| 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 2 2 | 5 3 I | 6 6 3 | 7 6 I | 8 7 | 9 6 I | 10 6 4 | 11 5 I | 12 11 5 | 13 11 I | 14 12 | 15 11 I | 16 11 6 | 17 10 I | 18 14 7 | 19 14 I | 20 14 8 | 21 14 I | 22 14 9 | 23 14 I | 24 14 10 | 25 14 I | 26 14 11 | 27 14 I | 28 14 12 | 29 14 I | 30 14 13 | 31 14 I | 32 14 14 | 33 15 I | 34 16 15 | 35 16 I | 36 17 | 37 16 I | 38 16 16 | 39 15 I | 40 14 17 | 41 3 I | 42 2 18 | 43 2 I | 44 2 19 | 45 2 I | 46 2 20 | 47 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_64075.1_Instance_1 J4_64075.1,J4_5J7L_026,C1833_G1972 | C | U | G | C | G | C | C | U | A | A | G | G | U | A | G | C | G | A | A | U | G | |||||||||||||||||||||||||||||||
| J4_64075.1_Sequence_1 J4_64075.15J7L_C_1833_G_1972 | C | U | G | * | C | G | * | C | C | U | A | A | G | G | U | A | G | * | C | G | A | A | U | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||
| J4_64075.1_Instance_2 J4_64075.1,J4_4Y4O_021,U1833_A1972 | U | U | G | C | G | C | C | U | A | A | G | G | U | A | G | C | G | A | A | A | A | |||||||||||||||||||||||||||||||
| J4_64075.1_Sequence_2 J4_64075.14Y4O_U_1833_A_1972 | U | U | G | * | C | G | * | C | C | U | A | A | G | G | U | A | G | * | C | G | A | A | A | A | true | 93 | 0 | 0 | 1.42 | |||||||||||||||||||||||
| J4_64075.1_Instance_3 J4_64075.1,J4_5TBW_007,C2192_G2315 | C | U | G | C | G | C | U | U | A | A | G | G | U | A | G | U | G | A | A | U | G | |||||||||||||||||||||||||||||||
| J4_64075.1_Sequence_3 J4_64075.15TBW_C_2192_G_2315 | C | U | G | * | C | G | * | C | U | U | A | A | G | G | U | A | G | * | U | G | A | A | U | G | true | 97 | 0 | 0 | 0.68 | |||||||||||||||||||||||
| J4_64075.1_Instance_4 J4_64075.1,J4_4V9F_008,C1889_G2013 | C | U | G | C | G | C | U | U | A | A | G | G | U | A | G | U | G | A | A | U | G | |||||||||||||||||||||||||||||||
| J4_64075.1_Sequence_4 J4_64075.14V9F_C_1889_G_2013 | C | U | G | * | C | G | * | C | U | U | A | A | G | G | U | A | G | * | U | G | A | A | U | G | true | 97 | 0 | 0 | 0.68 |
1 2 s35 1 18 tSS 1 20 cWW 2 19 cWH 2 20 s55 3 4 cWW 3 13 s55 4 12 s35 5 6 cWW 5 7 s55 5 11 s55 6 7 s35 7 8 s35 7 11 tWW 8 10 tSH 8 11 s53 9 10 s35 10 11 s33 12 13 cSH 12 17 s33 13 14 s35 13 17 s33 13 18 tWH 14 15 s35 14 17 tHS 14 18 s55 15 16 cWW 15 17 s55 16 17 s35 18 20 cSS 19 20 s55 8 11 6BPh 17 13 6BPh 12 18 6BPh 10 4 2BR 17 12 6BR 14 17 6BRJAR3D SCFG/MRF model for J4_64075.1:
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 [20] // Initial node ClusterNode | Deletion Probability [0.000000000000015524427799645559379460012814890536486428420510] | Num Left Bases [2] | Num Right Bases [3] | Left Index [1] | Right Index [20] | Norm Constant [0.015988623090801] // Cluster node 5J7L|1|DA|C|1833:5J7L|1|DA|U|1834 and 5J7L|1|DA|A|1969:5J7L|1|DA|G|1972 Interaction | Interacting Bases [1,3] | Pair Probability [[0.060096154,0.060096154,0.060096154,0.060096154,0.000000000],[0.088942308,0.060096154,0.060096154,0.060096154,0.000000000],[0.060096154,0.060096154,0.060096154,0.060096154,0.000000000],[0.069711538,0.060096154,0.060096154,0.060096154,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1833 - 5J7L|1|DA|A|1969 tSS Interaction | Interacting Bases [2,4] | Pair Probability [[0.003009274,0.003009274,0.012968037,0.013028877,0.000000000],[0.003009274,0.014471321,0.003009274,0.285028871,0.000000000],[0.011086743,0.003009274,0.010400724,0.003009274,0.000000000],[0.339388921,0.003009274,0.278445149,0.014116440,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1834 - 5J7L|1|DA|A|1970 cWH Interaction | Interacting Bases [1,5] | Pair Probability [[0.009230036,0.016881218,0.010494353,0.194361300,0.000000000],[0.020319858,0.009555111,0.230862069,0.012852202,0.000000000],[0.010589659,0.197055880,0.002038410,0.022912280,0.000000000],[0.207859340,0.012317386,0.032759727,0.009911172,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1833 - 5J7L|1|DA|G|1972 cWW Interaction | Interacting Bases [3,5] | Pair Probability [[0.086472048,0.076104746,0.108659211,0.072073014,0.000000000],[0.075412287,0.076719486,0.003403014,0.064300174,0.000000000],[0.073023686,0.003465765,0.007400953,0.060867279,0.000000000],[0.074810444,0.068877759,0.077447827,0.070962307,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1969 - 5J7L|1|DA|G|1972 cSS Insertion | Location [4] | Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000]// Insertion after nucleotide 19, position 4 in cluster node 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 [3] | Right Index [17] // Initial node 5J7L|1|DA|2MG|1835 - 5J7L|1|DA|G|1968 from node JunctionNode | Branches [2] | Left Index [3] | Right Index [17] // Junction node G1835 - G1968 ID J5852 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // Basepair G1835 - C1905 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [5] | Right Index [17] // Initial node 5J7L|1|DA|G|1906 - 5J7L|1|DA|G|1968 from node JunctionNode | Branches [2] | Left Index [5] | Right Index [17] // Junction node G1906 - G1968 ID J5497 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [6] // Basepair G1906 - C1924 cWW 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [17] // Initial node 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1968 from node ClusterNode | Deletion Probability [0.000000000000000000001953125000000000515889489244815448855715] | Num Left Bases [8] | Num Right Bases [1] | Left Index [7] | Right Index [17] | Norm Constant [1.000000000000000] // Cluster node 5J7L|1|DA|C|1925:5J7L|1|DA|A|1932 and 5J7L|1|DA|G|1968:5J7L|1|DA|G|1968 Interaction | Interacting Bases [8,9] | Pair Probability [[0.042857649,0.043176051,0.398595795,0.047840582,0.000000000],[0.045370598,0.045265538,0.003601343,0.045021164,0.000000000],[0.000514478,0.000514478,0.017605820,0.000514478,0.000000000],[0.002424734,0.000514478,0.305668340,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|1932 - 5J7L|1|DA|G|1968 tHS Interaction | Interacting Bases [2,4] | Pair Probability [[0.072312829,0.013210163,0.000160612,0.000790086,0.000000000],[0.072592178,0.013660448,0.000160612,0.000160612,0.000000000],[0.074675711,0.000160612,0.000992664,0.013333822,0.000000000],[0.631622605,0.103918470,0.001124287,0.001124287,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|U|1926 - 5J7L|1|DA|A|1928 tSH Interaction | Interacting Bases [1,5] | Pair Probability [[0.017121410,0.016023235,0.004960794,0.021367648,0.000000000],[0.100702211,0.023585581,0.426645111,0.023424167,0.000000000],[0.004960794,0.019524850,0.021175153,0.017390558,0.000000000],[0.094150901,0.024535264,0.159816286,0.024616037,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|C|1925 - 5J7L|1|DA|G|1929 tWW Interaction | Interacting Bases [6,7] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|G|1930 - 5J7L|1|DA|U|1931 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5J7L|1|DA|A|1927 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 [15] | Right Index [16] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012540860,0.155529775,0.012456608,0.140202703,0.000000000],[0.015113779,0.010952378,0.117426741,0.013578237,0.000000000],[0.012245828,0.142067698,0.002615550,0.191455955,0.000000000],[0.115398566,0.014477202,0.018565386,0.025372734,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [16] // Basepair G1933 - C1967 cWW HairpinNode | Num Bases [1] | Left Index [16] | Right Index [16] | 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 J4_64075.1:
> J4_64075.1 5J7L C 1833 G 1972 CUG*CG*CCUAAGGUAG*CGAAUG > J4_64075.1 4Y4O U 1833 A 1972 UUG*CG*CCUAAGGUAG*CGAAAA > J4_64075.1 5TBW C 2192 G 2315 CUG*CG*CUUAAGGUAG*UGAAUG > J4_64075.1 4V9F C 1889 G 2013 CUG*CG*CUUAAGGUAG*UGAAUG