| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 3 I | 16 3 8 | 17 3 I | 18 3 9 | 19 3 I | 20 3 10 | 21 2 I | 22 2 11 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_50622.6_Instance_1 HL_50622.6_HL_4WSM_225_C31_G41 | C | C | U | U | G | A | G | G | U | G | G | |||||||||||||||||
| HL_50622.6_Sequence_1 HL_50622.6_HL_4WSM_225_C31_G41 | C | C | U | U | G | A | G | G | U | G | G | true | 97 | 0 | 0 | 0.51 | ||||||||||||
| HL_50622.6_Instance_2 HL_50622.6_HL_6GSK_218_C30_G40 | C | C | U | U | G | G | U | A | A | G | G | |||||||||||||||||
| HL_50622.6_Sequence_2 HL_50622.6_HL_6GSK_218_C30_G40 | C | C | U | U | G | G | U | A | A | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_50622.6_Instance_3 HL_50622.6_HL_4UYK_001_G21_C31 | G | G | U | U | C | G | G | C | G | U | C | |||||||||||||||||
| HL_50622.6_Sequence_3 HL_50622.6_HL_4UYK_001_G21_C31 | G | G | U | U | C | G | G | C | G | U | C | true | 92 | 0 | 0 | 1.31 | ||||||||||||
| HL_50622.6_Instance_4 HL_50622.6_HL_4V7M_039_G29_C39 | G | A | U | U | G | U | G | A | U | U | C | |||||||||||||||||
| HL_50622.6_Sequence_4 HL_50622.6_HL_4V7M_039_G29_C39 | G | A | U | U | G | U | G | A | U | U | C | true | 98 | 0 | 0 | 0.29 | ||||||||||||
| HL_50622.6_Instance_5 HL_50622.6_HL_6CZR_101_G1338_C1349 | G | A | U | C | A | G | C | C | A | U | G | C | ||||||||||||||||
| HL_50622.6_Sequence_5 HL_50622.6_HL_6CZR_101_G_1338_C_1349 | G | A | U | C | A | G | C | C | A | U | G | C | true | 77 | 0 | 0 | 3.94 |
1 2 s35 1 11 cWW 2 3 s35 3 4 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35JAR3D SCFG/MRF model for HL_50622.6:
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 [11] // Initial node C31 - G41 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009378994,0.018460667,0.010720525,0.194585102,0.000000000],[0.017844226,0.009337380,0.218585035,0.013101324,0.000000000],[0.010696621,0.229254879,0.002029771,0.024718569,0.000000000],[0.194084748,0.013199104,0.024076884,0.009926171,0.000000000],[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 [11] // Basepair C31 - G41 cWW HairpinNode | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node C32:G40 Interaction | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C32 Interaction | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U33 Interaction | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.642857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U34 Interaction | Interacting Bases [4,4] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G35 Interaction | Interacting Bases [5,5] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A36 Interaction | Interacting Bases [6,6] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.214285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G37 Interaction | Interacting Bases [7,7] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.357142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G38 Interaction | Interacting Bases [8,8] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U39 Interaction | Interacting Bases [9,9] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G40 Insertion | Location [8] | Length Distribution [0.792098765,0.205432099,0.002370370,0.000098765] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 9, position 8Sequences of instances from HL_50622.6:
> HL_50622.6 HL_4WSM_225 C 31 G 41 CCUUGAGGUGG > HL_50622.6 HL_6GSK_218 C 30 G 40 CCUUGGUAAGG > HL_50622.6 HL_4UYK_001 G 21 C 31 GGUUCGGCGUC > HL_50622.6 HL_4V7M_039 G 29 C 39 GAUUGUGAUUC > HL_50622.6 HL_6CZR_101 G 1338 C 1349 GAUCAGCCAUGC