| 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 3 3 | 7 4 I | 8 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 6 | 13 7 I | 14 7 7 | 15 6 I | 16 6 8 | 17 5 I | 18 5 9 | 19 4 I | 20 3 10 | 21 3 I | 22 3 11 | 23 3 I | 24 3 12 | 25 2 I | 26 2 13 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_56677.4_Instance_1 HL_56677.4_HL_4V9F_068_C2780_G2794 | C | U | G | A | A | C | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_1 HL_56677.4_HL_4V9F_068_C_2780_G_2794 | C | U | G | A | A | C | G | C | A | U | C | U | A | A | G | true | 99 | 0 | 0 | 0.30 | ||||||||||||
| HL_56677.4_Instance_2 HL_56677.4_HL_5J7L_199_C2745_G2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_2 HL_56677.4_HL_5J7L_199_C_2745_G_2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_56677.4_Instance_3 HL_56677.4_HL_4WF9_062_C2772_G2786 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_3 HL_56677.4_HL_4WF9_062_C_2772_G_2786 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_56677.4_Instance_4 HL_56677.4_HL_5TBW_067_C3110_G3124 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_4 HL_56677.4_HL_5TBW_067_C_3110_G_3124 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | true | 93 | 0 | 0 | 1.61 | ||||||||||||
| HL_56677.4_Instance_5 HL_56677.4_HL_4Y4O_169_C2745_G2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_5 HL_56677.4_HL_4Y4O_169_C_2745_G_2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_56677.4_Instance_6 HL_56677.4_HL_7A0S_065_C2725_G2739 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_56677.4_Sequence_6 HL_56677.4_HL_7A0S_065_C_2725_G_2739 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 3 s35 2 10 tWH 2 12 tSH 2 13 s55 3 4 s35 3 9 s33 3 10 s55 3 11 tSH 4 5 s35 4 9 tHW 4 11 s55 5 6 s33 5 8 tHW 6 7 tSW 7 8 s35 8 9 s35 10 11 s53 10 12 cWH 10 13 s35 11 12 s35 12 13 s35 3 10 6BPh 11 3 6BR 7 6 7BRJAR3D SCFG/MRF model for HL_56677.4:
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 [13] // Initial node C2780 - G2794 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [1] | Right Index [13] // Basepair C2780 - G2794 cWW ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [2] | Num Right Bases [3] | Left Index [2] | Right Index [12] | Norm Constant [0.031373098575383] // Cluster node U2781:G2782 and U2791:A2793 Interaction | Interacting Bases [1,3] | Pair Probability [[0.018340435,0.003764121,0.032657415,0.003764121,0.000000000],[0.325525626,0.043924416,0.003764121,0.003764121,0.000000000],[0.003764121,0.011778114,0.024206194,0.035508032,0.000000000],[0.037075964,0.003764121,0.015383236,0.433015844,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2781 - U2791 tWH Interaction | Interacting Bases [2,4] | Pair Probability [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2782 - A2792 tSH Interaction | Interacting Bases [1,5] | Pair Probability [[0.115848656,0.105816603,0.001286545,0.006328779,0.000000000],[0.116296186,0.109423494,0.001286545,0.001286545,0.000000000],[0.119634107,0.001286545,0.007951482,0.106807141,0.000000000],[0.185258265,0.118916017,0.001286545,0.001286545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2781 - A2793 tSH Interaction | Interacting Bases [3,5] | Pair Probability [[0.002952495,0.002952495,0.012723357,0.012783050,0.000000000],[0.002952495,0.014198277,0.002952495,0.279650968,0.000000000],[0.010877559,0.002952495,0.010204484,0.002952495,0.000000000],[0.351853281,0.002952495,0.273191467,0.013850093,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2791 - A2793 cWH 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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018067094,0.040207941,0.003998277,0.456431444,0.000000000],[0.003998277,0.322184696,0.009584133,0.003998277,0.000000000],[0.018765634,0.003998277,0.030406557,0.023197522,0.000000000],[0.003998277,0.003998277,0.017782958,0.039382361,0.000000000],[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 [4] | Right Index [9] // Basepair A2783 - U2789 tHW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.342039969,0.091806375,0.003474987,0.018889658,0.000000000],[0.003474987,0.016497440,0.009191710,0.003474987,0.000000000],[0.272247212,0.003474987,0.111751524,0.016484687,0.000000000],[0.003474987,0.003474987,0.036339973,0.063901528,0.000000000],[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 [5] | Right Index [8] // Basepair A2784 - A2788 tHW HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C2785:C2787 Interaction | Interacting Bases [1,2] | Pair Probability [[0.024910016,0.240216583,0.003306393,0.016354853,0.000000000],[0.149732358,0.178534718,0.003306393,0.017293195,0.000000000],[0.149236317,0.003306393,0.003306393,0.011795353,0.000000000],[0.024035321,0.138536536,0.018365350,0.017763828,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C2785 - C2787 tSW Insertion | Location [1] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 1Sequences of instances from HL_56677.4:
> HL_56677.4 HL_4V9F_068 C 2780 G 2794 CUGAACGCAUCUAAG > HL_56677.4 HL_5J7L_199 C 2745 G 2759 CUGAAAGCAUCUAAG > HL_56677.4 HL_4WF9_062 C 2772 G 2786 CUGAAAGCAUCUAAG > HL_56677.4 HL_5TBW_067 C 3110 G 3124 CUGAACGCCUCUAAG > HL_56677.4 HL_4Y4O_169 C 2745 G 2759 CUGAAAGCAUCUAAG > HL_56677.4 HL_7A0S_065 C 2725 G 2739 CUGAAAGCAUCUAAG