| 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 4 I | 10 5 | 11 4 I | 12 4 5 | 13 3 I | 14 2 6 | 15 2 I | 16 2 7 | 17 2 I | 18 2 8 | 19 2 I | 20 2 9 | 21 2 I | 22 2 10 | 23 2 I | 24 2 11 | 25 2 I | 26 2 12 | 27 2 I | 28 2 13 | 29 2 I | 30 2 14 | 31 2 I | 32 2 15 | 33 2 I | 34 2 16 | 35 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_02359.3_Instance_1 IL_02359.3_IL_2QBG_016_G481_C509 | G | A | A | C | G | A | G | U | G | A | A | A | A | A | G | A | A | C | ||||||||||||||||||||||
| IL_02359.3_Sequence_1 IL_02359.3_IL_2QBG_016_G481_C509 | G | A | A | C | * | G | A | G | U | G | A | A | A | A | A | G | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_02359.3_Instance_2 IL_02359.3_IL_4IOA_009_G492_C519 | G | A | A | C | G | A | G | U | G | A | A | A | G | A | G | A | A | C | ||||||||||||||||||||||
| IL_02359.3_Sequence_2 IL_02359.3_IL_4IOA_009_G492_C519 | G | A | A | C | * | G | A | G | U | G | A | A | A | G | A | G | A | A | C | true | 98 | 0 | 0 | 0.51 | ||||||||||||||||
| IL_02359.3_Instance_3 IL_02359.3_IL_3V2F_014_G481_C509 | G | A | A | C | G | A | G | U | G | A | A | A | U | A | G | A | G | C | ||||||||||||||||||||||
| IL_02359.3_Sequence_3 IL_02359.3_IL_3V2F_014_G481_C509 | G | A | A | C | * | G | A | G | U | G | A | A | A | U | A | G | A | G | C | true | 94 | 0 | 0 | 1.36 | ||||||||||||||||
| IL_02359.3_Instance_4 IL_02359.3_IL_4A1B_012_G375_C400 | G | A | A | C | G | G | G | C | U | A | A | A | A | G | A | C | ||||||||||||||||||||||||
| IL_02359.3_Sequence_4 IL_02359.3_IL_4A1B_012_G375_C400 | G | A | A | C | * | G | G | G | C | U | A | A | A | A | G | A | C | true | 78 | 0 | 0 | 5.25 | ||||||||||||||||||
| IL_02359.3_Instance_5 IL_02359.3_IL_3U5H_015_G376_C403 | G | A | A | C | G | A | G | U | G | A | A | A | A | A | G | U | A | C | ||||||||||||||||||||||
| IL_02359.3_Sequence_5 IL_02359.3_IL_3U5H_015_G376_C403 | G | A | A | C | * | G | A | G | U | G | A | A | A | A | A | G | U | A | C | true | 88 | 0 | 0 | 2.85 |
1 14 tSS 1 15 s35 1 16 cWW 2 6 cSW 2 14 s53 2 15 tHH 3 4 s35 3 6 tHS 4 5 cWW 4 6 s55 5 6 s35 6 7 s35 7 8 s35 7 14 bif 8 9 s35 8 12 tWH 9 11 s33 9 12 s55 9 13 tSH 10 11 s35 11 13 s35 12 13 s53 12 14 s35 15 2 6BPh 4 3 7BPh 9 12 6BPh 3 6 6BR 11 9 7BR 2 14 6BRJAR3D SCFG/MRF model for IL_02359.3:
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 [16] // Initial node G481 - C509 from junction ClusterNode | Deletion Probability [0.000000000000000000000000000000000001211008282206275700000000] | Num Left Bases [3] | Num Right Bases [11] | Left Index [1] | Right Index [16] | Norm Constant [0.013279958585473] // Cluster node G481:A483 and A497:C509 Interaction | Interacting Bases [2,4] | Pair Probability [[0.478443015,0.036369758,0.158610950,0.021176618,0.000000000],[0.078468636,0.005641642,0.025667140,0.006056960,0.000000000],[0.072220953,0.005571037,0.012040718,0.003489910,0.000000000],[0.079476498,0.005921929,0.006958079,0.003886159,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A482 - A497 cSW Interaction | Interacting Bases [3,4] | Pair Probability [[0.183582475,0.141922579,0.138423704,0.137696516,0.000000000],[0.124538656,0.072141506,0.001499413,0.132557529,0.000000000],[0.001499413,0.001499413,0.012018634,0.001499413,0.000000000],[0.011041404,0.001499413,0.037080518,0.001499413,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A483 - A497 tHS Interaction | Interacting Bases [1,12] | Pair Probability [[0.010983645,0.013785681,0.023402995,0.013491197,0.000000000],[0.002396565,0.002396565,0.002396565,0.002396565,0.000000000],[0.215473637,0.222077550,0.287275572,0.194337201,0.000000000],[0.002396565,0.002396565,0.002396565,0.002396565,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G481 - G506 tSS Interaction | Interacting Bases [2,13] | Pair Probability [[0.740587879,0.040267265,0.009958255,0.042726002,0.000000000],[0.018144708,0.000398962,0.034298065,0.028339038,0.000000000],[0.008777237,0.033104331,0.000977408,0.000398962,0.000000000],[0.008633645,0.032590321,0.000398962,0.000398962,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A482 - A507 tHH Interaction | Interacting Bases [1,14] | Pair Probability [[0.009903804,0.020176037,0.011467133,0.187947036,0.000000000],[0.016710520,0.008166390,0.202428381,0.012884484,0.000000000],[0.011322786,0.256428223,0.002088092,0.026783299,0.000000000],[0.186861727,0.013524960,0.023103472,0.010203655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G481 - C509 cWW Interaction | Interacting Bases [6,10] | Pair Probability [[0.024041325,0.004721629,0.048139148,0.004721629,0.000000000],[0.100431499,0.037456340,0.073399645,0.004721629,0.000000000],[0.004721629,0.004721629,0.052877132,0.024792127,0.000000000],[0.466250249,0.004721629,0.054559658,0.089723102,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U499 - A503 tWH Interaction | Interacting Bases [7,11] | Pair Probability [[0.043376023,0.048520582,0.000511343,0.002468182,0.000000000],[0.043801785,0.044536745,0.000511343,0.000511343,0.000000000],[0.333835603,0.002967386,0.014466878,0.243064083,0.000000000],[0.117854180,0.101327801,0.001123361,0.001123361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G500 - A505 tSH Interaction | Interacting Bases [5,12] | Pair Probability [[0.032556401,0.250925245,0.004078006,0.004078006,0.000000000],[0.015466579,0.013181622,0.004078006,0.004078006,0.000000000],[0.004078006,0.004078006,0.455419622,0.191670474,0.000000000],[0.004078006,0.004078006,0.004078006,0.004078006,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G498 - G506 bif Interaction | Interacting Bases [8,8] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A501 Interaction | Interacting Bases [9,9] | Pair Probability [[0.944444444,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.018518519,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A502 Insertion | Location [10] | Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000]// Insertion after nucleotide 12, position 10 in cluster node Insertion | Location [13] | Length Distribution [0.204221895,0.787432499,0.007952872,0.000392734] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000]// Insertion after nucleotide 15, position 13 in cluster node 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 [4] | Right Index [5] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003776012,0.006476861,0.004388619,0.072426074,0.000000000],[0.054740466,0.022575992,0.614148123,0.036695147,0.000000000],[0.004444567,0.078459581,0.000809327,0.008954716,0.000000000],[0.072846731,0.004993921,0.010380987,0.003882877,0.000000000],[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 [4] | Right Index [5] // Basepair C484 - G496 cWW 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_02359.3:
> IL_02359.3 IL_2QBG_016 G 481 C 509 GAAC*GAGUGAAAAAGAAC > IL_02359.3 IL_4IOA_009 G 492 C 519 GAAC*GAGUGAAAGAGAAC > IL_02359.3 IL_3V2F_014 G 481 C 509 GAAC*GAGUGAAAUAGAGC > IL_02359.3 IL_4A1B_012 G 375 C 400 GAAC*GGGCUAAAAGAC > IL_02359.3 IL_3U5H_015 G 376 C 403 GAAC*GAGUGAAAAAGUAC