| 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 4 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 4 9 | 21 3 I | 22 3 10 | 23 2 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_88269.4_Instance_1 IL_88269.4,IL_4LFB_018,C483_G450 | C | G | G | U | A | C | G | G | A | C | G | |||||||||||||||||||
| IL_88269.4_Sequence_1 IL_88269.44LFB_C483_G450 | C | G | G | U | A | C | * | G | G | A | C | G | true | 97 | 0 | 0 | 0.57 | |||||||||||||
| IL_88269.4_Instance_2 IL_88269.4,IL_5J7L_309,U1712_A1746 | U | A | U | G | U | A | G | U | G | A | A | A | ||||||||||||||||||
| IL_88269.4_Sequence_2 IL_88269.45J7L_U_1712_A_1746 | U | A | U | G | U | A | G | * | U | G | A | A | A | true | 97 | 0 | 0 | 0.56 | ||||||||||||
| IL_88269.4_Instance_3 IL_88269.4,IL_5J7L_022,C483_G450 | C | G | U | U | A | C | G | G | A | G | G | |||||||||||||||||||
| IL_88269.4_Sequence_3 IL_88269.45J7L_C483_G450 | C | G | U | U | A | C | * | G | G | A | G | G | true | 100 | 0 | 0 | 0.00 |
1 2 s33 1 11 cWW 2 4 s55 2 10 tWW 3 4 cSH 3 8 s33 4 5 s35 4 8 s33 4 9 tWH 4 10 s55 5 6 s35 5 8 tHS 5 9 s55 6 7 cWW 6 8 s55 7 8 s35 9 10 s35 10 11 s35 8 4 6BPh 3 9 6BPh 5 8 6BRJAR3D SCFG/MRF model for IL_88269.4:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009278201,0.017081703,0.010509311,0.196044617,0.000000000],[0.020663004,0.009657695,0.222404933,0.012750390,0.000000000],[0.010596976,0.198258342,0.002054445,0.023100179,0.000000000],[0.210129795,0.012196624,0.035266599,0.010007185,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair C483 - G450 cWW BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.358978558,0.024629521,0.003627646,0.017351906,0.000000000],[0.034558768,0.013457670,0.011257965,0.013444602,0.000000000],[0.003627646,0.066769925,0.358662117,0.019201563,0.000000000],[0.017903732,0.013510193,0.025874138,0.017144051,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair G484 - C449 tWW ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [9] | Norm Constant [0.277797291791425] // Cluster node 4LFB|1|A|G|485:4LFB|1|A|U|486 and 4LFB|1|A|A|448:4LFB|1|A|A|448 Interaction | Interacting Bases [2,3] | Pair Probability [[0.018593320,0.004114731,0.019312206,0.004114731,0.000000000],[0.041379046,0.331568716,0.004114731,0.004114731,0.000000000],[0.004114731,0.009863283,0.031292185,0.018300908,0.000000000],[0.440599350,0.004114731,0.023873178,0.040529420,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|U|486 - 4LFB|1|A|A|448 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.029337147,0.029893207,0.001643621,0.029214219,0.000000000],[0.021902097,0.033006844,0.000363926,0.029275462,0.000000000],[0.179423483,0.002547479,0.218866065,0.274165405,0.000000000],[0.029792340,0.029613492,0.000363926,0.090591288,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4LFB|1|A|G|485 - 4LFB|1|A|U|486 cSH InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.043273743,0.043595236,0.392756919,0.048305054,0.000000000],[0.045811089,0.045705009,0.003636307,0.045458262,0.000000000],[0.000519472,0.000519472,0.017776750,0.000519472,0.000000000],[0.002448275,0.000519472,0.308635994,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A487 - G447 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011524674,0.109291750,0.011964229,0.159160108,0.000000000],[0.017916203,0.010634031,0.169407889,0.013859534,0.000000000],[0.011944263,0.147787249,0.002450608,0.132297401,0.000000000],[0.145015364,0.013965966,0.022426943,0.020353790,0.000000000],[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 C488 - G446 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_88269.4:
> IL_88269.4 4LFB C 483 G 450 CGGUAC*GGACG > IL_88269.4 5J7L U 1712 A 1746 UAUGUAG*UGAAA > IL_88269.4 5J7L C 483 G 450 CGUUAC*GGAGG