CACCCC1CA1AC11AC
r-9L20L CCCCA1CC1CACCC1C11AAACCCCCC1111C
r-9L22L CCCCAACCACCCCCACCC1CCA1C11AC11AC
r-9L24s C1CA11A1ACCAC1CACCA1111AACAAC1CC

!"
DOI: 10.1038/NCHEM.1070
D|agram for rectang|e w|th 10.67 bp]turn
wlLh poslLlons and lengLhs of loopouLs (black clrcles wlLh numbers) lndlcaLed

7 5 4 4 7
2
4
1
1
5 8
4
6
2
4
0
7 9 3
1
6
4
0
7
1
1
1
6
2
9
3
1
5
!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for rectang|e w|th 10.67 bp]turn

-
9

-
8

-
7

-
6

-
5

-
4

-
3

-
2

-
1

0

+
1

+
2

+
3

+
4

+
5

+
6

+
7

+
8

+
9

r
-
7
t
0
g

r
-
5
t
0
g

r
-
3
t
0
g

r
-
1
t
0
g

r
1
t
0
g

r
3
t
0
g

r
5
t
0
g

r
7
t
0
g

r
9
t
0
y

<
G
A
T
A
G
C
G
A
<

<
A
T
T
C
C
C
T
T
-
-
-
T
T
A
A
T
T
A
A
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<
T
C
T
T
C
G
T
T
-
-
-
C
C
A
A
T
A
A
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A
A
T
A
C
A
T
G
-
-
-
A
C
A
A
A
G
G
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T
T
T
A
C
T
T
T
-
-
-
A
A
C
A
A
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A
A
G
A
A
C
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-
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A
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C
A
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-
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G
C
A
A
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A
A
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-
-
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A
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A
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G
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A
A
T
G
A
C
A
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-
-
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A
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A
A
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A
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<
T
T
A
G
A
T
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>
C
T
A
T
C
G
C
T
-
-
-
A
T
G
T
T
T
T
C
-
-
-
A
A
G
G
A
T
T
C
-
-
-
T
A
A
G
G
G
A
A
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!"
DOI: 10.1038/NCHEM.1070
SS.3. 1a|| rectang|e

Core
Seq name Sequence
L0r11ml1 ACA111ACCCCCAAAACCAA11ACCCCCC1CA
L0r11mr1 C1AA11CAA11CAC11AACCCCAACAAACCCA
L0r11mr2 AAACCA11AA1C11ACCAACCC1ACC1CCCCA
L0r11mr_fr AAACACCCCAA1CAAA1ACCAA11AACCAC
L0r11seam_l 1CCCC1CACC1CC1CA11CAC1CAACA1AACC
L0r11seam_r CACCCA11AA111CCCAC11AC1AA1CCAC
L0r13ml1 AA1CC111CAAAAA1CACC1C111CC1111CA
L0r13mr1 CCACACCCA11A111A1CCCAA1CACAA11AA
L0r13mr2 C11CCCCC111CA1CC1ACCAA1CCC1C1C11
L0r13mr_fr 11A1CC1C1111C111AACC1CAAACA1AA
L0r13seam_l A1ACA1AACAA1ACCACA11CAACAAAA1AAA
L0r13seam_r ACAACCC1ACAACCC11A1CCCCACAA1CA
L0r13ml1 1AACACC1CAA1A1AA1CC1C1ACC1AA1AC1
L0r13mr1 A1CACA1ACACCCC1111ACCCAAACCACCC1
L0r13mr2 1CC11A1CAACC1AAAC1AA11C1CA1A111A
L0r13mr_fr C11111A1ACC1111CAACCC111ACAA11
L0r13seam_l CCA1AAA1AAACAC11CACAAAACC1A11C1A
L0r13seam_r A1C1ACAA1A1CCCA1CC1AA111ACACC1
L0r17ml1 AC1ACCA1CAA11ACCAAAA11AAAAAACCC1
L0r17mr1 CAAAAA1AAACCAA1CAA1AA1CCA11ACCCC
L0r17mr2 ACAACCCC11AC1ACAAAAACCC11CACC1AA
L0r17mr_fr ACCCACAAA11CCAACAACCCC1CCAACCC
L0r17seam_l 1AA11CC1CA11111CCCCA1CCC11ACCACC
L0r17seam_r AC1ACCCCCAC1A1AAACCCAAA1ACACCC
L0r19ml1 CACAAACC11CAACCC11C1ACC11AAA11C1
L0r19mr1 AA11C11AC11AA11CACAA1CCCC1CCACAC
L0r19mr2 A111AA1C1CA1ACC1C1CACACA111CCC11
L0r19mr_fr AA1CA1AAAACA1C1AA111ACCA1AAAC1
L0r19seam_l AACCCAAA1AACA1CCAA1AAA1CCCC1CAAC
L0r19seam_r A1A1111AACCCCACAAAAC11CACCA1CA
L0r1ml1 ACACCC11CC1AC1CACCACC11111CCACAC
L0r1ml_fl 11CC1CACACAACCCCCACCC1CAAAAC1ACA
L0r1mr2 ACCACCACACACCCACCACCCCAACCCC1111
L0r1seam_r ACCCACCACCC1CACAACCCCCCCAA1ACC
L0r1L_seam CCCAC1C1C1CAA111ACCC11CCAC1AACC
L0r1Ll1 C1CA1ACA1CCC1111CA1CA1AC1CCCC1CC
L0r1Ll2 AC1CC1AA1AAC1111AACCCCCCACAC1CC
L0r1Lr1 A11CACAAACAAA1AAA1CC1CA1CCACAACC
L0r21mr1 ACACAAACAC11AA111CA1C11CC111AC1A
L0r21mr_fr 1A1CAAAAC111CAAA1ACCCACACACCCC
L0r21seam_l A1A1CA1ACCCCACACAC1CAAA1111CAAA1
L0r23mr_fr A1CAACAA1CAAAACA1ACCCA1C1CAA11
L0r23ml1 CCAC1CACCCA1CCC1CCACC1CCCCC1CAC1
L0r23ml_fl CCCCA11ACCCC1ACCCACC1CCAC1CCCC1C
L0r23mr2 1AA1CCAAAACA11A1CA1111CCAC1A11AC
L0r23mr_fr 11CCC1ACACACCCCAA11A11CAACAAAC
L0r23seam_r 1AA1CC1CACA1CA1CCCAA11CCCCAC1C
L0r27ml1 CCCCCC111AA1CAA1CCCCCAACCCCAAA1C
L0r27ml_fl CC1AAC1CC111CCC1A11CCCCCCC111CCC
L0r27mr2 AC111ACAA1C1CC1CAC11CCCACCACCC1C
L0r27mr_fr C111CAC1CCC11ACAACC1ACCAAACAAA
L0r27seam_r CA1AA1AC1AA1ACA11ACACCC1CC1CCC
L0r29ml1 CCCAAAA1CC11CAC1C11C11CCAACCCCCC
L0r29ml2 ACACCCCACA11AA11CCC11CAC1C1ACA
L0r29mr1 AC1AACAACA111CACCA111ACACCAACAAA
L0r29mr2 ACACCCACC1AAAACA1CCCCA11CACC1CAA
L0r29mr_fr CAA1CAA1AACAA11CCACAAC1111AAAA
L0r29seam_l ACC1CCA11CCAC1CCCCAAACC1CC1CAA1A
L0r29seam_r 1A11AAC1AAAACACACC1CACCAA1ACCC
L0r31ml2 ACAACAC1C111CA1CC1CC11CCCCCCCC
L0r31mr1 CCACAACAACCCCC1CCAACAC1CAA1CAACA
L0r31mr_fr 1CA1ACCCCACCAAA1CAAAAA1AAACCC1
L0r31br2 ACCC1AACAA1ACC1CCCACACACCCCAAC
L0r31seam_l CCACA1ACCCC11A1AAA1CAAAACCCC1CAC
L0r31b_seam CAACC1CCCCACAAACCAACCCAAACA11C1C
L0r31bl1 CCCCA111ACACC11CACCCCCAAC111CCA
L0r31br1 CCCAACACACA1ACAACCC11C1AAAAA1AC
L0r3ml1 C11AC1AAC111CAACAC111CACACAA1CAC
L0r3ml2 CACCC1C1ACCACCCCCA1AACACCAC1C1
L0r3ml_fl AACCA1C1AACCAACAAC1AAACCCC1CAA11
L0r3mr1 CACCCCCCACCC1CACACCCCCCA1AAACCCA
L0r3mr2 CA1CCCCAAACCCCCCAAACC1CA1CAA11A1
L0r3mr_fr CCCCAACCACCCCCCCCCACCA1CC11CA1
L0r3seam_l 1C1A1CACCA1A1AAC1A1ACCCCACCC1CAC
L0r3seam_r 11CCC11AA1CAC1ACCCACACCCA1111C
L0r3ml1 AACAACCACACCC11CCACCCAC1AACAA1AC
L0r3ml2 CAA1ACAAAAC1111C1CC1C1AC1ACCCC
L0r3mr1 ACCACCC11ACCC1CACAC1C1ACCCCCC1CC
L0r3mr2 CACCC1CAACAA1CAA1ACAAAA1AAACC1AC
L0r3mr_fr CCA11ACC1111CCC1CA1ACCCAAAA1CA
L0r3seam_l C1AAACAAA1CAA1111C1C1A1CAA1CAAC1
L0r3seam_r 1CACCCAA11CACCCACCCAACCA1A1A11
L0r7ml1 AC1AAAACCCCCAAACAAAC1ACAAAA1CAAC
L0r7ml2 CC1111CCCCA1AC11CCCCCCCCCAC1CA
L0r7mr1 11CAACCCAA11A11CA11AAACCCCAA1CAA
L0r7mr2 AAAA1ACAACAAAC11ACCACAAC1AA1AACA
L0r7mr_fr A1111C1CCCCAC11CACCCA11ACCA11A
L0r7seam_l CCC1CCC11CCCCCACCCA1AACCC1AAA1A1
L0r7seam_r 1CC11A1AAAACAAC1CCCA1CCACCCA11
L0r9ml1 C1AACAAACCACAAACACCACAACA1CAC11C
L0r9mr1 CAA1ACCC1ACCCAC1A1C11ACC1CA1A1CC
L0r9mr2 CCAACAAAAACCCCA11ACACCCCCAAA1AAC
L0r9mr_fr A1ACCCCA1ACA1AAACC1CCCA1AAC111
L0r9seam_l A1ACCAACAC1CA1C111CACCCCA11AACAC
L0r9seam_r CACAACACCCC1AA1A1CACACA1AACCC1
L-1r0Ll4 11CAC1AACAC1CCCCC1A1AAA11A11C1
L-1r10fl2 CCAAC1CAC1CAA11ACC11A1CCCACC11

L-1r12fl2 CCCAACAACCA1AAAAACCAAAAACACCCC
L-1r14fl2 C1AA1AC11AACACCAACCCCCA1CAAACC
L-1r16fl2 CAACCACACA11CCA1A1AACACC111CAC
L-1r18fl2 CA11ACA111A1CACCC1C1AA1ACCA1AA
L-1r20fl2 AAA11111CCC1A1CACC1CA111CAACCC
L-1r22fl2 1AA1CC1AC1ACCCACC111CA1CCA11C1
L-1r24fl2 CCC1CCCACCCA11CACCC1CCCC11CCC1
L-1r26fl1 1CA1CC1CACC1CCCCAAACCCCCACCCAAAC
L-1r26fl2 A11ACCCCA1ACC1C111CC1C1ACA1ACC
L-1r28fl1 C11111C1CCA1AAAC1C1AAACCA11CC1AA
L-1r28fl2 ACCCCCAA111CACCAC1CACACCC1CACA
L-1r2fl1 ACCC1CACAAAC1A11AACACCC11CAC1CCC
L-1r2fl2 CAAACA1CACCCACCACCC1CA1C1ACCC1
L-1r30fl1 CAACC1CACCAACCCC1CCACCC1CCACCC1C
L-1r30fl2 CAC11CCAAACCCCCAAAAACCC1CACCCA
L-1r32bl2 AA1CAAC111111CCCC1CCACC1C1CCAC1C
L-1r4fl1 A1AA1AA1C111CC1CACCAC1ACCAACCCCC
L-1r4fl2 AACAC1CA11111CACC11CAAA1AA11C1
L-1r6fl1 AACACACCA1CACC11CC111CCAAA11CCCA
L-1r6fl2 A1CCC111A1CCCAACCACCC1AC11111C
L-1r8fl2 A1CACCAAC1CC1CCA1C11AC1ACCCAAC
Lr-rem1 C1AAAACAC1C1C1CCA1CACCCAAA11
Lr-rem2 AC1C11111A1AA1CAC1CACCCCACCCA
L0r29speclal_l1 CAAAA1CC1CCAC1A11AAACAACCCCC1AAACCCCA111

L1r0_edge_r_2 CACC1CACACCA11CC1CACACCACC11CACC
L1r2_edge_r_2 CCA1C1111CA1AA1CCCC11A11ACCC111C
L1r4_edge_r_2 CAAAA1CACCAC1ACC1CCCAA11ACACCCAC
L1r6_edge_r_2 CAAACACACCACCCAAACA1A1AAAACAAACC
L1r8_edge_r_2 CCC11111AACAAAACACC1A1C11ACCCAAC
L1r10_edge_r_2 CC111ACACACACAA1AAAA1CAAAA1ACCAC
L1r12_edge_r_2 C1A1111CCACCCACCAAA1CAACA11AC11C
L1r14_edge_r_2 CAC1CA1CCACAACAAA11AAACCAAC1ACCC
L1r16_edge_r_2 CCAC1AA1AACACAA1CACACCCA1111CCAC
L1r18_edge_r_2 CC11AAA1AACAA1AACC1C1CA1AAA1AACC
L1r20_edge_r_2 C1CACAACAC1CAA1AACC11ACA11AACACC
L1r22_edge_r_2 CAAAACAACA1CA1CAA111CAA11ACC1CAC
L1r24_edge_r_2 CACC1AAAACACAAA1A1A1CAAAA11A111C
L1r26_edge_r_2 CCCCAACC11A11AA1CC1A11AAA1CC111C
L1r28_edge_r_2 C1CAACC1CAAA1A1CC1AAACCA1CACC11C
L1r30_edge_r_2 C1A11AC1C111AA1CCAA1A11111CAA1CC

L-1r2_edge_l_2 CC1A111CCCAACC1ACAC11AA1CCCCCC1C
L-1r4_edge_l_2 CCCAA1ACCAACCCA1111CACCCA1ACCAAC
L-1r6_edge_l_2 C1CCAAAACCACCC11A1C1CCAAAAAAAACC
L-1r8_edge_l_2 C111CACCAC1AAACACCAACCCC1ACACACC
L-1r10_edge_l_2 CACACCC1CAA1CA1A1ACCCCCAACCACCCC
L-1r12_edge_l_2 C1CA11A1ACCAC1CACCA1111AACAAC1CC
L-1r14_edge_l_2 CAAAACAAC1111CCC1ACCCACACCC1111C
L-1r16_edge_l_2 CC1111AA11CCACC1AACAC11CAAA1A1CC
L-1r18_edge_l_2 CCAACCAC1ACA111A11CA11CCCAA11C1C
L-1r20_edge_l_2 CC111A111CAACCCAAC1111CCCCCACAAC
L-1r22_edge_l_2 CAAACAACACAA1CCACCC1CACAC1C1CCAC
L-1r24_edge_l_2 CCAC1AACAACCCC1CCAACA11AAA1C1CAC
L-1r26_edge_l_2 CCA1CCC1CCCCCCC1CAAC1C11CCCAACCC
L-1r28_edge_l_2 C1CACAA11CCACACAC1CAAA11C11A1CCC
L-1r30_edge_l_2 CCC11CACCCCC1CCCCCCCAACACC1CA11C
L-1r32_edge_l_2 CCCAC1ACC1CAACCA1C1A1CACCCCCA1CC

L-1r8fl1_hp 1CCCCCACC111CCA1LccLcLLLLgaggaacaagLLLLcLLgL1AAACCCCACCACCCA
L-1r10fl1_hp 1AA1CA11CCAAC111LccLcLLLLgaggaacaagLLLLcLLgLCAAACACC1C1CCAAA
L-1r12fl1_hp CCACACCAAAA1C1ACLccLcLLLLgaggaacaagLLLLcLLgLC11AA1AA11CAAC11
L-1r14fl1_hp AAAAACA1AAAA1C11LccLcLLLLgaggaacaagLLLLcLLgL1ACAC1CCC1CC111A
L0r3ml_fl_hp CC11CA1ACCCCA1CCLccLcLLLLgaggaacaagLLLLcLLgL1CACCC1C1AAAA1AC
L0r7ml_fl_hp CCAACC1AA1CCCC1CLccLcLLLLgaggaacaagLLLLcLLgLA1AAA11CACACA1CA
L0r9ml_fl_hp CAACAACCC11CACA1LccLcLLLLgaggaacaagLLLLcLLgLCC111AA1AACCAAC1
L0r11ml_fl_hp CA11A11ACAACAC1ALccLcLLLLgaggaacaagLLLLcLLgL1CA1AACCA1ACCC1C
L0r13ml_fl_hp A1CC1CA1C1CACAACLccLcLLLLgaggaacaagLLLLcLLgLCAAACCCCACACC1CA
L0r9ml2_hp 11C1A1CAAACCAAALccLcLLLLgaggaacaagLLLLcLLgLCACCCAA1AAACCCC
L0r11ml2_hp AA11CCCCCA1A11CLccLcLLLLgaggaacaagLLLLcLLgLA11ACCCACCCACA1
L0r13ml2_hp C1AACACCACC1ACALccLcLLLLgaggaacaagLLLLcLLgLAACA11CCAC1AC1A
L0r13ml2_hp 1A11A1AAAA1A11CLccLcLLLLgaggaacaagLLLLcLLgLA11CAA1CACCCA1A
L-1r16fl1_hp CCAAC111CCCCAACCLccLcLLLLgaggaacaagLLLLcLLgLAAAC1CCAA11CCA1C
L-1r18fl1_hp CAAAAACAACA111CCLccLcLLLLgaggaacaagLLLLcLLgLCAAA1CC1CCC1C1C1
L-1r20fl1_hp 1C1ACAAAACAACCC1LccLcLLLLgaggaacaagLLLLcLLgLCA1A1A11CC11C1AC
L-1r22fl1_hp CCC11CC1AAAC1ACCLccLcLLLLgaggaacaagLLLLcLLgLA1C1CAA111CACACA
L-1r24fl1_hp CCCCA11CACAAACCCLccLcLLLLgaggaacaagLLLLcLLgLCCCA11CACCCC1C1C
L0r13ml_fl_hp A11ACACAA1A1CCAALccLcLLLLgaggaacaagLLLLcLLgLC1AAAC1ACAA1AACC
L0r17ml_fl_hp C1CAAAACACCA1AAALccLcLLLLgaggaacaagLLLLcLLgLCC1AAA1C11AAA1CC
L0r19ml_fl_hp CAC1AA1CCACACCC1LccLcLLLLgaggaacaagLLLLcLLgLACC1A111CA1A1C1A
L0r21ml_fl_hp CCAACA11CCCA1CAALccLcLLLLgaggaacaagLLLLcLLgLAAA1AA11CCC1AA1C
L0r17ml2_hp C1111AAC1ACC111LccLcLLLLgaggaacaagLLLLcLLgLAA11CC1ACCC1CAC
L0r19ml2_hp CCC1CACC1CCCA1CLccLcLLLLgaggaacaagLLLLcLLgLAA11C1AC1CAACA1
L0r21ml2_hp AA1CCCC1C1ACC1ALccLcLLLLgaggaacaagLLLLcLLgLAACA11CCCAA1AAA
L0r23ml2_hp 1ACCAACC1A1AACCLccLcLLLLgaggaacaagLLLLcLLgLAAA1A11CA1AAA11
L0r23ml_fl_hp C1C1ACA11C1CC1CCLccLcLLLLgaggaacaagLLLLcLLgLCCCAAACCA1C1CC1C
L0r23ml2_hp CACCCC1CCCCCCA1LccLcLLLLgaggaacaagLLLLcLLgLCC1AACC11AACCAA
L0r27ml2_hp CCA1CCCAC11CCC1LccLcLLLLgaggaacaagLLLLcLLgLAACCCCAC111CCCC
L0r21ml1_hp AAACC11A1AAA1CACLccLcLLLLgaggaacaagLLLLcLLgLC1CA1111C1CCA1C1
L0r23ml1_hp CCCAC111A1CCCAC1LccLcLLLLgaggaacaagLLLLcLLgLCCACCCACCCC1111C
L0r23seam_l_hp A11111C1A1A1111CLccLcLLLLgaggaacaagLLLLcLLgL11AAAA1111CC11C1
L0r23seam_l_hp 1CACCAACCACCCCACLccLcLLLLgaggaacaagLLLLcLLgLCACCACAC1AACCCA1
L0r27seam_l_hp CCAACC11CACC11C1LccLcLLLLgaggaacaagLLLLcLLgLAAAACCACCA1CAA1A
L0r21seam_r_hp C1AAA1C1C1CAC1CLccLcLLLLgaggaacaagLLLLcLLgLAA1AACCCCCA11AA
L0r23seam_r_hp 1CCCC1CCA1CCCCALccLcLLLLgaggaacaagLLLLcLLgLCAAACAA1A1CCCCC
L0r23mr1_hp 1CAA1A1AC1CCC1A1LccLcLLLLgaggaacaagLLLLcLLgL1AA11AA1C1ACC111
L0r23mr1_hp ACC1111AA11CC111LccLcLLLLgaggaacaagLLLLcLLgLCAA1ACCA111AACAA
L0r27mr1_hp C1CA11A1CA11C111LccLcLLLLgaggaacaagLLLLcLLgLCCA11A1A1CACA1CA
L0r21mr2_hp ACAA1CC1AACAAAA1LccLcLLLLgaggaacaagLLLLcLLgL1AA11ACAAC11ACAA
L0r23mr2_hp AA1CCCCCA1111CACLccLcLLLLgaggaacaagLLLLcLLgLC111AACCC11C1CAA

na|rp|n-|ess stap|es correspond|ng to ha|rp|n-|abe|ed ones
(needed when generat|ng ha|rp|n patterns other than 'L')
L-1r8fl1_hp_org 1CCCCCACC111CCA11AAACCCCACCACCCA
L-1r10fl1_hp_org 1AA1CA11CCAAC111CAAACACC1C1CCAAA
L-1r12fl1_hp_org CCACACCAAAA1C1ACC11AA1AA11CAAC11
L-1r14fl1_hp_org AAAAACA1AAAA1C111ACAC1CCC1CC111A
L0r3ml_fl_hp_org CC11CA1ACCCCA1CC1CACCC1C1AAAA1AC
L0r7ml_fl_hp_org CCAACC1AA1CCCC1CA1AAA11CACACA1CA
L0r9ml_fl_hp_org CAACAACCC11CACA1CC111AA1AACCAAC1
L0r11ml_fl_hp_org CA11A11ACAACAC1A1CA1AACCA1ACCC1C
L0r13ml_fl_hp_org A1CC1CA1C1CACAACCAAACCCCACACC1CA
L0r9ml2_hp_org 11C1A1CAAACCAAACACCCAA1AAACCCC
L0r11ml2_hp_org AA11CCCCCA1A11CA11ACCCACCCACA1
L0r13ml2_hp_org C1AACACCACC1ACAAACA11CCAC1AC1A
L0r13ml2_hp_org 1A11A1AAAA1A11CA11CAA1CACCCA1A
L-1r16fl1_hp_org CCAAC111CCCCAACCAAAC1CCAA11CCA1C
L-1r18fl1_hp_org CAAAAACAACA111CCCAAA1CC1CCC1C1C1
L-1r20fl1_hp_org 1C1ACAAAACAACCC1CA1A1A11CC11C1AC
L-1r22fl1_hp_org CCC11CC1AAAC1ACCA1C1CAA111CACACA
L-1r24fl1_hp_org CCCCA11CACAAACCCCCCA11CACCCC1C1C
L0r13ml_fl_hp_org A11ACACAA1A1CCAAC1AAAC1ACAA1AACC
L0r17ml_fl_hp_org C1CAAAACACCA1AAACC1AAA1C11AAA1CC
L0r19ml_fl_hp_org CAC1AA1CCACACCC1ACC1A111CA1A1C1A
L0r21ml_fl_hp_org CCAACA11CCCA1CAAAAA1AA11CCC1AA1C
L0r17ml2_hp_org C1111AAC1ACC111AA11CC1ACCC1CAC
L0r19ml2_hp_org CCC1CACC1CCCA1CAA11C1AC1CAACA1
L0r21ml2_hp_org AA1CCCC1C1ACC1AAACA11CCCAA1AAA
L0r23ml2_hp_org 1ACCAACC1A1AACCAAA1A11CA1AAA11
L0r23ml_fl_hp_org C1C1ACA11C1CC1CCCCCAAACCA1C1CC1C
L0r23ml2_hp_org CACCCC1CCCCCCA1CC1AACC11AACCAA
L0r27ml2_hp_org CCA1CCCAC11CCC1AACCCCAC111CCCC
L0r21ml1_hp_org AAACC11A1AAA1CACC1CA1111C1CCA1C1
L0r23ml1_hp_org CCCAC111A1CCCAC1CCACCCACCCC1111C
L0r23seam_l_hp_org A11111C1A1A1111C11AAAA1111CC11C1
L0r23seam_l_hp_org 1CACCAACCACCCCACCACCACAC1AACCCA1
L0r27seam_l_hp_org CCAACC11CACC11C1AAAACCACCA1CAA1A
L0r21seam_r_hp_org C1AAA1C1C1CAC1CAA1AACCCCCA11AA
L0r23seam_r_hp_org 1CCCC1CCA1CCCCACAAACAA1A1CCCCC
L0r23mr1_hp_org 1CAA1A1AC1CCC1A11AA11AA1C1ACC111
L0r23mr1_hp_org ACC1111AA11CC111CAA1ACCA111AACAA
L0r27mr1_hp_org C1CA11A1CA11C111CCA11A1A1CACA1CA
L0r21mr2_hp_org ACAA1CC1AACAAAA11AA11ACAAC11ACAA
L0r23mr2_hp_orgAA1CCCCCA1111CACC111AACCC11C1CAA

!"
43
DOI: 10.1038/NCHEM.1070
D|agram for ta|| rectang|e
wlLh poslLlons of dumbbells (orange clrcles) and poslLlons and lengLhs of loopouLs (black clrcles wlLh numbers) lndlcaLed

9
29
40
9
20
55
10
12
2
31
7
33
15
3
12
44
10
4
12
30
18
26
16
72
16
63
41
15
36
28
4
14
!"
44
DOI: 10.1038/NCHEM.1070
Sequence d|agram for ta|| rectang|e

-1 0 +1
t-1r0t- t1r0_edge_r_2
< GTCCCCCGTAATTGACAAATATGCCCGTGACAATGAGTTCCGTGACTGGGGCAA< <AGTTCCGGTTAGCAGACTGGAC <
> CAGGGGGCATTAACTGTTTATACGGGCACTGTTACTCAAGGCACTGACCCCGTT---AAAACTTATTACCAGTACACTCCTGTATCATCAAAAGCCATGTATGACGCTTACTG-------GAACGGTAAATTCAGAGACTGCGTGGCTTTAATGAGGATTTATTTGTTTGTGAATA---TCAAGGCCAATCGTCTGACCTG >
/ <TTTTGAATAATGGTCATGTGAGGACATAGTAGTTTTCGGTACATACTGCGAATGAC-------CTTGCCATTTAAGTCTCTGACGCACCGAAATTACTCCTAAATAAACAAACACTTAT< \
| l2_temp_pre t0r1t0r1tt0 |
\ >CTTGCTCAGTACCAGGCGGATAAGTGCCGTCGAGAGGGTTGATATAAGTATAGCCC-------ACCCTCAGAGCCACCACCCTCAGAGCCGCCACCAGAACCACCACCAGAGCCGCCGC> /
< GGATAAAGCCTTGGATAATAAGACTTTGTACTTTCATAATTCTCCGACTCTGAG---GAACGAGTCATGGTCCGCCTATTCACGGCAGCTCTCCCAACTATATTCATATCGGG< <TGGGAGTCTCGGTGGTGGGAGTCTCGGCGGTGGTCTTGGTGGTGGTCTCGGCGGCG---GTCGTAACTGTCCTCCAACTCC <
CCTATTTCGGAACCTATTATTCTGAAACATGAAAGTATTAAGAGGCTGAGACTC> \ / >CAGCATTGACAGGAGGTTGAGG
( | | )
GAACGATAGGGACTTTTACTCCCACCACCGAGACTCCCACCGCCAAGACTCCCA< / \ <CTAAAACTAATACTTTTCTACC
> CTTGCTATCCCTGAAAATGAGGGTGGTGGCTCTGAGGGTGGCGGTTCTGAGGGT---GGCGGTTCTGAGGGTGGCGGTACTAAACCTCCTGAGTACGGTGATACACCTATTCC> >GGCGGTTCTGAGGGTGGCGGCTCGGAGGCGGTTCCGGTGGTGGCTCTGGTTCCGGT---GATTTTGATTATGAAAAGATGG >
/ <CCGCCAAGACTCCCACCGCCATGATTTGGAGGACTCATGCCACTATGTGGATAAGG-------CCGCCAAGACTCCCACCGCCGAGCCTCCGCCAAGGCCACCACCGAGACCAAGGCCA< \
| t0r3ml_fll t0r3seam_r |
\ >AAACGATCTAAAGTTTTGTCGTCTTTCCAGACGTTAGTAAATGAATTTTCTGTATG-------AATCAAGTTTGCCTTTAGCGTCAGACTGTAGCGCGTTTTCATCGGCATTTTCGGTC> /
< GGGTTATCCTTGGGTACATGGCATTGTGACTCAAAGCAGTGGTCATGTTTGATG---TTTGCTAGATTTCAAAACAGCAGAAAGGTCTGCAATCATTTACTTAAAAGACATAC< <TTAGTTCAAACGGAAATCGCAGTCTGACATCGCGCAAAAGTAGCCGTAAAAGCCAG---TATCGGGGGAATAATCGCAAAC <
CCCAATAGGAACCCATGTACCGTAACACTGAGTTTCGTCACCAGTACAAACTAC> \ / >ATAGCCCCCTTATTAGCGTTTG
( | | )
GGAAAAAAAACCTCTAAAAGTTGCACTTTTTTAATAATAAGCGTTAAGGAAATC< / \ <TTACCACGATGACCACTAAAAC
> CCTTTTTTTTGGAGATTTTCAACGTGAAAAAATTATTATTCGCAATTCCTTTAG---TTGTTCCTTTCTATTCTCACTCCGCTGAAACTGTTGAAAGTTGTTTAGCAAAATCC> >CTGTCGCTACTGATTACGGTGCTTTCATTGGTGACGTTTCCGGCCTTGCTAATGGT---AATGGTGCTACTGGTGATTTTG >
/ <AACAAGGAAAGATAAGAGTGAGGCGACTTTGACAACTTTCAACAAATCGTTTTAGG-------GACAGCGATGACTAATGCCACGAAAGTAACCACTGCAAAGGCCGGAACGATTACCA< \
\ >TGCTTGATACCGATAGTTGCGCCGACAATGACAACAACCATCGCCCACGCATAACC-------GTAAATATTGACGGAAATTATTCATTAAAGGTGAATTATCACCGTCACCGACTTGA> /
< GAGGTTTTCCTCGGAAATTAACATAGCCAAATAGTCGAACGAAAGCTCCACTTA---ACGAACTATGGCTATCAACGCGGCTGTTACTGTTGTTGGTAGCGGGTGCGTATTGG< <CATTTATAACTGCCTTTAATAAGTAATTTCCACTTAATAGTGGCAGTGGCTGAACT---CGGTAAACCCTTAATCTCGGTC <
CTCCAAAAGGAGCCTTTAATTGTATCGGTTTATCAGCTTGCTTTCGAGGTGAAT> \ / >GCCATTTGGGAATTAGAGCCAG
( | | )
GGAGACATCGGCAACGATGGGAGCAAGGCTACGACAGAAAGCGACGACTCCCAC< / \ <TTGAATAAGGCACCACAGAAAC
> CCTCTGTAGCCGTTGCTACCCTCGTTCCGATGCTGTCTTTCGCTGCTGAGGGTG---ACGATCCCGCAAAAGCGGCCTTTAACTCCCTGCAAGCCTCAGCGACCGAATATATC> >CTTCCCTCCCTCAATCGGTTGAACCATATGAATTTTCTATTGATTGTGACAAAATA---AACTTATTCCGTGGTGTCTTTG >
/ <TGCTAGGGCGTTTTCGCCGGAAATTGAGGGACGTTCGGAGTCGCTGGCTTATATAG-------GAAGGGAGGGAGTTAGCCAACTTGGTATACTTAAAAGATAACTAACACTGTTTTAT< \
\ >CCCAACCTAAAACGAAAGAGGCAAAAGAATACACTAAAACACTCATCTTTGACCCC-------ATTAAGACTCCTTATTACGCAGTATGTTAGCAAACGTAGAAAATACATACATAAAG> /
< GAAACTCCTGATTTCTGAAAAAGTACTCCTTCAAAGGTAATTTGCCCATTTTAT---GGGTTGGATTTTGCTTTCTCCGTTTTCTTATGTGATTTTGTGAGTAGAAACTGGGG< <TAATTCTGAGGAATAATGCGTCATACAATCGTTTGCATCTTTTATGTATGTATTTC---CACCGTTGTATATTTTCTTTGC <
CTTTGAGGACTAAAGACTTTTTCATGAGGAAGTTTCCATTAAACGGGTAAAATA> \ / >GTGGCAACATATAAAAGAAACG
( | | )
GCGGAGCAAGGCCGATTCATTGTACCTCGTCCAGCGCCTAAAGCTGTGTTAAAT< / \ <ACGAATGAAAAGAATTTTTCCC
> CGCCTCGTTCCGGCTAAGTAACATGGAGCAGGTCGCGGATTTCGACACAATTTA---TCAGGCGATGATACAAATCTCCGTTGTACTTTGTTTCGCGCTTGGTATAATCGCTG> >CATGCCAGTTCTTTTGGGTATTCTCGGTTTCCTTCTGGTAACTTTGTTCGGCTATC---TGCTTACTTTTCTTAAAAAGGG >
/ <AGTCCGCTACTATGTTTAGAGGCAACATGAAACAAAGCGCGAACCATATTAGCGAC-------GTACGGTCAAGAAAACCCATAAGAGCCAAAGGAAGACCATTGAAACAAGCCGATAG< \
\ >ACAAGAACCGGATATTCATTACCCAAATCAACGTAACAAAGCTGCTCATTCAGTGA-------AGATAACCCACAAGAATTGAGTTAAGCCCAATAATAAGAGCAAGAAACAATGAAAT> /
< GTCTGCCAGTTAGTATTCCCTTGGCTTGACTGGTTGAAACTTTCTCCTGTCTAC---TGTTCTTGGCCTATAAGTAATGGGTTTAGTTGCATTGTTTCGACGAGTAAGTCACT< <TCTATTGGGTGTTCTTAACTCAATTCGGGTTATTATTCTCGTTCTTTGTTACTTTA---TCGTTATCGATAGAATGGCTTC <
CAGACGGTCAATCATAAGGGAACCGAACTGACCAACTTTGAAAGAGGACAGATG> \ / >AGCAATAGCTATCTTACCGAAG
( | | )
GGTCAAGAATTTTAGCGTATTCCATTAAGTGTTACTAATTTCAACTTTAATTTG< / \ <ATACAATAAGAGAGACATTTCC
> CCAGTTCTTAAAATCGCATAAGGTAATTCACAATGATTAAAGTTGAAATTAAAC---CATCTCAAGCCCAATTTACTACTCGTTCTGGTGTTTCTCGTCAGGGCAAGCCTTAT> >CTCTGATATTAGCGCTCAATTACTTAATTCTCCCGTCTAATGCGCTTCCCTGTTTT---TATGTTATTCTCTCTGTAAAGG >
/ <GTAGAGTTCGGGTTAAATGATGAGCAAGACCACAAAGAGCAGTCCCGTTCGGAATA-------GAGACTATAATCGCGAGTTAATGAATTAAGAGGGCAGATTACGCGAAGGGACAAAA< \
\ >TCATTATTACAGGTAGAAAGATTCATCAGTTGAGATTTAGGAATACCACATTCAAC-------AAAATAAACAGCCATATTATTTATCCCAATCCAAATAAGAAACGATTTTTTGTTTA> /
< GAGTAATATGGTCAGTCCTGCAACCCTTCTTTTTAGATGCAATTATTTTGCTTG---AGTAATAATGTCCATCTTTCTAAGTAGTCAACTCTAAATCCTTATGGTGTAAGTTG< <TTTTATTTGTCGGTATAATAAATAGGGTTAGGTTTATTCTTTGCTAAAAAACAAAT---TGCAGTTTTTACTTTTATCGTC <
CTCATTATACCAGTCAGGACGTTGGGAAGAAAAATCTACGTTAATAAAACGAAC> \ / >ACGTCAAAAATGAAAATAGCAG
( | | )
GTTTTCGGAGAGCGATAAAACCAAAAATAGCAGCAGACCATTTGCTCCCAATAC< / \ <TAACATCGACCCACGTTTTATC
> CAAAAGCCTCTCGCTATTTTGGTTTTTATCGTCGTCTGGTAAACGAGGGTTATG---ATAGTGTTGCTCTTACTATGCCTCGTAATTCCTTTTGGCGTTATGTATCTGCATTA> >GTAACTGGCAAATTAGGCTCTGGACGCTCGTTAGCGTTGGTAAGATTCAGGATAAA---ATTGTAGCTGGGTGCAAAATAG >
/ <TATCACAACGAGAATGATACGGAGCATTAAGGAAAACCGCAATACATAGACGTAAT-------CATTGACCGTTTAATCCGAGACCTGCGAGCAATCGCAACCATTCTAAGTCCTATTT< \
\ >CATCGTCATAAATATTCATTGAATCCCCCTCAAATGCTTTAAACAGTTCAGAAAAC-------GTATTCTAAGAACGCGAGGCGTTTTAGCGAACCTCCCGACTTGCGGGAGGTTTTGA> /
< GTTTTCTTCAAAACGGTCTCCCCCATTATCATTTTACAAATCTGACCTATCGCA---GTAGCAGTATTTATAAGTAACTTAGGGGGAGTTTACGAAATTTGTCAAGTCTTTTG< <CATAAGATTCTTGCGCTCCGCAAAATCGCTTGGAGGGCTGAACGCCCTCCAAAACT---TCGGAATTTAGTTCTAATCAAC <
CAAAAGAAGTTTTGCCAGAGGGGGTAATAGTAAAATGTTTAGACTGGATAGCGT> \ / >AGCCTTAAATCAAGATTAGTTG
( | | )
GCTATAAACTTCAGAAAGCCCGAAGGAGAATTAGAAAAACTACGTTAGGCGAAA< / \ <CGAACGAACAAGAGCTACTCAC
> CGATATTTGAAGTCTTTCGGGCTTCCTCTTAATCTTTTTGATGCAATCCGCTTT---GCTTCTGACTATAATAGTCAGGGTAAAGACCTGATTTTTGATTTATGGTCATTCTC> >CGGATAAGCCTTCTATATCTGATGCGGTAATGATTCCTACGATGAAAATAAAAACG---GCTTGCTTGTTCTCGATGAGTG >
/ <CGAAGACTGATATTATCAGTCCCATTTCTGGACTAAAAACTAAATACCAGTAAGAG-------GCCTATTCGGAAGATATAGACTACGCCATTACTAAGGATGCTACTTTTATTTTTGC< \
\ >AATTAGAGAGTACCTTTAATTGCTCCTTTTGATAAGAGGTCATTTTTGCGGATGGC-------TTACGAGCATGTAGAAACCAATCAATAATCGGCTGTCTTTCCTTATCATTCCAAGA> /
< GCAAAATTAAGCTCGAAGTTTCGCTTGGTCTGGCCTTCGTTTGAGGTTGTCCAG---TTAATCTCTCATGGAAATTAACGAGGAAAACTATTCTCCAGTAAAAACGCCTACCG< <AATGCTCGTACATCTTTGGTTAGTTATTAGCCGACAGAAAGGAATAGTAAGGTTCT---TGCCCATAATTTGGTTCATGGC <
CGTTTTAATTCGAGCTTCAAAGCGAACCAGACCGGAAGCAAACTCCAACAGGTC> \ / >ACGGGTATTAAACCAAGTACCG
( | | )
GTCTTAACCCTTAGTTGACAATATACCTTACTTTGAAGGTCTGTGGCATGAAAT< / \ <GAAATATAAGAGAATAATGACC
> CAGAATTGGGAATCAACTGTTATATGGAATGAAACTTCCAGACACCGTACTTTA---GTTGCATATTTAAAACATGTTGAGCTACAGCATTATATTCAGCAATTAAGCTCTAA> >ATTAGGATGGGATATTATTTTTCGTCTGGACAGAATTACTTTACCTTTTGTCGGTA---CTTTATATTCTCTTATTACTGG >
/ <CAACGTATAAATTTTGTACAACTCGATGTCGTAATATAAGTCGTTAATTCGAGATT-------TAATCCTACCCTATAATAAAAAGCAGACCTGTCTTAATGAAATGGAAAACAGCCAT< \
\ >CCTGAAAAGGTGGCATCAATTCTACTAATAGTAGTAGCATTAACATCCAATAAATC-------CGCTCAACAGTAGGGCTTAATTGAGAATCGCCATATTTAACAACGCCAACATGTAA> /
< GCTTGCTCATCTAAATCAAACTGGTAATCTATGTAAAGCGTTTACCAGTTATTG---GGACTTTTCCACCGTAGTTAAGATGATTATCATCATCGTAATTGTAGGTTATTTAG< <GCGAGTTGTCATCCCGAATTAACTCTTAGCGGTATAAATTGTTGCGGTTGTACATT---AAATCCGTCTCCGTAAAAGCTC <
CGAACGAGTAGATTTAGTTTGACCATTAGATACATTTCGCAAATGGTCAATAAC> \ / >TTTAGGCAGAGGCATTTTCGAG
( | | )
GAAGAGGGCGTTTTCATAATGTCCCAGTATTACAAAAACCATGTTGGCTAAATC< / \ <GCCACAAATAAGAATAAATTGC
> CTTCTCCCGCAAAAGTATTACAGGGTCATAATGTTTTTGGTACAACCGATTTAG---CTTTATGCTCTGAGGCTTTATTGCTTAATTTTGCTAATTCTTTGCCTTGCCTGTAT> >TTGGCTTTATACTGGTAAGAATTTACTAAACAGGCTTTTTCTAGTAATTATGATTC---CGGTGTTTATTCTTATTTAACG >
/ <GAAATACGAGACTCCGAAATAACGAATTAAAACGATTAAGAAACGGAACGGACATA-------AACCGAAATATGACCATTCTTAAATGATTTGTCCGAAAAAGATCATTAATACTAAG< \
\ >CGAGTAATGTGTAGGTAAAGATTCAAAAGGGTGAGAAAGGCCGGAGACAGTCAAAT-------TTTCAAATATATTTTAGTTAATTTCATCTTCTGACCTAAATTTAATGGTTTGAAAT> /
< GGAAATAAAGTTGCGTTCCTATTTTTAAAAATCTTGGGAGTATATAAAATTTAC---GCTCATTACACATCCATTTCTAAGTTTTCCCACTCTTTCCGGCCTCTGTCAGTTTA< <AAAGTTTATATAAAATCAATTAAAGTAGAAGACTGGATTTAAATTACCAAACTTTA---TGGCTGGCACACTATTTATTCC <
CCTTTATTTCAACGCAAGGATAAAAATTTTTAGAACCCTCATATATTTTAAATG> \ / >ACCGACCGTGTGATAAATAAGG
( | | )
GAGGTCTGAGAGTCCGTTACTGGACTATCGGAAACATCTAGAGAGTTTTTATCG< / \ <TAAGTGATAACTGAGAAGAGTC
> CTCCAGACTCTCAGGCAATGACCTGATAGCCTTTGTAGATCTCTCAAAAATAGC---TACCCTCTCCGGCATTAATTTATCAGCTAGAACGGTTGAATATCATATTGATGGTG> >AAGTTTTCTCGCGTTCTTTGTCTAAAGGTAGTCTCTCAGACCTATGATTTTGATAA---ATTCACTATTGACTCTTCTCAG >
/ <ATGGGAGAGGCCGTAATTAAATAGTCGATCTTGCCAACTTATAGTATAACTACCAC-------TTCAAAAGAGCGCAAGAAACAGATTTCCATCAGAGAGTCTGGATACTAAAACTATT< \
\ >AGGAAGATTGTATAAGCAAATATTTAAATTGTAAACGTTAATATTTTGTTAAAATT-------TTGCTTCTGTAAATCGTCGCTATTAATTAATTTTCCCTTAGAATCCTTGAAAACAT> /
< GTTTGTTCTCTTAGCTACTTGCCATTAGCATTTTGATCGTACAGTTAGTATACA---TCCTTCTAACATATTCGTTTATAAATTTAACATTTGCAATTATAAAACAATTTTAA< <AACGAAGACATTTAGCAGCGATAATTAATTAAAAGGGAATCTTAGGAACTTTTGTA---TCGCTATCGAATCTAATTCTGC <
CAAACAAGAGAATCGATGAACGGTAATCGTAAAACTAGCATGTCAATCATATGT> \ / >AGCGATAGCTTAGATTAAGACG
( | | )
GAGTGTAAATTACAACTACTTTCGACCGATGTCCTTCCGGTCTGCGCTTAATAA< / \ <AAACAAAGTAGTAGAAGAAAAC
> CTCACATTTAATGTTGATGAAAGCTGGCTACAGGAAGGCCAGACGCGAATTATT---TTTGATGGCGTTCCTATTGGTTAAAAAATGAGCTGATTTAACAAAAATTTAATGCG> >GGTTATTCACTCACATATATTGATTGTTAAATGTAATTAATTTTGTTTTCTTGATG---TTTGTTTCATCATCTTCTTTTG >
/ <AAACTACCGCAAGGATAACCAATTTTTTACTCGACTAAATTGTTTTTAAATTACGC-------CCAATAAGTGAGTGTATATAACTAACAATTTACATTAATTAAAACAAAAGAACTAC< \
\ >GGTGTAGATGGGCGCATCGTAACCGTGCATCTGCCAGTTTGAGGGGACGACGACAG-------TAACGGATTCGCCTGATTGCTTTGAATACCAAGTTACAAAATCGCGCAGAGGCGAA> /
< GCTCATTGTTGGGCAGCCTAAGAGGCACCCTTGTTTGCCGCCTAACTGGCATTA---CCACATCTACCCGCGTAGCATTGGCACGTAGACGGTCAAACTCCCCTGCTGCTGTC< <ATTGCCTAAGCGGACTAACGAAACTTATGGTTCAATGTTTTAGCGCGTCTCCGCTT---AATAAGTAAAGTTAATGGACTC <
CGAGTAACAACCCGTCGGATTCTCCGTGGGAACAAACGGCGGATTGACCGTAAT> \ / >TTATTCATTTCAATTACCTGAG
( | | )
GGGAAGGGTTGTCAACGCGTCGGACTTACCGCTTACCGCGAAACGGACCAAAGG< / \ <AAGAAATAAAGACAAAATGCAC
> CCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGCGCTTTGCCTGGTTTCC---GGCACCAGAAGCGGTGCCGGAAAGCTGGCTGGAGTGCGATCTTCCTGAGGCCGATA> >TTGTTTCTCCCGATGTAAAAGGTTCATCTGACGTTAAACCTGAAAATCTACGCAAT---TTCTTTATTTCTGTTTTACGTG >
/ <CCGTGGTCTTCGCCACGGCCTTTCGACCGACCTCACGCTAGAAGGACTCCGGCTAT-------AACAAAGAGGGCTACATTTTCCAAGTAGACTGCAATTTGGACTTTTAGATGCGTTA< \
\ >GGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGAC-------CATCAATATAATCCTGATTGTTTGGATTATACTTCTGAATAATGGAAGGGTTAGAA> /
< GCTAGCCACGCCCGGAGAAGCGATAATGCGGTCGACCGCTTTCCCCCTACACGA---CCCGCTAATTCAACCCATTGCGGTCCCAAAAGGGTCAGTGCTGCAACATTTTGCTG< <GTAGTTATATTAGGACTAACAAACCTAATATGAAGACTTATTACCTTCCCAATCTT---GGATGGTATAGTTTTAATAAAC <
CGATCGGTGCGGGCCTCTTCGCTATTACGCCAGCTGGCGAAAGGGGGATGTGCT> \ / >CCTACCATATCAAAATTATTTG
( | | )
GCCTATTGTTAAAGTGTGTCCTTTGTCGATACTGGTACTAATGCTTAAGCTCGA< / \ <AAATTTTAATTATTGCAAGCCC
> CGGATAACAATTTCACACAGGAAACAGCTATGACCATGATTACGAATTCGAGCT---CGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTTGGCACTGGCC> >AATTGCCATCATCTGATAATCAGTTTGTTCCGCAAAATGATAATGTTACTCAAACT---TTTAAAATTAATAACGTTCGGG >
/ <GCCATGGGCCCCTAGGAGATCTCAGCTGGACGTCCGTACGTTCGAACCGTGACCGG-------TTAACGGTAGTAGACTATTAGTCAAACAAGGCGTTTTACTATTACAATGAGTTTGA< \
\ >GGCTAACTCACATTAATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCT-------CGTCAATAGATAATACATTTGAGGATTTAGAAGTATTAGACTTTACAAACAATTCG> /
< GAGTGTTAAGGTGTGTTGTATGCTCGGCCTTCGTATTTCACATTTCGGACCCCA---CCGATTGAGTGTAATTAACGCAACGCGAGTGACGGGCGAAAGGTCAGCCCTTTGGA< <GCAGTTATCTATTATGTAAACTCCTAAATCTTCATAATCTGAAATGTTTGTTAAGC---TGTTGAGCATAATTTAGGAAAC <
CTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGT> \ / >ACAACTCGTATTAAATCCTTTG
( | | )
GTTAGTCGACAACGGGCAGAGTGACCACTTTTCTTTTTGGTGGGACCGCGGGTT< / \ <CCCAAACTATAAACTCCAAGTC
> CAATCAGCTGTTGCCCGTCTCACTGGTGAAAAGAAAAACCACCCTGGCGCCCAA---TACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCATTAATGCAGCTGGCACGAC> >GCTCTAATCTATTAGTTGTTAGTTGTTGATTTGCCAACTGACCAGATATTGATTGA---GGGTTTGATATTTGAGGTTCAG >
/ <ATGCGTTTGGCGGAGAGGGGCGCGCAACCGGCTAAGTAATTACGTCGACCGTGCTG-------CGAGATTAGATAATCAACAATCAACAACTAAACGGTTGACTGGTCTATAACTAACT< \
\ >CGAAAATCCTGTTTGATGGTGGTTCCGAAATCGGCAAAATCCCTTATAAATCAAAA-------GCGGTCAGTATTAACACCGCCTGCAACAGTGCCACGCTGAGAGCCAGCAGCAAATG> /
< GGGAAGTGGCGGACCGGGACTCTCTCAACGTCGTTCGCCAGGTGCGACCAAACG---GCTTTTAGGACAAACTACCACCAAGGCTTTAGCCGTTTTAGGGAATATTTAGTTTT< <CGCCAGTCATAATTGTGGCGGACGTTGTCACGGTGCGACTCTCGGTCGTCGTTTAC---TTTTTAGATTTCGTAGTGGAAC <
CCCTTCACCGCCTGGCCCTGAGAGAGTTGCAGCAAGCGGTCCACGCTGGTTTGC> \ / >AAAAATCTAAAGCATCACCTTG
( | | )
GGTAGCGGGACTATCTGCCAAAAAGCGGGAAACTGCAACCTCAGGTGCAAGAAA< / \ <AAGCGCGTAATTTCTGATTATC
> CCATCGCCCTGATAGACGGTTTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTT---AATAGTGGACTCTTGTTCCAAACTGGAACAACACTCAACCCTATCTCGGGCTATTC> >CTCACCTCTGTTTTATCTTCTGCGTATTTTTAATGGCGATGTTTTAGGGCTATCAG---TTCGCGCATTAAAGACTAATAG >
/ <TTATCACCTGAGAACAAGGTTTGACCTTGTTGTGAGTTGGGATAGAGCCCGATAAG-------GAGTGGAGACAAAATAGAAGACGCATAAAAATTACCGCTACAAAATCCCGATAGTC< \
| t0r31b_seam_temp2 t0r3t0r31t0 |
\ >ACCCGATTTAGAGCTTGACGGGGAAAGCCGGCGAACGTGGCGAGAAAGGAAGGGAA-------ACATTCTGGCCAACAGAGATAGAACCCTTCTGACCTGAAAGCGTAAGAATACGTGG> /
< GGGTGATGCACTTGGTAGTGGGTTTAGTTCAAAAAACCCCAGCTCCACGGCATT---TGGGCTAAATCTCGAACTGCCCCTTTCGGCCGCTTGCACCGCTCTTTCCTTCCCTT< <TGTAAGACCGGTTGTCTCTATCTTGGGAAGACTGGACTTTCGCATTCTTATGCACC---GTGTCTGTTATAAAAACTTACC <
> CCCACTACGTGAACCATCACCCAAATCAAGTTTTTTGGGGTCGAGGTGCCGTAA> >CACAGACAATATTTTTGAATGG >
!! !2011!Macmillan Publishers Limited. All rights reserved.!
45
DOI: 10.1038/NCHEM.1070
SS.4. "A" or|gam|

Core
Seq name Sequence
10[143]-8[144] AC1ACAACCCCACCCA1AACCCA1ACAAC111
10[173]-8[176] ACCCCCACCCC11CCACCCAC11A1AAA1CAA
10[431]-8[432] CCCAC11AACA1ACCCCAACAAACC1ACAAAA
10[463]-8[464] CCC1AACCCCACCAAACCCAA1AAACAC1CC1
11[128]-13[127] AACCA1CCCCACA111C1A1CA1CAC111CAA
11[416]-13[413] AAC1AACCCAAAA1AAACACCCA1CCCC1111
11[64]-8[80] CC11CC111CCACC1CAA111C111AA11111
11[96]-13[93] 1CA1ACCC1CCAAA1CCCCCACC1ACCC1CAA
12[143]-10[144] 1AACCCAACA1CAACCC1C1ACACCCAAACAA
12[173]-10[176] CCCAACAA1CCC1CACC11CA1CACA1C111C
12[431]-10[432] AACAACA11CCCCAC11CCCCCACCC1AA111
12[463]-10[464] C1AAAC1AA1CAACA11AC11CC1C11ACCAA
13[128]-13[127] ACACCACACAACA11A11ACACC1C1A1CA1A
13[288]-12[272] C1ACCCCA11CCAACAACCCC1A1CCAC1AC1
13[384]-13[383] 1A1CCCC1AACAA1ACA1AAC1CCA11C11AC
13[416]-13[413] ACCCAACCC11CACC1AA1CCACAC1ACCCC1
13[96]-13[93] 1CA1AACC11CACA111ACCAA1AAAACCAA1
14[143]-12[144] CACC11CA11ACCACACCACCA1AAAACCAAC
14[173]-12[176] CCCAAACAACACCC1111CCAAAAACCACC11
14[239]-12[240] 1C111ACCCCCAA1CC1CA1AAA1111CAAC1
14[271]-13[287] AAACCACAC1CAAA1CC111AAACACCCACCC
14[367]-12[368] AA1CCCAACA1A1CCC11A1ACAA1CAACAAC
14[431]-12[432] 1ACC1111AA1CCCCA1A111AACCCACAA1A
14[463]-12[464] 1CAA111A111ACCCACACCCA11CACAAAAC
14[47]-17[31] CCA1CCC11ACACC11AA11CC1CA1A1CCAA
13[128]-17[127] ACCC1CC1AACCCAACCACACCCCACA111CC
13[384]-17[383] CAC1A1AAA1A1C1AAA1CC1CA1CCAAACAC
13[416]-17[413] 1AA11CAC1AACC1CCCCC11ACCCAA1AACC
13[96]-17[93] 1ACCACCCCC1CACCA11ACACACCCAACCAC
16[143]-14[144] ACA11CAACAA1AACC1C111ACC111AA11C
16[173]-14[176] 1AAA1CCACCCCCCACC1CAAAACCACCAACC
16[239]-14[240] C1111CCCACCCAAACAA11ACCAAAA1CACC
16[333]-14[336] CCCC1CA1CAAAA11AA11ACA11AAAAC111
16[367]-14[368] CC1111ACAA11ACC111111AA1CCAAA1CC
16[431]-14[432] ACACAAA1C1AAA1CC1CCC1A111CACACAC
16[463]-14[464] ACC1ACCAACAA1CC11CAAAACAC1CAA1AC
16[47]-14[48] CC1A1111CCC1C1C1CCAAC111A11111CC
16[79]-14[80] 1C1ACC1C11CA11CCCAA11C1C1ACC111A
17[128]-19[127] CAAA1CC1AACCC1CACAAACCCC11C1A1AA
17[32]-19[31] C1AAAC1A1CACACA1C1ACAAACCAAACAAC
17[320]-19[319] CAACAAAA1CC111CAA1ACCAACAA11CCAC
17[384]-19[383] 1ACA1AAA1CACA1CAA1A1ACAC11A1CA11
17[416]-19[413] 11CC11C1AAACAAA11CCC1ACAAACCACCC
17[96]-19[93] 1ACA111AACCA1CAA1A1CA1A1CA1AA1CA
18[143]-16[144] ACA1CCCA11AAA11C1AAACC11C1ACC1AA
18[173]-16[176] 1CACCCCA11CCCA11AAA11111A1A1A111
18[333]-16[336] 1A1C111A11AAA1CC111CCCCCAACCCA11
18[367]-16[368] C11CAAACAAAAC111CAC1AACA1AACAC1A
18[431]-16[432] 1CACC11CA1CA1A11CC1CA11ACACC1AAA
18[463]-16[464] ACACCCAC1CA1CAA1A1AA1CC1CCC11ACA
18[47]-16[48] CCCCA1CC1CAACCC1AA1CC1AAACACCC1A
18[79]-16[80] 1CCCCA11CA1A1C1ACCCCCC111CAACCC1
19[128]-21[127] CCAAA1A1C1CCACCCACC111CCC1C1ACAC
19[288]-18[272] 1ACAAC1ACAA1ACA1AA1ACA11ACAACCCC
19[32]-21[31] ACAA1CCAC1CCCCCCC1C11CCCC1CCAACC
19[320]-21[319] AAC1CC1ACCACCAC1AACAAC1AACACACA1
19[384]-21[383] 11CCCCAAA1C1CC1CAC11CCCA1CCC1A11
19[416]-21[413] CAA11A1CC1CAACC1CAAA1A1CCCCC1AAA
19[96]-21[93] CAAAACCCCCCCCAAACCACCCAACCAC1CCC
20[143]-18[144] CC1CA11CCC1ACCCACC1CCAA1CC1CACCA
20[173]-18[176] C11111C11ACC1C111CC1C1C11CCCAC11
20[271]-21[287] CCCCC111ACA11AA11CCC11CCACCACCAC
20[333]-18[336] 111CACCC1C1CACC1CAAACCC1A1C1AAAA
20[367]-18[368] ACACCAAAACACAA1A11111CAAAA1CAACA
20[431]-18[432] CAACAAC1A11AAAAA1ACCCAACC1AAACCA
20[463]-18[464] 11CA11ACCA1AAAACACACC1CACCACCC1C
20[47]-18[48] 1CCCAAA111CCC1AACCCCACCC11CCCAAC
20[79]-18[80] CCACCACCCC11C1AAAACCACCCACCCCCA1
21[128]-23[127] CA1CCCCCCCC11CACCCCC1CCC1ACC1CAA
21[288]-20[272] 1AA1AAAACACA11CACCAC1CACCC1CAC1C
21[32]-23[31] CCA11AACCCCCAAAA1CCC11A1AC1C11C1
21[320]-23[319] ACAACCC11CAA1CC1C1CAAA1CAC1A1CC1
21[384]-23[383] AC1C111AACAA1A11ACCCCCACAACACCAC
21[416]-23[413] ACA1CCCCCAAAC1A1CCCCC11CCCAACCC1
21[96]-23[93] AACC11CCCCAACCCC1CCACCC1CCAAAAAC
23[128]-20[144] CCA1CACCCAAA1CAAC111111CCCCCAACA
23[160]-20[176] CC1CCCC1AAACCAC1AAA1CCCACCACCC1C
23[224]-20[240] CCAACC1CCCCACAAACCAACCCAC1CC1CCC
23[236]-23[287] CAAACCACCCCCCCC1ACCCCCC1CCCCCCC1
23[32]-20[48] 1CCAC111CCAACAACAC1CCAC1A1CC1CC1
23[320]-20[336] 1CC111CACCACCACC1A1AACC1ACC1ACA1
23[416]-20[432] ACCCCACAA1CC1CACAAC1C111CC1CAC1A
23[64]-20[80] AACC1CCAC1CCAACC1CAAACCCCC111CCC
6[143]-9[127] 111AACCCCC1CAC1CCC11CAC1CA1A1AAC
6[303]-6[272] 1CACACCACC11CACCCACC1CACACCA11CC
6[333]-9[319] CCACAACCACCACCACACCCCCCCA1CACCC1
6[399]-9[383] CC1CCC1CACACCCCCCACCC1CAACCA11AC
8[143]-6[144] CAACAC11CCAA1ACC1C1A1CAC1AA1AAC1
8[173]-6[176] 1111C1C11AC1ACCCCCACCC1CCA1CCC11
8[239]-6[240] CACCCC1CCCA1ACCAACCCCAA1A1CC1CA1
8[271]-9[287] ACAAAC1AC1AACAC1CAC111CCA11CACCC
8[333]-6[336] CCACCCCC1CACCCA111CCCAA1ACCCCCCA
8[367]-6[368] C1CACAA1CACCAC1ACCACCA11CAACCCCC
8[463]-6[464] 1A11ACCCCCC111ACCC1CACACACCCCCC1
8[79]-6[80] 1CACC11CCCCCCC1111CC1CAC1CCC1A11
9[128]-11[127] 1A1ACCCC1CACCCCAC1CACAA1A1CACAAC
9[288]-8[272] AAA11A11CCCACCCAACC1AAA11CACCAC1
9[320]-11[319] CACCCAC1AAACACAAAACCCCCA1AA1A1CA
9[96]-11[93] CCA1AAC1AACCAA11CCCAA1AAAAACACC1
23[332]-20[368] CC11ACAA1CACACCCCCACC1ACCA11CCA
23[448]-20[464] AC1CACCCCACCCAC1AAAACACA1AC11C1
23[96]-20[112] CC1C1A1CACCCCCA1CCCCCACCC1CACAC
6[111]-9[93] CCC1A1AAACAC11AA1CCCCCC1ACCACCC
6[367]-9[331] ACCC1CACACCCACCACCC1CAC1ACACCCA
10[111]-8[112] AA11C1CA1AC11CCCCCCACAACAAACCA
11[160]-13[139] C1CCC1CACCA11A1ACCAACCCACCACCC
11[448]-13[447] ACCAAACACCC1C111CCACACC1111CAA
12[111]-10[112] 1CA1CACCAACCCAAC1CACCACCC1CA1A
12[399]-10[400] 1C111A1CA11C1AACAACCCCAA11A111
13[160]-13[139] CCA1ACCCAAA1C1ACC11AA1AAAAACCA
13[236]-13[233] 11CCCC1CC11CACA1CC111AAA11CA11
13[448]-13[447] CCC11AAA11C1C1CCACACCAAACCCCAA
14[111]-12[112] 1CCAACAA1AC1AACACCAACAACAAACA1
Core (cont|nued)
Seq name Sequence
14[399]-12[400] A1A1AAC1ACCCAACCC1CAACAACCCCCC
14[79]-17[63] A11CC1CC1111CA1AACACC1CCA11CCA
13[160]-17[139] AAA1ACCCC11CAAA1A1CCCC11A1A111
13[236]-17[233] CAA1CCCCA1CACCA1AAA1CAAAAA11AA
13[332]-17[331] 11AC1A1CACAAACAACCCCAC1AACAA11
13[448]-17[447] CA1C1AA1CAAAA1CA1ACC1CAA11AA11
16[111]-14[112] 1CAAA1CC111CACCA11ACA1AACCAAAC
16[399]-14[400] C111AACC1CAA1A1A1C1CAC111CCC11
17[160]-19[139] 1CA111CCA1CCC1CAC1AA1C1AA1A111
17[332]-19[331] 1CA111CA1CCCCACAAACAA1AACC11A1
17[448]-19[447] 11CCC111A1CAAAA11A111C1CACA1CA
17[64]-19[63] 1A1AACACA1AAA11AA1CCCCCAAC1ACC
18[111]-16[112] 11C1CC1CCAAAAACACCAACACCACACAC
18[303]-16[304] ACACCCC111ACAC111ACAAAC11ACAAA
18[399]-16[400] CAA1CAA1CAAACAAACCACCAC1111CAC
19[160]-21[139] 1C11AAAACCACCACAC1A1CCC1CC1AA1
19[332]-21[331] 1AA1111CAA11CACCAACC11AACAA1AC
19[448]-21[447] 1CCCAA1CACCAAA1CAAAAA1CAACCACC
19[64]-21[63] A1C1CAA1CACCC1CCCCAAC1C1111CCC
20[111]-18[112] AC11CCAA1CCC1CCACC1CCACCCACCCC
20[303]-18[304] 1ACA11CCCCCACA11C1CCCCAA1ACA11
20[399]-18[400] 1A1CCACAA1CCCCCAAC1CA1AAAACCC1
21[160]-23[139] CA1CC1CA111CACCAC1CACACCCC1CCA
21[236]-23[233] CC1AAC1CCCAC1CCCCAAACC1ACAAACC
21[332]-23[331] C1CCCACAACCC1CA1CCAAA1CC111CC1
21[448]-23[447] ACCACAA1AA1AACA1CAC11C11A1AA1C
21[64]-23[63] AC1CACCACCAAAA1CC1C111CA11AAAC
23[288]-20[304] 1AA1CCCCCCC1ACACCCCCCC1CA11A11
23[384]-20[400] CCCCA11AAACCCA1111ACACAC1CC1AA
6[173]-9[139] 11CA1CA1ACACCAC1C1AC1CCCC1AC1C
6[271]-9[233] CC11CA1A11CACAAACAAA1AAACCAACC
6[79]-9[63] 1CCCAACC1A11A11C1CAAACACAACCA1
8[111]-6[112] ACAAC1ACCCC1CCACACCC11AACAC1CC
8[303]-6[304] CCCA11CACA11AAACC1CAA11CCACCA1
9[160]-11[139] ACCACC11A1CCCA1111CC1AAA1A11CC
9[236]-11[233] CA1C1ACCCAACCCC1C1ACCA11ACACAC
9[332]-11[331] CCAAAA1CAA1ACAAAA11CA111AACCCC
9[448]-11[447] CAAC111AC1A1C11ACCAAAC11ACCACA
9[64]-11[63] 1ACCA11AAAAA1C1CCAAAAAA111A1CA
22[279]-23[267] CCCAAC1C1ACCCC1CACCC
23[268]-22[280] 1CCCCC1AACCACCACACCC

Left edge
9[40]-6[40] C1CACAC1CC1CAACA1CAAAC1A11AACACC
11[40]-8[40] CC111AA11C1A1CCCAACCC1CCAAAACCAC
13[72]-10[72] CCCCAACCACCCCCACCC1CCA1C11AC11AC
13[72]-12[72] CACA1ACA1AACCCCACCACA11CAAC1AA1C
17[8]-14[8] C1CAACA1C1111AAAA1A1AA1CC1C1AC
19[8]-16[8] CC1CACAC1C1CCACCC1A1CACC1CA11C
21[8]-18[8] CCAAACCCCCA1C1C1A11ACCCCACC1CC
23[8]-20[8] CCCCACA1ACCC11CAAA1CAAAACAA1AC

10[239]-8[240] CAC1ACCACCACCC1ALccLcLLLLgaggaacaagLLLLcLLgLCCAACCCC1CCACACA
10[271]-11[287] C111CCA1CAC1AAACLccLcLLLLgaggaacaagLLLLcLLgLAC11111CCCC1CAAC
10[333]-8[336] ACACACAAACCCACAALccLcLLLLgaggaacaagLLLLcLLgLCAA11CACA1CC111A
10[367]-8[368] 1AACC1CAACACCAACLccLcLLLLgaggaacaagLLLLcLLgLAAACAA1C111A1111
11[192]-13[191] 1111CCCCAA1ACAC1LccLcLLLLgaggaacaagLLLLcLLgLAAAACAC1ACAC1AA1
11[224]-13[223] CA1CCCAAACCCACCALccLcLLLLgaggaacaagLLLLcLLgLACC1AAAA1ACCCAAA
11[288]-10[272] AAAC1CACCACAA11ALccLcLLLLgaggaacaagLLLLcLLgLAC1CAACAA1CACCAA
11[320]-13[319] CACACA1A1AACA1AALccLcLLLLgaggaacaagLLLLcLLgLAAACACCCCAACCCC1
11[384]-13[383] A1ACC1A1CCAAA1AALccLcLLLLgaggaacaagLLLLcLLgLCAAACCA1ACAACCC1
12[239]-10[240] 11AA1CA1CC1CC1CALccLcLLLLgaggaacaagLLLLcLLgL11CAC1CACC1AA1CC
12[271]-13[287] AAA11CCCACCACAAALccLcLLLLgaggaacaagLLLLcLLgLCACCACAA1AAACCAA
12[333]-10[336] 1C1ACAAA1CA1CC1ALccLcLLLLgaggaacaagLLLLcLLgLCCAA1CA1CCC111AC
12[367]-10[368] AAAAA1AACAACCAAALccLcLLLLgaggaacaagLLLLcLLgL1CACA1A111111C11
13[192]-13[191] C11CACAACC1CA11ALccLcLLLLgaggaacaagLLLLcLLgL1ACCAC1CCAAC1111
13[224]-13[223] C1AACAAA1C1CAA11LccLcLLLLgaggaacaagLLLLcLLgLACC11A1CC111ACAC
13[320]-13[319] 1111A111CCAA1CAALccLcLLLLgaggaacaagLLLLcLLgL1AA1CCCCACAA1AAA
14[333]-12[336] 11CAAA1A1CA1AA11LccLcLLLLgaggaacaagLLLLcLLgLAC1ACAAA1ACCACCA
13[192]-17[191] CCCACACCCCA1CAAALccLcLLLLgaggaacaagLLLLcLLgLAACA11AAC1CCCA1C
13[224]-17[223] CAA1AC1CC1CAC1A1LccLcLLLLgaggaacaagLLLLcLLgL1A1AC1CA1AACA1CC
13[288]-14[272] 1C1CA1AA111AA1CCLccLcLLLLgaggaacaagLLLLcLLgL111CAAA1AC11CACA
13[320]-17[319] CACCCCAA1A1111ACLccLcLLLLgaggaacaagLLLLcLLgL11AA111CACAAACA1
16[271]-17[287] C11C1ACCCCC1CACALccLcLLLLgaggaacaagLLLLcLLgLCCA1AAAC11CAA11A
17[192]-19[191] AA11C1ACAA11111ALccLcLLLLgaggaacaagLLLLcLLgLCAACCC1CC11AAA1C
17[224]-19[223] 1ACACCCACCACAACCLccLcLLLLgaggaacaagLLLLcLLgLC111A111ACCCCA1C
17[288]-16[272] CC1CACCACACCCCAALccLcLLLLgaggaacaagLLLLcLLgL11A11CA1C1AAA1CC
18[239]-16[240] CACCC1AA1CCCC11CLccLcLLLLgaggaacaagLLLLcLLgLC1C1ACCCC1C1AA1A
18[271]-19[287] 1CCCA11C1AAA1C1CLccLcLLLLgaggaacaagLLLLcLLgLACCCAC1A1CACCA11
19[192]-21[191] ACC1CA11A1CC1AACLccLcLLLLgaggaacaagLLLLcLLgLCC1CCA1CCAAA11C1
19[224]-21[223] 11CCCC1C1CCCA1ACLccLcLLLLgaggaacaagLLLLcLLgLC1CACC11CA1ACCAC
20[239]-18[240] ACC1CCA1ACCC1CCCLccLcLLLLgaggaacaagLLLLcLLgLC1CCC1AACCCCCA11
21[192]-23[191] 1A1CCCC1C111CCC1LccLcLLLLgaggaacaagLLLLcLLgLA11CCCCCACCC1AAA
21[224]-23[223] AAC1C1AA1AA1CAA1LccLcLLLLgaggaacaagLLLLcLLgLCCCCCAACACCCCCAA
6[239]-9[223] 1AAACCCACAA1CCAALccLcLLLLgaggaacaagLLLLcLLgLACCCCAC1CACCCACC
6[431]-9[413] A1CACCCCAACCACACLccLcLLLLgaggaacaagLLLLcLLgLCCACCACCAAACCA1C
8[431]-6[432] 1ACA1ACACACCC1AALccLcLLLLgaggaacaagLLLLcLLgL1CAC1ACC1AA1CAAA
9[192]-11[191] CACCC1CA1C111CCALccLcLLLLgaggaacaagLLLLcLLgLCACC11ACAACCCCCC
9[224]-11[223] A1111CACA1AC11ACLccLcLLLLgaggaacaagLLLLcLLgLCC1AACCACACCCAAA
9[384]-11[383] CAACCCCCCACACCACLccLcLLLLgaggaacaagLLLLcLLgLCCAA1AACAAA1ACCA
9[416]-11[413] CA1ACCAC1AAACC1CLccLcLLLLgaggaacaagLLLLcLLgLCCAACA1A111AACAA
23[192]-20[208] CCCACCCCCCCA111LccLcLLLLgaggaacaagLLLLcLLgLACACC11CCCCCCCCC
6[207]-9[191] 11ACCC11CCAC1AALccLcLLLLgaggaacaagLLLLcLLgLCCC1CA1AACAACCCC
6[463]-9[447] 1A11ACCC111CCCALccLcLLLLgaggaacaagLLLLcLLgL1C1111CACACACAA1
10[207]-8[208] CCAAAACCA1CC1CALccLcLLLLgaggaacaagLLLLcLLgLCCC1CAC1C1AAAC1
10[303]-8[304] 11ACACCCACCC1AALccLcLLLLgaggaacaagLLLLcLLgL11CACCCCCA11CAA
10[399]-8[400] A1CCCAA1C11ACCCLccLcLLLLgaggaacaagLLLLcLLgLAACCCC111AAAACA
11[236]-13[233] CC111CAC1AAACCCLccLcLLLLgaggaacaagLLLLcLLgLC1AAAA1AA1AACCC
11[332]-13[331] AA1AA1AAAAA1CAALccLcLLLLgaggaacaagLLLLcLLgLAA1ACCA1ACCCCCC
12[207]-10[208] ACAAC1CCAACCCCALccLcLLLLgaggaacaagLLLLcLLgL1A11CA1CCAAACAC
12[303]-10[304] CC11A1CAC1CA1CCLccLcLLLLgaggaacaagLLLLcLLgLACAACAACAACCCCA
13[332]-13[331] CCAA1AC1A1CCCA1LccLcLLLLgaggaacaagLLLLcLLgLCC1AA11AACCC1C1
14[207]-12[208] CCCCA11CCC1AA1ALccLcLLLLgaggaacaagLLLLcLLgLC1AAAA1CCA1111A
14[303]-12[304] CACC1AAAA1AACCCLccLcLLLLgaggaacaagLLLLcLLgLC11AAA1A1C1C111
16[207]-14[208] CCA1AAA1AA1AC1ALccLcLLLLgaggaacaagLLLLcLLgLC1ACCA1CAACCAAA
16[303]-14[304] A1CCCCCAAAACAACLccLcLLLLgaggaacaagLLLLcLLgLA1CA1CAAA1C11C1
17[236]-19[233] CCAA1AAAAAAAACALccLcLLLLgaggaacaagLLLLcLLgL11A1CACCACC111C
18[207]-16[208] 1CCCCCC1111AACCLccLcLLLLgaggaacaagLLLLcLLgLAA1ACCACAACCCAA
19[236]-21[233] A1CAACA11CCC1CCLccLcLLLLgaggaacaagLLLLcLLgLCAACAAAC1CAC1CA
20[207]-18[208] ACACCCCCACAA11CLccLcLLLLgaggaacaagLLLLcLLgLCACACAACC1C1ACA
8[207]-6[208] 111C1CCCAACCCCCLccLcLLLLgaggaacaagLLLLcLLgLACCC1CAC1C1CAA1
8[399]-6[400] AACCCAAACAAACC1LccLcLLLLgaggaacaagLLLLcLLgLCACCAA1CCCAACCC
!" !2011!Macmillan Publishers Limited. All rights reserved.!
DOI: 10.1038/NCHEM.1070
oslLlons of dumbbells are lndlcaLed by Lhe red-colored
sLaple sLrands (28-nL dumbbell halrpln sequences are
lnserLed ln Lhe mlddle of each sLaple sLrand. See sequence llsL.)

7 6 9 8
1
1
1
0
1
3
1
2
1
5
1
4
1
7
1
6
1
9
1
8
2
1
2
0
2
3
2
2
2
5
6 9 8
1
1
1
0
1
3
1
2
1
5
1
4
1
7
1
6
1
9
1
8
2
1
2
0
2
3
2
2
2
5
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
3
8
4
3
9
2
4
0
0
4
0
8
4
1
6
4
2
4
4
3
2
4
4
0
4
4
8
4
5
6
4
6
4
4
7
2
4
8
0
4
8
8
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
3
8
4
3
9
2
4
0
0
4
0
8
4
1
6
4
2
4
4
3
2
4
4
0
4
4
8
4
5
6
4
6
4
4
7
2
4
8
0
4
8
8
6 5 5 11 9 8 11 6
C
C
T
C
T
T
A
A
T
A
C
T
T
T
C
A
T
G
T
T

T
C
A
G
A
A
T
A
A
T
A
G
G
T
T
C
C
G
A
A
A
T
A
G
G
C
A
G
G
G
G
G
C
A
T
T
A
A
C
T
G
T
T
T
A
T

A
C
G
G
G
C
A
C
T
G
T
T
A
C
T
C
A
A
G
G
C
A
C
T
G
A
C
C
C
C
G
T
T
A
A
A
A
C
T
T
A
T
T
A
C
C
A

G
T
A
C
A
C
T
C
C
T
G
T
A
T
C
A
T
C
A
A
A
A
G
C
C
A
T
G
T
A
T
G
A
C
G
C
T
T
A
C
T
G
G
A
A
C
G

G
T
A
A
A
T
T
C
A
G
A
G
A
C
T
G
C
G
C
T
T
T
C
C
A
T
T
C
T
G
G
C
T
T
T
A
A
T
G
A
G
G
A
T
T
T
A

T
T
T
G
T
T
T
G
T
G
A
A
T
A
T
C
A
A
G
G
C
C
A
A
T
C
G
T
C
T
G
A
C
C
T
G
C
C
T
C
A
A
C
C
T
C
C
T
G
T
C
A
A
T
G
C

T
G
G
C
G
G
C
G
G
C
T
C
T
G
G
T
G
G
T
G
G
T
T
C
T
G
G
T
G
G
C
G
G
C
T
C
T
G
A
G
G
G
T
G
G
T

G
G
C
T
C
T
G
A
G
G
G
T
G
G
C
G
G
T
T
C
T
G
A
G
G
G
T
G
G
C
G
G
C
T
C
T
G
A
G
G
G
A
G
G
C
G
G

T
T
C
C
G
G
T
G
G
T
G
G
C
T
C
T
G
G
T
T
C
C
G
G
T
G
A
T
T
T
T
G
A
T
T
A
T
G
A
A
A
A
G
A
T
G
G

C
A
A
A
C
G
C
T
A
A
T
A
A
G
G
G
G
G
C
T
A
T
G
A
C
C
G
A
A
A
A
T
G
C
C
G
C
G
A
A
A
C
T
C
A
G
T
G
T
T
A
C
G
G
T
A
C
A
T
G
G
G
T
T

C
C
T
A
T
T
G
G
G
C
T
T
G
C
T
A
T
C
C
C
T
G
A
A
A
A
T
G
G
T
G
G
C
T
C
T
G
A
G
G
G
T
G
G
C
G
G

T
T
C
T
G
A
G
G
G
T
G
G
C
G
G
T
T
C
T
G
A
G
G
G
T
G
G
C
G
G
T
A
C
T
A
A
A
C
C
T
C
C
T
G
A
G
T

A
C
G
G
T
G
A
T
A
C
A
C
C
T
A
T
T
C
C
G
G
G
C
T
A
T
A
C
T
T
A
T
A
T
C
A
A
C
C
C
T
C
T
C
G
A
C

G
G
C
A
C
T
T
A
T
C
C
G
C
C
T
G
G
T
A
C
T
G
A
G
C
A
A
A
A
C
C
C
C
G
C
T
A
A
T
C
C
T
A
A
T
C

C
T
T
C
T
C
T
T
G
A
G
G
A
G
T
C
T
C
A
G
A
T
G
A
A
A
A
C
G
C
G
C
T
A
C
A
G
T
C
T
G
A
C
G
C
T
A
A
A
G
G
C
A
A
A
C

T
T
G
A
T
T
C
T
G
T
C
G
C
T
A
C
T
G
A
T
T
A
C
G
G
T
G
C
T
G
C
T
A
T
C
G
A
T
G
G
T
T
T
C
A
T
T

G
G
T
G
A
C
G
T
T
T
C
C
G
G
C
C
T
T
G
C
T
A
A
T
G
G
T
A
A
T
G
G
T
G
C
T
A
C
T
G
G
T
G
A
T
T
T

T
G
C
T
G
G
C
T
C
T
A
A
T
T
C
C
C
A
A
A
T
G
G
C
T
C
A
A
G
T
C
G
G
T
G
A
C
G
G
T
G
A
T
A
A
T

T
C
A
C
C
T
T
T
A
A
T
G
A
A
T
A
A
T
T
T
C
C
G
T
C
A
A
T
C
T
C
C
T
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!"
47
DOI: 10.1038/NCHEM.1070
SS.S. "8" or|gam|

Core
Seq name Sequence
10[143]-8[144] 111C1A1C1CCCCCACCCA1AACCA1AA1AA1
10[173]-8[176] A1ACCAAC1CACCC11CCACCCACCAA1ACAA
10[271]-11[287] CCC1AAAA11CA1CACCAAC111CAAACAAC1
10[333]-8[336] CCCAACAAACC1ACAAAA1ACA1AAA1CACCA
10[367]-8[368] 1CAAA1ACA1A1AAAACAAACCCAAC11CACC
10[431]-8[432] CC1AA1A1A1A1CC111ACCACCC1CACCCAC
11[128]-13[127] AACAACCAA1CCCC1CA1AAA11CACACA1CA
11[192]-13[191] CCC1111CAC1CA1C111CACCCCCAACAACC
11[288]-10[272] CCCA1CA1AA1AACCCAA1ACCCACA11AAAC
11[384]-13[383] ACCCAA1ACCCAA1AA1AACACCA1AAACACC
11[416]-13[413] CAAAA11CCACACACA1AACCCAC1AACAAAC
11[96]-13[93] CC11CA1ACC1CC1CCA1C11AC1ACCCAACC
12[143]-10[144] 11CA1CACCACACCACCCCCA1ACAACCCACA
12[173]-10[176] 1AACCCAA1CAACAC1AA1C11CACACCCA11
12[271]-13[287] 11AA1CA1CC11CACA1CC111AAA11AC11C
12[333]-10[336] CACCCC11CAACCC1AACCACCC1CCAACCCC
12[367]-10[368] A11ACCCC111CCCAC11ACAAAAACAAACAA
12[431]-10[432] A11AAACCC111AACC1CAAAAA1AA11CACC
12[463]-10[464] CC1C1C111ACACACACAA1AACA1AAC1CAA
13[128]-13[127] ACCC1C1A11CACA111ACCAA1AAAAAACCA
13[192]-13[191] CCA1A11CAAAA1C1ACC11AA1AC111ACAC
13[384]-13[383] CA1A11A1C11111A1111CA1CCC1CCACAC
13[416]-13[413] CA111111AAC1ACCCCAC1CA1CCC1AA1CC
13[96]-13[93] CAAC1CACCCACA1ACA1AACCCCC1A1CA1A
14[143]-12[144] CCCCAACCACACCC1111CCAAAA1ACAAACA
14[173]-12[176] CC1111AACCCC1AA1AC1AAAA1AAACCAAC
14[367]-12[368] AA11AC1AAACC1AAAC1AA11C11ACCAA1C
14[431]-12[432] A1CC111CCC1C111A1CAACAA1CAACCCC1
14[463]-12[464] 11AC11AAAACAAAAA1AA1A1CCAA1AA1CC
14[47]-17[31] CC1CAA1A1AA1CC1C1ACC1CAAC1C1CCAA
13[128]-17[127] AAA1ACCCAAAC1CCAACACC1CAAACC1C11
13[192]-17[191] 1CCA1ACCAACCCCCAAACAC11CAC1AC1AC
13[384]-17[383] CACCACAAAA1AACAA1AAACACCA111A1CA
13[416]-17[413] ACAACCCCAAA1ACCCACCC1C1CC11111AA
13[96]-17[93] ACCC1CC1111AA11CC1CC1111CACCA11A
16[143]-14[144] ACAAACCC1111CA111CCCCCCCCAACCACA
16[173]-14[176] AC1AA1C1CA1CAA11C1AC1AA1AAA1A1CC
16[271]-17[287] 11A1CACCCC1AAA1CCC11C1AC11C1C1AA
16[431]-14[432] CCCCACAA11ACC11CCC11A1A11AAA111A
16[463]-14[464] CA1CAA1AC1CA1CCAAA1CCAA1AA1A1A11
16[47]-14[48] 1C1ACAAACCA1A1AACAC11CA1CC11AA11
16[79]-14[80] AA1CCCCCCCAC1ACA111AC111CA1AACAC
17[128]-19[127] 1ACC1A1ACCCACACAC1CAAA1C111AAA11
17[192]-19[191] CA11AACACA1A1A1111AAA1CC11111AAC
17[288]-16[272] A1CC1CCCCAC1CAA1AACC11CCCAAAAACA
17[32]-19[31] C111CA11CCC1A1CACC1CA11CA1CAACCC
17[320]-19[319] 1CC11CAA1AA1CCAAACAC1ACACCCCAACA
17[384]-19[383] AAA1CA1AACCAAC11ACAAAA1CCCAA11CA
17[416]-19[413] CC1CCCCCACAA1AACCCA11CCCA11A1AC1
17[96]-19[93] CA1ACA1111CAACCC11C1ACC1CCCAAAAA
18[143]-16[144] C11C1CC11AA1A1111C11AAAAAAACCC1C
18[173]-16[176] ACA1CCCA1C11AAA1CACC1CA1AA1CCC1C
18[271]-19[287] CACCC1AAC1CCC1CCCAACAAACA1111AAA
18[431]-16[432] CAA1CAA1A1CCAACCC11ACAAC1111ACA1
18[79]-16[80] CCCCA1CC1CA1AA1CACAAAACCCA1AAA11
19[128]-21[127] C1AAACC1CCCCCAAACCACCCAACCAC1CCC
19[192]-21[191] CAA1ACCAACCACCACAC1A1CCC1CC1AA1C
19[288]-18[272] AC111CAC1CCCCCAACC11A11ACCCCCA11
19[32]-16[48] 1AA1CC1AAAAC1ACCA1C1CAA111CACACA
19[320]-21[319] AACAAACCCAAACAA11CCACAACCCC1AAAA
19[384]-21[383] 1CAA1A1ACCAA11CACCAACC11CCCC1CAC
19[416]-21[413] 1C1CAA1AA1C1CC1CAC11CCCACCACCC1C
19[96]-21[93] CACCAACA1CACCC1CCCCAAC1C1111CCCA
20[143]-18[144] C11111C1A1CCC1CCACC1CCACCCCCACCC
20[173]-18[176] ACACCCCCCC1ACCCACC1CCAA1CC1CACCA
20[431]-18[432] A1ACC1ACCACCAAA1CAAAAA1CCAAACCC1
20[79]-18[80] AC11CCAC11CCC1AACCCCACCC11CCCAAC
21[128]-23[127] AACC11CC111CACCAC1CACACCC1C11C11
21[192]-23[191] A1CC1CA11AA1CAA1CCCCCAACCAAAAACC
21[384]-23[383] 1A11AACA111ACA11CCCACA11CA1CAC11
21[416]-23[413] ACACCCACA1111CACCC1CAA1CA1CCCCC1
21[96]-23[93] C1CACCACCCC11CACCCCC1CCCAAA1CAAA
23[128]-20[144] CCAC111CCAACAACAC1CCAC1ACCACCC1C
23[160]-20[176] ACC1CCAC1CCAACC1CAAACCCCCCCCCCCC
23[416]-20[432] 1CC1CC1AA1A1CCACAACAA1A11CA1CCAA
23[64]-20[80] 1CCCAAA1CCCCAAAA1CCC11A1CC1CACAC
6[143]-9[127] CA11ACCA11ACCCCCC1111CC1C1CACAAC
6[333]-9[319] CAA111ACCC11CCAC1AACCC1C1111CCC1
6[399]-9[383] 1CACACCA11CCCC11CA1A11CACACCCACC
6[431]-9[413] CCCCCCACCA11CACACCACC11CCCCCACCC
8[143]-6[144] 11111CAC1CACAACCCCCACCC1AACACAAC
8[173]-6[176] ACCAACAACA1111CACCCA1ACCACA1CAAA
8[333]-6[336] 1CAAACCACC11A11ACCC111CCCCAAACCC
8[367]-6[368] CA111CCCAAAA1CACCCCAACCACAAACAAA
8[431]-6[432] CCAACC1ACCCACCC1CACACCCACCACACCC
9[128]-11[127] CCCCACCCC11CAAAA1C1CCAAAACAA1CAC
9[192]-11[191] 1ACCAACCAC111CACCCCAC1CA11AAACCC
9[384]-11[383] ACCCCAACA11A1CACCC1CACCCAACACACC
9[416]-11[413] 1CACAACCAA1A11CACCCAAA11AA1CAA1A
9[96]-11[93] 1CACCACCCCACCC111AA11C1AC11AAACA
10[463]-13[447] CACCC1CAACAAAC1CACACCC1CAAAA1AC
19[448]-16[464] 1CAAAA11A111CCACC1AAAAC1AACC1CA
23[332]-20[368] AA1AC11C111CA11AC1AA1AACACCAC1C
23[96]-20[112] ACAA1ACCCCCACA1ACCC11CACCCAACAC
6[111]-9[93] CCCCCA1AAC1CCCC1CCACACCCACCC1AC
6[207]-9[191] A111CCCAACC1A11A11C1CAAAACCCCAA
6[367]-9[331] 1AAA1CC1CA11AAACCCACAA1CA1C1111
10[111]-8[112] 1CCCCCACCCA1AC11CCCCCCAAAAACCC
10[399]-8[400] CAC11AACAC111A1111C1CACA11CA11
11[160]-13[139] 1CCC1CCCCCCCAAACAAAC1ACCC1CCC1
11[236]-13[233] AACAC1111ACC1AA1CCCAC1ACCAC1AC
11[332]-13[331] 1CCCAACCAA1ACC1A1C11ACC111CCAC
12[111]-10[112] AAC1AA1CAAC111CAAACACC1C1CCAAA
12[399]-10[400] ACCAACCC11A1CCCAA1CCAAAAACAA11
13[160]-13[139] CACC11CACAACA11A11ACACCCAAC111
13[332]-13[331] ACCC1AACCCCAA1ACCAACCAA1AAAC1A
13[448]-13[447] CACCC111CC11A1CA11CCAAACA1AAC1
14[111]-12[112] CAC1ACC11ACCACACCACCA1CCACA11C
14[399]-12[400] ACCCC11A1AAACAACA1C11CACACAACA
14[79]-17[63] C1CA11111CCCCA1CCC11ACA1CCCAA1
13[160]-17[139] 1CCCACAC11CCACC11CAAACCCACC1CA
13[448]-17[447] CC1CAAC111CA1C11C1CACCAAC1A1A1
16[111]-14[112] 1A1CA1A1CCCAAA1CC1CAA1CCA11ACA
16[303]-14[304] A1A1A1C11A11AA11AA1111CCCC1CAA
16[399]-14[400] C111CAA1CC1C1CACACAC1ACA1AAA1A
17[160]-19[139] AAACC1CCC1ACC1AAACA11CA11CCCA1
17[236]-19[233] ACCA1AAAC1C1AA1AC1111CCACAACCC
17[448]-19[447] C1AAA1C1ACAC1AACAC1ACCC1ACCA1A
17[64]-19[63] 1C1CCCAAACACCC1ACC1A111CA1A1C1
18[111]-16[112] 1CCCCA111C1A1AACCAAA1AACCA1CAA
18[303]-16[304] AAA1CC111AACA11A1CA11111AAA1CA
18[399]-16[400] AC11CAAAA1CC1CA11C111CCC1CA11C
19[160]-21[139] 1AAA1111C1CCACCCACC111C1C1ACAC
19[236]-21[233] C1CCCA111CCCA1ACC1CACC1AACCA1A
19[64]-21[63] ACCCCCC1C1CCCCCCC1C11CC1CCAACC
20[111]-18[112] C1CA11CC11C1AAAACCACCCACCCCCA1
20[399]-18[400] A1CCA11ACCCCC1CCAACAC1CAA1CAAC
21[160]-23[139] CA1CCCCC111CCC1A11CCCCC11AAACA
21[64]-23[63] CCA11AACCAACCCC1CCACCC11CC1CC1
23[384]-20[400] CCC1CAC1ACAACAAC1CAAAC1C1C1CAA
6[173]-9[139] C1A11AACACCC1CACAC1CC1CCACACCC
8[111]-6[112] 1CCAAAA111AC1ACCCCCACCCAC1ACCA
8[399]-6[400] AAACC1CACCCC1CCC1CACACCACCCACC
9[160]-11[139] ACCACCC1C1AAACCAA11CCCACA1A1A1
9[332]-11[331] CA1AA1CAA11ACACCCACCAACA1AAACC
22[239]-23[233] AACCCAAACCACCCCCCCC1ACCCCCC1
22[307]-22[280] ACACACCAACCC1ACCCCACAA1CC1CA
22[333]-22[308] 1AAACACCACCCCCA11AAACCCA1111
23[284]-23[311] 1AA1CCCCCCC1ACACCCCCCC1AC1A1
23[312]-23[339] CC11CC111CACCACCACC1A1AACC1C
23[340]-22[336] C111CC1CC11ACAA1CACACCCCCACC
23[236]-23[239] CCCAAC1C1ACCCC1CACCC1CCC
23[260]-23[283] CC1AACCACCACACCCCCCCCCC1
22[239]-22[240] CCCCACAAACCAACCCAACA
22[279]-22[260] CCCCCAAACCCCCCCAACC1

k|ght Ldge
6[433]-9[433] CCACCACAACCACCACCACCC1CACACCCC
8[433]-11[433] CCACA11CAACCCA1CCAAACACAAAACCC
10[487]-13[487] CA11ACACCCCACAA11AAAAACACCCAACCC
12[487]-13[487] CA1C1ACAAACCAA1CCA1CC1AA111ACCAC
14[487]-17[487] CCACAAAAC11111CACCCAACACAAACAACC
16[487]-19[487] CC1ACA1111CACC11ACAAA1AAACAAA11C
18[433]-21[433] C1CAACC1CAAA1A11AAACCA1CACC11C
20[433]-23[433] CAACACCAAAAACCC1ACCCCCACCCA11C

Left Ldge
9[72]-6[72] CCCCCAA1ACC1C1A1C11CA1A1AAC1A1AC
11[72]-8[72] C111CCACC1CAA1111CCC111A1CACC11C
13[72]-10[72] CACACCC1CAA1CA1A1ACCCCCAACCACCCC
13[72]-12[72] CA1AC1AACACCAACAAAAACCAA11ACCACC
17[8]-14[8] CAAC1AAAC1ACCC1CA1C1111AAA1A1C
19[8]-16[8] CAAACAACACAA1CCCC1CACAC1C1CCAC
21[40]-18[40] CCAAACCCCCA1C1CCC1A11ACCCCACC1CC
23[40]-20[40] CCAAAA1CC1C111CACC111CCCCCACCACC

10[239]-8[240] CCAACC1ACCC1ACACLccLcLLLLgaggaacaagLLLLcLLgLACCC111C11AC1AAA
11[224]-13[223] C1ACCAACAAACCAAALccLcLLLLgaggaacaagLLLLcLLgLCACCCAAAC1AACAAA
11[320]-13[319] C11ACCAAAC11ACCALccLcLLLLgaggaacaagLLLLcLLgLCAACCAAA11A1CC1C
12[239]-10[240] AACAAC1CACCACAAALccLcLLLLgaggaacaagLLLLcLLgLCACCACAACCAACCCA
13[224]-13[223] 11CCCC1CCC1CA11ALccLcLLLLgaggaacaagLLLLcLLgL1ACCAC1CA1CC1CA1
13[288]-12[272] C1A1111CCAACCC11LccLcLLLLgaggaacaagLLLLcLLgLAAA1CAAC111CAAC1
13[320]-13[319] AA1C11AC11ACCCAALccLcLLLLgaggaacaagLLLLcLLgLCC1CCCCACACACCCA
14[239]-12[240] C1CACAACA11CAA1CLccLcLLLLgaggaacaagLLLLcLLgLCCCC1CAACCCA1111
14[271]-13[287] CAAAAA1CCACAAAACLccLcLLLLgaggaacaagLLLLcLLgLCACAA1CACA1A111A
14[333]-12[336] AAA11C11CCAC1AA1LccLcLLLLgaggaacaagLLLLcLLgLAACACAA1AA1CACA1
13[224]-17[223] AAA1A11CCAAACCCCLccLcLLLLgaggaacaagLLLLcLLgLA11CCA1CACCCAACC
13[288]-14[272] ACAACCCCC11AA11CLccLcLLLLgaggaacaagLLLLcLLgLACAA1CCCCCA1AAA1
13[320]-17[319] 1111CCACACCAC1A1LccLcLLLLgaggaacaagLLLLcLLgLAAACCCAACC11ACAA
16[239]-14[240] CC111A11AAAA11AALccLcLLLLgaggaacaagLLLLcLLgLCCAA1AAAC1A11A1A
16[333]-14[336] ACC11111AACA1ACCLccLcLLLLgaggaacaagLLLLcLLgLCA1ACC11C1A1CA1A
16[367]-14[368] CCCAA11ACAACAC1CLccLcLLLLgaggaacaagLLLLcLLgLAA1AC1CACCAA1CA1
17[224]-19[223] CAA11ACC1CAACCCALccLcLLLLgaggaacaagLLLLcLLgLACCA1AAAA11CCCC1
18[239]-16[240] A1CCCCCC1AAA1C1CLccLcLLLLgaggaacaagLLLLcLLgLACCCAC1ACCCACAAC
18[333]-16[336] ACAC111AACCACAACLccLcLLLLgaggaacaagLLLLcLLgLCACCCCAA1CACCAAA
18[367]-16[368] 1A1C111A1CA11A1CLccLcLLLLgaggaacaagLLLLcLLgLACA1CA1CCCCCACAC
19[224]-21[223] A1CAACA1A1CC1AACLccLcLLLLgaggaacaagLLLLcLLgLCC1CCA1CCAAA11C1
20[239]-18[240] CCCCC111ACAACA1ALccLcLLLLgaggaacaagLLLLcLLgLCCACCCCC1CC1C1AC
20[271]-21[287] C1AAC1CAACCC1CCCLccLcLLLLgaggaacaagLLLLcLLgLC1CCC1AACCC1A11A
20[333]-18[336] CAACCC1111AAAAA1LccLcLLLLgaggaacaagLLLLcLLgLACCCAACCAA1ACA11
20[367]-18[368] ACACCACCA1AAAACALccLcLLLLgaggaacaagLLLLcLLgLCACC1CACA1C1AAAA
21[224]-23[223] AA11CCACCCAC1CCCLccLcLLLLgaggaacaagLLLLcLLgLCAAACC1CACC1CAAC
21[288]-20[272] C1C111AACACAA1A1LccLcLLLLgaggaacaagLLLLcLLgL1111CAA11CAC1CAC
21[320]-23[319] CA1CCCCAC1CACC1CLccLcLLLLgaggaacaagLLLLcLLgLAAACCC1AC1AAAACA
23[224]-20[240] C1CCCC1AAACCAC1ALccLcLLLLgaggaacaagLLLLcLLgLAA1CCCAACC1CAC1C
23[236]-23[287] CCCACCCCCCCA111ALccLcLLLLgaggaacaagLLLLcLLgLCACC11CACAAC1C11
23[320]-20[336] C1C1C1CCA1CACCCALccLcLLLLgaggaacaagLLLLcLLgLAA11AACCA11C1CCC
6[239]-9[223] C1CCCCC1A1AAACACLccLcLLLLgaggaacaagLLLLcLLgL11AA1CCC1CAC111C
6[303]-6[272] CC1111CA1CA1ACACLccLcLLLLgaggaacaagLLLLcLLgLCAC1C1AC1CC1AA1A
8[239]-6[240] 1CAA1111AC1ACAACLccLcLLLLgaggaacaagLLLLcLLgLCCC1C1ACCAC1AACA
8[271]-9[287] AAC1111CCC1CA1ACLccLcLLLLgaggaacaagLLLLcLLgL11ACCC1AACCC1CAC
9[224]-11[223] CAC1ACAAC1C1A1CCLccLcLLLLgaggaacaagLLLLcLLgLCA1111CCCACCACCC
9[288]-8[272] AC1C1ACCAA1CAAC1LccLcLLLLgaggaacaagLLLLcLLgL11CCC111ACCA1C1A
9[320]-11[319] CA1ACCCC1CCA1ACCLccLcLLLLgaggaacaagLLLLcLLgLACCACCC1CCCAC1A1
23[192]-20[208] C1C1A1CACCCCCA1LccLcLLLLgaggaacaagLLLLcLLgLCCCCCAC11CC1CCCA
10[207]-8[208] C1AAAACCCCCA1CCLccLcLLLLgaggaacaagLLLLcLLgL1CACCC11AAACAAC
10[303]-8[304] AACCCAA11AACAC1LccLcLLLLgaggaacaagLLLLcLLgLCC11A11AAA1CAC1
12[207]-10[208] CCCAACAA11ACCCALccLcLLLLgaggaacaagLLLLcLLgLAA1CAACACAA1ACA
12[303]-10[304] CACC1111CACCCACLccLcLLLLgaggaacaagLLLLcLLgLC1ACAA11CCCACCA
13[236]-13[233] 1AAA11CC1C1CAA1LccLcLLLLgaggaacaagLLLLcLLgL1ACC11A1A1CC111
14[207]-12[208] 1AACACCC1CCAA1ALccLcLLLLgaggaacaagLLLLcLLgLC1CCCCAACCACC11
14[303]-12[304] CAC1ACCCAACA1C1LccLcLLLLgaggaacaagLLLLcLLgLAA111ACCC11CCCC
13[236]-17[233] AAACAC11ACC1C11LccLcLLLLgaggaacaagLLLLcLLgL1ACCC1CACCC1CAC
13[332]-17[331] CCCACAACAAAAACCLccLcLLLLgaggaacaagLLLLcLLgLC1C111AACA11AAC
16[207]-14[208] CAACCC11CCAA1AALccLcLLLLgaggaacaagLLLLcLLgLA1CA1ACAAAAACA1
17[332]-19[331] ACCC1CA11CA111CLccLcLLLLgaggaacaagLLLLcLLgLAA11ACC11A1CA1C
18[207]-16[208] 1CACCCCACCCCA1CLccLcLLLLgaggaacaagLLLLcLLgLAAAAA1AAA11111A
19[332]-21[331] A1A11CCCCACCAC1LccLcLLLLgaggaacaagLLLLcLLgLAACAAC1AACCACCA
20[207]-18[208] CC1CCA1ACC1C111LccLcLLLLgaggaacaagLLLLcLLgLCC1C1C11CCCAC11
20[303]-18[304] C1CCCACA1CCCCCALccLcLLLLgaggaacaagLLLLcLLgLAC1CA1AC1CC1A11
21[236]-23[233] AAC1C1AACA11AA1LccLcLLLLgaggaacaagLLLLcLLgL1CCC11CCCCC1AAA
21[332]-23[331] CCACAACAC1AA1AALccLcLLLLgaggaacaagLLLLcLLgLAACCCACC11C1ACC
23[288]-20[304] 111A1AA1CAC1CACLccLcLLLLgaggaacaagLLLLcLLgLCCCACCCAACAA1AC
6[271]-9[233] AC1111AACCCCC1CLccLcLLLLgaggaacaagLLLLcLLgLAC1CCC11CA11CCA
8[207]-6[208] 111CAACCA1C1ACCLccLcLLLLgaggaacaagLLLLcLLgLC1AACACCCC1CCC1
8[303]-6[304] ACCCACACCCC1111LccLcLLLLgaggaacaagLLLLcLLgLCA1CCCCAA1ACA1C
9[236]-11[233] CACACACC1CC1C11LccLcLLLLgaggaacaagLLLLcLLgL1CCACACCACCAC1A
DOI: 10.1038/NCHEM.1070


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G
T
A
T
A
A
C
G
T
G
C
T
T
T
C
C
T
C
G
T
T
A
!"
49
DOI: 10.1038/NCHEM.1070
SS.6. "C" or|gam|

Core
Seq name Sequence
6[111]-9[93] AACACACCA1CCCAACCACCC1AC11111CA
6[143]-9[127] CCC1111CCCCCA1CC1CACCC1C1AAAA1AC
6[173]-9[139] CCC1CCC1CACCC11CCACCCACCC1AAAA
6[207]-9[191] ACAACCA1CCCCCACCCA1AACCAAACAC1C
6[239]-9[223] CC11CA1ACCCA1AC11CCCCCCACCAACCCC
6[271]-9[233] CACC11CC111CCACC1CAA1111C11AC1
6[303]-6[272] 1CCAAAACCACCC111AA11C1A1CCC111A1
6[333]-9[319] 1111CACC11CAAAA1C1CCAAAAC1CACAC1
6[367]-9[331] CCCA1111CC1AAACAAC111CACCCCC111
6[399]-9[383] 111CCACACC11AC1AAA1CAA11CCCC1CCA
6[431]-9[413] AC11ACCC1AACCA1C1AAAC111CCAA1ACC
6[463]-9[447] ACCCC1C1ACCA11CCACACACAAC1ACCCC
6[493]-9[479] AACAC1CAC111CC1CACCAC1ACCAACCCCC
9[96]-11[93] 1CACCAACACCACAAACACCACAA11CAAC11
9[128]-11[127] C1AA1CCCCC1CC1CA11CAC1CACCA1111A
9[160]-11[139] CCAAACACCCA1A11CA11ACCCCCACC11
9[192]-11[191] A1C111CACACC11CA1CAACAC1AACCAAC1
9[332]-11[331] 1CC1CACAA1AAC1111AACCCCCCA1111
9[384]-11[383] CACCC11CCA1CCC1111CA1CA1111CCCA1
9[416]-11[413] 1C1A1CACC1C1CAA111ACCC11AACCACAC
9[448]-11[447] CACCC1C1CC1CA11AAACCCACACCCCCC
9[480]-11[479] ACCC1CACACCA11CCCC11CA1AACCCACCA
8[111]-6[112] 1CCCC1C111CCA11AAACCCCACCACCCA
8[143]-6[144] C1AACAAAAC1ACCAACCCACCAA11AAACCC
8[173]-6[176] CAACAACCCCAAAACAA1ACAC1ACA1A1A11
8[207]-6[208] CC1CCC1CCCCCACCCA11A1ACAA1CACA
8[333]-6[336] CC11CAC1CAACCA11ACCA11ACACAC111C
8[367]-6[368] C1AC1CC11ACCACCCCCA1AAC111C1C1A1
8[399]-6[400] CCC1CA1AA1A1AAC1A1ACCCC1C1CC1C
8[431]-6[432] ACCCCAC1CC1AC1CACCACC111CCCC1CA1
8[463]-6[464] CAAA1AAAACAACCCCCACCC1CAAAAC1ACA
8[493]-6[496] CACC1CACACCCACCACCC1CA1C1ACCC1
11[96]-8[112] 1AA1CA11C1CAA11ACC11A1CA1AACCC1
11[128]-13[127] ACAAC1CC1CA1AAA1A11CA11CAAAACCAC
11[160]-13[139] CCCAACAAACAC1CCA1ACCC1C1C111AC
11[192]-13[191] AACCCAACC1111CCCACACCCCCACCCCA11
11[236]-13[233] CCCCAAAACA1AACCC1CC111AAACCCAA
11[288]-10[272] CAC1ACCCAACCA1CCA1ACCACCC1AACACC
11[332]-13[331] CCC1CA11A11CA11AAACC1CAAAC11AC
11[384]-13[383] C1111CA111CACCCACCCAACC1A1AA1AAC
11[416]-13[413] CCACCACCCCCCAAACACAAAACCCA11AACA
11[448]-13[447] ACCC1CACAA1CAA1ACAAAA1AAACC1AC
11[480]-8[496] CCC1CACACCCCCCACCACAACCC11CACC
10[143]-8[144] CCCAA1CCC1CA11A1ACCAC1CAAAA1CAAC
10[173]-8[176] AAA1C111AAA1C1ACC11AA1AAAA1C11CA
10[207]-8[208] AAAACAAAACA11A11ACACC1CCCCA1AC
10[367]-8[368] ACCCAAA1ACCCCCC11A11ACCCACACCAC1
10[399]-8[400] 1CAACCCAAA1CAAAA1CACCCCCCAC1AA
10[431]-8[432] 111ACCACCCAACCCCC1CCC1CACAA1CCAA
10[463]-8[464] 1111C1CACAACCCCCACCC1CAC11CACAAA
13[128]-13[127] AA1CACCACA11CCA1A1AACAC1AC111CAC
13[160]-13[139] CC1CAC1A1A1CCAAC1AAAC1ACAA1AAC
13[192]-13[191] CCA1CAAACAA1A1AA1CC1C1ACCCCCCCAC
13[236]-13[233] CCACACCC1ACC111AA11CC1CAACCCAA
13[288]-12[272] ACCAA1ACAA1AACACCAACAAACCC1CACCA
13[320]-13[319] ACAAAAC1CA1AACCCACAACAA1CCC1A11C
13[332]-13[331] CACAACCACACCC1CAACAAACACC1CCCC
13[384]-13[383] CCAA1ACCACCCAACCCCA11ACA1AAA1CAA
13[416]-13[413] C1CC11A1CCACCC111ACACACACC1ACAA1
13[448]-13[447] AAAA1ACCA111111C111AACAACCACCC
12[143]-10[144] CCAAC1111AAA1CAAAAA1CACCCAA1AC1C
12[173]-10[176] C1111AAA11A1AC1CACAACCAA1AA1AC1A
12[271]-13[287] 11ACACACCAACCAAAC1CCAACAAA1CAAA1
12[333]-10[336] A1CACACAAACCACA1ACCCCAACAA11A1CA
12[367]-10[368] 11AAC1CAAAACCCACCAAACCCAAAA1A11C
12[399]-10[400] A1AAAAACCAAAACAAC1CCCA1CCCACA1
12[431]-10[432] 1CAAAA1A1ACCCAC1A1C11ACC1CA1A1CC
12[463]-10[464] 1AACAAACA1ACA1AAACC1CCCA1AAC111A
13[128]-17[127] CA11ACA11C1ACC1AAACA11CA1CACCA1C
13[160]-17[139] C1C111ACCA1A1A1111AAA1C1CA1AAA
13[192]-17[191] C1CAAAAC11CAACCCAACCA1AA111CACAC
13[236]-17[233] ACAA11ACCC1AAA1CCC11C1AA1C1ACC
13[288]-14[272] AAA1CACA1CA11ACCCCCCCCAAACCC1CAC
13[320]-17[319] 1AACAACCAACCAACCCC11111AAC11AA11
13[332]-17[331] AC11CCC11CC11A1CA11CCAC111CAAA
13[384]-17[383] CA11AC11CCA1C1ACAAACCAA1CC11AAA1
13[416]-17[413] 111A1CC1AACAAAAA1AA1A1CC11AC1ACA
13[448]-17[447] 1C111CCCC1C111A1CAACAAC11A1ACA
14[143]-12[144] CAC1AA1CACA111CCCAAA1CC1CCC1C1C1
14[173]-12[176] ACAACCC1C1A1A1111CA111CCC1CAACA1
14[271]-13[287] ACCA1AAACAAAA11AACCAA1AA1ACCAACC
14[303]-12[304] CC1ACCAA1A1ACAACCC11A1C1CAC11A
14[333]-12[336] 1CCACAACCCACCCC1111ACCCA1CACACCC
14[367]-12[368] CCC1C1C1CCACC1111CAACCC1CCCCACAA
14[399]-12[400] A111ACCACC1A1111CCACCCACAA1AAC
14[431]-12[432] 1CC1CAACCAA1C11ACCAACCC1C1CAAAAA
14[463]-12[464] ACAACCCCACACCC1AA111CCCAAA1CCAAA
14[493]-17[479] CCACCACAA1AAACAACA1C11CACCC1CAAC
14[327]-17[311] ACCCACAAAACC1AAAC1AA11C1CA1A111A
17[128]-19[127] AA1A1CA1C1ACCCACC111CA1CCCCA11C1
17[160]-19[139] 11AA1CCCCCA1CAAAAA1AA11CCC1AA1
17[192]-19[191] A1C1ACAA1AAA1CACC1CA1111CCCCCCA1
17[236]-19[233] CCCC11CA1A1AACCAAA1A11111C1CC1
17[288]-16[272] CAAAAC11CCAA1CCCAACACAAAAAAAACAC
17[332]-19[331] 1ACCCACA11AACACCC1CACAACCC11AC
17[384]-19[383] AACAA1AA11ACAA1CC11CAAAACCACC1AA
17[416]-19[413] AAAACCC1C1C1AAA1CC1CCC1ACA1111CA
17[448]-19[447] AA11C11AA1CAA1A1A1C1CAC1AACAC1
17[480]-19[479] AC1ACCCC1CAA11ACC111111A1AACCCA1
17[312]-19[311] ACAACCCCAACAAAA11AA11ACAAC11ACAA
16[143]-14[144] CCC11CC1A11CAACCC11C1ACCCAA1CCC1
16[173]-14[176] 1ACCAACCCCACACCC1ACC1A11AAA11111
16[271]-17[287] CAACA11C1AA1CACAAAACCCCCCAACCCCA
16[303]-14[304] A1CCAAA1111CAAA1A1A11111111CA1
16[333]-14[336] CC11CCC11CACC1AAA111AA1CACAACCCC
16[367]-14[368] 1ACC11ACCC1C1CA1AAA1AACCCAA1AA1C
16[399]-14[400] A1111CCCACACCCCAA1CA1AACA1CC1A
16[431]-14[432] CC11CC11C111AC1A1CA1A1CC1ACA1AAC
16[463]-14[464] AC1ACA1AACCAC1A1AAACCCAACC1AA1CC
16[493]-14[496] A111CA1111AA11CACAA1CCCC1CCACA
16[327]-14[328] A1CAACAAAACA1C1AA111ACCC1A1AAAC1
19[128]-21[127] CCC1CCCAACCACCCCCAC1CCCAA1CCCC1C
19[160]-21[139] CCCA1ACCCCCACCC1111CCCACCAACCA
19[192]-21[191] CC1AACCCCCA1C1CC1CCAACCCAA1CAC1C
19[332]-21[331] AACC1ACCAA11CCACAAC1CCACA1AAAA
19[384]-21[383] AACACAAA111CACCA111ACAACACACCCCC
19[416]-21[413] CC111AAC1AA1ACA11ACACCCCCACCACCA
19[448]-21[447] ACC11111A1C1AAAA1A1C111CC1CAAC
19[480]-16[496] 1CCCC1CA11CC111CAA1ACCA111AACA
19[312]-16[328] AA1CCCCCACACCCCAA11A11CAAAACAAAC
18[111]-21[93] 1CCC1CCACC1CCAC1C1ACACC1CC1CA1A
18[143]-16[144] C11C1AAAACAAACCCCCCA11CACCCC1C1C
18[173]-16[176] 1CCC1AAC1CACC11CC1C1ACA111AACCAA
18[271]-19[287] CACCC1CCCCACCCAAACCCCCA1A1CACA1C
18[367]-16[368] 111ACAAACA1A1CAAAA11A111CA1ACCCA
18[399]-16[400] A1AA1ACA1AAACAAA11CCC1A11AA11A
18[431]-16[432] C1AACAACC1CACA1CAA1A1ACAC1CAA1AA
18[463]-16[464] ACCAACC1ACA1CCCCACAAACAAA1CCAAAC
21[96]-23[93] CC1C111C1CCCCAAAA1CCC11AC1C11C11
21[128]-23[127] ACAA11CCCCCAAAA1CC1C111CA11AAACA
21[160]-23[139] 1AAAC1C1CCAACCCC1CCACCCCAAAAAC
21[192]-23[191] ACC1AAC1CCCC11CACCCCC1CCACC1CAAC
21[224]-23[223] CCCCCC111111CACCAC1CACACCCC1CCAC
21[320]-23[319] AA1ACCCAC1AACAA1ACC1CCCACACAA1CC
21[332]-23[331] CACACC1CCAACACACA1ACAAACCCCACC
21[384]-23[383] 1CCAACAC1CACACCACCAC1AA1CCAAA11A
21[416]-23[413] AA1CAAAAAA1CCA11A111ACA1A11AC1AA
21[448]-23[447] C1CAAA1AA1ACC1ACA1111CAAC1CAAA
20[111]-18[112] 1CCCAAAC1C1C1CAAA11C11ACC11CCA
20[143]-18[144] CCCACCACACACAACA1ACCACCCC1CACCAC
20[173]-18[176] CAC11CCAAAACCC1CCCC1CCC1CA11AAC1
20[207]-18[208] CC1CA11CACA11AA11CCC11CACC1CCC
20[333]-18[336] C1CAAACCACCAACCACCACCACA1A11AAA1
20[367]-18[368] CA11C1CCCACCCCC1CAC1A11A1A11ACAC
20[399]-18[400] 11CACCAC1CCCACCC1CACACC1CAA1AC
20[431]-18[432] 1CC1C1CAA1C1AAACCA1CACC11ACCACCA
20[463]-18[464] C1CA1CCAA1CAAACCC1CAA1CAACCAA11C
23[96]-20[112] CCAC111CCAACAACAC1CCAC1A1CC1CC1
23[128]-20[144] ACC1CCAC1CCAACC1CAAACCCC1CC111CC
23[160]-20[176] CC1C1A1CACCCCCA1CCCCCAC1CCC1CACA
23[192]-20[208] CA1CACCCAAA1CAAC111111CCCCCAACA
23[224]-20[240] C1CCCC1AAACCAC1AAA1CCCAACCCACCC1
23[236]-23[287] CCCACCCCCCCA111ACACC11CAA11AAACC
23[288]-20[304] CA1111ACACACCAACCC1ACCCCACACAA
23[320]-20[336] 1CACAAC1C11111A1AA1CAC1CCCC11C1C
23[332]-20[368] CAC1AAAACAC1C1C1CCA1CACAAAACCCA
23[384]-20[400] ACCC11C1ACCAA1AC11C111C1CCCACA
23[416]-20[432] 1AACA1CAC11CCC1CAC1ACAACACCC1CAA
23[448]-20[464] C1A1CCCCC11CC1CC1AA1A1CCAAAAACC
22[231]-23[239] CCACCCCCCCC1ACCCCCC1CCCA
22[233]-22[232] ACAAACCAACCCAACAAACCCAAA
22[279]-22[236] CCCCCAAACCCCCCCAACC1CCCC
22[303]-22[280] CACCCCCACC1AAACACCACCCCC
22[327]-22[304] AACC1CC111CC1CC11ACAA1CA
23[240]-23[263] AC1C1ACCCC1CACCC1CCCCC1A
23[264]-23[287] ACCACCACACCCCCCCCCC11AA1
23[288]-23[311] CCCCCCC1ACACCCCCCC1AC1A1
23[312]-22[328] CC11CC111CACCACCACC1A1

k|ght Ldge
6[319]-9[319] CCCAA1ACCAACCCA1111CACCCA1ACCAAC
8[319]-11[319] CCACCA11CACACCACACCACCACACCCCCCC
10[487]-13[487] CAAACACACCACCCAAACA1A1AAAACAAACC
12[487]-13[487] CCA1A11A111A1CCCC11ACAAAA1AAACAC
14[331]-17[331] CCAC1AA1AACACAAACACCCA1111CCAC
16[331]-19[331] CAAAACAACA1CA1C111CAA11ACC1CAC
18[487]-21[487] CAAA1CAACAC11CAAA1A1C1CC1CAC11CC
20[487]-23[487] CCACCCA11CCAACACCACAACAA1A11ACCC

Left Ldge
9[72]-6[72] C111CACCAC1AAACACCAACCCC1ACACACC
11[72]-8[72] C11CACA1CC111AA1CCAC1AC1AAA11CCC
13[104]-10[104] C111AAACAC11CACAA1CCCCC1CAAA1C
13[104]-12[104] CCAACCAC1ACA1111CA11CCCAA11C1C
17[104]-14[104] CCCCACACAC1CAAAAAACCC1CACAAACC
19[104]-16[104] CCAC1AACAACCCC1AACA11AAA1C1CAC
21[72]-18[72] C1CCAA11CC1AA1CAA1CCCCCCC1ACCCAC
23[72]-20[72] CCCCACA1ACCC11CA1AAA1CAAAACAA1AC

9[236]-11[233] 1ACCCCCACAAC1CALccLcLLLLgaggaacaagLLLLcLLgLCCAAC1111ACA1AA
8[303]-6[304] A1CCCCCCCAAAC1ALccLcLLLLgaggaacaagLLLLcLLgL11AACACCAAAACCC
10[303]-8[304] ACCAA1CAACACAA1LccLcLLLLgaggaacaagLLLLcLLgLCAAC111CACAC11A
12[207]-10[208] AA11CC1AACA11AALccLcLLLLgaggaacaagLLLLcLLgLCACCAACCC1111CC
12[303]-10[304] ACCCCAA1C1A1C11LccLcLLLLgaggaacaagLLLLcLLgLACCCAACCAAACC1C
14[207]-12[208] CC111A1C1CCCA1CLccLcLLLLgaggaacaagLLLLcLLgLAA11C1A1ACACC11
16[207]-14[208] 11111C1ACCC1A1CLccLcLLLLgaggaacaagLLLLcLLgLACC1CA1CCCACAAC
19[236]-21[233] CCCCCAAACCAAC1CLccLcLLLLgaggaacaagLLLLcLLgL11CCCAACC1CC1CC
18[207]-16[208] CAAACCC1CCA1C1CLccLcLLLLgaggaacaagLLLLcLLgLCCAC111CCA11AAA
18[303]-16[304] CCAA11A11CA1CAALccLcLLLLgaggaacaagLLLLcLLgL1A1AA1CCAA1CC1C
21[236]-23[233] CACC1CCAC111CCCLccLcLLLLgaggaacaagLLLLcLLgL1A11CCCCCCC1AAA
20[303]-18[304] 1A11111CACCCC1ALccLcLLLLgaggaacaagLLLLcLLgLAAACA1CCAACCACC
9[224]-11[223] 1C1CCAAAACCC1C1ALccLcLLLLgaggaacaagLLLLcLLgLCACACCACACAAACA1
9[288]-8[272] 1CAAACA11CCC1A11LccLcLLLLgaggaacaagLLLLcLLgL1CCCAACCCAA1CA1A
9[320]-11[319] CC1CAACAAACAC1CCLccLcLLLLgaggaacaagLLLLcLLgLCCC1A1AACC111ACC
8[239]-6[240] ACACA1CA1CCCCCACLccLcLLLLgaggaacaagLLLLcLLgLC1CC1CCAC11AAACA
8[271]-9[287] ACCCAACCACCACCCCLccLcLLLLgaggaacaagLLLLcLLgLCACACCC11A11A11C
11[224]-13[223] AA1ACCACACCAAAA1LccLcLLLLgaggaacaagLLLLcLLgLACCCACACCCCCAAAC
11[320]-13[319] C1CACAC1CCA11ACCLccLcLLLLgaggaacaagLLLLcLLgLAACCCCCCCC11111A
10[239]-8[240] CCA1AAAAA11CAAC1LccLcLLLLgaggaacaagLLLLcLLgLAA1CCACACAAACACC
10[271]-11[287] AACAC1A1CCAA11ACLccLcLLLLgaggaacaagLLLLcLLgLCACCCA1AACCC1AA1
10[333]-8[336] CACCA11AC1ACCCCCLccLcLLLLgaggaacaagLLLLcLLgL1111CA1CCC1CAC1C
13[224]-13[223] 1A1CCCC1A11111CCLccLcLLLLgaggaacaagLLLLcLLgLCCA1CCC1C1AA1AC1
12[239]-10[240] AACACC1C111AA11CLccLcLLLLgaggaacaagLLLLcLLgLCACC11CACCACACCA
13[224]-17[223] 1AACA1CCCC1C1AA1LccLcLLLLgaggaacaagLLLLcLLgLAC1111CC1CCC1CAC
14[239]-12[240] A11A1CACAA1AAA1CLccLcLLLLgaggaacaagLLLLcLLgLA1ACACCCC1111CA1
17[224]-19[223] 1CC1AAAA1A1111C1LccLcLLLLgaggaacaagLLLLcLLgL1AAAA11CCACCCCAC
17[320]-19[319] 1CA1C11C1A1A1AACLccLcLLLLgaggaacaagLLLLcLLgL1A1A1C1A1CA11C11
16[239]-14[240] AACC11AAC1ACCA1CLccLcLLLLgaggaacaagLLLLcLLgL1CAA1CA1CCAAAAAC
19[224]-21[223] C1CCACCCC1C11CCCLccLcLLLLgaggaacaagLLLLcLLgL1A11ACCCCCCC1CAC
19[288]-18[272] A1CCCAA1CA1CA1A1LccLcLLLLgaggaacaagLLLLcLLgL1CC1CA111CCCCA11
19[320]-21[319] 1CCA11A1ACAAACAALccLcLLLLgaggaacaagLLLLcLLgLACCACCACCCA11AAA
18[239]-16[240] C1CCCCCCACC111CCLccLcLLLLgaggaacaagLLLLcLLgLCCCACCCCAAA11C1A
18[333]-16[336] 111CCCCAAC11C1CALccLcLLLLgaggaacaagLLLLcLLgLA1AA1CCAACAC1CAA
21[288]-20[272] CAAC1CA1AA1CCC1ALccLcLLLLgaggaacaagLLLLcLLgL11AC1C11CCCCCCCC
20[239]-18[240] CC11111C1CCAC1CCLccLcLLLLgaggaacaagLLLLcLLgLCCAAACC1CCCCA1CC
20[271]-21[287] CACACCCC11AA1CAALccLcLLLLgaggaacaagLLLLcLLgL1CCCCCAA1AA1CCCC
DOI: 10.1038/NCHEM.1070

6 9 8 1
1
1
0
1
3
1
2
1
5
1
4
1
7
1
6
1
9
1
8
2
1
2
0
2
3
2
2
2
5
6 9 8 1
1
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1
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8
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7
6
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4
4
5
5
2
50
44 19
52
8
15
8
23
35
56
30
48
1
2
C
C
T
C
T
G
T
A
G
C
C
G
T
T
G
C
T
A
C
C
C
T
C
G
T
T
C
C
G
A
T
G
C
T
G

T
C
T
T
T
C
G
C
T
G
C
T
G
A
G
G
G
T
G
A
C
G
A
T
C
C
C
G
C
A
A
A
A
G
C
G
G
C
C
T
T
T
A
A
C
T
C

C
C
T
G
C
A
A
G
C
C
T
C
A
G
C
G
A
C
C
G
A
A
T
A
T
A
T
C
G
G
T
T
A
T
G
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!"
DOI: 10.1038/NCHEM.1070
SS.7. "D" or|gam|

Core
Seq name Sequence
6[111]-9[93] CCCAACC1A11A11C1CAAACA1A1A1AAC1
6[143]-9[127] CCC1A1AAACAC11AA1CCCCCC1CC1AC1CA
6[173]-9[139] 11AACCCCC1CAC1CCC11CAC1CAACCCC
6[207]-9[191] 1CA1CA1ACACCAC1C1AC1CC1ACCCACCA
6[239]-9[223] 11ACCC11CCAC1AACCC1CA1ACCCCAA1AC
6[271]-9[233] AAACCCACAA1CCAAACCCCAC11CC1CAC
6[303]-6[272] CC11CA1A11CACAAACAAA1AAA1CC1CA11
6[333]-9[319] CACACCACC11CACCCACC1CACA1ACCAACC
6[367]-9[331] 1CACACCCACCACCC1CACACCC1CCA1ACC
6[399]-9[383] CC1CACACCCCCCACCC1CACAACAA1CAAC1
6[431]-9[413] CCCCAACCACACCCACCACCCCAACCCC1111
6[79]-9[63] 1AACACCC1CACAC1CC1CAACAACCACCC
8[111]-6[112] 1111CACCAA1ACC1C1A1CACCCC1A111
8[143]-6[144] ACCAACAAAC1ACCCCCACCC1CAAACAC1CC
8[173]-6[176] 111CAACACAACCCCCACCC1CACAA1AAC11
8[333]-6[336] A11CA11AC1CACCAA1CAAACCACCCACCAC
8[367]-6[368] 1CAACCCA1AA1CAC1ACCCACACCCCCACCC
8[399]-6[400] C111ACCAACCC1CACAC1C1ACCCCCC1C
8[431]-6[432] A1111C1C1111CCC1CA1ACCCCCAAAA1CA
8[79]-6[80] 1CCAAAACCCCC1CCACACCC11CCAAAC1A1
9[128]-11[127] CCACC111C1AAACCAA11CCCAACCA1A1A1
9[160]-11[139] CACCC1CAC111CACCCCAC1CA11AAACC
9[332]-11[331] ACCACCC11CACCCACCCAACC1AA1AACC
9[384]-11[383] 11CCC111CCCCCAAACACAAAACA11AACAC
9[416]-11[413] CA1CCCCAACAA1CAA1ACAAAA1AAACC1AC
9[64]-11[63] CCA1AAC1CACCC111AA11C1AC11AAAC
9[96]-11[93] A1ACCCCCC11CAAAA1C1CCAAAACAA1CAC
10[111]-8[112] 1CCA1C11CCCCCACCCA1AAC1AA1AA11
10[143]-8[144] CC1CA1AA1CACCC11CCACCCACCAA1ACAA
10[173]-8[176] AAACAAACCCCCCA1CC1CACCC11AAACAAC
10[367]-8[368] 1CACCCC1CAAAACAAC1CCCA1CCCCCACA1
10[399]-8[400] AC1CAACAACCCAC1A1C11ACC1CA1A1C
10[431]-8[432] AAACACCC1ACA1AAACC1CCCAAA1AAC111
10[47]-13[31] C111CAAACACCACACA1CAACCCC11CA1CA
10[79]-8[80] CCC1CAA1ACCCA1AC11CCCCCCAAAAACCC
11[128]-13[127] 1CCC1CCCA11C1C1CCAAA1CCCACAAACAC
11[160]-13[139] CCCC11111ACAACCCACA111CCACA1CC
11[192]-13[191] AAACACACCCCCCACCCA11A1ACCAA11ACC
11[236]-13[233] 1CACCAACC1ACCAACCCACCAAC1ACC11
11[288]-10[272] CAAAAC1AC1A1C11ACCCAACCCAAAA1ACC
11[384]-13[383] 1CC11A11CCC1CAACAAAC1CACAAAA1AAA
11[416]-13[413] AAAA1ACAAACCCCA11ACACCCCCAAA1AAC
11[64]-13[63] ACC11CA1CA1AACCCAACCCAA1A11CA1
11[96]-13[93] AACAACCA1AC11ACCCCCAACCACC1CA11C
12[111]-10[112] AAAACAAACCC11CCCC1CACCCCACC1CC
12[143]-10[144] CCA1AAAAC1AC1AAA11CCCC111A1CA1CC
12[173]-10[176] AACAC1A1CAAC111AA1CA11C1CAACCCCC
12[239]-10[240] AA1ACCACCC11CCCAACAAAAA1CC1AAAAC
12[271]-13[287] ACC1ACAACAAC1AACCCAACAACCAACA11A
12[303]-10[304] CCCCCACC111CCACCCACC1ACA1CAAA1
12[367]-10[368] ACCAA1CAC1AA111CCCAC11ACACCC1AA1
12[399]-10[400] CACAACAA11A111A1CCCAA1CACAA11A
12[431]-10[432] AACCCC1A1111C111AACC1CAA1AACA1AA
12[47]-10[48] CCCAA1CCC11CACAACAACCCCAC1CACCAA
12[79]-10[80] AAA1C1111CAACC1AACAAACC1CCCCCACA
13[128]-13[127] CACAACCAACCAAAA1ACCCACACCCCCAAAC
13[160]-13[139] 111AA111CA1AACCC1CC111ACACC11C
13[192]-13[191] 11A1CCCACCAA11ACCACCCA1AC1CCAACA
13[236]-13[233] AA1AAAACACA11CA1CAC11CA1C1111A
13[288]-12[272] C11CC1A11111CAACCC11AAA1A11A11AC
13[32]-13[31] ACAC1AA11CA1AAA1A11CA11CAAAACCAC
13[384]-13[383] CACCCA1ACCAACCCC11111A11AACAA1AC
13[416]-13[413] AAACCA1111AAACCAAC1ACCCCA1A1CCCA
13[64]-13[63] 1ACCCAAAACAC1CCA1ACCC1C1C111AC
13[96]-13[93] AC1CAA1AC1111CCCACACCCCCACCCCA11
14[111]-12[112] 1AACA1CAACA11AACACCAACCC1111CC
14[143]-12[144] CC1CCCA11A1CCCC1111AA11CCCACACCA
14[173]-12[176] C1A1A111CCACACCCCAACCAAAC1AACACC
14[239]-12[240] CCCAACCAA1CC1C1ACC1CAACACA111ACC
14[271]-13[287] 1CA11CCAAC1AAAC1ACCC1C1CCACAA1A1
14[303]-12[304] CACCCA11CACAAAACC1AAAC1CCCAC11
14[367]-12[368] AAACCCAAAACCCCCC1C111A1C11CA1CC1
14[399]-12[400] A1CA1A1C1CAACAACAAAAA1AAC1CA1C
14[431]-12[432] AA1CA1AA1ACCACCA1C1ACAAAA11CCAAC
13[128]-17[127] AC11CAAACAA11C1AC1AA1AC1CCAAAAAC
13[160]-17[139] AAACCCAA1CA111CCCCCCCCACCCACAA
13[236]-17[233] AA1A1CCA1A1AACAC11CA11CCAAACCC
13[288]-14[272] AAAC1ACC11CCACCCAC1AA1AA1CCAAC11
13[32]-12[48] AA1CACCA1AAA1CAAAAA1CACCCAA1AC1C
13[384]-17[383] A1AAC1CCCC11A1ACAAA11C11111CAAA1
13[416]-17[413] 1CC1AA1111AC1ACAAAAACCC11CACC1AA
13[64]-12[80] CC1CAC1A11A1AC1CACAACCAA1AA1AC1A
13[96]-17[93] CCA1CAAACAA1AAA1CA1ACACCACCC1CAC
16[111]-14[112] A1AA1CACC1AAA1CCC11C1AAC1ACCA1
16[143]-14[144] AAC1ACCACC1C1AA1AC1111CCCC1CAAAA
16[173]-14[176] AAACAACA11CAACCCAACCA1AAC1C111AC
16[239]-14[240] ACACCC1AACA11CAAAACCC1CACCAA11C1
16[271]-17[287] 1CAACCC1C1CAAA1CACCA1CAAC1ACC111
16[303]-14[304] 1A1CAAAACCCC11ACC11CCC111ACCCA
16[367]-14[368] AC1ACA1ACAACCCCACAAAAC11ACCAC1A1
16[399]-14[400] A111CA11C11AA111CA1C11CC111AC1
16[431]-14[432] A1CAACAAC111CAAA1ACCCACCAACACCCC
17[128]-19[127] A11A1CAC1C1CAA1CA1A1C1ACAA11111C
17[160]-19[139] CCC111A1CAA1CCA1CAACCC1A1ACCAA
17[224]-19[223] C1ACC1AACC1A11111CACACA1AAA1C1CA
17[236]-19[233] CCCACACA1C1ACC1CA1AAA111CCCA1A
17[288]-16[272] 11AACC1C1CA1ACC1C1CACACA1A1CA1A1
17[332]-19[331] ACACAAAAA1CAA1A1A1C1CAC1AACAC1
17[384]-19[383] A1A1111A1CAA11ACC111111A1AACCCA1
17[416]-19[413] A111AA1CAACAAAA11AA11ACAAC11ACAA
17[96]-19[93] ACCA1AAACAAAACCCCCAAAAACAAACC11A
18[111]-16[112] C1C11CC11AAAA11CCCA11ACCCCC11C
18[143]-16[144] CCCAAC1CCC1CA111111AACCAAA1CC1AA
18[173]-16[176] CCACCCAAAAAA1AA11CCCC1C11C1CCACC
18[239]-16[240] AC1A1CCCCCCCCA11CACCC1AAAA1CCCCC
18[271]-19[287] CC1CCA1C1CC1C1ACA1CCCCCCCCACC1AA
18[367]-16[368] 1A11CC1CACA1CCCCACAAACAAA1CCAAAC
18[399]-16[400] ACAAACCA11CC111CAA1ACCA111AACA
18[431]-16[432] C111CAC1ACACCCCAA11A11CAAAACAAAC
18[47]-21[31] CCCCACCC1111CCCAC1CACCACCA1CCC1C
18[79]-21[63] CCA1C1CC1CCAACCCCA11AACCC1ACCC
19[128]-21[127] 11AAA1CA11CCCAACCCCCA1CC1CACAA11
19[160]-21[139] CCCCA1CAACCCCCA11CCCCA1A1AAAC1
19[332]-21[331] ACC1111A11A1CACA1CA1CC11ACCACC
19[384]-21[383] 1CCCC1CACCACAACCACCCCAA1CC1CAA1A
19[416]-21[413] AA1CCCCCAACA11A1CA1111CCAC1A11AC
19[96]-21[93] A1A1111CC1A11ACCCCACC1CC1ACC1C11
20[111]-18[112] 1CCC11ACAAA11C11A1CCCCC1CCCCCC
20[143]-18[144] CC1C111CCA1ACCACCCCCAACC1CACCC1C
20[333]-18[336] AAA1CAAAC11A1C1AAAA1A1C1CAA11CA1
20[367]-18[368] AACACCCCAC1AA1ACA11ACACC1A1CA1CA
20[399]-18[400] CAACA1AAA111CACCA111ACACCAACAA
20[431]-18[432] CCCA11AAAACAA11CCACAAC1C1111AAAA
20[47]-18[48] AC1CCAC1C1C1ACACCA1CCCCC11CCC1AA
20[79]-18[80] ACCC11CA11CC1AA1CA1CC1CACCAAACCC
21[128]-23[127] CCACACAAA1CC1CC11CCCAAA1CCCCA111
21[32]-23[31] CACC1CCAA11AAACAACC1CCACCACCCCCA
21[320]-23[319] 1CACCAACAA1C1AAACCA1CACC111ACA11
21[332]-23[331] AC1AACAC1CCAACAC1CCCACAC1AA1AA
21[384]-23[383] CA1AA1ACAACACACC1CACCCCCA1ACAACC
21[416]-23[413] AC111ACAAAA1ACCCAACCAACC1ACC1CCC
21[64]-23[63] ACC1CCAAC1C11C11CCAC111CAAA1CA
21[96]-23[93] 1CC1C1C11AAA1CAAAACAA1ACAAACCAC1
23[128]-20[144] ACACC11CACCCCCAAACCCCCCCCCCAAAA1
23[160]-20[176] CCACAAACCAACCCAACAAACCCACCAACCCC
23[192]-20[208] CCCCC1ACCCCCCCC11CC1CC1CCC11CAC
23[224]-20[240] CAACAA1A11ACCCCCACCCA11C1111CACC
23[236]-23[287] AAAAACCC1CA1CCAAA1ACC1ACA1111CAC
23[288]-20[304] CC1CAA1CC1C1CAAA1CCA11A11CC1CA
23[32]-20[48] 1CCCCCAC1ACC1CAACCA1CACCCCAACAAC
23[320]-20[336] CCCACA11CACCAC1CACACCACCCC1CACAC
23[332]-20[368] AACCCACA11C1CCCCAACACAC1CAC1A11
23[384]-20[400] C11C1CACC1CAAACCC1AACAAACCACCA
23[416]-20[432] ACACACAA1A11111CAA1CCC1AAAAACA1C
23[64]-20[80] AC111111CCCC1CCACC1CCCC1CCCCACA1
23[96]-20[112] AAA1CCCAACCC1AAACCCACCCCCCCAAAA

k|ght Ldge
6[433]-9[433] CCA1C1111CA1AA1CC11A11ACCC111C
8[433]-11[433] CAAACACACCACCCACA1A1AAAACAAACC
10[433]-13[433] CC111ACACACACAAAAA1CAAAA1ACCAC
12[433]-13[433] C1C1C111CC11A1CCCAA1CAA1AA1CCC
14[433]-17[433] CC11AAA1AACAA1AC1C1CA1AAA1AACC
16[433]-19[433] CAAAACAACA1CA1C111CAA11ACC1CAC
18[433]-21[433] CCCCAACC11A11AAC1A11AAA1CC111C
20[433]-23[433] CCAAC1CA1ACCCC111AC1C111AA1CCC

Left Ldge
9[40]-6[40] CCCCC1111CC1CAC1CAACCA11ACCA11AC
11[40]-8[40] C111CCACC1CAA1111CCC111A1CACC11C
13[8]-10[8] CA1ACCC1CCC1CAC1C1ACACACCACCCC
13[8]-12[8] C111AAACAC11CACAA1CCCCC1CAAA1C
17[72]-14[72] CAAAA11AACCAA1AACAACCCAAACAA11AC
19[72]-16[72] CAAA1A111AAA11C1ACCAACA11C1A1AAC
21[8]-18[8] CCAC1CCCAACC11CC11C1AAAACCACCC
23[8]-20[8] CCAAAAACCC1C1A11CCAACC1CAAACCC

10[207]-8[208] 1C111CACA1CCCAALccLcLLLLgaggaacaagLLLLcLLgLCCACCC11AC1AAA1
10[239]-8[240] CAAACACC111CACCALccLcLLLLgaggaacaagLLLLcLLgLC1AAACACACCA1C1A
10[271]-11[287] 1AA1CCCA111CCA11LccLcLLLLgaggaacaagLLLLcLLgLAAACCCC1C11111AA
10[303]-8[304] ACCAA1ACACCACA1LccLcLLLLgaggaacaagLLLLcLLgLACCCCAACC1CACCC
10[333]-8[336] CCCCAA1AAACCCACCLccLcLLLLgaggaacaagLLLLcLLgLAAACCCAA1AAA1A11
11[224]-13[223] ACACACCCCAAAACAALccLcLLLLgaggaacaagLLLLcLLgL1ACAC1AACA11A1AC
11[320]-13[319] CACAACCAA1AACACCLccLcLLLLgaggaacaagLLLLcLLgLAACAAACAAA1111A1
11[332]-13[331] CAA1ACCAA1A1CACLccLcLLLLgaggaacaagLLLLcLLgLACACA1ACCC1C111
12[207]-10[208] CCCAAAA1111AACALccLcLLLLgaggaacaagLLLLcLLgLAC1CCC1AACAC1CA
12[333]-10[336] ACCCCACC11ACCAACLccLcLLLLgaggaacaagLLLLcLLgLCC1AACCAACCCACAA
13[224]-13[223] AC1CACCAA11CAAC1LccLcLLLLgaggaacaagLLLLcLLgLAA1CCACAAA11CC1C
13[320]-13[319] CC1CAA1CCC1111ACLccLcLLLLgaggaacaagLLLLcLLgLCCAACC1CAA11C1C1
13[332]-13[331] CCACACC11ACCCCCLccLcLLLLgaggaacaagLLLLcLLgLCCCAA1AC11CACC1
14[207]-12[208] ACA111C11ACACACLccLcLLLLgaggaacaagLLLLcLLgL1ACC1111ACA1AAC
14[333]-12[336] 1A111AACCCACAA1ALccLcLLLLgaggaacaagLLLLcLLgLAACAACA1CCAACCAA
13[192]-17[191] CC1CACCACCAAA1CCLccLcLLLLgaggaacaagLLLLcLLgL1CAA1AACAAA11111
13[224]-17[223] 1CAA1A1AC1ACA111LccLcLLLLgaggaacaagLLLLcLLgLAC111CACCAA1CCC1
13[320]-17[319] CCACACCAAACCCCAALccLcLLLLgaggaacaagLLLLcLLgLCA1C1AA11A1A1AAC
13[332]-17[331] AA1CCACCCC1CAACLccLcLLLLgaggaacaagLLLLcLLgLAC1ACCCCAA1CCCA
16[207]-14[208] CC1A1CACA1A1A11LccLcLLLLgaggaacaagLLLLcLLgL11AAA1CCA11ACA1
16[333]-14[336] 11AACACCAA1CC1CALccLcLLLLgaggaacaagLLLLcLLgL1CCAAA1CC11AA11C
17[192]-19[191] ACAACCC1CC1CA11CLccLcLLLLgaggaacaagLLLLcLLgLCC1CACACCCCC11CC
17[320]-19[319] 1A1A1C1AC1CACAACLccLcLLLLgaggaacaagLLLLcLLgLAC1CAA1ACA1111CA
18[207]-16[208] ACC111CCC111CA1LccLcLLLLgaggaacaagLLLLcLLgLCAACA11C1ACAAAC
18[303]-16[304] CAACC1AC1AAACAALccLcLLLLgaggaacaagLLLLcLLgLA11CCC1AC1CAA11
18[333]-16[336] 1CCA11A1C1CACA1CLccLcLLLLgaggaacaagLLLLcLLgLAA1A1ACAC1CAA1AA
19[192]-21[191] 1C1ACCCACCCCACCCLccLcLLLLgaggaacaagLLLLcLLgLC11C1CC11CACC1AA
19[224]-21[223] CAACAAACCC1CACCALccLcLLLLgaggaacaagLLLLcLLgLACA1CCCAAC1CCCCC
19[236]-21[233] CC1CACC11CCCAC1LccLcLLLLgaggaacaagLLLLcLLgL11CACCCC1AA1CAA
19[288]-18[272] AACACAAACA1A1CAALccLcLLLLgaggaacaagLLLLcLLgLAA11A111A1CC1AAC
19[320]-21[319] CC111AACAC11C1CALccLcLLLLgaggaacaagLLLLcLLgLA1AA1CCAAAACCAA1
20[173]-18[176] 1CCACCC11CCCC1CCLccLcLLLLgaggaacaagLLLLcLLgLC1AA1CACCCCCCAAA
20[207]-18[208] CCCC1CCAA11CCC1LccLcLLLLgaggaacaagLLLLcLLgL1CCCC1CC1CCACCC
20[239]-18[240] AC1CACACC1CC1CCCLccLcLLLLgaggaacaagLLLLcLLgLACC1CCA1ACCACCAC
20[271]-21[287] A11CCCCCCCCCCCCCLccLcLLLLgaggaacaagLLLLcLLgLCACACCCCAA1A1C1C
20[303]-18[304] ACC1CAAACCAAA1CLccLcLLLLgaggaacaagLLLLcLLgLAACAC11CACCC11A
21[160]-23[139] C1AAACCCCC111CCLccLcLLLLgaggaacaagLLLLcLLgLCCCACCACAACC1CC
21[192]-23[191] C1CACA11CCC1CACALccLcLLLLgaggaacaagLLLLcLLgLCAC11CCAAACCACCC
21[224]-23[223] CCAAACC1CCCCAACALccLcLLLLgaggaacaagLLLLcLLgLCC1CA11CAA1A1CCA
21[236]-23[233] 1CCCCCAACCACCC1LccLcLLLLgaggaacaagLLLLcLLgLCC11111CCAACACC
21[288]-20[272] C1CAC11C1A1CAAACLccLcLLLLgaggaacaagLLLLcLLgLCC1CAA1CC111CCC1
8[207]-6[208] CAA111111CACCCALccLcLLLLgaggaacaagLLLLcLLgL1ACCAACA1CCC111
8[239]-6[240] AAC1111CACCC1AACLccLcLLLLgaggaacaagLLLLcLLgLAC1CAC11C1C1CAA1
8[271]-9[287] ACACACCCAC1ACAACLccLcLLLLgaggaacaagLLLLcLLgLCCC1C1ACCCACCAAA
8[303]-6[304] AC11CACC1ACCACCLccLcLLLLgaggaacaagLLLLcLLgLA11ACCA1CCA11CC
9[192]-11[191] CCC1CA11C1C1A1CCLccLcLLLLgaggaacaagLLLLcLLgLCA1111CCCACCACCC
9[224]-11[223] ACCCA1C11CC1C111LccLcLLLLgaggaacaagLLLLcLLgLCCACACC1ACCAACCC
9[236]-11[233] CAC1ACAAC1CA1ACLccLcLLLLgaggaacaagLLLLcLLgL11ACCC1A11111CA
9[288]-8[272] A1CACCACCA111CCCLccLcLLLLgaggaacaagLLLLcLLgLAA11ACACCA11CCAC
9[320]-11[319] CCCCAAACAACC1CAALccLcLLLLgaggaacaagLLLLcLLgL11A1CACCAAAC11AC

!"
DOI: 10.1038/NCHEM.1070

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A
C
G
G
T
A
C
G
C
C
A
G
A
A
T
C
C
T
G
A
G
A
A
G
T
G
T
T
T
T
T
A
T
A
A
T
C
A
G
T
G
A
G
G
C
C
A
C
C
G
A
G
T
A
A
A
A
G
A
G
T
C
T
G
T
C
C
A
T
C
A
C
G
C
!"
DOI: 10.1038/NCHEM.1070
SS.8. 60 corner or|gam| w|th stra|ght edges

arm 1
core
arm 2
core
plate flat-v-top-core (arm1)
A1,flatv-h1-b32,AATATTTTATGGGATAGGTCACGTTCTGCCAG
B1,flatv-h3-b32,TTTGAGGGAACGACGGCCAGTGCCGGATCCCC
C1,flatv-h5-b32,GGGTACCGGCAGCAAGCGGTCCACTTTGATGG
D1,flatv-h7-b32,TGGTTCCGTCAATCGTCTGAAATGCACGACCA
E1,flatv-h9-b32,GTAATAAAAACAATTCGACAACTCTTTTAAAA
F1,flatv-h11-b32,GTTTGAGTTGAAAACATAGCGATAAGTGAATT
G1,flatv-h13-b32,TATCAAAACCAAGTACCGCACTCATCGTAGGAATCATTAC
A2,flatv-h1-b48,TCGCATTACCCGGTTGATAATCAGAAAAGCCCCAAAAACATAAACGTT
B2,flatv-h3-b48,CAGTATCGCGGCGGATTGACCGTAGTTAAAAT
C2,flatv-h5-b48,TTCGTAATAGTCACGACGTTGTAAGACGACGA
D2,flatv-h7-b48,AAAATCCCTGGCCCTGAGAGAGTTAGCTCGAA
E2,flatv-h9-b48,TCTGGCCAACCTACATTTTGACGCAAATCGGC
F2,flatv-h11-b48,CATTTTGCAGTATTAGACTTTACAAGGGACAT
G2,flatv-h13-b48,CTGAGAGATTTCCCTTAGAATCCTAACATTAT
H2,flatv-h15-b40,CGCGCCCAATAGCAAGAAGAACGGGTATTAAATCATAGGT
A3,flatv-h1-b64,GTTAAATCCTCCGTGGGAACAAAGCCTCAG
B3,flatv-h3-b64,GAAGATCGCGCCAGGGTTTTCCCCATGGTC
C3,flatv-h5-b64,ATAGCTGTTTGCCCTTCACCGCCTTATAAA
D3,flatv-h7-b64,TCAAAAGAAACGCTCATGGAAATACAGAGA
E3,flatv-h9-b64,TAGAACCCATTTGAGGATTTAGAGGAACAA
F3,flatv-h11-b64,AGAAACCATCGCTATTAATTAATCTACCTT
G3,flatv-h13-b64,TTTAACCTTTTCCTTATCATTCCCAAATCAGATATAGA
A4,flatv-h1-b80,TTTTAACCATCGTAAAACTAGCATGTCAATCATATGTACAATTTTT
B4,flatv-h3-b80,CCAGCTTTTAAATGTGGTCGGATTAGCTCATT
C4,flatv-h5-b80,TGAAATTGCTGCAAGGTTGGGTAACACTCCAG
D4,flatv-h7-b80,AGATAGGGGGCGCCAGACAGCTGATTCCTGTG
E4,flatv-h9-b80,TGAAAGCGCTAGGGCGACAGGAAAATAGCCCG
F4,flatv-h11-b80,AGCGGAATAATAGATTGATAATACTTCTGACC
G4,flatv-h13-b80,GGTTGGGTATAAATCAGTAAATCGCCAGAAGG
H4,flatv-h15-b72,AGGCTTATCGGTATTCAAGAAAAACGGCTGTCCCGGCTTA
A5,flatv-h3-b96,GCTTCTGGGCGAAAGGGGGATGTGTTATCCGC
B5,flatv-h5-b96,TCACAATTGGCGGTTTGCGTATTGTTGAGTGT
C5,flatv-h7-b96,TGTTCCAGGCGAAAGGAGCGGGCGTAAGAATA
D5,flatv-h9-b96,CGTGGCACAGGAGCACTAACAACTTATCATCA
E5,flatv-h11-b96,TATTCCTGTTAATGGAAACAGTACTATATAAC
F5,flatv-h13-b96,TATATGTATAGATAAGTCCTGAACTAAGAACGCGAGGCGT
A6,flatv-h5-b112,ACATACGACTATTACGCCAGCTGTGCCGGA
B6,flatv-h7-b112,CAAGAGTCCAACGCGCGGGGAGACCACACA
C6,flatv-h9-b112,ATTTTTGAAAGGAAGGGAAGAAATTTGGAA
D6,flatv-h11-b112,GATGATGGATCTAAAATATCTTTAGACAAT
E6,flatv-h13-b112,ATGCAAATTTTGAATTACCTTTTATTATCA
F6,flatv-h15-b104,TTTAGCGAACCTCCCCCTGTTTATCAACAAAATGCTG
A7,flatv-h3-b120,AAAGCGCCATTCGCCAGGTGCGGGCCTCTTCGGCCGGAAG
B7,flatv-h5-b128,CATAAAGTGCATTAATGAATCGGCCACTATTA
C7,flatv-h7-b128,AAGAACGTGGCGAACGTGGCGAGAATGGCTAT
D7,flatv-h9-b128,TAGTCTTTGGAATTGAGGAAGGTTCAATTCAT
E7,flatv-h11-b128,CAATATAAACATTTAACAATTTCACCAATCGC
F7,flatv-h13-b128,AAGACAAAGCTAATGCAGAACGCGGACTTGCGGGAGGTTT
A8,flatv-h7-b144,ACGTCAAAACCTGTCGTGCCAGCTGTAAAGCC
B8,flatv-h9-b144,AACTGATACTTGACGGGGAAAGCCGGACTCCA
C8,flatv-h11-b144,GTTTGGATAAATCAACAGTTGAAAAATGCGCG
D8,flatv-h13-b144,GAAAACTTGAAAACAAAATTAATTTCCTGATT
E8,flatv-h15-b136,TGAAGCCTTAAATCAAATAAACAACATGTTCAGAACGCGA
A9,flatv-h5-b152,CTAATGAGTGAGCTACTTTCCAGTCGGGAAGGGCGAA
B9,flatv-h7-b160,AAACCGTCGCCCCCGATTTAGAGGCCCTAA
C9,flatv-h9-b160,AACATCGCATCTGGTCAGTTGGCTATACTT
D9,flatv-h11-b160,CTGAATAATGAAACAAACATCAATTTCAAA
E9,flatv-h13-b160,TATATTTTGTCCAGACGACGACAGATTAGTTGCTATTT
A10,flatv-h9-b176,ATACCGAACGGAACCCTAAAGGGATATCAGGG
B10,flatv-h11-b176,TTAGAACCCAAACCCTCAATCAATCATTAAAA
C10,flatv-h13-b176,TCATCTTCGAGCAAAAGAAGATGATGGAAGGG
D10,flatv-h15-b168,TGCACCCAGCTACAATAAGGTAAAGTAATTCTAGTTAATT
E10,flatv-h7-b184,CACTACGTGAACCATCCCGTAAAGCACTAAATCGAACCAC
F10,flatv-h9-b192,CAGCAGAAGCTGAACCTCAAATATTACCATAT
G10,flatv-h11-b192,CAAAATTATTCATTTCAATTACCTTGACCTAA
H10,flatv-h13-b192,ATTTAATGTATAAAGTACCGACAATTTATCCTGAATCTTA
A11,flatv-h11-b208,GTAAAACACTAAAGCATCACCTTGATAAAA
B11,flatv-h13-b208,ATACCGACCGCAGAGGCGAATTATTTGCAC
C11,flatv-h15-b200,CCAACGCTAACGAGCCCAGTAATAAGAGAAGTTTGAA
D11,flatv-h9-b216,AGGCGGTCAGTATTAAGCAGCAAATGAAAAATGAAATAAA
E11,flatv-h11-b224,GAAATTGCCCAAGTTACAAAATCGCGTGTGAT
F11,flatv-h13-b224,AAATAAGGCAGAGGCATTTTCGAGGTCTTTCCAGAGCCTA
G11,flatv-h13-b240,AAGAATAACTGATTGCTTTGAATAGTAGATTT
H11,flatv-h15-b232,ATTTGCCAGTTACAAACAACATGTAATTTAGGCGTTAAAT
A12,flatv-h11-b248,AACGTCAGATGAATACAATAACGGATTCGCACACCGG
B12,flatv-h13-b256,AATCATAACATATTTAACAACGCATAAACAGCCATATT
C12,flatv-h15-b264,ATTTATCCCAATCCAACTTAATTGAGAATCGCTTACTAGA
D12,flatv-h13-b280,GTTTAGTATCATATGCACGCTCAACAGTAGGGATAAGAAA
plate flat-v-bottom-core (arm 2)
A1,flatv-h16-b39,ATACATAAAGGTGGCATAAGTTTATTTTGTCAGAATTTAC
B1,flatv-h18-b31,CGTTCCAGAGTGTACTGGTAATAAGTGAGAAT
C1,flatv-h20-b31,AGAAAGGACACGTTGAAAATCTCCCCTGCTCC
D1,flatv-h22-b31,ATGTTACTAGGGAACCGAACTGACATACCACA
E1,flatv-h24-b31,TTCAACTAGGCATAGTAAGAGCAAAATTCGAG
F1,flatv-h26-b31,CTTCAAAGAGGATTAGAGAGTACCAAAGGTGG
G1,flatv-h28-b31,CATCAATTATCATACAGGCAAGGCGTGTAGGT
H1,flatv-h30-b31,AAAGATTCCACCATCAATATGATATTCAACCGTTCTAGCCAATGCCT
A2,flatv-h18-b47,AGTCTCTCAATCAATAGAAAATAAACGTAGAAAATAC
B2,flatv-h20-b47,CAGCGGAGTTTTAACGGGGTCAGAAAGCGC
C2,flatv-h22-b47,TCCGCGAAAAAAAAAGGCTCCAAACAGTTT
D2,flatv-h24-b47,TTTAGGACAACTTTGAAAGAGGTGTCGAAA
E2,flatv-h26-b47,GCGTTTTCACTATCATAACCCTAGTTGAGA
F2,flatv-h28-b47,GAGCTGATTTAATTGCTCCTTTCAAATATC
G2,flatv-h30-b47,GAGTAATAAAGAATTAGCAAAATGGGGCGC
A3,flatv-h16-b71,TACGCAGTATGTTAGCTCATATGGTTTACCAGCATTAAAG
B3,flatv-h18-b63,CCAGAATGGTGCCTTGAGTAACAGTTGCTAAA
C3,flatv-h20-b63,CAACTTTCAAAGGAGCCTTTAATTATCGCCTG
D3,flatv-h22-b63,ATAAATTGACAGATGAACGGTGTAGGTAGAAA
E3,flatv-h24-b63,GATTCATCCGTTTACCAGACGACGGAAGCCCG
F3,flatv-h26-b63,AAAGACTTTGATAAGAGGTCATTTTAGCTATA
G3,flatv-h28-b63,TTTTCATTTTAAGCAATAAAGCCTTCATATAT
H3,flatv-h30-b63,TTTAAATGTGATAAATTAATGCCGGAGAGGGTGTCATTGCAAAATTTT
A4,flatv-h18-b79,TAAATCCTCGCCAAAGGAGGGAGGGATTAAGACTCCTTAT
B4,flatv-h20-b79,ATGGGATTTGCCCGTATTTCGGAACAAACAAA
C4,flatv-h22-b79,TTTGTATCGTATCGGTTACCGATATTTTCTGT
D4,flatv-h24-b79,TTATTACACAGACCAGTAGGCTGGAACGGAGA
E4,flatv-h26-b79,ATTAAGAGATAAAAACTTTTGCAAGAACAACA
F4,flatv-h28-b79,AACCTGTTTTGCGGATTAATGCTGTCAAAAAG
G4,flatv-h30-b79,TAGAACCCCAGAGCATCGGTTGTATGGTCAAT
A5,flatv-h16-b103,CAAAAGAACTGGCATGAAGGTAAATATTGATGGCCTTG
B5,flatv-h18-b95,ATATTCACCTATTATTCTGAAAACGTTAGT
C5,flatv-h20-b95,AAATGAAGTTGCGCCGACAATGCGCGAAAC
D5,flatv-h22-b95,AAAGTACCTGACCTTCATCAAGTAAAACGA
E5,flatv-h24-b95,ACTAACGAAGAAGTTTTGCCAGGCAAAGCG
F5,flatv-h26-b95,GATTGCATAGCTCAACATGTTTGATACATT
A6,flatv-h18-b111,CAGACGATCGGAAATTATTCATTAATAATAACGGAATACC
B6,flatv-h20-b111,CTTTCCAGCATGAAAGTATTAAGAAGGCAGGT
C6,flatv-h22-b111,ATACCAAGACAACAACCATCGCCCTTTGTCGT
D6,flatv-h24-b111,TACGTTAAAGTAATCTTGACAAGACAGCGATT
E6,flatv-h26-b111,AGTCAGAAAGGGGGTAATAGTAAAGAAAAATC
F6,flatv-h28-b111,GACCATTATAAATATGCAACTAAAACTATTAT
A7,flatv-h16-b135,AAACCGAGGAAACGCAAAGGTGAATTATCACCCATTGACA
B7,flatv-h18-b127,GGAGGTTGGGCTGAGACTCCTCAACGTAACGA
C7,flatv-h20-b127,TCTAAAGTACGCATAACCGATATAACTCATCT
D7,flatv-h22-b127,TTGACCCCACCGGATATTCATTACGTCAGGAC
E7,flatv-h24-b127,GTTGGGAAATGTTTAGACTGGATATCAGGTCT
F7,flatv-h26-b127,TTACCCTGGTACGGTGTCTGGAAGTCTGCGAACGAGTAGA
A8,flatv-h18-b143,CCGCCAGGTCACCGACTTGAGCAAAGTTACCAGAAGG
B8,flatv-h20-b143,TAGTTAGGAGAAGGATTAGGATCAGAGCCG
C8,flatv-h22-b143,CTAAAACTTCGGTCGCTGAGGCAGCCCTCA
D8,flatv-h24-b143,TATACCACCAAATCAACGTAACAGAATACA
E8,flatv-h26-b143,TCAAAAAGCGTCCAATACTGCGTGGCTCAT
A9,flatv-h16-b167,AAGCAGATAGCCGAACCATTTGGGAATTAGAGCCACCAGA
B9,flatv-h18-b159,ACCACCACTAGCGGGGTTTTGCTCGTAGCATT
C9,flatv-h20-b159,CCACAGACTTGCAGGGAGTTAAAGAAACGAAA
D9,flatv-h22-b159,GAGGCAAAAAAGCTGCTCATTCAGATGCGATT
E9,flatv-h24-b159,TTAAGAACGAATCGTCATAAATATTCAGAAAACGAGAATG
A10,flatv-h18-b175,CAGAGCCGCCAGCAAAATCACCAGCCTTTTTAAGAAAAGT
B10,flatv-h20-b175,CAACGCCTAGTACCAGGCGGATAAACCACCCT
C10,flatv-h22-b175,CCAACCTAGCCGCTTTTGCGGGATACAAACTA
D10,flatv-h24-b175,ATTACCTTTGAATAAGGCTTGCCCCGAAGGCA
E10,flatv-h16-b199,CTATCTTACCGAAGCTAGCACCATTACCATGCCACCCT
F10,flatv-h18-b191,CAGAGCCGTGCCGTCGAGAGGGAGTTTCGT
G10,flatv-h20-b191,CACCAGTCGTCACCCTCAGCAGTACGTAAT
H10,flatv-h22-b191,GCCACTATGACGAGAAACACCAAATTTCAACTTTAAT
A11,flatv-h18-b207,TCAGAACCTAGCAAGGCCGGAAACAATGAAATAGCAATAG
B11,flatv-h20-b207,TAACACTGTTGATATAAGTATAGCCGCCACCC
C11,flatv-h22-b207,GGGTAAAACGAAAGACAGCATCGGATGTACCG
D11,flatv-h16-b231,AATAAGAGCAAGAAACGTCACCAATGAAACCACCGCCTCC
E11,flatv-h18-b223,CTCAGAGCCCGGAATAGGTGTATCAGCCCAAT
F11,flatv-h20-b223,AGGAACCCAACGAGGGTAGCAACGTTCATGAGGAAGTTTC
G11,flatv-h18-b239,ACCGGAATCGATAGCAGCACCGTGAGTTAAGCCCAAT
H11,flatv-h20-b239,GATAGCAACCGTACTCAGGAGGGAGCCACC
A12,flatv-h16-b263,GATAACCCACAAGAATTAATCAGTAGCGACAGAAAATCAC
B12,flatv-h18-b255,CGGAACCATTTAGTACCGCCACCCAGAGCCACCACCCTCA
C12,flatv-h18-b271,TCATAATCAATCAAGTTTGCCTTTGCGCTAATATCAGAGA
D12,flatv-h16-b287,TAATTGAAGCGTCAGACTGTAGCCTTATTAGCGTTTG
!"
DOI: 10.1038/NCHEM.1070

edge staples
arm 1
arm 2
arm 1
arm 2
plate flat-v-edges-bridges
A1,flatv-h1-b8-II,CAAATATTTAAATTGGGAAGATTGTATAAG
B1,flatv-h3-b8-II,CATCGTAACCGTGCATGGTGTAGATGGGCG
C1,flatv-h5-b8-II,CAGGTCGACTCTAGAAAGCTTGCATGCCTG
D1,flatv-h7-b8-II,CAGGCGAAAATCCTGGCTGGTTTGCCCCAG
E1,flatv-h9-b8-II,CAGATTCACCAGTCAGATTATTTACATTGG
F1,flatv-h11-b8-II,CCCGAACGTTATTAAGTATTAAATCCTTTG
G1,flatv-h13-b8-II,CTGAGAAGAGTCAATGCTTAGATTAAGACG
H1,flatv-h15-b8-II,CCGTTTTTATTTTCATCGAGAACAAGCAAG
A2,flatv-h17-b8-II,CAAAGACACCACGGAAACATATAAAAGAAACG
B2,flatv-h19-b8-II,CTTTTGATGATACAGGTAAGCGTCATACATGG
C2,flatv-h21-b8-II,CGAATAATAATTTTTTACAACTAAAGGAATTG
D2,flatv-h23-b8-II,CAGACGGTCAATCATATAGCCGGAACGAGGCG
E2,Flatv-h25-b8-II,CCAAAAGGAATTACGAATGCAGATACATAACG
F2,flatv-h27-b8-II,CAAACTCCAACAGGTCCGAACCAGACCGGAAG
G2,flatv-h29-b8-II,CATTAACATCCAATAACTACTAATAGTAGTAG
H2,flatv-h31-b8-II,CCGGAGACAGTCAAATAAAAGGGTGAGAAAGG
plate flat-v-edges-bridges
A5,flatv-h0-b92,CGGTAAATAGGAACGCCATCACAGCTTTCATCAACATCCGGCACC
B5,flatv-h3-b112,AACCAGGCTGGCCTTCCTGTAGCAAAAT
C5,flatv-h5-b144,TGGGGTGCGTTGGGAAGGGCGATCTTCAG
D5,flatv-h7-b176,CGATGGCCTTGCGCTCACTGCCCGACTCA
E5,flatv-h9-b208,CAGAGGTGTTTGGGGTCGAGGTGACCCA
F5,flatv-h11-b240,TCAGGTTTGCCACGCTGAGAGCCACACCG
G5,flatv-h13-b272,AAAAGCCTTTTACATCGGGAGAAATACAG
H5,flatv-h15-b288,CGATTTTTTGTTTAACGTCAAAAACCAGTATAAAGCCAGTTAT
A6,flatv-h18-b300,AGCCCCGCGTTTTCATCGGCAAACACCCTGAACAAAGTCAGAGGG
B6,flatv-h20-b268,CCCTCTCAGAACCGCCACCCTCCATCTTT
C6,flatv-h22-b236,ACTTTGCTACAGAGGCTTTGTTTTCAGG
D6,flatv-h24-b204,GGTTTGAACGAGTAGTAAATTCATTAAAC
E6,flatv-h26-b172,ACAGTTCATTGAATCCCCCTCCATTGTGA
F6,flatv-h28-b140,CCAATTTTCATTCCATATAAACCATAAA
G6,flatv-h30-b108,TTTATCCCTGTAATACTTTTGTTTAGTTT
H6,flatv-h28-b95,TCGCAAACCAAAAACATTATGATTCAACGCAAGGATACTGAG
A7,flatv-h31-b93,AGTCTGGAGCGAATCGATGAA
B7,flatv-h1-b109,AATTCGCGTCCGGGAGAAGCC
C7,flatv-h3-b141,GCTGCGCAACTCAGTTGATTC
D7,flatv-h5-b173,CATTAATTGCGAAATGCTTTAA
E7,flatv-h7-b205,AATCAAGTTTGGGCTTGAGAT
F7,flatv-h9-b237,CCTGCAACAGTAGGACTAAAG
G7,flatv-h11-b269,TAACAGTACCTCAGAACCGCCA
H7,flatv-h13-b301,ACAAATTCTTTTTTCGGTCAT
A8,flatv-h15-b333,GAGAGAATAACAGGGAAGCGC
B8,flatv-h15-b312,ATGAAAATAGCAGCCTTTACA
C8,flatv-h16-b332,ATTAGACGGGAGAATTAACTG
bridge !"#$%&!
bridges
strands at corner
strands adjacent to bridges
!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for 60 corner or|gam| w|th stra|ght edges
1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
2
3
3
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
2
3
3
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
8
25 24 41 5 16 24 10 33
8
15 8 32 13 28 46 1
C
G
T
T
T
C
T
T
T
T
A
T
A
T
G
T
T
G
C
C
A
C
C
T
T
T
A
T
G
T
A
T
G
T
A
T
T
T
T

C
T
A
C
G
T
T
T
G
C
T
A
A
C
A
T
A
C
T
G
C
G
T
A
A
T
A
A
G
G
A
G
T
C
T
T
A
A
T
C
A
T
G
C
C
A
G

T
T
C
T
T
T
T
G
G
G
T
A
T
T
C
C
G
T
T
A
T
T
A
T
T
G
C
G
T
T
T
C
C
T
C
G
G
T
T
T
C
C
T
T
C
T
G

G
T
A
A
C
T
T
T
G
T
T
C
G
G
C
T
A
T
C
T
G
C
T
T
A
C
T
T
T
T
C
T
T
A
A
A
A
A
G
G
G
C
T
T
C
G
G

T
A
A
G
A
T
A
G
C
T
A
T
T
G
C
T
A
T
T
T
C
A
T
T
G
T
T
T
C
T
T
G
C
T
C
T
T
A
T
T
A
T
T
G
G
G
C

T
T
A
A
C
T
C
A
A
T
T
C
T
T
G
T
G
G
G
T
T
A
T
C
T
C
T
C
T
G
A
T
A
T
T
A
G
C
G
C
T
C
A
A
T
T
A

C
C
C
T
C
T
G
A
C
T
T
T
G
T
T
C
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A
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A
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G
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C
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A
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T
A
A
G
A
A
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C
G
A
T
T
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G
T
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T
A
A
C
G
T
C
A
A
A
A
A
T
G
A
A
A
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T
A
G
C
A
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T
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A
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G
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A
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A
A
C
!!
DOI: 10.1038/NCHEM.1070
SS.9. 60 corner or|gam| w|th e!g"#$%&'"$

plate shape-U-top-core (arm 1)
A1, h1-b64,CGAACTGAGTGAATTACCTTATGCAGGACGTTGGGAAGAA
B1, h13-b64,TGCCAGCTCTTGCCTGAGTAGAAGCCAGAACAATATTACC
C1, h1-b80,GAAAGAGGTGTCGAAATCCGCGACCTGCTCCATGTTACTTAAGGGAAC
D1, h15-b72,GCCAGCCATTGCAACAATTAGTAATAACATCAGCATTAAT
A2, h1-b96,AACGGTGTTTGAGATGGTTTAATAACGAAC
B2, h3-b96,TAACGGAATCATAAATATTCATTAAACGAG
C2, h5-b96,AATGACCACATTCCATATAACAGGTTTGAC
D2, h7-b96,CATTAGATTGTAGGTAAAGATTCCACCATC
E2, h9-b96,AATATGATAACCCGTCGGATTCTGGATAGG
F2, h11-b96,TCACGTTGTAAAGCCTGGGGTGCCAACGCG
G2, h13-b96,CGGGGAGAAGCAATACTTCTTTGGGAAAAACGCTCATG
A3, h1-b112,GGCGCATAACGGAGATTTGTATCATCGCCTGATAAATTGACAGATG
B3, h3-b112,TTACAGGTCGTAACAAAATTGGGCACAGACCA
C3, h5-b112,AAATCAGGAAAACCAACGGAATCGCAACATTA
D3, h7-b112,CAAATGGTGGATGGCTGGAAGTTTTAAATCAA
E3, h9-b112,GTTCTAGCTTTAAATGGAGTAATGACATTTCG
F3, h11-b112,GGGCGCATATCAACATCGAGTAACATTCAACC
G3, h13-b112,GCGTATTGCAATTCCAATAAAGTGGTGTAGAT
H3, h15-b104,GAAATACCATTTTGACCTAGGGCGACCGTTGTGGCGGTTT
A4, h3-b128,TCATCAGTTTACCAGACGACGATATCTTTACC
B4, h5-b128,CTGACTATAAGAGGTCATTTTTGCCAATAACC
C4, h7-b128,TGTTTAGCTAGAACCCTCATATATTGATAAAT
D4, h9-b128,TAATGCCGCCTGTAGCCAGCTTTCCGTAACCG
E4, h11-b128,TGCATCTGAATTGTTATCCGCTCAGGCGCCAG
F4, h13-b128,GGTGGTTTGCGAAAGGAGCGGGCGGCTCAATCGTCTGAAA
A5, h5-b144,AGAAGCAATATCATAACCCTCGTTGAGATT
B5, h7-b144,TCATTTGGATTGCTCCTTTTGATTATAGTC
C5, h9-b144,TAGCTATTAAGGATAAAAATTTTTATATTT
D5, h11-b144,GAGGGGACTTCGCGTCTGGCCTTGAGAGGG
E5, h13-b144,CACCAGTGCTGTTTCCTGTGTGACCAGTTT
F5, h15-b136,TGGATTATTTACATTAAGGAAGGGAAGAAATTCTTTT
A6, h3-b152,CCACATTCAACTAATGATAGTAAGAGCAACACAGCGGATT
B6, h5-b160,GCATCAAATTAGAGAGTACCTTTAGGCGCGAG
C6, h7-b160,CTGAAAAGGCCTTTATTTCAACGCTTTGAGAG
D6, h9-b160,ATCTACAAACGCCATCAAAAATAAGACGACAG
E6, h11-b160,TATCGGCCGTAATCATGGTCATAGAGACGGGC
F6, h13-b160,AACAGCTGGGCGAACGTGGCGAGAGGCAGATTCACCAGTC
A7, h7-b176,AATTCTACCTCCAACAGGTCAGGAAAGATTAA
B7, h9-b176,AGGTCATTTACTTTTGCGGGAGAAGTGGCATC
C7, h11-b176,ATCGCACTTTTTTAACCAATAGGAAGGCTATC
D7, h13-b176,TCACCGCCTACCGAGCTCGAATTCTCAGGAAG
E7, h15-b168,ACACGACCAGTAATAACTTGACGGGGAAAGCCATTGCCCT
A8, h5-b184,CCGAAAGACTTCAAACAGACCGGAAGCAAATAATAGT
B8, h7-b192,AGTAGCATATTATGACCCTGTAAGCCTGAG
C8, h9-b192,AGTCTGGAGTTAAATCAGCTCATCCAGCCA
D8, h11-b192,GCTTTCCGTAGAGGATCCCCGGGTGGCCCT
E8, h13-b192,GAGAGAGTGCCCCCGATTTAGAGAAGGGACATTCTGGC
A9, h9-b208,GAGAATCGCGGTTGTACCAAAAACTAACATCC
B9, h11-b208,TCTGGTGCTTCGCATTAAATTTTTGCAAACAA
C9, h13-b208,GCGGTCCAGCCTGCAGGTCGACTCGCACCGCT
D9, h15-b200,CAACAGAGATAGAACCCGGAACCCTAAAGGGATGCAGCAA
E9, h7-b216,ATACAGGCAAGGCAAAGAGCATAAAGCTAAATATGAACGG
F9, h9-b224,TAATCGTATAATATTTTGTTAAAACGGAAACC
G9, h11-b224,AGGCAAAGAGTGCCAAGCTTGCATCGCTGGTT
H9, h13-b224,TGCCCCAGCCGTAAAGCACTAAATCTTCTGACCTGAAAGC
A10, h11-b240,CGCCATTCTTAAATTGTAAACGTAAACTAG
B10, h13-b240,AAATCCTGTGTAAAACGACGGCCCGCCATT
C10, h15-b232,GTAAGAATACGTGGCTTTGGGGTCGAGGTGCAGGCGA
D10, h9-b248,TCATATGTACCCCGGTTTGTATAAGCAAATATAGGCTGCG
E10, h11-b256,CAACTGTTTTCCCAGTCACGACGTTTTGATGG
F10, h13-b256,TGGTTCCGCACCCAAATCAAGTTTACAGACAATATTTTTG
G10, h13-b272,AAAATCCCGGGTAACGCCAGGGTTGGGAAGGG
H10, h15-b264,AATGGCTATTAGTCTTCCACTACGTGAACCATAAATCGGC
A11, h11-b280,GCGGGCCTCTTCGCTCAAGGCGATTAAGTTTTATAAA
B11, h13-b288,TCAAAAGATATCAGGGCGATGGCTAATGCGCGAACTGA
C11, h15-b296,TAGCCCTAAAACATCGAGGGCGAAAAACCGTCATAGCCCG
D11, h13-b312,TTGAGTGTTGTTCCAGTGGACTCCAACGTCAACCATTAAA
plate bottom-core (arm 2)
A1, h20-b39,CGAACCTCCCGACTTGTTGCTATTTTGCACTACATAAA
B1, h22-b31,GGTGGCATAAGTTTATTTTGTCCCACCAGA
C1, h24-b31,ACCACCAAGGCAGGTCAGACGAAGGAGGTT
D1, h24-b47,CAGAGCCGACAATCAATAGAAAATAAACGTAG
E1, h26-b47,CCGTACTCTTGGCCTTGATATTCAACCACCCT
A2, h16-b71,ATTTTGCGGAACAAAGTTCCTGATTATCAGATCTGATGCA
B2, h18-b63,AATCCAATAATATATTTTAGTTAAATCCGGTA
C2, h20-b63,TTCTAAGACCTGAATCTTACCAACTACGCAGT
D2, h22-b63,ATGTTAGCTCATATGGTTTACCAGCGCCACCC
E2, h24-b63,TCAGAGCCCAAACAAATAAATCCTGTATAGCC
F2, h26-b63,CGGAATAGGATAGCAAGCCCAATATTTTTTCA
G2, h28-b63,CGTTGAAATAATTGTATCGGTTTACATCGGAA
H2, h30-b63,CGAGGGTACTTTTTCATGAGGAAGTTTCCATTAAACGGGAGCAGCGA
A3, h18-b79,GTAAATGGATGGCAATTCATCATTGAGTAACATTATC
B3, h20-b79,AAGGCTTTTTCATCTTCTGACCAACTATAT
C3, h22-b79,TCCTTATGCTAACGAGCGTCTTAGATATAG
D3, h24-b79,TCAGAACCGCCAAAGACAAAAGATTAAGAC
E3, h26-b79,GATATAACATTAAAGCCAGAATCGCCACCC
F3, h28-b79,ATAATAAGGAACCCATGTACCGAGAGGGTT
G3, h30-b79,AAGACAGTCAGCTTGCTTTCGAAATTGCGA
A4, h16-b103,TATTAATTTTAAAAGTATATAATCCTGATTGTTTAGGTTG
B4, h18-b95,GGTTATATTAAATTTAATGGTTTGCAATAGCA
C4, h20-b95,AGCAAATCTCCAGAGCCTAATTTGCAAAAGAA
D4, h22-b95,CTGGCATGGGCGACATTCAACCGACCGCCTCC
E4, h24-b95,CTCAGAGCGGAAAGCGCAGTCTCTCGGATAAG
F4, h26-b95,TGCCGTCGTAACACTGAGTTTCGTAAGGAACA
G4, h28-b95,ACTAAAGGGGTGAATTTCTTAAACCGGGATCG
H4, h30-b95,TCACCCTCTAAAATACGTAATGCCACTACGAACTCATCTTTTAAAGGC
A5, h18-b111,CCTCCGGCTTGGATTATAGAACCTTCCTTTGCCCGAACGT
B5, h20-b111,ACCGCGCCAAATACCGTATGCGTTCTTTTTAA
C5, h22-b111,GGAATACCCCAGTTACTAAACAGCGAATCATT
D5, h24-b111,CACCGGAATTGAGGGAATTCATTAATAATAAC
E5, h26-b111,GTACCAGGGAATTTACTTCCAGTAAGAGCCAC
F5, h28-b111,AGAATAGACACCAGTAACTACAACTTTGCTCA
G5, h30-b111,CGCTTTTGAGCTTGATTGCGCCGAGCGGAGTG
A6, h16-b135,ACAACTCGTATTAAAACCATATCAAAATTAGGTCTGAG
B6, h18-b127,AGACTACATACAAATTCTTACCTTATTTTC
C6, h20-b127,ATCGTAGCATATTATTTATCCCAACCGAGG
D6, h22-b127,AAACGCAAAGGTGAATTATCACAAAATCAC
E6, h24-b127,CGGAACCAGCGTCATACATGGCTAGGATTA
F6, h26-b127,GCGGGGTGCCTGTAGCATTCCACTTTCAAC
A7, h18-b143,AAATCATATTTGCACGTAAAACAGCTTTACAAACAATTCG
B7, h20-b143,AGCCGTTTAGTATAAAGCCAACGCATTTATCA
C7, h22-b143,CAGAAGGAAATCCAAATAAGAAACAACAAGCA
D7, h24-b143,TCATAATCCGTCACCGACTTGAGCAAAGTTAC
E7, h26-b143,AGAAGGATTTTTGATGATACAGGACCATCTTT
F7, h28-b143,CTAAACAACAGACAGCCCTCATAGTCCTCAAG
A8, h16-b167,ATTTAGAAGTATTAGAAAATAAAGAAATTGCGGAAGAGTC
B8, h18-b159,AATAGTGATCAACAGTAGGGCTTATACCGCAC
C8, h20-b159,TCATCGAGGATTTTTTGTTTAACGAAGCAGAT
D8, h22-b159,AGCCGAACCATTTGGGAATTAGAGCCCTTATT
E8, h24-b159,AGCGTTTGGTGTACTGGTAATAAGATTAAGAG
F8, h26-b159,GCTGAGACTTAGCGTAACGATCTAATGAATTTTCTGTATG
A9, h18-b175,ACGCTGATAGATTTTCAGGTTTATAATACATTTGAGG
B9, h20-b175,AACCAAGATTGAGAATCGCCATAGATTAAG
C9, h22-b175,GAAAAGTTCAAAAATGAAAATAGGGTATTA
D9, h24-b175,CATAGCCCCAGCAAAATCACCACTTTTTAA
E9, h26-b175,TGAAAGTTTTTAACGGGGTCAGTTTTCGGT
G9, h16-b295,CTCAATCAATATCTGGCGCAGAGGCGAATTATTAATGGAA
H9, h18-b287,ACAGTACACAGACGACGACAATAATTTATCAACAATAGAT
A10, h16-b199,TTAGAGCCGTCAATAGAACGTCAGATGAATATAACATAGC
B10, h18-b191,GATAGCTTATTTAACAACGCCAACTTATCATT
C10, h20-b191,CCAAGAACGCAGCCTTTACAGAGACTATCTTA
D10, h22-b191,CCGAAGCCGTAGCACCATTACCATCGCGTTTT
E10, h24-b191,CATCGGCATGCCTTGAGTAACAGTTTCGGAACCTATTATT
G10, h18-b303,ACCTTTTTTCATTTCAATTACCTGCCTCAAATATCAAACC
H10, h16-b319,TGCTGAAAGCAAAAGAAGATGACATTTAACAATTTCA
A11, h18-b207,TCCTTGAAACAGTAACAGTACCTTACTAACAACTAATAGA
B11, h20-b207,GTCTTTCCATGTAATTTAGGCAGACCTTAGAA
C11, h22-b207,AGCAATAGGAATAACATAAAAACAAATCGGCT
D11, h24-b207,GACTGTAGTAGCAAGGCCGGAAACAATGAAAT
E11, h16-b231,AATATCTTTAGGAGCTTACATCGGGAGAAATATTAATT
F11, h18-b223,AATTTTCGGCATTTTCGAGCCATAGAAACC
G11, h20-b223,AATCAATGGGAAGCGCATTAGAATAAGAGC
H11, h22-b223,AAGAAACGTCACCAATGAAACCAATCAAGTTTGCCTT
A12, h18-b239,ATCGTCGCCAATAACGGATTCGCCGAGGAAGGTTATCTAA
B12, h20-b239,CGAGCATGGTAATAAGAGAATATATTCTGTAA
C12, h22-b239,GCCCAATACGGGAGAATTAACTGACTAATTTA
D12, h16-b263,ACAGTTGAAAGGAATTTGATTGCTTTGAATACGAGTGAAT
E12, h18-b255,AACCTTGCAAGTACCGACAAAAGGAAAATAAT
F12, h20-b255,ATCCCATCACACCCTGAACAAAGTGATAACCCACAAGAAT
G12, h18-b271,TATATGTCAAGTTACAAAATCGTCAGTTGGCAAATCA
H12, h20-b271,AACAAGATAAAGTAATTCTGTCTAAATCAA
arm 1
core
arm 2
core
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
shapeU-
!"
DOI: 10.1038/NCHEM.1070

plate shape-U-edges
A1,shapeU-h1-b40-II,CAGACGGTCAATCATAGCCGGAACGAGGCG
B1,shapeU-h3-b40-II,CTCATTATACCAGTCGATTTTAAGAACTGG
C1,shapeU-h3-b72-II,AAATCTACGTTAATAATTCAACTTTAATCATTCCAACTTT
D1,shapeU-h5-b72-II,CTTTAAACAGTTCAGAGAATCCCCCTCAAATG
E1,shapeU-h7-b72-II,CGAACGAGTAGATTTATTGATTCCCAATTCTG
F1,shapeU-h9-b72-II,CCGGAGACAGTCAAATAAAAGGGTGAGAAAGG
G1,shapeU-h11-b72-II,CGGATTGACCGTAATGCCGTGGGAACAAACGG
H1,shapeU-h13-b80-II,GAATCGGCCTAATGAGTGAGCTAACTCACATTAATTGCGTACCTGTCG
A2,shapeU-h13-b40-II,CTTTCCAGTCGGGAATGCGCTCACTGCCCG
B2,shapeU-h15-b40-II,CCTTGCTGGTAATATAACTCAAACTATCGG
A3,shapeU-h17-b40-II,CGGAATTATCATCATAAAACCACCAGAAGGAG
B3,shapeU-h19-b40-II,CGAGAAAACTTTTTCACGCAAGACAAAGAACG
C3,shapeU-h22-b47-II,AAAATACACCAGCTACAATTTTATACGCGAGGCGTTTTAG
D3,shapeU-h21-b8-II,CCTTAAATCAAGATTAGCGGGAGGTTTTGAAG
E3,shapeU-h23-b8-II,CAAAGACACCACGGAAACATATAAAAGAAACG
F3,shapeU-h25-b8-II,CATTGACAGGAGGTTGCCAGAGCCGCCGCCAG
G3,shapeU-h27-b8-II,CCACCCTCAGAACCGCGCCACCCTCAGAACCG
H3,shapeU-h26-b31-II,TAGTACCCACCCTCAGAGCCACCACCCTCATTTTCAGGGTGTATCA
A4,shapeU-h29-b40-II,CTCCAAAAGGAGCCTTATCTCCAAAAAAAAGG
B4,shapeU-h31-b40-II,CTTTGAGGACTAAAGAGCAACGGCTACAGAGG
edge!"#$%&'"
bridge!"#$%&'!
arm 1
arm 2
arm 1
arm 2
plate shape-U-bridges
A1,shapeU-h0-b124,GTACAGGCTGGCTGACCTTCATCATTACCCAAATCAAAGAAAGAT
B1,shapeU-h3-b144,TAGGAATAACAAGAACCGGATATTCAAG
C1,shapeU-h5-b176,GAGGAAGCAAAGGAATTACGAGGCCAGAT
D1,shapeU-h7-b208,AATAAATCGAGCTTCAAAGCGAACTATCG
E1,shapeU-h9-b240,CATGTCAAAGCAATAAAGCCTCAGAATT
F1,shapeU-h11-b272,CGATCGGTCCCAAAAACAGGAAGATGATA
G1,shapeU-h13-b304,AGATAGGGAAAGGGGGATGTGCTGATTAC
H1,shapeU-h15-b320,AATACCGAACGAACCACCAGCAGCACTATTAAAGAACGTTTGG
A2,shapeU-h18-b332,AATTATGAAACAAACATCAAGAATGAAAAATCTAAAGCATCACCT
B2,shapeU-h20-b300,GCCTGACAACATGTTCAGCTATTTGAATT
C2,shapeU-h22-b268,AGAGACAGAGGGTAATTGAGAAGTCCTG
D2,shapeU-h24-b236,GACAGATCGATAGCAGCACCGTGAGTTAA
E2,shapeU-h26-b204,CCTATGCCCGTATAAACAGTTTAGCGTCA
F2,shapeU-h28-b172,AGTAAAAGTTTTGTCGTCTTCTGAAACA
G2,shapeU-h30-b140,TCGCTTCGCCCACGCATAACCGGATTTTG
H2,shapeU-h28-b127,AGTTTCACAATGACAACAACCAGAGGCTTGCAGGGAGTGACC
A3,shapeU-h31-b125,CCCAGCGATTCGCGAAACAAA
B3,shapeU-h1-b141,AGTAATCTTGGATATATTCGG
C3,shapeU-h3-b173,ACATAACGCCATCCAGACGTT
D3,shapeU-h5-b205,CGTTTTAATTCAATGCCCCCTG
E3,shapeU-h7-b237,AGCAAAATTATAATCAGTAGC
F3,shapeU-h9-b269,ATCAGAAAAGCCGCTAATATC
G3,shapeU-h11-b301,GCCAGCTGGCGATGCAGAACGC
H3,shapeU-h13-b333,AACAAGAGTCAAAACAAAATT
A4,shapeU-h15-b365,GGTCAGTATTATGCAACAGTG
B4,shapeU-h15-b344,AAGATAAAACAGAGGTGAGGC
C4,shapeU-h16-b364,CCACGCTGAGAGCCAGCAGCA
bridges
strands at corner
!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for 60 corner or|gam| w|th e!"#$%&'(#%

1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
2
3
3
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
2
3
3
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
8
22 76 4 25 2 3 9 44
8
57 81 70 8 10 21 3
C
T
C
C
T
T
C
T
G
G
T
G
G
T
T
T
C
T
T
T
G
T
T
C
C
G
C
A
A
A
A
T
G
A
T
A
A
T
G

T
T
A
C
T
C
A
A
A
C
T
T
T
T
A
A
A
A
T
T
A
A
T
A
A
C
G
T
T
C
G
G
G
C
A
A
A
G
G
A
T
T
T
A
A
T
A

C
G
A
G
T
T
G
T
C
G
A
A
T
T
G
T
T
T
G
T
A
A
A
G
T
C
T
A
A
T
A
C
T
T
C
T
A
A
A
T
C
C
T
C
A
A
A

T
G
T
A
T
T
A
T
C
T
A
T
T
G
A
C
G
G
C
T
C
T
A
A
T
C
T
A
T
T
A
G
T
T
G
T
T
A
G
T
G
C
T
C
C
T
A

A
A
G
A
T
A
T
T
T
T
A
G
A
T
A
A
C
C
T
T
C
C
T
C
A
A
T
T
C
C
T
T
T
C
A
A
C
T
G
T
T
G
A
T
T
T
G

C
C
A
A
C
T
G
A
C
C
A
G
A
T
A
T
T
G
A
T
T
G
A
G
G
G
T
T
T
G
A
T
A
T
T
T
G
A
G
G
T
T
C
A
G
C
A

A
G
G
T
G
A
T
G
C
T
T
T
A
G
A
T
T
T
T
T
C
A
T
T
T
G
C
T
G
C
T
G
G
C
T
C
T
C
A
G
C
G
T
G
G
C
A

C
T
G
T
T
G
C
A
C
T
T
G
A
T
G
T
T
T
G
T
T
T
C
A
T
C
A
T
C
T
T
C

T
T
T
T
G
C
T
C
A
G
G
T
A
A
T
T
G
A
A
A
T
G
A
A
T
A
A
T
T
C
G
C
C
T
C
T
G
C
G
C
G
A
T
T
T
T
G

T
A
A
C
T
T
G
G
T
A
T
T
C
A
A
A
G
C
A
A
T
C
A
G
G
C
G
A
A
T
C
C
G
T
T
A
T
T
G
T
T
T
C
T
C
C
C

G
A
T
G
T
A
A
A
A
G
G
T
A
C
T
G
T
T
A
C
T
G
T
A
T
A
T
T
C
A
T
C
T
G
A
C
G
T
T
A
A
A
C
C
T
G
A

A
A
A
T
C
T
A
C
G
C
A
A
T
T
T
C
T
T
T
A
T
T
T
C
T
G
T
T
T
T
A
C
G
T
G
C
A
A
A
T
A
A
T
T
T
T
G

A
T
A
T
G
G
T
A
G
G
T
T
C
T
A
T
A
A
T
C
C
A
A
A
C
A
A
T
C
A
G
G
A
T
T
A
T
A
T
T
G
A
T
G
A
A
T

T
G
C
C
A
T
C
A
T
C
T
G
A
T
A
A
T
C
A
G
G
A
A
T
A
T
G
A
T
G
A
T
A
A
T
T
C
C
G
C
G
T
T
C
T
T
T
G
T
C
T
T
G
C
G
A
T
T
G
G
A
T
T
T
G
C
A
T
C
A
G
C
A
T
T
T
A
C

A
T
A
T
A
G
T
T
A
T
A
T
A
A
C
C
C
A
A
C
C
T
A
A
G
C
C
G
G
A
G
G
T
T
A
A
A
A
A
G
G
T
A
G
T
C
T

C
T
C
A
G
A
C
C
T
A
T
G
A
T
T
T
T
G
A
T
A
A
A
T
T
C
A
C
T
A
T
T
G
A
C
T
C
T
T
C
T
C
A
G
C
G
T

C
T
T
A
A
T
C
T
A
A
G
C
T
A
T
C
G
C
T
A
T
G
T
T
T
T
C
A
A
G
G
A
T
T
C
T
A
A
G
G
G
A
A
A
A
T
T

A
A
T
T
A
A
T
A
G
C
G
A
C
G
A
T
T
T
A
C
A
G
A
A
G
C
A
A
G
G
T
T
A
T
T
C
A
C
T
C
A
C
A
T
A
T
A

T
T
G
A
T
T
T
A
T
G
T
A
C
T
G
T
T
T
C
C
A
T
T
A
A
A
A
A
A
G
G
T
A
A
T
T
C
A
A
A
T
G
A
A
A
T
T

G
T
T
A
A
A
T
G
T
A
A
T
T
A
A
T
T
T
T
G
T
T
T
T
T
A
G
C
T
G
A
A
C
A
T
G
T
T
G
T
T
T
A
T
T
G
T
C
G
T
C
G
T
C
T
G
G
A
C
A
G
A
A
T

T
A
C
T
T
T
A
C
C
T
T
T
T
G
T
C
G
G
T
A
C
T
T
T
A
T
A
T
T
C
T
C
T
T
A
T
T
A
C
T
G
G
C
T
C
G
A

A
A
A
T
G
C
C
T
C
T
G
C
C
T
A
A
A
T
T
A
C
A
T
G
T
T
G
G
C
G
T
T
G
T
T
A
A
A
T
A
T
G
G
C
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C
A
A
T
T
C
C
A
A
T
A
A
A
G
T
G
A
A
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G
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A
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C
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C
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A
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A
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A
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C
A
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A
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A
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A
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A
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A
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A
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C
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A
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A
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A
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C
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A
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A
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A
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C
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A
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A
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A
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A
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A
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A
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!"
DOI: 10.1038/NCHEM.1070
SS.10. 60 corner or|gam| w|th e!"#$%&'(#%$')!$*#+#*%#!$!"#$%&'($(,-'*./0

arm 1
core
arm 2
core
plate shape-flip-top-core (arm1)
A1, h1-b96,ATCATAAGCGAGAAACACCAGAACTTTCAACTTTAATCAT
B1, h13-b96,AGCTGTTTCGGAACCCTAAAGGGACGGCGAACGTGGCGAG
C1, h1-b112,ACTGACCAGCCTGATAAATTGTGTCGAAATCCGCGACCTGGACGGTCA
D1, h15-b104,AAAGGAAGGGAAGAAACCGTAAAGCACTAAATCCTGTGTG
A2, h1-b128,AAGAGGACCTGCTCATTCAGTGACGATTTT
B2, h3-b128,AAGAACTGGTTTACCAGACGACGAAGAAGT
C2, h5-b128,TTTGCCAGATTCGAGCTTCAAAGAGGATTA
D2, h7-b128,GAGAGTACAAATTAAGCAATAAAAAAAACA
E2, h9-b128,TTATGACCATTGTAAACGTTAATAATCAGC
F2, h11-b128,TCATTTTTCGACGGCCAGTGCCAATCCGCT
G2, h13-b128,CACAATTCTTTGGGGTCGAGGTGGCGAAAGGAGCGGGC
A3, h1-b144,GGTGTACAGCGCGAAAGTACAACGGAGATTTGTATCATCACTTTGA
B3, h3-b144,TACCAGTCTTACCCAATAACAAAGAGATGAAC
C3, h5-b144,ATAGTAAAAAAGGAATTAACCCTCGCTCATTA
D3, h7-b144,GCTCCTTTTCAAATATGCGTTTTAAGGGGGTA
E3, h9-b144,CTTTTGCGTAGTAGTAAATTAGCACTTTAATT
F3, h11-b144,AGGAACGCCAAAAACAATATTTAACTGTAATA
G3, h13-b144,ATACGAGCAGGGTTTTTTGTAAAATAACCAAT
H3, h15-b136,GCTAGGGCCGATTAAAACTACGTGTCAAGTTTCACACAAC
A4, h3-b160,GGGAAGAACAGATACATAACGCCAATGTTTAG
B4, h5-b160,ACTGGATAGGAAGCCCGAAAGACTTGATAAGA
C4, h7-b160,GGTCATTTGCATCAATTCTACTAAGGAGAAGC
D4, h9-b160,CTTTATTTATAATCAGAAAAGCCCCATCAAAA
E4, h11-b160,ATAATTCGTAAGTTGGGTAACGCCCGGAAGCA
F4, h13-b160,TAAAGTGTATCAGGGCGATGGCCCGGGATTTTAGACAGGA
A5, h5-b176,ATACTGCGCACATTCAACTAATGAAATCTA
B5, h7-b176,TGGCTTAGTCAAAAAGATTAAGAGCGTCCA
C5, h9-b176,AGGATAAACGAGCTGAAAAGGTGTTGCGGA
D5, h11-b176,CCTTCCTGTATGTACCCCGGTTGCAACGCA
E5, h13-b176,GGGGTGCCGTGCTGCAAGGCGATCGTCTGG
F5, h15-b168,ACGGTACGCCAGAATGGCGAAAAACCGTCTAAAGCCT
A6, h3-b184,AAACGAACTAACGGAATGAGATTTAGGAATACGAATCGTC
B6, h5-b192,ATAAATATAGCAAAGCGGATTGCAAGCTTAAT
C6, h7-b192,TGCTGAATATTTTCATTTGGGGCGAATTTTTA
D6, h9-b192,GAACCCTCACTAGCATGTCAATCATAGCCAGC
E6, h11-b192,TTTCATCACTGGCGAAAGGGGGATTAATGAGT
F6, h13-b192,GAGCTAACGACTCCAACGTCAAAGCCTGAGAAGTGTTTTT
A7, h7-b208,GTAGCTCAGACTATTATAGTCAGATCATTGAA
B7, h9-b208,TAAATGCATAACCTGTTTAGCTATATAATGCT
C7, h11-b208,TGTGAGCGGAACGGTAATCGTAAAATATATTT
D7, h13-b208,ATTGCGTTTTCGCTATTACGCCAGACATTAAA
E7, h15-b200,ATAATCAGTGAGGCCAACTATTAAAGAACGTGTCACATTA
A8, h5-b216,AAATGCTTTAAACAGTCAGGTCTTTACCCTACATGTT
B8, h7-b224,TTAAATATTTCGCAAATGGTCAAATGCCTG
C8, h9-b224,AGTAATGTAACAAGAGAATCGATAGTAACA
D8, h11-b224,ACCCGTCGATCGGTGCGGGCCTCGCGCTCA
E8, h13-b224,CTGCCCGCTTGGAACAAGAGTCCCCGAGTAAAAGAGTC
A9, h9-b240,AGATTCAATGACCATTAGATACATGCAACTAA
B9, h11-b240,GTGGGAACCTGAGAGTCTGGAGCAGTAGGTAA
C9, h13-b240,CGGGAAACACTGTTGGGAAGGGCGGATTCTCC
D9, h15-b232,TGTCCATCACGCAAATTGAGTGTTGTTCCAGTTTTCCAGT
E9, h7-b248,GTCTGGAAGTTTCATTACGAGTAGATTTAGTTAAGGGTGA
F9, h9-b256,GAAAGGCCGCTATCAGGTCATTGCAAACGGCG
G9, h11-b256,GATTGACCCCATTCAGGCTGCGCACTGTCGTG
H9, h13-b256,CCAGCTGCTAGCCCGAGATAGGGTTAACCGTTGTAGCAAT
A10 h15-b264,ACTTCTTTGATTAGTTATAAATCAAAAGAAATTAATG
B10, h11-b272,GATAGGTCGAGAGATCTACAAAGGGAGACA
C10, h13-b272,AATCGGCCGCAAAGCGCCATTCGGTAATGG
D10, h9-b280,ACCATCAATATGATATGAGGGTAGCTATTTTTACGTTGGT
E10, h11-b288,GTAGATGGTGGTGCCGGAAACCAGAACGCGCG
F10, h13-b288,GGGAGAGGAATCGGCAAAATCCCTAATAACATCACTTGCC
G10, h13-b304,GTATTGGGTTTCCGGCACCGCTTCGCGCATCG
H10, h15-b296,TGAGTAGAAGAACTCATTGATGGTGGTTCCGACGGTTTGC
A11, h11-b312,CATCTGCCAGTTTGACGCACTCCAGCCAGCCGCCAGG
B11, h13-b320,GTGGTTTTAGGCGAAAATCCTGTAACTATCGGCCTTGC
C11, h15-b328,TGGTAATATCCAGAACGCTGGTTTGCCCCAGCTCTTTTCA
D11, h13-b344,ACGGGCAACAGCTGATGCAGCAAGCGGTCCACAATATTAC
plate shape-flip-bottom-core (arm2)
A1, h22-b47,ATTTAGGATAAAGTACCGACAAAGAAAAAT
B1, h24-b47,TACCGACACACCGGAATCATAAAACATGTA
C1, h26-b55,TGAAAACATAGCGATGTGAATTTATCAAAAGTTTGAAA
D1, h20-b63,CCTGAACAAAGGTAAAGTAATTCTCATATTTA
E1, h22-b63,ACAACGCCTTACTAGAAAAAGCCTTGACCTAA
A2, h16-b79,GAAGCCTTTACAATTTTATCCTGAATCTTAC
B2, h18-b79,ATCATTACGGCTTATCAGAACGCGGAGGTTTT
C2, h20-b79,TCAACAATGAACGGGTCGCACTCATCGTAGGA
D2, h22-b79,AGAATCGCGTCCAGACACGACAATCCTGTTTA
E2, h24-b79,TCATCTTCGTTTAGTAAATTCTTACTTAATTG
F2, h26-b79,TAATTAATCTACCTTTAGACAAAGAGTTAATT
G2, h28-b79,AATTATTCAACAAACATCAATATAGTCGCTAT
H2, h30-b87,TATTTGCACGTAAAACTAACGTCATCGCCTGACAGAGGCG
A3, h33-b96,CAACGCTAACGAGCGTCTTTCCAGAGCCTAATTTG
B3, h16-b95,CTTGCGGAGGCGTTTTAGCGAACACCTTGC
C3, h18-b95,ATTTTCATCGAGAACAAGCAAGAATCAACA
D3, h20-b95,GAACGCGAAACAACATGTTCAGTAACAACT
E3, h22-b95,AGTAGGGCCAGTATAAAGCCAATATTAGAC
F3, h24-b95,ATATTTTAACGCGAGAAAACTTTATTAATT
G3, h26-b95,GTAAATCTGTGAGTGAATAACCCAGAAGGA
H3, h28-b95,AATCGCGTTGCTTTGAATACCACAATATAA
A4, h17-b112,TGAACCTCGAAAAATCTAAAGCATCCTCCCGA
B4, h19-b112,GTTGAAAGATCTGGTCAGTTGGCACCGTTTTT
C4, h21-b112,AATAGATTATATCTTTAGGAGCACCTAATGCA
D4, h23-b112,TTTACAAATTTGAGGATTTAGAAGCGCTCAAC
E4, h25-b112,TTAAAAGTTCCTTTGCCCGAACGTTTTCAAAT
F4, h27-b112,GCGGAATTGGAACAAAGAAACCACTTGCTTCT
G4, h29-b112,TCCTGATTGATGATGGCAATTCATAGTTACAA
H4, h30-b119,ATGGAAGGGTTAGAACCTACCATATCAAAAT
A5, h16-b151,AACAGTGCCACGCTGACAGCAGCAAAT
B5, h17-b120,AAATATCAAACAAAATAAACAGCCATA
C5, h18-b151,TTTATTTTGTCACAATCCTCAATCAAT
D5, h19-b120,GAATTGAGGAACAATAGAAAATTCATA
E5, h20-b151,GAACCGCCACCCTCAGGGTTATCTAAA
F5, h21-b120,AGAGCCGTCAAAGCCACCACCCTCAGA
G5, h22-b151,AGAAGGATTAGGATTATAGATAATACA
H5, h23-b120,CAATTCGACAAGCGGGGTTTTGCTCAG
A6, h24-b151,GTAACGATCTAAAGTTCTCGTATTAAA
B6, h25-b120,TTGAGTAACATTTGTCGTCTTTCCAGA
C6, h26-b151,TTTCTTAAACAGCTTGTATCATTTTGC
D6, h27-b120,ATCATCATATTATACCGATAGTTGCGC
E6, h28-b151,GGTAGCAACGGCTACACCTGATTATCA
F6, h29-b120,GTTTGGATTATGAGGCTTTGAGGACTA
G6, h31-b136,AGAGGCAAAAGAATACACCAACCTAAAACGAAACTTCTGAATA
A7, h16-b167,ATTAACACCGCCTGCTTATTTATCCCAATCACACCACG
B7, h18-b159,GAATAAGTGGTTTACCAGCGCCGAGCCGCC
C7, h20-b159,ACCCTCAGCCGCCACCAGAACCCTGAGACT
D7, h22-b159,CCTCAAGTACCAGGCGGATAAGGCCCTCAT
E7, h24-b159,AGTTAGCCGTTAGTAAATGAATTGCTTTCG
F7, h26-b159,AGGTGAACGACAATGACAACAACAGCATCG
G7, h18-b175,ACGCAAAGCAAATAAGAAACGATTAGGTGAGGCGGTCAGT
H7, h20-b175,CTCCCTCAAAAGACAAAAGGGCGATAAAAGAA
A8, h22-b175,TTAAGAGGACCACCAGAGCCGCCGGGAACCGC
B8, h24-b175,CACAGACATGCCGTCGAGAGGGTTTGAAAGTA
C8, h26-b175,TATCAGCTTTTCTGTATGGGATTTTAGCATTC
D8, h28-b175,GCGAAAGACCATCGCCCACGCATATATCGGTT
E8, h16-b199,GCAGAAGATAAAACAGTTTTGTTTAACGTCAATAAAGGTG
F8, h18-b191,GCAACATACATTCAACCGATTGAGAACCAGAG
G8, h20-b191,CCACCACCCCAGCATTGACAGGAGCTATTATT
H8, h22-b191,CTGAAACAGATATAAGTATAGCCCCAAACTAC
A9, h24-b191,AACGCCTGTGCTAAACAACTTTCAAAGGAGCC
B9, h26-b191,TTTAATTGACCGATATATTCGGTCTTTGCGGGATCGTCAC
C9, h18-b207,ACATACAAAATGAAAATAGCAGCCGAACGAACCACCA
D9, h20-b207,TCACCGGGGAGGGAAGGTAAATTAGAAAAT
E9, h22-b207,TCGGAACGTTGAGGCAGGTCAGAATCAAAA
F9, h24-b207,ACCAGTAGGAATAGGTGTATCATGCCTATT
G9, h26-b207,GCTCCAAACAGTTTCAGCGGAGGTTTCGTC
H9, h16-b231,ATCGCCATTAAAAATACCTTTACAGAGAGAATAGTATGTT
A10 h18-b223,AGCAAACGATTGACGGAAATTATTTTTGCCAT
B10, h20-b223,CTTTTCATACGATTGGCCTTGATAAACAGTTA
C10, h22-b223,ATGCCCCCCCGTACTCAGGAGGTTTGTACCGT
D10, h24-b223,AACACTGATGAGAATAGAAAGGAAACGTTGAAAATCTCCA
E10, h18-b239,TATTACGCAACATAAAAACAGGGACTGATAGCCCTAAAAC
F10, h20-b239,TATTAGCGCATTAAAGGTGAATTAAGACTCCT
G10, h22-b239,CCCGTATATTCACAAACAAATAAAAGCCCCCT
H10, h24-b239,GGAACCCATAGTACCGCCACCCTCTAACAGTG
A11, h16-b263,TCTTTAATGCGCGAAAGCGCATTAGACGGGGAACTGGC
B11, h18-b255,ATGATTATCACCGTCACCGACTGGCATTTT
C11, h20-b255,CGGTCATTCCTCATTAAAGCCAGGTCAGTG
D11, h22-b255,CCTTGAGAGAACCGCCACCCTCTTTCAGGGATAGCAA
E11, h18-b271,ACCCAAAAAGAATTAACTGAACACTTTGAATGGCTATTAG
F11, h20-b271,TTTTCATCTGAGCCATTTGGGAATAACGGAAT
G11, h22-b271,TTTAACGGGAATGGAAAGCGCAGTGTAGCGCG
H11, h16-b295,TGGCACAGACAATATTCCTGAACAAAGTCAGAGAGGAAAC
plate shape-flip-bottom-core (arm2) continued....
A12, h18-b287,GCAATAATTAGAGCCAGCAAAATCCCTTTAGC
B12, h20-b287,GTCAGACTCTCTGAATTTACCGTTTACAGGAGTGTACTGG
C12, h18-b303,GGAAACCGGGTAATTGAGCGCTAAGCGTAAGAATACG
D12, h20-b303,AAGTTTGACCAGTAGCACCATTTACCAGAA
E12, h16-b327,AACCCTTCTGACCTGAAATATCAGAGAGATAAGATAGCCG
F12, h18-b319,AACAAAGTACCATTAGCAAGGCCGACCGTAATCAGTAGCG
G12, h18-b335,AGTAAGCACCCACAAGAATTGAGTTGGCCAACAGAGATAG
H12, h16-b351,GACATTCTAAGCCCAATAATAATTACCGAAGCCCTTT
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shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
!"
DOI: 10.1038/NCHEM.1070

A1, h1-b72,CCGGAACGAGGCGCACTCCATGTTACTTAG
B1, h3-b72,CTTGAGATGGTTTAAGAGTAGTAAATTGGG
C1, h3-b104,TGTGAATTACCTTATGATAAGGCTTGCCCTGAGGAACCGA
D1, h5-b104,CGAGAGGCTTTTGCAAATAAAAACCAAAATAG
E1, h7-b104,CAAACTCCAACAGGTCCGAACCAGACCGGAAG
F1, h9-b104,CTAAATCGGTTGTACCGCCTCAGAGCATAAAG
G1, h11-b104,CATTAAATTTTTGTTAATTTTGTTAAAATTCG
H1, h13-b112,AAATTGTTAGCTTGCATGCCTGCAGGTCGACTCTAGAGGAATGGTCAT
A2, h13-b72,CTCGAATTCGTAATCTCCCCGGGTACCGAG
B2, h15-b72,CTTGACGGGGAAAGCGCCCCCGATTTAGAG
A3, h33-b56,CTATTTTGCACCCAGCAAATCAAGATTAGTTG
B3, h17-b56,CAAATCAGATATAGAACGCGCCCAATAGCAAG
C3, h20-b47,AATATCCAATAATCGGCTGTCTTTCCTTATCATTCCAAAGATAAGT
D3, h19-b24,CATGTAGAAACCAATCCATCCTAATTTACGAG
E3, h21-b24,CCAGTAATAAGAGAATCAGAGGCATTTTCGAG
F3, h23-b24,CGTTAAATAAGAATAACGTGTGATAAATAAGG
G3, h25-b24,CTGAGAAGAGTCAATAAGCTTAGATTAAGACG
H3, h24-b63,ATTTAATGTCATAGGTCTGAGAGATTTCCCTTAGAATCCT
A4, h27-b56,CAAAAGAAGATGATGAATTTCAATTACCTGAG
B4, h29-b56,CGTAGATTTTCAGGTTAGAAATAAAGAAATTG
edge!"#$%&'"
arm 1
arm 2
arm 1
arm 2
plate shape-flip-bridges
A1, h0-b156,ACCAAGACCAGGCGCATAGGCAAGAACCGGATATTCAAGGACGTT
B1, h3-b176,CGTTAATAAAGAGTAATCTTGACTGGCT
C1, h5-b208,TCCCCCTCAGAAAGATTCATCAGTCAACA
D1, h7-b240,AGTACGGTGACCATAAATCAAAAATTCAG
E1, h9-b272,GTCAAATCTTCCCAATTCTGCGACCATA
F1, h11-b304,TAACCGTGATAAATTAATGCCGGATCAAC
G1, h13-b336,CCAGTGAGTCGGCCTCAGGAAGATGGGGA
H1, h15-b352,CGCCAGCCATTGCAACAGGAAAAGGCCCTGAGAGAGTTTGCCC
A2, h18-b364,CTATCGAGCAAGAAACAATGAAGTCACACGACCAGTAATAAAAGG
B2, h20-b332,GCAGCGAAACGTCACCAATGATTAAGAAA
C2, h22-b300,GATGACCAGTAAGCGTCATAACAGAATC
D2, h24-b268,CTCATAGAACCGCCACCCTCATAATAAGT
E2, h26-b236,TTTTCCAACTAAAGGAATTGCGCCCAATA
F2, h28-b159,GAACGAGAAGACTTTTTCATGATGCCACTACGAAGGCACTAA
G2, h30-b172,CGTAAGGAAGTTTCCATTAAACCTCAGCA
H2, h28-b204,CCGCTGCTGAGGCTTGCAGGAAAAAAAG
A3, h31-b157,AACACTCATCCCAGCGATTAT
B3, h1-b173,GACCTTCATCCGGGTAAAATA
C3, h3-b205,TTATTACAGGTGAGTTAAAGG
D3, h5-b237,AAAACGAGAATGAATAATAATT
E3, h7-b269,TAACAGTTGAGAGCCACCACC
F3, h9-b301,CGTTCTAGCTGCATGGCTTTT
G3, h11-b333,CGACGACAGTAAACCATCGATA
H3, h13-b365,TTCACCGCCTAATAGCAATAG
A4, h15-b397,TTTTGACGCTCGAAATGGAT
B4, h15-b376,ACGCTCATGGAAATACCTACA
C4, h16-b396,ATTTACATTGGCAGATTCACC
bridge !"#$%&!
bridges
strands at corner
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
shflip-
!"
DOI: 10.1038/NCHEM.1070
Sequence d|agram for 60 corner or|gam| !"#$%&'(&%)$*+&)%*,'%-&.&-)&'%!"#$%&'(%+/0*-"#1

3
4
3
3
1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
5
3
7
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
3
2
3
4
3
3
1
6
1
7
1
8
1
9
2
0
2
1
2
2
2
3
2
4
2
5
2
6
2
7
2
8
2
9
3
0
3
1
3
5
3
7
0 1 2 3 4 5 6 7 8 9 1
0
1
1
1
2
1
3
1
4
1
5
3
2
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
3
8
4
3
9
2
4
0
0
4
0
8
1
6
2
4
3
2
4
0
4
8
5
6
6
4
7
2
8
0
8
8
9
6
1
0
4
1
1
2
1
2
0
1
2
8
1
3
6
1
4
4
1
5
2
1
6
0
1
6
8
1
7
6
1
8
4
1
9
2
2
0
0
2
0
8
2
1
6
2
2
4
2
3
2
2
4
0
2
4
8
2
5
6
2
6
4
2
7
2
2
8
0
2
8
8
2
9
6
3
0
4
3
1
2
3
2
0
3
2
8
3
3
6
3
4
4
3
5
2
3
6
0
3
6
8
3
7
6
3
8
4
3
9
2
4
0
0
4
0
8
4
8
10
8
14 1 16 63 72 51
4
8
7 29 1 37 18 13 14
C
A
A
A
T
T
A
G
G
C
T
C
T
G
G
A
A
A
G
A
C
G
C
T
C
G
T
T
A
G
C
G
T
T
G

G
T
A
A
G
A
T
T
C
A
G
G
A
T
A
A
A
A
T
T
G
T
A
G
C
T
G
G
G
T
G
C
A
A
A
A
T
A
G
C
A
A
C
T
A
A
T
C
T
T
G
A
T
T
T
A
A
G
G
C
T
T
C
A
A
A
A
C
C
T
C
C
C
G
C
A
A
G

T
C
G
G
G
A
G
G
A
T
G
C
T
T
T
A
G
A
T
T
T
T
T
C
A
T
T
T
G
C
T
G
C
T
G
T
C
A
G
C
G
T
G
G
C
A
C
T
G
T
T
G
C
A
G
G
C
G

G
T
G
T
T
A
A
T
A
C
T
G
A
C
C
G
C
C
T
C
A
C
C
T
C
T
G
T
T
T
T
A
T
C
T
T
C
T
G
C
T
G
G
T
G
G
T

T
C
G
T
T
C
G
G
T
A
T
T
T
T
T
A
A
T
G
G
C
G
A
T
G
T
T
T
T
A
G
G
G
C
T
A
T
C
A
G
T
T
C
G
C
G
C

A
T
T
A
A
A
G
A
C
T
A
A
T
A
G
C
C
A
T
T
C
A
A
A
A
A
T
A
T
T
G
T
C
T
G
T
G
C
C
A
C
G
T
A
T
T
C

T
T
A
C
G
C
T
T
T
C
A
G
G
T
C
A
G
A
A
G
G
G
T
T
C
T
A
T
C
T
C
T
G
T
T
G
G
C
C
A
G
A
A
T
G
T
C

C
C
T
T
T
T
A
T
T
A
C
T
G
G
T
C
G
T
G
T
G
A
C
T
G
G
T
G
A
A
T
C
T
G
C
C
A
A
T
G
T
A
A
A
T
A
A

T
C
C
A
T
T
T
C
T
T
C
G
C
T
A
A

A
A
C
G
C
C
T
C
G
C
G
T
T
C
T
G
A
T
A
A
G
C
C
T
T
C
T
A
T
A
T
C
T
G
A
T
T
T
G
G
T
T
T
G
A
T
A
T
T
T
G
A
G
G
T
T
C
A
G
C
A
A
G
G
T
G
T
C
A
T
T
G
T
T
T
C
T
T
G
C
T
C
T
T
A
T
T
A
T
T

G
G
G
C
T
T
A
A
C
T
C
A
A
T
T
C
T
T
G
T
G
G
G
T
T
A
T
C
T
C
T
C
T
G
A
T
A
T
T
A
G
C
G
C
T
C
A

A
T
T
A
C
C
C
T
C
T
G
A
C
T
T
T
G
T
T
C
A
G
G
G
T
G
T
T
C
A
G
T
T
A
A
T
T
C
T
C
C
C
G
T
C
T
A

A
T
G
C
G
C
T
T
C
C
C
T
G
T
T
T
T
T
A
T
G
T
T
A
T
T
C
T
C
T
C
T
G
T
A
A
A
G
G
C
T
G
C
T
A
T
T

T
T
C
A
T
T
T
T
T
G
A
C
G
T
T
A
A
A
C
A
A
A
A
A
A
T
C
G
T
T
T
C
T
T
A
T
T
T
G
G
A
T
T
G
G
G
A

T
A
A
A
T
A
A
T
A
T
G
G
C
T
G
T
T
T
A
T
T
T
T
C
T
T
G
C
T
A
T
T
G
G
G
C
G
C
G
G
T
A
A
T
G
A
T
T
C
C
T
A
C
G
A
T
G
A
A
A
A
T

A
A
A
A
A
C
G
G
T
G
C
C
A
A
C
T
G
A
C
C
A
G
A
T
A
T
T
G
A
T
T
G
A
G
G
A
T
T
G
T
G
A
C
A
A
A
A
T
A
A
A
C
T
T
A
T
T
C

C
G
T
G
G
T
G
T
C
T
T
T
G
C
G
T
T
T
C
T
T
T
T
A
T
A
T
G
T
T
G
C
C
A
C
C
T
T
T
A
T
G
T
A
T
G
T

A
T
T
T
T
C
T
A
C
G
T
T
T
G
C
T
A
A
C
A
T
A
C
T
G
C
G
T
A
A
T
A
A
G
G
A
G
T
C
T
T
A
A
T
C
A
T

G
C
C
A
G
T
T
C
T
T
T
T
G
G
G
T
A
T
T
C
C
G
T
T
A
T
T
A
T
T
G
C
G
T
T
T
C
C
T
C
G
G
T
T
T
C
C

T
T
C
T
G
G
T
A
A
C
T
T
T
G
T
T
C
G
G
C
T
A
T
C
T
G
C
T
T
A
C
T
T
T
T
C
T
T
A
A
A
A
A
G
G
G
C

T
T
C
G
G
T
A
A
G
A
T
A
G
C
T
A
T
T
G
C
T
A
T
T
C
T
T
G
C
T
T
G

T
T
C
T
C
G
A
T
G
A
G
T
G
C
G
A
C
C
C
G
T
T
C
T
T
G
G
A
A
T
G
A
T
A
A
G
G
A
A
A
G
A
C
A
G
C
C

G
A
T
T
A
T
T
G
A
T
T
G
G
T
T
T
C
T
A
C
A
T
G
T
T
C
C
T
C
A
A
T
T
C
C
T
T
T
C
A
A
C
T
G
T
T
G
A
T
T
T
C
A
T
T
G
G
T
G
A
C
G
T
T
T
C
C
G
G
C
C
T
T
G
C
T
A
A
T
G
G
T
A
A
T
G
G
T
G
C

T
A
C
T
G
G
T
G
A
T
T
T
T
G
C
T
G
G
C
T
C
T
A
A
T
T
C
C
C
A
A
A
T
G
G
C
T
C
A
A
G
T
C
G
G
T
G

A
C
G
G
T
G
A
T
A
A
T
T
C
A
C
C
T
T
T
A
A
T
G
A
A
T
A
A
T
T
T
C
C
G
T
C
A
A
T
A
T
T
T
A
C
C
T

T
C
C
C
T
C
C
C
T
C
A
A
T
C
G
G
T
T
G
A
A
T
G
T
C
G
C
C
C
T
T
T
T
G
T
C
T
T
T
G
G
C
G
C
T
G
G

T
A
A
A
C
C
A
T
A
T
G
A
A
T
T
T
T
C
T
A
T
T
G
C
T
C
G
T
A
A
A
T
T
A
G
G
A
T
G
G
G
A
T
A
T
T

A
T
T
T
T
T
C
T
T
G
T
T
C
A
G
G
A
C
T
T
A
T
C
T
A
T
T
G
T
T
G
A
T
A
A
A
C
A
G
G
C
G
C
G
T
T
C

T
G
C
A
T
T
A
G
G
T
G
C
T
C
C
T
A
A
A
G
A
T
A
T
T
T
T
A
G
A
T
A
A
C
C
C
T
G
A
G
G
G
T
G
G
C
G
G
T
T
C
T
G
A
G
G
G
T

G
G
C
G
G
C
T
C
T
G
A
G
G
G
A
G
G
C
G
G
T
T
C
C
G
G
T
G
G
T
G
G
C
T
C
T
G
G
T
T
C
C
G
G
T
G
A

T
T
T
T
G
A
T
T
A
T
G
A
A
A
A
G
A
T
G
G
C
A
A
A
C
G
C
T
A
A
T
A
A
G
G
G
G
G
C
T
A
T
G
A
C
C
G

A
A
A
A
T
G
C
C
G
A
T
G
A
A
A
A
C
G
C
G
C
T
A
C
A
G
T
C
T
G
A
C
G
C
T
A
A
A
G
G
C
A
A
A
C
T
T

G
A
T
T
C
T
G
T
C
G
C
T
A
C
T
G
A
T
T
A
C
G
G
T
G
C
T
G
C
T
A
T
C
G
A
T
G
G
T
T
C
T
G
A
A
C
A
T

G
T
T
G
T
T
T
A
T
T
G
T
C
G
T
G
T
C
T
G
G
A
C
A
G
A
A
T
T
A
C
T
T
T
A
C
C
T
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61
Two 8-nt loopouts to relieve
stress in the corners.
A 4-nt loopout and an 8-nt
loopout provide slack for
the seam reversal.

Sungwook Woo and Paul W.K. Rothemund - Programmable Molecular Recognition Based On The Geometry of DNA Nanostructures

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