ANALYSIS OF NUCLEOTIDE BASES

By :
Aficko Razaky Pratama
B1B017040

POPULATION GENETIC PRACTICAL REPORT

MINISTRY OF RESEARCH, TECHNOLOGY, AND HIGHER EDUCATION

JENDERAL SOEDIRMAN UNIVERSITY
FACULTY OF BIOLOGY
PURWOKERTO
2019
 I. RESULT AND DISCUSSION
A. Result

!Domain=Data property=Coding CodonStart=1;

#gi|Populus TGG CTT CAT CTT CAG TAT AAT CTT G-- -TT AGT GTC ATT ATT TGT TCT [ 48]

#gi|Pyrus ... ..C ..G ..C ... ..C ... ..C .-- -.C ... ... ... ... .TC ... [ 48]

#gi|Musa ... ..C ..C ..C ... ..C ..C ..C .-- -.C ..C ..A C.G G.C ..C ..C [ 48]

#gi|Jatropha ... A.. TG. ..G T-- .GC ..C A.. C-- -C. TA. T.T TC. .G. CC. .T. [ 48]

#gi|Nelumbo .TT AC. TG. ... TGT .CG ..A T.A ACG T.. TA. C.. T.. CCC AT. ... [ 48]

#gi|Populus GCT TTT CTT GTT TTT GGA GCC ACG GTT TAT ATT ATG ACC AGG CCC AGA [ 96]

#gi|Pyrus ... A.G G.. ..C ... ... T.. ..C ... ..C ... ... ... C.C ..G ... [ 96]

#gi|Musa ..C ..C ..C ..C ..C ..C A.. ..C ..C ..C ..C ... ..G G.. ..T C.C [ 96]

#gi|Jatropha .T. ..C --. AG. ..C ATT .T. .AA AA. ..C G.. T.A .-- -AA T.. TTT [ 96]

#gi|Nelumbo .TC .CC AA. A.. A.C A.T AA. -TC A.C A.C T.. ..T .GT ..T TT. CTG [ 96]

#gi|Populus TCC CTT TTT CTT G-- -TT GAT TAT GCT TGT TAC AAG CCT CCA TCA AAC [ 144]

#gi|Pyrus ... G.. .AC ... .-- -.G ..C ... T.A ... ... ... ..G ..G ..G C.T [ 144]

#gi|Musa C.T G.G .AC ..C .-- -.C ..C ... ..G ..C ... CGC ..C ..G C.C ... [ 144]

#gi|Jatropha A.A G.. .AC ..C A-- -.A ... .TC T.. ... .T. ..A ..A ..C AAC TC. [ 144]

#gi|Nelumbo .TT AA. .GG T.C AAG A.. .GC .C. ... .A. A.G TTA TAA AG. C.. TGT [ 144]

#gi|Populus TTA CAA GTC AAA TTT GAG CAA -TT CAT GGA G-C ATT CAA ATC TGA CTG [ 192]

#gi|Pyrus ... ... ..G .G. .AC C.. ..G -.. T.. ... .-. ... .G. .G. ... .A. [ 192]

#gi|Musa C.C .GG .CG CCC ..C CCC .GC -.. ... .A. .-. .C. .GC .G. .CT GC. [ 192]

#gi|Jatropha .GC A.. ..T CCT ..C TCT GT. -.. TC. T.. A-. ..G ..T CCA ... TC. [ 192]

#gi|Nelumbo .GC ..T ..T CCT GA. T.. G.. A.. A.. ... .GT ... ATT GG. CCC T.C [ 192]

#gi|Populus GTG ATT TTG ATG ATT CTT CGT TGG A-- ATT TCA AAG G-A AGA TT- --T [ 240]

#gi|Pyrus .G. .C. .C. ... .G. .A. ..C .C. .-- G.. C.. GC. C-. ... ..- --C [ 240]

#gi|Musa .A. .G. .CA .C. .G. .CG ..C .C. .-- G.. C.. GC. C-C G.. .C- --C [ 240]

#gi|Jatropha AGT CG. ... ..- .G. GAA A.C GTT T-- C.. ... TG. CT. .A. .C- --C [ 240]

#gi|Nelumbo AGA TAA ... .C- .G. .AC .A. C.A .CC .C. CTT TGT CTT C.. ..G TA. [ 240]

#gi|Populus TGG AAA GAT CAG GTC TTG GTG AAG A-- AAC TTA TGT --- --C CCC GAA [ 288]

#gi|Pyrus .C. .GC .C. .T. .C. ... .A. .G. .-- G.. ... ... --- --. ..T ... [ 288]

#gi|Musa .C. .GC .T. .C. .C. .C. ..C .G. .-- G.. G.. CC. --- --G ... AGC [ 288]

#gi|Jatropha .CA GTT CT. .T. .G. AAA ..C ... .-- G.. C.. .C. --- --T ..T CCG [ 288]

#gi|Nelumbo .TA G.C T.A GC. .C. .AA .CC GGA .CG G.T ... .A. AGT TGG T.T CG. [ 288]

#gi|Populus GCT ATG CAT TAT ATT CCA CCA AGA CCA TCA ATG GCA GCA GCT AGA GAA [ 336]

#gi|Pyrus ..A ... ... ..C ... ..G ..G ..G ..T ... ... ..G ..G ... C.C ..G [ 336]

#gi|Musa ..C C.A ..C ... C.. ..G ..C C.C ..C ..C ... ..C T.T ..C C.C ..G [ 336]

#gi|Jatropha ..A T.. ..C .GC ... ..T ..T .A. A.- .A. CCA A.. A.. ATC CAT A.. [ 336]

#gi|Nelumbo .GA .CC GT. C.A TC. AAT T.T GA. TT. .A. .GA AA. .TG AAC CAT TTG [ 336]
#gi|Populus -GA GGC A-- -CA GCA GGT GAT GT- --- --- --- -TT GGT GCA CTG AAT [ 384]

#gi|Pyrus -.. ... .-- -G. ... ... ... T.- --- --- --- -.. ... ... T.. G.. [ 384]

#gi|Musa -.. ... C-- -G. .G. ... C.. ..- --- --- --- -.C ..C ..T ..C G.C [ 384]

#gi|Jatropha A.. A.T .-- -.. .AT ... TC. T.- --- --- --- -.C CC. ATT ..A C.A [ 384]

#gi|Nelumbo GT. ATT .AG TTG .T. ... C.G ..C CCT GAA TAT G.. TT. A.T ..C T.A [ 384]

#gi|Populus GTT TTA TTT GCA -AA TAC TAA TAT C-- --- --- -AA GCC TAA AGA TAT [ 432]

#gi|Pyrus AA. C.G ... ..T -.. ... G.. .G. T-- --- --- -.. ... C.. G.. CT. [ 432]

#gi|Musa .CC C.C ..C AGG -.. C.. CGG CG. T-- --- --- -.. ... C.. G.. C.. [ 432]

#gi|Jatropha .A. C.T C.. T.T -.. A.. ... A.. A-- --- --- -TC C.. .CG T.. C.. [ 432]

#gi|Nelumbo CGG ..G ..G ..T C.. C.A ... AT. TGT TTG TTT GT. ... ..T .CC ... [ 432]

#gi|Populus TGG TAT TCT TGT TGT GAA TTG TAG TTT GTT TAA TCC TAC ACC CTC GTT [ 480]

#gi|Pyrus ... ... ... ... ... ... ... ... ... ... ... ... A.. ... T.. AC. [ 480]

#gi|Musa C.. C.. C.. C.. C.. C.. ... C.. CC. C.. C.. C.. C.. C.. G.. CC. [ 480]

#gi|Jatropha C.A ... A.. .A. ... A.. ... ... CGG ... .TG ... GT. ... T.. C.. [ 480]

#gi|Nelumbo ... .GG C.. G.. .T. A.C ..T ..T C.. .G. GG. .T. .GT TGT TCT ... [ 480]

#gi|Populus -AT CTG CGA TGA TTG TTA ACA AGT ATA AAT TGA GAG GGA ATA TTA GAT [ 528]

#gi|Pyrus -G. ... .T. ... ... ... .T. ... .C. ... ... .G. ... ... ... .GA [ 528]

#gi|Musa -C. .C. .C. ... .C. .C. ..C GC. .C. .G. .CC .T. .C. .C. .C. AGA [ 528]

#gi|Jatropha -.. .AT .C. .T. ..A ... ... .A. .CT CCA ... ... CTG ... ... A.A [ 528]

#gi|Nelumbo G.A G.. AA. .CG ACC CA. .T. ... CCT GT. .CT .G. TTT T.. A-. TGA [ 528]

#gi|Populus CTT TTA ATC TTG GGG GAA TGG GGT GTA GT- -GC TGG GGT TAT TGC TGT [ 576]

#gi|Pyrus G.. ... ..T .G. ... .T. ... ... ... ..- -.. ... A.. ... A.. ... [ 576]

#gi|Musa GC. .C. ... .C. .T. .G. ... .C. .C. .C- -.. C.. C.. C.. CT. CA. [ 576]

#gi|Jatropha GC. A.. ... ..T CT. .T. ... ... .C. ..- -.. A.. A.C C.. .T. CA. [ 576]

#gi|Nelumbo T.A A.. T.A CAA .TA ATT ATA .AA .A. A.T A.. AA. T.A .GA .CT CA. [ 576]

#gi|Populus TGA CCT TGC TAA AGA TAT GTT GCA AGT TCA TAG GAA TAC CTA TGC TGT [ 624]

#gi|Pyrus ... T.. ... ... G.. ... ... ... .A. ... ... ... ... G.. ... G.. [ 624]

#gi|Musa C.. T.. C.. GCG G.. CC. CC. C.. GA. C.. CC. CTC C.. ... C.. G.. [ 624]

#gi|Jatropha ... .T. G.. .TT TA. CC. TC. CA. ... ... A.A ... .G. T.. C.. GC. [ 624]

#gi|Nelumbo GC. TT. G.G C.T CA. ATA A-- A.. G.. G.. .CC ... CT. ... C.. .C. [ 624]

#gi|Populus TGT TGT AAG TAC TGA GAA CAT TAC ACA G-A ATT GGT ATT TTG GGA ACA [ 672]

#gi|Pyrus ... ... T.. ... ... A.. T.. ... T.. .-. ... ... .C. ... ... ... [ 672]

#gi|Musa C.. ... ... C.. ... ... ... C.. C.. .-. .C. ... .C. .C. .C. ..C [ 672]

#gi|Jatropha .A. .C. T.. C.. C.. -.. T.. ..T CA. CCG G.. ... ... C.. .CC ..G [ 672]

#gi|Nelumbo A.. G.. T.. C.. A.. ... ... A.. T.T T-. ... ... .C. GG. .C. ... [ 672]

#gi|Populus AGA AGT CAA TGT TGA TAC CGA ATT GCT TGT TTA GAG TCG GCG GTT CTG [ 720]

#gi|Pyrus ... .A. .C. ... ... ... .C. .C. .T. ... .CC .T. .T. .T. .G. .G. [ 720]

#gi|Musa GC. ... .G. ..C .C. .C. .C. ... ..C ... .CC ... ... ... CCG .C. [ 720]
#gi|Jatropha ... .A. .T. A.. .AC .C. TT. .C. ..C .A. ... ..A .G. .AA .CG .A. [ 720]

#gi|Nelumbo .CC GC. .C. A.C .CG .TT .C. ... ..C .C. .CC .CA .G. ... CCG GC. [ 720]

#gi|Populus CCG TTT TGT TGT CAA ATA AAG CTA AAG ATA AGA GAA GAG CGA AGT ATA [ 768]

#gi|Pyrus .A. ... ..C .T. .G. ... .GT .CG TG. ... G.C .TC .G. .A. ... ... [ 768]

#gi|Musa ..A .G. ..C .C. .C. ..C GCT .GG CG. ..C GCT .GC .CT .C. ... .C. [ 768]

#gi|Jatropha .AA ... ..C .CA ... ... ..A A.G ... C.. .A. A.T C.T .A. .A. .C. [ 768]

#gi|Nelumbo ... .CC .CC .T. ... .C. .GA TGT CC. .CC GCC ACC .C. .C. ... .CG [ 768]

#gi|Populus AGC TTG TTC ATG TGG TTA GAA CTC ATA AAG GAG CTG ACG ACA AGG CGT [ 816]

#gi|Pyrus ... ... .C. ... .T. .G. .G. ... ..T GT. .C. ... .T. .T. ... .A. [ 816]

#gi|Musa ... .A. .C. .C. .C. ..C .C. .C. .C. GT. .C. .C. .T. ... G.. .C. [ 816]

#gi|Jatropha ... ..T ..T GCA CA. .A. .GG .C. .A. G.. CTT ... ... ... .AA GT. [ 816]

#gi|Nelumbo ... .CC .C. .CA CCC .CC .C. .A. .CT .C. .T. .G. .G. .GC GT. G.. [ 816]

#gi|Populus TCA AGT GTG TCT ATC AGG AGC AGG ATG ATG CTG GAA AAA CAG GGG TTT [ 864]

#gi|Pyrus .T. G.. ... .T. ... .A. ... ... ... ... .C. .G. ... .T. ... ... [ 864]

#gi|Musa .TC GC. .C. .G. .C. ... ... .A. .C. .C. ... .C. ..G TG. .T. .G. [ 864]

#gi|Jatropha ATC .T. CG. CGA T.. GC. .AG ... ..T CCA A.. ... G.C TC. ... ..A [ 864]

#gi|Nelumbo A.C GC. CC. CA. .C. ... .AG .A. .C. .AA ... ... TTG TT. .T. .GA [ 864]

#gi|Populus CTT TGT CAA AAG AGC TCA TGG CAA TTG CTG GTG GTG CAC TTA AGA CTA [ 912]

#gi|Pyrus ... ... .C. .G. .T. ... ... ... ... .C. ... .G. .T. ... ... ... [ 912]

#gi|Musa .CC .C. .C. .G. .C. ... ... .C. ... .C. .G. AG. .G. ... ... TC. [ 912]

#gi|Jatropha .GC .TA GG. GG. .TT .AC .TC A.G .G. ... .A. AAA .T. .C. G.C .C. [ 912]

#gi|Nelumbo .CC .C. .C. G.. .C. .AG CCA ... CG. .A. .A. A.. .G. .G. G.. .C. [ 912]

#gi|Populus ATA TTA CAA CCT TGG GTC CTT TGG TTC TTC CCA TTA GTG AGC AAC TTT [ 960]

#gi|Pyrus .C. .C. ... .A. ... ... .GC .T. .C. .G. ..T .A. ... ... .G. ..C [ 960]

#gi|Musa .C. .C. .C. ..C .T. ... .CC .C. .C. ... .A. .C. .C. .A. .G. .CC [ 960]

#gi|Jatropha .C. .A. ... TTC .T. ..T .AC GTA ..T .G. .TT .CC CA. .AA TG. .AC [ 960]

#gi|Nelumbo .C. .C. .T. AGC .A. ... ..C .A. .G. ... .TC C.T CG. ... ... .C. [ 960]

#gi|Populus TGT TCT TCT CAA CTT TAG TTG CTA AGA AAT TGT TCA ATG CAA AAG TGA [1008]

#gi|Pyrus .C. ... .TG TT. ... .G. ... .G. ... .G. ... ... .C. .G. .G. ... [1008]

#gi|Musa .C. ... .TG .G. ..C .C. .G. .C. ... .GC .C. ... ... GC. .G. ... [1008]

#gi|Jatropha GA. ATA ..G TTT .GA ..A ..C AA. .C. GG. ACA .TG ..A A.T C.. GAC [1008]

#gi|Nelumbo .C. A.. .GG .C. A.. .GA ... .A. G.. .GG ... .T. .GA TG. .GA .A. [1008]

#gi|Populus AGC CGT ATA TCC CAG ATT TTA AGC TTG CCT TCG ATC ATT TCT GTA TTC [1056]

#gi|Pyrus ... .T. ... .A. ... ... .C. ... ... .T. .T. ... ... .T. .C. .A. [1056]

#gi|Musa ... .C. ... ... ... .C. .C. ... ... ... .T. .A. ... ... .C. .C. [1056]

#gi|Jatropha ..G TA. .CG .G. ..A ... .C. ..A GG. TGA .AC .G. ... .T. .CC .G. [1056]

#gi|Nelumbo ..T .T. .C. .G. ... .C. .C. ... GG. .T. ... .G. ... ... .C. .C. [1056]

#gi|Populus ATG CTG GAG GGA GAG CCG TGA TTG ATG AGC TTG AGA AGA ATC TGC AGC [1104]
#gi|Pyrus .C. .G. ... .A. .G. .T. ... ... ... ... ... ... ... ..T ... ... [1104]

#gi|Musa .C. ... .G. .A. .G. ... .C. .C. ... ... .A. ... ... ... ... ... [1104]

#gi|Jatropha CCA ..T C.. ... .GC .G. ... .AA .A. ..A .A. CA. .AG GGT .AA ... [1104]

#gi|Nelumbo ... .A. ... .T. ... .T. .CC ... .CA GCG .A. ... ... ... ... .T. [1104]

#gi|Populus TTT TGC CTA TTC ATG TTG AAG CTT CCA GGA TGA CTC TTC ATC GGT TTG [1152]

#gi|Pyrus ..C .A. .AG ... ... ... .G. .G. .TC ... ... .A. .C. .CA ... .C. [1152]

#gi|Musa .CC G.. .AG AC. ... .G. .G. ... ..C ... ... .C. .G. .C. ... ... [1152]

#gi|Jatropha ..G GTG A.. GAG .A. .G. ... ..G .AT T.. ... .A. .G. ..A ... ... [1152]

#gi|Nelumbo .GA C.G A.T GG. .GA .G. .GC ... .A. .A. ... .C. ..T .CA ... ... [1152]

#gi|Populus GTA ACA CTT CGT CAA GCT CGA TTT GGT ACG AGT TGG CTT ACA CTG AGG [1200]

#gi|Pyrus ... ... .C. ... .T. .T. ... ... ... .T. ... ... ... .T. .A. ... [1200]

#gi|Musa .C. ... .G. .C. .C. ... .C. .C. ... .T. ..C .T. ... ... ... ... [1200]

#gi|Jatropha .C. .TC AA. .T. .TT CA. ... ... ... .T. .AC .T. .G. .T. TG. .A. [1200]

#gi|Nelumbo .C. ... .A. .CA GC. ... .CT .G. ... .T. .AC .T. .C. ..T .C. ... [1200]

#gi|Populus CAA AGG AAA GAG TAC GGA GGG GGG ACC GTG TTT GGC AGA TTG CTT TTG [1248]

#gi|Pyrus ... ... GG. .GA .G. AA. A.. ..A ... ... .C. ... ... ... ... ... [1248]

#gi|Musa ... ... GGC .GA .G. ... A.. .CC ... .G. ... ... ... ... .C. .C. [1248]

#gi|Jatropha .C. .A. ... A.. .GA AA. AA. .CC ..A AG. .G. ... ..T ... GGA .G. [1248]

#gi|Nelumbo .T. ... GG. .G. .CA A.. A.. ..C .T. .G. .G. ... ... ... .AC .G. [1248]

#gi|Populus GCA GTG GTT TCA AGT GCA ACA GTG CAA TTT GGG AGG CTC TGA GG- --C [1296]

#gi|Pyrus .T. .C. ... ... ... .T. ... ... ..G .G. ... ... ... .TC A.- --A [1296]

#gi|Musa .G. ... .C. ... ... ... .T. ... .TG .G. ..C ... .G. .TT .C- --A [1296]

#gi|Jatropha .A. C.. .GC CT. .A. ..G CT. ... TCG ... ... ..T G.T .A. ..C CCA [1296]

#gi|Nelumbo .TT C.. ... .T. ... ... ... ... .TG .G. ..C G.. .A. .C. ..- --A [1296]

#gi|Populus ATG TTA AGC CAT CTT CTA GTA A-- -TC CAT GGC AGG ATT GCA TTG ACA [1344]

#gi|Pyrus G.. .A. .A. .T. ..C ..C A.. G-- -C. ... ..G .A. ... ... ..C ..G [1344]

#gi|Musa ... .G. ... .C. ..C .AG A.G G-- -.. ... ..G ... ... ... .CC .T. [1344]

#gi|Jatropha T.A ..G GAG AG. .CA AG. AAG G-- -C. ... ..G CT. .C. .T. ... .TC [1344]

#gi|Nelumbo CC. .AG .T. .CA .CA AGG AC. GGA A.G .T. ..T CC. ..G AG. ... .TG [1344]

#gi|Populus GGT ATC CGG TGC AGA TAG TCA TGT AGC T-- --- [1377]

#gi|Pyrus ... ... ... ..G ... CC. .TG CC. ... AGA GGT [1377]

#gi|Musa ... .C. .T. ..G .A. .T. .TG ATG G.T .TC CT- [1377]

#gi|Jatropha ... ... .AA .CT T.G CC. .TG ATC TAG GCA TTT [1377]

#gi|Nelumbo AC. TC. ... .TA TCG .GC C.. A.C T.G CCT --- [1377]

Data 1.1 Data of Five Nucleotide Base Sequence

 gi|Populus TGG AAA GAT CAG GTC TTG GTG [288]
gi|Pyrus TCG AGC GCT CTG GCC TTG GAG [288]
gi|Musa TCG AGC GTT CCG GCC TCG GAC [288]
gi|Jatropha TCA GTT CTT CTG GGC AAA GAC [288]
gi|Nelumbo TTA GTC TTA GCG GCC AAA GCC [288]
Data 1.2 Data of 20 Nitrogen Basa on Length of 288-309 Sequence
 B. Discussion

Clustal is a series of widely used computer programs used in Bioinformatics for

multiple sequence alignment. There have been many versions of Clustal over the
development of the algorithm that are listed below. The analysis of each tool and its
algorithm are also detailed in their respective categories. Available operating systems
listed in the sidebar are a combination of the software availability and may not be
supported for every current version of the Clustal tools. Clustal Omega has the widest
variety of operating systems out of all the Clustal tools. Based on the above analysis
of the data, obtained the order of nucleotides contained punctuation dots (.) and also
the sign of the dash (-). This sign has a meaning which is used in the analysis of
nucleotide. The dot shows the similarity of base sequences at nucleotide, while the
sign of the strip indicates the insertion or deletion to optimize the alignment. There is
also a value that is inside the brackets. This value indicates the number of nucleotides
in one line (Chenna et al., 2003).
Based on the result, the total bases that were obtained are 1377 bases from the 5
different sequences, with 390 conserved sites and 5 conserved sites, in the 20th
nitrogen base sequence of 5 sample with the 288 – 309 length sequence. This
alignment of genes indicates that this gene are a high on diversity based on the variaton
base on the site on each species. This difference is due to mutation events such as point
mutations (single amino acid or nucleotide changes) that appear as differing characters
in a single alignment column, and insertion or deletion mutations (indels or gaps) that
appear as hyphens in one or more of the sequences in the alignment. Multiple sequence
alignment is often used to assess sequence conservation of protein domains, tertiary
and secondary structures, and even individual amino acids or nucleotides (Higgins &
Sharp, 1988).
 II. CONCLUSION

Based on result and discussion above, it can be concluded that were obtained are
1377 bases from the 5 different sequences, with 390 conserved sites and 5 conserved
sites, in the 20th nitrogen base sequence of 5 sample with the 288 – 309 length
sequence.
 REFERENCE

Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T. J., Higgins, D. G. &
Thompson, J. D., 2003. Multiple Sequence Alignment with The Clustal Series
of Programs. Nucleic Acids Research. 31 (13), pp. 3497–500.
Higgins, D. G. & Sharp P. M., 1988. CLUSTAL: A Package for Performing Multiple
Sequence Alignment on A Microcomputer. Gene. 73 (1), pp. 237–244.