| 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 3 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_49196.2_Instance_1 HL_49196.2_HL_4QEI_005_A31_U39 | A | U | U | C | CCA | U | U | |||||||||||
| HL_49196.2_Sequence_1 HL_49196.2_HL_4QEI_005_A31_U39 | A | U | U | C | CCA | U | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_49196.2_Instance_2 HL_49196.2_HL_4QEI_002_A31_U39 | A | U | U | C | CCA | U | U | |||||||||||
| HL_49196.2_Sequence_2 HL_49196.2_HL_4QEI_002_A31_U39 | A | U | U | C | CCA | U | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_49196.2_Instance_3 HL_49196.2_HL_5E6M_002_A31_U39 | A | U | U | C | CCA | U | U | |||||||||||
| HL_49196.2_Sequence_3 HL_49196.2_HL_5E6M_002_A31_U39 | A | U | U | C | CCA | U | U | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_49196.2_Instance_4 HL_49196.2_HL_4Y4O_121_C612_G615 | C | G | U | U | G | A | G | |||||||||||
| HL_49196.2_Sequence_4 HL_49196.2_HL_4Y4O_121_C612_G615 | C | G | U | U | G | A | G | true | 69 | 0 | 0 | 3.77 |
1 2 s35 1 6 cWW 2 3 s33 2 5 cWW 3 4 s55 5 6 s35JAR3D SCFG/MRF model for HL_49196.2:
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 A31 - U39 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009166602,0.020383573,0.009980938,0.227730182,0.000000000],[0.017857579,0.009428504,0.203678568,0.011001082,0.000000000],[0.009996931,0.194467451,0.002013816,0.044896561,0.000000000],[0.193563959,0.011369935,0.023491652,0.010972668,0.000000000],[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 [1] | Right Index [6] // Basepair A31 - U39 cWW BasepairNode | Deletion Probability [0.0000000000429844] | Pair Probability [[0.014642936,0.268569294,0.013073672,0.022833987,0.000000000],[0.016183920,0.017450268,0.019517606,0.014351871,0.000000000],[0.053433362,0.019882520,0.004035860,0.051558882,0.000000000],[0.019947010,0.015543066,0.016543547,0.432432199,0.000000000],[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 [0.003046923,0.243753809,0.012187690,0.731413772,0.009140768,0.000457038] | Right Letter Distribution [0.291666667,0.541666667,0.125000000,0.041666667,0.000000000] | Left Index [2] | Right Index [5] // Basepair U32 - U38 cWW HairpinNode | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U33:C34 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [2,2] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.583333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C34Sequences of instances from HL_49196.2:
> HL_49196.2 HL_4QEI_005 A 31 U 39 AUUCCCAUU > HL_49196.2 HL_4QEI_002 A 31 U 39 AUUCCCAUU > HL_49196.2 HL_5E6M_002 A 31 U 39 AUUCCCAUU > HL_49196.2 HL_4Y4O_121 C 612 G 615 CGUUGAG