| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_93324.4_Instance_1 HL_93324.4,HL_4FRN_006,U44_A51 | U | U | A | C | U | U | G | A | ||||||||||||||
| HL_93324.4_Sequence_1 HL_93324.44FRN_U44_A51 | U | U | A | C | U | U | G | A | true | 66 | 0 | 0 | 3.27 | |||||||||
| HL_93324.4_Instance_2 HL_93324.4,HL_6R47_001,G6_C13 | G | U | U | C | G | G | G | C | ||||||||||||||
| HL_93324.4_Sequence_2 HL_93324.46R47_G6_C13 | G | U | U | C | G | G | G | C | true | 75 | 0 | 0 | 2.35 | |||||||||
| HL_93324.4_Instance_3 HL_93324.4,HL_6UFJ_003,G5_C12 | G | U | U | U | G | A | G | C | ||||||||||||||
| HL_93324.4_Sequence_3 HL_93324.46UFJ_G5_C12 | G | U | U | U | G | A | G | C | true | 67 | 0 | 0 | 3.14 | |||||||||
| HL_93324.4_Instance_4 HL_93324.4,HL_5K7D_001,G5_C12 | G | U | U | A | G | G | G | C | ||||||||||||||
| HL_93324.4_Sequence_4 HL_93324.45K7D_G5_C12 | G | U | U | A | G | G | G | C | true | 87 | 0 | 0 | 1.25 | |||||||||
| HL_93324.4_Instance_5 HL_93324.4,HL_9DFE_054,C2324_G2331 | C | G | C | A | A | G | G | G | ||||||||||||||
| HL_93324.4_Sequence_5 HL_93324.49DFE_C_2324_G_2331 | C | G | C | A | A | G | G | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| HL_93324.4_Instance_6 HL_93324.4,HL_2JLT_002,C5_G12 | C | C | U | G | G | G | A | G | ||||||||||||||
| HL_93324.4_Sequence_6 HL_93324.42JLT_C5_G12 | C | C | U | G | G | G | A | G | true | 60 | 0 | 0 | 3.83 | |||||||||
| HL_93324.4_Instance_7 HL_93324.4,HL_8CRE_056,C2665_G2672 | C | A | A | A | A | G | G | G | ||||||||||||||
| HL_93324.4_Sequence_7 HL_93324.48CRE_C_2665_G_2672 | C | A | A | A | A | G | G | G | true | 89 | 0 | 0 | 1.01 | |||||||||
| HL_93324.4_Instance_8 HL_93324.4,HL_7A0S_055,C2303_G2310 | C | G | C | A | A | A | G | G | ||||||||||||||
| HL_93324.4_Sequence_8 HL_93324.47A0S_C_2303_G_2310 | C | G | C | A | A | A | G | G | true | 89 | 0 | 0 | 1.00 | |||||||||
| HL_93324.4_Instance_9 HL_93324.4,HL_3SKI_002,G53_C60 | G | A | C | C | C | C | G | C | ||||||||||||||
| HL_93324.4_Sequence_9 HL_93324.43SKI_G53_C60 | G | A | C | C | C | C | G | C | true | 76 | 0 | 0 | 2.32 | |||||||||
| HL_93324.4_Instance_10 HL_93324.4,HL_8P9A_168,C2693_G2700 | C | A | A | A | A | G | G | G | ||||||||||||||
| HL_93324.4_Sequence_10 HL_93324.48P9A_C_2693_G_2700 | C | A | A | A | A | G | G | G | true | 89 | 0 | 0 | 1.01 | |||||||||
| HL_93324.4_Instance_11 HL_93324.4,HL_4WF9_052,U2351_G2358 | U | G | U | A | A | A | G | G | ||||||||||||||
| HL_93324.4_Sequence_11 HL_93324.44WF9_U_2351_G_2358 | U | G | U | A | A | A | G | G | true | 81 | 0 | 0 | 1.83 | |||||||||
| HL_93324.4_Instance_12 HL_93324.4,HL_3SKL_005,G52_C59 | G | A | C | C | C | C | G | C | ||||||||||||||
| HL_93324.4_Sequence_12 HL_93324.43SKL_G52_C59 | G | A | C | C | C | C | G | C | true | 76 | 0 | 0 | 2.32 | |||||||||
| HL_93324.4_Instance_13 HL_93324.4,HL_4V9F_058,U2358_G2365 | U | G | C | A | A | G | A | G | ||||||||||||||
| HL_93324.4_Sequence_13 HL_93324.44V9F_U_2358_G_2365 | U | G | C | A | A | G | A | G | true | 88 | 0 | 0 | 1.13 | |||||||||
| HL_93324.4_Instance_14 HL_93324.4,HL_5J7L_189,U2324_G2331 | U | G | C | A | A | U | G | G | ||||||||||||||
| HL_93324.4_Sequence_14 HL_93324.45J7L_U_2324_G_2331 | U | G | C | A | A | U | G | G | true | 90 | 0 | 0 | 0.95 | |||||||||
| HL_93324.4_Instance_15 HL_93324.4,HL_4V9F_014,G416_C424 | G | G | C | A | U | C | G | A | C | |||||||||||||
| HL_93324.4_Sequence_15 HL_93324.44V9F_G416_C424 | G | G | C | A | U | C | G | A | C | true | 50 | 0 | 0 | 4.79 | ||||||||
| HL_93324.4_Instance_16 HL_93324.4,HL_8P9A_171,C2776_G2784 | C | G | G | A | A | U | U | U | G | |||||||||||||
| HL_93324.4_Sequence_16 HL_93324.48P9A_C_2776_G_2784 | C | G | G | A | A | U | U | U | G | true | 51 | 0 | 0 | 4.62 | ||||||||
| HL_93324.4_Instance_17 HL_93324.4,HL_3D0U_002,U90_G98 | U | U | C | C | U | C | C | C | G | |||||||||||||
| HL_93324.4_Sequence_17 HL_93324.43D0U_U90_G98 | U | U | C | C | U | C | C | C | G | true | 36 | 0 | 0 | 6.06 | ||||||||
| HL_93324.4_Instance_18 HL_93324.4,HL_2NZ4_007,G71_C79 | G | U | U | C | A | U | C | A | C | |||||||||||||
| HL_93324.4_Sequence_18 HL_93324.42NZ4_G71_C79 | G | U | U | C | A | U | C | A | C | true | 62 | 0 | 0 | 3.65 | ||||||||
| HL_93324.4_Instance_19 HL_93324.4,HL_8CRE_059,C2748_G2756 | C | G | G | A | A | U | U | U | G | |||||||||||||
| HL_93324.4_Sequence_19 HL_93324.48CRE_C_2748_G_2756 | C | G | G | A | A | U | U | U | G | true | 51 | 0 | 0 | 4.62 | ||||||||
| HL_93324.4_Instance_20 HL_93324.4,HL_3DIL_002,U93_G101 | U | U | C | C | U | C | C | C | G | |||||||||||||
| HL_93324.4_Sequence_20 HL_93324.43DIL_U93_G101 | U | U | C | C | U | C | C | C | G | true | 36 | 0 | 0 | 6.06 | ||||||||
| HL_93324.4_Instance_21 HL_93324.4,HL_4V9F_061,G2442_C2450 | G | C | U | U | G | A | U | G | C | |||||||||||||
| HL_93324.4_Sequence_21 HL_93324.44V9F_G_2442_C_2450 | G | C | U | U | G | A | U | G | C | true | 46 | 0 | 0 | 5.13 | ||||||||
| HL_93324.4_Instance_22 HL_93324.4,HL_6N5P_003,U76_G84 | U | A | C | C | U | U | C | U | G | |||||||||||||
| HL_93324.4_Sequence_22 HL_93324.46N5P_U76_G84 | U | A | C | C | U | U | C | U | G | true | 31 | 0 | 0 | 6.57 | ||||||||
| HL_93324.4_Instance_23 HL_93324.4,HL_4V9F_002,C83_G91 | C | G | C | A | C | G | G | A | G | |||||||||||||
| HL_93324.4_Sequence_23 HL_93324.44V9F_C83_G91 | C | G | C | A | C | G | G | A | G | true | 47 | 0 | 0 | 4.99 | ||||||||
| HL_93324.4_Instance_24 HL_93324.4,HL_3IGI_005,U178_A187 | U | GC | A | U | A | A | C | A | A | |||||||||||||
| HL_93324.4_Sequence_24 HL_93324.43IGI_U178_A187 | U | GC | A | U | A | A | C | A | A | true | 23 | 0 | 0 | 7.31 |
1 8 cWW 2 3 s35 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_93324.4:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000026904167381] | Pair Probability [[0.008215789,0.014325884,0.009660735,0.130830449,0.000000000],[0.073974265,0.011702188,0.199697140,0.011478144,0.000000000],[0.009726346,0.198448680,0.001965888,0.018370220,0.000000000],[0.157574942,0.011153516,0.133803005,0.009072811,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.623842412,0.333731457,0.042300635,0.000121168,0.000004327] | Left Letter Distribution [0.125000000,0.208333333,0.375000000,0.291666667,0.000000000] | 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 [8] // Basepair U44 - A51 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U45:G50 Interaction | Interacting Bases [1,1] | Pair Probability [[0.211538462,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.211538462,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.326923077,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U45 Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.442307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.019230769,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.288461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A46 Interaction | Interacting Bases [3,3] | Pair Probability [[0.519230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.173076923,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.096153846,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.211538462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C47 Interaction | Interacting Bases [4,4] | Pair Probability [[0.365384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.211538462,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.211538462,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.211538462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U48 Interaction | Interacting Bases [5,5] | Pair Probability [[0.134615385,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.288461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.365384615,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.211538462,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U49 Interaction | Interacting Bases [6,6] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.096153846,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.519230769,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.134615385,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G50 Insertion | Location [3] | Length Distribution [0.956245345,0.043564116,0.000186208,0.000004330] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3Sequences of instances from HL_93324.4:
> HL_93324.4 4FRN U 44 A 51 UUACUUGA > HL_93324.4 6R47 G 6 C 13 GUUCGGGC > HL_93324.4 6UFJ G 5 C 12 GUUUGAGC > HL_93324.4 5K7D G 5 C 12 GUUAGGGC > HL_93324.4 9DFE C 2324 G 2331 CGCAAGGG > HL_93324.4 2JLT C 5 G 12 CCUGGGAG > HL_93324.4 8CRE C 2665 G 2672 CAAAAGGG > HL_93324.4 7A0S C 2303 G 2310 CGCAAAGG > HL_93324.4 3SKI G 53 C 60 GACCCCGC > HL_93324.4 8P9A C 2693 G 2700 CAAAAGGG > HL_93324.4 4WF9 U 2351 G 2358 UGUAAAGG > HL_93324.4 3SKL G 52 C 59 GACCCCGC > HL_93324.4 4V9F U 2358 G 2365 UGCAAGAG > HL_93324.4 5J7L U 2324 G 2331 UGCAAUGG > HL_93324.4 4V9F G 416 C 424 GGCAUCGAC > HL_93324.4 8P9A C 2776 G 2784 CGGAAUUUG > HL_93324.4 3D0U U 90 G 98 UUCCUCCCG > HL_93324.4 2NZ4 G 71 C 79 GUUCAUCAC > HL_93324.4 8CRE C 2748 G 2756 CGGAAUUUG > HL_93324.4 3DIL U 93 G 101 UUCCUCCCG > HL_93324.4 4V9F G 2442 C 2450 GCUUGAUGC > HL_93324.4 6N5P U 76 G 84 UACCUUCUG > HL_93324.4 4V9F C 83 G 91 CGCACGGAG > HL_93324.4 3IGI U 178 A 187 UGCAUAACAA