| 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 4 I | 10 4 5 | 11 5 I | 12 6 6 | 13 6 I | 14 7 7 | 15 7 I | 16 8 | 17 7 I | 18 7 8 | 19 6 I | 20 6 9 | 21 5 I | 22 4 10 | 23 4 I | 24 4 11 | 25 4 I | 26 4 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_05221.1_Instance_1 IL_05221.1_IL_3U5H_021_G531_C561 | G | A | A | U | G | U | A | G | U | A | U | U | A | U | A | G | C | |||||||||||||||||||||
| IL_05221.1_Sequence_1 IL_05221.1_IL_3U5H_021_G531_C561 | G | A | A | U | G | U | A | G | * | U | A | U | U | A | U | A | G | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 15 cWW 2 3 s35 2 10 s33 2 14 cWW 3 4 s35 3 10 tHW 3 13 bif 4 5 cSH 4 9 s33 4 10 s55 4 12 tSW 5 6 s35 5 11 s55 5 12 cWH 5 13 s55 6 7 s35 6 9 tHS 6 12 s53 7 8 cWW 8 9 s35 10 11 cSH 11 12 s55 11 13 cWH 11 14 s35 13 14 s35 14 15 s35 6 9 6BR 2 10 7BR 4 10 6BRJAR3D SCFG/MRF model for IL_05221.1:
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 G531 - C561 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.010296034,0.020975088,0.011921277,0.195390483,0.000000000],[0.017372323,0.008489812,0.210445347,0.013394761,0.000000000],[0.011771213,0.226979836,0.002170788,0.027844024,0.000000000],[0.194262192,0.014060602,0.024018461,0.010607760,0.000000000],[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 G531 - C561 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.315343748,0.019630589,0.493904012,0.022103230,0.000000000],[0.003833930,0.001478680,0.005249063,0.011169182,0.000000000],[0.093002083,0.005315980,0.000968006,0.004364346,0.000000000],[0.004413113,0.011881031,0.004267756,0.003075251,0.000000000],[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 A532 - G560 cWW ClusterNode | Deletion Probability [0.000000000000000000001861482761166059500000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [13] | Norm Constant [0.002186805502869] // Cluster node A533:U536 and U555:A559 Interaction | Interacting Bases [1,4] | Pair Probability [[0.026228946,0.054639536,0.005500826,0.559983562,0.000000000],[0.005500826,0.045670107,0.005500826,0.005500826,0.000000000],[0.026982756,0.036513624,0.064376936,0.067861159,0.000000000],[0.005500826,0.005500826,0.025659745,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - U555 tHW Interaction | Interacting Bases [2,6] | Pair Probability [[0.011713255,0.098795318,0.001115418,0.005321145,0.000000000],[0.103847303,0.005193506,0.005039138,0.004579369,0.000000000],[0.567609822,0.151988445,0.005577088,0.018128417,0.000000000],[0.006756583,0.004694656,0.006215599,0.003424936,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - A557 tSW Interaction | Interacting Bases [3,6] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U536 - A557 cWH Interaction | Interacting Bases [1,7] | Pair Probability [[0.738708947,0.033322493,0.007288080,0.007288080,0.000000000],[0.027777766,0.025772735,0.007288080,0.007288080,0.000000000],[0.007288080,0.007288080,0.058183744,0.043353518,0.000000000],[0.007288080,0.007288080,0.007288080,0.007288080,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A533 - A559 bif Interaction | Interacting Bases [2,3] | Pair Probability [[0.066577006,0.068586257,0.003740469,0.003094775,0.000000000],[0.064400289,0.074806542,0.000795565,0.075390323,0.000000000],[0.032523262,0.017785442,0.036355651,0.407683380,0.000000000],[0.005728730,0.066713376,0.000795565,0.075023369,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G535 - U536 cSH Interaction | Interacting Bases [4,5] | Pair Probability [[0.111957140,0.109553485,0.005904964,0.004876169,0.000000000],[0.106210408,0.127560275,0.001323815,0.126229679,0.000000000],[0.010119885,0.005598590,0.008485208,0.124838481,0.000000000],[0.007055763,0.106679783,0.001323815,0.142282540,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U555 - U556 cSH Interaction | Interacting Bases [5,7] | Pair Probability [[0.003495037,0.003495037,0.017334262,0.012470772,0.000000000],[0.003495037,0.037384026,0.017149526,0.190754110,0.000000000],[0.015332069,0.003495037,0.013986624,0.003495037,0.000000000],[0.359404723,0.003495037,0.280049403,0.035164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U556 - A559 cWH Insertion | Location [1] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node Insertion | Location [6] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 12, position 6 in cluster node 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 [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.170710115,0.155925473,0.133465681,0.148228098,0.000000000],[0.128906975,0.063872294,0.001608091,0.142674762,0.000000000],[0.001608091,0.001608091,0.013969090,0.001608091,0.000000000],[0.012727400,0.001608091,0.019871564,0.001608091,0.000000000],[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 [6] | Right Index [9] // Basepair A537 - A554 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.016663800,0.313360908,0.015725272,0.045114411,0.000000000],[0.014618495,0.011663950,0.038590886,0.015584762,0.000000000],[0.015377247,0.044737484,0.003487844,0.358685405,0.000000000],[0.038297587,0.017266078,0.015312095,0.035513776,0.000000000],[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 G538 - U553 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_05221.1:
> IL_05221.1 IL_3U5H_021 G 531 C 561 GAAUGUAG*UAUUAUAGC