Nyeo2 Week 5
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- Nyeo2 Week 14
Class Journals
- BIOL368/S20:Class Journal Week 1
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- Class Journal Week 9
- 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
The purpose of this assignment is to acquaint ourselves with online databases in order to find relevant biological information on HIV-1 test subjects and with resources, create phylogenetic trees, sequence alignments, and calculate statistical values from the information gathered.
Methods/Results
Activity 1
Part 1
- How did you search for the PubMed entry?
- I searched for the PubMed entry by entering the full name of the article(Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline) into the search bar, with the category set to "All Databases". I then clicked on PubMed under the literature category to find the article that we used in class.
- What other ways might you have searched?
- Another way I may have searched for the PubMed entry of the article could be by typing the authors, the date of publication, or the publisher into advanced search.
- What other types of related information are available?
- On the right side of the screen, the page provides access to tabs such as related information on MedGen, published nucleotide sequences, references for the article, protein sequences, and search details.
Part 2
- What was the accession number of the sequence you chose?
- AF089138
- Which subject of the study was that HIV sequence from?
- Subject 3(S3V5-7)
- Which section of the record contains information about who the HIV was collected from?
- The section titled "Features" with the source, gene, and CDS information
Part 3
- Phylogeny alignment
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
AF089124.1 GATGTAGTAATTAGATCCGCCAATTTCGCGGACAATGCTAAAACCATACTAGTACAGCTG AF089138.1 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATATTAGTACAGCTG AF089128.1 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAACCATAATAGTACAGCTG AF089116.1 GATGTAGTAATTAGATCCGCCAATTTCACGGACAATGCTAAAATCATAATAGTACAGCTG *************************** ** ************ **** ***********
AF089124.1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT AF089138.1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT AF089128.1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT AF089116.1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT ************************************************************
AF089124.1 CTAGGACCAGGCAAAGTATATTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA AF089138.1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA AF089128.1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA AF089116.1 CTAGGACCAGGCAGAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA ************* ****** ***************************************
AF089124.1 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA AF089138.1 CATTGTAACCTTAGTAGAGCAGGTTGAAATAACACTTTAGAAAGGATAGCTATAAAATTA AF089128.1 CATTGTAACCTTAGTAGAGCAGGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA AF089116.1 CATTGTAACCTTAGTAGAGCAAGTTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA ********************* *** ************ ********************
AF089124.1 AGAGAACAATTTCAGAATAAAACAATAGGCTTTAATCAATCCTCA AF089138.1 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA AF089128.1 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA AF089116.1 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCAATCCTCA ******************* ******** ****************
- Phylogenetic tree
Activity 2
Part 1
- Multiple sequence alignment
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S3V1-1 GATGTAGTAATTAGATCCGCCAATTTCTCGGACAATGCTAAAACCATACTAGTACAGCTG S3V1-3 GATGTAGTAATTAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S3V1-4 GATGTAGTAATCAGATCCGCCAATTTCACGAACAATGCTAAAACCATACTAGTACAGCTG S13V1-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-3 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S1V1-2 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-5 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S1V1-4 GAGGTAGTAATTAGATCCGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S7V1-6 GAGGTAGTAATTAGATCTGCCAATTTCACGGACAATACTAAGACCATAATAGTACAGCTG S7V1-3 GAGATAGTAATTAGATCTGCCAATCTCTCGGACAATGCTAAGACCATAATAGTACAGCTG S7V1-8 GAGATAGTAATTAGATCTGCCAATCTCTCGGACAATGCTAAAACCATAATAGTACAGCTG ** ******* ***** * *** ** * ***** **** * **** ***********
S3V1-1 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGGGTAACT S3V1-3 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S3V1-4 AATGAAACTGTAGTAATGAATTGTACAAGACCCGGCAACAATACAAGAAAAAGAGTAACT S13V1-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S1V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S1V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S7V1-6 AATGTATCTGTAGAAATTAATTGTACGAGACCCAACAACAATACAAGAAAAAGTATACCT S7V1-3 AATGCACCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGGAAAAGTATATCT S7V1-8 AATGCACCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGGAAAAGTATATCT ** * * ****** *** ******** ***** ************ * *** ** *
S3V1-1 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-3 CTAGGACCAGGCAAAGTATACTACACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S3V1-4 CTAGGACCAGGCAAAGTATACTATACAACAGGACAAATAATAGGAGATATAAGAAAAGCA S13V1-4 ATGGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-3 ATAGGACCAGGGAGAGCATTCTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S1V1-2 ATAAGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAAGAGATATAAGACAAGCA S1V1-5 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACCAGCA S1V1-4 ATAGGACCAGGTAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S7V1-6 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAATAGGAAATATAAGACAAGCA S7V1-3 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAATAGGAAATATAAGACAAGCA S7V1-8 ATAGGACCAGGGAGAGCATTTTATGCTACAGGAGAAATAGTAGGAAATATAAGACAAGCA * ******* * ** ** ** * ** ** *** ** ** ******** ****
S3V1-1 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-3 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S3V1-4 CATTGTAACCTTAGTAGAGCAGATTGGAATAACACTTTAAAAAGGATAGCTATAAAATTA S13V1-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S1V1-2 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTATAAAATTA S1V1-5 TATTGTAACATTAGTAGAGCAGAATGGAATAACACTTTAAAACAGATAGTTAACAAATTA S1V1-4 TATTGTAACATTAGTAGAGCAGAATGGAATAACACCTTAAAACACATAGTTATAAAATTA S7V1-6 CATTGTACCGTAAGTAGAGTAAAATGGAATAACACTTTAAAACAGATAGTTACAAAATTA S7V1-3 CATTGTAACATTAATAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTACAAAATTA S7V1-8 CATTGTAACATTAGTAGAGCAAAATGGAATAACACTTTAAAACAGATAGCTACAAAATTA ****** * * * ** ** * * *** ******* *** * *** * ******
S3V1-1 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S3V1-3 AGAGAACAATTTCAGAATAAAACAATAGCCTTTAATCAATCCTCA S3V1-4 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCAATCCTCA S13V1-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S1V1-2 AGAGAACACTTTAGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-5 AGAGAACACTTTGGGAATAAAACAATAGTCTTTAATCACTCCTCA S1V1-4 AGAGAACACTTTGGCAACAAAACAATAGTCTTTAATCACTCTTCA S7V1-6 AGAGAACAATTTGGGAATAAAACAATAGTCTTTAATCAATCCTCA S7V1-3 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAATCAATCCTCA S7V1-8 AGAAAACAATTTGAGAATAAAACAATAGTCTTTAATCAATCCTCA *** **** *** ** ******* ********* ** ***
- Phylogenetic tree
Subject | Clone # |
1 | 2 |
4 | |
5 | |
3 | 1 |
3 | |
4 | |
7 | 3 |
6 | |
8 | |
13 | 1 |
3 | |
4 |
- Do the clones from each subject cluster together?
- The clones from each subject seem to be clustered together, as each node of three all have clones from the same subject.
- Do some subjects' clones show more diversity than others?
- Subject 7 seems to be the most diverse because there is greater distance between when it branches off in the node. Subject 3 is also more diverse than the other subjects, but not quite as diverse as subject 7 because while it branches, the distance between branching is not as long.
- Do some of the subjects cluster together?
- There is not that much clustering between subjects; however, subjects 1 and 13 and subjects 3 and 7 could be said to be clustered because each pair is under a respective overarching branch that connects them.
- Write a brief description of your tree and how you interpret the clustering pattern with respect to the similarities and potential evolutionary relationships between subjects' HIV sequences.
- This phylogenetic tree shows the evolutionary relationship between subjects 1, 3, 7, and 13. Subject 3 and 13 had the longest time before they diverged into their branches, which shows that they have the greatest genetic distance among the subjects. Subjects 7 and 3 branch off within their nodes, hinting that they are more genetically diverse.
Part 2
- Sequence alignment for Subject 5
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S5V4-7 GAGGTAGTAATTAGATCCCAAAATCTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V4-1 GAGGTAGTAATTAGATCTCAAAATCTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V4-2 GAGGTAGTAATTAGATCTCAAAATCTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V4-6 GAGGTAGTAATTAGATCTCAAAATCTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V3-3 GAGGTAGTAATTAGATCCAAAAATTTCACGGACAATGCAAAAATCATAATAGTACATCTA S5V3-4 GAGGTAGTAATTAGATCCAAAAATTTCACTGACAATGCTAAAATCATAATAGTACATCTA S5V4-3 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V4-4 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V4-5 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V3-1 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V3-2 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V3-5 GAGGTAGTAATTAGATCCATAAATTTCTCAGACAATGCTAAAATCATAATAGTACATCTA S5V5-4 GAGGTAGTAATTAGATCCACAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V5-5 GAGGTAGTAATTAGATCCACAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V5-1 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V5-3 GAGGTAGTAATTAGATCCACAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-3 GAGGTAGTTATTAGATCCAAAAATTTCTCGGACAATGTAAAAATCATAATAGTACATCTA S5V3-6 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-6 GAGGTAGTTATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V3-8 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V3-10 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATGATAGTACATCTA S5V3-11 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATGATAGTACATCTA S5V2-10 AAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-11 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCAAAAATCATAATAGTACATCTA S5V2-5 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-1 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-9 GAAGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-2 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-12 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-7 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-8 GAGGTAGTAATTAGATCCAAAAATTTCTCGGAAAATGCTAAAATCATAATAGTACATCTA S5V1-3 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-5 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-7 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V3-7 GAGGTGGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-8 GAAGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V3-9 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-1 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAGTAGTACATCTA S5V1-6 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-4 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V2-4 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V1-2 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA S5V5-2 GAGGTAGTAATTAGATCCAAAAATTTCTCGGACAATGCTAAAATCATAATAGTACATCTA * ** ** ******** **** ** * ** **** ******** ***********
S5V4-7 AATGAATCTGTAGAAATTAATTGTACAGGACCCGGCAACAATACAAGAAGAAGTATACAT S5V4-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V4-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V4-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-3 AATGAATCTGTAGAAATTAATTGTACAAGACACGGCAACAACACAAGAAGAAGTATACAT S5V3-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAACACAAGAAGAAGTATACCT S5V4-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V4-4 AATGAATCTGTAGAAATTAATTGCATAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V4-5 AATGAATCTGTAGAAATTAATTGCACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V5-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V5-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V5-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V5-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-3 AATGAATCTGTAGAAATTAATTGCACAAGACCCGGCAACAATACAAGAAGAAGTATACCT S5V3-6 AATGAATCTGTAGAAATTAATTGCACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S5V3-10 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-11 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-10 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-11 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACCT S5V2-5 AATGAATTTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-1 AATGAATTTGTAAAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S5V2-2 AATGAATCTGTAGAAATTAATTGTGCAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S5V2-12 AATGAATCTGTAGAAATTAATTGTGCAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S5V1-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAGCAACAATACAAGAAGAAGTATACAT S5V1-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-5 AATGAATCTGTAGAAATTAATTGTACAAGGCCCGGCAACAATACAAGAAGAAGTATACTT S5V2-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACCT S5V3-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V3-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-6 AATGAGTCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V2-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S5V5-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT ***** * **** ********** * * * * ******* *************** *
S5V4-7 ATAGGGCCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V4-1 ATAGGGCCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V4-2 ATAGGGCCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCG S5V4-6 ATAGGGCCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-3 ATAGGACCAAACAGAGCATTTTATACAACAGGAGACGTAATAGGAGATATAAGACAAGCA S5V3-4 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V4-3 ATAGGACCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V4-4 ATAGGACCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V4-5 ATAGGACCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-1 ATAGGACCAAACAGAGCATTCTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-2 ATAGGACCAAACAGAGCATTCTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-5 ATAGGACCAAACAGAGCATTCTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V5-4 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V5-5 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V5-1 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V5-3 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-3 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-6 ATAGGACCAAACAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-6 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-8 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-10 ATAGGACCAGGCGGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-11 ATAGGACCAGGCGGAGCATTTTATACAACAGGAGACATAATAGGAGGTATAAGACAAGCA S5V2-10 GTAGGACCAGGCAGAGCATTTTATACAATAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-11 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-5 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-1 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-9 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-2 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-12 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V1-7 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGACATAAGACAAGCA S5V1-8 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGACATAAGACAAGCA S5V1-3 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGACATAAGACAAGCA S5V1-5 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-7 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-7 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-8 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V3-9 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V1-1 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V1-6 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V1-4 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V2-4 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V1-2 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA S5V5-2 ATAGGACCAGGCAGAGCATTTTATACAACAGGAGACATAATAGGAGATATAAGACAAGCA **** *** * ******* ******* ******* ********* ***********
S5V4-7 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V4-1 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V4-2 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V4-6 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V3-3 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGCTATAAAATTA S5V3-4 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGCTATAAAATTA S5V4-3 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGTTATAAAATTA S5V4-4 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGTTATAAAATTA S5V4-5 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGTTATAAAATTA S5V3-1 CATTGTAACATTAGTGAAGAAGAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V3-2 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V3-5 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V5-4 CATTGTAACATTAGTAAAGGAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V5-5 CATTGTAACATTAGTGAAGGAAAATGGAATGAAACCTTAAAAAAGATAGCTATAAAATTA S5V5-1 CATTGTAACATTAGTGAAGGAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V5-3 CATTGTAACATTAGTGAAGGAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V2-3 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGCTATAAAATTA S5V3-6 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-6 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGCTATAAAATTA S5V3-8 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGCTATAAAATTA S5V3-10 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V3-11 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-10 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-11 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-5 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-1 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-9 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-2 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-12 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-7 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-8 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-3 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-5 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-7 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACCTTAAAAAAGATAGTTATAAAATTA S5V3-7 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-8 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V3-9 CATTGTAATATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-1 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-6 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-4 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V2-4 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V1-2 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA S5V5-2 CATTGTAACATTAGTGAAGAAAAATGGAATGAAACTTTAAAAAAGATAGTTATAAAATTA ******** ****** *** * ************* ************* **********
S5V4-7 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATTCATCCTCA S5V4-1 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAACTCATCCTCA S5V4-2 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATTCATCCTCA S5V4-6 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATTCATCCTCA S5V3-3 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATCCATCCTCA S5V3-4 AGAAAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V4-3 AGAGAACAATTTAAGAATAA---AACAATAGTATTTAAGTCATCCTCA S5V4-4 AGAGAACAATTTAAGAATAA---AACAATAGTATTTAAGTCATCCTCA S5V4-5 AGAGAACAATTTAAGAATAA---AACAATAGTATTTAAGTCATCCTCA S5V3-1 AGAGAACAATTTAGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V3-2 AGAAAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V3-5 AGAGAACAATTTAGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V5-4 AGAGAACAATTTAGGAATAA---AACAATAGTCTTTAATTCATCCTCA S5V5-5 AGAGAACAATTTAGGAATAA---AACAATAGCATTTAATCCATCCTCA S5V5-1 AGAGAACAATTTAGGAATAA---AACAATAGCATTTAATTCATCCTCA S5V5-3 AGAGAACAATTTAGGAATAA---AACAATAGCATTTAATTCATCCTCA S5V2-3 AGAGAACAATTTGTGAATAA---AACAATAGTATTTAATCCATCCTCA S5V3-6 AGAAAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V2-6 AGAGAACAATTTGTGAATAA---AACAATAGTATTTAATCCATCCTCA S5V3-8 AGAGAACAATTTGTGAATAA---AACAATAGTATTTAATCCATCCTCA S5V3-10 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATTCATCCTCA S5V3-11 AGAGAACAATTTGAGAATAA---AACAATAGTATTTAATCCATCCTCA S5V2-10 AGAGAACAATTTGGGAATAAAACAACAATAGTATTTAATTCATCCTCA S5V2-11 AGAGAACAATTTGGGAATAA---AACGATAGTATTTAATTCATCCTCA S5V2-5 AGGGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V2-1 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V2-9 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V2-2 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V2-12 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V1-7 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCGCA S5V1-8 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCGCA S5V1-3 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCGCA S5V1-5 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V2-7 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V3-7 AGAAAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V2-8 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V3-9 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V1-1 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V1-6 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V1-4 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V2-4 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATTCATCCTCA S5V1-2 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA S5V5-2 AGAGAACAATTTGGGAATAA---AACAATAGTATTTAATCCATCCTCA ** ******** ****** *** **** ***** ***** **
- Sequence alignment for Subject 9
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S9V7-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGATAATGCTAAAACCATAATAGTACAGCTG S9V7-8 GAGGTAGTGGTTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-9 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-10 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V7-6 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V6-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V6-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V6-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGTTG S9V6-8 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGTTG S9V6-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAACTG S9V6-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAACTG S9V4-6 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-2 GAGGTAGTGGTTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-11 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-6 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-8 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V6-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V6-6 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-10 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-8 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V4-9 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V1-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTGCAGCTG S9V1-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTGCAGCTG S9V5-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V5-9 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V1-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-6 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V2-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V2-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V1-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V2-1 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-2 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V2-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V1-3 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTGCAGCTG S9V2-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-4 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-5 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V3-8 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V8-1 GAGGTAGTGCTTAGATCCGCCAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S9V8-4 GAGGTAGTGCTTAGATCCGCCAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S9V8-5 GAGGTAGTGCTTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V8-2 GAGGTAGTGCTTAGATCCGCCAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S9V8-3 GAGGTAGTGGTTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V8-6 GAGGTAGTGCTTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V8-7 GAGGTAGTGATTAGATCCGCCAATTTCACAGACAATGCTAAAACCATAATAGTACAGCTG S9V8-8 GAGGTAGTGGTTAGATCCGCCAATTTCACAAACAATGCTAAAACCATAATAGTACGGCTG ********* ******************** * ******************** * **
S9V7-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAGCAACAATACAAGAAAAAGTATAAAT S9V7-8 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-7 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-9 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAACT S9V7-10 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V7-6 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-2 AAAGAACATGTAAAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-5 AAAGAACATGTAAAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-8 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAACT S9V6-7 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAACT S9V4-6 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-11 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-7 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-6 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-8 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAACACAAGAAAAAGTATAAAT S9V4-7 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S9V5-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V6-6 AAAGAACATGTAAAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-10 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-8 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V4-9 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V1-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V1-4 AAAGAACATGTAGAAATAAATTGCACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V5-9 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-7 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V1-2 AAAGAACATGTAGAAATAAATTGTGCAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-6 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V2-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAGCAACAATACAAGAAAAAGTATAAAT S9V2-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V1-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V2-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V2-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V1-3 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V2-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-4 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V3-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAGTACAAGAAAAAGTATAAAT S9V3-8 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-1 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-4 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-5 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-2 AAAGAACATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-3 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAGGAAAAAGTATACAT S9V8-6 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S9V8-7 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S9V8-8 AAAGACCATGTAGAAATAAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT ***** ****** ********** ********* ***** *** *** ******* *
S9V7-2 ATAGGACCAGGAAGAGCATTTTATGCAACAGGAGAAATAATAGGAGACATAAGACAAGCA S9V7-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATACGACAAGCA S9V7-3 ATAGGACCAGGAAGAGCATTTTATGCAACAGGAACAATAATAGGGGATATACGACAAGCA S9V7-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-10 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V7-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V6-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V6-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V6-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V6-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V6-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V6-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAGGCA S9V4-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V5-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V4-11 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V5-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGGGAAATAATAGGAGATATAAGACAAGCA S9V5-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCAATAATAGGAGATATAAGGCAAGCA S9V5-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V6-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V5-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V5-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCAATAATAGGAGATATAAGACAAGCA S9V5-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAGGCA S9V6-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V3-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCC S9V4-10 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V4-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V1-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V1-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V5-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V5-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCA S9V3-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCAATAATAGGAGATATAAGACAAGCA S9V1-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V2-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V2-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V1-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V2-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V2-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V1-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V2-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V3-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAACAATAATAGGAGATATAAGACAAGCA S9V8-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA S9V8-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAAATATAAGACAAGCA *********** ******************** ********* * *** * ** **
S9V7-2 CATTGTAACATTAGTAGAACAAAATGGAATGAGACCTTAAGACAGATAGTAGAAAAATTA S9V7-4 CATTGTAACATCAGTGGAGCAAAATGGAATGAGACCTTAAAACAGATAGCTAAAAAATTA S9V7-1 CATTGTAACATCAGTGGAACAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V7-3 CATTGTAACATCAGTGGAACAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V7-5 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGGAAAATTA S9V7-8 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGCTGGAAAATTA S9V7-7 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGGAAAATTA S9V7-9 CATTGTAACATTAGTGGAACAAAATGGAATGACACCTTAAGACAGATAGCTGGAAAATTA S9V7-10 CATTGTAACATTAGTGGAACAAAATGGAATGACACCTTAAGACAGATAGCTGGAAAATTA S9V7-6 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAGACAGATAGCTGGAAAATTA S9V6-2 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAGACAGATAGCTGGAAAATTA S9V6-5 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGCTGGAAAATTA S9V6-3 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGCTGAAAAATTA S9V6-8 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAGACAGATAGCTGAAAAATTA S9V6-4 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V6-7 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V4-6 CATTGTAATATTAGTGGAGCAAAATGGAATAACACATTAAAACAGACAGCTGAAAAATTA S9V5-2 CATTGTAACGTTAGTGGAGCAAAATGGCATAACACCTTAAAACAGATAGTTGAAAAATTA S9V4-11 CATTGTAATATTAGTGGAGCAAAATGGCATGACACCTTAAAACAGATAGTTGAAAAATTA S9V4-2 CATTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAACTA S9V5-7 CATTGTAACATTAGTGGAACAAAATGGAATAACACCTTAAAACAGATAGTTGAAAAATTA S9V5-6 CATTGTAACATTAGTGGAGCAAAATGGAATAACACCTTAAAACAGATAGTTGAAAAATTA S9V5-8 CATTGTAACATTAGTGGAACAAAATGGAATAACACCTTAAAACAGATAGTTGAAAAATTA S9V6-1 CATTGTAACATTAGTGGAGCAAAATGGAATAACACCTTAAAACAGATAGTTGAAAAATTA S9V5-4 CACTGTAACATTAGTGGAGTAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V5-5 CATTGTAACATTAGTGGAGTAAAATGGAATGACACCTTAAAACAGATAGCTGAAAAATTA S9V4-5 CACTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTCGAAAAATTA S9V4-7 CATTGTAATATTAGTGGAGCAAAATGGAATGGCACCTTAAAACAGATAGTTGAAAAATTA S9V5-3 CATTGTAACATTAGTGGAGCAAAATGGAATAACACCTTAAAACAGATAGTTGAAAAATTA S9V6-6 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-3 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-1 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V4-1 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTCGAAAAATTA S9V4-4 CATTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTCGAAAAATTA S9V4-3 CATTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGCTGAAAAATTA S9V4-10 CATTGTAATATTAGTGGAGCAAAATGGAATGGCACCTTAAAACAGATAGTTGAAAAATTA S9V4-8 CATTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V4-9 CATTGTAATATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V1-5 CATTGTAACATTAGTGGAGCAAAATGGAAGGACACCTTAAAACAGATAGTTGAAAAATTA S9V1-4 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V5-1 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V5-9 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-7 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAATTA S9V1-2 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAGATTA S9V3-6 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCCTAAAACAGATAGTTGAAAAATTA S9V2-2 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V2-3 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAATTA S9V1-1 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V2-1 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-2 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V2-5 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAATTA S9V1-3 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V2-4 CATTGTAACATTAGTGGAGCAAAATGGAATGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-4 CATTGTAACATTAGTGGGGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-5 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAATTA S9V3-8 CATTGTAACATTAGTGGAGCAAAATGGAAAGACACCTTAAAACAGATAGTTGAAAAACTA S9V8-1 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-4 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-5 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-2 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-3 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-6 CATTGTAATATTAGCAG---AAAATGGAATAACACCTTAGAACAGATAGTTAAAAAATTA S9V8-7 CATTGTAATATTAGTAGAGGAAAATGGAATAACACCTTAAAACAGATAGTTAAAAAATTA S9V8-8 CATTGTAATATTAGTAGAACAAAATGGAATAACACCTTAAAACAGATAGTTAAAAAATTA ** ***** * ** * ******* * ** ** ***** ** ** * **
S9V7-2 AGAGAACAATTTAGAAATAAAATAATAATCTTTAATCACTCCTCA S9V7-4 AGAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-1 AGAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-3 AGAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-5 AAAGAACAATTTGGGAATAAAATAATAATCTTTAATCACTCCTCA S9V7-8 AGAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-7 AGAGAACAATTTGGAAATAAAACAATAATCTTTAATCACTCCTCA S9V7-9 AGAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-10 AAAGAACAATTTGGGAATAAAACAATAATCTTTAATCACTCCTCA S9V7-6 AGAAAACAATTTAGCAATAAAATAATAGTCTTTAATCACTCCTCA S9V6-2 AGAGAACAATTTCAGGATAAAACAATAGTCTTTAATCACTCCTCA S9V6-5 AGAGAACAATTTCAGAATAAAATAATAGTCTTTAGTCACTCCTCA S9V6-3 AGAGAACAGTTTCATGATAGAACAATAATCTTTAATCACTCCTCA S9V6-8 AGAGAACAATTTCATAATAAAACAATAATCTTTAATCACTCCTCA S9V6-4 AGAAAACAATTTCAGGATAAAACAATAATCTTTAATCACTCCTCA S9V6-7 AGAAAACAATTTCAGGATAAAACAATAATCTTTAATCACTCCTCA S9V4-6 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-2 AAAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V4-11 AAAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V4-2 AAAGAACAATTTAAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V5-7 AAAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-6 AAAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-8 AGAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V6-1 AGAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-4 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-5 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V4-5 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V4-7 AGAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-3 AAAGAACAATTTCAGAATAAAATAATAGTCTTTAATCACTCCTCA S9V6-6 AGAGAACAATTTCAGAATAAAACAATAATCTTTAATCACTCCTCA S9V3-3 AGAGAACAATTTCAGAATAGAACAGTAGTCTTTAATCACTCCTCA S9V3-1 AAAGAACAATTTCAGAATAAAACAGTAGTCTTTAATCACTCCTCA S9V4-1 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V4-4 AGAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V4-3 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V4-10 AGAGAACAATTTAAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V4-8 AGAGAACAATTTAAGAATAGAATAATAGTCTTTAATCACTCCTCA S9V4-9 AGAGAACAATTTCAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V1-5 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V1-4 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-1 AAAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V5-9 AAAGAACAATTTCAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V3-7 AGAGAACAATTTGAGAATAGAACAATAGTCTTTAATCACTCCTCA S9V1-2 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V3-6 AGAGAACAATTTAAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V2-2 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V2-3 AGAGAACAATTTGAGAATAAAATAATAGTCTTTAATCACTCCTCA S9V1-1 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V2-1 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V3-2 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V2-5 AGAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V1-3 AAAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V2-4 AAAGAACAATTTGAGAATAAAACAATAGTCTTTAATCACTCCTCA S9V3-4 AGAGAACAATTTCATAATAAAACAGTAGTCTTTAATCACTCCTCA S9V3-5 AGAGAACAATTTAAGAATAAAACAGTAGTCTTTAATCACTCCTCA S9V3-8 AGAGAACAATTTAAGAATAGAACAGTAGTCTTTAATCACTCCTCA S9V8-1 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCCCA S9V8-4 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCTCA S9V8-5 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCTCA S9V8-2 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCTCA S9V8-3 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCTCA S9V8-6 AGAGAACAATTTCCGGGTAGAACAATAGTCTTTAATCACTCCTCA S9V8-7 AGAGAACAATTT---AATAAAACAATAGTCTTTAATCACTCCTCA S9V8-8 AGAGAACAATTT---AATAAAACAATAGTCTTTAATCACTCCTCA * * **** *** ** ** * ** ****** ******* **
- Sequence alignment for Subject 13
CLUSTAL FORMAT: MUSCLE (3.8) multiple sequence alignment
S13V4-1 GAGATAGTAATCAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-3 GAGATAGTAATCAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-6 GAGATAGTAATTAGATCTGAAAATTTCACAAACAGTGCTAAAATCATAATAGTACAGCTG S13V5-3 GAGATAGTAATTAGATTTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-3 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V2-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-5 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATGATAGTACAGCTG S13V3-7 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-5 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V2-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-2 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V1-1 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V3-3 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-5 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-6 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V4-7 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG S13V5-6 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAACCATAATAGTACAGCTG S13V5-4 GAGATAGTAATTAGATCTGAAAATTTCACAAACAATGCTAAAATCATAATAGTACAGCTG *********** **** ***************** ******** *** ************
S13V4-1 AAGGAATCTGTAGAGATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S13V4-3 AAGGAATCTGTAGAGATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S13V4-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V4-4 AAGGAGTCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-6 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V1-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V1-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V2-2 AAGGAATTTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-5 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-7 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-5 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V1-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V2-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V3-2 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V1-1 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V3-3 AAGGAATCTGTAGAAATTAATTGTACAAGACCTGGCAACAATACAAGAAGAAGTATAAAT S13V4-5 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V4-6 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATACAT S13V4-7 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-6 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT S13V5-4 AAGGAATCTGTAGAAATTAATTGTACAAGACCCGGCAACAATACAAGAAGAAGTATAAAT ***** * ****** ***************** ************************ **
S13V4-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAAAGGAATAATAGGAGATATAAGACAAGCA S13V4-3 ATAGGACCAGGGAGAGCATTTTATGCATCAAAAGGAATAATAGGAGATATAAGACAAGCA S13V4-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAAAGGAATAATAGGAGATATAAGACAAGCA S13V4-4 ATAGGACCAGGGAGAGCATTTTATGCATCAAAAGGAATAATAGGAGATATAAGACAAGCA S13V3-6 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-3 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-3 ATAGGACCAGGGAGAGCATTCTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-4 ATGGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V2-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-1 ATAGGACCAGGGAGAGCGTTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-4 ATAGAACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-5 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-7 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-5 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V2-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-2 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V1-1 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V3-3 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V4-5 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V4-6 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V4-7 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-6 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA S13V5-4 ATAGGACCAGGGAGAGCATTTTATGCATCAAGAGGAATAATAGGAGATATAAGACAAGCA ** * ************ ** ********** ****************************
S13V4-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V4-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V4-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGAAAGGTAGCTGCAAAATTA S13V4-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGAAAGGTAGCTGCAAAATTA S13V3-6 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-3 TATTGTAACATCAGTAAAGCGAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V2-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-5 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-7 TATTGTAACACCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-2 TATTGTAACATCAGTAAAGCAAAATGGGACAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-5 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V2-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-2 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V5-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V1-1 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V3-3 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAGGACAGGTAGCTGCAAAATTA S13V4-5 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V4-6 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V4-7 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V5-6 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA S13V5-4 TATTGTAACATCAGTAAAGCAAAATGGGATAACACTTTAAGACAGGTAGCTGCAAAATTA ********** ********* ******** ********* ** *****************
S13V4-1 AGAGGACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-3 AGAGAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-2 AGAGAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-4 AGAGAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-6 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAGTCAATCATCA S13V5-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V2-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-5 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-7 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-5 AGAGAACAATTTAAGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V2-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-2 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V1-1 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V3-3 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-5 AGAGAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-6 AGAAAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V4-7 AGAAAACAATTTGGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-6 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA S13V5-4 AGAGAACAATTTAGGAATGCTACAATAGTCTTTAATCAATCATCA *** ******* ******************** **********
Subject | Number of Clones | S | Theta |
---|---|---|---|
5 | 43 | 54 | 12.41 |
9 | 64 | 64 | 13.49 |
13 | 26 | 25 | 6.49 |
Data and Files
- Activity 1 Part 3 Phylogenetic Tree
- Activity 2 Part 2 Phylogenetic Tree
- HIV-1 isolate S3V3-4 from USA envelope glycoprotein (env) gene, partial cds
- HIV-1 isolate S3V4-2 from USA envelope glycoprotein (env) gene, partial cds
- HIV-1 isolate S3V4-6 from USA envelope glycoprotein (env) gene, partial cds
- HIV-1 isolate S3V5-7 from USA envelope glycoprotein (env) pseudogene, partial sequence
- Visit 1 Subjects 1-9
- Visit 1 Subjects 10-15
Activity 3: Defining your HIV evolution research project
- Our question was if there is a relationship between CD4 T cell levels and average pairwise genetic distance (theta). To do this, we wanted to see if there is statistical significance between these two values within and between each progressor group.
- We predict that there will be statistical significance between the theta value and CD4 T Cell levels. To test this, we plan to use linear regression.
Subjects
- We will use subjects 2, 12, 13, 6, 5, 8, 1, 15, 10, 9, 11, and 4.
Visits
- We will use all visits for each subject.
Clones
- We will use all clones for each subject.
- We chose these subjects, visits, and clones on the basis of ensuring each progression group was represented and enough visits and clones were included.
Scientific Conclusion
Overall, this assignment showed that using online tools to make phylogenetic trees and sequence alignments for genomic data is helpful in determining relationships between subjects in relation to the virus at hand. Subject 3 in Activity 2 showed great genetic diversity and genetic distance because it branched off more and further along than the other subjects. In Activity 3, Subject 9 was the more diverse subject out of subjects 3, 9, and 15 because the calculated theta value was greater.
Acknowledgements
- I worked with my homework partner, Jenny Chua, during class to figure out our research project and ask questions about how to do the assignment. We also texted about the assignment outside of class.
- I used the citation for the Week 5 assignment page.
- I followed the protocol on the assignment page for this week and copied the wiki syntax for the tables from the page.
- My partner and I talked with our professor, Kam D. Dahlquist, Ph.D., about our research idea during class and how to go about testing the hypothesis.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Nyeo2 (talk) 23:17, 19 February 2020 (PST)
References
- Markham, R. B., Wang, W. C., Weisstein, A. E., Wang, Z., Munoz, A., Templeton, A., ... & Yu, X. F. (1998). Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline. Proceedings of the National Academy of Sciences, 95(21), 12568-12573. doi: 10.1073/pnas.95.21.12568
- OpenWetWare. (2020). BIOL368/S20:Week 5. Retrieved February 19, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_5
- HIV-1 isolate S3V3-4 from USA envelope glycoprotein (env) gene, partial cds. (n.d.). Retrieved February 19, 2020, from https://www.ncbi.nlm.nih.gov/nuccore?LinkName=pubmed_nuccore&from_uid=9770526
- Home - PubMed - NCBI. (n.d.). Retrieved February 19, 2020, from https://www.ncbi.nlm.nih.gov/pubmed
- Nucleotide Sequences. (n.d.). Retrieved February 19, 2020, from http://bioquest.org/bedrock/problem_spaces/hiv/nucleotide_sequences.php
- Phylogeny.fr: Home. (n.d.). Retrieved February 19, 2020, from http://www.phylogeny.fr/
- Visit_1_Subjects_1_thru_9_HIV. (n.d.). Retrieved from https://s3-us-west-2.amazonaws.com/oww-files-public/9/9b/Visit_1_Subjects_1_thru_9_HIV.txt
- Visit_1_Subjects_10_thru_15_HIV. (n.d.). Retrieved from https://s3-us-west-2.amazonaws.com/oww-files-public/4/4c/Visit_1_Subjects_10_thru_15_HIV.txt
- The harmonic series. (n.d.). Retrieved February 19, 2020, from https://www.math.utah.edu/~carlson/teaching/calculus/harmonic.html