| 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 5 2 | 5 5 I | 6 6 | 7 5 I | 8 5 3 | 9 4 I | 10 10 4 | 11 10 I | 12 11 5 | 13 11 I | 14 11 6 | 15 12 I | 16 13 7 | 17 13 I | 18 14 8 | 19 14 I | 20 15 | 21 14 I | 22 14 9 | 23 13 I | 24 13 10 | 25 12 I | 26 11 11 | 27 10 I | 28 10 12 | 29 9 I | 30 17 13 | 31 18 I | 32 19 14 | 33 20 I | 34 25 15 | 35 25 I | 36 26 | 37 25 I | 38 25 16 | 39 24 I | 40 23 17 | 41 22 I | 42 21 18 | 43 2 I | 44 2 19 | 45 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_45801.2_Instance_1 J4_45801.2,J4_7A0S_001,C245_G437 | C | C | G | A | G | U | A | G | U | G | A | A | U | C | C | G | C | A | A | G | ||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_1 J4_45801.27A0S_C245_G437 | C | C | * | G | A | G | U | A | G | * | U | G | A | A | U | C | C | G | * | C | A | A | G | true | 93 | 0 | 0 | 1.36 | ||||||||||||||||||||||
| J4_45801.2_Instance_2 J4_45801.2,J4_4V9F_001,C239_G431 | C | C | G | A | G | U | A | G | C | G | A | A | U | A | A | C | G | A | A | G | ||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_2 J4_45801.24V9F_C239_G431 | C | C | * | G | A | G | U | A | G | * | C | G | A | A | U | A | A | C | * | G | A | A | G | true | 92 | 0 | 0 | 1.62 | ||||||||||||||||||||||
| J4_45801.2_Instance_3 J4_45801.2,J4_5J7L_018,C268_G424 | C | C | G | A | G | U | A | G | U | G | A | A | U | A | U | G | C | A | A | G | ||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_3 J4_45801.25J7L_C268_G424 | C | C | * | G | A | G | U | A | G | * | U | G | A | A | U | A | U | G | * | C | A | A | G | true | 96 | 0 | 0 | 0.85 | ||||||||||||||||||||||
| J4_45801.2_Instance_4 J4_45801.2,J4_4WF9_001,C271_G470 | C | C | G | A | G | U | A | C | G | G | A | A | U | C | U | G | U | A | A | G | ||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_4 J4_45801.24WF9_C271_G470 | C | C | * | G | A | G | U | A | C | * | G | G | A | A | U | C | U | G | * | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||||||
| J4_45801.2_Instance_5 J4_45801.2,J4_4Y4O_014,C268_G424 | C | U | G | A | G | U | A | C | G | G | A | A | U | C | U | G | U | A | A | G | ||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_5 J4_45801.24Y4O_C268_G424 | C | U | * | G | A | G | U | A | C | * | G | G | A | A | U | C | U | G | * | U | A | A | G | true | 95 | 0 | 0 | 0.97 | ||||||||||||||||||||||
| J4_45801.2_Instance_6 J4_45801.2,J4_5TBW_001,U112_A319 | U | C | G | A | G | U | C | G | C | U | A | A | G | U | G | U | A | A | A | |||||||||||||||||||||||||||||||
| J4_45801.2_Sequence_6 J4_45801.25TBW_U112_A319 | U | C | * | G | A | G | U | C | G | * | C | U | A | A | G | U | G | * | U | A | A | A | true | 76 | 0 | 0 | 4.85 |
1 2 s35 1 19 cWW 2 3 cWW 2 19 s55 3 18 perp 3 19 s35 4 6 s55 4 11 s53 4 12 tHH 5 6 cSH 5 10 s33 6 7 s35 6 10 s33 6 11 tWH 6 18 cSS 7 8 s35 7 10 tHS 7 11 s55 8 9 cWW 8 10 s55 9 10 s35 11 12 s35 11 17 tWW 12 13 s35 12 18 tWW 14 15 s55 15 16 cWW 17 18 s35 18 3 7BPh 10 6 6BPh 5 11 6BPh 4 12 6BPh 17 6 2BR 17 7 2BR 7 10 6BRJAR3D SCFG/MRF model for J4_45801.2:
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 [19] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009096159,0.016527150,0.010380816,0.190892026,0.000000000],[0.019794727,0.009365287,0.246335869,0.012829884,0.000000000],[0.010482647,0.194028432,0.002003598,0.022513545,0.000000000],[0.203692206,0.012318528,0.030014751,0.009724374,0.000000000],[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 [19] // Basepair C245 - G437 cWW JunctionNode | Branches [2] | Left Index [2] | Right Index [18] // Junction node C246 - A436 ID J6550 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 [2] | Right Index [3] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009450884,0.015956080,0.011081266,0.165384558,0.000000000],[0.064779646,0.012271176,0.221537108,0.013630044,0.000000000],[0.011230126,0.168795395,0.002205978,0.021170298,0.000000000],[0.175296480,0.013008887,0.083924597,0.010277478,0.000000000],[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 [2] | Right Index [3] // Basepair C246 - G383 cWW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | 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 [4] | Right Index [18] // Initial node 7A0S|1|X|A|384 - 7A0S|1|X|A|436 from node JunctionNode | Branches [2] | Left Index [4] | Right Index [18] // Junction node A384 - A436 ID J1626 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 [4] | Right Index [12] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.417171827,0.289668157,0.017287202,0.017637068,0.000000000],[0.067920990,0.000772046,0.065817481,0.007336049,0.000000000],[0.003849208,0.064976341,0.001927026,0.000772046,0.000000000],[0.005243791,0.038076678,0.000772046,0.000772046,0.000000000],[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 [4] | Right Index [12] // Basepair A384 - A415 tHH ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.283040840551315] // Cluster node 7A0S|1|X|G|385:7A0S|1|X|U|386 and 7A0S|1|X|A|414:7A0S|1|X|A|414 Interaction | Interacting Bases [2,3] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|386 - 7A0S|1|X|A|414 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.037660918,0.038374747,0.002109963,0.037503112,0.000000000],[0.028116336,0.042371811,0.000467182,0.037581732,0.000000000],[0.163663517,0.002323717,0.199641593,0.288975486,0.000000000],[0.038245262,0.038015670,0.000467182,0.044481773,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|385 - 7A0S|1|X|U|386 cSH 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 [7] | Right Index [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.056207763,0.056830275,0.362233015,0.060888198,0.000000000],[0.052349381,0.057195926,0.003180057,0.069800068,0.000000000],[0.000656205,0.000656205,0.015617141,0.000656205,0.000000000],[0.003098284,0.000656205,0.259318862,0.000656205,0.000000000],[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 [7] | Right Index [10] // Basepair A387 - G413 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011261729,0.107215514,0.011664304,0.155467535,0.000000000],[0.016389492,0.010279223,0.162705215,0.013304776,0.000000000],[0.011565927,0.164350628,0.002381099,0.139045256,0.000000000],[0.140070064,0.013731238,0.020730402,0.019837597,0.000000000],[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 [8] | Right Index [9] // Basepair G388 - U412 cWW HairpinNode | Num Bases [1] | Left Index [9] | Right Index [9] | 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 [0.400000000,0.200000000,0.200000000,0.200000000,0.000000000] | Left Index [13] | Right Index [18] // Initial node 7A0S|1|X|U|416 - 7A0S|1|X|A|436 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.187500000,0.687500000,0.000000000] | Position [1] | Left Index [13] | Right Index [18] // Fixed node on left for 7A0S|1|X|U|416 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 [14] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.312500000,0.437500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [14] | Right Index [18] // Fixed node on left for 7A0S|1|X|C|417 InitialNode | Left Length Distribution [0.170928484,0.821824149,0.006905511,0.000341857] | Left Letter Distribution [0.214285714,0.214285714,0.071428571,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [15] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.965909091,0.011363636,0.011363636,0.011363636,0.000000000] | Position [2] | Left Index [15] | Right Index [18] // Fixed node on right for 7A0S|1|X|A|435 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 [15] | Right Index [17] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.953125000,0.015625000,0.015625000,0.015625000,0.000000000] | Position [2] | Left Index [15] | Right Index [17] // Fixed node on right for 7A0S|1|X|C|434 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 [15] | Right Index [16] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012272627,0.152086787,0.012202235,0.137151389,0.000000000],[0.015338437,0.010772651,0.125599160,0.013403298,0.000000000],[0.012034920,0.138448119,0.002566276,0.196748461,0.000000000],[0.113641780,0.014123779,0.018746004,0.024864074,0.000000000],[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 G419 - C434 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_45801.2:
> J4_45801.2 7A0S C 245 G 437 CC*GAGUAG*UGAAUCCG*CAAG > J4_45801.2 4V9F C 239 G 431 CC*GAGUAG*CGAAUAAC*GAAG > J4_45801.2 5J7L C 268 G 424 CC*GAGUAG*UGAAUAUG*CAAG > J4_45801.2 4WF9 C 271 G 470 CC*GAGUAC*GGAAUCUG*UAAG > J4_45801.2 4Y4O C 268 G 424 CU*GAGUAC*GGAAUCUG*UAAG > J4_45801.2 5TBW U 112 A 319 UC*GAGUCG*CUAAGUG*UAAA