| 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 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 5 5 | 11 6 I | 12 11 6 | 13 11 I | 14 12 | 15 11 I | 16 11 7 | 17 10 I | 18 14 8 | 19 15 I | 20 16 9 | 21 16 I | 22 17 | 23 16 I | 24 16 10 | 25 8 I | 26 7 11 | 27 4 I | 28 3 12 | 29 2 I | 30 2 13 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J3_84189.2_Instance_1 J3_84189.2,J3_7A0S_007,C1621_G1322 | C | G | C | A | A | A | C | G | U | G | C | A | A | G | ||||||||||||||||||||||
| J3_84189.2_Sequence_1 J3_84189.27A0S_C_1621_G_1322 | C | G | C | A | A | A | C | * | G | U | G | * | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||||
| J3_84189.2_Instance_2 J3_84189.2,J3_4V9F_005,C1404_G1718 | C | U | A | A | U | G | C | A | U | G | C | A | A | G | ||||||||||||||||||||||
| J3_84189.2_Sequence_2 J3_84189.24V9F_C_1404_G_1718 | C | U | A | A | U | G | * | C | A | U | G | * | C | A | A | G | true | 78 | 0 | 0 | 4.34 | |||||||||||||||
| J3_84189.2_Instance_3 J3_84189.2,J3_4Y4O_023,C1605_G1309 | C | G | C | A | A | A | C | G | U | G | C | A | A | G | ||||||||||||||||||||||
| J3_84189.2_Sequence_3 J3_84189.24Y4O_C_1605_G_1309 | C | G | C | A | A | A | C | * | G | U | G | * | C | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 12 tSH 2 13 s55 3 8 s53 3 9 tHH 4 6 s35 4 8 tHW 4 12 tWW 6 7 cWW 7 8 s35 9 10 cWW 9 11 s55 10 11 s35 11 12 s35 12 13 s35 6 5 7BPh 3 9 6BPh 13 6 2BRJAR3D SCFG/MRF model for J3_84189.2:
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 [13] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.004686603,0.008404204,0.026939134,0.097691925,0.000000000],[0.009964519,0.004773169,0.542614836,0.006777195,0.000000000],[0.005448334,0.099796923,0.005134886,0.011532100,0.000000000],[0.098958403,0.006529697,0.065781563,0.004966509,0.000000000],[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 [13] // Basepair C1621 - G1322 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [12] | Norm Constant [0.285003745332375] // Cluster node 7A0S|1|X|G|1622:7A0S|1|X|A|1624 and 7A0S|1|X|A|1321:7A0S|1|X|A|1321 Interaction | Interacting Bases [1,4] | Pair Probability [[0.106334440,0.112569335,0.001276474,0.006016026,0.000000000],[0.107124428,0.112308671,0.001276474,0.001276474,0.000000000],[0.147064882,0.001276474,0.006240276,0.108342292,0.000000000],[0.174638455,0.111702351,0.001276474,0.001276474,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|G|1622 - 7A0S|1|X|A|1321 tSH Interaction | Interacting Bases [3,4] | Pair Probability [[0.414443196,0.029718936,0.003853170,0.018419488,0.000000000],[0.028948610,0.014046437,0.011475468,0.014056646,0.000000000],[0.003853170,0.011491976,0.356313449,0.021716090,0.000000000],[0.018397520,0.014053216,0.021246137,0.017966491,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 7A0S|1|X|A|1624 - 7A0S|1|X|A|1321 tWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.326086957,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.630434783,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.021739130,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 7A0S|1|X|C|1623 InitialNode | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [11] // Initial node 7A0S|1|X|A|1626 - 7A0S|1|X|A|1320 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.100000000,0.300000000,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // Fixed node on left for 7A0S|1|X|C|1621 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 [6] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [6] | Right Index [11] // Fixed node on right for 7A0S|1|X|C|1627 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 [6] | Right Index [10] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [6] | Right Index [10] // Junction node C1627 - C1319 ID J5472 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 [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.005685123,0.011124657,0.006500758,0.117985306,0.000000000],[0.042435980,0.020774777,0.465628354,0.029408551,0.000000000],[0.006492041,0.131315512,0.001231369,0.014917984,0.000000000],[0.117802838,0.007995460,0.014683976,0.006017314,0.000000000],[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 [6] | Right Index [7] // Basepair C1627 - G1636 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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 [10] // Initial node 7A0S|1|X|U|1637 - 7A0S|1|X|C|1319 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.300000000,0.100000000,0.100000000,0.500000000,0.000000000] | Position [1] | Left Index [8] | Right Index [10] // Fixed node on left for 7A0S|1|X|A|1624 InitialNode | Left Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [9] | Right Index [10] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | 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 [0.990049834,0.009900498,0.000049502,0.000000165] | 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 G1638 - C1319 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 truncationSequences of instances from J3_84189.2:
> J3_84189.2 7A0S C 1621 G 1322 CGCAAAC*GUG*CAAG > J3_84189.2 4V9F C 1404 G 1718 CUAAUG*CAUG*CAAG > J3_84189.2 4Y4O C 1605 G 1309 CGCAAAC*GUG*CAAG