| 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 11 4 | 9 11 I | 10 12 | 11 11 I | 12 11 5 | 13 10 I | 14 14 6 | 15 15 I | 16 16 7 | 17 16 I | 18 17 | 19 16 I | 20 16 8 | 21 8 I | 22 7 9 | 23 2 I | 24 2 10 | 25 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_82365.1_Instance_1 J3_82365.1,J3_4V88_040,G1386_C1338 | G | G | A | C | G | U | U | U | A | A | C | |||||||||||||||||||
| J3_82365.1_Sequence_1 J3_82365.14V88_G_1386_C_1338 | G | G | A | C | * | G | U | U | U | * | A | A | C | true | 97 | 0 | 0 | 0.30 | ||||||||||||
| J3_82365.1_Instance_2 J3_82365.1,J3_5J7L_010,A1155_U1118 | A | G | A | C | G | G | U | G | U | A | U | |||||||||||||||||||
| J3_82365.1_Sequence_2 J3_82365.15J7L_A_1155_U_1118 | A | G | A | C | * | G | G | U | G | * | U | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| J3_82365.1_Instance_3 J3_82365.1,J3_4LFB_008,G1155_C1118 | G | G | A | C | G | G | A | G | C | G | C | |||||||||||||||||||
| J3_82365.1_Sequence_3 J3_82365.14LFB_G_1155_C_1118 | G | G | A | C | * | G | G | A | G | * | C | G | C | true | 93 | 0 | 0 | 0.80 |
1 2 s35 1 10 cWW 2 10 s55 3 4 s53 3 5 s55 4 5 cWW 7 8 cWW 7 9 s55 8 9 s35 3 5 2BRJAR3D SCFG/MRF model for J3_82365.1:
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 [10] // 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 [10] // Basepair G1386 - C1338 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 4V88|1|A6|A|1337 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 [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.911764706,0.029411765,0.029411765,0.029411765,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 4V88|1|A6|C|1338 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 [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 4V88|1|A6|U|1413 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 [4] | Right Index [8] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [4] | Right Index [8] // Junction node C1389 - A1336 ID J6990 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 C1389 - G1412 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 [8] // Initial node 4V88|1|A6|U|1413 - 4V88|1|A6|A|1336 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.500000000,0.300000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left for 4V88|1|A6|A|1388 InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011423951,0.110484656,0.011656322,0.159180973,0.000000000],[0.017450321,0.010617882,0.144067618,0.012785933,0.000000000],[0.011520818,0.156585994,0.002435430,0.133248182,0.000000000],[0.154868126,0.013169784,0.030089465,0.020414546,0.000000000],[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 U1415 - A1336 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 truncationSequences of instances from J3_82365.1:
> J3_82365.1 4V88 G 1386 C 1338 GGAC*GUUU*AAC > J3_82365.1 5J7L A 1155 U 1118 AGAC*GGUG*UAU > J3_82365.1 4LFB G 1155 C 1118 GGAC*GGAG*CGC