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"

1. 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"

1. After pasting sequence data(same as above) into the Phylogeny.fr website, clicked on "6. Tree Rendering"

• Phylogenetic tree for Subject 14

Graphical Analysis

1. 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
2. Deleted data points for which theta was not calculated in the table.
3. Added trendline for each graph and added R squared values.
4. 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.