| 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 5 3 | 7 6 I | 8 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 8 I | 14 14 6 | 15 14 I | 16 15 7 | 17 15 I | 18 16 | 19 15 I | 20 15 8 | 21 14 I | 22 14 9 | 23 13 I | 24 18 10 | 25 19 I | 26 20 11 | 27 20 I | 28 21 12 | 29 21 I | 30 22 | 31 21 I | 32 21 13 | 33 20 I | 34 20 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_77044.1_Instance_1 J4_77044.1,J4_5J7L_028,G2643_C2771 | G | G | G | C | G | A | C | G | G | A | A | G | U | G | C | |||||||||||||||||||||||||||
| J4_77044.1_Sequence_1 J4_77044.15J7L_G_2643_C_2771 | G | G | G | C | * | G | A | C | * | G | G | A | A | G | * | U | G | C | true | 99 | 0 | 0 | 0.24 | |||||||||||||||||||
| J4_77044.1_Instance_2 J4_77044.1,J4_4Y4O_023,G2643_C2771 | G | G | G | C | G | A | C | G | G | A | A | G | C | G | C | |||||||||||||||||||||||||||
| J4_77044.1_Sequence_2 J4_77044.14Y4O_G_2643_C_2771 | G | G | G | C | * | G | A | C | * | G | G | A | A | G | * | C | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||
| J4_77044.1_Instance_3 J4_77044.1,J4_4WF9_009,G2670_C2798 | G | A | G | C | G | A | C | G | G | A | C | G | C | C | C | |||||||||||||||||||||||||||
| J4_77044.1_Sequence_3 J4_77044.14WF9_G_2670_C_2798 | G | A | G | C | * | G | A | C | * | G | G | A | C | G | * | C | C | C | true | 97 | 0 | 0 | 0.60 |
1 2 s35 1 15 cWW 2 3 s35 4 5 cWW 4 9 s53 5 6 s35 6 7 s35 6 9 cWW 7 8 cWW 8 9 s35 10 11 s35 11 12 s35 11 14 tHS 12 13 cWW 12 14 s55 13 14 s35 9 3 2BPh 11 14 6BRJAR3D SCFG/MRF model for J4_77044.1:
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 [15] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009639190,0.020074982,0.010976465,0.199366183,0.000000000],[0.016931500,0.009452194,0.201055505,0.013155030,0.000000000],[0.010854565,0.236025807,0.002068996,0.026505317,0.000000000],[0.196814677,0.013653651,0.023233104,0.010192834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [15] // Basepair G2643 - C2771 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.500000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [14] // Fixed node on left for 5J7L|1|DA|G|2644 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [14] // Fixed node on left for 5J7L|1|DA|G|2645 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [14] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [14] // Junction node C2646 - G2770 ID J4505 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 C2646 - G2674 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 [6] | Right Index [14] // Initial node 5J7L|1|DA|A|2675 - 5J7L|1|DA|G|2770 from node JunctionNode | Branches [2] | Left Index [6] | Right Index [14] // Junction node A2675 - G2770 ID J838 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.008589120,0.004207307,0.755260582,0.005038585,0.000000000],[0.004108517,0.002798182,0.038095159,0.012229032,0.000000000],[0.099662909,0.005503283,0.007261344,0.004577802,0.000000000],[0.005028777,0.012920973,0.031358110,0.003360318,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // Basepair A2675 - G2732 cWW BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009443990,0.016935343,0.010857030,0.196859360,0.000000000],[0.020079540,0.009618431,0.236072779,0.013656751,0.000000000],[0.010978957,0.201101150,0.002069466,0.023238378,0.000000000],[0.199411444,0.013158017,0.026511334,0.010008030,0.000000000],[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 [7] | Right Index [8] // Basepair C2676 - G2731 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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 [10] | Right Index [14] // Initial node 5J7L|1|DA|A|2733 - 5J7L|1|DA|G|2770 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [1] | Left Index [10] | Right Index [14] // Fixed node on left for 5J7L|1|DA|A|2733 InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [14] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.096397716,0.113677305,0.157422936,0.130119698,0.000000000],[0.128471263,0.143621845,0.001446502,0.125577863,0.000000000],[0.001446502,0.001446502,0.006796528,0.001446502,0.000000000],[0.006512560,0.001446502,0.082723273,0.001446502,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [11] | Right Index [14] // Basepair A2734 - G2770 tHS BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011654807,0.111384843,0.012043853,0.160831324,0.000000000],[0.015817510,0.010523206,0.146063039,0.013525053,0.000000000],[0.011861335,0.171070354,0.002450295,0.134475360,0.000000000],[0.143284186,0.014296389,0.020241456,0.020476992,0.000000000],[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 G2735 - U2769 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_77044.1:
> J4_77044.1 5J7L G 2643 C 2771 GGGC*GAC*GGAAG*UGC > J4_77044.1 4Y4O G 2643 C 2771 GGGC*GAC*GGAAG*CGC > J4_77044.1 4WF9 G 2670 C 2798 GAGC*GAC*GGACG*CCC