| 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 12 I | 14 13 7 | 15 14 I | 16 15 8 | 17 15 I | 18 15 9 | 19 15 I | 20 15 10 | 21 16 I | 22 17 11 | 23 17 I | 24 17 12 | 25 17 I | 26 17 13 | 27 16 I | 28 15 14 | 29 2 I | 30 2 15 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_73247.1_Instance_1 HL_73247.1,HL_7JJU_001,C14_G30 | C | AU | A | C | A | C | G | A | G | U | U | G | C | A | A | G | ||||||||||||||||||||
| HL_73247.1_Sequence_1 HL_73247.17JJU_C14_G30 | C | AU | A | C | A | C | G | A | G | U | U | G | C | A | A | G | true | 100 | 0 | 0 | 0.04 | |||||||||||||||
| HL_73247.1_Instance_2 HL_73247.1,HL_7JJU_002,C14_G30 | C | AU | A | C | A | C | G | A | G | U | U | G | C | A | A | G | ||||||||||||||||||||
| HL_73247.1_Sequence_2 HL_73247.17JJU_C14_G30 | C | AU | A | C | A | C | G | A | G | U | U | G | C | A | A | G | true | 100 | 0 | 0 | 0.04 | |||||||||||||||
| HL_73247.1_Instance_3 HL_73247.1,HL_6D3P_002,C13_G27 | C | A | U | C | C | G | A | G | U | U | G | C | A | A | G | |||||||||||||||||||||
| HL_73247.1_Sequence_3 HL_73247.16D3P_C13_G27 | C | A | U | C | C | G | A | G | U | U | G | C | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 3 s35 1 15 cWW 2 4 s55 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35 10 11 s35 10 14 tWH 11 14 s55 12 13 s35 11 14 6BPh 13 11 7BRJAR3D SCFG/MRF model for HL_73247.1:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000000191968215] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.324061572,0.016203079,0.648393195,0.010802052,0.000540103] | Left Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair C14 - G30 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 7JJU|1|A|A|15 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 [14] // 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 [3] | Right Index [14] // Fixed node on left for 7JJU|1|A|U|16 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 [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [4] | Right Index [14] // Fixed node on left for 7JJU|1|A|A|17 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 [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [5] | Right Index [14] // Fixed node on left for 7JJU|1|A|C|18 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 [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [6] | Right Index [14] // Fixed node on left for 7JJU|1|A|A|19 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 [7] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [7] | Right Index [14] // Fixed node on left for 7JJU|1|A|C|20 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 [8] | Right Index [14] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [8] | Right Index [14] | Norm Constant [1.000000000000000] // Cluster node 7JJU|1|A|G|23:7JJU|1|A|U|25 and 7JJU|1|A|A|29:7JJU|1|A|A|29 Interaction | Interacting Bases [3,4] | 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 7JJU|1|A|U|25 - 7JJU|1|A|A|29 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 7JJU|1|A|G|23 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7JJU|1|A|U|24 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 [11] | Right Index [13] // New Initial node after Cluster HairpinNode | Num Bases [3] | Left Index [11] | Right Index [13] | Norm Constant [1.000000000000000] // Hairpin node G26:A28 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 G26 Interaction | Interacting Bases [2,2] | 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 C27 Interaction | Interacting Bases [3,3] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A28Sequences of instances from HL_73247.1:
> HL_73247.1 7JJU C 14 G 30 CAUACACGAGUUGCAAG > HL_73247.1 7JJU C 14 G 30 CAUACACGAGUUGCAAG > HL_73247.1 6D3P C 13 G 27 CAUCCGAGUUGCAAG