| 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 3 I | 10 3 5 | 11 4 I | 12 5 | 13 4 I | 14 3 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_22373.1_Instance_1 IL_22373.1,IL_5U3G_002,G10_C29 | G | G | U | U | C | G | U | C | ||||||||||||||||
| IL_22373.1_Sequence_1 IL_22373.15U3G_G10_C29 | G | G | U | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_22373.1_Instance_2 IL_22373.1,IL_5T83_002,G16_C41 | G | G | U | U | C | G | U | C | ||||||||||||||||
| IL_22373.1_Sequence_2 IL_22373.15T83_G16_C41 | G | G | U | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_22373.1_Instance_3 IL_22373.1,IL_7MLW_003,G11_C50 | G | G | U | U | C | G | U | C | ||||||||||||||||
| IL_22373.1_Sequence_3 IL_22373.17MLW_G11_C50 | G | G | U | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_22373.1_Instance_4 IL_22373.1,IL_6DLR_002,G16_C44 | G | G | U | U | C | G | U | C | ||||||||||||||||
| IL_22373.1_Sequence_4 IL_22373.16DLR_G16_C44 | G | G | U | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 3 s35 2 7 bif 3 4 cSH 3 5 cSH 4 5 s35 4 7 cWW 5 6 cWW 6 7 s35 7 8 s35JAR3D SCFG/MRF model for IL_22373.1:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | 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 [0.995990040,0.003999960,0.000010000] | 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 [1] | Right Index [8] // Basepair G10 - C29 cWW ClusterNode | Deletion Probability [0.000000000000015625000000000002841172490091166211760239940914] | Num Left Bases [4] | Num Right Bases [2] | Left Index [2] | Right Index [7] | Norm Constant [0.007328414636428] // Cluster node 5U3G|1|B|G|11:5U3G|1|B|C|14 and 5U3G|1|B|G|27:5U3G|1|B|U|28 Interaction | Interacting Bases [4,5] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|C|14 - 5U3G|1|B|G|27 cWW Interaction | Interacting Bases [1,6] | Pair Probability [[0.045965469,0.300684085,0.003676754,0.003676754,0.000000000],[0.023538170,0.014096579,0.003676754,0.003676754,0.000000000],[0.003676754,0.003676754,0.172811225,0.406136932,0.000000000],[0.003676754,0.003676754,0.003676754,0.003676754,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|G|11 - 5U3G|1|B|U|28 bif Interaction | Interacting Bases [3,6] | Pair Probability [[0.015131034,0.277521604,0.013509461,0.023595120,0.000000000],[0.016723384,0.018031943,0.020168192,0.014830267,0.000000000],[0.013227295,0.020545271,0.004170389,0.053277511,0.000000000],[0.020611910,0.016061168,0.017094999,0.455500452,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|13 - 5U3G|1|B|U|28 cWW Interaction | Interacting Bases [2,3] | Pair Probability [[0.075162086,0.075504064,0.004224789,0.076442643,0.000000000],[0.074797160,0.086127893,0.000932278,0.077317705,0.000000000],[0.076126663,0.000932278,0.078408891,0.088765037,0.000000000],[0.076691089,0.075945794,0.000932278,0.131689351,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|12 - 5U3G|1|B|U|13 cSH Interaction | Interacting Bases [2,4] | Pair Probability [[0.088942412,0.095317025,0.008286587,0.090773273,0.000000000],[0.090993081,0.093096767,0.001058558,0.011953521,0.000000000],[0.013374065,0.001058558,0.096560837,0.086137347,0.000000000],[0.090839268,0.144317297,0.001058558,0.086232846,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5U3G|1|B|U|12 - 5U3G|1|B|C|14 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 [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_22373.1:
> IL_22373.1 5U3G G 10 C 29 GGUUC*GUC > IL_22373.1 5T83 G 16 C 41 GGUUC*GUC > IL_22373.1 7MLW G 11 C 50 GGUUC*GUC > IL_22373.1 6DLR G 16 C 44 GGUUC*GUC