| 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 4 I | 6 7 3 | 7 7 I | 8 7 4 | 9 7 I | 10 7 5 | 11 7 I | 12 7 6 | 13 7 I | 14 7 7 | 15 7 I | 16 7 8 | 17 7 I | 18 7 9 | 19 7 I | 20 7 10 | 21 8 I | 22 9 | 23 8 I | 24 7 11 | 25 6 I | 26 5 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_04332.3_Instance_1 IL_04332.3,IL_7A0S_072,C1917_G1947 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | U | G | ||||||||||||||||||
| IL_04332.3_Sequence_1 IL_04332.37A0S_C_1917_G_1947 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | U | G | true | 93 | 0 | 0 | 1.59 | ||||||||||||
| IL_04332.3_Instance_2 IL_04332.3,IL_4V9F_071,C1975_G2005 | C | G | U | A | G | U | A | C | C | U | U | G | C | U | U | G | ||||||||||||||||||
| IL_04332.3_Sequence_2 IL_04332.34V9F_C_1975_G_2005 | C | G | U | A | G | U | A | C | C | U | U | G | * | C | U | U | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 12 s33 2 13 s55 3 6 s53 3 9 cWW 3 10 s35 4 5 s35 4 6 perp 6 8 tSW 7 8 s35 8 9 s33 10 11 cWW 11 12 s35 11 3 7BPh 12 3 6BPh 7 6 7BR 2 13 2BRJAR3D SCFG/MRF model for IL_04332.3:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C1917 - G1947 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.041666667,0.875000000,0.041666667,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 7A0S|1|X|G|1918 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [3] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.031250000,0.468750000,0.031250000,0.468750000,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right for 7A0S|1|X|G|1928 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [11] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000047613026806972809848148273455744644] | Num Left Bases [8] | Num Right Bases [1] | Left Index [3] | Right Index [11] | Norm Constant [0.999999999999999] // Cluster node 7A0S|1|X|A|1919:7A0S|1|X|G|1928 and 7A0S|1|X|C|1944:7A0S|1|X|C|1944 Interaction | Interacting Bases [8,9] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|1928 - 7A0S|1|X|C|1944 cWW Interaction | Interacting Bases [4,6] | Pair Probability [[0.019829543,0.295643567,0.002858396,0.014078274,0.000000000],[0.229276560,0.011247462,0.002858396,0.011119265,0.000000000],[0.228871501,0.002858396,0.002858396,0.008972368,0.000000000],[0.026862862,0.110612460,0.018243500,0.013809051,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|1923 - 7A0S|1|X|C|1925 tSW Interaction | Interacting Bases [1,7] | Pair Probability [[0.012355323,0.152486873,0.011844359,0.123890391,0.000000000],[0.017284732,0.013982885,0.107364811,0.012739948,0.000000000],[0.011690860,0.108815631,0.003146657,0.053767974,0.000000000],[0.108519843,0.013702127,0.020221404,0.228186183,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|1919 - 7A0S|1|X|U|1926 cWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|A|1920 Interaction | Interacting Bases [3,3] | Pair Probability [[0.125000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.625000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|U|1922 Interaction | Interacting Bases [5,5] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.875000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|C|1924 Insertion | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node Insertion | Location [7] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion after nucleotide 9, position 7 in cluster node InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [10] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_04332.3:
> IL_04332.3 7A0S C 1917 G 1947 CGAAAUUCCUUG*CCUG > IL_04332.3 4V9F C 1975 G 2005 CGUAGUACCUUG*CUUG