| 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 5 5 | 11 5 I | 12 5 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_06226.4_Instance_1 HL_06226.4,HL_8P9A_199,C393_G404 | C | C | U | G | A | G | A | A | A | CG | G | |||||||||||||
| HL_06226.4_Sequence_1 HL_06226.48P9A_C393_G404 | C | C | U | G | A | G | A | A | A | CG | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_06226.4_Instance_2 HL_06226.4,HL_8CRE_200,C391_G402 | C | C | U | G | A | G | A | A | A | CG | G | |||||||||||||
| HL_06226.4_Sequence_2 HL_06226.48CRE_C391_G402 | C | C | U | G | A | G | A | A | A | CG | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_06226.4_Instance_3 HL_06226.4,HL_5J7L_029,G1356_C1366 | G | A | U | C | A | G | A | A | UG | C | ||||||||||||||
| HL_06226.4_Sequence_3 HL_06226.45J7L_G_1356_C_1366 | G | A | U | C | A | G | A | A | UG | C | true | 93 | 0 | 0 | 1.30 | |||||||||
| HL_06226.4_Instance_4 HL_06226.4,HL_4LFB_030,G1356_C1366 | G | A | U | C | A | G | C | C | A | UG | C | |||||||||||||
| HL_06226.4_Sequence_4 HL_06226.44LFB_G_1356_C_1366 | G | A | U | C | A | G | C | C | A | UG | C | true | 82 | 0 | 0 | 3.49 |
1 2 s35 1 9 cWW 2 3 s35 2 8 tWH 2 9 s55 3 4 s35 3 7 tWH 4 7 s55 5 6 s35 6 7 s35 7 8 s35 8 9 s35JAR3D SCFG/MRF model for HL_06226.4:
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 [0.0000000006078908] | Pair Probability [[0.009449844,0.018327229,0.010811779,0.196207841,0.000000000],[0.018327582,0.009443627,0.221270256,0.013276988,0.000000000],[0.010811792,0.221269599,0.002049334,0.024632695,0.000000000],[0.196208128,0.013276932,0.024633063,0.010003312,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.050000000,0.250000000,0.450000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair C393 - G404 cWW BasepairNode | Deletion Probability [0.0000004444241139] | Pair Probability [[0.134031167,0.003199733,0.091534441,0.003199733,0.000000000],[0.339204095,0.023312121,0.003199733,0.003199733,0.000000000],[0.003199733,0.011171182,0.028773770,0.029494493,0.000000000],[0.032177534,0.003199733,0.014386067,0.276716730,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Right Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C394 - A401 tWH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.016740489,0.003704697,0.017387738,0.003704697,0.000000000],[0.037255609,0.298527778,0.003704697,0.003704697,0.000000000],[0.003704697,0.008880403,0.028173908,0.016477216,0.000000000],[0.443022142,0.057026375,0.021494207,0.036490649,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // Basepair U395 - A399 tWH HairpinNode | Num Bases [3] | Left Index [4] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G396:G398 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G396 Interaction | Interacting Bases [2,2] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A397 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G398Sequences of instances from HL_06226.4:
> HL_06226.4 8P9A C 393 G 404 CCUGAGAAACGG > HL_06226.4 8CRE C 391 G 402 CCUGAGAAACGG > HL_06226.4 5J7L G 1356 C 1366 GAUCAGAAUGC > HL_06226.4 4LFB G 1356 C 1366 GAUCAGCCAUGC