| 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 4 I | 6 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 10 I | 12 11 6 | 13 11 I | 14 11 7 | 15 12 I | 16 13 8 | 17 13 I | 18 13 9 | 19 13 I | 20 13 10 | 21 12 I | 22 11 11 | 23 2 I | 24 2 12 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_86109.1_Instance_1 HL_86109.1,HL_4MGN_001,G51_C63 | G | G | G | C | G | G | U | G | G | G | A | G | C | |||||||||||||||||
| HL_86109.1_Sequence_1 HL_86109.14MGN_G51_C63 | G | G | G | C | G | G | U | G | G | G | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_86109.1_Instance_2 HL_86109.1,HL_4JRC_002,G51_C63 | G | G | G | C | G | G | U | G | G | G | A | G | C | |||||||||||||||||
| HL_86109.1_Sequence_2 HL_86109.14JRC_G51_C63 | G | G | G | C | G | G | U | G | G | G | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_86109.1_Instance_3 HL_86109.1,HL_4LCK_010,G52_C64 | G | G | A | U | A | G | U | G | A | A | A | G | C | |||||||||||||||||
| HL_86109.1_Sequence_3 HL_86109.14LCK_G52_C64 | G | G | A | U | A | G | U | G | A | A | A | G | C | true | 86 | 0 | 0 | 2.70 |
1 2 s35 1 12 cWW 2 3 s35 2 12 s55 3 4 s35 5 6 s35 6 7 s35 7 8 s35 7 11 tWH 8 11 s55 9 10 s35 3 11 6BPh 8 11 6BPhJAR3D SCFG/MRF model for HL_86109.1:
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 [12] // Initial node 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 [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G51 - C63 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|52 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.326086957,0.021739130,0.630434783,0.021739130,0.000000000] | Position [1] | Left Index [3] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|53 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.500000000,0.100000000,0.300000000,0.000000000] | Position [1] | Left Index [4] | Right Index [11] // Fixed node on left for 4MGN|1|A|C|54 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left for 4MGN|1|A|G|55 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [11] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [6] | Right Index [11] | Norm Constant [1.000000000000000] // Cluster node 4MGN|1|A|G|56:4MGN|1|A|U|57 and 4MGN|1|A|A|61:4MGN|1|A|A|61 Interaction | Interacting Bases [2,3] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4MGN|1|A|U|57 - 4MGN|1|A|A|61 tWH Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 4MGN|1|A|G|56 InitialNode | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [10] // New Initial node after Cluster HairpinNode | Num Bases [3] | Left Index [8] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node G58:G60 Interaction | Interacting Bases [1,1] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G58 Interaction | Interacting Bases [2,2] | 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 G59 Interaction | Interacting Bases [3,3] | 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 G60Sequences of instances from HL_86109.1:
> HL_86109.1 4MGN G 51 C 63 GGGCGGUGGGAGC > HL_86109.1 4JRC G 51 C 63 GGGCGGUGGGAGC > HL_86109.1 4LCK G 52 C 64 GGAUAGUGAAAGC