| 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 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_12703.2_Instance_1 HL_12703.2_HL_1HMH_006_G101_C111 | G | G | C | C | C | |||||||||||
| HL_12703.2_Sequence_1 HL_12703.2_HL_1HMH_006_G101_C111 | G | G | C | C | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_12703.2_Instance_2 HL_12703.2_HL_1HMH_004_G101_C111 | G | G | C | C | C | |||||||||||
| HL_12703.2_Sequence_2 HL_12703.2_HL_1HMH_004_G101_C111 | G | G | C | C | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_12703.2_Instance_3 HL_12703.2_HL_6AAY_001_C37_G44 | C | A | U | UU | U | G | G | |||||||||
| HL_12703.2_Sequence_3 HL_12703.2_HL_6AAY_001_C37_G44 | C | A | U | UU | U | G | G | true | 52 | 0 | 0 | 4.58 |
1 2 s35 1 5 cWW 2 3 s35 2 5 s55 3 4 s35JAR3D SCFG/MRF model for HL_12703.2:
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 [5] // Initial node G101 - C111 from junction BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair G101 - C111 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G102:C104 Interaction | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G102 Interaction | Interacting Bases [2,2] | 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 C103 Interaction | Interacting Bases [3,3] | 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 C104 Insertion | Location [2] | Length Distribution [0.651642683,0.016291067,0.326364377,0.005430356,0.000271518] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_12703.2:
> HL_12703.2 HL_1HMH_006 G 101 C 111 GGCCC > HL_12703.2 HL_1HMH_004 G 101 C 111 GGCCC > HL_12703.2 HL_6AAY_001 C 37 G 44 CAUUUUGG