| 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 4 I | 10 4 5 | 11 5 I | 12 6 6 | 13 6 I | 14 7 7 | 15 7 I | 16 8 8 | 17 8 I | 18 9 | 19 8 I | 20 8 9 | 21 7 I | 22 7 10 | 23 6 I | 24 6 11 | 25 5 I | 26 4 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_64900.1_Instance_1 IL_64900.1,IL_6HCT_003,C2_G18 | C | C | G | A | U | G | A | A | U | A | U | G | A | A | G | |||||||||||||||||||||
| IL_64900.1_Sequence_1 IL_64900.16HCT_C2_G18 | C | C | G | A | U | G | A | A | U | * | A | U | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_64900.1_Instance_2 IL_64900.1,IL_6HCT_002,C2_G18 | C | C | G | A | U | G | A | A | U | A | U | G | A | A | G | |||||||||||||||||||||
| IL_64900.1_Sequence_2 IL_64900.16HCT_C2_G18 | C | C | G | A | U | G | A | A | U | * | A | U | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| IL_64900.1_Instance_3 IL_64900.1,IL_6HCT_001,C2_G18 | C | C | G | A | U | G | A | A | U | A | U | G | A | A | G | |||||||||||||||||||||
| IL_64900.1_Sequence_3 IL_64900.16HCT_C2_G18 | C | C | G | A | U | G | A | A | U | * | A | U | G | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 3 s35 2 13 cWW 2 14 s55 3 12 tSS 3 13 s55 4 5 s35 4 12 s33 5 11 s33 5 12 tSH 6 7 s35 6 11 tHS 6 12 s55 7 8 s35 7 10 tHS 8 9 cWW 9 10 s35 10 11 s35 13 14 s35 11 6 6BPh 11 5 6BR 12 5 6BR 5 11 6BR 6 11 6BR 4 12 6BRJAR3D SCFG/MRF model for IL_64900.1:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [14] // Basepair C2 - G18 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.011060734,0.014482797,0.014081613,0.030514044,0.000000000],[0.384664447,0.040594609,0.034497041,0.015724453,0.000000000],[0.014420209,0.029095250,0.003555382,0.015038155,0.000000000],[0.038339089,0.014329933,0.325345055,0.014257188,0.000000000],[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 [2] | Right Index [13] // Basepair C3 - A17 cWW ClusterNode | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.392931951529007] // Cluster node 6HCT|1|E|G|4:6HCT|1|E|G|7 and 6HCT|1|F|A|16:6HCT|1|F|A|16 Interaction | Interacting Bases [1,4] | Pair Probability [[0.046690699,0.007676303,0.008842876,0.005613701,0.000000000],[0.005638926,0.001127785,0.098122071,0.001127785,0.000000000],[0.639250862,0.001127785,0.109634108,0.066124819,0.000000000],[0.005638926,0.001127785,0.001127785,0.001127785,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6HCT|1|E|G|4 - 6HCT|1|F|A|16 tSS Interaction | Interacting Bases [3,4] | Pair Probability [[0.054373565,0.057561746,0.000652718,0.003076264,0.000000000],[0.054777521,0.057428457,0.000652718,0.000652718,0.000000000],[0.355485412,0.003263592,0.015954665,0.277001348,0.000000000],[0.060695419,0.057118419,0.000652718,0.000652718,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6HCT|1|E|G|7 - 6HCT|1|F|A|16 tSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6HCT|1|E|A|5 Insertion | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node 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 [6] | Right Index [11] // 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 [6] | Right Index [11] // Basepair A8 - G15 tHS BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.113545609,0.113984241,0.117255805,0.201455165,0.000000000],[0.103712991,0.107248177,0.001260969,0.116551990,0.000000000],[0.001260969,0.001260969,0.007793409,0.001260969,0.000000000],[0.006202964,0.001260969,0.104683837,0.001260969,0.000000000],[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 [7] | Right Index [10] // Basepair A9 - U14 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008946623,0.017374423,0.009813872,0.194415132,0.000000000],[0.021829934,0.009736222,0.195069241,0.010937668,0.000000000],[0.009833013,0.192572728,0.002024403,0.022823782,0.000000000],[0.231566497,0.010273839,0.052777129,0.010005495,0.000000000],[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 [8] | Right Index [9] // Basepair U10 - A13 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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_64900.1:
> IL_64900.1 6HCT C 2 G 18 CCGAUGAAU*AUGAAG > IL_64900.1 6HCT C 2 G 18 CCGAUGAAU*AUGAAG > IL_64900.1 6HCT C 2 G 18 CCGAUGAAU*AUGAAG