| 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 4 3 | 7 5 I | 8 6 4 | 9 7 I | 10 12 5 | 11 12 I | 12 13 6 | 13 13 I | 14 13 7 | 15 12 I | 16 12 8 | 17 11 I | 18 10 9 | 19 9 I | 20 8 10 | 21 3 I | 22 3 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_07583.1_Instance_1 HL_07583.1,HL_4WSM_208,U11_A25 | U | G | G | A | A | U | UG | G | U | A | G | A | C | A | ||||||||||||||||
| HL_07583.1_Sequence_1 HL_07583.14WSM_U11_A25 | U | G | G | A | A | U | UG | G | U | A | G | A | C | A | true | 87 | 0 | 0 | 1.90 | |||||||||||
| HL_07583.1_Instance_2 HL_07583.1,HL_9IWF_004,A15_U27 | A | U | U | A | A | U | A | C | G | G | U | U | U | |||||||||||||||||
| HL_07583.1_Sequence_2 HL_07583.19IWF_A15_U27 | A | U | U | A | A | U | A | C | G | G | U | U | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 12 cWW 2 3 s35 2 11 cWW 2 12 s55 3 4 s35 3 11 s55 4 5 s35 4 10 s55 5 6 s35 5 8 cSS 5 9 s55 7 8 s55 8 9 s35 10 11 s35 11 12 s35JAR3D SCFG/MRF model for HL_07583.1:
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 [0.0000229437914523] | Pair Probability [[0.009158630,0.019777652,0.009912226,0.210022087,0.000000000],[0.019781061,0.009705967,0.195573829,0.010701870,0.000000000],[0.009912241,0.195571919,0.002042701,0.038130662,0.000000000],[0.210028228,0.010701362,0.038153583,0.010825982,0.000000000],[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 [12] // Basepair U11 - A25 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.012580706,0.151617500,0.012429215,0.112689261,0.000000000],[0.017074394,0.013965187,0.111795142,0.014202529,0.000000000],[0.012223818,0.124741992,0.003170721,0.040543671,0.000000000],[0.109880149,0.015081802,0.020445537,0.227558377,0.000000000],[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 [11] // Basepair G12 - C24 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 4WSM|1|1K|G|13 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 4WSM|1|1K|A|14 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [2] | Left Index [5] | Right Index [10] // Fixed node on right for 4WSM|1|1K|U|20 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // Fixed node on right for 4WSM|1|1K|G|19 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.074779183,0.077704083,0.090642274,0.175204246,0.000000000],[0.070059069,0.076370390,0.003134090,0.070332545,0.000000000],[0.071723371,0.003066455,0.006948844,0.070890762,0.000000000],[0.066229747,0.010445680,0.055745967,0.076723295,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Left Index [5] | Right Index [8] // Basepair A15 - U20 cSS HairpinNode | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U16:G19 Interaction | Interacting Bases [1,1] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16 Interaction | Interacting Bases [2,2] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.375000000,0.000000000,0.000000000],[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 G19 Insertion | Location [1] | Length Distribution [0.481347774,0.024067389,0.481949458,0.012033694,0.000601685] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 1Sequences of instances from HL_07583.1:
> HL_07583.1 4WSM U 11 A 25 UGGAAUUGGUAGACA > HL_07583.1 9IWF A 15 U 27 AUUAAUACGGUUU