| 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 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 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_64690.6_Instance_1 HL_64690.6,HL_5J7L_201,G2819_C2827 | G | A | A | G | A | C | G | A | C | |||||||||||||
| HL_64690.6_Sequence_1 HL_64690.65J7L_G_2819_C_2827 | G | A | A | G | A | C | G | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_64690.6_Instance_2 HL_64690.6,HL_7A0S_067,G2794_C2802 | G | A | A | G | A | C | C | A | C | |||||||||||||
| HL_64690.6_Sequence_2 HL_64690.67A0S_G_2794_C_2802 | G | A | A | G | A | C | C | A | C | true | 94 | 0 | 0 | 0.79 | ||||||||
| HL_64690.6_Instance_3 HL_64690.6,HL_8CRE_069,G3268_C3276 | G | C | A | U | A | C | G | A | C | |||||||||||||
| HL_64690.6_Sequence_3 HL_64690.68CRE_G_3268_C_3276 | G | C | A | U | A | C | G | A | C | true | 91 | 0 | 0 | 1.10 | ||||||||
| HL_64690.6_Instance_4 HL_64690.6,HL_9DFE_065,G2819_C2827 | G | A | A | G | A | C | C | A | C | |||||||||||||
| HL_64690.6_Sequence_4 HL_64690.69DFE_G_2819_C_2827 | G | A | A | G | A | C | C | A | C | true | 94 | 0 | 0 | 0.79 | ||||||||
| HL_64690.6_Instance_5 HL_64690.6,HL_4WF9_064,A2839_U2847 | A | A | A | G | A | U | G | A | U | |||||||||||||
| HL_64690.6_Sequence_5 HL_64690.64WF9_A_2839_U_2847 | A | A | A | G | A | U | G | A | U | true | 91 | 0 | 0 | 1.18 | ||||||||
| HL_64690.6_Instance_6 HL_64690.6,HL_8P9A_181,G3303_C3311 | G | U | A | U | A | C | G | A | C | |||||||||||||
| HL_64690.6_Sequence_6 HL_64690.68P9A_G_3303_C_3311 | G | U | A | U | A | C | G | A | C | true | 95 | 0 | 0 | 0.59 | ||||||||
| HL_64690.6_Instance_7 HL_64690.6,HL_4V9F_069,G2836_C2844 | G | U | A | C | A | A | G | A | C | |||||||||||||
| HL_64690.6_Sequence_7 HL_64690.64V9F_G_2836_C_2844 | G | U | A | C | A | A | G | A | C | true | 75 | 0 | 0 | 3.15 | ||||||||
| HL_64690.6_Instance_8 HL_64690.6,HL_2DER_005,C31_G39 | C | C | U | U | U | C | A | C | G | |||||||||||||
| HL_64690.6_Sequence_8 HL_64690.62DER_C31_G39 | C | C | U | U | U | C | A | C | G | true | 47 | 0 | 0 | 6.75 | ||||||||
| HL_64690.6_Instance_9 HL_64690.6,HL_8CRE_203,C487_G495 | C | C | C | U | U | U | U | G | G | |||||||||||||
| HL_64690.6_Sequence_9 HL_64690.68CRE_C487_G495 | C | C | C | U | U | U | U | G | G | true | 45 | 0 | 0 | 7.03 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cSW 4 5 s35 5 6 s33 6 7 s55 7 8 s35JAR3D SCFG/MRF model for HL_64690.6:
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 [0.0000003956735078] | Pair Probability [[0.009020734,0.018491432,0.010225554,0.197330353,0.000000000],[0.016704287,0.008970478,0.208652624,0.012232111,0.000000000],[0.010172358,0.248065715,0.001950201,0.027110293,0.000000000],[0.186243259,0.012511091,0.022596004,0.009723506,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.224265942,0.771181521,0.004338660,0.000213878] | Left Letter Distribution [0.500000000,0.166666667,0.055555556,0.277777778,0.000000000] | 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 G2819 - C2827 cWW BasepairNode | Deletion Probability [0.0000132986348294] | Pair Probability [[0.264283267,0.014703421,0.019881487,0.007142341,0.000000000],[0.184023312,0.033908760,0.023917043,0.007534271,0.000000000],[0.194473311,0.002000631,0.025481599,0.005962327,0.000000000],[0.187977629,0.012170621,0.009516546,0.007023433,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A2821 - A2826 cSW HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node G2822:G2825 Interaction | Interacting Bases [1,1] | Pair Probability [[0.045454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.136363636,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.409090909,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.409090909,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2822 Interaction | Interacting Bases [2,2] | Pair Probability [[0.681818182,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.227272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2823 Interaction | Interacting Bases [3,3] | Pair Probability [[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],[0.000000000,0.000000000,0.000000000,0.227272727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2824 Interaction | Interacting Bases [4,4] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.136363636,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2825 Insertion | Location [1] | Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 1Sequences of instances from HL_64690.6:
> HL_64690.6 5J7L G 2819 C 2827 GAAGACGAC > HL_64690.6 7A0S G 2794 C 2802 GAAGACCAC > HL_64690.6 8CRE G 3268 C 3276 GCAUACGAC > HL_64690.6 9DFE G 2819 C 2827 GAAGACCAC > HL_64690.6 4WF9 A 2839 U 2847 AAAGAUGAU > HL_64690.6 8P9A G 3303 C 3311 GUAUACGAC > HL_64690.6 4V9F G 2836 C 2844 GUACAAGAC > HL_64690.6 2DER C 31 G 39 CCUUUCACG > HL_64690.6 8CRE C 487 G 495 CCCUUUUGG