Jennymchua Week 6 Assignment

Purpose

The purpose of this experiment was to estimate a graphical relationship between CD4 T-cell levels and genetic diversity within three HIV-1 progressor groups - rapid, moderate, and non-progressors - based on linear regression.

Combined Methods/Results

Methods

CD4 T-cell levels and Θ (genetic diversity) were selected from a data table from Markham et. al. (1998), separated into progression group, and plotted against each other in Microsoft Excel.
- Independent variable = Θ, dependent variable = CD4 T-cell levels
- Individuals with no Θ values were excluded from the analysis as
Trendlines and their equations and R² values were added to each figure.
After each progressor group was plotted, one graph for all three progressor groups and one graph for Subject 14 were created as well.
- Subject 14 was selected as they had multiple data points for CD4 T-cell values and Θ.
Nucleotide sequences from Subject 14 were copied from BEDROCK Nucleotide Sequences and pasted into a "One Click" phylogenetic analysis to generate a clustered sequence alignment and a phylogenetic tree.
LINEST and FDIST on Microsoft Excel were used to statistically analyze the correlation between the dependent and independent variables for each group.

Results

Alignment in clustal form 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 of clones for Subject 14

The figure below is a phylogenetic tree of Subject 14's HIV-1 clones throughout their multiple visits. Subject 14 was chosen because they had the most data points to further analyze.

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

Non-progressors
Moderate progressors
Rapid progressors
All subjects
Subject 14 scaled
Phylogenetic tree for Subject 14

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.

Acknowledgments

I worked with my homework and project partner Nick Yeo in class, over text, and in person once to discuss our presentation and formulate questions to ask Dr. Dahlquist in office hours.
I asked Dr. Dahlquist several questions and got some helpful tips during office hours once.
I asked Annika Dinulos a clarifying question about genetic diversity versus genetic divergence.
I referenced data from Markham et. al. (1998) and Gaardbo et. al. (2012) to guide my background and discussion information.
I used BEDROCK Nucleotide Sequences for Subject 14 in data analysis.
I used Phylogeny.fr to create a phylogenetic tree for Subject 14.
I copied Wikipedia syntax for a superscript from this Wiki page.
Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Jennymchua (talk) 21:49, 25 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.

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