| 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 8 4 | 9 9 I | 10 12 5 | 11 12 I | 12 13 | 13 12 I | 14 12 6 | 15 11 I | 16 10 7 | 17 7 I | 18 7 8 | 19 6 I | 20 17 9 | 21 17 I | 22 28 10 | 23 28 I | 24 29 | 25 28 I | 26 28 11 | 27 27 I | 28 31 12 | 29 31 I | 30 32 | 31 31 I | 32 31 13 | 33 25 I | 34 24 14 | 35 23 I | 36 22 15 | 37 21 I | 38 20 16 | 39 19 I | 40 18 17 | 41 17 I | 42 17 18 | 43 16 I | 44 15 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_69051.2_Instance_1 J4_69051.2,J4_5TBW_004,G1492_C1836 | G | G | U | U | C | G | G | U | U | A | G | C | C | G | G | U | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_1 J4_69051.25TBW_G_1492_C_1836 | G | G | U | U | C | * | G | G | U | U | A | G | * | C | C | * | G | G | U | C | G | U | A | C | true | 93 | 0 | 0 | 1.34 | |||||||||||||||||||||||
| J4_69051.2_Instance_2 J4_69051.2,J4_4V9F_004,G1416_C1679 | G | G | U | U | C | G | G | U | U | A | G | C | C | G | U | C | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_2 J4_69051.24V9F_G_1416_C_1679 | G | G | U | U | C | * | G | G | U | U | A | G | * | C | C | * | G | U | C | C | G | U | A | C | true | 96 | 0 | 0 | 0.75 | |||||||||||||||||||||||
| J4_69051.2_Instance_3 J4_69051.2,J4_5J7L_022,G1310_C1604 | G | G | U | U | C | G | G | U | G | A | G | C | U | A | A | U | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_3 J4_69051.25J7L_G_1310_C_1604 | G | G | U | U | C | * | G | G | U | G | A | G | * | C | U | * | A | A | U | C | G | U | A | C | true | 87 | 0 | 0 | 2.53 | |||||||||||||||||||||||
| J4_69051.2_Instance_4 J4_69051.2,J4_4Y4O_017,G1310_C1604 | G | G | U | U | C | G | G | U | U | A | G | C | U | A | C | C | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_4 J4_69051.24Y4O_G_1310_C_1604 | G | G | U | U | C | * | G | G | U | U | A | G | * | C | U | * | A | C | C | C | G | U | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||
| J4_69051.2_Instance_5 J4_69051.2,J4_4WF9_005,G1347_C1648 | G | U | U | U | C | G | G | U | U | A | G | C | C | G | C | C | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_5 J4_69051.24WF9_G_1347_C_1648 | G | U | U | U | C | * | G | G | U | U | A | G | * | C | C | * | G | C | C | C | G | U | A | C | true | 93 | 0 | 0 | 1.46 | |||||||||||||||||||||||
| J4_69051.2_Instance_6 J4_69051.2,J4_7A0S_005,G1323_C1620 | G | G | U | U | C | G | G | A | A | A | G | C | C | G | C | C | C | G | U | A | C | |||||||||||||||||||||||||||||||
| J4_69051.2_Sequence_6 J4_69051.27A0S_G_1323_C_1620 | G | G | U | U | C | * | G | G | A | A | A | G | * | C | C | * | G | C | C | C | G | U | A | C | true | 87 | 0 | 0 | 2.56 |
1 2 s33 1 4 s35 1 20 cWW 3 5 perp 3 8 tWW 3 19 s55 4 19 cWW 5 6 cWW 5 7 s55 5 19 perp 6 7 s35 8 19 s55 9 18 tHW 10 11 cWW 10 12 s55 10 13 s53 11 12 s35 12 13 cWW 14 15 s35 15 16 s35 16 17 s35 17 18 s35 19 20 s35 2 2 2BPh 5 4 7BPh 20 19 7BPh 3 2 7BR 7 19 2BRJAR3D SCFG/MRF model for J4_69051.2:
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 [20] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003679589,0.053642867,0.004190070,0.076104487,0.000000000],[0.006463298,0.025257446,0.076749356,0.005021698,0.000000000],[0.004143537,0.609465400,0.000789802,0.010117932,0.000000000],[0.075130495,0.036484266,0.008868823,0.003890933,0.000000000],[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 [1] | Right Index [20] // Basepair G1492 - C1836 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.011363636,0.011363636,0.806818182,0.170454545,0.000000000] | Position [1] | Left Index [2] | Right Index [19] // Fixed node on left for 5TBW|1|1|G|1493 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 [19] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [19] // Junction node U1494 - A1835 ID J758 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.187500000,0.062500000,0.187500000,0.562500000,0.000000000] | Left Index [3] | Right Index [8] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.006056150,0.007192874,0.001295320,0.009495516,0.000000000],[0.011827738,0.008041874,0.004799143,0.007268339,0.000000000],[0.001295320,0.004494765,0.006250557,0.009083267,0.000000000],[0.132556854,0.039706769,0.122545730,0.628089785,0.000000000],[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 [3] | Right Index [8] // Basepair U1494 - U1522 tWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.062500000,0.812500000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 5TBW|1|1|U|1495 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 [5] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.015625000,0.015625000,0.953125000,0.015625000,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 5TBW|1|1|G|1521 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 [5] | Right Index [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.003603143,0.006461301,0.004142256,0.075107278,0.000000000],[0.053626290,0.025687878,0.609294550,0.036472991,0.000000000],[0.004188775,0.076725638,0.000789558,0.008866083,0.000000000],[0.076080968,0.005020146,0.010114806,0.003818340,0.000000000],[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 C1496 - G1520 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 [0.333333333,0.222222222,0.222222222,0.222222222,0.000000000] | Left Index [9] | Right Index [19] // Initial node 5TBW|1|1|A|1524 - 5TBW|1|1|A|1835 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [9] | Right Index [19] // Fixed node on right for 5TBW|1|1|U|1834 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 [9] | Right Index [18] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018067094,0.040207941,0.003998277,0.456431444,0.000000000],[0.003998277,0.322184696,0.009584133,0.003998277,0.000000000],[0.018765634,0.003998277,0.030406557,0.023197522,0.000000000],[0.003998277,0.003998277,0.017782958,0.039382361,0.000000000],[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 [9] | Right Index [18] // Basepair A1524 - U1834 tHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [2] | Left Index [10] | Right Index [17] // Fixed node on right for 5TBW|1|1|C|1832 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 [10] | Right Index [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [10] | Right Index [16] // Fixed node on right for 5TBW|1|1|U|1831 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 [10] | Right Index [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.562500000,0.062500000,0.312500000,0.000000000] | Position [2] | Left Index [10] | Right Index [15] // Fixed node on right for 5TBW|1|1|G|1830 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 [10] | Right Index [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.437500000,0.187500000,0.187500000,0.000000000] | Position [2] | Left Index [10] | Right Index [14] // Fixed node on right for 5TBW|1|1|G|1829 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 [10] | Right Index [13] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [10] | Right Index [13] // Junction node G1525 - G1829 ID J539 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[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 [10] | Right Index [11] // Basepair G1525 - C1614 cWW 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 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 [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [12] | Right Index [13] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009015611,0.016598259,0.010211877,0.190496184,0.000000000],[0.020078202,0.009384364,0.234978378,0.012389530,0.000000000],[0.010297061,0.192647257,0.001996300,0.022446401,0.000000000],[0.213616688,0.011851437,0.034268488,0.009723963,0.000000000],[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 [12] | Right Index [13] // Basepair C1615 - G1829 cWW HairpinNode | Num Bases [1] | Left Index [13] | Right Index [13] | 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_69051.2:
> J4_69051.2 5TBW G 1492 C 1836 GGUUC*GGUUAG*CC*GGUCGUAC > J4_69051.2 4V9F G 1416 C 1679 GGUUC*GGUUAG*CC*GUCCGUAC > J4_69051.2 5J7L G 1310 C 1604 GGUUC*GGUGAG*CU*AAUCGUAC > J4_69051.2 4Y4O G 1310 C 1604 GGUUC*GGUUAG*CU*ACCCGUAC > J4_69051.2 4WF9 G 1347 C 1648 GUUUC*GGUUAG*CC*GCCCGUAC > J4_69051.2 7A0S G 1323 C 1620 GGUUC*GGAAAG*CC*GCCCGUAC