| 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 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 6 | 13 7 I | 14 8 7 | 15 9 I | 16 10 8 | 17 10 I | 18 11 9 | 19 11 I | 20 12 | 21 11 I | 22 11 10 | 23 10 I | 24 10 11 | 25 7 I | 26 7 12 | 27 6 I | 28 6 13 | 29 5 I | 30 5 14 | 31 4 I | 32 4 15 | 33 3 I | 34 3 16 | 35 2 I | 36 2 17 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_60797.1_Instance_1 IL_60797.1,IL_2P7E_001,G19_C45 | G | A | G | A | A | A | C | A | C | G | G | U | A | C | A | U | U | A | C | C | ||||||||||||||||||||||
| IL_60797.1_Sequence_1 IL_60797.12P7E_G19_C45 | G | A | G | A | A | A | C | A | C | * | G | G | U | A | C | A | U | U | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_60797.1_Instance_2 IL_60797.1,IL_3BBM_002,G19_C45 | G | A | G | A | A | A | C | A | C | G | G | U | C | C | A | U | U | A | C | C | ||||||||||||||||||||||
| IL_60797.1_Sequence_2 IL_60797.13BBM_G19_C45 | G | A | G | A | A | A | C | A | C | * | G | G | U | C | C | A | U | U | A | C | C | true | 91 | 0 | 0 | 2.13 | ||||||||||||||||
| IL_60797.1_Instance_3 IL_60797.1,IL_3GS5_002,G31_C58 | G | A | G | A | A | A | C | A | C | G | G | U | A | C | A | U | U | A | C | C | ||||||||||||||||||||||
| IL_60797.1_Sequence_3 IL_60797.13GS5_G31_C58 | G | A | G | A | A | A | C | A | C | * | G | G | U | A | C | A | U | U | A | C | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_60797.1_Instance_4 IL_60797.1,IL_1M5K_003,G19_C64 | G | A | G | A | A | A | C | A | C | G | G | U | A | U | A | U | U | A | C | C | ||||||||||||||||||||||
| IL_60797.1_Sequence_4 IL_60797.11M5K_G19_C64 | G | A | G | A | A | A | C | A | C | * | G | G | U | A | U | A | U | U | A | C | C | true | 97 | 0 | 0 | 0.85 |
1 2 s35 1 17 cWW 2 3 s35 2 16 cWW 2 17 s55 3 14 s33 3 15 tSH 4 5 s35 4 14 tHW 4 15 s55 5 6 s35 5 13 tHW 6 7 s35 6 12 tWH 7 8 s35 8 9 s35 8 11 cWW 9 10 cWW 10 11 s35 12 13 s35 13 14 s35 15 16 s35 16 17 s35 16 15 7BPh 15 3 6BR 3 14 6BRJAR3D SCFG/MRF model for IL_60797.1:
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 [17] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [17] // Basepair G19 - C45 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.004305574,0.687018922,0.003757817,0.009990928,0.000000000],[0.003774127,0.025319498,0.007582041,0.003734291,0.000000000],[0.003669581,0.062928002,0.000926511,0.084782900,0.000000000],[0.007951770,0.028683864,0.003918850,0.061655324,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [16] // Basepair A20 - C44 cWW BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.068032455,0.072021522,0.000816684,0.003849035,0.000000000],[0.068537887,0.071854750,0.000816684,0.000816684,0.000000000],[0.314062643,0.002756011,0.013473263,0.233919797,0.000000000],[0.075942388,0.071466829,0.000816684,0.000816684,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [3] | Right Index [15] // Basepair G21 - A43 tSH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.018414538,0.040981170,0.004075167,0.445978203,0.000000000],[0.004075167,0.328380556,0.009768444,0.004075167,0.000000000],[0.019126511,0.004075167,0.030991298,0.023643628,0.000000000],[0.004075167,0.004075167,0.018124938,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [14] // Basepair A22 - U41 tHW BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.393085105,0.030353665,0.003546236,0.016024447,0.000000000],[0.003546236,0.015048971,0.008784509,0.003546236,0.000000000],[0.312841705,0.003546236,0.130350480,0.016997105,0.000000000],[0.003546236,0.003546236,0.037957794,0.017278804,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.583333333,0.083333333,0.250000000,0.000000000] | Left Index [5] | Right Index [13] // Basepair A23 - A40 tHW BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.372030251,0.044064595,0.302750037,0.003431841,0.000000000],[0.029374515,0.014563521,0.003431841,0.003431841,0.000000000],[0.003431841,0.008501137,0.126145626,0.036733349,0.000000000],[0.015507529,0.003431841,0.016448812,0.016721423,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Left Index [6] | Right Index [12] // Basepair A24 - A38 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [11] // Fixed node on left for 2P7E|1|C|C|25 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.029212090,0.014309292,0.391265048,0.017136517,0.000000000],[0.013973300,0.009516777,0.018509117,0.041591637,0.000000000],[0.338959260,0.018716979,0.003528035,0.015569366,0.000000000],[0.017103160,0.043944969,0.015235818,0.011428634,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [11] // Basepair A26 - G36 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [9] | Right Index [10] // Basepair C27 - G35 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_60797.1:
> IL_60797.1 2P7E G 19 C 45 GAGAAACAC*GGUACAUUACC > IL_60797.1 3BBM G 19 C 45 GAGAAACAC*GGUCCAUUACC > IL_60797.1 3GS5 G 31 C 58 GAGAAACAC*GGUACAUUACC > IL_60797.1 1M5K G 19 C 64 GAGAAACAC*GGUAUAUUACC