| 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 5 I | 8 7 I | 9 8 4 | 10 8 I | 11 8 5 | 12 8 I | 13 8 6 | 14 8 I | 15 8 7 | 16 7 I | 17 6 8 | 18 3 I | 19 3 9 | 20 2 I | 21 2 10 | 22 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_04171.2_Instance_1 HL_04171.2_HL_5SWD_004_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | ||||||||||||||||
| HL_04171.2_Sequence_1 HL_04171.2_HL_5SWD_004_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_04171.2_Instance_2 HL_04171.2_HL_3LA5_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | ||||||||||||||||
| HL_04171.2_Sequence_2 HL_04171.2_HL_3LA5_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_04171.2_Instance_3 HL_04171.2_HL_4LX6_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | ||||||||||||||||
| HL_04171.2_Sequence_3 HL_04171.2_HL_4LX6_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_04171.2_Instance_4 HL_04171.2_HL_1Y26_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | ||||||||||||||||
| HL_04171.2_Sequence_4 HL_04171.2_HL_1Y26_001_A30_U40 | A | U | G | A | U | A | U | G | G | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_04171.2_Instance_5 HL_04171.2_HL_3IVN_001_A21_U31 | A | U | G | A | U | A | U | G | G | U | U | ||||||||||||||||
| HL_04171.2_Sequence_5 HL_04171.2_HL_3IVN_001_A21_U31 | A | U | G | A | U | A | U | G | G | U | U | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_04171.2_Instance_6 HL_04171.2_HL_4ATO_003_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | ||||||||||||||||
| HL_04171.2_Sequence_6 HL_04171.2_HL_4ATO_003_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | true | 95 | 0 | 0 | 0.96 | |||||||||||
| HL_04171.2_Instance_7 HL_04171.2_HL_4ATO_001_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | ||||||||||||||||
| HL_04171.2_Sequence_7 HL_04171.2_HL_4ATO_001_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | true | 95 | 0 | 0 | 0.96 | |||||||||||
| HL_04171.2_Instance_8 HL_04171.2_HL_4ATO_002_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | ||||||||||||||||
| HL_04171.2_Sequence_8 HL_04171.2_HL_4ATO_002_U15_A25 | U | U | A | C | C | G | U | A | G | U | A | true | 95 | 0 | 0 | 0.96 | |||||||||||
| HL_04171.2_Instance_9 HL_04171.2_HL_2D6F_004_G912_C923 | G | U | A | G | U | G | GU | A | A | U | C | ||||||||||||||||
| HL_04171.2_Sequence_9 HL_04171.2_HL_2D6F_004_G912_C923 | G | U | A | G | U | G | GU | A | A | U | C | true | 61 | 0 | 0 | 7.06 |
1 2 s35 1 10 cWW 2 3 s35 2 9 cWW 2 10 s55 3 4 s35 3 9 s55 4 5 s35 4 7 cSS 5 7 cSS 6 7 s55 7 8 s35 9 10 s35JAR3D SCFG/MRF model for HL_04171.2:
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 [10] // Initial node A30 - U40 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008656101,0.019023238,0.009397950,0.234156706,0.000000000],[0.017761122,0.009039756,0.183496187,0.010211739,0.000000000],[0.009381147,0.193806354,0.001916039,0.037636721,0.000000000],[0.213861372,0.010402960,0.031027090,0.010225516,0.000000000],[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 [10] // Basepair A30 - U40 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [9] // Basepair U31 - U39 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.409090909,0.045454545,0.500000000,0.045454545,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.136363636,0.045454545,0.772727273,0.045454545,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right 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 [4] | Right Index [7] // New Initial node after Fixed node HairpinNode | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.261529643730035] // Hairpin node A33:G37 Interaction | Interacting Bases [1,4] | Pair Probability [[0.071703980,0.073208534,0.132869395,0.072674192,0.000000000],[0.099926616,0.073031471,0.003157041,0.066347042,0.000000000],[0.093619001,0.003097427,0.006610608,0.071752232,0.000000000],[0.067116411,0.034167437,0.059908779,0.070809834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A33 - G37 cSS Interaction | Interacting Bases [2,4] | Pair Probability [[0.071212161,0.071893141,0.072699428,0.066762370,0.000000000],[0.099834189,0.072423742,0.003167868,0.055492012,0.000000000],[0.069797814,0.003219472,0.007219597,0.061775210,0.000000000],[0.091529489,0.065448457,0.119896235,0.067628816,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U34 - G37 cSS Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.409090909,0.000000000,0.000000000],[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 A35 Insertion | Location [3] | Length Distribution [0.004882663,0.879489762,0.114742592,0.000854466,0.000030517] | Letter Distribution [0.041666667,0.041666667,0.125000000,0.791666667,0.000000000]// Insertion in Hairpin after nucleotide 6, position 3Sequences of instances from HL_04171.2:
> HL_04171.2 HL_5SWD_004 A 30 U 40 AUGAUAUGGUU > HL_04171.2 HL_3LA5_001 A 30 U 40 AUGAUAUGGUU > HL_04171.2 HL_4LX6_001 A 30 U 40 AUGAUAUGGUU > HL_04171.2 HL_1Y26_001 A 30 U 40 AUGAUAUGGUU > HL_04171.2 HL_3IVN_001 A 21 U 31 AUGAUAUGGUU > HL_04171.2 HL_4ATO_003 U 15 A 25 UUACCGUAGUA > HL_04171.2 HL_4ATO_001 U 15 A 25 UUACCGUAGUA > HL_04171.2 HL_4ATO_002 U 15 A 25 UUACCGUAGUA > HL_04171.2 HL_2D6F_004 G 912 C 923 GUAGUGGUAAUC