| 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 6 3 | 7 6 I | 8 6 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 6 | 13 10 I | 14 13 7 | 15 14 I | 16 15 | 17 14 I | 18 13 8 | 19 13 I | 20 13 9 | 21 12 I | 22 11 10 | 23 8 I | 24 8 11 | 25 7 I | 26 6 12 | 27 5 I | 28 4 13 | 29 3 I | 30 3 14 | 31 2 I | 32 2 15 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_88367.1_Instance_1 IL_88367.1_IL_4A1B_045_A1018_U1083 | A | G | G | U | A | A | A | U | U | U | A | A | A | U | U | |||||||||||||||||||||||
| IL_88367.1_Sequence_1 IL_88367.1_IL_4A1B_045_A_1018_U_1083 | A | G | G | U | A | A | A | * | U | U | U | A | A | A | U | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 15 cWW 2 14 bif 3 4 cSH 3 11 s33 4 5 s35 4 12 tWH 5 6 s35 5 11 tHS 5 12 s55 6 7 s35 7 8 cWW 7 9 tSH 9 10 s35 10 11 s35 12 13 s35 13 14 s35 14 15 s35 11 3 6BR 5 11 6BRJAR3D SCFG/MRF model for IL_88367.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | 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 [1] | Right Index [15] // Initial node A1018 - U1083 from junction BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair A1018 - U1083 cWW BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.022972337,0.326477442,0.003861837,0.003861837,0.000000000],[0.018596955,0.015739896,0.003861837,0.003861837,0.000000000],[0.003861837,0.003861837,0.181510317,0.396084684,0.000000000],[0.003861837,0.003861837,0.003861837,0.003861837,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [14] // Basepair G1019 - U1082 bif FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [13] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.339207964837216] // Cluster node G1020:U1021 and A1080:A1080 Interaction | Interacting Bases [2,3] | Pair Probability [[0.026228946,0.005500826,0.026982756,0.005500826,0.000000000],[0.054639536,0.045670107,0.036513624,0.005500826,0.000000000],[0.005500826,0.005500826,0.064376936,0.025659745,0.000000000],[0.559983562,0.005500826,0.067861159,0.059078674,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1021 - A1080 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.109399626,0.112701236,0.006146356,0.005085348,0.000000000],[0.105822836,0.122922437,0.001307276,0.123881708,0.000000000],[0.010688473,0.005845023,0.011947953,0.140628542,0.000000000],[0.009413474,0.109623711,0.001307276,0.123278727,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1020 - U1021 cSH InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [11] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.370723561,0.069972932,0.059893903,0.066518667,0.000000000],[0.289240714,0.028663256,0.000721645,0.064026559,0.000000000],[0.003608226,0.000721645,0.006268752,0.000721645,0.000000000],[0.028557666,0.000721645,0.008917540,0.000721645,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [11] // Basepair A1022 - A1079 tHS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [6] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [2] | Left Index [7] | Right Index [10] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [9] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [7] | Right Index [9] | Norm Constant [0.253218861320121] // Cluster node A1024:A1024 and U1076:U1077 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009342473,0.024677534,0.009906945,0.226837217,0.000000000],[0.020281602,0.009395363,0.194134563,0.010378776,0.000000000],[0.009890064,0.195262113,0.002169362,0.028060170,0.000000000],[0.208798271,0.010452176,0.023820256,0.016593115,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1024 - U1076 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.032237520,0.018923185,0.004073171,0.417218066,0.000000000],[0.025930022,0.017417610,0.004073171,0.004073171,0.000000000],[0.019395920,0.004073171,0.379996231,0.023911335,0.000000000],[0.020722872,0.019808215,0.004073171,0.004073171,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1024 - U1077 tSH InitialNode | 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 [7] // New Initial node after Cluster 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_88367.1:
> IL_88367.1 IL_4A1B_045 A 1018 U 1083 AGGUAAA*UUUAAAUU