| 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 9 3 | 7 9 I | 8 10 4 | 9 10 I | 10 11 | 11 10 I | 12 10 5 | 13 9 I | 14 9 6 | 15 8 I | 16 15 7 | 17 15 I | 18 16 8 | 19 17 I | 20 18 9 | 21 18 I | 22 19 | 23 18 I | 24 18 10 | 25 15 I | 26 15 11 | 27 14 I | 28 21 12 | 29 21 I | 30 22 | 31 21 I | 32 21 13 | 33 6 I | 34 5 14 | 35 2 I | 36 2 15 | 37 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_04930.2_Instance_1 J4_04930.2,J4_4Y4O_022,C2285_G2383 | C | A | A | A | G | C | U | G | A | C | G | G | G | C | G | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_1 J4_04930.24Y4O_C_2285_G_2383 | C | A | A | A | G | * | C | U | G | A | C | * | G | G | G | * | C | G | G | true | 94 | 0 | 0 | 1.25 | ||||||||||||||||||
| J4_04930.2_Instance_2 J4_04930.2,J4_5J7L_027,C2285_G2383 | C | G | A | A | G | U | U | G | A | C | G | G | U | A | G | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_2 J4_04930.25J7L_C_2285_G_2383 | C | G | A | A | G | * | U | U | G | A | C | * | G | G | U | * | A | G | G | true | 95 | 0 | 0 | 0.95 | ||||||||||||||||||
| J4_04930.2_Instance_3 J4_04930.2,J4_4WF9_008,C2312_G2410 | C | A | A | A | G | U | U | G | A | C | G | G | G | C | G | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_3 J4_04930.24WF9_C_2312_G_2410 | C | A | A | A | G | * | U | U | G | A | C | * | G | G | G | * | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| J4_04930.2_Instance_4 J4_04930.2,J4_7A0S_009,C2264_G2362 | C | A | A | A | G | U | U | G | A | C | G | G | G | C | G | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_4 J4_04930.27A0S_C_2264_G_2362 | C | A | A | A | G | * | U | U | G | A | C | * | G | G | G | * | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||||
| J4_04930.2_Instance_5 J4_04930.2,J4_5TBW_008,C2654_G2753 | C | U | A | A | G | U | U | G | A | U | A | C | C | G | U | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_5 J4_04930.25TBW_C_2654_G_2753 | C | U | A | A | G | * | U | U | G | A | U | * | A | C | C | * | G | U | G | true | 82 | 0 | 0 | 3.59 | ||||||||||||||||||
| J4_04930.2_Instance_6 J4_04930.2,J4_4V9F_009,C2319_G2420 | C | U | A | U | G | U | U | G | A | C | G | A | C | G | U | G | ||||||||||||||||||||||||||
| J4_04930.2_Sequence_6 J4_04930.24V9F_C_2319_G_2420 | C | U | A | U | G | * | U | U | G | A | C | * | G | A | C | * | G | U | G | true | 84 | 0 | 0 | 3.21 |
1 15 cWW 2 3 s53 2 8 s53 3 4 s55 3 6 tWW 4 5 cWW 4 6 s55 5 6 s35 7 9 s55 7 11 cHW 7 12 s35 7 13 s33 7 14 perp 8 15 s55 9 10 cWW 9 14 s35 10 11 s35 11 12 s35 12 13 cWW 4 8 2BPh 7 14 2BPh 15 4 2BRJAR3D SCFG/MRF model for J4_04930.2:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004553963,0.008166350,0.026176706,0.094927059,0.000000000],[0.009682505,0.004638079,0.555559699,0.006585388,0.000000000],[0.005294135,0.096972482,0.004989559,0.011205720,0.000000000],[0.096157693,0.006344894,0.063919821,0.004825947,0.000000000],[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 [15] // Basepair C2285 - G2383 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.062500000,0.187500000,0.312500000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 4Y4O|1|2A|A|2286 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 [14] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.562500000,0.312500000,0.000000000] | Position [2] | Left Index [3] | Right Index [14] // Fixed node on right for 4Y4O|1|2A|C|2381 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 [13] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [13] // Junction node A2287 - C2381 ID J6323 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 [3] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.015768747,0.038966363,0.003298662,0.431393572,0.000000000],[0.015484946,0.035535304,0.013737323,0.038098902,0.000000000],[0.003298662,0.016351027,0.015788067,0.264238191,0.000000000],[0.037682318,0.031632851,0.016261599,0.022463465,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | 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 [6] // Basepair A2287 - U2344 tWW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004415529,0.072449384,0.004136539,0.033074219,0.000000000],[0.004376309,0.003672370,0.021641442,0.004297347,0.000000000],[0.028386345,0.172159827,0.006373413,0.603433192,0.000000000],[0.021404270,0.004648070,0.004942750,0.010588996,0.000000000],[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 [4] | Right Index [5] // Basepair G2289 - C2343 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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 [13] // Initial node 4Y4O|1|2A|G|2345 - 4Y4O|1|2A|C|2381 from node JunctionNode | Branches [2] | Left Index [7] | Right Index [13] // Junction node G2345 - C2381 ID J975 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 [7] | Right Index [11] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005428049,0.005428049,0.046000828,0.007552856,0.000000000],[0.005428049,0.013114330,0.005428049,0.005428049,0.000000000],[0.210874063,0.047430306,0.539876129,0.051111671,0.000000000],[0.025251681,0.007664253,0.005428049,0.018555587,0.000000000],[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 [11] // Basepair G2345 - G2371 cHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 4Y4O|1|2A|G|2345 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 [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 [9] | Right Index [10] // Basepair C2347 - G2370 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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 [[0.009190997,0.018052541,0.010438844,0.192109964,0.000000000],[0.018265254,0.009284521,0.215171816,0.012586124,0.000000000],[0.010422211,0.225147488,0.002003370,0.024100784,0.000000000],[0.202430569,0.012559332,0.028422025,0.009814160,0.000000000],[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 G2372 - C2381 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_04930.2:
> J4_04930.2 4Y4O C 2285 G 2383 CAAAG*CUGAC*GGG*CGG > J4_04930.2 5J7L C 2285 G 2383 CGAAG*UUGAC*GGU*AGG > J4_04930.2 4WF9 C 2312 G 2410 CAAAG*UUGAC*GGG*CGG > J4_04930.2 7A0S C 2264 G 2362 CAAAG*UUGAC*GGG*CGG > J4_04930.2 5TBW C 2654 G 2753 CUAAG*UUGAU*ACC*GUG > J4_04930.2 4V9F C 2319 G 2420 CUAUG*UUGAC*GAC*GUG