1.

Helicobacter pylori B38 complete

genome, strain B38
Marimea secventei 1576758 bp
Sursa DNA
Tipul molecule circular
DEFINITION Helicobacter pylori B38 complete genome, strain B38.
ACCESSION FM991728
VERSION FM991728.1
SOURCE Helicobacter pylori B38
ORGANISM Helicobacter pylori B38
Bacteria; Proteobacteria; Epsilonproteobacteria;
Campylobacterales;
Helicobacteraceae; Helicobacter.

Secventa: FM991728.1:c521-105 Helicobacter pylori B38 complete genome, strain

B38
1 ATGGCGACAC GAACTCAAGC CAGGGGGGCT GTGGTTGAAT TGTTGTATGC GTTTGAGAGC
61 GGTAATGAAG AAATTAAAAA AATCGCTTCC AGCATGTTAG AAGAAAAAAA GATTAAAAAC
121 AACCAGCTCG CTTTCGCTTT AAGCCTTTTT AATGGCGTGT TAGAAAAAAT CAATGAAATT
181 GACGCCCTCA TTGAGCCGCA TTTAAAAGAC TGGGATTTCA AGCGATTAGG GAGCATGGAA
241 AAGGCGATTT TACGCTTAGG AGCGTATGAA ATTGGCTTCA CGCCCACACA AAACCCCATC
301 ATCATCAACG AATGCATAGA GCTTGGCAAA CTCTACGCTG AGCCTAACAC CCCTAAATTT
361 TTAAACGCTA TCTTGGATTC TTTGAGCAAA AAACTCGCTC AAAAACCCTT GAATTGA

2. Generarea fisierului FASTA:

1
 3. Crearea hartii de restrictie:

Restriction Enzyme Map:

1
ATGGCGACACGAACTCAAGCCAGGGGGGCTGTGGTTGAATTGTTGTATGCGTTTGAGAGCGGTAATGAAGAAATTAA
AAA 80
1
TACCGCTGTGCTTGAGTTCGGTCCCCCCGACACCAACTTAACAACATACGCAAACTCTCGCCATTACTTCTTTAATT
TTT 80
SmlI BsaJI XcmI BsrBI
MboII
BglI
MwoI
HpyF10VI
Hin4I

81
AATCGCTTCCAGCATGTTAGAAGAAAAAAAGATTAAAAACAACCAGCTCGCTTTCGCTTTAAGCCTTTTTAATGGCG
TGT 160
81
TTAGCGAAGGTCGTACAATCTTCTTTTTTTCTAATTTTTGTTGGTCGAGCGAAAGCGAAATTCGGAAAAATTACCGC
ACA 160
TspDTI NspI MboII Cac8I

161
TAGAAAAAATCAATGAAATTGACGCCCTCATTGAGCCGCATTTAAAAGACTGGGATTTCAAGCGATTAGGGAGCATG
GAA 240
161
ATCTTTTTTAGTTACTTTAACTGCGGGAGTAACTCGGCGTAAATTTTCTGACCCTAAAGTTCGCTAATCCCTCGTAC
CTT 240
BsaHI HgaI MnlI DraI BsrI
TspDTI BmrI

241
AAGGCGATTTTACGCTTAGGAGCGTATGAAATTGGCTTCACGCCCACACAAAACCCCATCATCATCAACGAATGCAT
AGA 320
241
TTCCGCTAAAATGCGAATCCTCGCATACTTTAACCGAAGTGCGGGTGTGTTTTGGGGTAGTAGTAGTTGCTTACGTA
TCT 320
Bpu10I TspDTI
BfrBI

BsmI

NsiI

2
321
GCTTGGCAAACTCTACGCTGAGCCTAACACCCCTAAATTTTTAAACGCTATCTTGGATTCTTTGAGCAAAAAACTCG
CTC 400
321
CGAACCGTTTGAGATGCGACTCGGATTGTGGGGATTTAAAAATTTGCGATAGAACCTAAGAAACTCGTTTTTTGAGC
GAG 400
BseMII BlpI ApoI DraI BcgI
BspCNI

401 AAAAACCCTTGAATTGA 417

401 TTTTTGGGAACTTAACT 417
BcgI BpuEI
Hin4I

4. Compozitie in nucleotide
DNA molecule: lcl|FM991728.1_cds_CAX28559.1_1 [gene=nusB]
[locus_tag=HELPY_0001] [db_xref=EnsemblGenomes-Gn:HELPY_0001,EnsemblGenomes-
Tr:CAX28559,GOA:C7BXH4,InterPro:IPR006027,InterPro:IPR011605,UniProtKB/TrEMBL
:C7BXH4] [protein=N utilization substance protein B homolog (Protein nusB),
transcriptional antitermination factor] [protein_id=CAX28559.1]
[location=complement(105..521)] [gbkey=CDS]

Length = 417 base pairs

Molecular Weight = 126853,00 Daltons, single stranded

Molecular Weight = 252926,00 Daltons, double stranded

G+C content = 41,49%

A+T content = 58,51%

Nucleotide Number Mol%

A 140 33,57
C 85 20,38
G 88 21,10
T 104 24,94

5. Modificarea secventei ADN: complement / revers complement

Secventa complementara
1 TACCGCTGTG CTTGAGTTCG GTCCCCCCGA CACCAACTTA ACAACATACG CAAACTCTCG
61 CCATTACTTC TTTAATTTTT TTAGCGAAGG TCGTACAATC TTCTTTTTTT CTAATTTTTG
121 TTGGTCGAGC GAAAGCGAAA TTCGGAAAAA TTACCGCACA ATCTTTTTTA GTTACTTTAA
181 CTGCGGGAGT AACTCGGCGT AAATTTTCTG ACCCTAAAGT TCGCTAATCC CTCGTACCTT
241 TTCCGCTAAA ATGCGAATCC TCGCATACTT TAACCGAAGT GCGGGTGTGT TTTGGGGTAG
301 TAGTAGTTGC TTACGTATCT CGAACCGTTT GAGATGCGAC TCGGATTGTG GGGATTTAAA
361 AATTTGCGAT AGAACCTAAG AAACTCGTTT TTTGAGCGAG TTTTTGGGAA CTTAACT

3
Secventa revers-complementara

1 TCAATTCAAG GGTTTTTGAG CGAGTTTTTT GCTCAAAGAA TCCAAGATAG CGTTTAAAAA

61 TTTAGGGGTG TTAGGCTCAG CGTAGAGTTT GCCAAGCTCT ATGCATTCGT TGATGATGAT
121 GGGGTTTTGT GTGGGCGTGA AGCCAATTTC ATACGCTCCT AAGCGTAAAA TCGCCTTTTC
181 CATGCTCCCT AATCGCTTGA AATCCCAGTC TTTTAAATGC GGCTCAATGA GGGCGTCAAT
241 TTCATTGATT TTTTCTAACA CGCCATTAAA AAGGCTTAAA GCGAAAGCGA GCTGGTTGTT
301 TTTAATCTTT TTTTCTTCTA ACATGCTGGA AGCGATTTTT TTAATTTCTT CATTACCGCT
361 CTCAAACGCA TACAACAATT CAACCACAGC CCCCCTGGCT TGAGTTCGTG TCGCCAT

6. Transformarea ADN în ARN

1 AUGGCGACAC GAACUCAAGC CAGGGGGGCU GUGGUUGAAU UGUUGUAUGC GUUUGAGAGC
61 GGUAAUGAAG AAAUUAAAAA AAUCGCUUCC AGCAUGUUAG AAGAAAAAAA GAUUAAAAAC
121 AACCAGCUCG CUUUCGCUUU AAGCCUUUUU AAUGGCGUGU UAGAAAAAAU CAAUGAAAUU
181 GACGCCCUCA UUGAGCCGCA UUUAAAAGAC UGGGAUUUCA AGCGAUUAGG GAGCAUGGAA
241 AAGGCGAUUU UACGCUUAGG AGCGUAUGAA AUUGGCUUCA CGCCCACACA AAACCCCAUC
301 AUCAUCAACG AAUGCAUAGA GCUUGGCAAA CUCUACGCUG AGCCUAACAC CCCUAAAUUU
361 UUAAACGCUA UCUUGGAUUC UUUGAGCAAA AAACUCGCUC AAAAACCCUU GAAUUGA

7. Identificare cadru de citire major (ORF/CDS) din secventa

ATGCATTCGTTGATGATGATGGGGTTTTGTGTGGGCGTGAAGCCAATTTC
ATACGCTCCTAAGCGTAAAATCGCCTTTTCCATGCTCCCTAATCGCTTGA
AATCCCAGTCTTTTAAATGCGGCTCAATGAGGGCGTCAATTTCATTGATT
TTTTCTAACACGCCATTAAAAAGGCTTAAAGCGAAAGCGAGCTGGTTGTT
TTTAATCTTTTTTTCTTCTAACATGCTGGAAGCGATTTTTTTAATTTCTT
CATTACCGCTCTCAAACGCATACAACAATTCAACCACAGCCCCCCTGGCT
TGA

8. Traducerea secventei din fisier în secventa de aminoacizi

1 ATG GCG ACA CGA ACT CAA GCC AGG GGG GCT GTG GTT GAA TTG TTG 45
1 Met Ala Thr Arg Thr Gln Ala Arg Gly Ala Val Val Glu Leu Leu 15

46 TAT GCG TTT GAG AGC GGT AAT GAA GAA ATT AAA AAA ATC GCT TCC 90
16 Tyr Ala Phe Glu Ser Gly Asn Glu Glu Ile Lys Lys Ile Ala Ser 30

91 AGC ATG TTA GAA GAA AAA AAG ATT AAA AAC AAC CAG CTC GCT TTC 135
31 Ser Met Leu Glu Glu Lys Lys Ile Lys Asn Asn Gln Leu Ala Phe 45

136 GCT TTA AGC CTT TTT AAT GGC GTG TTA GAA AAA ATC AAT GAA ATT 180
46 Ala Leu Ser Leu Phe Asn Gly Val Leu Glu Lys Ile Asn Glu Ile 60

181 GAC GCC CTC ATT GAG CCG CAT TTA AAA GAC TGG GAT TTC AAG CGA 225
61 Asp Ala Leu Ile Glu Pro His Leu Lys Asp Trp Asp Phe Lys Arg 75

226 TTA GGG AGC ATG GAA AAG GCG ATT TTA CGC TTA GGA GCG TAT GAA 270
76 Leu Gly Ser Met Glu Lys Ala Ile Leu Arg Leu Gly Ala Tyr Glu 90

271 ATT GGC TTC ACG CCC ACA CAA AAC CCC ATC ATC ATC AAC GAA TGC 315

4
91 Ile Gly Phe Thr Pro Thr Gln Asn Pro Ile Ile Ile Asn Glu Cys 105

316 ATA GAG CTT GGC AAA CTC TAC GCT GAG CCT AAC ACC CCT AAA TTT 360
106 Ile Glu Leu Gly Lys Leu Tyr Ala Glu Pro Asn Thr Pro Lys Phe 120

361 TTA AAC GCT ATC TTG GAT TCT TTG AGC AAA AAA CTC GCT CAA AAA 405
121 Leu Asn Ala Ile Leu Asp Ser Leu Ser Lys Lys Leu Ala Gln Lys 135

406 CCC TTG AAT TGA 417

136 Pro Leu Asn End

9. Alinierea a doua secvente ADN (aliniament in perechi)

Helicobacter hepaticus ATCC 51449 si Helicobacter pylori B38

Pairwise Alignment
Sequence 1: lcl|FM991728.1_cds_CAX28559.1_1 [gene=nusB]
[locus_tag=HELPY_0001] [db_xref=EnsemblGenomes-Gn:HELPY_0001,EnsemblGenomes-
Tr:CAX28559,GOA:C7BXH4,InterPro:IPR006027,InterPro:IPR011605,UniProtKB/TrEMBL
:C7BXH4] [protein=N utilization substance protein B homolog (Protein nusB),
transcriptional antitermination factor] [protein_id=CAX28559.1]
[location=complement(105..521)] [gbkey=CDS]
Sequence 2: lcl|AE017125.1_cds_AAP76598.1_1 [locus_tag=HH_0001]
[protein=conserved hypothetical protein] [protein_id=AAP76598.1]
[location=141..2423] [gbkey=CDS]
Optimal Global aligment
Alignment score: -1419

Identities: 0,1725799

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
5 15 25 35 45 55
lcl|FM9917 ATG------- ---------- GCGA------ ---------- ---------- ---------
-
lcl|AE0171 ATGCAAAACA CAAACATAGT GCAATATAAA ACTTTTTTCA TTGTGTTTTT
ACTTTCTATG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
65 75 85 95 105 115
lcl|FM9917 ---------- ---------C AC-------- ----GAA--- -------CTC ---------
-
lcl|AE0171 GCTTTTTTCT CGCTCAAAGC ACAAAACTAT ACTAGAAATC TTCCAAGCTC
CATTATCTTG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
125 135 145 155 165 175

5
lcl|FM9917 ---------- -------AAG C--------- ----CAG--- --GGG----- ---------
-
lcl|AE0171 CAAAATGGAG AGAGTAGAAG CGATATTCTT ACTTCAGTAT GTGGGAATCA
ATATTGCGCA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
185 195 205 215 225 235
lcl|FM9917 ---GGCT--- ---------- ---------- ---------- G--------- ------
TGGT
lcl|AE0171 TTTGGCTTAA TGAGCAATAA TGCTGGAAGC TATGACTTCA GCTATTCTAC
CCATAATGGT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
245 255 265 275 285 295
lcl|FM9917 T----GAA-- -TT-----GT TG-------- ---------- --TAT----- ---GCGTT-
-
lcl|AE0171 TCTTCGAAGC TTTCTCTCGT TGCAAATACT CCTACAAATC CTTATAACCA
TAGGCATTCT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
305 315 325 335 345 355
lcl|FM9917 ---------- TGAGA----- --------GC G--------- ------GTA- --ATGA---
-
lcl|AE0171 GTATTTTATA TGAGACATCT TAATGTAGGA GAAAATTCAA CATTAAGTAT
AAATGATTTT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
365 375 385 395 405 415
lcl|FM9917 ---------- ---------- ---------- -------AGA A--------- ----ATTA-
-
lcl|AE0171 CATACATTTG CCCTCTCTGG TGGGCTTACA CTTAATAATA ATGCTGCTCT
TGAGATTATT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
425 435 445 455 465 475
lcl|FM9917 ---------- ---AAAAAAT -----CG--- ---------- CTTC--CA-- ---
GCATGTT
lcl|AE0171 TTGCAAAAAG GAGAAAAAAT ACCTGCGAGT GAATTTGCCC CTTCATCAAA
AGTGCATTTT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
485 495 505 515 525 535
lcl|FM9917 ---------- ---------- ---------- ---------- ---------- ---------
-
lcl|AE0171 TCACGCAATG CAAATTTTTA TCTTGGCAAT GGCTCAACAC TTAATATAAG
CAATACTGAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
545 555 565 575 585 595

6
lcl|FM9917 ---------- --AG-----A AG-------A AA-------- ---AAA---- ---------
-
lcl|AE0171 TTTGTCATAA TAAGCTCTAA AGGCATTATA AATAATAATG CACAAATGAT
TTTAGATTCT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
605 615 625 635 645 655
lcl|FM9917 ---------A GATT--AAAA ---------- ---------- ---------- ---------
-
lcl|AE0171 AGCACAATAA GATTCCAAAA TACTCTCCAC AATAAGGGCA CAATAGAACT
TACAGGAGAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
665 675 685 695 705 715
lcl|FM9917 ---------- ---------- ----ACAACC A--------- GC---TCGC- ---------
-
lcl|AE0171 GTATATAACA TAGGACAAAG CCAAACAATC ACAAATCTTG GCACTTCGCA
TTTTATTAAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
725 735 745 755 765 775
lcl|FM9917 ---------- ---------- --------TT T--------- ------CGC- ------
TTTA
lcl|AE0171 TATGGCAATG TCAAAGTGAA TGGGAATTTT TATAATGGTG GCACTCCGCG
TGCTGATTCA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
785 795 805 815 825 835
lcl|FM9917 ---------- ---------- ---------- ---AGCC--- ---------- ---------
-
lcl|AE0171 GTGCAAGGAA GCTGGTGGCA AAATGATGCA CCAAGCCCGG GTGGAGGGAA
TCTTATAAAC

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
845 855 865 875 885 895
lcl|FM9917 ---------- ---------- ---------- -TTTTTAATG ------GCGT -G---
TTAGA
lcl|AE0171 TATGGTGGAA CAATTCATAT TACGGGTAAC CTTATTAATG CGCAAGGCGT
TGAACTTGGA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
905 915 925 935 945 955
lcl|FM9917 AAAA------ AT-CAA---T G-AAATTGAC G----CCC-- TCA---TTGA ---------
-
lcl|AE0171 AAAACACAAA ATTCAAGTGT GCAAATTTAT GGTGGCACAA TCAAAGTTGA
TGGAGGAATG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
965 975 985 995 1005 1015

7
lcl|FM9917 ---------G C--------C GC--ATTT-- ---------- -----AAAA- ------
GACT
lcl|AE0171 AACAACGGAG CTAATAATAC ACTTATTTTA GGTTGGTATA ATGGGAAAAT
GGGGCAGATT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1025 1035 1045 1055 1065 1075
lcl|FM9917 G--GGA--TT T---CAAGCG ---------- ---------A TTAG-GGAGC A--------
-
lcl|AE0171 GATGGAAATG TAACCAATCG TGGTATAGCT AAAGTTGATA TTACAGGAGC
AACGCTTAAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1085 1095 1105 1115 1125 1135
lcl|FM9917 ---------- ---------- ---------- ---------- ---------- ---------
-
lcl|AE0171 ACAGATCATA GAATCGCTGG TGGTTGGCAT ACTGGCAGGC TTAATGCAAA
TCGAGATGTC

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1145 1155 1165 1175 1185 1195
lcl|FM9917 --------TG G----AAAAG ---------- ---GCGA--- ---------- ---------
-
lcl|AE0171 TTACTAAATG GGAGCAAAAG TGAATTTTTA AACGCGAGAA TTAGTCATTA
CCAAAATAGC

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1205 1215 1225 1235 1245 1255
lcl|FM9917 ---------- ---------- ---------- ---------- -TTTTA---- ---------
-
lcl|AE0171 ACAACAATCA CACTTAATAA AAACACTCAA GCCATTAACG CTTTTATGAA
CACTCTTCCT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1265 1275 1285 1295 1305 1315
lcl|FM9917 ---------- ---------- -----CGCTT ---------- ---------- ---------
A
lcl|AE0171 ATACAATCAA AAACTATTCT TACCGCGCTT GAAAATAGTC TTTACAATCC
TAATACAATA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1325 1335 1345 1355 1365 1375
lcl|FM9917 GGA------- --------GC GTATG----- --AAATT--- ---------- ---------
-
lcl|AE0171 GGACAACAAA GTATTTATGC TTATGGCAAT AAAAATTACC TTACAAAACT
AGGAAATAAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1385 1395 1405 1415 1425 1435

8
lcl|FM9917 ---------- ---------- ---------- ---------- ---------- ---GGCT--
-
lcl|AE0171 ATTAATGAAA GCGCAGAATC TATGCTCCTT TATGCCTCTC CTTTAAATAT
ATGGGCTATA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1445 1455 1465 1475 1485 1495
lcl|FM9917 ---------- ---------- ---------- ---------- ---------- ---------
-
lcl|AE0171 GTTCAAAATA GTATTATGCC GCTTAAAGCT CAAGTAACGC CCCCTCCGCG
CAAATCTGTT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1505 1515 1525 1535 1545 1555
lcl|FM9917 ---------- ---------- ---------- TCACG----- ---------- ---------
-
lcl|AE0171 TTAAACATAG CTCCTTTAAG CTCTATTGCT TCACGTGGCT CACTTAAATC
CCCTCTTAAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1565 1575 1585 1595 1605 1615
lcl|FM9917 ---------- ------CCCA ---------- ----CACA-- ---------- ---------
-
lcl|AE0171 GGTGTAAATA TTAGTGCCCA AATTCCTTAT AAGACACATT TTCTTAGCGC
TTTTGCTGCT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1625 1635 1645 1655 1665 1675
lcl|FM9917 ---------- -AAAC----C CCAT------ ---------C A---TCAT-- -----CAA-
-
lcl|AE0171 TATGGAAATA CAAACGCTAC CCATACACTT ACCCACTTGC AAACTCATTT
TGACACAAAC

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1685 1695 1705 1715 1725 1735
lcl|FM9917 ------C--- ---------- -----GAAT- ---------- ---------- ---------
-
lcl|AE0171 TCTTTTCTTG TAGGTTTATA TGATAGAATC TCCCTACCAT ATATAGAAGT
TTCACTCCTT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1745 1755 1765 1775 1785 1795
lcl|FM9917 GCATA----- ---------- ---------- ---------- ---------- ---------
-
lcl|AE0171 GCATACTATG GTGCTAGTTT TAACAAAGCT AAACGACATC TTTTATTAAA
CAACAGTGCT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1805 1815 1825 1835 1845 1855

9
lcl|FM9917 ---------- ---------- ----GAGCTT GG-------- --CAAA---C TC---TA--
-
lcl|AE0171 TTTCAAACAC GCTATTCTTA TCACGAGCTT GGTTTATCAG CCCAAATCGC
TCATCTATTG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1865 1875 1885 1895 1905 1915
lcl|FM9917 CGCT------ -------GA- ---GCC---- --------TA AC-------- ------AC-
-
lcl|AE0171 CGCTTTGAAA AACTATGGAT AAAGCCATTT ATAGGGATTA ACTATGCTTT
TGGCTTACAA

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1925 1935 1945 1955 1965 1975
lcl|FM9917 ----CCCT-- ----AAAT-- --TTTTAAA- --------CG CTAT------ ---------
-
lcl|AE0171 AGTGCCTTCA AAGAAAATCT TGTTTCAGAT ACCACCTCCG CTATGCTTAC
AGCTCCTATG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
1985 1995 2005 2015 2025 2035
lcl|FM9917 ---------- ---------- -------CTT GG-------- ----AT---- ---------
-
lcl|AE0171 TGGCTTTCTC ATTTGCCACA ACTCTCACTT GGCACACAAG GGCAATACTA
CTTAAAAAAG

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
2045 2055 2065 2075 2085 2095
lcl|FM9917 ---------- TCTTTG---- AGC------- -AA------- ----AAA--- ---------
-
lcl|AE0171 CAACACTTTC TCTTTGGAGG AGCGCAGATT CAATATGCAC TCACAAATTC
CTCTTTTTCC

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
2105 2115 2125 2135 2145 2155
lcl|FM9917 ---------- ---------- -----ACT-- --CGCTCAAA A--------- ----
ACCCTT
lcl|AE0171 GCTCATTTTG GCTCTTCAGT TCTTAACTTT AACCCTCAAA ATTCACTTGG
GCTTACACTT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
2165 2175 2185 2195 2205 2215
lcl|FM9917 ---------- ---------- ---------- GAATT----- ---------- ---------
-
lcl|AE0171 CATTTTGGTG GCTCTATGCC TATAGCTAAA GAATTCTCTC TTAGTGCTTA
TACATTTTAT

....|....| ....|....| ....|....| ....|....| ....|....|

....|....|
2225 2235 2245 2255 2265 2275

10
lcl|FM9917 ---------- ---------- ---------- ----G----- ---------- ---------
-
lcl|AE0171 TCACGCTCAC ACTTGGCATT TCAAAGTTAT TCAGGCACAA TCAATCTCTC
ATATTATTTC

...

lcl|FM9917 -A-
lcl|AE0171 TAG

10. Crearea de aliniamente multiple*;

*in fisierul Crearea de aliniamente multiple;.xps

11. Realizarea designului unor primeri

Varianta 1
ATGGCGACACGAACTCAAGC Tm=50,01°C

AAACCCTTGAATTGA Tm=45,26°C

Most stable 3' extensible primer-dimers (at 37°C), if any

More stable non-extensible primer-dimers (at 37°C), if any

Forward vs. Forward: -3.25 kcal/mol

5' ATGGCGACACGAA 3'

.||.||.||.

3' AAGCACAGCGGTA 5'

11
Varianta 2
TCAATTCAAG GGTTTTTGAG Tm=55,04°C

AATTCAAGGGTTTTTGAG Tm=50,57°C

Most stable 3' extensible primer-dimers (at 37°C), if any

More stable non-extensible primer-dimers (at 37°C), if any

Forward vs. Forward: -3.25 kcal/mol

5' ATGGCGACACGAACT 3'

.||.||.||.

3' TCAAGCACAGCGGTA 5'

Forward vs. Reverse: -0.03 kcal/mol

5' ATGGCGACACGAACT 3'

..||..|||.

3' GAGTTTTTGGGAACTTAA 5'

Reverse vs. Reverse: -2.54 kcal/mol

5' AATTCAAGGGTTTTTGAG 3'

.||||......||||.

12
3' GAGTTTTTGGGAACTTAA 5'

12. BLAST

CGCGCCCATATGGCGACACGAACT

13
TGGTGGGATCCAATTCAAGGGTTTTTGAG

13. Clonarea in silico

14