| 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 13 5 | 11 13 I | 12 14 6 | 13 13 I | 14 13 7 | 15 12 I | 16 11 8 | 17 10 I | 18 9 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_93438.2_Instance_1 HL_93438.2,HL_7A0S_001,C58_G67 | C | G | A | U | U | A | C | C | U | G | ||||||||||||||||
| HL_93438.2_Sequence_1 HL_93438.27A0S_C58_G67 | C | G | A | U | U | A | C | C | U | G | true | 90 | 0 | 0 | 1.70 | |||||||||||
| HL_93438.2_Instance_2 HL_93438.2,HL_4V9F_001,U55_G64 | U | G | C | C | A | A | G | C | U | G | ||||||||||||||||
| HL_93438.2_Sequence_2 HL_93438.24V9F_U55_G64 | U | G | C | C | A | A | G | C | U | G | true | 97 | 0 | 0 | 0.47 | |||||||||||
| HL_93438.2_Instance_3 HL_93438.2,HL_4WF9_067,U59_A68 | U | U | A | C | U | A | A | C | G | A | ||||||||||||||||
| HL_93438.2_Sequence_3 HL_93438.24WF9_U59_A68 | U | U | A | C | U | A | A | C | G | A | true | 85 | 0 | 0 | 2.53 | |||||||||||
| HL_93438.2_Instance_4 HL_93438.2,HL_9DFE_001,U59_G68 | U | G | G | C | U | A | C | C | U | G | ||||||||||||||||
| HL_93438.2_Sequence_4 HL_93438.29DFE_U59_G68 | U | G | G | C | U | A | C | C | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_93438.2_Instance_5 HL_93438.2,HL_8CRE_074,C47_G56 | C | A | G | C | G | A | A | A | U | G | ||||||||||||||||
| HL_93438.2_Sequence_5 HL_93438.28CRE_C47_G56 | C | A | G | C | G | A | A | A | U | G | true | 94 | 0 | 0 | 1.01 | |||||||||||
| HL_93438.2_Instance_6 HL_93438.2,HL_8P9A_186,C47_G56 | C | A | G | C | G | A | A | A | U | G | ||||||||||||||||
| HL_93438.2_Sequence_6 HL_93438.28P9A_C47_G56 | C | A | G | C | G | A | A | A | U | G | true | 94 | 0 | 0 | 1.01 |
1 10 cWW 2 5 s33 3 4 s35 5 7 cSH 6 7 s35 7 8 s35 8 9 s35 9 10 s35 4 2 7BRJAR3D SCFG/MRF model for HL_93438.2:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009644511,0.015527228,0.011443838,0.139085405,0.000000000],[0.110331516,0.015215217,0.174023365,0.013549495,0.000000000],[0.011606434,0.140800008,0.002393762,0.019692765,0.000000000],[0.166749717,0.012765061,0.146341917,0.010829761,0.000000000],[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 [10] // Basepair C58 - G67 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.062500000,0.437500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 7A0S|1|X|G|59 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.187500000,0.437500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 7A0S|1|X|A|60 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.015625000,0.796875000,0.015625000,0.171875000,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 7A0S|1|X|U|61 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.187500000,0.687500000,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // Fixed node on right for 7A0S|1|X|U|66 InitialNode | Left Length Distribution [1.000000000] | 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 [5] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.562500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [5] | Right Index [8] // Fixed node on right for 7A0S|1|X|C|65 InitialNode | Left Length Distribution [1.000000000] | 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 [5] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.073367185,0.075458306,0.148940336,0.057373787,0.000000000],[0.074011572,0.073408955,0.002105538,0.014004024,0.000000000],[0.078838155,0.002105538,0.075152692,0.068176470,0.000000000],[0.084841134,0.101762745,0.002105538,0.068348021,0.000000000],[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 [5] | Right Index [7] // Basepair U62 - C64 cSH HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A63:A63 Interaction | Interacting Bases [1,1] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A63Sequences of instances from HL_93438.2:
> HL_93438.2 7A0S C 58 G 67 CGAUUACCUG > HL_93438.2 4V9F U 55 G 64 UGCCAAGCUG > HL_93438.2 4WF9 U 59 A 68 UUACUAACGA > HL_93438.2 9DFE U 59 G 68 UGGCUACCUG > HL_93438.2 8CRE C 47 G 56 CAGCGAAAUG > HL_93438.2 8P9A C 47 G 56 CAGCGAAAUG