| 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 6 3 | 7 6 I | 8 7 4 | 9 7 I | 10 8 | 11 7 I | 12 7 5 | 13 6 I | 14 6 6 | 15 5 I | 16 4 7 | 17 3 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_93424.4_Instance_1 IL_93424.4_IL_2QBG_054_C1417_G1581 | C | G | A | A | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_1 IL_93424.4_IL_2QBG_054_C_1417_G_1581 | C | G | A | A | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_93424.4_Instance_2 IL_93424.4_IL_3V2F_052_C1417_G1581 | C | G | A | U | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_2 IL_93424.4_IL_3V2F_052_C_1417_G_1581 | C | G | A | U | G | * | C | U | A | A | G | true | 91 | 0 | 0 | 1.04 | ||||||||||
| IL_93424.4_Instance_3 IL_93424.4_IL_3V2F_049_C1376_G1355 | C | G | A | A | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_3 IL_93424.4_IL_3V2F_049_C_1376_G_1355 | C | G | A | A | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_93424.4_Instance_4 IL_93424.4_IL_2QBG_051_C1376_G1355 | C | G | A | U | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_4 IL_93424.4_IL_2QBG_051_C_1376_G_1355 | C | G | A | U | G | * | C | U | A | A | G | true | 91 | 0 | 0 | 1.04 | ||||||||||
| IL_93424.4_Instance_5 IL_93424.4_IL_1S72_038_C1257_G1099 | C | G | A | G | A | U | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_5 IL_93424.4_IL_1S72_038_C_1257_G_1099 | C | G | A | G | A | * | U | U | A | A | G | true | 75 | 0 | 0 | 2.83 | ||||||||||
| IL_93424.4_Instance_6 IL_93424.4_IL_2QBG_036_C1153_G1002 | C | G | A | A | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_6 IL_93424.4_IL_2QBG_036_C_1153_G_1002 | C | G | A | A | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_93424.4_Instance_7 IL_93424.4_IL_1S72_052_C1483_G1460 | C | G | A | AAU | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_7 IL_93424.4_IL_1S72_052_C_1483_G_1460 | C | G | A | AAU | G | * | C | U | A | A | G | true | 66 | 0 | 0 | 3.86 | ||||||||||
| IL_93424.4_Instance_8 IL_93424.4_IL_4IOA_032_C1164_G1013 | C | G | A | A | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_8 IL_93424.4_IL_4IOA_032_C_1164_G_1013 | C | G | A | A | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_93424.4_Instance_9 IL_93424.4_IL_3V2F_036_C1153_G1002 | C | G | A | A | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_9 IL_93424.4_IL_3V2F_036_C_1153_G_1002 | C | G | A | A | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_93424.4_Instance_10 IL_93424.4_IL_3U5H_069_C1585_G1536 | C | G | A | AA | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_10 IL_93424.4_IL_3U5H_069_C_1585_G_1536 | C | G | A | AA | G | * | C | U | A | A | G | true | 79 | 0 | 0 | 2.33 | ||||||||||
| IL_93424.4_Instance_11 IL_93424.4_IL_3U5H_126_A3127_U3107 | A | G | A | A | U | A | U | U | A | U | ||||||||||||||||
| IL_93424.4_Sequence_11 IL_93424.4_IL_3U5H_126_A_3127_U_3107 | A | G | A | A | U | * | A | U | U | A | U | true | 78 | 0 | 0 | 2.45 | ||||||||||
| IL_93424.4_Instance_12 IL_93424.4_IL_4A1B_122_A3116_U3096 | A | G | A | A | U | A | U | U | A | U | ||||||||||||||||
| IL_93424.4_Sequence_12 IL_93424.4_IL_4A1B_122_A_3116_U_3096 | A | G | A | A | U | * | A | U | U | A | U | true | 78 | 0 | 0 | 2.45 | ||||||||||
| IL_93424.4_Instance_13 IL_93424.4_IL_4A1B_067_C1610_G1562 | C | A | A | AA | G | C | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_13 IL_93424.4_IL_4A1B_067_C_1610_G_1562 | C | A | A | AA | G | * | C | U | A | A | G | true | 61 | 0 | 0 | 4.36 | ||||||||||
| IL_93424.4_Instance_14 IL_93424.4_IL_2XXA_014_C31_G66 | C | G | A | ACC | U | A | U | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_14 IL_93424.4_IL_2XXA_014_C31_G66 | C | G | A | ACC | U | * | A | U | A | A | G | true | 39 | 0 | 0 | 6.83 | ||||||||||
| IL_93424.4_Instance_15 IL_93424.4_IL_4IOA_053_U1431_A1597 | U | G | A | U | G | C | U | A | A | A | ||||||||||||||||
| IL_93424.4_Sequence_15 IL_93424.4_IL_4IOA_053_U_1431_A_1597 | U | G | A | U | G | * | C | U | A | A | A | true | 86 | 0 | 0 | 1.56 | ||||||||||
| IL_93424.4_Instance_16 IL_93424.4_IL_1S72_092_U2724_G2758 | U | G | U | A | C | G | G | U | A | G | ||||||||||||||||
| IL_93424.4_Sequence_16 IL_93424.4_IL_1S72_092_U_2724_G_2758 | U | G | U | A | C | * | G | G | U | A | G | true | 52 | 0 | 0 | 5.46 | ||||||||||
| IL_93424.4_Instance_17 IL_93424.4_IL_3U5H_024_G725_C745 | G | G | G | G | U | G | C | A | C | |||||||||||||||||
| IL_93424.4_Sequence_17 IL_93424.4_IL_3U5H_024_G725_C745 | G | G | G | G | * | U | G | C | A | C | true | 34 | 0 | 0 | 7.47 | |||||||||||
| IL_93424.4_Instance_18 IL_93424.4_IL_3U5H_124_U3054_G3088 | U | U | U | U | U | G | C | G | A | A | G | |||||||||||||||
| IL_93424.4_Sequence_18 IL_93424.4_IL_3U5H_124_U_3054_G_3088 | U | U | U | U | U | G | * | C | G | A | A | G | true | 17 | 0 | 0 | 9.33 | |||||||||
| IL_93424.4_Instance_19 IL_93424.4_IL_1X8W_006_U253_G220 | U | G | C | A | G | C | C | A | A | G | ||||||||||||||||
| IL_93424.4_Sequence_19 IL_93424.4_IL_1X8W_006_U253_G220 | U | G | C | A | G | * | C | C | A | A | G | true | 73 | 0 | 0 | 3.05 | ||||||||||
| IL_93424.4_Instance_20 IL_93424.4_IL_4A1B_126_U3212_G3199 | U | G | A | C | G | G | A | A | G | |||||||||||||||||
| IL_93424.4_Sequence_20 IL_93424.4_IL_4A1B_126_U_3212_G_3199 | U | G | A | C | * | G | G | A | A | G | true | 59 | 0 | 0 | 4.63 | |||||||||||
| IL_93424.4_Instance_21 IL_93424.4_IL_3V2F_057_U1518_G1473 | U | G | G | U | A | G | A | A | G | |||||||||||||||||
| IL_93424.4_Sequence_21 IL_93424.4_IL_3V2F_057_U_1518_G_1473 | U | G | G | U | * | A | G | A | A | G | true | 68 | 0 | 0 | 3.66 |
1 2 s35 1 9 cWW 2 6 s33 2 7 s33 2 8 tSH 2 9 s55 3 4 s35 3 6 tHW 3 7 s55 4 5 cWW 4 6 s55 5 6 s35 7 8 s35 8 9 s35 2 7 6BPh 8 2 6BRJAR3D SCFG/MRF model for IL_93424.4:
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 [9] // Initial node C1417 - G1581 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008962558,0.014859592,0.010393278,0.150315095,0.000000000],[0.076913212,0.008817731,0.243398715,0.011987446,0.000000000],[0.010528894,0.148385406,0.002088945,0.018854073,0.000000000],[0.143605439,0.011357816,0.129384680,0.010147120,0.000000000],[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 [9] // Basepair C1417 - G1581 cWW BasepairNode | Deletion Probability [0.0000147294218142] | Pair Probability [[0.059544634,0.053787320,0.000584169,0.003300211,0.000000000],[0.037422832,0.037770072,0.000443210,0.000443210,0.000000000],[0.452776205,0.002961509,0.014438148,0.244674219,0.000000000],[0.052405994,0.038561849,0.000443210,0.000443210,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.902527688,0.097127447,0.000333558,0.000011307] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G1418 - A1580 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.760869565,0.065217391,0.021739130,0.152173913,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | 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] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000000741983018] | Pair Probability [[0.021051522,0.043854046,0.031539389,0.565466781,0.000000000],[0.004414998,0.050217320,0.004414998,0.004414998,0.000000000],[0.021656535,0.029306072,0.078793737,0.054465806,0.000000000],[0.004414998,0.004414998,0.034156873,0.047416927,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.191104012,0.616996179,0.096534053,0.095117422,0.000237046,0.000011288] | Left Letter Distribution [0.620000000,0.100000000,0.060000000,0.220000000,0.000000000] | 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 A1419 - U1578 tHW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008622968,0.028889233,0.009691427,0.168375221,0.000000000],[0.015965643,0.007442493,0.182909660,0.010737626,0.000000000],[0.009614004,0.276828393,0.001864995,0.043338082,0.000000000],[0.193378178,0.011086787,0.020653500,0.010601790,0.000000000],[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 G1421 - C1577 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_93424.4:
> IL_93424.4 IL_2QBG_054 C 1417 G 1581 CGAAG*CUAAG > IL_93424.4 IL_3V2F_052 C 1417 G 1581 CGAUG*CUAAG > IL_93424.4 IL_3V2F_049 C 1376 G 1355 CGAAG*CUAAG > IL_93424.4 IL_2QBG_051 C 1376 G 1355 CGAUG*CUAAG > IL_93424.4 IL_1S72_038 C 1257 G 1099 CGAGA*UUAAG > IL_93424.4 IL_2QBG_036 C 1153 G 1002 CGAAG*CUAAG > IL_93424.4 IL_1S72_052 C 1483 G 1460 CGAAAUG*CUAAG > IL_93424.4 IL_4IOA_032 C 1164 G 1013 CGAAG*CUAAG > IL_93424.4 IL_3V2F_036 C 1153 G 1002 CGAAG*CUAAG > IL_93424.4 IL_3U5H_069 C 1585 G 1536 CGAAAG*CUAAG > IL_93424.4 IL_3U5H_126 A 3127 U 3107 AGAAU*AUUAU > IL_93424.4 IL_4A1B_122 A 3116 U 3096 AGAAU*AUUAU > IL_93424.4 IL_4A1B_067 C 1610 G 1562 CAAAAG*CUAAG > IL_93424.4 IL_2XXA_014 C 31 G 66 CGAACCU*AUAAG > IL_93424.4 IL_4IOA_053 U 1431 A 1597 UGAUG*CUAAA > IL_93424.4 IL_1S72_092 U 2724 G 2758 UGUAC*GGUAG > IL_93424.4 IL_3U5H_024 G 725 C 745 GGGG*UGCAC > IL_93424.4 IL_3U5H_124 U 3054 G 3088 UUUUUG*CGAAG > IL_93424.4 IL_1X8W_006 U 253 G 220 UGCAG*CCAAG > IL_93424.4 IL_4A1B_126 U 3212 G 3199 UGAC*GGAAG > IL_93424.4 IL_3V2F_057 U 1518 G 1473 UGGU*AGAAG