| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 4 I | 6 7 3 | 7 8 I | 8 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 6 I | 14 14 6 | 15 14 I | 16 15 | 17 14 I | 18 14 7 | 19 13 I | 20 17 8 | 21 18 I | 22 19 9 | 23 19 I | 24 20 | 25 19 I | 26 19 10 | 27 2 I | 28 2 11 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_64571.2_Instance_1 J4_64571.2,J4_5J7L_021,C1270_G2010 | C | GAU | A | A | A | U | C | G | C | U | U | A | G | |||||||||||||||||||||
| J4_64571.2_Sequence_1 J4_64571.25J7L_C_1270_G_2010 | C | GAU | A | A | A | * | U | C | * | G | C | U | U | * | A | G | true | 94 | 0 | 0 | 0.95 | |||||||||||||
| J4_64571.2_Instance_2 J4_64571.2,J4_7A0S_004,C1283_G1993 | C | GAU | A | A | A | U | C | G | C | G | C | G | G | |||||||||||||||||||||
| J4_64571.2_Sequence_2 J4_64571.27A0S_C_1283_G_1993 | C | GAU | A | A | A | * | U | C | * | G | C | G | C | * | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| J4_64571.2_Instance_3 J4_64571.2,J4_4Y4O_016,C1270_G2010 | C | GAU | A | A | A | U | C | G | C | G | C | G | G | |||||||||||||||||||||
| J4_64571.2_Sequence_3 J4_64571.24Y4O_C_1270_G_2010 | C | GAU | A | A | A | * | U | C | * | G | C | G | C | * | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| J4_64571.2_Instance_4 J4_64571.2,J4_4WF9_004,C1308_G2037 | C | GA | A | A | G | C | C | G | A | G | C | G | G | |||||||||||||||||||||
| J4_64571.2_Sequence_4 J4_64571.24WF9_C_1308_G_2037 | C | GA | A | A | G | * | C | C | * | G | A | G | C | * | G | G | true | 94 | 0 | 0 | 0.95 |
1 9 s35 1 11 cWW 2 8 s35 3 6 tSS 4 5 cWW 4 6 s55 4 7 s53 5 6 s35 6 7 cWW 9 10 cWW 9 11 s55 10 11 s35 8 2 6BPh 8 3 7BPh 7 3 2BRJAR3D SCFG/MRF model for J4_64571.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [11] // Initial node BasepairNode | Deletion Probability [0.0000000000114302] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.003046923,0.252894576,0.734308349,0.009293114,0.000457038] | Left Letter Distribution [0.346153846,0.038461538,0.346153846,0.269230769,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C1270 - G2010 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [10] // Fixed node on left for 5J7L|1|DA|G|1271 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [10] // Junction node A1275 - A2009 ID J9171 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.333333333,0.222222222,0.222222222,0.222222222,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // Initial node 5J7L|1|DA|A|1275 - 5J7L|1|DA|U|1294 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left for 5J7L|1|DA|A|1272 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009214932,0.021160936,0.010010509,0.228350862,0.000000000],[0.017078136,0.009387344,0.192604579,0.010876858,0.000000000],[0.009966132,0.205518508,0.002013700,0.045705442,0.000000000],[0.192921009,0.011492652,0.022679975,0.011018425,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair A1276 - U1294 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [10] // Initial node 5J7L|1|DA|C|1295 - 5J7L|1|DA|A|2009 from node JunctionNode | Branches [2] | Left Index [6] | Right Index [10] // Junction node C1295 - A2009 ID J2858 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.005819450,0.010435672,0.022698237,0.121306055,0.000000000],[0.012373147,0.005926941,0.471114136,0.008415381,0.000000000],[0.006765307,0.123919874,0.004326526,0.014319644,0.000000000],[0.122878666,0.008108058,0.055425890,0.006167015,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair C1295 - G1645 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // Initial node 5J7L|1|DA|C|1646 - 5J7L|1|DA|A|2009 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.744949495,0.002525253,0.002525253,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 5J7L|1|DA|U|1294 InitialNode | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.083333333,0.583333333,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009230036,0.016881218,0.010494353,0.194361300,0.000000000],[0.020319858,0.009555111,0.230862069,0.012852202,0.000000000],[0.010589659,0.197055880,0.002038410,0.022912280,0.000000000],[0.207859340,0.012317386,0.032759727,0.009911172,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Basepair U1648 - A2009 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from J4_64571.2:
> J4_64571.2 5J7L C 1270 G 2010 CGAUAAA*UC*GCUU*AG > J4_64571.2 7A0S C 1283 G 1993 CGAUAAA*UC*GCGC*GG > J4_64571.2 4Y4O C 1270 G 2010 CGAUAAA*UC*GCGC*GG > J4_64571.2 4WF9 C 1308 G 2037 CGAAAG*CC*GAGC*GG