| 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 7 3 | 7 7 I | 8 7 4 | 9 7 I | 10 7 5 | 11 8 I | 12 9 | 13 8 I | 14 7 6 | 15 6 I | 16 5 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_69440.3_Instance_1 IL_69440.3,IL_5J7L_254,C343_G295 | C | A | A | A | A | U | A | G | ||||||||||||||||
| IL_69440.3_Sequence_1 IL_69440.35J7L_C343_G295 | C | A | A | A | A | * | U | A | G | true | 95 | 0 | 0 | 0.51 | ||||||||||
| IL_69440.3_Instance_2 IL_69440.3,IL_9DFE_011,C343_G295 | C | G | A | A | A | U | A | G | ||||||||||||||||
| IL_69440.3_Sequence_2 IL_69440.39DFE_C343_G295 | C | G | A | A | A | * | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_69440.3_Instance_3 IL_69440.3,IL_4WF9_014,C386_G338 | C | G | A | A | A | U | A | G | ||||||||||||||||
| IL_69440.3_Sequence_3 IL_69440.34WF9_C386_G338 | C | G | A | A | A | * | U | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 8 s55 3 4 cSH 3 5 s35 3 6 s33 3 7 s55 4 5 s35 5 6 cWW 5 3 7BRJAR3D SCFG/MRF model for IL_69440.3:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | 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 [0.993970181,0.005999820,0.000029999] | 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 [8] // Basepair C343 - G295 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 [7] // Fixed node on left for 5J7L|1|DA|A|294 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 [7] // 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 [3] | Right Index [7] // Fixed node on right for 5J7L|1|DA|A|346 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 [3] | Right Index [6] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [3] | Num Right Bases [1] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Cluster node 5J7L|1|DA|A|345:5J7L|1|DA|A|347 and 5J7L|1|DA|U|293:5J7L|1|DA|U|293 Interaction | Interacting Bases [3,4] | Pair Probability [[0.022971459,0.054467125,0.024534015,0.534228079,0.000000000],[0.008670066,0.004741447,0.096096332,0.005126781,0.000000000],[0.004897252,0.097342125,0.001010204,0.026336484,0.000000000],[0.097015716,0.005458041,0.011389368,0.005715505,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|347 - 5J7L|1|DA|U|293 cWW Interaction | Interacting Bases [1,2] | Pair Probability [[0.187259051,0.101614492,0.005090369,0.012801197,0.000000000],[0.102841136,0.096103725,0.001119008,0.007902860,0.000000000],[0.007928601,0.001119008,0.092976433,0.090206588,0.000000000],[0.107680396,0.094021553,0.001119008,0.090216576,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5J7L|1|DA|A|345 - 5J7L|1|DA|A|346 cSH InitialNode | Left Length Distribution [0.952380952,0.047619048] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.952380952,0.047619048] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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 IL_69440.3:
> IL_69440.3 5J7L C 343 G 295 CAAAA*UAG > IL_69440.3 9DFE C 343 G 295 CGAAA*UAG > IL_69440.3 4WF9 C 386 G 338 CGAAA*UAG