| 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 3 I | 6 4 3 | 7 4 I | 8 5 4 | 9 5 I | 10 5 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 | 17 8 I | 18 8 8 | 19 7 I | 20 7 9 | 21 6 I | 22 5 10 | 23 4 I | 24 4 11 | 25 3 I | 26 3 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_26307.2_Instance_1 IL_26307.2,IL_5J7L_251,C239_G258 | C | C | A | G | U | A | G | C | G | A | A | C | G | |||||||||||||||||||||
| IL_26307.2_Sequence_1 IL_26307.25J7L_C239_G258 | C | C | A | G | U | A | G | * | C | G | A | A | C | G | true | 99 | 0 | 0 | 0.18 | |||||||||||||||
| IL_26307.2_Instance_2 IL_26307.2,IL_9DFE_007,U239_G258 | U | G | A | G | U | A | G | C | G | A | A | A | G | |||||||||||||||||||||
| IL_26307.2_Sequence_2 IL_26307.29DFE_U239_G258 | U | G | A | G | U | A | G | * | C | G | A | A | A | G | true | 98 | 0 | 0 | 0.32 | |||||||||||||||
| IL_26307.2_Instance_3 IL_26307.2,IL_4V9F_007,U210_G229 | U | U | A | G | U | A | A | U | G | A | A | C | G | |||||||||||||||||||||
| IL_26307.2_Sequence_3 IL_26307.24V9F_U210_G229 | U | U | A | G | U | A | A | * | U | G | A | A | C | G | true | 98 | 0 | 0 | 0.46 | |||||||||||||||
| IL_26307.2_Instance_4 IL_26307.2,IL_8CRE_065,G1440_C2337 | G | U | A | G | U | A | G | C | G | A | A | A | C | |||||||||||||||||||||
| IL_26307.2_Sequence_4 IL_26307.28CRE_G_1440_C_2337 | G | U | A | G | U | A | G | * | C | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_26307.2_Instance_5 IL_26307.2,IL_8P9A_289,G1444_C2359 | G | U | A | G | U | A | G | C | G | A | A | A | C | |||||||||||||||||||||
| IL_26307.2_Sequence_5 IL_26307.28P9A_G_1444_C_2359 | G | U | A | G | U | A | G | * | C | G | A | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_26307.2_Instance_6 IL_26307.2,IL_4V9F_049,A1367_U2057 | A | U | A | G | U | A | G | U | G | A | A | C | U | |||||||||||||||||||||
| IL_26307.2_Sequence_6 IL_26307.24V9F_A_1367_U_2057 | A | U | A | G | U | A | G | * | U | G | A | A | C | U | true | 94 | 0 | 0 | 1.07 | |||||||||||||||
| IL_26307.2_Instance_7 IL_26307.2,IL_4V9F_106,G75_U106 | G | G | A | G | U | A | C | G | G | A | A | A | U | |||||||||||||||||||||
| IL_26307.2_Sequence_7 IL_26307.24V9F_G75_U106 | G | G | A | G | U | A | C | * | G | G | A | A | A | U | true | 95 | 0 | 0 | 0.88 | |||||||||||||||
| IL_26307.2_Instance_8 IL_26307.2,IL_4V9F_092,A2689_U2705 | A | U | A | G | U | A | C | G | G | A | A | C | U | |||||||||||||||||||||
| IL_26307.2_Sequence_8 IL_26307.24V9F_A_2689_U_2705 | A | U | A | G | U | A | C | * | G | G | A | A | C | U | true | 100 | 0 | 0 | 0.02 | |||||||||||||||
| IL_26307.2_Instance_9 IL_26307.2,IL_1NBS_007,U165_A143 | U | G | A | G | U | A | U | A | A | A | A | A | A | |||||||||||||||||||||
| IL_26307.2_Sequence_9 IL_26307.21NBS_U165_A143 | U | G | A | G | U | A | U | * | A | A | A | A | A | A | true | 92 | 0 | 0 | 1.52 |
1 2 s35 1 13 cWW 2 3 s33 2 11 s33 2 12 tSH 3 4 s55 3 5 s55 3 10 s53 3 11 tHH 4 5 cSH 4 9 s33 5 6 s35 5 9 s33 5 10 tWH 6 7 s35 6 9 tHS 6 10 s55 7 8 cWW 7 9 s55 8 9 s35 10 11 s35 11 12 s35 12 13 s35 9 5 6BPh 4 10 6BPh 3 11 6BPh 12 2 6BR 9 4 6BR 6 9 6BRJAR3D SCFG/MRF model for IL_26307.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009871049,0.046171971,0.010994713,0.160287119,0.000000000],[0.075938610,0.013151401,0.146576152,0.012330920,0.000000000],[0.011013021,0.156071426,0.002313617,0.067427105,0.000000000],[0.155186233,0.012309232,0.106586450,0.013770981,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C239 - G258 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.108290885,0.105412437,0.001332541,0.006252454,0.000000000],[0.114621927,0.126644956,0.001332541,0.001332541,0.000000000],[0.151011558,0.001332541,0.006924724,0.079367587,0.000000000],[0.142571113,0.150907115,0.001332541,0.001332541,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [12] // Basepair C240 - C257 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.468359047,0.309930808,0.018496463,0.018870803,0.000000000],[0.048485738,0.000551129,0.046984138,0.005236875,0.000000000],[0.002747776,0.046383686,0.001375617,0.000551129,0.000000000],[0.003743306,0.027181227,0.000551129,0.000551129,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // Basepair A241 - A256 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.287755810051411] // Cluster node 5J7L|1|DA|G|242:5J7L|1|DA|U|243 and 5J7L|1|DA|A|255:5J7L|1|DA|A|255 Interaction | Interacting Bases [2,3] | Pair Probability [[0.017569834,0.003888232,0.018249148,0.003888232,0.000000000],[0.039101300,0.313317227,0.003888232,0.003888232,0.000000000],[0.003888232,0.009320350,0.029569679,0.017293519,0.000000000],[0.471392047,0.003888232,0.022559058,0.038298443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|243 - 5J7L|1|DA|A|255 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.029108371,0.029660095,0.001630804,0.028986401,0.000000000],[0.021731301,0.032749451,0.000361088,0.029047168,0.000000000],[0.178024309,0.002527614,0.217159311,0.335330170,0.000000000],[0.029560014,0.029382561,0.000361088,0.034380255,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|242 - 5J7L|1|DA|U|243 cSH InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.095042800,0.046221503,0.387079866,0.049492520,0.000000000],[0.044258638,0.042324170,0.003153390,0.047082533,0.000000000],[0.000931539,0.000535376,0.015792087,0.000535376,0.000000000],[0.005076173,0.000535376,0.261403276,0.000535376,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A244 - G254 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009582906,0.046969097,0.010439699,0.184672626,0.000000000],[0.016867708,0.009337652,0.190702311,0.012115851,0.000000000],[0.010382217,0.210810972,0.002065622,0.066848871,0.000000000],[0.179146945,0.012358680,0.024755653,0.012943189,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Basepair G245 - C253 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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 IL_26307.2:
> IL_26307.2 5J7L C 239 G 258 CCAGUAG*CGAACG > IL_26307.2 9DFE U 239 G 258 UGAGUAG*CGAAAG > IL_26307.2 4V9F U 210 G 229 UUAGUAA*UGAACG > IL_26307.2 8CRE G 1440 C 2337 GUAGUAG*CGAAAC > IL_26307.2 8P9A G 1444 C 2359 GUAGUAG*CGAAAC > IL_26307.2 4V9F A 1367 U 2057 AUAGUAG*UGAACU > IL_26307.2 4V9F G 75 U 106 GGAGUAC*GGAAAU > IL_26307.2 4V9F A 2689 U 2705 AUAGUAC*GGAACU > IL_26307.2 1NBS U 165 A 143 UGAGUAU*AAAAAA