| 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 5 4 | 9 5 I | 10 6 | 11 5 I | 12 5 5 | 13 4 I | 14 4 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_13959.4_Instance_1 IL_13959.4_IL_1SAQ_002_C111_G106 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_1 IL_13959.4_IL_1SAQ_002_C111_G106 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_2 IL_13959.4_IL_1SA9_001_C111_G106 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_2 IL_13959.4_IL_1SA9_001_C111_G106 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_3 IL_13959.4_IL_3V2F_086_C2364_G2353 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_3 IL_13959.4_IL_3V2F_086_C_2364_G_2353 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_4 IL_13959.4_IL_2QBG_088_C2364_G2353 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_4 IL_13959.4_IL_2QBG_088_C_2364_G_2353 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_5 IL_13959.4_IL_4IOA_083_C2343_G2332 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_5 IL_13959.4_IL_4IOA_083_C_2343_G_2332 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_6 IL_13959.4_IL_3D0U_002_C67_G19 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_6 IL_13959.4_IL_3D0U_002_C67_G19 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_7 IL_13959.4_IL_4BPP_087_U1682_A1643 | U | A | A | A | U | G | A | A | ||||||||||||||||
| IL_13959.4_Sequence_7 IL_13959.4_IL_4BPP_087_U_1682_A_1643 | U | A | A | A | * | U | G | A | A | true | 86 | 0 | 0 | 1.29 | ||||||||||
| IL_13959.4_Instance_8 IL_13959.4_IL_4BPP_085_U1625_A1700 | U | A | A | C | G | G | A | A | ||||||||||||||||
| IL_13959.4_Sequence_8 IL_13959.4_IL_4BPP_085_U_1625_A_1700 | U | A | A | C | * | G | G | A | A | true | 88 | 0 | 0 | 1.15 | ||||||||||
| IL_13959.4_Instance_9 IL_13959.4_IL_3U5F_088_C1729_G1672 | C | A | A | A | U | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_9 IL_13959.4_IL_3U5F_088_C_1729_G_1672 | C | A | A | A | * | U | G | A | G | true | 92 | 0 | 0 | 0.72 | ||||||||||
| IL_13959.4_Instance_10 IL_13959.4_IL_4A1B_007_C162_G257 | C | A | A | C | G | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_10 IL_13959.4_IL_4A1B_007_C162_G257 | C | A | A | C | * | G | G | A | G | true | 94 | 0 | 0 | 0.58 | ||||||||||
| IL_13959.4_Instance_11 IL_13959.4_IL_2QBG_017_G536_C557 | G | G | A | G | U | G | A | C | ||||||||||||||||
| IL_13959.4_Sequence_11 IL_13959.4_IL_2QBG_017_G536_C557 | G | G | A | G | * | U | G | A | C | true | 75 | 0 | 0 | 2.42 | ||||||||||
| IL_13959.4_Instance_12 IL_13959.4_IL_4BPP_003_U37_A462 | U | A | A | A | U | G | A | C | A | |||||||||||||||
| IL_13959.4_Sequence_12 IL_13959.4_IL_4BPP_003_U37_A462 | U | A | A | A | * | U | G | A | C | A | true | 58 | 0 | 0 | 3.96 | |||||||||
| IL_13959.4_Instance_13 IL_13959.4_IL_4A1B_117_C2993_G3133 | C | G | A | C | G | G | A | A | A | G | ||||||||||||||
| IL_13959.4_Sequence_13 IL_13959.4_IL_4A1B_117_C_2993_G_3133 | C | G | A | C | * | G | G | A | AA | G | true | 51 | 0 | 0 | 4.63 | |||||||||
| IL_13959.4_Instance_14 IL_13959.4_IL_3U5H_120_C3004_G3144 | C | A | A | U | A | G | A | AC | G | |||||||||||||||
| IL_13959.4_Sequence_14 IL_13959.4_IL_3U5H_120_C_3004_G_3144 | C | A | A | U | * | A | G | A | AC | G | true | 39 | 0 | 0 | 5.75 | |||||||||
| IL_13959.4_Instance_15 IL_13959.4_IL_1FJG_059_U1481_G1419 | U | G | A | C | G | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_15 IL_13959.4_IL_1FJG_059_U_1481_G_1419 | U | G | A | C | * | G | G | A | G | true | 85 | 0 | 0 | 1.44 | ||||||||||
| IL_13959.4_Instance_16 IL_13959.4_IL_3U5F_013_C186_G199 | C | G | A | C | G | A | A | G | ||||||||||||||||
| IL_13959.4_Sequence_16 IL_13959.4_IL_3U5F_013_C186_G199 | C | G | A | C | * | G | A | A | G | true | 90 | 0 | 0 | 0.93 | ||||||||||
| IL_13959.4_Instance_17 IL_13959.4_IL_4IOA_058_U1530_G1494 | U | C | A | G | C | A | A | G | ||||||||||||||||
| IL_13959.4_Sequence_17 IL_13959.4_IL_4IOA_058_U_1530_G_1494 | U | C | A | G | * | C | A | A | G | true | 68 | 0 | 0 | 3.05 | ||||||||||
| IL_13959.4_Instance_18 IL_13959.4_IL_4A1B_005_C138_G128 | C | A | A | C | G | A | A | G | ||||||||||||||||
| IL_13959.4_Sequence_18 IL_13959.4_IL_4A1B_005_C138_G128 | C | A | A | C | * | G | A | A | G | true | 85 | 0 | 0 | 1.44 | ||||||||||
| IL_13959.4_Instance_19 IL_13959.4_IL_3U5F_085_C1653_G1747 | C | G | A | U | A | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_19 IL_13959.4_IL_3U5F_085_C_1653_G_1747 | C | G | A | U | * | A | G | A | G | true | 98 | 0 | 0 | 0.17 | ||||||||||
| IL_13959.4_Instance_20 IL_13959.4_IL_1S72_098_C2873_G2884 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_20 IL_13959.4_IL_1S72_098_C_2873_G_2884 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_21 IL_13959.4_IL_4A1B_132_C3316_G3303 | C | G | A | U | A | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_21 IL_13959.4_IL_4A1B_132_C_3316_G_3303 | C | G | A | U | * | A | G | A | G | true | 98 | 0 | 0 | 0.17 | ||||||||||
| IL_13959.4_Instance_22 IL_13959.4_IL_3DIR_002_C70_G22 | C | G | A | G | C | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_22 IL_13959.4_IL_3DIR_002_C70_G22 | C | G | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_13959.4_Instance_23 IL_13959.4_IL_2AW7_065_U1481_G1419 | U | G | A | C | G | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_23 IL_13959.4_IL_2AW7_065_U_1481_G_1419 | U | G | A | C | * | G | G | A | G | true | 85 | 0 | 0 | 1.44 | ||||||||||
| IL_13959.4_Instance_24 IL_13959.4_IL_3U5H_141_C3360_G3345 | C | G | A | U | A | G | A | G | ||||||||||||||||
| IL_13959.4_Sequence_24 IL_13959.4_IL_3U5H_141_C_3360_G_3345 | C | G | A | U | * | A | G | A | G | true | 98 | 0 | 0 | 0.17 | ||||||||||
| IL_13959.4_Instance_25 IL_13959.4_IL_2IL9_002_A6058_U6021 | A | A | U | A | U | A | U | U | ||||||||||||||||
| IL_13959.4_Sequence_25 IL_13959.4_IL_2IL9_002_A_6058_U_6021 | A | A | U | A | * | U | A | U | U | true | 38 | 0 | 0 | 5.86 | ||||||||||
| IL_13959.4_Instance_26 IL_13959.4_IL_2O3V_002_C7_G42 | C | G | C | U | A | A | A | A | G | |||||||||||||||
| IL_13959.4_Sequence_26 IL_13959.4_IL_2O3V_002_C7_G42 | C | G | C | U | * | A | A | A | A | G | true | 64 | 0 | 0 | 3.43 |
1 2 s35 1 8 cWW 2 6 s33 2 7 tSH 2 8 s55 3 4 s35 3 6 tHS 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 7 8 s35 7 2 6BR 3 6 6BRJAR3D SCFG/MRF model for IL_13959.4:
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 [8] // Initial node C111 - G106 from junction BasepairNode | Deletion Probability [0.0000132678587784] | Pair Probability [[0.008294599,0.014312172,0.009576747,0.151456887,0.000000000],[0.044699620,0.007743685,0.298156428,0.011138058,0.000000000],[0.009689343,0.159107771,0.001869446,0.018710913,0.000000000],[0.169069254,0.010625603,0.076296475,0.009253001,0.000000000],[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 [0.921154598,0.040223480,0.038540736,0.000077495,0.000003690] | Right Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C111 - G106 cWW BasepairNode | Deletion Probability [0.0000132736577717] | Pair Probability [[0.145487941,0.108926192,0.001227015,0.027212787,0.000000000],[0.105368082,0.081170457,0.001227015,0.001227015,0.000000000],[0.242216542,0.001227015,0.018730957,0.066681200,0.000000000],[0.100258643,0.096585107,0.001227015,0.001227015,0.000000000],[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 [0.882858682,0.116823982,0.000306266,0.000011070] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G112 - A105 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.118163166,0.094541409,0.277534671,0.099817256,0.000000000],[0.115282494,0.088817694,0.001102839,0.096148385,0.000000000],[0.001102839,0.001102839,0.005980668,0.001102839,0.000000000],[0.017117566,0.001102839,0.079979660,0.001102839,0.000000000],[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 [3] | Right Index [6] // Basepair A113 - G104 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008128108,0.025408901,0.009083861,0.188309537,0.000000000],[0.016113918,0.007225292,0.216116288,0.010127624,0.000000000],[0.009064412,0.232552318,0.001781266,0.038742155,0.000000000],[0.196220574,0.010218194,0.020421330,0.010486221,0.000000000],[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 G114 - C103 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_13959.4:
> IL_13959.4 IL_1SAQ_002 C 111 G 106 CGAG*CGAG > IL_13959.4 IL_1SA9_001 C 111 G 106 CGAG*CGAG > IL_13959.4 IL_3V2F_086 C 2364 G 2353 CGAG*CGAG > IL_13959.4 IL_2QBG_088 C 2364 G 2353 CGAG*CGAG > IL_13959.4 IL_4IOA_083 C 2343 G 2332 CGAG*CGAG > IL_13959.4 IL_3D0U_002 C 67 G 19 CGAG*CGAG > IL_13959.4 IL_4BPP_087 U 1682 A 1643 UAAA*UGAA > IL_13959.4 IL_4BPP_085 U 1625 A 1700 UAAC*GGAA > IL_13959.4 IL_3U5F_088 C 1729 G 1672 CAAA*UGAG > IL_13959.4 IL_4A1B_007 C 162 G 257 CAAC*GGAG > IL_13959.4 IL_2QBG_017 G 536 C 557 GGAG*UGAC > IL_13959.4 IL_4BPP_003 U 37 A 462 UAAA*UGACA > IL_13959.4 IL_4A1B_117 C 2993 G 3133 CGAC*GGAAAG > IL_13959.4 IL_3U5H_120 C 3004 G 3144 CAAU*AGAACG > IL_13959.4 IL_1FJG_059 U 1481 G 1419 UGAC*GGAG > IL_13959.4 IL_3U5F_013 C 186 G 199 CGAC*GAAG > IL_13959.4 IL_4IOA_058 U 1530 G 1494 UCAG*CAAG > IL_13959.4 IL_4A1B_005 C 138 G 128 CAAC*GAAG > IL_13959.4 IL_3U5F_085 C 1653 G 1747 CGAU*AGAG > IL_13959.4 IL_1S72_098 C 2873 G 2884 CGAG*CGAG > IL_13959.4 IL_4A1B_132 C 3316 G 3303 CGAU*AGAG > IL_13959.4 IL_3DIR_002 C 70 G 22 CGAG*CGAG > IL_13959.4 IL_2AW7_065 U 1481 G 1419 UGAC*GGAG > IL_13959.4 IL_3U5H_141 C 3360 G 3345 CGAU*AGAG > IL_13959.4 IL_2IL9_002 A 6058 U 6021 AAUA*UAUU > IL_13959.4 IL_2O3V_002 C 7 G 42 CGCU*AAAAG