| 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 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 3 I | 12 4 6 | 13 4 I | 14 5 7 | 15 5 I | 16 6 | 17 5 I | 18 5 8 | 19 4 I | 20 4 9 | 21 3 I | 22 2 10 | 23 2 I | 24 2 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_01488.3_Instance_1 IL_01488.3,IL_6UFM_001,C3_G27 | C | G | A | C | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_1 IL_01488.36UFM_C3_G27 | C | G | A | C | G | A | U | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_01488.3_Instance_2 IL_01488.3,IL_6UFG_001,C3_G27 | C | A | U | C | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_2 IL_01488.36UFG_C3_G27 | C | A | U | C | G | A | U | C | * | G | G | G | A | G | true | 98 | 0 | 0 | 0.42 | |||||||||||||
| IL_01488.3_Instance_3 IL_01488.3,IL_9DFE_004,C97_G85 | C | G | U | G | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_3 IL_01488.39DFE_C97_G85 | C | G | U | G | G | A | U | C | * | G | G | G | A | G | true | 99 | 0 | 0 | 0.14 | |||||||||||||
| IL_01488.3_Instance_4 IL_01488.3,IL_1T0K_001,C54_G13 | C | A | G | A | G | A | U | G | C | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_4 IL_01488.31T0K_C54_G13 | C | A | G | A | G | A | U | G | * | C | G | G | A | G | true | 83 | 0 | 0 | 3.07 | |||||||||||||
| IL_01488.3_Instance_5 IL_01488.3,IL_4GXY_005,C139_G86 | C | G | A | G | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_5 IL_01488.34GXY_C139_G86 | C | G | A | G | G | A | U | C | * | G | G | G | A | G | true | 98 | 0 | 0 | 0.34 | |||||||||||||
| IL_01488.3_Instance_6 IL_01488.3,IL_4WF9_004,C97_G85 | C | U | U | U | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_6 IL_01488.34WF9_C97_G85 | C | U | U | U | G | A | U | C | * | G | G | G | A | G | true | 88 | 0 | 0 | 2.12 | |||||||||||||
| IL_01488.3_Instance_7 IL_01488.3,IL_9L6Y_001,C21_G10 | C | C | A | U | G | A | C | G | C | A | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_7 IL_01488.39L6Y_C21_G10 | C | C | A | U | G | A | C | G | * | C | A | G | A | G | true | 67 | 0 | 0 | 6.11 | |||||||||||||
| IL_01488.3_Instance_8 IL_01488.3,IL_6UFH_001,C3_G27 | C | A | U | C | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_8 IL_01488.36UFH_C3_G27 | C | A | U | C | G | A | U | C | * | G | G | G | A | G | true | 98 | 0 | 0 | 0.42 | |||||||||||||
| IL_01488.3_Instance_9 IL_01488.3,IL_5J7L_035,C699_G688 | C | G | U | A | G | A | G | A | U | G | U | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_9 IL_01488.35J7L_C699_G688 | C | G | U | A | G | A | G | A | * | U | G | U | A | G | true | 76 | 0 | 0 | 4.47 | |||||||||||||
| IL_01488.3_Instance_10 IL_01488.3,IL_4V9F_004,C93_G81 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_01488.3_Sequence_10 IL_01488.34V9F_C93_G81 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 99 | 0 | 0 | 0.27 |
1 2 s35 1 12 cWW 2 11 tSS 2 12 s55 3 4 s35 3 11 s33 4 10 s33 4 11 tSH 5 6 s35 5 10 tHS 5 11 s55 5 12 tSS 6 7 s35 6 9 tHS 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 10 11 s35 9 5 6BPh 10 5 6BPh 7 6 7BPh 10 4 6BR 4 10 6BRJAR3D SCFG/MRF model for IL_01488.3:
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 [12] // Initial node ClusterNode | Deletion Probability [0.000000000000000000001948010068092961341050756773210484931265] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.033621768617430] // Cluster node 6UFM|1|B|C|3:6UFM|1|B|A|8 and 6UFM|1|B|G|25:6UFM|1|B|G|27 Interaction | Interacting Bases [5,6] | Pair Probability [[0.039531668,0.039825360,0.425090578,0.064305282,0.000000000],[0.041849598,0.041752691,0.003321859,0.041527282,0.000000000],[0.000474551,0.000474551,0.016239515,0.000474551,0.000000000],[0.002236562,0.000474551,0.281946850,0.000474551,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|A|8 - 6UFM|1|B|G|25 tHS Interaction | Interacting Bases [2,7] | Pair Probability [[0.111101318,0.052400834,0.054200741,0.049388083,0.000000000],[0.028255171,0.019164262,0.118559039,0.019164262,0.000000000],[0.206476690,0.019164262,0.129550183,0.106827196,0.000000000],[0.028255171,0.019164262,0.019164262,0.019164262,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|G|4 - 6UFM|1|B|A|26 tSS Interaction | Interacting Bases [4,7] | Pair Probability [[0.067003226,0.070931945,0.000804329,0.003790805,0.000000000],[0.067501012,0.070767696,0.000804329,0.000804329,0.000000000],[0.342472894,0.002515638,0.012298155,0.213517844,0.000000000],[0.074793495,0.070385643,0.000804329,0.000804329,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|G|7 - 6UFM|1|B|A|26 tSH Interaction | Interacting Bases [1,8] | Pair Probability [[0.008843009,0.015857640,0.010166128,0.184331946,0.000000000],[0.018801751,0.009006349,0.284686329,0.012787685,0.000000000],[0.010280296,0.188303804,0.001937772,0.021759572,0.000000000],[0.186721625,0.012320688,0.024824249,0.009371156,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|C|3 - 6UFM|1|B|G|27 cWW Interaction | Interacting Bases [5,8] | Pair Probability [[0.168972788,0.168568456,0.301674653,0.159859182,0.000000000],[0.001734057,0.001734057,0.017968699,0.001734057,0.000000000],[0.013596605,0.001734057,0.014161773,0.141325392,0.000000000],[0.001734057,0.001734057,0.001734057,0.001734057,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6UFM|1|B|A|8 - 6UFM|1|B|G|27 tSS Interaction | Interacting Bases [3,3] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.458333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6UFM|1|B|A|5 Insertion | Location [3] | Length Distribution [0.004949270,0.989853997,0.004949270,0.000247463] | Letter Distribution [0.291666667,0.291666667,0.208333333,0.208333333,0.000000000]// Insertion after nucleotide 3, position 3 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 [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.015178830,0.010913304,0.316584574,0.042859977,0.000000000],[0.036613397,0.010759673,0.004270706,0.023132666,0.000000000],[0.000610101,0.000610101,0.109226680,0.000610101,0.000000000],[0.012748860,0.000610101,0.414660830,0.000610101,0.000000000],[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 [6] | Right Index [9] // Basepair U9 - G24 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.005096422,0.010158915,0.005769065,0.116017074,0.000000000],[0.040968590,0.019986131,0.492108108,0.028026816,0.000000000],[0.005775826,0.126921291,0.001109330,0.015878667,0.000000000],[0.106354829,0.006965885,0.013307720,0.005555333,0.000000000],[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 C10 - G23 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_01488.3:
> IL_01488.3 6UFM C 3 G 27 CGACGAUC*GGGAG > IL_01488.3 6UFG C 3 G 27 CAUCGAUC*GGGAG > IL_01488.3 9DFE C 97 G 85 CGUGGAUC*GGGAG > IL_01488.3 1T0K C 54 G 13 CAGAGAUG*CGGAG > IL_01488.3 4GXY C 139 G 86 CGAGGAUC*GGGAG > IL_01488.3 4WF9 C 97 G 85 CUUUGAUC*GGGAG > IL_01488.3 9L6Y C 21 G 10 CCAUGACG*CAGAG > IL_01488.3 6UFH C 3 G 27 CAUCGAUC*GGGAG > IL_01488.3 5J7L C 699 G 688 CGUAGAGA*UGUAG > IL_01488.3 4V9F C 93 G 81 CGAAGAAC*GGGAG