| 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_01181.4_Instance_1 HL_01181.4_HL_1L2X_001_G7_C14 | G | C | A | C | C | G | U | C | ||||||||||||
| HL_01181.4_Sequence_1 HL_01181.4_HL_1L2X_001_G7_C14 | G | C | A | C | C | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_01181.4_Instance_2 HL_01181.4_HL_2A43_001_G6_C13 | G | C | A | C | C | G | U | C | ||||||||||||
| HL_01181.4_Sequence_2 HL_01181.4_HL_2A43_001_G6_C13 | G | C | A | C | C | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_01181.4_Instance_3 HL_01181.4_HL_4V88_220_G1594_C1602 | G | U | C | A | U | C | A | G | C | |||||||||||
| HL_01181.4_Sequence_3 HL_01181.4_HL_4V88_220_G_1594_C_1602 | G | U | C | A | U | C | A | G | C | true | 85 | 0 | 0 | 2.14 |
1 2 s35 1 7 cWW 2 5 s33 2 6 tWH 3 4 s35 4 5 s35 5 6 s35 6 7 s35 4 3 7BPhJAR3D SCFG/MRF model for HL_01181.4:
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 [7] // Initial node G7 - C14 from junction BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.100000000,0.300000000,0.500000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair G7 - C14 cWW BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.057790106,0.057790106,0.057790106,0.057790106,0.000000000],[0.057790106,0.057790106,0.077207582,0.057790106,0.000000000],[0.057790106,0.057790106,0.057790106,0.057790106,0.000000000],[0.113730929,0.057790106,0.057790106,0.057790106,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | 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 [6] // Basepair C8 - G12 tWH HairpinNode | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [0.999999999999999] // Hairpin node A9:C11 Interaction | Interacting Bases [1,1] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 A9 Interaction | Interacting Bases [2,2] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.326086957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C10 Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C11Sequences of instances from HL_01181.4:
> HL_01181.4 HL_1L2X_001 G 7 C 14 GCACCGUC > HL_01181.4 HL_2A43_001 G 6 C 13 GCACCGUC > HL_01181.4 HL_4V88_220 G 1594 C 1602 GUCAUCAGC