| 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_76486.1_Instance_1 IL_76486.1_IL_3U5H_006_C82_G103 | C | U | U | A | G | U | A | A | U | G | A | A | G | C | G | |||||||||||||||||||||||
| IL_76486.1_Sequence_1 IL_76486.1_IL_3U5H_006_C82_G103 | C | U | U | A | G | U | A | A | * | U | G | A | A | G | C | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 15 cWW 2 3 s35 2 14 tSH 3 4 s33 3 13 tSW 4 6 s55 4 11 s53 4 12 tHH 5 6 cSH 5 10 s33 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 s33 13 14 s55 14 15 s35 10 6 6BPh 5 11 6BPh 4 12 6BPh 13 13 2BPh 3 4 7BR 7 10 6BRJAR3D SCFG/MRF model for IL_76486.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | 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 [1] | Right Index [15] // Initial node C82 - G103 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010130121,0.017375838,0.011773595,0.194301502,0.000000000],[0.020979332,0.008652269,0.227023763,0.014063448,0.000000000],[0.011923689,0.210487931,0.002171228,0.024023321,0.000000000],[0.195430021,0.013397471,0.027849658,0.010416811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair C82 - G103 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.133633771,0.127486748,0.001506190,0.007324744,0.000000000],[0.135810798,0.130305286,0.001506190,0.001506190,0.000000000],[0.130902608,0.001506190,0.007522744,0.018755504,0.000000000],[0.138700667,0.160519989,0.001506190,0.001506190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [14] // Basepair U83 - C102 tSH BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.001889513,0.001111336,0.001593034,0.013225307,0.000000000],[0.001554591,0.001207481,0.135152057,0.002075013,0.000000000],[0.001268155,0.015077930,0.001593034,0.001383172,0.000000000],[0.005493426,0.005490697,0.806417865,0.005467389,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [13] // Basepair U84 - G101 tSW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.557926848,0.110624637,0.027357914,0.027399489,0.000000000],[0.010110700,0.000782894,0.067304067,0.055610500,0.000000000],[0.004890903,0.064961568,0.001917995,0.000782894,0.000000000],[0.004810890,0.063952913,0.000782894,0.000782894,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [12] // Basepair A85 - A100 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.460751978306534] // Cluster node G86:U87 and A99:A99 Interaction | Interacting Bases [2,3] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U87 - A99 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.055679592,0.057359966,0.003128224,0.002588218,0.000000000],[0.053859163,0.062562107,0.000665346,0.063050334,0.000000000],[0.038079735,0.020824015,0.042566873,0.475642955,0.000000000],[0.004791044,0.055793641,0.000665346,0.062743443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G86 - U87 cSH InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [0.0000224390099112] | Pair Probability [[0.044149057,0.044541851,0.382258874,0.047988462,0.000000000],[0.051461378,0.046686356,0.003723579,0.046230763,0.000000000],[0.000531940,0.000531940,0.018039957,0.000531940,0.000000000],[0.002533030,0.000531940,0.309726994,0.000531940,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // Basepair A88 - G98 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[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 A89 - U97 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_76486.1:
> IL_76486.1 IL_3U5H_006 C 82 G 103 CUUAGUAA*UGAAGCG