| 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 8 3 | 7 8 I | 8 11 4 | 9 11 I | 10 12 5 | 11 12 I | 12 12 6 | 13 12 I | 14 12 7 | 15 11 I | 16 11 8 | 17 10 I | 18 9 9 | 19 8 I | 20 8 10 | 21 7 I | 22 6 11 | 23 5 I | 24 4 12 | 25 3 I | 26 3 13 | 27 2 I | 28 2 14 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_81205.3_Instance_1 HL_81205.3,HL_4LFB_008,C320_G333 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | ||||||||||||||||||||
| HL_81205.3_Sequence_1 HL_81205.34LFB_C320_G333 | C | A | C | U | G | A | G | A | C | A | C | G | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| HL_81205.3_Instance_2 HL_81205.3,HL_5J7L_008,A320_U333 | A | A | C | U | G | A | G | A | C | A | C | G | G | U | ||||||||||||||||||||
| HL_81205.3_Sequence_2 HL_81205.35J7L_A320_U333 | A | A | C | U | G | A | G | A | C | A | C | G | G | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 3 s35 2 9 s35 2 13 cWW 2 14 s55 3 4 s35 3 10 tWH 4 5 s35 4 8 tWH 5 8 s55 6 7 s35 8 10 s35 10 13 s35 13 14 s35 5 8 6BPh 1 10 7BPh 2 10 7BPhJAR3D SCFG/MRF model for HL_81205.3:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.014861164,0.034155142,0.016024821,0.334434203,0.000000000],[0.031366346,0.015262620,0.335798204,0.021022280,0.000000000],[0.004154445,0.079182220,0.000818266,0.015243784,0.000000000],[0.078715413,0.004812926,0.009855722,0.004292443,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [14] // Basepair C320 - G333 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.058238598,0.028527678,0.722973527,0.034164167,0.000000000],[0.003979690,0.002710442,0.005271521,0.011845578,0.000000000],[0.096537877,0.005330722,0.001004808,0.004434260,0.000000000],[0.004871095,0.012515823,0.004339264,0.003254952,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [13] // Basepair A321 - G332 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right for 4LFB|1|A|G|331 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [3] | Right Index [11] // Fixed node on right for 4LFB|1|A|C|330 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.030717309,0.003588720,0.102662158,0.003588720,0.000000000],[0.378479886,0.026146144,0.003588720,0.003588720,0.000000000],[0.003588720,0.012529247,0.032271758,0.033080098,0.000000000],[0.036089313,0.003588720,0.016134962,0.310356803,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Basepair C322 - A329 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 4LFB|1|A|C|328 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.018775607,0.004155072,0.019501541,0.004155072,0.000000000],[0.041784723,0.334819390,0.004155072,0.004155072,0.000000000],[0.004155072,0.009959982,0.031598971,0.018480329,0.000000000],[0.435115030,0.004155072,0.024107229,0.040926768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // Basepair U323 - A327 tWH HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G324:G326 Interaction | Interacting Bases [1,1] | Pair Probability [[0.031250000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.031250000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.906250000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.031250000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G324 Interaction | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A325 Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.625000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G326Sequences of instances from HL_81205.3:
> HL_81205.3 4LFB C 320 G 333 CACUGAGACACGGG > HL_81205.3 5J7L A 320 U 333 AACUGAGACACGGU