Nyeo2 Week 5

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Assignments

Individual Journals

Class Journals

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

  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.
  2. 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.
  3. 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

  1. What was the accession number of the sequence you chose?
    • AF089138
  2. Which subject of the study was that HIV sequence from?
    • Subject 3(S3V5-7)
  3. 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

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

Phylogenetic tree

Table 2
Subject Clone #
1 2
4
5
3 1
3
4
7 3
6
8
13 1
3
4
  1. 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.
  2. 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.
  3. 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.
  4. 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
                ***  *******  ******************** **********


Table 3
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 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

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