| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 3 I | 4 4 2 | 5 5 I | 6 16 3 | 7 16 I | 8 17 4 | 9 17 I | 10 18 | 11 17 I | 12 17 5 | 13 16 I | 14 16 6 | 15 15 I | 16 20 7 | 17 21 I | 18 22 8 | 19 23 I | 20 26 9 | 21 26 I | 22 27 | 23 26 I | 24 26 10 | 25 25 I | 26 29 11 | 27 30 I | 28 31 12 | 29 31 I | 30 32 13 | 31 32 I | 32 33 | 33 32 I | 34 32 14 | 35 31 I | 36 31 15 | 37 13 I | 38 12 16 | 39 11 I | 40 10 17 | 41 9 I | 42 8 18 | 43 7 I | 44 6 19 | 45 3 I | 46 2 20 | 47 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_60168.1_Instance_1 J4_60168.1,J4_4WF9_003,C644_G701 | C | A | A | G | C | G | U | A | G | C | G | A | G | U | G | C | G | U | U | U | A | G | ||||||||||||||||||||||||||||||
| J4_60168.1_Sequence_1 J4_60168.14WF9_C644_G701 | C | A | A | G | * | C | G | U | A | G | * | C | G | A | G | U | * | G | C | G | U | U | U | A | G | true | 96 | 0 | 0 | 0.73 | ||||||||||||||||||||||
| J4_60168.1_Instance_2 J4_60168.1,J4_5J7L_020,C601_G656 | C | A | A | G | C | G | A | A | G | C | G | A | G | C | G | U | U | A | A | G | ||||||||||||||||||||||||||||||||
| J4_60168.1_Sequence_2 J4_60168.15J7L_C601_G656 | C | A | A | G | * | C | G | A | A | G | * | C | G | A | G | * | C | G | U | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 20 cWW 2 19 perp 2 20 s55 3 6 tSS 3 19 s55 4 5 cWW 4 6 s55 4 20 rib 6 7 s35 8 9 perp 8 11 perp 8 12 s55 9 10 cWW 9 11 s55 9 12 perp 9 13 rib 10 11 s35 12 15 tSS 13 14 cWW 13 15 s55 14 15 s35 15 16 s35 19 20 perp 19 3 6BPh 8 12 6BPh 12 9 2BR 4 20 2BRJAR3D SCFG/MRF model for J4_60168.1:
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 ClusterNode | Deletion Probability [0.0000250000000000] | Num Left Bases [1] | Num Right Bases [1] | Left Index [1] | Right Index [20] | Norm Constant [1.000000000000000] // Cluster node 4WF9|1|X|C|644:4WF9|1|X|C|644 and 4WF9|1|X|G|701:4WF9|1|X|G|701 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009536579,0.017101376,0.010963471,0.198789353,0.000000000],[0.020276398,0.009712729,0.228583296,0.013790641,0.000000000],[0.011086594,0.203072729,0.002089755,0.023466206,0.000000000],[0.201366458,0.013287017,0.026771249,0.010106148,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 4WF9|1|X|C|644 - 4WF9|1|X|G|701 cWW InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [19] // Initial node 4WF9|1|X|A|645 - 4WF9|1|X|A|700 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [2] | Right Index [19] // Fixed node on left for 4WF9|1|X|A|645 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [2] | Left Index [3] | Right Index [19] // Fixed node on right for 4WF9|1|X|U|698 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [18] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [2] | Left Index [3] | Right Index [18] // Fixed node on right for 4WF9|1|X|U|697 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [17] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [3] | Right Index [17] // Fixed node on right for 4WF9|1|X|G|696 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [16] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Position [2] | Left Index [3] | Right Index [16] // Fixed node on right for 4WF9|1|X|C|695 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [3] | Right Index [15] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [15] // Junction node A646 - C695 ID J9292 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Initial node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.190035222,0.189580490,0.214628497,0.179785606,0.000000000],[0.001950207,0.001950207,0.020208495,0.001950207,0.000000000],[0.015291419,0.001950207,0.015927036,0.158941582,0.000000000],[0.001950207,0.001950207,0.001950207,0.001950207,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A646 - G670 tSS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.004830920,0.010061077,0.005501129,0.099917326,0.000000000],[0.008485643,0.004737202,0.100763972,0.006592971,0.000000000],[0.027200179,0.538072256,0.005184644,0.066418997,0.000000000],[0.098638576,0.006842867,0.011643848,0.005108392,0.000000000],[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 G647 - C669 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 [15] // Initial node 4WF9|1|X|U|671 - 4WF9|1|X|C|695 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [1] | Left Index [7] | Right Index [15] // Fixed node on left for 4WF9|1|X|U|671 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [15] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.906250000,0.031250000,0.031250000,0.031250000,0.000000000] | Position [1] | Left Index [8] | Right Index [15] // Fixed node on left for 4WF9|1|X|A|672 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [15] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [9] | Right Index [15] // Junction node G673 - C695 ID J3499 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009733692,0.020271796,0.011084078,0.201320753,0.000000000],[0.017097495,0.009544863,0.203026637,0.013284001,0.000000000],[0.010960983,0.228535864,0.002089280,0.026765173,0.000000000],[0.198744233,0.013787510,0.023460879,0.010292763,0.000000000],[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 G673 - C680 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 [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [15] // Initial node 4WF9|1|X|G|681 - 4WF9|1|X|C|695 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.125000000,0.625000000,0.125000000,0.000000000] | Position [1] | Left Index [11] | Right Index [15] // Fixed node on left for 4WF9|1|X|G|681 InitialNode | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [12] | Right Index [15] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.211816489,0.310240118,0.227177257,0.200392093,0.000000000],[0.000434747,0.000434747,0.004504946,0.000434747,0.000000000],[0.003408815,0.000434747,0.003550509,0.035431798,0.000000000],[0.000434747,0.000434747,0.000434747,0.000434747,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [12] | Right Index [15] // Basepair A682 - C695 tSS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010489920,0.017127883,0.012680838,0.119297674,0.000000000],[0.159817824,0.018747803,0.122690376,0.014659067,0.000000000],[0.012775575,0.132830577,0.002697714,0.020718591,0.000000000],[0.142468525,0.014233330,0.186841746,0.011922559,0.000000000],[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 [13] | Right Index [14] // Basepair U684 - G694 cWW HairpinNode | Num Bases [1] | Left Index [14] | Right Index [14] | 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_60168.1:
> J4_60168.1 4WF9 C 644 G 701 CAAG*CGUAG*CGAGU*GCGUUUAG > J4_60168.1 5J7L C 601 G 656 CAAG*CGAAG*CGAG*CGUUAAG