| 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 4 3 | 7 4 I | 8 7 4 | 9 7 I | 10 8 5 | 11 8 I | 12 9 | 13 8 I | 14 8 6 | 15 7 I | 16 7 7 | 17 6 I | 18 11 8 | 19 12 I | 20 13 9 | 21 14 I | 22 15 10 | 23 15 I | 24 16 | 25 15 I | 26 15 11 | 27 4 I | 28 4 12 | 29 3 I | 30 3 13 | 31 2 I | 32 2 14 | 33 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_85054.2_Instance_1 J3_85054.2,J3_4WF9_005,C1342_G1667 | C | U | A | A | G | C | G | C | A | AA | C | G | U | A | G | |||||||||||||||||||||||
| J3_85054.2_Sequence_1 J3_85054.24WF9_C_1342_G_1667 | C | U | A | A | G | * | C | G | C | A | A | A | C | * | G | U | A | G | true | 79 | 0 | 0 | 4.29 | |||||||||||||||
| J3_85054.2_Instance_2 J3_85054.2,J3_6CZR_018,C835_G813 | C | G | A | A | G | C | G | U | U | A | A | G | C | U | A | G | ||||||||||||||||||||||
| J3_85054.2_Sequence_2 J3_85054.26CZR_C835_G813 | C | G | A | A | G | * | C | G | U | U | A | A | G | * | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_85054.2_Instance_3 J3_85054.2,J3_4LFB_001,C857_G829 | C | G | A | A | G | C | G | U | U | A | A | G | C | U | A | G | ||||||||||||||||||||||
| J3_85054.2_Sequence_3 J3_85054.24LFB_C857_G829 | C | G | A | A | G | * | C | G | U | U | A | A | G | * | C | U | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_85054.2_Instance_4 J3_85054.2,J3_5J7L_004,C857_G829 | C | G | G | A | G | C | G | U | U | A | A | G | C | U | U | G | ||||||||||||||||||||||
| J3_85054.2_Sequence_4 J3_85054.25J7L_C857_G829 | C | G | G | A | G | * | C | G | U | U | A | A | G | * | C | U | U | G | true | 93 | 0 | 0 | 1.44 |
1 2 s35 1 14 cWW 2 7 s33 2 13 tSH 2 14 s55 3 4 s35 3 12 cWS 3 13 s55 4 5 s35 4 7 tHS 5 6 cWW 5 7 s55 6 7 s35 8 12 s53 9 10 s55 9 12 tWW 10 11 cWW 10 12 s55 11 12 s35 13 14 s35 7 3 6BPh 2 8 6BPh 5 10 2BRJAR3D SCFG/MRF model for J3_85054.2:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009353183,0.016772504,0.010752635,0.194966481,0.000000000],[0.019886467,0.009525946,0.243418233,0.013525436,0.000000000],[0.010873390,0.199167485,0.002049567,0.023014932,0.000000000],[0.197494026,0.013031497,0.026256418,0.009911799,0.000000000],[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 [14] // Basepair C1342 - G1667 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.054311612,0.053894558,0.000739175,0.003760316,0.000000000],[0.053172276,0.052433222,0.000739175,0.000739175,0.000000000],[0.321346456,0.003207298,0.018558805,0.297545310,0.000000000],[0.079112236,0.058962034,0.000739175,0.000739175,0.000000000],[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 [2] | Right Index [13] // Basepair U1343 - A1666 tSH BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.159374624,0.152845990,0.157201766,0.242173582,0.000000000],[0.015147788,0.012253258,0.001696211,0.012417102,0.000000000],[0.021968543,0.001696211,0.136926738,0.061666390,0.000000000],[0.006363449,0.006674066,0.005334703,0.006259579,0.000000000],[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 [3] | Right Index [12] // Basepair A1344 - U1665 cWS JunctionNode | Branches [2] | Left Index [4] | Right Index [11] // Junction node A1345 - G1664 ID J1492 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 [4] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | 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]] | 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 [4] | Right Index [7] // Basepair A1345 - G1650 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004738018,0.009867595,0.005395338,0.097995839,0.000000000],[0.008322457,0.004646102,0.098826203,0.006466183,0.000000000],[0.026677098,0.546955482,0.005084939,0.065141709,0.000000000],[0.096741680,0.006711274,0.011419928,0.005010154,0.000000000],[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 G1346 - C1649 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 [8] | Right Index [11] // Initial node 4WF9|1|X|C|1651 - 4WF9|1|X|G|1664 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000] | Position [1] | Left Index [8] | Right Index [11] // Fixed node on left for 4WF9|1|X|C|1651 InitialNode | Left Length Distribution [0.253667482,0.736552567,0.009321516,0.000458435] | Left Letter Distribution [0.100000000,0.100000000,0.100000000,0.700000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [9] | Right Index [11] // Fixed node on left for 4WF9|1|X|A|1652 InitialNode | Left Length Distribution [0.009140768,0.734308349,0.252894576,0.003503961,0.000152346] | Left Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009498175,0.019104591,0.010841350,0.196828520,0.000000000],[0.017548139,0.009402467,0.210196267,0.013152764,0.000000000],[0.010780994,0.232320656,0.002049218,0.025441577,0.000000000],[0.195565178,0.013399649,0.023821386,0.010049069,0.000000000],[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 C1655 - G1664 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 truncationSequences of instances from J3_85054.2:
> J3_85054.2 4WF9 C 1342 G 1667 CUAAG*CGCAAAC*GUAG > J3_85054.2 6CZR C 835 G 813 CGAAG*CGUUAAG*CUAG > J3_85054.2 4LFB C 857 G 829 CGAAG*CGUUAAG*CUAG > J3_85054.2 5J7L C 857 G 829 CGGAG*CGUUAAG*CUUG