| 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 2 2 | 5 2 I | 6 2 3 | 7 3 I | 8 4 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 6 | 13 8 I | 14 13 7 | 15 13 I | 16 14 | 17 13 I | 18 13 8 | 19 12 I | 20 16 9 | 21 17 I | 22 18 10 | 23 18 I | 24 19 11 | 25 19 I | 26 20 | 27 19 I | 28 19 12 | 29 18 I | 30 18 13 | 31 10 I | 32 9 14 | 33 6 I | 34 6 15 | 35 3 I | 36 2 16 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_96372.1_Instance_1 J3_96372.1,J3_3MXH_001,G14_C93 | G | C | A | C | A | G | G | G | C | A | A | A | G | U | U | A | C | C | ||||||||||||||||||||||||
| J3_96372.1_Sequence_1 J3_96372.13MXH_G14_C93 | G | C | A | C | A | G | G | G | * | C | A | A | A | G | * | U | U | A | C | C | true | 98 | 0 | 0 | 0.30 | |||||||||||||||||
| J3_96372.1_Instance_2 J3_96372.1,J3_4YAZ_002,G8_C76 | G | A | C | A | A | U | A | C | G | A | A | A | G | C | U | G | C | C | ||||||||||||||||||||||||
| J3_96372.1_Sequence_2 J3_96372.14YAZ_G8_C76 | G | A | C | A | A | U | A | C | * | G | A | A | A | G | * | C | U | G | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 cSH 1 16 cWW 2 3 s35 3 4 s35 3 16 cWS 4 5 s35 5 6 s35 5 9 wat 5 15 cWS 6 7 s35 6 9 s55 7 8 cWW 10 11 s35 10 13 tHW 10 14 s55 11 12 cWW 11 13 s55 12 13 s35 13 14 s35 14 15 s35 15 16 s35 4 16 2BRJAR3D SCFG/MRF model for J3_96372.1:
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 [16] // Initial node ClusterNode | Deletion Probability [0.0000000000025160] | Num Left Bases [3] | Num Right Bases [1] | Left Index [1] | Right Index [16] | Norm Constant [0.062995478238493] // Cluster node 3MXH|1|R|G|14:3MXH|1|R|C|17 and 3MXH|1|R|C|93:3MXH|1|R|C|93 Interaction | Interacting Bases [1,4] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|G|14 - 3MXH|1|R|C|93 cWW Interaction | Interacting Bases [3,4] | Pair Probability [[0.107679378,0.128747765,0.106682031,0.107285303,0.000000000],[0.134823572,0.151413186,0.002414108,0.136448280,0.000000000],[0.020746290,0.002414108,0.040865269,0.010122944,0.000000000],[0.012099297,0.017402507,0.009561675,0.011294287,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|C|17 - 3MXH|1|R|C|93 cWS Interaction | Interacting Bases [1,2] | Pair Probability [[0.012110736,0.014906893,0.008290727,0.149390441,0.000000000],[0.015118535,0.125816550,0.001709255,0.161217910,0.000000000],[0.190533378,0.001709255,0.021344674,0.120385885,0.000000000],[0.014589390,0.021595133,0.001709255,0.139571982,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 3MXH|1|R|G|14 - 3MXH|1|R|A|16 cSH Insertion | Location [1] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 1, position 1 in cluster node Insertion | Location [2] | Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [15] // Initial node 3MXH|1|R|A|18 - 3MXH|1|R|C|92 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.875000000,0.041666667,0.041666667,0.041666667,0.000000000] | Position [1] | Left Index [4] | Right Index [15] // Fixed node on left for 3MXH|1|R|C|17 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [5] | Right Index [15] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.007954761,0.008168861,0.007762277,0.008311193,0.000000000],[0.020519004,0.020978457,0.002112287,0.022140132,0.000000000],[0.009804957,0.101042768,0.009260923,0.007352509,0.000000000],[0.190527041,0.221032582,0.174161696,0.188870550,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [15] // Basepair G19 - C92 cWS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [6] | Right Index [14] // Fixed node on left for 3MXH|1|R|G|19 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [7] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [7] | Right Index [14] // Fixed node on right for 3MXH|1|R|U|89 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [13] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [7] | Right Index [13] // Junction node G21 - U90 ID J8308 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009635135,0.018686586,0.011023774,0.200055053,0.000000000],[0.018686946,0.009628796,0.215804967,0.013537321,0.000000000],[0.011023788,0.215804297,0.002089517,0.025115689,0.000000000],[0.200055346,0.013537264,0.025116064,0.010199456,0.000000000],[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 [7] | Right Index [8] // Basepair G21 - C46 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 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 [9] | Right Index [13] // Initial node 3MXH|1|R|A|47 - 3MXH|1|R|U|90 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [9] | Right Index [13] // Fixed node on left for 3MXH|1|R|C|46 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [10] | Right Index [13] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.018775607,0.041784723,0.004155072,0.435115030,0.000000000],[0.004155072,0.334819390,0.009959982,0.004155072,0.000000000],[0.019501541,0.004155072,0.031598971,0.024107229,0.000000000],[0.004155072,0.004155072,0.018480329,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [13] // Basepair A48 - U90 tHW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012786759,0.158579378,0.012700856,0.142951775,0.000000000],[0.015410127,0.011167131,0.119729226,0.013844477,0.000000000],[0.012485943,0.135049418,0.002666836,0.185406071,0.000000000],[0.117661282,0.014761069,0.018929413,0.025870238,0.000000000],[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 [11] | Right Index [12] // Basepair G50 - U89 cWW HairpinNode | Num Bases [1] | Left Index [12] | Right Index [12] | 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 J3_96372.1:
> J3_96372.1 3MXH G 14 C 93 GCACAGGG*CAAAG*UUACC > J3_96372.1 4YAZ G 8 C 76 GACAAUAC*GAAAG*CUGCC