| 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 4 I | 6 5 | 7 4 I | 8 3 3 | 9 3 I | 10 3 4 | 11 3 I | 12 3 5 | 13 2 I | 14 2 6 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_92027.3_Instance_1 IL_92027.3_IL_1S03_007_G37_C15 | G | U | A | A | A | C | ||||||||||||||
| IL_92027.3_Sequence_1 IL_92027.3_IL_1S03_007_G37_C15 | G | U | * | A | A | A | C | true | 94 | 0 | 0 | 0.60 | ||||||||
| IL_92027.3_Instance_2 IL_92027.3_IL_1FJG_025_G597_C643 | G | U | A | U | A | C | ||||||||||||||
| IL_92027.3_Sequence_2 IL_92027.3_IL_1FJG_025_G597_C643 | G | U | * | A | U | A | C | true | 89 | 0 | 0 | 1.09 | ||||||||
| IL_92027.3_Instance_3 IL_92027.3_IL_1I6U_004_G12_C27 | G | U | A | U | A | C | ||||||||||||||
| IL_92027.3_Sequence_3 IL_92027.3_IL_1I6U_004_G12_C27 | G | U | * | A | U | A | C | true | 89 | 0 | 0 | 1.09 | ||||||||
| IL_92027.3_Instance_4 IL_92027.3_IL_2AW7_032_G597_C643 | G | U | A | U | A | C | ||||||||||||||
| IL_92027.3_Sequence_4 IL_92027.3_IL_2AW7_032_G597_C643 | G | U | * | A | U | A | C | true | 89 | 0 | 0 | 1.09 | ||||||||
| IL_92027.3_Instance_5 IL_92027.3_IL_3U5F_040_A746_U805 | A | C | G | A | A | U | ||||||||||||||
| IL_92027.3_Sequence_5 IL_92027.3_IL_3U5F_040_A746_U805 | A | C | * | G | A | A | U | true | 97 | 0 | 0 | 0.29 | ||||||||
| IL_92027.3_Instance_6 IL_92027.3_IL_1S72_101_C29_G53 | C | C | G | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_6 IL_92027.3_IL_1S72_101_C29_G53 | C | C | * | G | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_92027.3_Instance_7 IL_92027.3_IL_4IOA_068_C1876_G1841 | C | C | G | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_7 IL_92027.3_IL_4IOA_068_C_1876_G_1841 | C | C | * | G | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_92027.3_Instance_8 IL_92027.3_IL_4A1C_006_C28_G51 | C | C | G | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_8 IL_92027.3_IL_4A1C_006_C28_G51 | C | C | * | G | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_92027.3_Instance_9 IL_92027.3_IL_4A1B_019_U469_A510 | U | C | G | A | A | A | ||||||||||||||
| IL_92027.3_Sequence_9 IL_92027.3_IL_4A1B_019_U469_A510 | U | C | * | G | A | A | A | true | 96 | 0 | 0 | 0.33 | ||||||||
| IL_92027.3_Instance_10 IL_92027.3_IL_1S72_068_A1934_U1905 | A | C | G | U | A | U | ||||||||||||||
| IL_92027.3_Sequence_10 IL_92027.3_IL_1S72_068_A_1934_U_1905 | A | C | * | G | U | A | U | true | 92 | 0 | 0 | 0.77 | ||||||||
| IL_92027.3_Instance_11 IL_92027.3_IL_1U9S_005_G161_C139 | G | G | C | A | G | C | ||||||||||||||
| IL_92027.3_Sequence_11 IL_92027.3_IL_1U9S_005_G161_C139 | G | G | * | C | A | G | C | true | 67 | 0 | 0 | 3.12 | ||||||||
| IL_92027.3_Instance_12 IL_92027.3_IL_3U5H_091_C2245_G2199 | C | G | C | C | A | G | ||||||||||||||
| IL_92027.3_Sequence_12 IL_92027.3_IL_3U5H_091_C_2245_G_2199 | C | G | * | C | C | A | G | true | 84 | 0 | 0 | 1.49 | ||||||||
| IL_92027.3_Instance_13 IL_92027.3_IL_1U9S_002_C228_G115 | C | C | G | A | A | A | G | |||||||||||||
| IL_92027.3_Sequence_13 IL_92027.3_IL_1U9S_002_C228_G115 | C | C | * | G | A | A | A | G | true | 63 | 0 | 0 | 3.54 | |||||||
| IL_92027.3_Instance_14 IL_92027.3_IL_3Q1Q_005_C126_G151 | C | G | C | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_14 IL_92027.3_IL_3Q1Q_005_C126_G151 | C | G | * | C | A | A | G | true | 94 | 0 | 0 | 0.53 | ||||||||
| IL_92027.3_Instance_15 IL_92027.3_IL_1U9S_004_C133_G167 | C | G | C | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_15 IL_92027.3_IL_1U9S_004_C133_G167 | C | G | * | C | A | A | G | true | 94 | 0 | 0 | 0.53 | ||||||||
| IL_92027.3_Instance_16 IL_92027.3_IL_3TZR_001_G110_C58 | G | C | G | A | ACU | A | C | |||||||||||||
| IL_92027.3_Sequence_16 IL_92027.3_IL_3TZR_001_G110_C58 | G | C | * | G | A | ACU | A | C | true | 32 | 0 | 0 | 6.43 | |||||||
| IL_92027.3_Instance_17 IL_92027.3_IL_2QBG_074_C1893_G1849 | C | C | G | A | A | G | ||||||||||||||
| IL_92027.3_Sequence_17 IL_92027.3_IL_2QBG_074_C_1893_G_1849 | C | C | * | G | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 6 cWW 2 3 cWW 2 5 cSW 3 4 s35 4 5 cSH 5 6 s35JAR3D SCFG/MRF model for IL_92027.3:
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 [6] // Initial node G37 - C15 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008668452,0.016988087,0.009924636,0.188219101,0.000000000],[0.017131643,0.007544544,0.250353907,0.011380325,0.000000000],[0.009939034,0.232642761,0.001874181,0.022305022,0.000000000],[0.179374627,0.011316366,0.022479125,0.009858189,0.000000000],[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 [6] // Basepair G37 - C15 cWW ClusterNode | Deletion Probability [0.0000000001763743] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.094752302846867] // Cluster node U38:U38 and A12:A14 Interaction | Interacting Bases [1,2] | Pair Probability [[0.008590864,0.016331836,0.009816266,0.171008313,0.000000000],[0.018142150,0.007634138,0.258662220,0.011276526,0.000000000],[0.009857818,0.214012712,0.001875006,0.021485688,0.000000000],[0.207140253,0.011092461,0.023320816,0.009752934,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A12 cWW Interaction | Interacting Bases [1,4] | Pair Probability [[0.148845005,0.016642779,0.008840780,0.006304384,0.000000000],[0.259403036,0.012911978,0.009864416,0.006983616,0.000000000],[0.184512997,0.013990132,0.108087970,0.005348851,0.000000000],[0.190360302,0.014390467,0.007769248,0.005744039,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U38 - A14 cSW Interaction | Interacting Bases [3,4] | Pair Probability [[0.213394359,0.097711652,0.029298823,0.008073800,0.000000000],[0.081617278,0.055476529,0.001516816,0.058595049,0.000000000],[0.006792689,0.077315958,0.022342735,0.056169929,0.000000000],[0.131754900,0.103459442,0.001516816,0.054963226,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A13 - A14 cSH Insertion | Location [3] | Length Distribution [0.879505504,0.061208480,0.000474150,0.058630827,0.000172418,0.000008621] | Letter Distribution [0.416666667,0.250000000,0.083333333,0.250000000,0.000000000]// Insertion after nucleotide 4, position 3 in cluster node 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 [3] | Right Index [2] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | 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_92027.3:
> IL_92027.3 IL_1S03_007 G 37 C 15 GU*AAAC > IL_92027.3 IL_1FJG_025 G 597 C 643 GU*AUAC > IL_92027.3 IL_1I6U_004 G 12 C 27 GU*AUAC > IL_92027.3 IL_2AW7_032 G 597 C 643 GU*AUAC > IL_92027.3 IL_3U5F_040 A 746 U 805 AC*GAAU > IL_92027.3 IL_1S72_101 C 29 G 53 CC*GAAG > IL_92027.3 IL_4IOA_068 C 1876 G 1841 CC*GAAG > IL_92027.3 IL_4A1C_006 C 28 G 51 CC*GAAG > IL_92027.3 IL_4A1B_019 U 469 A 510 UC*GAAA > IL_92027.3 IL_1S72_068 A 1934 U 1905 AC*GUAU > IL_92027.3 IL_1U9S_005 G 161 C 139 GG*CAGC > IL_92027.3 IL_3U5H_091 C 2245 G 2199 CG*CCAG > IL_92027.3 IL_1U9S_002 C 228 G 115 CC*GAAAG > IL_92027.3 IL_3Q1Q_005 C 126 G 151 CG*CAAG > IL_92027.3 IL_1U9S_004 C 133 G 167 CG*CAAG > IL_92027.3 IL_3TZR_001 G 110 C 58 GC*GAACUAC > IL_92027.3 IL_2QBG_074 C 1893 G 1849 CC*GAAG