TUGAS GENETIKA POPULASI I

Nama: Flafiani Cios Conara

NIM: 18/426459/BI/10051
Kelas: Genpop B

a. Choose 5 DNA sequences from GenBank (1 target gene & 1 species with 5
populations/strains/voucher)

>MK567495.1 Nemacheilus fasciatus voucher BIF0173 cytochrome oxidase

subunit 1 (COI) gene, partial cds; mitochondrial
GTATTTGGTGCCTGGGCCGGAATAGTCGGTACCGCCCTTAGCCTTCTAATTCGAGCCGAACTAAGTCAAC
CAGGGTCCCTCCTGGGTGATGACCAGATTTATAATGTTATTGTTACTGCCCACGCCTTTGTTATAATCTT
CTTTATAGTGATACCAATCCTCATCGGAGGGTTTGGGAATTGACTAGTTCCCCTAATGATCGGAGCCCCC
GACATGGCATTCCCCCGGATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCTTACTATTACTAG
CCTCTTCGGGCGTTGAGGCCGGGGCCGGTACGGGGTGAACAGTCTACCCGCCTTTAGCAGGCAACCTTGC
CCACGCAGGAGCATCCGTAGATCTAACCATCTTCTCACTTCATCTGGCAGGTGTGTCCTCCATCCTCGGG
GCAATCAACTTTATCACAACAACCATCAATATGAAACCCCCAGCCATCTCTCAGTACCAAACCCCATTAT
TTGTTTGAGCCGTCCTTGTAACAGCCGTTCTCCTGCTTTTGTCACTTCCAGTTCTAGCTGCAGGGATTAC
CATGCTTTTAACAGACCGAAACCTAAACACCACATTCTTTGACCCCGCCGGAGGGGGGGACCCAATTCTC
TACCAACACCTC

>MK567494.1 Nemacheilus fasciatus voucher BIF0097 cytochrome oxidase

subunit 1 (COI) gene, partial cds; mitochondrial
CCTTTATTTAGTATTTGGTGCCTGGGCCGGAATAGTCGGTACCGCCCTTAGCCTTCTAATTCGAGCCGAA
CTAAGTCAACCAGGGTCCCTCCTGGGTGATGACCAGATTTATAATGTTATTGTTACTGCCCACGCCTTTG
TTATAATCTTCTTTATAGTGATACCAATCCTCATCGGAGGGTTTGGGAATTGACTAGTTCCCCTAATGAT
CGGAGCCCCCGACATGGCATTCCCCCGGATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCTTA
CTATTACTAGCCTCTTCGGGCGTTGAGGCCGGGGCCGGTACGGGGTGAACAGTCTACCCGCCTTTAGCAG
GCAACCTTGCCCACGCAGGAGCATCCGTAGATCTAACCATCTTCTCACTTCATCTGGCAGGTGTGTCCTC
CATCCTCGGGGCAATCAACTTTATCACAACAACCATCAATATGAAACCCCCAGCCATCTCTCAGTACCAA
ACCCCATTATTTGTTTGAGCCGTCCTTGTAACAGCCGTTCTCCTGCTTTTGTCACTTCCAGTTCTAGCTG
CAGGGATTACCATGCTTTTAACAGACCGAAACCTAAACACCACATTCTTTGACCCCGCCGGAGGGGGGGA
CCCAATTCTCTACCAACACCTC
>KT960790.1 Nemacheilus fasciatus voucher BIF3493 cytochrome oxidase
subunit 1 (COI) gene, partial cds; mitochondrial
CACCCTATATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCTAATTCGAGCC
GAACTAAGCCAACCAGGATCCCTCCTGGGAGATGACCAAATCTACAATGTTATTGTTACTGCACACGCCT
TTGTTATAATCTTCTTTATAGTAATGCCTATCCTCATTGGGGGATTTGGAAACTGACTAGTGCCGCTGAT
AATTGGAGCCCCCGACATGGCATTCCCCCGAATAAACAACATAAGCTTCTGACTCCTGCCGCCTTCCTTC
CTCCTGCTTCTAGCCTCATCAGGTGTTGAAGCCGGAGCCGGGACAGGGTGAACGGTCTACCCGCCACTGG
CAGGAAACCTTGCCCACGCAGGCGCATCCGTAGATCTGACCATTTTCTCCCTTCACCTGGCAGGTGTGTC
TTCCATCCTCGGGGCAATTAACTTTATTACTACAACTATTAACATAAAACCCCCAGCCATCTCTCAATAC
CAAACTCCCCTGTTCGTGTGGGCGGTCCTGGTAACAGCAGTCCTTCTGCTCCTATCACTCCCAGTCCTGG
CCGCTGGAATTACCATGCTCTTAACAGACCGAAATTTAAACACCACATTCTTTGACCCCGCCGGAGGAGG
GGACCCAATTCTATATCAGCACCTGTTC

>KT960795.1 Nemacheilus fasciatus voucher BIF2197 cytochrome oxidase

subunit 1 (COI) gene, partial cds; mitochondrial
CCTATATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCTAATTCGAGCCGAA
CTAAGCCAACCAGGATCCCTCCTGGGAGATGACCAGATCTACAATGTTATTGTTACTGCACACGCCTTTG
TTATAATCTTCTTTATAGTAATACCTATCCTTATTGGGGGATTTGGAAACTGACTAGTGCCGCTGATAAT
CGGGGCCCCCGACATGGCATTCCCCCGAATAAACAACATAAGCTTCTGACTCCTGCCGCCCTCCTTCCTC
CTGCTTCTAGCCTCATCAGGTGTTGAAGCCGGAGCCGGGACAGGATGAACGGTCTACCCGCCACTGGCAG
GAAACCTTGCCCACGCAGGCGCATCCGTAGATCTGACCATTTTCTCCCTTCACCTGGCAGGTGTGTCTTC
CATCCTCGGGGCAATTAACTTTATTACTACAACTATTAACATAAAACCCCCAGCCATCTCTCAATACCAA
ACTCCCCTGTTCGTGTGGGCGGTCCTGGTAACAGCAGTCCTTCTGCTCCTGTCACTCCCAGTCCTGGCCG
CTGGAATTACCATGCTCTTAACAGACCGAAATTTAAACACCACATTCTTTGACCCCGCCGGAGGCGGAGA
CCCAATTCTATATCAGCACCTG

>MN852339.1 Nemacheilus fasciatus isolate 2005-0971 cytochrome c

oxidase subunit I (COX1) gene, partial cds; mitochondrial
CTTTATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCTAATTCGAGCCGAAC
TAAGCCAACCAGGATCCCTCCTGGGAGATGACCAAATCTACAATGTTATTGTTACTGCACACGCCTTTGT
TATAATCTTCTTTATAGTAATGCCTATCCTCATCGGAGGATTTGGAAACTGACTAGTGCCGCTGATAATT
GGAGCCCCCGACATGGCATTTCCCCGAATAAATAATATGAGCTTCTGACTCCTGCCACCTTCCTTCCTCC
TGCTACTAGCCTCATCAGGCGTTGAAGCCGGGGCCGGGACAGGGTGAACGGTTTACCCGCCACTGGCAGG
AAACCTTGCCCACGCAGGCGCATCCGTAGATCTGACTATTTTCTCCCTCCACCTGGCAGGTGTGTCTTCT
ATCCTAGGGGCAATTAACTTTATTACTACAACTATCAACATAAAACCCCCAGCCATCTCCCAATACCAAA
CCCCCCTGTTCGTATGGGCGGTCCTAGTAACAGCAGTACTTCTGCTTCTATCACTCCCAGTCCTGGCCGC
TGGAATTACCATGCTCTTAACAGACCGAAATTTAAACACCACATTCTTTGACCCAGCCGGAGGAGGAGAC
CCAATTCTATATCAACACCTG

Table % Similarity
NEM_BIF017 NEM_BIF009 NEM_BIF34 NEM_BIF219 NEM_2005_0971
3 7 93 7
NEM_BIF0173 -
NEM_BIF0097 100,00% -
NEM_BIF3493 86,54% 86,48% -
NEM_BIF2197 86,70% 86,64% 98,47% -
NEM_2005_0971 86,38% 86,46% 96,01% 94,78% -
Note abbreviation :
1. NEM_BIF0173 = Nemacheilus fasciatus voucher BIF0173
2. NEM_BIF0097 = Nemacheilus fasciatus voucher BIF0097
3. NEM_BIF3439 = Nemacheilus fasciatus voucher BIF3439
4. NEM_BIF2197 = Nemacheilus fasciatus voucher BIF2197
5. NEM_2005_0971 = Nemacheilus fasciatus isolate 2005-0971

Alignment with Clustal Omega

NEM_BIF0173 -------------GTATTTGGTGCCTGGGCCGGAATAGTCGGTACCGCCCTTAGCCTTCT 47
NEM_BIF0097 ---CCTTTATTTAGTATTTGGTGCCTGGGCCGGAATAGTCGGTACCGCCCTTAGCCTTCT 57
NEM_2005_0971 ----CTTTATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCT 56
NEM_BIF3493 CACCCTATATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCT 60
NEM_BIF2197 ---CCTATATTTAGTTTTCGGTGCCTGAGCCGGAATAGTCGGTACCGCCCTTAGCCTTCT 57
** ** ******** ********************************

NEM_BIF0173 AATTCGAGCCGAACTAAGTCAACCAGGGTCCCTCCTGGGTGATGACCAGATTTATAATGT 107

NEM_BIF0097 AATTCGAGCCGAACTAAGTCAACCAGGGTCCCTCCTGGGTGATGACCAGATTTATAATGT 117
NEM_2005_0971 AATTCGAGCCGAACTAAGCCAACCAGGATCCCTCCTGGGAGATGACCAAATCTACAATGT 116
NEM_BIF3493 AATTCGAGCCGAACTAAGCCAACCAGGATCCCTCCTGGGAGATGACCAAATCTACAATGT 120
NEM_BIF2197 AATTCGAGCCGAACTAAGCCAACCAGGATCCCTCCTGGGAGATGACCAGATCTACAATGT 117
****************** ******** *********** ******** ** ** *****

NEM_BIF0173 TATTGTTACTGCCCACGCCTTTGTTATAATCTTCTTTATAGTGATACCAATCCTCATCGG 167

NEM_BIF0097 TATTGTTACTGCCCACGCCTTTGTTATAATCTTCTTTATAGTGATACCAATCCTCATCGG 177
NEM_2005_0971 TATTGTTACTGCACACGCCTTTGTTATAATCTTCTTTATAGTAATGCCTATCCTCATCGG 176
NEM_BIF3493 TATTGTTACTGCACACGCCTTTGTTATAATCTTCTTTATAGTAATGCCTATCCTCATTGG 180
NEM_BIF2197 TATTGTTACTGCACACGCCTTTGTTATAATCTTCTTTATAGTAATACCTATCCTTATTGG 177
************ ***************************** ** ** ***** ** **

NEM_BIF0173 AGGGTTTGGGAATTGACTAGTTCCCCTAATGATCGGAGCCCCCGACATGGCATTCCCCCG 227

NEM_BIF0097 AGGGTTTGGGAATTGACTAGTTCCCCTAATGATCGGAGCCCCCGACATGGCATTCCCCCG 237
NEM_2005_0971 AGGATTTGGAAACTGACTAGTGCCGCTGATAATTGGAGCCCCCGACATGGCATTTCCCCG 236
NEM_BIF3493 GGGATTTGGAAACTGACTAGTGCCGCTGATAATTGGAGCCCCCGACATGGCATTCCCCCG 240
NEM_BIF2197 GGGATTTGGAAACTGACTAGTGCCGCTGATAATCGGGGCCCCCGACATGGCATTCCCCCG 237
 ** ***** ** ******** ** ** ** ** ** ***************** *****

NEM_BIF0173 GATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCTTACTATTACTAGCCTCTTC 287

NEM_BIF0097 GATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCTTACTATTACTAGCCTCTTC 297
NEM_2005_0971 AATAAATAATATGAGCTTCTGACTCCTGCCACCTTCCTTCCTCCTGCTACTAGCCTCATC 296
NEM_BIF3493 AATAAACAACATAAGCTTCTGACTCCTGCCGCCTTCCTTCCTCCTGCTTCTAGCCTCATC 300
NEM_BIF2197 AATAAACAACATAAGCTTCTGACTCCTGCCGCCCTCCTTCCTCCTGCTTCTAGCCTCATC 297
***** ** ** ************** ** ** ****** * ** * ******** **

NEM_BIF0173 GGGCGTTGAGGCCGGGGCCGGTACGGGGTGAACAGTCTACCCGCCTTTAGCAGGCAACCT 347

NEM_BIF0097 GGGCGTTGAGGCCGGGGCCGGTACGGGGTGAACAGTCTACCCGCCTTTAGCAGGCAACCT 357
NEM_2005_0971 AGGCGTTGAAGCCGGGGCCGGGACAGGGTGAACGGTTTACCCGCCACTGGCAGGAAACCT 356
NEM_BIF3493 AGGTGTTGAAGCCGGAGCCGGGACAGGGTGAACGGTCTACCCGCCACTGGCAGGAAACCT 360
NEM_BIF2197 AGGTGTTGAAGCCGGAGCCGGGACAGGATGAACGGTCTACCCGCCACTGGCAGGAAACCT 357
** ***** ***** ***** ** ** ***** ** ******** * ***** *****

NEM_BIF0173 TGCCCACGCAGGAGCATCCGTAGATCTAACCATCTTCTCACTTCATCTGGCAGGTGTGTC 407

NEM_BIF0097 TGCCCACGCAGGAGCATCCGTAGATCTAACCATCTTCTCACTTCATCTGGCAGGTGTGTC 417
NEM_2005_0971 TGCCCACGCAGGCGCATCCGTAGATCTGACTATTTTCTCCCTCCACCTGGCAGGTGTGTC 416
NEM_BIF3493 TGCCCACGCAGGCGCATCCGTAGATCTGACCATTTTCTCCCTTCACCTGGCAGGTGTGTC 420
NEM_BIF2197 TGCCCACGCAGGCGCATCCGTAGATCTGACCATTTTCTCCCTTCACCTGGCAGGTGTGTC 417
************ ************** ** ** ***** ** ** **************

NEM_BIF0173 CTCCATCCTCGGGGCAATCAACTTTATCACAACAACCATCAATATGAAACCCCCAGCCAT 467

NEM_BIF0097 CTCCATCCTCGGGGCAATCAACTTTATCACAACAACCATCAATATGAAACCCCCAGCCAT 477
NEM_2005_0971 TTCTATCCTAGGGGCAATTAACTTTATTACTACAACTATCAACATAAAACCCCCAGCCAT 476
NEM_BIF3493 TTCCATCCTCGGGGCAATTAACTTTATTACTACAACTATTAACATAAAACCCCCAGCCAT 480
NEM_BIF2197 TTCCATCCTCGGGGCAATTAACTTTATTACTACAACTATTAACATAAAACCCCCAGCCAT 477
** ***** ******** ******** ** ***** ** ** ** **************

NEM_BIF0173 CTCTCAGTACCAAACCCCATTATTTGTTTGAGCCGTCCTTGTAACAGCCGTTCTCCTGCT 527

NEM_BIF0097 CTCTCAGTACCAAACCCCATTATTTGTTTGAGCCGTCCTTGTAACAGCCGTTCTCCTGCT 537
NEM_2005_0971 CTCCCAATACCAAACCCCCCTGTTCGTATGGGCGGTCCTAGTAACAGCAGTACTTCTGCT 536
NEM_BIF3493 CTCTCAATACCAAACTCCCCTGTTCGTGTGGGCGGTCCTGGTAACAGCAGTCCTTCTGCT 540
NEM_BIF2197 CTCTCAATACCAAACTCCCCTGTTCGTGTGGGCGGTCCTGGTAACAGCAGTCCTTCTGCT 537
*** ** ******** ** * ** ** ** ** ***** ******** ** ** *****

NEM_BIF0173 TTTGTCACTTCCAGTTCTAGCTGCAGGGATTACCATGCTTTTAACAGACCGAAACCTAAA 587

NEM_BIF0097 TTTGTCACTTCCAGTTCTAGCTGCAGGGATTACCATGCTTTTAACAGACCGAAACCTAAA 597
NEM_2005_0971 TCTATCACTCCCAGTCCTGGCCGCTGGAATTACCATGCTCTTAACAGACCGAAATTTAAA 596
NEM_BIF3493 CCTATCACTCCCAGTCCTGGCCGCTGGAATTACCATGCTCTTAACAGACCGAAATTTAAA 600
NEM_BIF2197 CCTGTCACTCCCAGTCCTGGCCGCTGGAATTACCATGCTCTTAACAGACCGAAATTTAAA 597
* ***** ***** ** ** ** ** *********** ************** ****

NEM_BIF0173 CACCACATTCTTTGACCCCGCCGGAGGGGGGGACCCAATTCTCTACCAACACCTC--- 642

NEM_BIF0097 CACCACATTCTTTGACCCCGCCGGAGGGGGGGACCCAATTCTCTACCAACACCTC--- 652
NEM_2005_0971 CACCACATTCTTTGACCCAGCCGGAGGAGGAGACCCAATTCTATATCAACACCTG--- 651
NEM_BIF3493 CACCACATTCTTTGACCCCGCCGGAGGAGGGGACCCAATTCTATATCAGCACCTGTTC 658
NEM_BIF2197 CACCACATTCTTTGACCCCGCCGGAGGCGGAGACCCAATTCTATATCAGCACCTG--- 652
****************** ******** ** *********** ** ** *****