| 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 4 4 | 9 5 I | 10 6 | 11 5 I | 12 4 5 | 13 3 I | 14 3 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_55516.2_Instance_1 IL_55516.2,IL_6DME_003,G33_C22 | G | A | A | G | C | A | C | |||||||||||||||
| IL_55516.2_Sequence_1 IL_55516.26DME_G33_C22 | G | A | A | G | * | C | A | C | true | 90 | 0 | 0 | 0.91 | |||||||||
| IL_55516.2_Instance_2 IL_55516.2,IL_4V9F_072,G2090_C2654 | G | G | G | G | U | A | C | |||||||||||||||
| IL_55516.2_Sequence_2 IL_55516.24V9F_G_2090_C_2654 | G | G | G | G | * | U | A | C | true | 90 | 0 | 0 | 0.94 | |||||||||
| IL_55516.2_Instance_3 IL_55516.2,IL_7SZU_003,G49_C27 | G | C | A | C | G | A | C | |||||||||||||||
| IL_55516.2_Sequence_3 IL_55516.27SZU_G49_C27 | G | C | A | C | * | G | A | C | true | 95 | 0 | 0 | 0.49 | |||||||||
| IL_55516.2_Instance_4 IL_55516.2,IL_8CRE_096,G2369_C2960 | G | C | G | G | U | A | C | |||||||||||||||
| IL_55516.2_Sequence_4 IL_55516.28CRE_G_2369_C_2960 | G | C | G | G | * | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_55516.2_Instance_5 IL_55516.2,IL_8P9A_319,G2391_C2988 | G | C | G | G | U | A | C | |||||||||||||||
| IL_55516.2_Sequence_5 IL_55516.28P9A_G_2391_C_2988 | G | C | G | G | * | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_55516.2_Instance_6 IL_55516.2,IL_3DD2_004,G3_C23 | G | A | A | CA | A | U | A | C | ||||||||||||||
| IL_55516.2_Sequence_6 IL_55516.23DD2_G3_C23 | G | A | A | CA | A | * | U | A | C | true | 57 | 0 | 0 | 4.11 | ||||||||
| IL_55516.2_Instance_7 IL_55516.2,IL_2A64_008,G237_C193 | G | U | A | A | A | U | G | C | ||||||||||||||
| IL_55516.2_Sequence_7 IL_55516.22A64_G237_C193 | G | U | A | A | A | * | U | G | C | true | 73 | 0 | 0 | 2.56 |
1 2 s35 1 7 cWW 2 3 s35 2 6 cWW 3 4 cSH 4 5 cWW 4 6 s55 5 6 s35 6 7 s35JAR3D SCFG/MRF model for IL_55516.2:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009278847,0.019324516,0.010566130,0.191913241,0.000000000],[0.016298546,0.009098841,0.193539411,0.012663253,0.000000000],[0.010448787,0.264585590,0.001991650,0.025514464,0.000000000],[0.189457119,0.013143234,0.022364576,0.009811793,0.000000000],[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 [7] // Basepair G33 - C22 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.156208382,0.015747833,0.080665831,0.025131707,0.000000000],[0.231578224,0.026301300,0.027664507,0.021823405,0.000000000],[0.090678134,0.024729616,0.003730569,0.016550662,0.000000000],[0.029343356,0.021214564,0.214645878,0.013986030,0.000000000],[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 [6] // Basepair A34 - A21 cWW ClusterNode | Deletion Probability [0.0000000123740933] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.249846784555315] // Cluster node 6DME|1|A|A|35:6DME|1|A|G|36 and 6DME|1|A|C|20:6DME|1|A|C|20 Interaction | Interacting Bases [2,3] | Pair Probability [[0.011623860,0.132376000,0.011552172,0.163328520,0.000000000],[0.015467301,0.010456880,0.133220571,0.012393501,0.000000000],[0.011421606,0.136002279,0.002450521,0.181919338,0.000000000],[0.122821200,0.013119015,0.018990684,0.022856552,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|G|36 - 6DME|1|A|C|20 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.105488956,0.098299466,0.093939886,0.053122947,0.000000000],[0.083214750,0.083846198,0.001719570,0.012338546,0.000000000],[0.013044424,0.001719570,0.117710338,0.080417647,0.000000000],[0.086228482,0.087736867,0.001719570,0.079452783,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6DME|1|A|A|35 - 6DME|1|A|G|36 cSH Insertion | Location [1] | Length Distribution [0.708546015,0.147571638,0.142770506,0.001061303,0.000050538] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node InitialNode | Left Length Distribution [0.992332775,0.007314709,0.000352516] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.992332775,0.007314709,0.000352516] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [4] // New Initial node after Cluster 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 truncationSequences of instances from IL_55516.2:
> IL_55516.2 6DME G 33 C 22 GAAG*CAC > IL_55516.2 4V9F G 2090 C 2654 GGGG*UAC > IL_55516.2 7SZU G 49 C 27 GCAC*GAC > IL_55516.2 8CRE G 2369 C 2960 GCGG*UAC > IL_55516.2 8P9A G 2391 C 2988 GCGG*UAC > IL_55516.2 3DD2 G 3 C 23 GAACAA*UAC > IL_55516.2 2A64 G 237 C 193 GUAAA*UGC