| 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 5 2 | 5 5 I | 6 5 3 | 7 5 I | 8 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 5 I | 16 5 8 | 17 6 I | 18 7 | 19 6 I | 20 5 9 | 21 4 I | 22 9 10 | 23 9 I | 24 10 | 25 9 I | 26 9 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_65070.2_Instance_1 J3_65070.2,J3_7A0S_001,G485_C31 | G | U | G | A | A | A | A | G | C | C | G | C | ||||||||||||||||||||||
| J3_65070.2_Sequence_1 J3_65070.27A0S_G485_C31 | G | U | G | A | A | A | A | G | * | C | C | * | G | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_65070.2_Instance_2 J3_65070.2,J3_5J7L_036,G474_C31 | G | C | G | A | A | A | A | G | C | C | G | C | ||||||||||||||||||||||
| J3_65070.2_Sequence_2 J3_65070.25J7L_G474_C31 | G | C | G | A | A | A | A | G | * | C | C | * | G | C | true | 96 | 0 | 0 | 0.67 | |||||||||||||||
| J3_65070.2_Instance_3 J3_65070.2,J3_5TBW_002,A369_U20 | A | U | G | A | A | A | A | G | C | G | C | U | ||||||||||||||||||||||
| J3_65070.2_Sequence_3 J3_65070.25TBW_A369_U20 | A | U | G | A | A | A | A | G | * | C | G | * | C | U | true | 99 | 0 | 0 | 0.11 |
1 10 s35 1 12 cWW 2 3 s35 2 6 tWH 2 8 s55 2 9 s53 3 5 s33 3 6 s55 3 7 tSH 4 5 s35 5 7 s35 6 7 s53 6 8 s35 8 9 cWW 10 11 cWW 11 12 s35 3 6 6BPh 5 3 7BRJAR3D SCFG/MRF model for J3_65070.2:
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 [0.0000234451146992] | Pair Probability [[0.009490394,0.020648938,0.010590347,0.209997349,0.000000000],[0.017070363,0.009463878,0.198130626,0.012189443,0.000000000],[0.010502710,0.222275070,0.002053109,0.035235925,0.000000000],[0.195916611,0.012742798,0.023085133,0.010607307,0.000000000],[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 [12] // Basepair G485 - C31 cWW JunctionNode | Branches [2] | Left Index [2] | Right Index [11] // Junction node U486 - G30 ID J1189 InitialNode | Left Length Distribution [1.000000000] | 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 [2] | Right Index [9] // Initial node 7A0S|1|X|U|486 - 7A0S|1|X|C|519 from node ClusterNode | Deletion Probability [0.000000000000000000390625000000000088131570158437809669143083] | Num Left Bases [7] | Num Right Bases [1] | Left Index [2] | Right Index [9] | Norm Constant [1.000000000000001] // Cluster node 7A0S|1|X|U|486:7A0S|1|X|G|492 and 7A0S|1|X|C|519:7A0S|1|X|C|519 Interaction | Interacting Bases [7,8] | 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]] // Cluster Interaction 7A0S|1|X|G|492 - 7A0S|1|X|C|519 cWW Interaction | Interacting Bases [1,5] | Pair Probability [[0.022535241,0.003927780,0.046763283,0.003927780,0.000000000],[0.155757385,0.229676577,0.003927780,0.003927780,0.000000000],[0.003927780,0.010711390,0.031514270,0.023120249,0.000000000],[0.305645877,0.003927780,0.021241556,0.129467490,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|U|486 - 7A0S|1|X|A|490 tWH Interaction | Interacting Bases [2,6] | Pair Probability [[0.043273743,0.045811089,0.000519472,0.002448275,0.000000000],[0.043595236,0.045705009,0.000519472,0.000519472,0.000000000],[0.392756919,0.003636307,0.017776750,0.308635994,0.000000000],[0.048305054,0.045458262,0.000519472,0.000519472,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|487 - 7A0S|1|X|A|491 tSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|A|488 Interaction | Interacting Bases [4,4] | Pair Probability [[0.911764706,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|A|489 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [8] // New Initial node after Cluster 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 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 [10] | Right Index [11] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009509057,0.017981890,0.010896842,0.197694967,0.000000000],[0.019030193,0.009563019,0.224400354,0.013489511,0.000000000],[0.010937493,0.212742702,0.002069309,0.024327358,0.000000000],[0.198545855,0.013323228,0.025418591,0.010069631,0.000000000],[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 C520 - G30 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_65070.2:
> J3_65070.2 7A0S G 485 C 31 GUGAAAAG*CC*GC > J3_65070.2 5J7L G 474 C 31 GCGAAAAG*CC*GC > J3_65070.2 5TBW A 369 U 20 AUGAAAAG*CG*CU