Table 3. Different patterns of nucleotide substitution for ss and ds nucleotides in HIV-1 subtype B RNA genomes.
| Qss | A | U | C | G | Qds | A | U | C | G |
|---|---|---|---|---|---|---|---|---|---|
| A |
-0.699428 |
0.081518 |
0.156830 |
0.461079 |
A |
-1.499043 |
0.254533 |
0.339833 |
0.904678 |
| U |
0.138854 |
-0.899975 |
0.568940 |
0.192180 |
U |
0.175181 |
-0.868417 |
0.532371 |
0.160865 |
| C |
0.574634 |
1.007012 |
-1.776556 |
0.194910 |
C |
0.300107 |
0.471187 |
-0.837239 |
0.065945 |
| G | 1.148242 | 0.084045 | 0.114724 | -1.347011 | G | 0.736551 | 0.068547 | 0.064782 | -0.869880 |
Patterns of nucleotide substitution are presented as rate matrices (Qss and Qds). A positive value of a row represents the rate of substitution of the row nucleotide into one of the column nucleotides. A negative value on the matrix diagonal is the quantity by which the sum of the positive row becomes reduced to zero (meaning a zero rate of substitution). An unrestricted model of nucleotide substitution was used. The two alignments of ss and ds nucleotides were analyzed in five batches of 80 sequences. The resulting matrices (Table S1) were arithmetically averaged to obtain the two “consensus” matrices (Qss and Qds).