| 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_74055.2_Instance_1 HL_74055.2,HL_5J7L_199,C2745_G2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_1 HL_74055.25J7L_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_74055.2_Instance_2 HL_74055.2,HL_4V9F_068,C2780_G2794 | C | U | G | A | A | C | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_2 HL_74055.24V9F_C_2780_G_2794 | C | U | G | A | A | C | G | C | A | U | C | U | A | A | G | true | 99 | 0 | 0 | 0.15 | ||||||||||||
| HL_74055.2_Instance_3 HL_74055.2,HL_9DFE_064,C2745_G2759 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_3 HL_74055.29DFE_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_74055.2_Instance_4 HL_74055.2,HL_4WF9_062,C2772_G2786 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_4 HL_74055.24WF9_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_74055.2_Instance_5 HL_74055.2,HL_8CRE_066,C3082_G3096 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_5 HL_74055.28CRE_C_3082_G_3096 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | true | 96 | 0 | 0 | 0.94 | ||||||||||||
| HL_74055.2_Instance_6 HL_74055.2,HL_8P9A_178,C3110_G3124 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_6 HL_74055.28P9A_C_3110_G_3124 | C | U | G | A | A | C | G | C | C | U | C | U | A | A | G | true | 96 | 0 | 0 | 0.94 | ||||||||||||
| HL_74055.2_Instance_7 HL_74055.2,HL_7A0S_065,C2725_G2739 | C | U | G | A | A | A | G | C | A | U | C | U | A | A | G | |||||||||||||||||
| HL_74055.2_Sequence_7 HL_74055.27A0S_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_74055.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009090944,0.016302246,0.010451159,0.189500131,0.000000000],[0.019328903,0.009258863,0.264630806,0.013146218,0.000000000],[0.010568529,0.193583350,0.001992102,0.022369654,0.000000000],[0.191956811,0.012666128,0.025520256,0.009633898,0.000000000],[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 C2745 - G2759 cWW ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [2] | Num Right Bases [3] | Left Index [2] | Right Index [12] | Norm Constant [0.033373703837395] // Cluster node 5J7L|1|DA|U|2746:5J7L|1|DA|G|2747 and 5J7L|1|DA|U|2756:5J7L|1|DA|A|2758 Interaction | Interacting Bases [1,3] | Pair Probability [[0.018169029,0.003728942,0.032352206,0.003728942,0.000000000],[0.322483331,0.043513907,0.003728942,0.003728942,0.000000000],[0.003728942,0.011668038,0.023979968,0.035176181,0.000000000],[0.036729459,0.003728942,0.015239468,0.438314762,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2746 - 5J7L|1|DA|U|2756 tWH Interaction | Interacting Bases [2,4] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|2747 - 5J7L|1|DA|A|2757 tSH Interaction | Interacting Bases [1,5] | Pair Probability [[0.114765959,0.104827663,0.001274521,0.006269632,0.000000000],[0.115209306,0.108400844,0.001274521,0.001274521,0.000000000],[0.118516031,0.001274521,0.007877169,0.105808943,0.000000000],[0.192872673,0.117804652,0.001274521,0.001274521,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2746 - 5J7L|1|DA|A|2758 tSH Interaction | Interacting Bases [3,5] | Pair Probability [[0.002924902,0.002924902,0.012604447,0.012663582,0.000000000],[0.002924902,0.014065583,0.002924902,0.277037407,0.000000000],[0.010775899,0.002924902,0.010109115,0.002924902,0.000000000],[0.357910727,0.002924902,0.270638276,0.013720652,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|2756 - 5J7L|1|DA|A|2758 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 [0.007039775,0.985568462,0.007039775,0.000351989] | Right Letter Distribution [0.055555556,0.833333333,0.055555556,0.055555556,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017898242,0.039832166,0.003960910,0.461511524,0.000000000],[0.003960910,0.319173624,0.009494562,0.003960910,0.000000000],[0.018590254,0.003960910,0.030122383,0.022980723,0.000000000],[0.003960910,0.003960910,0.017616762,0.039014302,0.000000000],[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 A2748 - U2754 tHW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.301295842,0.137508415,0.003439441,0.020954516,0.000000000],[0.003439441,0.017569130,0.009511229,0.003439441,0.000000000],[0.245154562,0.003439441,0.099286633,0.016194963,0.000000000],[0.003439441,0.003439441,0.035362340,0.096525722,0.000000000],[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 A2749 - A2753 tHW HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node A2750:C2752 Interaction | Interacting Bases [1,2] | Pair Probability [[0.024202650,0.234114099,0.003212502,0.015890427,0.000000000],[0.145480432,0.201142827,0.003212502,0.016802123,0.000000000],[0.144998478,0.003212502,0.003212502,0.011460402,0.000000000],[0.023352794,0.134602537,0.017843833,0.017259392,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A2750 - C2752 tSW Insertion | Location [1] | Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000]// Insertion in Hairpin after nucleotide 6, position 1Sequences of instances from HL_74055.2:
> HL_74055.2 5J7L C 2745 G 2759 CUGAAAGCAUCUAAG > HL_74055.2 4V9F C 2780 G 2794 CUGAACGCAUCUAAG > HL_74055.2 9DFE C 2745 G 2759 CUGAAAGCAUCUAAG > HL_74055.2 4WF9 C 2772 G 2786 CUGAAAGCAUCUAAG > HL_74055.2 8CRE C 3082 G 3096 CUGAACGCCUCUAAG > HL_74055.2 8P9A C 3110 G 3124 CUGAACGCCUCUAAG > HL_74055.2 7A0S C 2725 G 2739 CUGAAAGCAUCUAAG