COURSE

STAB3343 MOLECULAR SYSTEMATICS

SEMESTER 2 2022/2023
SET 1

TITLE
LABORATORY REPORT ON PRACTICAL 2 – MULTIPLE SEQUENCE ALLIGNMENT

LECTURER
PROF. MADYA DR. CHOONG CHEE YEN

NAME
ADILAH AIMAN BINTI ZAFIR KHAN (A184381)
1.0 TITLE
Multiple Sequence Allignment

2.0 OBJECTIVE
To carry out multiple sequence allignment by using CLUSTALW under BioEdit software and to
calculate the pairwise genetic distance of different characters state.

3.0 RESULT
....|....| ....|....| ....|....| ....|....| ....|....| ....|....|
5 15 25 35 45 55
Anisoptera TCACTTTTTT TGGAAAATGC GGGTTCGGGC AATAAATTCA GTTTACTGAT TGTAAAACGT
Vatica TCACTTTTTT TGGAAAATGC GGGTTCGGAC AATAAATTCA GTTTACTGAT TGTAAAACGT
Shorea TCACTTTTTT TGGAAAATGC GGGTTCTGAC AATAAATTCA GTTTACTGAT TGTAAAACGT
Hopea TCACTTTTTT TGGAAAATTC GGGTTCTGAC AATAAATTCA GTTTACTGAT TGTAAAACGT
Dipterocarpus TCACTTTTTT TGGAAAATGC GGGTTCCGAC AATAAATTCA GTTTACTGAT TGTAAAACGT
Dryobalanops TCACTTTTTT TGGAAAATGC GGGTTCGGAC AGTAAATTCA GTTTACTGAT TGTAAAACGT
Upuna TCACTTTTTT TGGAAAATGC GGGTTCGGAC AATAAATTCA GTTTACTGAT TGTAAAACGT

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

65 75 85 95 105 115
Anisoptera TTGATTACTC GAATGTATCA ACAGAATCAT TTTATTAGTT TTTCTAATGA TTCTAATCAA
Vatica TTGATTACTC GAATGTATCA ACAGAATCAT TTTATTAGTT TTTCTAATGA TTCTAATCAA
Shorea TTGATTACTC GAATGTATCA ACAAAATCTT TTGATTAGTT TTTCTAATGA TTCTAATCAA
Hopea TTGATTACTC GAATGTATCA ACAAAATCTT TTGATTAGTT TTTCTAATGA TTCTAATCAA
Dipterocarpus TTGATTACTC GAATGTATCA ACAGAATCAT TTGATTAGTT TTTCTAATGA TTCTAATCAA
Dryobalanops TTGATTACTC GAATGTATCA ACAAAATCAT TTGATTAGTT TTTCTAATGA TTCTAATCAA
Upuna TTGATTACTC GAATGTATCA ACAGAATCAT TTTATTAGTT TTTCTAATGA TTCTAATCAA

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

125 135 145 155 165 175
Anisoptera AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC CGGATTTGCA
Vatica AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC CGGATTTGCA
Shorea AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC TGGGTTTGCA
Hopea AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC TGGGTTTGCA
Dipterocarpus AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC TGGATTTGCA
Dryobalanops AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC TGGATTTGCA
Upuna AATCCCTTTT TTGGGCACAA TAAGAATTTG TATTCTCAAA TGATATCGGC CGGATTTGCA

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

185 195 205 215 225 235
Anisoptera ATCATTGTGG AAATTCCATT TTCCCTACAA TTAGGATCTT ATTTACAAGG GAAAGAAGGA
Vatica ATCATTGTGG AAATTCCATT TTCCCTACAA TTAGGATCTT ATTTACAAGG GAAAGAAAGA
Shorea ATCATTGTGG AAATTCCATT TTCCCTACAA TTAGTATCTT ATTTACAAGG GAAAGAAGGA
Hopea ATTATTGTGG AAATTCCATT TTCCCCACAA TTCGTATCTT ATTTACAAGG GAAAGAAGGG
Dipterocarpus ATCATTGGGG AAATTCCATT TTCCCTACAA TTAGTATCTT ATTTACAAGG GAAAGAAGGA
Dryobalanops ATCATTGTGG AAATTCCATT TTCCCTACAA TTAGTATCTT ATTTACAAGG GAAAGAAGGA
Upuna ATCATTGTGG AAATTCCATT TTCCCTACAA TTAGGATCTT ATTCACAAGG GAAAGAAAGA

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

245 255 265 275 285 295
Anisoptera GTAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Vatica GTAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Shorea GTAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Hopea GGAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Dipterocarpus GTAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Dryobalanops GTAAAATATC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC
Upuna GTAAAATCTC ATAATTTCCA ATCAATTCAT TCAATATTTC CTTTTTTAGA GGACAAATTC

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

305 315 325 335 345 355
Anisoptera TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATCCATCT GGAAATCTTG
Vatica TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATCCATCT GGAAATCTTG
Shorea TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATTCATCT GGAAATCCTG
Hopea TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATCCATCT GGAAATCCTG
Dipterocarpus TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATCCATCT GGAAATCTTG
Dryobalanops TCCCATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCATGCATCT GGAAATCCTG
Upuna TCACATTTAA ATTATGTGTT AGATGTACTA ATACCTCATC CCCTCCATCT GGAAATCTTG

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

365 375 385 395 405 415
Anisoptera ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCTTCTT TGCATTTATT ACGATTCCTT
Vatica ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCTTCTT TGCATTTATT ACGATTCCTT
Shorea ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCCTCTT TGCATTTATT ACGGTTCCTT
Hopea ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCCTCTT TGCATTTATT ACGGTTCCTT
Dipterocarpus ATTCAAGTCC TTCGCTACTG GGTAAGGGAG TCCTCCTCTT TGCATTTATT ACGGTTCCTT
Dryobalanops ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCCTCTT TGCATTTATT ACGGTTCCTT
Upuna ATTCAAGTCC TTCGCTACTG GGTAAAGGAG TCCTCTTCTT TGCATTTATT ACGATTCCTT

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

425 435 445 455 465 475
Anisoptera CTCTACAAAT ATTGCAATTT TAAGAGTCTT ATTACTCCAA AGAAATCCCT TTTTATTTTG
Vatica CTCTACAAGT ATTGCAATTT TAAGAGTCTT ATTACTCCAA AGAAATCCCT TTTTATTTTG
Shorea CTCTACAAGT ATTGTAATTT TAAGAGTCTT ATTACTCCAA AGAAATCCCC CGTTTTTTTG
Hopea CTCTACAAGT ATTGTCATTT TAAGAGTCTT ATTACTTCAA AGAAATCCCT TTTTTTTTTG
Dipterocarpus CTCTACAAGT ATTGTAATTT TAAGAGTCTT TTTACTCCAA AGAAATCCCC TTTTTTTTTG
Dryobalanops CTCTACAAGT ATTGTAATTT TAAGAGTCTT ATTACTCCAA AGAAATCCCT TTTTATTTTG
Upuna CTCTACAAGT ATTGCAATTT TAAGAGTCTT ATTACTCCAA AGAAATCCCT TTTTATTTTG

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

485 495 505 515 525 535
Anisoptera AATCCAAGAT TTTTCTTATT CCTATATAAT TCTTATATAT GTGAATACGA ATCCATTTTC
Vatica AATCCAAGAT TTTTCTTATT CCTATATAAT TCTTATGTAT GTGAATACGA ATCCATTTTC
Shorea AATCCAAGAT TGTTCTTGTT CCTATATAAT TCTTATGTAT GTGAATACGA ATCCATTTTC
Hopea AATCCAAGAT TTTTCTTGTT CCTATATAAT TCTTATGTAT GTGAATACGA ATCCATTTTC
Dipterocarpus AATCCAAGAT TTTTCTTGTT CCTATATAAT TCTTACGTAT GTGAATACGA ATCCATTTTC
Dryobalanops AATCTAAGAT TTTTCTTGTT CCTATATAAT TCTTATGTAT GTGAATACGA ATCCATTTTC
Upuna AATCCAAGAT TTTTCTTATT CCTATATAAT TCTTATGTAT GTGAATACGA ATCCATTTTC

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

545 555 565 575 585 595
Anisoptera CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAGT CTTTCTTGAA
Vatica CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAGT CTTTCTTGAA
Shorea CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAGT CTTTCTTGAA
Hopea CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAAT CTTTCTTGAA
Dipterocarpus CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAGT CTTTCTTGAA
Dryobalanops CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAACTG CTTCTGGAGT CTTTCTTGAA
Upuna CTTTTTCTCC GTAACCAATC CTCTCATTTA CGATCAATTG TTTCTGGAGT CTTTCTTGAA

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

605 615 625 635 645 655
Anisoptera CGAATCCATT TCTATCGAAA AATAGAGCAT CTCGTAGAAG TCTTTGCTAA TGATTTTCAG
Vatica CGAATCCATT TCTATCGAAA AATAGAACAT CTCGTAGAAG TTTTTGCTAA TGATTTTCAG
Shorea CGAATCCATT TCTATCGAAA AATAGAGCAT CTCGTAGAAG TTTTTGCTAA TGATTTTCAG
Hopea CGAATCCATT TCTATCGAAA AATAGAGCAT CTCGTAGAAG TTTGTGCTAA TGATTTTCAG
Dipterocarpus CGAATCCATT TCTATCGAAA AATAGAGGAT CTCGTAGAAG TTTTTGCTAA TGATTTTCAG
Dryobalanops CGAATCCATT TCTATCGAAA AATAGAACAT CTTATAGAAG TTTTTTCTAA TGATTTTCAG
Upuna CGAATCCATT TCTATCGAAA AATAGAGCAT CTCGTAGAAG TTTTTGCTAA TGATTTTCAG

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

665 675 685 695 705 715
Anisoptera GCTAACTTAT GTTTGTTCAA GGACCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Vatica ACTAACTTAT GTTTGTTCAA GGACCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Shorea GCTAACCTAT GTTTGTTCAA GGATCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Hopea GCTAACCTAT GTTTGTTCAA GGATCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Dipterocarpus GCTAACCTAT GTTTGTTCAA GGATCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Dryobalanops GCTAACCTAT TTTTGTTCAA GGATCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
Upuna GCTAACTTAT GTTTGTTCAA GGACCCTTTC ATACATTTTG TTAGATATCA AAGAAAATCA
 ....|....| ....|....| ....|....| ....|....| ....|....| ....|....|
725 735 745 755 765 775
Anisoptera ATTCTGTCTT CCAAGGATAC GCCTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCGAT
Vatica ATTCTGTCTT CCAAGGATAC GCCTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCCAT
Shorea ATTCTTTCTT CCAAGGATAC GCCTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCGAT
Hopea ATTCTTTTTT CCAAGGATAC GCCTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCAAT
Dipterocarpus ATTCTGTTTT CCAAGGATAC GCCTCTTCTG ATGACTAAGT GGAAATTCTA CTTTGTCGAT
Dryobalanops ATTCTGTCTT CCAAGGATAC GCCTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCGAT
Upuna ATTCTGTCTT CCAAGGATAC GCTTCTTCTG ATGAATAAGT GGAAATTTTA CTTTGTCGAT

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

785 795 805 815 825 835
Anisoptera TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT CCGGATAAAC
Vatica TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT CCGGATAAAC
Shorea TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATAAAGAT CCGGATAAAC
Hopea TTATGGCAAT ATTCTTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT TCGGATAAAC
Dipterocarpus TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT CCGGATAAAC
Dryobalanops TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT CCGGATAAAC
Upuna TTATGGCAAT ATTATTTTTA CATGTGGTCT CAATCAGGAA GGATACGGAT CCGGATAAAC

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

845 855 865 875 885 895
Anisoptera CAATTATCAA AAAAGTCTCT CAATTTTCTG GGTTATCGTT CAAGTATGCG ATTAGATTCT
Vatica CAATTATCAA AAAATTCTCT CGATTTTCTG GGTTATCGTT CAAGTATGCG ATTAGATTCT
Shorea CAATTATCAA AAAATTCTAT CGATTTTCTG GGTTATCGTT CAAGTATGCG ATTAGATTCT
Hopea CAATTATCAA AAAATTCTCT CGATTTTCTG GGTTATCGTT CAAGTATACG ATTAGATTCC
Dipterocarpus CAATTATCAA AAAATTCTCT CGATTTTCTG AGTTATCGTT CAAGTATGCG ATTAGATTCT
Dryobalanops CAATTATCAA AAAATTCTAT CGATTTTCTG GGTTATCGTT CAAGTATGCG ATTAGATTCT
Upuna CAATTATCAA AAAATTCTCT CAATTTTCTG GGTTATCGTT CAAGTATGCG ATTAGATTCT

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

905 915 925 935 945 955
Anisoptera TTAGTGGTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG
Vatica TTAGTGGTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG
Shorea TTAGTGGTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG
Hopea TTAGTGGTGC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG
Dipterocarpus TTAGTGTTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGAGAATGT TATGAAGAAG
Dryobalanops TTAGTGGTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG
Upuna TTAGTGGTAC GGAGTCAAAT GCTAGAAAAC TCATTTATAG TAGATAATGT TATGAAGAAG

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

965 975 985 995 1005
Anisoptera CTGGAAACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A
Vatica CTGGAAACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A
Shorea CTGGAGACAA AAATTCCAAT TCTCGCCTTG ATTGGATCAT TGTCCAAAGC A
Hopea CTGGAGACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A
Dipterocarpus CTGGAGACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A
Dryobalanops CTGGAGACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A
Upuna CTGGAAACAA AAATTCCAAT TCTAGCCTTG ATTGGATCAT TGTCCAAAGC A

3.1 Based on the DNA alignment, determine the number of constant and variable characters.
Give all the variable characters.
Constant characters : 936
Variable characters : 75
List of variable characters
Character 19 Character 27 Character 29 Character 32 Character 84 Character 89
Character 93 Character 171 Character 174 Character 183 Character 188 Character 206
Character 213 Character 215 Character 224 Character 238 Character 240 Character 242
Character 248 Character 303 Character 343 Character 345 Character 358 Character 386
Character 396 Character 414 Character 429 Character 435 Character 436 Character 451
Character 457 Character 470 Character 471 Character 472 Character 475 Character 485
Character 492 Character 498 Character 516 Character 517 Character 578 Character 581
Character 589 Character 627 Character 628 Character 633 Character 634 Character 642
Character 644 Character 646 Character 661 Character 667 Character 671 Character 684
Character 726 Character 728 Character 743 Character 755 Character 768 Character 778
Character 794 Character 826 Character 827 Character 831 Character 855 Character 859
Character 862 Character 871 Character 888 Character 900 Character 907 Character 909
Character 945 Character 966 Character 984

3.2 Give (separately) all the autapomorphic and synapomorphic characters.

Autapomorphic characters Synapomorphic characters
19 581 27
29 589 84
32 628 89
183 633 93
188 634 171
206 642 174
213 644 215
 224 646 238
240 661 345
242 671 358
248 743 396
303 755 414
343 768 435
386 794 470
429 826 475
436 827 498
451 831 627
457 855 667
471 871 684
472 888 726
485 900 728
492 907 778
516 909 859
517 945 862
578 984 966

3.3 Do you observe length mutation in the DNA allignment? Why?

No length mutation. This is because there is no gaps in the sequences from the allignment. Gaps in this
context means mutations due to insertions or deletions.

3.4 Determine the pairwise genetic distance between dipterocarp taxa.

Anisoptera Vatica Shorea Hopea Dipterocarpus Dryobalanops Upuna

Anisoptera

10
Vatica 1011
= 0.009891
32 30
Shorea 1011 1011
= 0.03165 = 0.02967
40 37 26
Hopea 1011 1011 1011
= 0.03956 = 0.0366 = 0.0257
 30 28 25 33
Dipterocarpus 1011 1011 1011 1011
= 0.02967 = 0.0277 = 0.02473 = 0.03264
29 25 22 33 27
Dryobalanops 1011 1011 1011 1011 1011
= 0.02868 = 0.0247 = 0.02176 = 0.03264 = 0.02671
11 9 33 41 31 30
Upuna 1011 1011 1011 1011 1011 1011
= 0.01088 = 0.0089 = 0.03264 = 0.04055 = 0.03066 = 0.02967