| 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 7 3 | 7 7 I | 8 8 4 | 9 8 I | 10 8 5 | 11 8 I | 12 8 6 | 13 8 I | 14 8 7 | 15 7 I | 16 7 8 | 17 6 I | 18 5 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_87219.4_Instance_1 HL_87219.4_HL_5J7L_017_G786_C796 | G | A | U | U | A | G | A | U | A | C | C | |||||||||||||||
| HL_87219.4_Sequence_1 HL_87219.4_HL_5J7L_017_G786_C796 | G | A | U | U | A | G | A | U | A | C | C | true | 93 | 0 | 0 | 1.07 | ||||||||||
| HL_87219.4_Instance_2 HL_87219.4_HL_4LFB_017_G786_C796 | G | A | U | U | A | G | A | U | A | C | C | |||||||||||||||
| HL_87219.4_Sequence_2 HL_87219.4_HL_4LFB_017_G786_C796 | G | A | U | U | A | G | A | U | A | C | C | true | 93 | 0 | 0 | 1.07 | ||||||||||
| HL_87219.4_Instance_3 HL_87219.4_HL_6CZR_088_G770_C780 | G | A | U | U | A | G | A | U | A | C | C | |||||||||||||||
| HL_87219.4_Sequence_3 HL_87219.4_HL_6CZR_088_G770_C780 | G | A | U | U | A | G | A | U | A | C | C | true | 93 | 0 | 0 | 1.07 | ||||||||||
| HL_87219.4_Instance_4 HL_87219.4_HL_4V88_208_G997_C1007 | G | A | U | C | A | G | A | U | A | C | C | |||||||||||||||
| HL_87219.4_Sequence_4 HL_87219.4_HL_4V88_208_G997_C_1007 | G | A | U | C | A | G | A | U | A | C | C | true | 80 | 0 | 0 | 3.20 | ||||||||||
| HL_87219.4_Instance_5 HL_87219.4_HL_5J7L_015_C689_G698 | C | G | G | U | G | A | A | A | U | G | ||||||||||||||||
| HL_87219.4_Sequence_5 HL_87219.4_HL_5J7L_015_C689_G698 | C | G | G | U | G | A | A | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_87219.4_Instance_6 HL_87219.4_HL_4LFB_015_C689_G698 | C | G | G | U | G | A | A | A | U | G | ||||||||||||||||
| HL_87219.4_Sequence_6 HL_87219.4_HL_4LFB_015_C689_G698 | C | G | G | U | G | A | A | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_87219.4_Instance_7 HL_87219.4_HL_6CZR_086_C673_G682 | C | G | G | U | G | A | A | A | U | G | ||||||||||||||||
| HL_87219.4_Sequence_7 HL_87219.4_HL_6CZR_086_C673_G682 | C | G | G | U | G | A | A | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_87219.4_Instance_8 HL_87219.4_HL_4V88_206_A900_U909 | A | G | G | U | G | A | A | A | U | U | ||||||||||||||||
| HL_87219.4_Sequence_8 HL_87219.4_HL_4V88_206_A900_U909 | A | G | G | U | G | A | A | A | U | U | true | 100 | 0 | 0 | 0.05 | |||||||||||
| HL_87219.4_Instance_9 HL_87219.4_HL_3R9X_001_A1513_U1522 | A | G | G | G | G | A | A | C | C | U | ||||||||||||||||
| HL_87219.4_Sequence_9 HL_87219.4_HL_3R9X_001_A_1513_U_1522 | A | G | G | G | G | A | A | C | C | U | true | 75 | 0 | 0 | 3.85 | |||||||||||
| HL_87219.4_Instance_10 HL_87219.4_HL_5TBW_028_G1266_C1275 | G | U | G | U | A | A | C | A | A | C | ||||||||||||||||
| HL_87219.4_Sequence_10 HL_87219.4_HL_5TBW_028_G_1266_C_1275 | G | U | G | U | A | A | C | A | A | C | true | 72 | 0 | 0 | 4.38 | |||||||||||
| HL_87219.4_Instance_11 HL_87219.4_HL_4WSM_226_G63_C73 | G | G | U | U | C | A | A | G | U | C | C | |||||||||||||||
| HL_87219.4_Sequence_11 HL_87219.4_HL_4WSM_226_G63_C73 | G | G | U | U | C | A | A | G | U | C | C | true | 71 | 0 | 0 | 4.56 |
1 2 s35 1 10 cWW 2 3 s35 2 10 s55 3 4 s35 3 8 tSH 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 4 7 6BPhJAR3D SCFG/MRF model for HL_87219.4:
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 [10] // Initial node G786 - C796 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008819762,0.018124088,0.009959712,0.202847942,0.000000000],[0.016578175,0.008818938,0.213602497,0.011845166,0.000000000],[0.009925645,0.242528718,0.001911957,0.028187187,0.000000000],[0.182832453,0.012083152,0.022313377,0.009621229,0.000000000],[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 [10] // Basepair G786 - C796 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.346153846,0.038461538,0.500000000,0.115384615,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.115384615,0.500000000,0.038461538,0.346153846,0.000000000] | Position [2] | Left Index [3] | Right Index [9] // 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 [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000021781539185] | Pair Probability [[0.100852388,0.100252221,0.001170348,0.005618559,0.000000000],[0.101441703,0.101511325,0.001170348,0.001170348,0.000000000],[0.170762009,0.022353694,0.006364883,0.098409479,0.000000000],[0.160531682,0.104866972,0.001170348,0.022353694,0.000000000],[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 [0.543801687,0.453920502,0.002175207,0.000102604] | Right Letter Distribution [0.071428571,0.071428571,0.214285714,0.642857143,0.000000000] | Left Index [3] | Right Index [8] // Basepair U788 - A794 tSH HairpinNode | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U789:A792 Interaction | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.094936709,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.094936709,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.803797468,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U789 Interaction | Interacting Bases [2,2] | Pair Probability [[0.423076923,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.115384615,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.423076923,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A790 Interaction | Interacting Bases [3,3] | Pair Probability [[0.576923077,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.346153846,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G791 Interaction | Interacting Bases [4,4] | Pair Probability [[0.807692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.115384615,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A792Sequences of instances from HL_87219.4:
> HL_87219.4 HL_5J7L_017 G 786 C 796 GAUUAGAUACC > HL_87219.4 HL_4LFB_017 G 786 C 796 GAUUAGAUACC > HL_87219.4 HL_6CZR_088 G 770 C 780 GAUUAGAUACC > HL_87219.4 HL_4V88_208 G 997 C 1007 GAUCAGAUACC > HL_87219.4 HL_5J7L_015 C 689 G 698 CGGUGAAAUG > HL_87219.4 HL_4LFB_015 C 689 G 698 CGGUGAAAUG > HL_87219.4 HL_6CZR_086 C 673 G 682 CGGUGAAAUG > HL_87219.4 HL_4V88_206 A 900 U 909 AGGUGAAAUU > HL_87219.4 HL_3R9X_001 A 1513 U 1522 AGGGGAACCU > HL_87219.4 HL_5TBW_028 G 1266 C 1275 GUGUAACAAC > HL_87219.4 HL_4WSM_226 G 63 C 73 GGUUCAAGUCC