| 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 | 15 7 I | 16 7 7 | 17 6 I | 18 6 8 | 19 5 I | 20 5 9 | 21 4 I | 22 4 10 | 23 3 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_92321.4_Instance_1 IL_92321.4_IL_1FJG_053_A1329_U1308 | A | U | G | A | A | G | C | G | G | A | U | U | ||||||||||||||||||||
| IL_92321.4_Sequence_1 IL_92321.4_IL_1FJG_053_A_1329_U_1308 | A | U | G | A | A | G | * | C | G | G | A | U | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_92321.4_Instance_2 IL_92321.4_IL_2AW7_059_A1329_U1308 | A | U | G | A | A | G | C | G | G | A | U | U | ||||||||||||||||||||
| IL_92321.4_Sequence_2 IL_92321.4_IL_2AW7_059_A_1329_U_1308 | A | U | G | A | A | G | * | C | G | G | A | U | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| IL_92321.4_Instance_3 IL_92321.4_IL_4BPP_078_U1538_A1517 | U | U | G | A | A | C | G | G | G | A | U | A | ||||||||||||||||||||
| IL_92321.4_Sequence_3 IL_92321.4_IL_4BPP_078_U_1538_A_1517 | U | U | G | A | A | C | * | G | G | G | A | U | A | true | 99 | 0 | 0 | 0.10 | ||||||||||||||
| IL_92321.4_Instance_4 IL_92321.4_IL_3U5F_079_U1566_A1545 | U | U | C | A | A | C | G | G | G | A | U | A | ||||||||||||||||||||
| IL_92321.4_Sequence_4 IL_92321.4_IL_3U5F_079_U_1566_A_1545 | U | U | C | A | A | C | * | G | G | G | A | U | A | true | 97 | 0 | 0 | 0.51 | ||||||||||||||
| IL_92321.4_Instance_5 IL_92321.4_IL_4A1B_037_G858_C886 | G | U | G | A | A | G | U | G | G | A | A | G | C | |||||||||||||||||||
| IL_92321.4_Sequence_5 IL_92321.4_IL_4A1B_037_G858_C886 | G | U | G | A | A | G | * | U | G | G | A | A | G | C | true | 65 | 0 | 0 | 5.66 | |||||||||||||
| IL_92321.4_Instance_6 IL_92321.4_IL_3U5H_027_C758_G773 | C | U | G | A | U | G | C | G | G | A | U | G | ||||||||||||||||||||
| IL_92321.4_Sequence_6 IL_92321.4_IL_3U5H_027_C758_G773 | C | U | G | A | U | G | * | C | G | G | A | U | G | true | 98 | 0 | 0 | 0.30 | ||||||||||||||
| IL_92321.4_Instance_7 IL_92321.4_IL_4A1B_017_G457_C521 | G | G | G | A | A | G | C | A | G | A | A | C | ||||||||||||||||||||
| IL_92321.4_Sequence_7 IL_92321.4_IL_4A1B_017_G457_C521 | G | G | G | A | A | G | * | C | A | G | A | A | C | true | 74 | 0 | 0 | 4.25 |
1 2 s35 1 12 cWW 2 3 s35 2 11 cWW 2 12 s55 3 9 s33 3 10 tSH 4 5 s35 4 9 tHS 4 10 s55 5 6 s35 5 8 tHS 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 10 11 s35 11 12 s35 8 4 6BPh 9 4 6BPh 5 8 6BRJAR3D SCFG/MRF model for IL_92321.4:
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 [12] // Initial node A1329 - U1308 from junction BasepairNode | Deletion Probability [0.0000111424121612] | Pair Probability [[0.009145256,0.020139538,0.010148883,0.212554478,0.000000000],[0.019656953,0.008586697,0.200536528,0.011134298,0.000000000],[0.010128663,0.210775841,0.002049900,0.024757579,0.000000000],[0.212408170,0.011224014,0.024244846,0.012508357,0.000000000],[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 [0.850913138,0.147720949,0.001315324,0.000050589] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [12] // Basepair A1329 - U1308 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014910173,0.157123927,0.014352410,0.034555578,0.000000000],[0.018417960,0.018747039,0.021674633,0.015823830,0.000000000],[0.041393014,0.022076413,0.004517751,0.046000453,0.000000000],[0.056336058,0.017176575,0.018390073,0.498504113,0.000000000],[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 [11] // Basepair U1330 - U1307 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.111467105,0.123315345,0.001308267,0.006561247,0.000000000],[0.122253852,0.111144321,0.001308267,0.001308267,0.000000000],[0.183540869,0.001308267,0.006770963,0.094042494,0.000000000],[0.118679724,0.114374477,0.001308267,0.001308267,0.000000000],[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 [10] // Basepair G1331 - A1306 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.051645759,0.052105251,0.389908136,0.056137112,0.000000000],[0.060199743,0.054613902,0.003091666,0.054080947,0.000000000],[0.000622266,0.000622266,0.014978472,0.000622266,0.000000000],[0.002963149,0.000622266,0.257164535,0.000622266,0.000000000],[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 [4] | Right Index [9] // Basepair A1332 - G1305 tHS BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.063824391,0.039175388,0.368475929,0.055855887,0.000000000],[0.073443977,0.040643600,0.003285515,0.040806707,0.000000000],[0.000816114,0.000816114,0.016634154,0.000816114,0.000000000],[0.004334704,0.000816114,0.289439177,0.000816114,0.000000000],[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 [5] | Right Index [8] // Basepair A1333 - G1304 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010532611,0.058255416,0.011725921,0.163876120,0.000000000],[0.016999615,0.008485582,0.195963150,0.013119307,0.000000000],[0.011638528,0.217272232,0.002226781,0.077875731,0.000000000],[0.162652665,0.013525563,0.022530856,0.013319923,0.000000000],[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 [6] | Right Index [7] // Basepair G1334 - C1303 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_92321.4:
> IL_92321.4 IL_1FJG_053 A 1329 U 1308 AUGAAG*CGGAUU > IL_92321.4 IL_2AW7_059 A 1329 U 1308 AUGAAG*CGGAUU > IL_92321.4 IL_4BPP_078 U 1538 A 1517 UUGAAC*GGGAUA > IL_92321.4 IL_3U5F_079 U 1566 A 1545 UUCAAC*GGGAUA > IL_92321.4 IL_4A1B_037 G 858 C 886 GUGAAG*UGGAAGC > IL_92321.4 IL_3U5H_027 C 758 G 773 CUGAUG*CGGAUG > IL_92321.4 IL_4A1B_017 G 457 C 521 GGGAAG*CAGAAC