| 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 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_32617.1_Instance_1 HL_32617.1_HL_3AM1_005_U18_A23 | U | U | G | G | U | A | ||||||||||
| HL_32617.1_Sequence_1 HL_32617.1_HL_3AM1_005_U18_A23 | U | U | G | G | U | A | true | 99 | 0 | 0 | 0.14 | |||||
| HL_32617.1_Instance_2 HL_32617.1_HL_3AM1_001_U18_A23 | U | U | G | G | U | A | ||||||||||
| HL_32617.1_Sequence_2 HL_32617.1_HL_3AM1_001_U18_A23 | U | U | G | G | U | A | true | 99 | 0 | 0 | 0.14 | |||||
| HL_32617.1_Instance_3 HL_32617.1_HL_3W3S_005_C15_G20A | C | U | G | G | U | G | ||||||||||
| HL_32617.1_Sequence_3 HL_32617.1_HL_3W3S_005_C15_G20A | C | U | G | G | U | G | true | 99 | 0 | 0 | 0.13 | |||||
| HL_32617.1_Instance_4 HL_32617.1_HL_3W3S_001_C15_G20A | C | U | G | G | U | G | ||||||||||
| HL_32617.1_Sequence_4 HL_32617.1_HL_3W3S_001_C15_G20A | C | U | G | G | U | G | true | 99 | 0 | 0 | 0.13 | |||||
| HL_32617.1_Instance_5 HL_32617.1_HL_4ZDO_001_G15_C20A | G | U | G | G | U | C | ||||||||||
| HL_32617.1_Sequence_5 HL_32617.1_HL_4ZDO_001_G15_C20A | G | U | G | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_32617.1_Instance_6 HL_32617.1_HL_3RG5_009_G15_C20A | G | U | G | G | U | C | ||||||||||
| HL_32617.1_Sequence_6 HL_32617.1_HL_3RG5_009_G15_C20A | G | U | G | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_32617.1_Instance_7 HL_32617.1_HL_3RG5_005_G15_C20A | G | U | G | G | U | C | ||||||||||
| HL_32617.1_Sequence_7 HL_32617.1_HL_3RG5_005_G15_C20A | G | U | G | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_32617.1_Instance_8 HL_32617.1_HL_3ADD_001_G15_C20A | G | U | G | G | U | C | ||||||||||
| HL_32617.1_Sequence_8 HL_32617.1_HL_3ADD_001_G15_C20A | G | U | G | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_32617.1_Instance_9 HL_32617.1_HL_5F9R_004_G105_C109 | G | A | G | U | C | |||||||||||
| HL_32617.1_Sequence_9 HL_32617.1_HL_5F9R_004_G105_C109 | G | A | G | U | C | true | 62 | 0 | 0 | 3.61 |
1 2 s35 1 5 cWW 3 4 cSHJAR3D SCFG/MRF model for HL_32617.1:
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 [5] // Initial node U18 - A23 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008922170,0.017743555,0.010103043,0.186825820,0.000000000],[0.017689168,0.009026441,0.208316861,0.012070633,0.000000000],[0.010068672,0.237156075,0.001945841,0.023587200,0.000000000],[0.206056080,0.012088270,0.028846556,0.009553614,0.000000000],[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 [1] | Right Index [5] // Basepair U18 - A23 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U19:U22 Interaction | Interacting Bases [2,3] | Pair Probability [[0.074204418,0.075610898,0.004157321,0.073893488,0.000000000],[0.055398446,0.083486430,0.000920502,0.074048396,0.000000000],[0.064832555,0.000920502,0.079084665,0.174618960,0.000000000],[0.075355769,0.074903398,0.000920502,0.087643751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G21 - U22 cSH Interaction | Interacting Bases [1,1] | Pair Probability [[0.136363636,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.772727273,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U19 Insertion | Location [1] | Length Distribution [0.114812666,0.880026871,0.004916181,0.000244282] | Letter Distribution [0.050000000,0.050000000,0.850000000,0.050000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_32617.1:
> HL_32617.1 HL_3AM1_005 U 18 A 23 UUGGUA > HL_32617.1 HL_3AM1_001 U 18 A 23 UUGGUA > HL_32617.1 HL_3W3S_005 C 15 G 20A CUGGUG > HL_32617.1 HL_3W3S_001 C 15 G 20A CUGGUG > HL_32617.1 HL_4ZDO_001 G 15 C 20A GUGGUC > HL_32617.1 HL_3RG5_009 G 15 C 20A GUGGUC > HL_32617.1 HL_3RG5_005 G 15 C 20A GUGGUC > HL_32617.1 HL_3ADD_001 G 15 C 20A GUGGUC > HL_32617.1 HL_5F9R_004 G 105 C 109 GAGUC