| 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 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_98995.6_Instance_1 HL_98995.6_HL_7A0S_064_U2680_A2685 | U | A | C | C | A | A | ||||||||||||
| HL_98995.6_Sequence_1 HL_98995.6_HL_7A0S_064_U_2680_A_2685 | U | A | C | C | A | A | true | 90 | 0 | 0 | 0.96 | |||||||
| HL_98995.6_Instance_2 HL_98995.6_HL_5J7L_198_U2701_A2706 | U | G | C | C | A | A | ||||||||||||
| HL_98995.6_Sequence_2 HL_98995.6_HL_5J7L_198_U_2701_A_2706 | U | G | C | C | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_98995.6_Instance_3 HL_98995.6_HL_4WF9_061_U2728_A2733 | U | G | C | C | A | A | ||||||||||||
| HL_98995.6_Sequence_3 HL_98995.6_HL_4WF9_061_U_2728_A_2733 | U | G | C | C | A | A | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_98995.6_Instance_4 HL_98995.6_HL_4V9F_067_C2737_G2742 | C | G | A | G | A | G | ||||||||||||
| HL_98995.6_Sequence_4 HL_98995.6_HL_4V9F_067_C_2737_G_2742 | C | G | A | G | A | G | true | 83 | 0 | 0 | 1.59 | |||||||
| HL_98995.6_Instance_5 HL_98995.6_HL_5TBW_066_U3068_A3073 | U | G | A | U | C | A | ||||||||||||
| HL_98995.6_Sequence_5 HL_98995.6_HL_5TBW_066_U_3068_A_3073 | U | G | A | U | C | A | true | 74 | 0 | 0 | 2.46 | |||||||
| HL_98995.6_Instance_6 HL_98995.6_HL_6UFM_005_G50_C55 | G | G | A | A | A | C | ||||||||||||
| HL_98995.6_Sequence_6 HL_98995.6_HL_6UFM_005_G50_C55 | G | G | A | A | A | C | true | 89 | 0 | 0 | 1.03 | |||||||
| HL_98995.6_Instance_7 HL_98995.6_HL_4GXY_003_G65_C71 | G | U | C | C | C | G | C | |||||||||||
| HL_98995.6_Sequence_7 HL_98995.6_HL_4GXY_003_G65_C71 | G | U | C | C | C | G | C | true | 41 | 0 | 0 | 5.57 | ||||||
| HL_98995.6_Instance_8 HL_98995.6_HL_1U6B_002_C70_G75 | C | G | C | C | C | G | ||||||||||||
| HL_98995.6_Sequence_8 HL_98995.6_HL_1U6B_002_C70_G75 | C | G | C | C | C | G | true | 89 | 0 | 0 | 1.04 | |||||||
| HL_98995.6_Instance_9 HL_98995.6_HL_6JXM_002_G41_C48 | G | CU | A | A | A | A | C | |||||||||||
| HL_98995.6_Sequence_9 HL_98995.6_HL_6JXM_002_G41_C48 | G | CU | A | A | A | A | C | true | 39 | 0 | 0 | 5.83 |
1 6 cWW 2 3 s35 3 4 s35 4 5 s35 5 6 s35JAR3D SCFG/MRF model for HL_98995.6:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Initial node U2680 - A2685 from junction BasepairNode | Deletion Probability [0.0000040911808346] | Pair Probability [[0.008776738,0.017176466,0.009858911,0.185786150,0.000000000],[0.018717789,0.009086084,0.207059807,0.011605009,0.000000000],[0.009854156,0.215798955,0.001936477,0.022814115,0.000000000],[0.225586024,0.011378544,0.035050500,0.009514275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.772932054,0.115234914,0.111158785,0.000643599,0.000030648] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | 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 [6] // Basepair U2680 - A2685 cWW HairpinNode | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A2681:A2684 Interaction | Interacting Bases [1,1] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.136363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.590909091,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2681 Interaction | Interacting Bases [2,2] | Pair Probability [[0.409090909,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2682 Interaction | Interacting Bases [3,3] | Pair Probability [[0.227272727,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2683 Interaction | Interacting Bases [4,4] | Pair Probability [[0.590909091,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2684Sequences of instances from HL_98995.6:
> HL_98995.6 HL_7A0S_064 U 2680 A 2685 UACCAA > HL_98995.6 HL_5J7L_198 U 2701 A 2706 UGCCAA > HL_98995.6 HL_4WF9_061 U 2728 A 2733 UGCCAA > HL_98995.6 HL_4V9F_067 C 2737 G 2742 CGAGAG > HL_98995.6 HL_5TBW_066 U 3068 A 3073 UGAUCA > HL_98995.6 HL_6UFM_005 G 50 C 55 GGAAAC > HL_98995.6 HL_4GXY_003 G 65 C 71 GUCCCGC > HL_98995.6 HL_1U6B_002 C 70 G 75 CGCCCG > HL_98995.6 HL_6JXM_002 G 41 C 48 GCUAAAAC