| 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 3 I | 6 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 9 5 | 11 9 I | 12 10 | 13 9 I | 14 9 6 | 15 8 I | 16 12 7 | 17 13 I | 18 14 8 | 19 14 I | 20 15 | 21 14 I | 22 14 9 | 23 6 I | 24 5 10 | 25 4 I | 26 3 11 | 27 2 I | 28 2 12 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_32852.2_Instance_1 J3_32852.2,J3_7A0S_006,C1311_G1659 | C | G | U | A | A | G | C | G | A | U | A | A | G | |||||||||||||||||||||
| J3_32852.2_Sequence_1 J3_32852.27A0S_C_1311_G_1659 | C | G | U | A | A | G | * | C | G | A | * | U | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||
| J3_32852.2_Instance_2 J3_32852.2,J3_4Y4O_022,C1298_G1642 | C | G | U | A | A | G | C | G | G | U | C | A | G | |||||||||||||||||||||
| J3_32852.2_Sequence_2 J3_32852.24Y4O_C_1298_G_1642 | C | G | U | A | A | G | * | C | G | G | * | U | C | A | G | true | 92 | 0 | 0 | 1.48 | ||||||||||||||
| J3_32852.2_Instance_3 J3_32852.2,J3_4WF9_004,C1335_G1686 | C | G | A | U | U | G | C | A | A | U | A | A | G | |||||||||||||||||||||
| J3_32852.2_Sequence_3 J3_32852.24WF9_C_1335_G_1686 | C | G | A | U | U | G | * | C | A | A | * | U | A | A | G | true | 81 | 0 | 0 | 3.49 | ||||||||||||||
| J3_32852.2_Instance_4 J3_32852.2,J3_5J7L_041,C1298_G1642 | C | G | G | A | A | G | C | A | G | C | A | A | G | |||||||||||||||||||||
| J3_32852.2_Sequence_4 J3_32852.25J7L_C_1298_G_1642 | C | G | G | A | A | G | * | C | A | G | * | C | A | A | G | true | 97 | 0 | 0 | 0.63 |
1 2 s35 1 12 cWW 2 9 s33 2 11 tSH 2 12 s55 3 7 s53 4 5 s55 4 7 tSS 4 11 tHW 5 6 cWW 6 7 s35 8 9 cWW 8 10 s55 10 11 s35 11 12 s35 2 10 6BPh 10 2 7BR 12 5 2BRJAR3D SCFG/MRF model for J3_32852.2:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.004641539,0.008323395,0.026680104,0.096752579,0.000000000],[0.009868707,0.004727273,0.547012770,0.006712030,0.000000000],[0.005395946,0.098837337,0.005085512,0.011421215,0.000000000],[0.098006880,0.006466912,0.065149048,0.004918754,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [1] | Right Index [12] // Basepair C1311 - G1659 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.411121066118020] // Cluster node 7A0S|1|X|G|1312:7A0S|1|X|A|1314 and 7A0S|1|X|A|1658:7A0S|1|X|A|1658 Interaction | Interacting Bases [1,4] | Pair Probability [[0.042857649,0.045370598,0.000514478,0.002424734,0.000000000],[0.043176051,0.045265538,0.000514478,0.000514478,0.000000000],[0.398595795,0.003601343,0.017605820,0.305668340,0.000000000],[0.047840582,0.045021164,0.000514478,0.000514478,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|1312 - 7A0S|1|X|A|1658 tSH Interaction | Interacting Bases [3,4] | Pair Probability [[0.372030251,0.029374515,0.003431841,0.015507529,0.000000000],[0.003431841,0.014563521,0.008501137,0.003431841,0.000000000],[0.302750037,0.003431841,0.126145626,0.016448812,0.000000000],[0.044064595,0.003431841,0.036733349,0.016721423,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|1314 - 7A0S|1|X|A|1658 tHW Interaction | Interacting Bases [2,2] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|U|1313 InitialNode | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // Initial node 7A0S|1|X|G|1316 - 7A0S|1|X|A|1657 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.704545455,0.250000000,0.022727273,0.022727273,0.000000000] | Position [2] | Left Index [5] | Right Index [10] // Fixed node on right for 7A0S|1|X|U|1656 InitialNode | Left Length Distribution [1.000000000] | 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 [5] | Right Index [9] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [5] | Right Index [9] // Junction node G1316 - U1656 ID J6787 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 G1316 - C1641 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 [9] // Initial node 7A0S|1|X|G|1642 - 7A0S|1|X|U|1656 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [9] // Fixed node on left for 7A0S|1|X|C|1641 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010822634,0.088558519,0.011090157,0.189427059,0.000000000],[0.016147531,0.010174201,0.153929377,0.011868934,0.000000000],[0.010975303,0.167484236,0.002308725,0.121823196,0.000000000],[0.153826251,0.012646641,0.020567725,0.018349512,0.000000000],[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 A1643 - U1656 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 truncationSequences of instances from J3_32852.2:
> J3_32852.2 7A0S C 1311 G 1659 CGUAAG*CGA*UAAG > J3_32852.2 4Y4O C 1298 G 1642 CGUAAG*CGG*UCAG > J3_32852.2 4WF9 C 1335 G 1686 CGAUUG*CAA*UAAG > J3_32852.2 5J7L C 1298 G 1642 CGGAAG*CAG*CAAG