| 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 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 5 5 | 11 5 I | 12 6 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 | 17 8 I | 18 8 8 | 19 5 I | 20 5 9 | 21 4 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_74051.1_Instance_1 IL_74051.1,IL_5XTM_003,C16_G33 | C | G | G | U | G | A | A | G | C | G | A | G | ||||||||||||||||||
| IL_74051.1_Sequence_1 IL_74051.15XTM_C16_G33 | C | G | G | U | G | A | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_74051.1_Instance_2 IL_74051.1,IL_5DCV_008,C18_G35 | C | G | G | U | G | A | A | G | C | G | A | G | ||||||||||||||||||
| IL_74051.1_Sequence_2 IL_74051.15DCV_C18_G35 | C | G | G | U | G | A | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_74051.1_Instance_3 IL_74051.1,IL_5XTM_007,C16_G33 | C | G | G | U | G | A | A | G | C | G | A | G | ||||||||||||||||||
| IL_74051.1_Sequence_3 IL_74051.15XTM_C16_G33 | C | G | G | U | G | A | A | G | * | C | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 11 cWW 2 10 tSS 2 11 s55 3 4 s35 3 10 s33 4 9 s33 4 10 tSH 5 6 s35 5 9 tHS 5 10 s55 6 7 s35 7 8 cWW 9 4 6BR 10 4 6BR 11 5 2BR 4 9 6BR 3 10 6BRJAR3D SCFG/MRF model for IL_74051.1:
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 [11] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.006272399,0.011247917,0.021578432,0.130747736,0.000000000],[0.013336193,0.006388256,0.440434150,0.009070380,0.000000000],[0.007291875,0.133564998,0.004113079,0.015434193,0.000000000],[0.132442750,0.008739137,0.052691487,0.006647016,0.000000000],[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 C16 - G33 cWW ClusterNode | Deletion Probability [0.0000000000030984] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [10] | Norm Constant [0.332341503555430] // Cluster node 5XTM|1|B|G|17:5XTM|1|B|G|20 and 5XTM|1|B|A|32:5XTM|1|B|A|32 Interaction | Interacting Bases [1,4] | Pair Probability [[0.039758362,0.011189224,0.012889659,0.008182709,0.000000000],[0.004801694,0.001643896,0.143025861,0.001643896,0.000000000],[0.509295606,0.001643896,0.159806172,0.096385645,0.000000000],[0.004801694,0.001643896,0.001643896,0.001643896,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5XTM|1|B|G|17 - 5XTM|1|B|A|32 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 5XTM|1|B|G|20 - 5XTM|1|B|A|32 tSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.911764706,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5XTM|1|B|G|18 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 3, 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 [5] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.054373565,0.054777521,0.355485412,0.060695419,0.000000000],[0.057561746,0.057428457,0.003263592,0.057118419,0.000000000],[0.000652718,0.000652718,0.015954665,0.000652718,0.000000000],[0.003076264,0.000652718,0.277001348,0.000652718,0.000000000],[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 [9] // Basepair A21 - G31 tHS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 5XTM|1|B|A|21 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[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 [7] | Right Index [8] // Basepair G23 - C30 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_74051.1:
> IL_74051.1 5XTM C 16 G 33 CGGUGAAG*CGAG > IL_74051.1 5DCV C 18 G 35 CGGUGAAG*CGAG > IL_74051.1 5XTM C 16 G 33 CGGUGAAG*CGAG