| 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 5 | 11 6 I | 12 6 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 8 | 17 9 I | 18 10 | 19 9 I | 20 9 9 | 21 8 I | 22 8 10 | 23 7 I | 24 6 11 | 25 5 I | 26 5 12 | 27 4 I | 28 4 13 | 29 3 I | 30 3 14 | 31 2 I | 32 2 15 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_85647.3_Instance_1 IL_85647.3_IL_1Q96_001_C6_G24 | C | U | C | A | G | U | A | U | A | G | A | A | C | C | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_1 IL_85647.3_IL_1Q96_001_C6_G24 | C | U | C | A | G | U | A | U | * | A | G | A | A | C | C | G | true | 91 | 0 | 0 | 1.75 | |||||||||||||||||
| IL_85647.3_Instance_2 IL_85647.3_IL_1JBR_001_C6_G24 | C | U | C | A | G | U | A | C | G | G | A | A | C | C | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_2 IL_85647.3_IL_1JBR_001_C6_G24 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | C | G | true | 92 | 0 | 0 | 1.58 | |||||||||||||||||
| IL_85647.3_Instance_3 IL_85647.3_IL_1Q96_003_C6_G24 | C | U | C | A | G | U | A | U | A | G | A | A | C | C | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_3 IL_85647.3_IL_1Q96_003_C6_G24 | C | U | C | A | G | U | A | U | * | A | G | A | A | C | C | G | true | 91 | 0 | 0 | 1.75 | |||||||||||||||||
| IL_85647.3_Instance_4 IL_85647.3_IL_3U5H_122_C3018_G3036 | C | U | U | A | G | U | A | C | G | G | A | A | C | A | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_4 IL_85647.3_IL_3U5H_122_C_3018_G_3036 | C | U | U | A | G | U | A | C | * | G | G | A | A | C | A | G | true | 89 | 0 | 0 | 2.15 | |||||||||||||||||
| IL_85647.3_Instance_5 IL_85647.3_IL_4A1B_003_C80_G101 | C | C | C | A | G | U | A | A | U | G | A | A | C | A | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_5 IL_85647.3_IL_4A1B_003_C80_G101 | C | C | C | A | G | U | A | A | * | U | G | A | A | C | A | G | true | 87 | 0 | 0 | 2.61 | |||||||||||||||||
| IL_85647.3_Instance_6 IL_85647.3_IL_4IOA_007_G215_C236 | G | U | U | A | G | U | A | G | C | G | A | A | C | C | C | |||||||||||||||||||||||
| IL_85647.3_Sequence_6 IL_85647.3_IL_4IOA_007_G215_C236 | G | U | U | A | G | U | A | G | * | C | G | A | A | C | C | C | true | 89 | 0 | 0 | 2.23 | |||||||||||||||||
| IL_85647.3_Instance_7 IL_85647.3_IL_3V2F_006_C201_G194 | C | U | C | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_7 IL_85647.3_IL_3V2F_006_C201_G194 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_85647.3_Instance_8 IL_85647.3_IL_2QBG_011_C201_G194 | C | U | A | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_8 IL_85647.3_IL_2QBG_011_C201_G194 | C | U | A | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 98 | 0 | 0 | 0.35 | |||||||||||||||||
| IL_85647.3_Instance_9 IL_85647.3_IL_4A1B_118_G3007_C3025 | G | U | U | A | G | U | A | C | G | G | A | A | C | A | C | |||||||||||||||||||||||
| IL_85647.3_Sequence_9 IL_85647.3_IL_4A1B_118_G_3007_C_3025 | G | U | U | A | G | U | A | C | * | G | G | A | A | C | A | C | true | 88 | 0 | 0 | 2.38 | |||||||||||||||||
| IL_85647.3_Instance_10 IL_85647.3_IL_1S72_006_C171_G164 | C | U | C | A | G | U | A | U | A | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_10 IL_85647.3_IL_1S72_006_C171_G164 | C | U | C | A | G | U | A | U | * | A | G | A | A | C | U | G | true | 99 | 0 | 0 | 0.17 | |||||||||||||||||
| IL_85647.3_Instance_11 IL_85647.3_IL_4IOA_006_C178_G171 | C | U | C | A | G | U | A | C | G | G | A | A | C | U | G | |||||||||||||||||||||||
| IL_85647.3_Sequence_11 IL_85647.3_IL_4IOA_006_C178_G171 | C | U | C | A | G | U | A | C | * | G | G | A | A | C | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||
| IL_85647.3_Instance_12 IL_85647.3_IL_4A1C_008_G71_C104 | G | U | U | A | G | U | A | C | G | G | A | A | G | U | C | |||||||||||||||||||||||
| IL_85647.3_Sequence_12 IL_85647.3_IL_4A1C_008_G71_C104 | G | U | U | A | G | U | A | C | * | G | G | A | A | G | U | C | true | 87 | 0 | 0 | 2.69 | |||||||||||||||||
| IL_85647.3_Instance_13 IL_85647.3_IL_3V2F_046_A1262_U2017 | A | U | G | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_85647.3_Sequence_13 IL_85647.3_IL_3V2F_046_A_1262_U_2017 | A | U | G | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 97 | 0 | 0 | 0.56 | |||||||||||||||||
| IL_85647.3_Instance_14 IL_85647.3_IL_3U5H_148_A72_U106 | A | C | C | G | A | G | U | A | G | C | G | A | A | A | C | U | ||||||||||||||||||||||
| IL_85647.3_Sequence_14 IL_85647.3_IL_3U5H_148_A72_U106 | A | C | C | G | A | G | U | A | G | * | C | G | A | A | A | C | U | true | 73 | 0 | 0 | 5.56 | ||||||||||||||||
| IL_85647.3_Instance_15 IL_85647.3_IL_2QBG_048_A1262_U2017 | A | U | A | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_85647.3_Sequence_15 IL_85647.3_IL_2QBG_048_A_1262_U_2017 | A | U | A | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 95 | 0 | 0 | 1.01 | |||||||||||||||||
| IL_85647.3_Instance_16 IL_85647.3_IL_4IOA_047_A1275_U2000 | A | U | G | A | G | U | A | A | U | G | A | A | A | U | U | |||||||||||||||||||||||
| IL_85647.3_Sequence_16 IL_85647.3_IL_4IOA_047_A_1275_U_2000 | A | U | G | A | G | U | A | A | * | U | G | A | A | A | U | U | true | 97 | 0 | 0 | 0.56 |
1 2 s35 1 15 cWW 2 3 s35 2 14 cWW 2 15 s55 3 4 s33 3 13 tSH 4 5 s55 4 6 s55 4 11 s53 4 12 tHH 5 6 cSH 5 10 s33 6 7 s35 6 10 s33 6 11 tWH 7 8 s35 7 10 tHS 7 11 s55 8 9 cWW 8 10 s55 9 10 s35 11 12 s35 12 13 s35 13 14 s35 14 15 s35 10 6 6BPh 5 11 6BPh 4 12 6BPh 13 3 6BR 7 10 6BRJAR3D SCFG/MRF model for IL_85647.3:
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 [15] // Initial node C6 - G24 from junction BasepairNode | Deletion Probability [0.0000174430812709] | Pair Probability [[0.008675828,0.017305933,0.009868939,0.208763802,0.000000000],[0.017525751,0.007668670,0.260538742,0.011333681,0.000000000],[0.009914276,0.206893488,0.001889988,0.022419314,0.000000000],[0.172878144,0.011132189,0.022745860,0.010445394,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | 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 [15] // Basepair C6 - G24 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012043709,0.122205117,0.011969405,0.029253075,0.000000000],[0.035781168,0.089520195,0.019193391,0.013829750,0.000000000],[0.011822882,0.019450683,0.004113380,0.037329396,0.000000000],[0.061924409,0.088229224,0.017064970,0.426269247,0.000000000],[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 [2] | Right Index [14] // Basepair U7 - C23 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.094201538,0.129338943,0.001354713,0.006427133,0.000000000],[0.106675245,0.182885554,0.001354713,0.001354713,0.000000000],[0.147691304,0.001354713,0.006637998,0.038275031,0.000000000],[0.118683445,0.146725775,0.015684468,0.001354713,0.000000000],[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 [13] // Basepair C8 - C22 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.617640543,0.095681848,0.023662502,0.023698462,0.000000000],[0.008744982,0.000677143,0.058212869,0.048098828,0.000000000],[0.004230257,0.056186787,0.001658919,0.000677143,0.000000000],[0.004161052,0.055314377,0.000677143,0.000677143,0.000000000],[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 [12] // Basepair A9 - A21 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.511983607588030] // Cluster node G10:U11 and A20:A20 Interaction | Interacting Bases [2,3] | Pair Probability [[0.022837272,0.004789512,0.023493607,0.004789512,0.000000000],[0.047574079,0.039764490,0.031792035,0.004789512,0.000000000],[0.004789512,0.004789512,0.056052332,0.022341674,0.000000000],[0.616882239,0.004789512,0.059086009,0.051439190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U11 - A20 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.048479644,0.049942729,0.002723713,0.002253535,0.000000000],[0.046894616,0.054472179,0.000579310,0.054897273,0.000000000],[0.033155631,0.018131255,0.037062536,0.543447746,0.000000000],[0.004171512,0.048578946,0.000579310,0.054630067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - U11 cSH 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 [7] | Right Index [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.038440127,0.038782129,0.462139192,0.041783058,0.000000000],[0.044806889,0.040649327,0.003242082,0.040252647,0.000000000],[0.000463155,0.000463155,0.015707204,0.000463155,0.000000000],[0.002205483,0.000463155,0.269676090,0.000463155,0.000000000],[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 [7] | Right Index [10] // Basepair A12 - G19 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008515984,0.017593209,0.009557680,0.211161401,0.000000000],[0.018336446,0.007836719,0.240176240,0.010785029,0.000000000],[0.009597611,0.195328240,0.001890644,0.022188538,0.000000000],[0.202408459,0.010607771,0.023000835,0.011015193,0.000000000],[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 [8] | Right Index [9] // Basepair U13 - A18 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_85647.3:
> IL_85647.3 IL_1Q96_001 C 6 G 24 CUCAGUAU*AGAACCG > IL_85647.3 IL_1JBR_001 C 6 G 24 CUCAGUAC*GGAACCG > IL_85647.3 IL_1Q96_003 C 6 G 24 CUCAGUAU*AGAACCG > IL_85647.3 IL_3U5H_122 C 3018 G 3036 CUUAGUAC*GGAACAG > IL_85647.3 IL_4A1B_003 C 80 G 101 CCCAGUAA*UGAACAG > IL_85647.3 IL_4IOA_007 G 215 C 236 GUUAGUAG*CGAACCC > IL_85647.3 IL_3V2F_006 C 201 G 194 CUCAGUAC*GGAACUG > IL_85647.3 IL_2QBG_011 C 201 G 194 CUAAGUAC*GGAACUG > IL_85647.3 IL_4A1B_118 G 3007 C 3025 GUUAGUAC*GGAACAC > IL_85647.3 IL_1S72_006 C 171 G 164 CUCAGUAU*AGAACUG > IL_85647.3 IL_4IOA_006 C 178 G 171 CUCAGUAC*GGAACUG > IL_85647.3 IL_4A1C_008 G 71 C 104 GUUAGUAC*GGAAGUC > IL_85647.3 IL_3V2F_046 A 1262 U 2017 AUGAGUAA*UGAAAUU > IL_85647.3 IL_3U5H_148 A 72 U 106 ACCGAGUAG*CGAAACU > IL_85647.3 IL_2QBG_048 A 1262 U 2017 AUAAGUAA*UGAAAUU > IL_85647.3 IL_4IOA_047 A 1275 U 2000 AUGAGUAA*UGAAAUU