| 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_85367.2_Instance_1 HL_85367.2,HL_4WF9_049,C2275_G2283 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_1 HL_85367.24WF9_C_2275_G_2283 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_2 HL_85367.2,HL_5J7L_186,C2248_G2256 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_2 HL_85367.25J7L_C_2248_G_2256 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_3 HL_85367.2,HL_8P9A_165,C2616_G2624 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_3 HL_85367.28P9A_C_2616_G_2624 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_4 HL_85367.2,HL_7A0S_052,C2227_G2235 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_4 HL_85367.27A0S_C_2227_G_2235 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_5 HL_85367.2,HL_8CRE_053,C2588_G2596 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_5 HL_85367.28CRE_C_2588_G_2596 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_6 HL_85367.2,HL_9DFE_051,C2248_G2256 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_6 HL_85367.29DFE_C_2248_G_2256 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_7 HL_85367.2,HL_4V9F_055,C2281_G2289 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_85367.2_Sequence_7 HL_85367.24V9F_C_2281_G_2289 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_85367.2_Instance_8 HL_85367.2,HL_4V83_220,U6161_G6168 | U | U | A | A | G | U | G | G | ||||||||||||||
| HL_85367.2_Sequence_8 HL_85367.24V83_U_6161_G_6168 | U | U | A | A | G | U | G | G | true | 68 | 0 | 0 | 4.51 | |||||||||
| HL_85367.2_Instance_9 HL_85367.2,HL_4V84_034,U6185_G6192 | U | U | A | G | G | U | A | G | ||||||||||||||
| HL_85367.2_Sequence_9 HL_85367.24V84_U_6185_G_6192 | U | U | A | G | G | U | A | G | true | 74 | 0 | 0 | 3.66 | |||||||||
| HL_85367.2_Instance_10 HL_85367.2,HL_8CRE_207,U749_G757 | U | G | U | U | C | A | A | A | G | |||||||||||||
| HL_85367.2_Sequence_10 HL_85367.28CRE_U749_G757 | U | G | U | U | C | A | A | A | G | true | 43 | 0 | 0 | 8.18 | ||||||||
| HL_85367.2_Instance_11 HL_85367.2,HL_8P9A_206,U764_G772 | U | G | U | U | C | A | A | A | G | |||||||||||||
| HL_85367.2_Sequence_11 HL_85367.28P9A_U764_G772 | U | G | U | U | C | A | A | A | G | true | 43 | 0 | 0 | 8.18 |
1 2 s35 1 8 cWW 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 2 5 6BPhJAR3D SCFG/MRF model for HL_85367.2:
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 [0.0000092008008274] | Pair Probability [[0.009334599,0.014673090,0.011181964,0.128700764,0.000000000],[0.112950790,0.015019486,0.199417652,0.013422149,0.000000000],[0.011358408,0.131155648,0.002326776,0.018624939,0.000000000],[0.146553907,0.012674875,0.162166665,0.010438289,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.814448029,0.184504119,0.001006760,0.000041092] | Left Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | 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 C2275 - G2283 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U2276:G2282 Interaction | Interacting Bases [1,1] | Pair Probability [[0.006329114,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.006329114,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.006329114,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.981012658,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2276 Interaction | Interacting Bases [2,2] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.576923077,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2278 Interaction | Interacting Bases [3,3] | Pair Probability [[0.115384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.192307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2279 Interaction | Interacting Bases [4,4] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.730769231,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2280 Interaction | Interacting Bases [5,5] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.576923077,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.038461538,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2281 Interaction | Interacting Bases [6,6] | Pair Probability [[0.269230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2282 Insertion | Location [1] | Length Distribution [0.363740748,0.633163150,0.002952574,0.000143528] | Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_85367.2:
> HL_85367.2 4WF9 C 2275 G 2283 CUGGGGCGG > HL_85367.2 5J7L C 2248 G 2256 CUGGGGCGG > HL_85367.2 8P9A C 2616 G 2624 CUGGGGCGG > HL_85367.2 7A0S C 2227 G 2235 CUGGGGCGG > HL_85367.2 8CRE C 2588 G 2596 CUGGGGCGG > HL_85367.2 9DFE C 2248 G 2256 CUGGGGCGG > HL_85367.2 4V9F C 2281 G 2289 CUGGGGCGG > HL_85367.2 4V83 U 6161 G 6168 UUAAGUGG > HL_85367.2 4V84 U 6185 G 6192 UUAGGUAG > HL_85367.2 8CRE U 749 G 757 UGUUCAAAG > HL_85367.2 8P9A U 764 G 772 UGUUCAAAG