| 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 4 4 | 9 4 I | 10 4 5 | 11 3 I | 12 3 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_54035.5_Instance_1 HL_54035.5_HL_3R4F_001_A24_U31 | A | U | U | G | A | G | U | U | ||||||||||||
| HL_54035.5_Sequence_1 HL_54035.5_HL_3R4F_001_A24_U31 | A | U | U | G | A | G | U | U | true | 95 | 0 | 0 | 0.56 | |||||||
| HL_54035.5_Instance_2 HL_54035.5_HL_3R4F_003_A24_U31 | A | U | U | G | A | G | U | U | ||||||||||||
| HL_54035.5_Sequence_2 HL_54035.5_HL_3R4F_003_A24_U31 | A | U | U | G | A | G | U | U | true | 95 | 0 | 0 | 0.56 | |||||||
| HL_54035.5_Instance_3 HL_54035.5_HL_5J7L_024_G1089_C1096 | G | U | U | A | A | G | U | C | ||||||||||||
| HL_54035.5_Sequence_3 HL_54035.5_HL_5J7L_024_G_1089_C_1096 | G | U | U | A | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_54035.5_Instance_4 HL_54035.5_HL_5TBW_008_U278_G287 | U | U | U | G | G | GAA | U | G | ||||||||||||
| HL_54035.5_Sequence_4 HL_54035.5_HL_5TBW_008_U278_G287 | U | U | U | G | G | GAA | U | G | true | 29 | 0 | 0 | 8.46 | |||||||
| HL_54035.5_Instance_5 HL_54035.5_HL_4LFB_025_G1089_C1096 | G | U | U | A | A | G | U | C | ||||||||||||
| HL_54035.5_Sequence_5 HL_54035.5_HL_4LFB_025_G_1089_C_1096 | G | U | U | A | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_54035.5_Instance_6 HL_54035.5_HL_5TBW_024_C1076_G1083 | C | U | U | A | A | U | U | G | ||||||||||||
| HL_54035.5_Sequence_6 HL_54035.5_HL_5TBW_024_C_1076_G_1083 | C | U | U | A | A | U | U | G | true | 91 | 0 | 0 | 1.05 | |||||||
| HL_54035.5_Instance_7 HL_54035.5_HL_4V88_215_C1309_G1316 | C | U | U | A | A | U | U | G | ||||||||||||
| HL_54035.5_Sequence_7 HL_54035.5_HL_4V88_215_C_1309_G_1316 | C | U | U | A | A | U | U | G | true | 91 | 0 | 0 | 1.05 | |||||||
| HL_54035.5_Instance_8 HL_54035.5_HL_6CZR_096_G1072_C1079 | G | U | U | A | A | G | U | C | ||||||||||||
| HL_54035.5_Sequence_8 HL_54035.5_HL_6CZR_096_G_1072_C_1079 | G | U | U | A | A | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_54035.5_Instance_9 HL_54035.5_HL_5TBW_038_G1719_C1725 | G | U | U | U | A | U | C | |||||||||||||
| HL_54035.5_Sequence_9 HL_54035.5_HL_5TBW_038_G_1719_C_1725 | G | U | U | U | A | U | C | true | 78 | 0 | 0 | 2.59 |
1 2 s35 1 7 cWW 2 3 s35 2 6 cWW 3 6 s55 4 5 s35 5 6 s35 6 7 s35JAR3D SCFG/MRF model for HL_54035.5:
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 [7] // Initial node A24 - U31 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009131124,0.018018440,0.010435981,0.189738429,0.000000000],[0.046426872,0.010887920,0.191025320,0.012213912,0.000000000],[0.010438876,0.210580642,0.002071721,0.028602908,0.000000000],[0.174257789,0.012316895,0.063660197,0.010192977,0.000000000],[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 [7] // Basepair A24 - U31 cWW BasepairNode | Deletion Probability [0.0000000679767832] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [0.114201960,0.770099850,0.004916181,0.110140768,0.000610706,0.000030535] | Right Letter Distribution [0.208333333,0.041666667,0.541666667,0.208333333,0.000000000] | Left Index [2] | Right Index [6] // Basepair U25 - U30 cWW HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U26:A28 Interaction | Interacting Bases [1,1] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.863636364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U26 Interaction | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.318181818,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G27 Interaction | Interacting Bases [3,3] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A28Sequences of instances from HL_54035.5:
> HL_54035.5 HL_3R4F_001 A 24 U 31 AUUGAGUU > HL_54035.5 HL_3R4F_003 A 24 U 31 AUUGAGUU > HL_54035.5 HL_5J7L_024 G 1089 C 1096 GUUAAGUC > HL_54035.5 HL_5TBW_008 U 278 G 287 UUUGGGAAUG > HL_54035.5 HL_4LFB_025 G 1089 C 1096 GUUAAGUC > HL_54035.5 HL_5TBW_024 C 1076 G 1083 CUUAAUUG > HL_54035.5 HL_4V88_215 C 1309 G 1316 CUUAAUUG > HL_54035.5 HL_6CZR_096 G 1072 C 1079 GUUAAGUC > HL_54035.5 HL_5TBW_038 G 1719 C 1725 GUUUAUC