Adinulos Week 5
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- BIOL368/S20:Week 1
- BIOL368/S20:Week 2
- BIOL368/S20:Week 3
- BIOL368/S20:Week 4
- BIOL368/S20:Week 5
- BIOL368/S20:Week 6
- BIOL368/S20:Week 8
- BIOL368/S20:Week 9
- BIOL368/S20:Week 10
- BIOL368/S20:Week 11
- BIOL368/S20:Week 13
- BIOL368/S20:Week 14
Journal Pages
- adinulos Week 2
- adinulos Week 3
- adinulos Week 4
- adinulos Week 5
- adinulos Week 6
- adinulos Week 8
- adinulos Week 10
- adinulos Week 11
- adinulos Week 13
- adinulos Week 14
Class Journal Pages
- BIOL368/S20:Class Journal Week 1
- BIOL368/S20:Class Journal Week 2
- BIOL368/S20:Class Journal Week 3
- BIOL368/S20:Class Journal Week 4
- BIOL368/S20:Class Journal Week 5
- BIOL368/S20:Class Journal Week 6
- BIOL368/S20:Class Journal Week 10
- BIOL368/S20:Class Journal Week 11
- BIOL368/S20:Class Journal Week 13
- BIOL368/S20:Class Journal Week 14
Purpose
Methods/Results
Activity 1
Part 1: Pubmed
- I was able to access the PubMed entry by going to the NCBI website, clicking on the link for the PubMed Search Engine, and then entering the PubMed ID found in the article citation into the search bar. The sequences were all listed on the side under related information, with sections like MedGen, Nucleotide, and others.
- Other ways for obtaining the article information could have been typing in the authors names or the title of the journal article.
- Other related information include references, taxonomy and protein sequences.
Part 2 GenBank
- The accession number of the sequence I chose was AF089153.
- The sequence was obtained from Subject 4.
- The definition section of the record contains information about the subject, the visit, the clone and the type of isolate of HIV.
Part 3: Introduction to Phylogeny.fr
Alignment in Clustal Format CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
AF089141.1 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG AF089501.1 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG AF016767.2 GGGGTAGTAATTAGATCCGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG AF089481.1 GAGGTAGTAATAAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG AF089153.2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATTATAATAGTACAGCTG * *** **** ***** * ****** * ************ *** ***********
AF089141.1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAA-- AF089501.1 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA AF016767.2 AATGAATCTGTAAAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAC-- AF089481.1 AATAAAGCTGTAGAAATTAATTGCACAAGACCCAACAACAATAAAAGAAGAAGAATAA-- AF089153.2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACCATACAGTAAGAAAGATAC-- *** ** ***** *** ***** ********* **** ** * * ** **
AF089141.1 -CTCTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGGGATATAAGAAAA AF089501.1 CATATAGGACCAGGGAGACCATTCTATACAACAGG---AATAAAAGGAAATATAAGACAA AF016767.2 -ATATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACCA AF089481.1 -GTATGGGACCAGGGAGAGTATTGTATACAACAGGAGAAATAATAGGAGATATAAGGCAA AF089153.2 -CTATAGGACCAGGGAGAGCATTTTATACAACAGG---CAGAATAGGAGATATAAGGCAA * * ******** *** ** *********** * ** *** ******* *
AF089141.1 GCACATTGTAACCTTAGTAGAGCAGGTTGAAATAACACTTTAGAAAGAATAGCTATAAAA AF089501.1 GCACATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTGGAAAA AF016767.2 GCATATTGTAACATTAGTAGAGCAGAATGGGATAACACTTTAAAACAGATAGTTATAAAA AF089481.1 GCACATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTAACAAA AF089153.2 GCACATTGTAACATTAGTAGAACAAAATGGAATAACACTTTAAAACTGATAGTTAACAAA *** ******** ******** * ** ** * ****** ** *** * ***
AF089141.1 TTAAGAGAACAATTTCA---GAATAAAACAATAGCCTTTAATCAATCCTCA AF089501.1 TTAAGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA AF016767.2 TTAAGAGAACACTTTGG---GAATAAAACAATAGTCTTTAATCACTCTTCA AF089481.1 TTAAGGGAACAATTTAG---GAATAAAACAATAATCTTTAATCAATCCTCA AF089153.2 TTAAGAGAACAATTTAG---GAATAAAACAATAATCTTTAATCAATCCTCA ***** ***** * * ************* ****** ** * *
Phylogenetic Tree
- Differences in the sequences are seen in the distances between the branches as well as the number of branches present for each strain.
Activity 2
Part 1
Alignment in Clustal Format CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S7V1-6 GAGGTAGTAATTAGATCTGCCAATTTCACGGACAATACTAAGACCATAATAGTACAGCTG S7V1-9 GAGATAGTAATTAGATCTGCCAATTTCTCGGACAATACTAAGACCATAATAGTACAGCTG S7V1-7 GAGATAGTAATTAGATCTGCCAATTTCTCGGACAATACTAAAACCATAATAGTACAGCTG S10V1-3 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-7 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S10V1-5 GAGGTAGTAATTAGATCTGAAAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG S1V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S15V1-8 GGGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S15V1-6 GGGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S15V1-10 GGGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG * * ************* * ****** ** ***** **** * ****************
S7V1-6 AATGTATCTGTAGAAATTAATTGTACGAGACCCAACAACAATACAAGAAAAAGTATACCT S7V1-9 AGTGTATCTGTAGAAATTAATTGTACGAGACCCAACAACAATACAAGAAAAAGTATACCT S7V1-7 AATGTATCTGTAGAAATTAATTGTACGAGACCCAACAACAATACAAGAAAAAGTATACCT S10V1-3 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-7 AATAAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S10V1-5 AATAAATCTGTAGAAATTAATCGCACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S1V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-6 AATGAATCTGTAGAAATTAACTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S15V1-8 AAGGAAGCTGTAAGAATTAATTGTATAAGACCCAACAACAATACAAGAAGAAGTATACCT S15V1-6 AAGGAAGTTGTAAGAATTAATTGTATAAGACCCAACAACAATACAAGAAGAAGGATACCT S15V1-10 AAGGAAGCTGTAAGAATTAATTGTATAAGACCCAACAATAATACAAGAAGAAGGATACCT * * **** ****** * * *********** ********** *** *** *
S7V1-6 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAATAGGAAATATAAGACAAGCA S7V1-9 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAATAGGAAATATAAGACAAGCA S7V1-7 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAATAGGAAATATAAGACAAGCA S10V1-3 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAACAGGAGATATAAGGCAAGCA S10V1-7 ATGGGACCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S10V1-5 ATGGGGCCAGGGAGAGCATTTTATACAACAGGAGAAATAATAGGAGATATAAGGCAAGCA S1V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACCAGCA S1V1-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S1V1-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S15V1-8 ATGGGACCAGGGAAAGCATTTTAT---ACAGGAGAGATAATAGGAGATATAAGGCAAGCA S15V1-6 ATAGGACCAGGGAGCGCATTTTATACAACAGG---CATAATAGGAGATATAAGGCAAGCA S15V1-10 ATAGGACCAGGGAGCGCATTTTATACAACAGG---CATAATAGGAGATATAAGGCAAGCA ** ** ***** * ********* ***** **** **** ******* * ****
S7V1-6 CATTGTACCGTAAGTAGAGTAAAATGGAATAACACTTTAAAACAGATAGTTACAAAATTA S7V1-9 CATTGTAACATTAATAGAGCAAAATGGAATAACACTTTAAAGCAGATGGCTACAAAATTA S7V1-7 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTACAAAATTA S10V1-3 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-7 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S10V1-5 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGGTAGTTGACAAATTA S1V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAACAAATTA S1V1-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAGACAGATAGTTATAAAATTA S15V1-8 CATTGTAACATTAGTAGATCAAAATGGAATCACACTTTAAAACAGATAGTTAACAAATTA S15V1-6 CATTGTAACATTAGTATAACAGAATGGAATAACACTTTAAAACAGATAGTTAACAATTTA S15V1-10 CATTGTAACATTAGTGGATCAAAATGGAATAGCACTTTAAAACAGATAGTTAACAAATTA ****** * * * * * * ******** ******** *** * * * ** ***
S7V1-6 AGAGAACAATTTGGGAATAAAACAATAGTCTTTAATCAATCCTCA S7V1-9 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAATCAATCCTCA S7V1-7 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAATCAATCCTCA S10V1-3 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-7 GGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S10V1-5 AGAGAACAATTTAGGAATAAAACAATAATCTTTAATCAATCCTCA S1V1-5 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-3 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S15V1-8 AGAGAACAATTTGTGAATAAAACAATAATATTTAATCAATCCTCA S15V1-6 AGAGAACAATTTGTGAATAAAACAATAGTCTTTAACCAATCCTCA S15V1-10 AGAGAACAATTTGTGAATAAACCAATAATCTTTAATCAATCCTCA ** **** *** ******* ***** * ***** ** ******
Activity 2 Phylogenetic Tree
Subject | Clone # |
Subject 1 | 3 |
5 | |
6 | |
Subject 7 | 6 |
7 | |
9 | |
Subject 10 | 3 |
5 | |
7 | |
Subject 15 | 6 |
8 | |
10 |
- The clones from each subject do seem to cluster together, it is especially apparent with subject 10.
- Subjects 1, 7. and 15. show diversity with because each clones has their own branch.
- None of the subjects seem to cluster together
- The clustering pattern of the tree seems to be conserved within the subjects. Subject 10 shows clustering within the clones, indicating how closely related they are.
Part 2
Subject 3 Clustal Format
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S3V6-2 GATGTAGTAATCAGATCTGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-4 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-5 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-3 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-6 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V6-1 GATATAGTAATTAGATCTGCCAATTTCTCGGACAATGCTAAAACCATATTAGTACAGCTG S3V4-5 GAGGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V3-2 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATTCTAAAACCATAATAGTACAGCTG S3V3-1 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATAATAGTACAGCTG S3V1-3 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V1-4 GATGTAGTAATCAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V5-3 GATGTAGTAATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATACTAGTACAGCTG S3V4-7 GATGTAGTAATCAGATCCGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V5-2 GATGTAGTAATCAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-9 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-1 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V5-10 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-7 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-8 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-4 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-5 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V5-6 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG S3V3-6 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATATTAGTACAGCTG S3V3-10 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATATTAGTACAGCTG S3V3-9 GATGTAGTAATTAGATCCGCCAATTTCACAGACAATGCTAAAATCATAATAGTACAGCTG S3V3-3 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATAATAGTACAGCTG S3V3-7 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATACTAGTACAGCTG S3V4-8 GATGTAGTAATTAGATCCGCCAATTTCGCGGACAATGCTAAAACCATACTAGTACAGCTG S3V1-1 GATGTAGTAATTAGATCCGCCAATTTCTCGGACAATGCTAAAACCATACTAGTACAGCTG S3V1-2 GATGTAGTAATTAGATCCGCCAATTTCTCGGACAATGCTAAAACCATACTAGTACAGCTG S3V4-2 GATGTAGTAATTAGATCCGCCAATTTCGCGGACAATGCTAAAACCATACTAGTACAGCTG S3V4-3 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V4-1 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V4-4 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAGACCATATTAGTACAGCTG S3V3-5 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATATTAGTACAGCTG S3V4-9 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATATTAGTACAGCTG S3V3-8 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATATTAGTACAGCTG S3V3-4 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATAATAGTACAGCTG S3V4-6 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG ** ******* ***** ********* * ***** **** * **** ***********
S3V6-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V6-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V6-5 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V6-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V6-6 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V6-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-5 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V3-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V1-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V1-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V5-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-7 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-9 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-10 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-7 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-8 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-5 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V5-6 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-6 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-10 AATGAAACTGTAGTAATGAATTGTACAAGACCCGACAACAATACAAGAAAAAGGGTAACT S3V3-9 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-7 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-8 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V1-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V1-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-2 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAATAATACAAGAAAAAGGGTAACT S3V4-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-5 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-9 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-8 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V3-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V4-6 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT ********************************** *** ************** ******
S3V6-2 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V6-4 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V6-5 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V6-3 CTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V6-6 CTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V6-1 CTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-5 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-2 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-3 CTAGGACCAGGCAAAGTATACTACACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-4 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-3 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-7 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-2 CTAGGACCGGGCAGAGTATACTATACAACAGGACAAATAATAGGGGATATAAGAAAAGCA S3V5-9 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATGAGAAAAGCA S3V5-1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-10 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGGGATATAAGAAAAGCA S3V5-7 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-8 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-4 CTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-5 CTAGGACCAGGCAGAGTATACTATACCACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V5-6 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-6 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-10 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-9 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-3 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-7 CTAGGACCAGGCAGAGTATACTATACAATAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-8 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-1 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-2 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-2 CTAGGACCAGGCAAAGTATATTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-3 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-4 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-5 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-9 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-8 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V3-4 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V4-6 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA ******** **** ****** ** ** * *************** ***** *********
S3V6-2 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V6-4 CATTGTAACCTTAGTAGAGCGGATTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V6-5 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V6-3 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V6-6 CATTGTAACCTTAGTAGAGCAGGTTGGAATAGCACTTTAGAAAGGATAGCTATAAAATTA S3V6-1 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V4-5 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAACAAGGATAGCTATAAAATTA S3V3-2 CATTGTAACCTTAGTAGAGCAGGTTGGGCTAACACTTTAGAAAGGATAGCTGTAAAATTA S3V3-1 CATTGTAACCTTAGTAGAACAGGTTGGAGTAACACTTTAAAAAGGATAGCTGTAAAATTA S3V1-3 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-4 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V5-3 CATTGTAACCTTAGTAGAGCGGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V4-7 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAAAAGGGATAGCTATAAAATTA S3V5-2 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V5-9 CATTGTAACCTTAGTTGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V5-1 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V5-10 CATTGTAACCTTAGTAGAGCAGGTTGAAATAACACTTTAGAAAGAATAGCTATAAAATTA S3V5-7 CATTGTAACCTTAGTAGAGCAGGTTGAAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V5-8 CATTGTAACCTTAGTAGAGCAGGTTGAAATAACACTTTAGAAAGAATAGCTATAAAATTA S3V5-4 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V5-5 CATTGTAACCTTAGTAGAGCAGGTTGGACTAACACTTTAGAAAGAATAGCTATAAAATTA S3V5-6 CATTGTAACCTTAGTAGAGCAGGTTGGACTAACACTTTAGAAAGGATAGCTATAAAATTA S3V3-6 CATTGTAACCTTAGTAGAGCAGATTGGAGTAACACTTTAGAAAGAATAGCTATAAAATTA S3V3-10 CATTGTAACCTTAGCAGAGCAGGTTGGACTAACACTTTAGAAAGAATAGCTATAAAATTA S3V3-9 CATTGTAACCTTAGTAGAGCAGGTTGGAGTAACACTTTAGAAAGGATAGCTATAAAATTA S3V3-3 CATTGTAACCTTAGTAGAGCAGGTTGGACTAACACTTTAGAAAGAATAGCTATAAAATTA S3V3-7 CATTGTAACCTTAGTAGAGCAGGTTGGACTAACACTTTAGAAAGAATAGCTATAAAATTA S3V4-8 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-1 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-2 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V4-2 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V4-3 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V4-1 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V4-4 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAGAAAGGATAGCTATAAAATTA S3V3-5 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V4-9 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V3-8 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V3-4 CATTGTAACCTTAGTAGAGCAAGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V4-6 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA ************** ** * *** ** ******* * * ****** ********
S3V6-2 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-4 TGAGAACAATTTCAGAATAAAACAATAGGCTTTAATCAATCCTCA S3V6-5 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-3 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAACCAATCCTCA S3V6-6 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V6-1 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V4-5 AGAGAACAATTTCAGAATAGAACAATAGGCTTTAATCAATCCTCA S3V3-2 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-1 AGAGAACAATTTCAGAATAGAACAATAGGCTTTAATCAATCCTCA S3V1-3 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V1-4 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V5-3 AGAGAACAATTTCAGAATAAAACAATAGGCTTTAATCAATCCTCA S3V4-7 TGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V5-2 AGAGAACAATTTCAGAATAAAACAATATTCTTTAATCAATCCTCA S3V5-9 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V5-1 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V5-10 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V5-7 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V5-8 AGAGAACAATTTCAGAATAAAACAATATTCTTTAATCAATCCTCA S3V5-4 AGAGAACAATTTCAGAATAAAACAATATTCTTTAATCAATCCTCA S3V5-5 AGAGAACAATTTCAGAATAAAACAATATTCTTTAATCAATCCTCA S3V5-6 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V3-6 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-10 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-9 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-3 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-7 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V4-8 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V1-1 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V1-2 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V4-2 AGAGAACAATTTCAGAATAAAACAATAGGCTTTAATCAATCCTCA S3V4-3 AGAGAACAATTTCAGAATAGAACAATATTCTTTAATCAATCCTCA S3V4-1 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V4-4 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-5 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V4-9 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-8 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V3-4 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA S3V4-6 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA ****************** ******* ****** *********
Subject 11 Clustal Format
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S11V1-4 GAGGTAATAATTAGATCTAAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-8 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-2 GAGGTAATAATTAGATCTGAGAATTTCTCAAATAATGCTAAAAACATAATAGTACAGCTG S11V3-5 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-2 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-2 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-6 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-5 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-1 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-9 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-7 GAGGTAATAATTAGATCTAAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-1 GAGGTAATAATTAGATCTAAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-4 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-1 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-3 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-10 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-8 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-5 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-6 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-4 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-3 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-5 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-6 GAGGTAATAATTAGGTCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-1 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-3 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-4 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-6 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-9 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V4-7 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V1-3 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V2-2 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG S11V3-7 GAGGTAATAATTAGATCTGAGAATTTCTCAAACAATGCTAAAAACATAATAGTACAGCTG ************** *** ************* ***************************
S11V1-4 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-8 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-2 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACCAAGGATAATA S11V3-5 AATAAATCTGTAGTAATTAATTGTACAAGACCCGATAACACTATAAAACAAAGGATAATA S11V1-2 AATGAATCTGTAGTAATTACTTGTACAAGACCCGACAACACTATCAAACAAAGGATAATA S11V4-2 AATGAATCTGTAGTAATTAATTGTGCAAGACCCGACTACACTATAAAACAAAGGATAATA S11V4-6 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACTACACTATAAAACAAAGGATAATA S11V4-5 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-1 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-9 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACTACACTATAAAACAAAGGATAATA S11V1-7 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V1-1 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-4 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-1 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-3 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-10 AATGAATCTGTAGTAATTAATTGTACGAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-8 AATGAATCTGTAGTAATTAATTGTACCAGACCCGACAACACTATAAAACAAAGGATAATA S11V1-5 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V1-6 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-4 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-3 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-5 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-6 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-1 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-3 AATGGATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-4 AATGAATCTGTAGTGATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-6 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-9 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V4-7 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V1-3 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V2-2 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA S11V3-7 AATGAATCTGTAGTAATTAATTGTACAAGACCCGACAACACTATAAAACAAAGGATAATA *** ********* **** **** * ******** ******* **** **********
S11V1-4 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-8 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-2 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAGATATAAGACAAGCA S11V3-5 CATATAGGACCAGGGAGACCATTCTATACAACAGAAATAAAAGGAAATATAAGACAAGCA S11V1-2 CATATAGGACCAGGGAGACCATTCTATACGACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-2 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-6 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-5 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V2-1 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-9 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V1-7 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V1-1 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-4 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V4-1 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAGATATAAGACAAGCA S11V4-3 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAGATATAAGACAAGCA S11V3-10 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-8 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V1-5 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V1-6 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V2-4 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V2-3 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V2-5 CATATAGGACCAGGGAGACCATTCTATACAACAAGAATAAAAGGAAATATAAGACAAGCA S11V2-6 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-1 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-3 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-4 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-6 CATGTAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-9 CATATAGGACCAGGGAGACCATTCTATACAGCAGGAATAAAAGGAAATATAAGACAAGCA S11V4-7 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V1-3 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V2-2 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA S11V3-7 CATATAGGACCAGGGAGACCATTCTATACAACAGGAATAAAAGGAAATATAAGACAAGCA *** ************************* ** ********** **************
S11V1-4 CATTGTAACGTTAGTGAGGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-8 CATTGTAACGTTAGTGGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAAAAACTTA S11V3-2 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-5 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V1-2 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-2 CATTGTAACGTTAGTGGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-6 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTATAAAATTA S11V4-5 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V2-1 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTAAGAAAATTA S11V4-9 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAAAAAATTA S11V1-7 CATTGTAACGTTAGTAGAGGACAATGGGATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V1-1 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-4 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-1 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-3 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAAAAAATTA S11V3-10 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-8 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V1-5 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTGGAAAATTA S11V1-6 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAGATTA S11V2-4 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAGATTA S11V2-3 CATTGTAACGTTAGTAGAGGACAATGGAATAGAACTTTAGAACAGGTAGTTAGAAAATTA S11V2-5 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V2-6 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-1 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-3 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-4 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-6 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-9 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V4-7 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V1-3 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V2-2 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA S11V3-7 CATTGTAACGTTAGTAGAGGACAATGGAATAAAACTTTAGAACAGGTAGTTAGAAAATTA *************** ********* *** ****************** ** ***
S11V1-4 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-8 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-2 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-5 AGAGAACAATATGGACCGAATAAAACAATAGTCTTTAAGCAACCCATA S11V1-2 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-2 AGAGAACAATATGGACTAAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-6 AGAGAACAATATGGGCCTAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-5 AGAGAACAATATGGGCCTAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-1 AGAGAACAATATGGACTGAACAAAACAATAGTCTTTAAGCAACCCATA S11V4-9 AGAGAACAATATGGACTAAATAAAACAATAGTCTTTAAGCAACCCATA S11V1-7 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V1-1 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-4 AGAGAACAATATGGACTAAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-1 AGAGAACAATATGGACTAAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-3 AGAGAACAATATGGACTAAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-10 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-8 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V1-5 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V1-6 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-4 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-3 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-5 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-6 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-1 AGAGAACAATATGGACCGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-3 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-4 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-6 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-9 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V4-7 AGAGAACAATATGGACTGAATAAAACAATAGCCTTTAAGCAACCCATA S11V1-3 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V2-2 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA S11V3-7 AGAGAACAATATGGACTGAATAAAACAATAGTCTTTAAGCAACCCATA ************** * ** ********** ****************
Subject 2 Clustal Sequence
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S2V4-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCCG S2V4-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-8 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-4 GAGGTAGTAATTAGATCCGAAAATTTCATGAGCAATGCTAGAATCATAATAGTACAGCTG S2V3-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-3 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTGAAATCATAATAGTACAGCTG S2V1-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-9 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V1-1 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-6 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATTATAATAGTACAGCTG S2V3-9 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-7 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-8 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V3-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTA S2V4-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S2V4-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG ***************** ********** ** ******* *** *************
S2V4-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-7 AATGAATCTGTAGAAATTAATTGTACAAAACCCAACAACAATACAAGAAAAAGTATACAT S2V3-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-3 AATAAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACAAGAAAAAGTATACAT S2V4-6 AATGAGTCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAGAAAGTATACAT S2V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-1 AATGGATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V3-7 AATAAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACAAGAAAAAGTATACAT S2V3-8 AATAAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACAAGAAAAAGTATACAT S2V3-5 AATAAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACGAGAAAAAGTATACAT S2V4-4 AATGAATCTGTAGAAATTAATTGCACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S2V4-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT *** ***************** **** ************** *** ***********
S2V4-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V4-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V4-8 ATAAGACCAGGTAGAGCATTTTATACAACAAGAGACATAATAAGAGAGATAAGACAAGCA S2V4-7 ATAGGACCAGGTAGAGCATTTTATACAACAGGAAACATAATAGGAGATATAAGACAAGCA S2V3-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-3 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAAGAGATATAAGACAAGCA S2V1-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-9 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V1-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-6 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-9 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-7 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-8 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V3-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-1 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S2V4-2 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA *** ************************** ** ******** **** ************
S2V4-3 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-5 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-8 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-7 CATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V3-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V3-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACTCTTTAAAACAGATAGTTATAAAATTG S2V1-3 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V1-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V3-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-9 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V1-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTG S2V3-6 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V3-9 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V3-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V3-7 CATTGTAACATTAGTAGAGCAGAATGGAATAACACTTCAAAACAGATAGTTAAAAAATTA S2V3-8 CATTGTAACATTAGTAGAGCAGAGTGGAATAACACTTTAAAACAGATAGTTAAAAAATTA S2V3-5 CATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAATTA S2V4-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S2V4-1 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAATTA S2V4-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAAAAAATTA ******************** * ********* *** ************** ******
S2V4-3 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAGCCACTCCTCA S2V4-5 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V4-8 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-7 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-4 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-3 AGAAAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V1-5 AGAGAACACTTTGGAAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-4 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-3 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V1-2 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAGTCACTCCTCA S2V3-1 AGAAAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-9 AGAAAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V1-1 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-6 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-9 AGAGAACACTTTGGGAATAAAACAATCGTCTTTAATCACTCCTCA S2V3-2 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-7 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-8 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V3-5 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-4 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-1 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S2V4-2 AGAGAACACTTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA *** **** *** *********** ******* *********
Subject | Number of Clones | S | Theta |
---|---|---|---|
3 | 39 | 45 | 10.6 |
11 | 31 | 35 | 8.7 |
2 | 24 | 36 | 9.6 |
Activity 3
- Our question is: How does the grouping of Subject 7 as a moderate progressor as compared to Subject 7 as a rapid progressor change slope of diversity/divergence as well as compare to rapid progressor phylogenetic trees?
- Hypothesis: We hypothesis that changing Subject 7 to a rapid progressor would increase signficance between moderate and rapid progressor group slope of diversity and divergence. We also hypothesis that Subject 7's phylogenetic tree would more closely resemble rapid progressor phylogenetic trees as opposed to moderate progreessor phylogenetic trees.
- Subjects, Visits, Clones:
- Subjects: Subjects 4, 10, 11, 15, 3, 1 (rapid progressors) and Subjects 8, 14, 5, 9, 6, 7 (moderate progressors)
- Visits: All visits
- Clones: All clones pertaining to subjects used
- We justified our subjects, visits, and clones based on wanting to compare slope of diversity/diversity and phylogenetic trees of all rapid progressors to all moderate progressors when subject 7 is moved from moderate to rapid.
Data and Files
Activity 1 Phylogenetic Tree Activity 2 Phylogenetic Tree Visit_1_Subjects_1_thru_9_HIV.txt Visit_1_Subjects_10_thru_15_HIV.txt
Conclusion
- The tools bioinformatics tools that were used this week were very helpful to visualize data on phylogenetic trees and in sequence. It allowed for easier comparison and analysis of sequences within and between subjects which is very useful for our future project.
Acknowledgments
- I worked with my partner Christina Dominguez on the class assignment and refining our question
- I copied the wiki syntax for Table 2 and Table 3 from the Week 5 assignment page to organize my collected data
- Sequences were obtained from PubMed
- Harmonic Sum calculator from Math Utah was used to calculate harmonic sum
- Data for all the subjects was obtained from the BEDROCK website
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Adinulos (talk) 14:14, 13 February 2020 (PST)
References
- Markham, R.B., Wang, W.C., Weisstein, A.E., Wang, Z., Munoz, A., Templeton, A., Margolick, J., Vlahov, D., Quinn, T., Farzadegan, H., & Yu, X.F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proc Natl Acad Sci U S A. 95, 12568-12573. doi: 10.1073/pnas.95.21.12568 (PubMed ID: 9770526)
- NCBI (2020). PubMed. Retrieved February 13, 2020, from https://www.ncbi.nlm.nih.gov/pubmed/?term=Patterns+of+HIV-1+evolution+in+individuals+with+differing+rates+of+CD4+T+cell+decline.
- OpenWetWare. (2020). BIOL368/S20:Week 5. Retrieved February 13, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_5