Nyeo2 Week 6
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Purpose
The purpose of our experiment was to predict a graphical relationship between CD4 T-cell levels and genetic diversity(theta) within the three HIV-1 progressor groups based on linear regression and statistical tests.
Methods and Results
Sequence Alignment
- "One Click" under "Phylogeny Analysis"
- Copied and pasted the nucleotide sequence data of Subject 14 from Nucleotide Sequence Data into Phylogeny.fr website
- Under "3. Alignment", clicked on "Alignment in Clustal format" under "Outputs".
- Exported clustered sequence alignment.
- We focused in on Subject 14 because there was the most data points with CD4 and corresponding theta values in the Markham Data Table the was provided in the assignment page.
- Sequence alignment for Subject 14
S14V7-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-9 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACGGCTG S14V6-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAGTAGTACAGCTG S14V4-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCCG S14V4-10 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V3-1 GAGGTAGTAGTTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-9 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V5-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-8 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-6 GAGGTAGTAGTTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V2-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V3-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V3-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V3-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAACGCTAAAATCATAATAGTACAGCTG S14V3-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-8 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V1-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V3-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V4-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-9 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-8 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-3 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-12 GAGGTGGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-10 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V5-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAACAGTACAGCTG S14V7-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-3 GAGGTAGTAATTAGATCTGAAAATTACACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAATAATGCTAAAATCATAATAGTACAGCTG S14V9-10 GAGGTAGTAATTAGATCTGAAAATTTCACGAATAATGCTAAAATCATAATAGTACAGCTG S14V5-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V5-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-10 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-8 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-11 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V5-1 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACTGCTG S14V7-6 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V7-7 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-9 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACATCTG S14V5-2 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V6-11 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V5-3 GAGGTAGTAATTAGAACTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-5 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCAG S14V7-4 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V8-8 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG S14V9-9 GAGGTAGTAATTAGATCTGAAAATTTCACGAACAATGCTAAAATCATAATAGTACAGCTG ***** *** ***** ********* ****** ** ************ ***** * *
S14V7-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAGGTATACAT S14V8-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V8-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAGAAAGTATACAT S14V6-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTGTAAAT S14V6-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V7-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCATCGACAATACAAGAAAAAGTATAAAT S14V4-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-10 AATGAATCTGTAGAAATTAATTGTACAAGACC---CAACAATACAAGAAGAAGTATAAAT S14V1-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-6 AATGAATCTGTAGAAATTAATTGTACAAGACACAACAACAATACAAGAAGAAGTATAAAT S14V4-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V5-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V6-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-1 AATGAGTCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-5 AATGAGTCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-6 AATGAATCTGTAGAAAGTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V1-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V1-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V1-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V1-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V2-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V1-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V3-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V4-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAGAAGTATAAAT S14V7-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V8-1 AATGAATCTGTAGAAATTGATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAACACAAGAAAAAGTATAAAT S14V9-2 AATGAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAACACAAGAAAAAGTATAAAT S14V8-3 AATGAATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACAAGAAAAAGTATAAAT S14V9-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-12 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V8-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V7-10 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V5-4 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V7-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V8-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAGCAATACAAGAAAAAGTATAAAT S14V9-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCCACAACAATACAAGAAAAAGTATACAT S14V9-5 AATGAATCTGTAGAAGTTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-10 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V5-5 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V5-7 AATGGATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V6-10 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V7-8 AATGAATCTGTAAAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V9-11 AATGAATCTGTAGAAATTAATTGTACAAGACCCCACAACAATACAAGAAAAAGTATAAAT S14V5-1 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V8-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATAAAT S14V7-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCCACAACAATACAAGAAAAAGTATACAT S14V7-6 AATGAATCTGTAGAAATTAATTGTACAAGACCCCACAACAATACAAGAAAAAGTATACAT S14V7-7 AATGAATCTGTAGAAATTAATTGTACAAGACCCCACAACAATACAAGAAAAAGTATACAT S14V6-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V5-2 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V6-11 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V5-3 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V8-5 AATAAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V7-4 AATGAATCTGTAGAAATCAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V8-8 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT S14V9-9 AATGAATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATACAT *** ****** ** ********** * * *** ****** * ** ** **
S14V7-1 CTAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGGCAAGCA S14V8-4 CTAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATGGGAGATATAAGGCAAGCA S14V8-9 CTAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAAAGGGAGATATAAGGCAAGCA S14V6-4 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V6-1 ATAGAACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V6-2 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V6-3 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCG S14V6-5 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V6-7 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V7-3 ATAGGGCCAGGGAGAGCATTGTATGCAACAGGAGCTATAATGGGAGATATAAGGCAAGCA S14V4-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V4-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGGCAAGCA S14V4-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGGCAAGCA S14V4-10 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGGCAAGCA S14V1-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATGTAATAGGAGATATAGGGCAAGCA S14V4-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAATATAATAGGAGATATAAGGCAAGCA S14V4-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V4-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V4-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V5-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V6-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V2-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V2-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V2-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V2-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V1-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V1-4 ACAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V1-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V1-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V2-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAGGGCAAGCA S14V2-4 GTAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCATGCA S14V4-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V1-1 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V3-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V4-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAGATATAATAGGAGATATAAGGCAAGCA S14V7-9 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTTTAATGGGAGATATAAGGCAAGCA S14V8-1 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V9-8 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V9-2 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V8-3 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V9-4 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGGGATATAAGGCAAGCA S14V9-1 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V9-12 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V8-6 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V9-7 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCGAGCA S14V7-10 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATGGGAGATATAAGGCAAGCG S14V5-4 ATAGGACCAGGGAGAGCGTTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V7-5 ATAGGACCAGGGAGAGCGTTGTATGCAACAGGAGCTATAATGGGAGATATAAGGCAAGCA S14V6-6 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAAATATAAGGCAAGCA S14V8-7 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V9-3 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V9-5 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V9-10 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V5-5 ATAGGACCAGGGAGAGCATCGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V5-7 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V6-10 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAAATATAAGGCAAGCA S14V9-6 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAAATATAAGGCAAGCA S14V7-8 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V9-11 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V5-1 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V8-2 ATAGGACCAGGGAGAGCATTGTATGCAACAGGAGCTATAATAGGAGATATAAGGCAAGCA S14V7-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V7-6 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCG S14V7-7 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V6-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V5-2 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V6-11 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V5-3 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAGAATAATAGGAGATATAAGGCAAGCA S14V8-5 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGACAAGCA S14V7-4 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGGCAAGCA S14V8-8 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGACAAGCA S14V9-9 ATAGGACCAGGGAGAGCATTTTATGCAACAGGAAAGATAATAGGAGATATAAGACAAGCA ** *********** * ************ *** ** ***** * * **
S14V7-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAGAACAGATAGTTTACAAATTA S14V8-4 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAGAACAGATAGTTTACAAATTA S14V8-9 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAGAACAGATAGTTTACAAATTA S14V6-4 CATTGTAACCTCAGTAGAGCAAAATGGAACGACACTTTAAAACAGATAGTTTACAAATTA S14V6-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTCCAAATTA S14V6-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-7 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-4 CATTGTAACCTTAGTAAAGCAAAGTGGGATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-10 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V1-3 CATTGTAACCTTAGTAGGGCAAAATGGAATGACACTTTAAAACAGACAGTTTACAAATTA S14V3-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-9 CATTGTAACCTTAGTAGTGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-8 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V1-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTCTAAAACAGATAGTTTACAAATTA S14V1-4 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V1-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACGCTTTAAAACAGATAGTTTACAAATTA S14V1-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V2-4 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V3-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V3-4 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAGTTA S14V3-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V3-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-8 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTATAAATTA S14V1-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V3-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V4-7 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-9 CATTGTAACCTTAGTAGGGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-1 CATTGTAACATTAGTAGAGCAAAATGGAATGATACTTTAAAACAGATAGTTTACAAATTA S14V9-8 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-2 TATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-3 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-4 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-1 CATTGTAACATTAGTAGAGCAAGATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-12 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-6 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-7 CATTGTAACATTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-10 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-4 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-6 CATTGTAACCTTAGTAAAGCAAAATGGGATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-7 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-10 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-5 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-7 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-10 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-8 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-11 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-1 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-6 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-7 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-9 CATTGTAACCTTAGTAGAGCAAGATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-2 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V6-11 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V5-3 CATTGTAACCTTAGTAGAGCAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-5 CATTATAACCTTAGTAGAACAAGATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V7-4 CATTGTAACCTTAGTAGAGCAAGATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V8-8 CATTGTAACCTTAGTAGAACAAAATGGAATGACACTTTAAAACAGATAGTTTACAAATTA S14V9-9 CATTGTAACCTTAGTAGAACAAGATGGAATGACACTTTAAAACAGATAGTTTACAAATTA *** **** * **** *** *** * ** ** ** ****** ***** ** ***
S14V7-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATTCTCA S14V8-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-9 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-4 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-1 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-2 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-3 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-5 AGAGAACAATTTGGAAATAATATAACAATAATCTTTAATCAATCCTCA S14V6-7 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-2 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-10 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAGTCAATCCTCA S14V4-5 AGAGAACAATTTAGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-9 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-8 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-5 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-6 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-2 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-2 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V2-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-3 AGAGAACAATTGGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-8 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V1-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V3-2 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V4-7 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-9 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-1 AGAGAACAATTTGGGACTAATAAAACAATAATCTTTAATCAATCCTCA S14V9-8 AGAGAACAATTTGGGACTAATAAAACAATAATCTTTAATCAATCCTCA S14V9-2 AGAGAACAATTTGGGACTAATAAAACAATAATCTTTAATCAATCCTCA S14V8-3 AGAGAACAATTTGGGACTAATAAAACAATAATCTTTAATCAATCCTCA S14V9-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-12 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-7 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-10 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-7 AGAGAACAATTTGGGAGTAATAAAACAATAATCTTTAATCAATCCTCA S14V9-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-10 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-7 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-10 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-6 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-8 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-11 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-1 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-2 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-2 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-6 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-7 AGAGAACAATTTGGAAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-9 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-2 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V6-11 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V5-3 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-5 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V7-4 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V8-8 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA S14V9-9 AGAGAACAATTTGGGAATAATAAAACAATAATCTTTAATCAATCCTCA *********** * * ***** ************** ***** ****
Phylogenetic Tree
- "One Click" under "Phylogeny Analysis"
- After pasting sequence data(same as above) into the Phylogeny.fr website, clicked on "6. Tree Rendering"
- Phylogenetic tree for Subject 14
Graphical Analysis
- Took theta and CD4 T-cell values from Markham et al. 1998 data table and plotted them against each other for each progressor group (rapid, moderate, non) in Microsoft Excel.
- Independent=theta, dependent=CD4 levels
- Deleted data points for which theta was not calculated in the table.
- Added trendline for each graph and added R squared values.
- Used =LINEST and =FDIST on Microsoft Excel to statistically analyze the correlation between the dependent and independent variables for each group.
- Null: There is not an inverse relationship between Θ vs. CD4 T-cell levels in the HIV-1 patients in the study.
- Alternate: There is an inverse relationship between Θ vs. CD4 T-cell levels in the HIV-1 patients in the study.
- Scatterplot for non-progressors
- Scatterplot for moderate progressors
- Scatterplot for rapid progressors
- Scatterplot for all subjects
- Scatterplot for Subject 14
Table for p-value significance
Progressor group | p-value |
Non-progressor | 0.936 |
Moderate Progressor | 0.903 |
Rapid Progressor | 0.007 |
All Subjects | 6.56x10-5 |
Subject 14 | 0.02 |
Note that the p-value was considered significant if the value was ≤ 0.05.
Data and Files
- Subject 14 Sequence Alignment
- Subject 14 Phylogenetic Tree
- Scatterplot for non-progressors
- Scatterplot for moderate progressors
- Scatterplot for rapid progressors
- Scatterplot for all subjects
- Scatterplot for Subject 14
Scientific Conclusion
It was found that the data from Markham et. al. (1998) matched our model of an inverse relationship between CD4 T-cell levels and genetic divergence, except in the case of non-progressors who showed a direct correlation instead. However, Gaardbo et. al. (2012) found that some non-progressors, in addition to preserved CD4 T-cell levels, had very low or undetectable viral replication. Genetic divergence cannot happen without the DNA constantly making copies, so this makes sense as to why, perhaps, we saw a slightly positive slope. In terms of R2, none of the groups when plotted showed a "strong" correlation; that is, a R2 value above 0.5, which means that the data did not fit closely with the best fit trend line. Though, as stated earlier, the slopes of the best fit lines revealed an inverse relationship based on their negative "m" value. In terms of statistical significance, the data for rapid progressors, all subjects, and Subject 14 were significant, meaning that their correlation probably did not happen by chance, which makes sense given the findings from Markham et. al. (1998) and the findings from Gaardbo et. al. (2012) that non- and moderate progressors did not have as much of a change in CD4 T-cell levels. In conclusion, our model supports the Markham et. al. (1998) data for rapid progressors and all subjects, and that non- and moderate progressors do not have as much of a change in CD4 T-cell levels because there is a lack of genetic divergence.
Acknowledgements
- I worked with my partner Jenny Chua during class, over text, and once in person to complete our presentation.
- Jenny went to office hours to ask our professor, Dr. Dahlquist, some questions about our research project.
- I copied the conclusion and data table from my partner's wiki page.
- I referenced data from Markham et. al. (1998) and Gaardbo et. al. (2012) to guide my background and discussion information.
- I used the citation for the Week 6 assignment page.
- I followed the protocol on the assignment page for this week.
- Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
Nyeo2 (talk) 22:57, 26 February 2020 (PST)
References
- BEDROCK Nucleotide Sequences. (2015). Subject 14 all visits. Retrieved February 25, 2020, from http://bioquest.org/bedrock/problem_spaces/hiv/hiv_data/dna/Subject_14.txt.
- Gaardbo, J. C., Hartling, H. J., Gerstoft, J., & Nielsen, S. D. (2012). Thirty years with HIV infection—nonprogression is still puzzling: lessons to be learned from controllers and long-term nonprogressors. AIDS research and treatment, 2012.
- 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.
- Minitab (2013). Regression Analysis: How Do I Interpret R-squared and Assess the Goodness-of-Fit? Retrieved February 25, 2020, from https://blog.minitab.com/blog/adventures-in-statistics-2/regression-analysis-how-do-i-interpret-r-squared-and-assess-the-goodness-of-fit.
- OpenWetWare. (2020). BIOL368/S20:Week 6. Retrieved February 25, 2020, from https://openwetware.org/wiki/BIOL368/S20:Week_6.
- Phylogeny.fr. (2020) Phylogeny.fr:Home. Retrieved February 25, 2020, from http://www.phylogeny.fr/.
- Wikipedia. (2010). Wikipedia:Manual of Style/Superscripts and subscripts. Retrieved February 25, 2020, from https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Superscripts_and_subscripts.