| 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 2 2 | 5 3 I | 6 4 3 | 7 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 9 I | 12 10 6 | 13 11 I | 14 12 7 | 15 13 I | 16 14 8 | 17 15 I | 18 16 9 | 19 16 I | 20 17 | 21 16 I | 22 16 10 | 23 3 I | 24 2 11 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_04650.2_Instance_1 IL_04650.2,IL_6TFF_001,A7_U46 | A | A | C | A | A | C | C | C | C | G | C | U | ||||||||||||||||||
| IL_04650.2_Sequence_1 IL_04650.26TFF_A7_U46 | A | A | C | A | A | C | C | C | C | G | * | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_04650.2_Instance_2 IL_04650.2,IL_7D7W_001,A7_U46 | A | A | C | A | A | C | C | C | C | G | C | U | ||||||||||||||||||
| IL_04650.2_Sequence_2 IL_04650.27D7W_A7_U46 | A | A | C | A | A | C | C | C | C | G | * | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_04650.2_Instance_3 IL_04650.2,IL_7D7V_001,A6_U53 | A | A | C | A | U | C | C | C | C | G | C | U | ||||||||||||||||||
| IL_04650.2_Sequence_3 IL_04650.27D7V_A6_U53 | A | A | C | A | U | C | C | C | C | G | * | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_04650.2_Instance_4 IL_04650.2,IL_7D81_001,A7_U44 | A | A | C | A | U | C | C | C | C | G | C | U | ||||||||||||||||||
| IL_04650.2_Sequence_4 IL_04650.27D81_A7_U44 | A | A | C | A | U | C | C | C | C | G | * | C | U | true | 100 | 0 | 0 | 0.00 |
1 2 cSH 1 9 s35 1 11 cWW 2 3 s35 4 8 s33 5 6 s35 6 7 s35 7 8 s35 9 10 cWW 9 11 s55 10 11 s35 3 2 7BPh 4 2 7BPh 3 1 7BR 3 9 6BRJAR3D SCFG/MRF model for IL_04650.2:
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 ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [1] | Right Index [11] | Norm Constant [0.250562202458820] // Cluster node 6TFF|1|A|A|7:6TFF|1|A|A|8 and 6TFF|1|A|U|46:6TFF|1|A|U|46 Interaction | Interacting Bases [1,3] | Pair Probability [[0.009104408,0.021587263,0.009723705,0.238651416,0.000000000],[0.017181282,0.009396023,0.190432013,0.010159631,0.000000000],[0.009704777,0.192900773,0.002001899,0.052190437,0.000000000],[0.192253936,0.010816081,0.022570064,0.011326291,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6TFF|1|A|A|7 - 6TFF|1|A|U|46 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.154827561,0.105669301,0.005293494,0.013312014,0.000000000],[0.106944893,0.099938633,0.001163660,0.008218214,0.000000000],[0.008244983,0.001163660,0.096686550,0.093806178,0.000000000],[0.111977258,0.097773375,0.001163660,0.093816564,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6TFF|1|A|A|7 - 6TFF|1|A|A|8 cSH 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [10] // Initial node 6TFF|1|A|C|9 - 6TFF|1|A|C|45 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.003521127,0.989436620,0.003521127,0.003521127,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left for 6TFF|1|A|C|9 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 [4] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.950000000,0.016666667,0.016666667,0.016666667,0.000000000] | Position [1] | Left Index [4] | Right Index [10] // Fixed node on left for 6TFF|1|A|A|10 InitialNode | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [10] // Fixed node on left for 6TFF|1|A|A|11 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 [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left for 6TFF|1|A|C|12 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 [7] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [10] // Fixed node on left for 6TFF|1|A|C|13 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 6TFF|1|A|C|14 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 [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | 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 [0.999900000,0.000100000] | 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 G16 - C45 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_04650.2:
> IL_04650.2 6TFF A 7 U 46 AACAACCCCG*CU > IL_04650.2 7D7W A 7 U 46 AACAACCCCG*CU > IL_04650.2 7D7V A 6 U 53 AACAUCCCCG*CU > IL_04650.2 7D81 A 7 U 44 AACAUCCCCG*CU