| 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_42218.2_Instance_1 IL_42218.2,IL_5J7L_319,C1934_G1964 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | U | G | ||||||||||||||||||
| IL_42218.2_Sequence_1 IL_42218.25J7L_C_1934_G_1964 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | U | G | true | 98 | 0 | 0 | 0.34 | ||||||||||||
| IL_42218.2_Instance_2 IL_42218.2,IL_9DFE_077,C1934_G1964 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | U | G | ||||||||||||||||||
| IL_42218.2_Sequence_2 IL_42218.29DFE_C_1934_G_1964 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | U | G | true | 98 | 0 | 0 | 0.34 | ||||||||||||
| IL_42218.2_Instance_3 IL_42218.2,IL_4WF9_077,C1961_G1991 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | C | G | ||||||||||||||||||
| IL_42218.2_Sequence_3 IL_42218.24WF9_C_1961_G_1991 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_42218.2_Instance_4 IL_42218.2,IL_8CRE_095,C2255_G2285 | C | C | A | A | A | U | G | C | C | U | C | G | C | G | C | G | ||||||||||||||||||
| IL_42218.2_Sequence_4 IL_42218.28CRE_C_2255_G_2285 | C | C | A | A | A | U | G | C | C | U | C | G | * | C | G | C | G | true | 93 | 0 | 0 | 1.41 | ||||||||||||
| IL_42218.2_Instance_5 IL_42218.2,IL_8P9A_318,C2277_G2307 | C | C | A | A | A | U | G | C | C | U | C | G | C | G | C | G | ||||||||||||||||||
| IL_42218.2_Sequence_5 IL_42218.28P9A_C_2277_G_2307 | C | C | A | A | A | U | G | C | C | U | C | G | * | C | G | C | G | true | 93 | 0 | 0 | 1.41 |
1 2 s35 1 13 cWW 2 12 s33 2 13 s55 3 6 s33 3 9 cHW 3 10 s55 4 5 s33 4 6 perp 6 7 cSH 6 8 tSW 7 8 s35 8 9 s33 10 11 cWW 11 12 s35 11 3 7BPh 12 3 6BPh 8 7 7BPh 2 13 6BPh 7 6 7BR 2 12 6BR 2 13 2BRJAR3D SCFG/MRF model for IL_42218.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.071428571,0.500000000,0.071428571,0.357142857,0.000000000] | Left Index [1] | Right Index [13] // Basepair C1934 - G1964 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.002824859,0.398305085,0.596045198,0.002824859,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left for 5J7L|1|DA|G|1935 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 [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 [0.013513514,0.581081081,0.391891892,0.013513514,0.000000000] | Position [2] | Left Index [3] | Right Index [12] // Fixed node on right for 5J7L|1|DA|G|1945 InitialNode | Left Length Distribution [1.000000000] | 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 [3] | Right Index [11] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000000000048323728403170814589206297593745167] | Num Left Bases [8] | Num Right Bases [1] | Left Index [3] | Right Index [11] | Norm Constant [0.248855558641365] // Cluster node 5J7L|1|DA|A|1936:5J7L|1|DA|G|1945 and 5J7L|1|DA|C|1961:5J7L|1|DA|C|1961 Interaction | Interacting Bases [8,9] | Pair Probability [[0.003714633,0.054153751,0.004229975,0.076829292,0.000000000],[0.006524853,0.025497993,0.077480302,0.005069524,0.000000000],[0.004182999,0.605746023,0.000797324,0.010214294,0.000000000],[0.075846024,0.036831735,0.008953288,0.003927989,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1945 - 5J7L|1|DA|C|1961 cWW Interaction | Interacting Bases [4,5] | Pair Probability [[0.078978008,0.083597937,0.020523612,0.080304904,0.000000000],[0.080464208,0.081988830,0.015285180,0.023181182,0.000000000],[0.024210704,0.057561603,0.084499376,0.076945069,0.000000000],[0.080352733,0.119807193,0.015285180,0.077014281,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1940 - 5J7L|1|DA|C|1941 cSH Interaction | Interacting Bases [4,6] | Pair Probability [[0.002600388,0.013803359,0.000950158,0.003911621,0.000000000],[0.002113814,0.203551233,0.011680332,0.004865762,0.000000000],[0.002057656,0.454778136,0.000950158,0.002074797,0.000000000],[0.002133219,0.287831381,0.002211871,0.004486114,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1940 - 5J7L|1|DA|C|1942 tSW Interaction | Interacting Bases [1,7] | Pair Probability [[0.002980614,0.002980614,0.010981155,0.345680455,0.000000000],[0.002980614,0.014333499,0.002980614,0.002980614,0.000000000],[0.012844532,0.002980614,0.010301669,0.275793290,0.000000000],[0.012904793,0.282314310,0.002980614,0.013981998,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1936 - 5J7L|1|DA|U|1943 cHW Interaction | Interacting Bases [2,2] | Pair Probability [[0.785714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|1937 Interaction | Interacting Bases [3,3] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.785714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|5MU|1939 Insertion | Location [2] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node Insertion | Location [7] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.071428571,0.357142857,0.071428571,0.500000000,0.000000000]// Insertion after nucleotide 9, position 7 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 [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_42218.2:
> IL_42218.2 5J7L C 1934 G 1964 CGAAAUUCCUUG*CCUG > IL_42218.2 9DFE C 1934 G 1964 CGAAAUUCCUUG*CCUG > IL_42218.2 4WF9 C 1961 G 1991 CGAAAUUCCUUG*CCCG > IL_42218.2 8CRE C 2255 G 2285 CCAAAUGCCUCG*CGCG > IL_42218.2 8P9A C 2277 G 2307 CCAAAUGCCUCG*CGCG