| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 3 I | 4 4 2 | 5 4 I | 6 5 3 | 7 5 I | 8 6 | 9 5 I | 10 5 4 | 11 4 I | 12 4 5 | 13 3 I | 14 2 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_43124.2_Instance_1 IL_43124.2_IL_3GX5_003_G56_C47 | G | U | G | C | A | A | C | |||||||||||||||
| IL_43124.2_Sequence_1 IL_43124.2_IL_3GX5_003_G56_C47 | G | U | G | * | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_43124.2_Instance_2 IL_43124.2_IL_4AOB_003_G56_C47 | G | U | G | C | A | A | C | |||||||||||||||
| IL_43124.2_Sequence_2 IL_43124.2_IL_4AOB_003_G56_C47 | G | U | G | * | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_43124.2_Instance_3 IL_43124.2_IL_3V7E_007_G288_C247 | G | U | G | C | A | A | C | |||||||||||||||
| IL_43124.2_Sequence_3 IL_43124.2_IL_3V7E_007_G288_C247 | G | U | G | * | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_43124.2_Instance_4 IL_43124.2_IL_4KQY_003_G77_C48 | G | U | G | C | A | A | C | |||||||||||||||
| IL_43124.2_Sequence_4 IL_43124.2_IL_4KQY_003_G77_C48 | G | U | G | * | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_43124.2_Instance_5 IL_43124.2_IL_4B5R_003_G56_C47 | G | U | G | C | A | A | C | |||||||||||||||
| IL_43124.2_Sequence_5 IL_43124.2_IL_4B5R_003_G56_C47 | G | U | G | * | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_43124.2_Instance_6 IL_43124.2_IL_1J2B_003_C926_G947 | C | G | C | G | A | G | G | |||||||||||||||
| IL_43124.2_Sequence_6 IL_43124.2_IL_1J2B_003_C926_G947 | C | G | C | * | G | A | G | G | true | 78 | 0 | 0 | 2.12 | |||||||||
| IL_43124.2_Instance_7 IL_43124.2_IL_4A1B_093_U2974_G2389 | U | A | C | G | C | G | G | |||||||||||||||
| IL_43124.2_Sequence_7 IL_43124.2_IL_4A1B_093_U_2974_G_2389 | U | A | C | * | G | C | G | G | true | 69 | 0 | 0 | 2.91 | |||||||||
| IL_43124.2_Instance_8 IL_43124.2_IL_3U5H_071_U1824_A1621 | U | G | C | G | A | U | A | |||||||||||||||
| IL_43124.2_Sequence_8 IL_43124.2_IL_3U5H_071_U_1824_A_1621 | U | G | C | * | G | A | U | A | true | 71 | 0 | 0 | 2.75 | |||||||||
| IL_43124.2_Instance_9 IL_43124.2_IL_3U5H_012_U177_G241 | U | U | C | G | A | G | U | G | ||||||||||||||
| IL_43124.2_Sequence_9 IL_43124.2_IL_3U5H_012_U177_G241 | U | U | C | * | G | A | G | U | G | true | 61 | 0 | 0 | 3.70 | ||||||||
| IL_43124.2_Instance_10 IL_43124.2_IL_1X8W_009_C316_G405 | C | U | C | G | U | U | G | |||||||||||||||
| IL_43124.2_Sequence_10 IL_43124.2_IL_1X8W_009_C316_G405 | C | U | C | * | G | U | U | G | true | 53 | 0 | 0 | 4.50 | |||||||||
| IL_43124.2_Instance_11 IL_43124.2_IL_3Q1Q_006_A179_U201 | A | G | C | G | G | C | U | |||||||||||||||
| IL_43124.2_Sequence_11 IL_43124.2_IL_3Q1Q_006_A179_U201 | A | G | C | * | G | G | C | U | true | 92 | 0 | 0 | 0.73 |
1 2 s35 1 7 cWW 2 3 s35 2 5 tHS 2 7 s55 3 4 cWW 3 5 s55 4 5 s35 5 6 s35 6 7 cSHJAR3D SCFG/MRF model for IL_43124.2:
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 [7] // Initial node G56 - C47 from junction ClusterNode | Deletion Probability [0.0000000752256015] | Num Left Bases [1] | Num Right Bases [2] | Left Index [1] | Right Index [7] | Norm Constant [0.249241205320160] // Cluster node G56:G56 and A46:C47 Interaction | Interacting Bases [1,3] | Pair Probability [[0.009643656,0.017743843,0.011116974,0.163701052,0.000000000],[0.067339819,0.009199884,0.180791773,0.012510100,0.000000000],[0.011138561,0.208425677,0.002205865,0.022375070,0.000000000],[0.164574954,0.012391145,0.095803274,0.011038354,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G56 - C47 cWW Interaction | Interacting Bases [2,3] | Pair Probability [[0.070820127,0.131469830,0.074440085,0.009251830,0.000000000],[0.075385232,0.070175051,0.001590324,0.093328000,0.000000000],[0.009938947,0.010256490,0.130627801,0.073632882,0.000000000],[0.076767980,0.080806256,0.022773670,0.068735496,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A46 - C47 cSH Insertion | Location [2] | Length Distribution [0.904811823,0.094550986,0.000616637,0.000020555] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000]// Insertion after nucleotide 6, position 2 in cluster node InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.026190392,0.046162582,0.015757625,0.016835666,0.000000000],[0.015373566,0.014150407,0.003309124,0.016092581,0.000000000],[0.053502174,0.003309124,0.333812897,0.003309124,0.000000000],[0.401053931,0.003309124,0.019426036,0.028405649,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair U57 - A45 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009286118,0.017299080,0.010773992,0.177247259,0.000000000],[0.017597460,0.007805594,0.248854464,0.012519905,0.000000000],[0.010786420,0.239296072,0.001975440,0.023439283,0.000000000],[0.177340704,0.012464760,0.023756114,0.009557335,0.000000000],[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 [3] | Right Index [4] // Basepair G58 - C44 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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_43124.2:
> IL_43124.2 IL_3GX5_003 G 56 C 47 GUG*CAAC > IL_43124.2 IL_4AOB_003 G 56 C 47 GUG*CAAC > IL_43124.2 IL_3V7E_007 G 288 C 247 GUG*CAAC > IL_43124.2 IL_4KQY_003 G 77 C 48 GUG*CAAC > IL_43124.2 IL_4B5R_003 G 56 C 47 GUG*CAAC > IL_43124.2 IL_1J2B_003 C 926 G 947 CGC*GAGG > IL_43124.2 IL_4A1B_093 U 2974 G 2389 UAC*GCGG > IL_43124.2 IL_3U5H_071 U 1824 A 1621 UGC*GAUA > IL_43124.2 IL_3U5H_012 U 177 G 241 UUC*GAGUG > IL_43124.2 IL_1X8W_009 C 316 G 405 CUC*GUUG > IL_43124.2 IL_3Q1Q_006 A 179 U 201 AGC*GGCU