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Table 2 Percentage conservations for the combinations

From: Multiple shRNA combinations for near-complete coverage of all HIV-1 strains

   229 sequences 995 sequences 127 sequences 549 sequences
   Clade B d Others e Clade B (LTR) f Others (LTR) g
# a Combin.c 4+ 5+ 6+ 7+ 4+ 5+ 6+ 7+ 4+ 5+ 6+ 7+ 4+ 5+ 6+ 7+
5.1 3.4.7.2.9 89 48 - - 54 15 - - 91 53 - - 58 15 - -
5.2 b 3.4.7.2.0 n/a n/a - - n/a n/a - - 94 57 - - 57 23 - -
5.3 3.8.9.2.7 92 49 - - 40 13 - - 94 54 - - 41 15 - -
5.4 b 3.8.5.9.0 n/a n/a - - n/a n/a - - 95 64 - - 58 20 - -
5.5 3.8.5.2.9 92 53 - - 48 12 - - 94 59 - - 54 13 - -
5.6 b 3.8.5.2.1 n/a n/a - - n/a n/a - - 97 65 - - 53 10 - -
6.2 b 3.4.7.2.0.5 n/a n/a n/a - n/a n/a n/a - 100 89 51 - 81 50 15 -
6.3 3.8.9.2.7.6 100 86 46 - 65 26 4 - 99 89 49 - 67 23 3 -
6.4 b 3.8.5.9.0.6 n/a n/a n/a - n/a n/a n/a - 100 88 60 - 75 38 5 -
6.5 b 3.8.5.2.9.0 n/a n/a n/a - n/a n/a n/a - 99 94 58 - 80 45 13 -
6.6 3.8.5.2.9.7 99 87 43 - 68 31 9 - 98 92 47 - 73 34 10 -
6.7 b 3.8.5.2.1.7 n/a n/a n/a - n/a n/a n/a - 100 94 53 - 75 30 7 -
6.8 b 3.4.7.2.0.6 n/a n/a n/a - n/a n/a n/a - 99 88 52 - 77 40 5 -
6.9 3.4.7.2.9.5 98 84 43 - 75 45 9 - 98 87 47 - 79 50 10 -
7.3 b 3.8.9.2.7.6.0 n/a n/a n/a n/a n/a n/a n/a n/a 100 98 89 48 87 57 22 3
7.5 3.8.5.2.9.7.6 100 99 81 41 84 56 18 3 100 98 84 44 85 58 17 2
7.7 3.4.7.2.9.5.6 100 96 80 40 86 64 31 3 100 94 83 43 86 64 34 2
  1. a Combination reference number (#) used in this study.
  2. b As these combinations contained an LTR shRNA (0 or 1) the intersecting conservations calculated on all sequences (where a large number lacked LTR sequence coverage), were not applicable (n/a); only the LTR containing subset were used, as shown.
  3. c The component shRNAs (in order of arrangement) for each combination.
  4. d The clade B sequences only.
  5. e The sequences of all other clades (excluding clade B).
  6. f The subset of clade B sequences that contain LTR sequence coverage.
  7. g The subset of all other sequences (non B) that contain LTR sequence coverage.