| 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 6 5 | 11 6 I | 12 6 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 8 | 17 9 I | 18 10 | 19 9 I | 20 9 9 | 21 8 I | 22 8 10 | 23 7 I | 24 6 11 | 25 5 I | 26 5 12 | 27 4 I | 28 4 13 | 29 3 I | 30 3 14 | 31 2 I | 32 2 15 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_04346.10_Instance_1 IL_04346.10,IL_9DFE_006,C201_G194 | C | U | C | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_1 IL_04346.109DFE_C201_G194 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_04346.10_Instance_2 IL_04346.10,IL_5J7L_250,C201_G194 | C | U | A | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_2 IL_04346.105J7L_C201_G194 | C | U | A | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 99 | 0 | 0 | 0.28 | |||||||||||||||||
| IL_04346.10_Instance_3 IL_04346.10,IL_4V9F_006,C171_G164 | C | U | C | A | G | U | A | U | A | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_3 IL_04346.104V9F_C171_G164 | C | U | C | A | G | U | A | U | * | A | G | A | A | C | U | G | true | 99 | 0 | 0 | 0.23 | |||||||||||||||||
| IL_04346.10_Instance_4 IL_04346.10,IL_7A0S_006,C178_G171 | C | U | C | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_4 IL_04346.107A0S_C178_G171 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_04346.10_Instance_5 IL_04346.10,IL_1JBR_001,C6_G24 | C | U | C | A | G | U | A | C | G | G | A | A | C | C | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_5 IL_04346.101JBR_C6_G24 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | C | G | true | 93 | 0 | 0 | 1.48 | |||||||||||||||||
| IL_04346.10_Instance_6 IL_04346.10,IL_7A0S_007,G215_C236 | G | U | U | A | G | U | A | G | C | G | A | A | C | C | C | |||||||||||||||||||||||
| IL_04346.10_Sequence_6 IL_04346.107A0S_G215_C236 | G | U | U | A | G | U | A | G | * | C | G | A | A | C | C | C | true | 91 | 0 | 0 | 1.86 | |||||||||||||||||
| IL_04346.10_Instance_7 IL_04346.10,IL_4WF9_009,C241_G262 | C | U | U | A | G | U | A | G | C | G | A | A | A | C | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_7 IL_04346.104WF9_C241_G262 | C | U | U | A | G | U | A | G | * | C | G | A | A | A | C | G | true | 91 | 0 | 0 | 1.72 | |||||||||||||||||
| IL_04346.10_Instance_8 IL_04346.10,IL_8OI5_139,A72_U106 | A | C | C | G | A | G | U | A | G | C | G | A | A | A | C | U | ||||||||||||||||||||||
| IL_04346.10_Sequence_8 IL_04346.108OI5_A72_U106 | A | C | C | G | A | G | U | A | G | * | C | G | A | A | A | C | U | true | 83 | 0 | 0 | 3.46 | ||||||||||||||||
| IL_04346.10_Instance_9 IL_04346.10,IL_8P9A_369,A72_U106 | A | C | C | G | A | G | U | A | G | C | G | A | A | A | C | U | ||||||||||||||||||||||
| IL_04346.10_Sequence_9 IL_04346.108P9A_A72_U106 | A | C | C | G | A | G | U | A | G | * | C | G | A | A | A | C | U | true | 83 | 0 | 0 | 3.46 | ||||||||||||||||
| IL_04346.10_Instance_10 IL_04346.10,IL_8P9A_344,C3018_G3036 | C | U | U | A | G | U | A | C | G | G | A | A | C | A | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_10 IL_04346.108P9A_C_3018_G_3036 | C | U | U | A | G | U | A | C | * | G | G | A | A | C | A | G | true | 88 | 0 | 0 | 2.36 | |||||||||||||||||
| IL_04346.10_Instance_11 IL_04346.10,IL_9DFE_048,A1262_U2017 | A | U | G | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_04346.10_Sequence_11 IL_04346.109DFE_A_1262_U_2017 | A | U | G | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 99 | 0 | 0 | 0.15 | |||||||||||||||||
| IL_04346.10_Instance_12 IL_04346.10,IL_5J7L_289,A1262_U2017 | A | U | A | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_04346.10_Sequence_12 IL_04346.105J7L_A_1262_U_2017 | A | U | A | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 97 | 0 | 0 | 0.67 | |||||||||||||||||
| IL_04346.10_Instance_13 IL_04346.10,IL_7A0S_045,A1275_U2000 | A | U | G | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_04346.10_Sequence_13 IL_04346.107A0S_A_1275_U_2000 | A | U | G | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 99 | 0 | 0 | 0.15 | |||||||||||||||||
| IL_04346.10_Instance_14 IL_04346.10,IL_8CRE_125,C2990_G3008 | C | U | U | A | G | U | A | C | G | G | A | A | C | C | G | |||||||||||||||||||||||
| IL_04346.10_Sequence_14 IL_04346.108CRE_C_2990_G_3008 | C | U | U | A | G | U | A | C | * | G | G | A | A | C | C | G | true | 92 | 0 | 0 | 1.53 | |||||||||||||||||
| IL_04346.10_Instance_15 IL_04346.10,IL_4WF9_048,G1300_C2044 | G | U | G | A | G | U | A | G | U | G | A | A | A | U | C | |||||||||||||||||||||||
| IL_04346.10_Sequence_15 IL_04346.104WF9_G_1300_C_2044 | G | U | G | A | G | U | A | G | * | U | G | A | A | A | U | C | true | 92 | 0 | 0 | 1.58 |
1 2 s35 1 15 cWW 2 3 s35 2 14 cWW 2 15 s55 3 4 s33 3 12 s33 3 13 tSH 3 14 s55 4 5 s55 4 6 s55 4 11 s53 4 12 tHH 5 6 cSH 5 10 s33 6 7 s35 6 10 s33 6 11 tWH 7 8 s35 7 10 tHS 7 11 s55 8 9 cWW 8 10 s55 9 10 s35 11 12 s35 12 13 s35 13 14 s35 14 15 s35 10 6 6BPh 5 11 6BPh 4 12 6BPh 13 3 6BR 7 10 6BRJAR3D SCFG/MRF model for IL_04346.10:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000119734646324] | Pair Probability [[0.008406848,0.016994520,0.009428215,0.221669729,0.000000000],[0.016792868,0.008555751,0.249835392,0.011157163,0.000000000],[0.009466194,0.196311342,0.001839096,0.029998578,0.000000000],[0.176713565,0.011176359,0.022242198,0.009412181,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.863704278,0.135687012,0.000586575,0.000022135] | Left Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | 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 [15] // Basepair C201 - G194 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012160827,0.195122844,0.012005175,0.020950047,0.000000000],[0.022937778,0.129790632,0.018543042,0.013683443,0.000000000],[0.011916535,0.018723588,0.003873259,0.040650650,0.000000000],[0.035987605,0.082184646,0.020230959,0.361238969,0.000000000],[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 [14] // Basepair U202 - U193 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.100135932,0.115971362,0.001358589,0.006285828,0.000000000],[0.103887646,0.153417806,0.001358589,0.001358589,0.000000000],[0.167626521,0.001358589,0.006952824,0.061391833,0.000000000],[0.130718205,0.145460507,0.001358589,0.001358589,0.000000000],[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 [13] // Basepair C203 - C192 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.499670618,0.291677097,0.017407094,0.017759386,0.000000000],[0.045630118,0.000518670,0.044216956,0.004928444,0.000000000],[0.002585943,0.043651869,0.001294599,0.000518670,0.000000000],[0.003522840,0.025580359,0.000518670,0.000518670,0.000000000],[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 [4] | Right Index [12] // Basepair A204 - A191 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.311752728833310] // Cluster node 9DFE|1|1A|G|205:9DFE|1|1A|U|206 and 9DFE|1|1A|A|190:9DFE|1|1A|A|190 Interaction | Interacting Bases [2,3] | Pair Probability [[0.016535040,0.003659231,0.017174345,0.003659231,0.000000000],[0.036798387,0.294864070,0.003659231,0.003659231,0.000000000],[0.003659231,0.008771418,0.027828141,0.016274998,0.000000000],[0.502524985,0.003659231,0.021230418,0.036042815,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|U|206 - 9DFE|1|1A|A|190 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.027394002,0.027913231,0.001534756,0.027279216,0.000000000],[0.020451412,0.030820637,0.000339821,0.027336403,0.000000000],[0.167539375,0.002378747,0.204369478,0.374476620,0.000000000],[0.027819045,0.027652044,0.000339821,0.032355393,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 9DFE|1|1A|G|205 - 9DFE|1|1A|U|206 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 [7] | Right Index [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.038758222,0.039046168,0.456121414,0.043264526,0.000000000],[0.041030801,0.040935791,0.003256866,0.040714791,0.000000000],[0.000465267,0.000465267,0.015921785,0.000465267,0.000000000],[0.002192803,0.000465267,0.276430499,0.000465267,0.000000000],[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 [7] | Right Index [10] // Basepair A207 - G189 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008803172,0.033358955,0.009702592,0.197048926,0.000000000],[0.016460115,0.008740523,0.222580180,0.011377063,0.000000000],[0.009696742,0.205091361,0.001910371,0.053338299,0.000000000],[0.176167818,0.011475196,0.023131906,0.011116780,0.000000000],[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 [8] | Right Index [9] // Basepair C208 - G188 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_04346.10:
> IL_04346.10 9DFE C 201 G 194 CUCAGUAC*GGAACUG > IL_04346.10 5J7L C 201 G 194 CUAAGUAC*GGAACUG > IL_04346.10 4V9F C 171 G 164 CUCAGUAU*AGAACUG > IL_04346.10 7A0S C 178 G 171 CUCAGUAC*GGAACUG > IL_04346.10 1JBR C 6 G 24 CUCAGUAC*GGAACCG > IL_04346.10 7A0S G 215 C 236 GUUAGUAG*CGAACCC > IL_04346.10 4WF9 C 241 G 262 CUUAGUAG*CGAAACG > IL_04346.10 8OI5 A 72 U 106 ACCGAGUAG*CGAAACU > IL_04346.10 8P9A A 72 U 106 ACCGAGUAG*CGAAACU > IL_04346.10 8P9A C 3018 G 3036 CUUAGUAC*GGAACAG > IL_04346.10 9DFE A 1262 U 2017 AUGAGUAA*UGAAAUU > IL_04346.10 5J7L A 1262 U 2017 AUAAGUAA*UGAAAUU > IL_04346.10 7A0S A 1275 U 2000 AUGAGUAA*UGAAAUU > IL_04346.10 8CRE C 2990 G 3008 CUUAGUAC*GGAACCG > IL_04346.10 4WF9 G 1300 C 2044 GUGAGUAG*UGAAAUC