| 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 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_80599.2_Instance_1 HL_80599.2,HL_8P9A_169,U2724_G2732 | U | U | C | A | G | U | G | U | G | |||||||||||||||
| HL_80599.2_Sequence_1 HL_80599.28P9A_U_2724_G_2732 | U | U | C | A | G | U | G | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_80599.2_Instance_2 HL_80599.2,HL_8CRE_057,U2696_G2704 | U | U | C | A | G | U | G | U | G | |||||||||||||||
| HL_80599.2_Sequence_2 HL_80599.28CRE_U_2696_G_2704 | U | U | C | A | G | U | G | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_80599.2_Instance_3 HL_80599.2,HL_1J2B_001,C932_G940 | C | C | U | U | A | C | G | A | G | |||||||||||||||
| HL_80599.2_Sequence_3 HL_80599.21J2B_C932_G940 | C | C | U | U | A | C | G | A | G | true | 78 | 0 | 0 | 3.95 |
1 2 s35 1 9 cWW 2 8 cWW 2 9 s55 3 5 s53 4 6 s35 6 7 s35 7 8 s35 8 9 s35 5 4 2BPh 6 3 7BRJAR3D SCFG/MRF model for HL_80599.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.010572638,0.014877250,0.013044997,0.090228256,0.000000000],[0.206427106,0.021659062,0.106652866,0.015137891,0.000000000],[0.013291996,0.091543616,0.002872521,0.017432502,0.000000000],[0.123374477,0.014077094,0.246524532,0.012283196,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair U2724 - G2732 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.013872203,0.191638258,0.013787618,0.026054147,0.000000000],[0.139478647,0.025669544,0.025075014,0.015224318,0.000000000],[0.013710547,0.023528243,0.003992380,0.040875897,0.000000000],[0.026654380,0.015588045,0.119955665,0.304895095,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U2725 - U2731 cWW HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C2726:G2730 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2726 Interaction | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2727 Interaction | Interacting Bases [3,3] | Pair Probability [[0.326086957,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.630434783,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2728 Interaction | Interacting Bases [4,4] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.323529412,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.617647059,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2729 Interaction | Interacting Bases [5,5] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2730Sequences of instances from HL_80599.2:
> HL_80599.2 8P9A U 2724 G 2732 UUCAGUGUG > HL_80599.2 8CRE U 2696 G 2704 UUCAGUGUG > HL_80599.2 1J2B C 932 G 940 CCUUACGAG