| 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 6 3 | 7 6 I | 8 7 4 | 9 6 I | 10 6 5 | 11 5 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_78457.3_Instance_1 HL_78457.3_HL_4V9F_037_G1498_C1507 | G | U | U | A | A | U | A | UU | C | |||||||||||||
| HL_78457.3_Sequence_1 HL_78457.3_HL_4V9F_037_G_1498_C_1507 | G | U | U | A | A | U | A | UU | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_78457.3_Instance_2 HL_78457.3_HL_5J7L_168_G1389_C1398 | G | U | U | A | A | U | A | UU | C | |||||||||||||
| HL_78457.3_Sequence_2 HL_78457.3_HL_5J7L_168_G_1389_C_1398 | G | U | U | A | A | U | A | UU | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_78457.3_Instance_3 HL_78457.3_HL_4Y4O_137_G1389_C1398 | G | U | U | A | A | U | A | UU | C | |||||||||||||
| HL_78457.3_Sequence_3 HL_78457.3_HL_4Y4O_137_G_1389_C_1398 | G | U | U | A | A | U | A | UU | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_78457.3_Instance_4 HL_78457.3_HL_4WF9_035_G1426_C1435 | G | U | U | G | A | U | A | UU | C | |||||||||||||
| HL_78457.3_Sequence_4 HL_78457.3_HL_4WF9_035_G_1426_C_1435 | G | U | U | G | A | U | A | UU | C | true | 92 | 0 | 0 | 1.30 | ||||||||
| HL_78457.3_Instance_5 HL_78457.3_HL_5TBW_035_G1599_C1608 | G | U | U | A | A | G | A | UU | C | |||||||||||||
| HL_78457.3_Sequence_5 HL_78457.3_HL_5TBW_035_G_1599_C_1608 | G | U | U | A | A | G | A | UU | C | true | 93 | 0 | 0 | 1.10 | ||||||||
| HL_78457.3_Instance_6 HL_78457.3_HL_5X2G_003_G73_C81 | G | U | U | A | C | A | A | U | C | |||||||||||||
| HL_78457.3_Sequence_6 HL_78457.3_HL_5X2G_003_G73_C81 | G | U | U | A | C | A | A | U | C | true | 84 | 0 | 0 | 2.67 |
1 2 s35 1 8 cWW 2 7 tWH 3 5 tSH 3 6 s55 4 5 s35 6 7 s35 7 8 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_78457.3:
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 [8] // Initial node G1498 - C1507 from junction BasepairNode | Deletion Probability [0.0000000014888525] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.001365561,0.170695070,0.820701898,0.006896081,0.000341390] | Right Letter Distribution [0.038461538,0.038461538,0.038461538,0.884615385,0.000000000] | Left Index [1] | Right Index [8] // Basepair G1498 - C1507 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | 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 U1499 - A1504 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.062500000,0.187500000,0.562500000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043836710,0.040040618,0.000486824,0.002394787,0.000000000],[0.044006054,0.041405452,0.000486824,0.000486824,0.000000000],[0.045269111,0.000486824,0.003008812,0.040415433,0.000000000],[0.387946550,0.342913643,0.003407767,0.003407767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // Basepair U1500 - A1502 tSH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1501:A1501 Interaction | Interacting Bases [1,1] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1501Sequences of instances from HL_78457.3:
> HL_78457.3 HL_4V9F_037 G 1498 C 1507 GUUAAUAUUC > HL_78457.3 HL_5J7L_168 G 1389 C 1398 GUUAAUAUUC > HL_78457.3 HL_4Y4O_137 G 1389 C 1398 GUUAAUAUUC > HL_78457.3 HL_4WF9_035 G 1426 C 1435 GUUGAUAUUC > HL_78457.3 HL_5TBW_035 G 1599 C 1608 GUUAAGAUUC > HL_78457.3 HL_5X2G_003 G 73 C 81 GUUACAAUC