| 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 8 4 | 9 8 I | 10 9 | 11 8 I | 12 8 5 | 13 7 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_05684.1_Instance_1 IL_05684.1_IL_3BNP_003_C5_G18 | C | A | C | C | G | C | A | A | G | |||||||||||||||
| IL_05684.1_Sequence_1 IL_05684.1_IL_3BNP_003_C5_G18 | C | A | C | C | * | G | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_05684.1_Instance_2 IL_05684.1_IL_3BNP_002_C6_G17 | C | A | C | C | G | C | A | A | G | |||||||||||||||
| IL_05684.1_Sequence_2 IL_05684.1_IL_3BNP_002_C6_G17 | C | A | C | C | * | G | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_05684.1_Instance_3 IL_05684.1_IL_3BNQ_005_C7_G19 | C | A | C | C | G | C | A | A | G | |||||||||||||||
| IL_05684.1_Sequence_3 IL_05684.1_IL_3BNQ_005_C7_G19 | C | A | C | C | * | G | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_05684.1_Instance_4 IL_05684.1_IL_2QBG_057_U1468_G1524 | U | A | A | G | U | G | A | U | G | |||||||||||||||
| IL_05684.1_Sequence_4 IL_05684.1_IL_2QBG_057_U_1468_G_1524 | U | A | A | G | * | U | G | A | U | G | true | 88 | 0 | 0 | 1.45 | |||||||||
| IL_05684.1_Instance_5 IL_05684.1_IL_3V2F_043_U1240_G1206 | U | A | A | G | C | G | A | U | G | |||||||||||||||
| IL_05684.1_Sequence_5 IL_05684.1_IL_3V2F_043_U_1240_G_1206 | U | A | A | G | * | C | G | A | U | G | true | 93 | 0 | 0 | 0.81 |
1 7 s35 1 8 cWW 2 3 s35 2 6 s33 3 4 s35 3 6 tHS 4 5 cWW 5 6 s35 6 7 s33 7 8 s55JAR3D SCFG/MRF model for IL_05684.1:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Initial node C5 - G18 from junction BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.010904993,0.015774246,0.012839185,0.127192867,0.000000000],[0.135276838,0.011234809,0.171466677,0.014903175,0.000000000],[0.013062604,0.136650032,0.002624031,0.019883418,0.000000000],[0.130523585,0.013857958,0.172213082,0.011592499,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.500000000,0.071428571,0.071428571,0.357142857,0.000000000] | Left Index [1] | Right Index [8] // Basepair C5 - G18 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | 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 BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.088238881,0.104302184,0.145760343,0.116988883,0.000000000],[0.124232993,0.211045704,0.001329649,0.115356801,0.000000000],[0.001329649,0.001329649,0.006210180,0.001329649,0.000000000],[0.006083401,0.001329649,0.073802737,0.001329649,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair C7 - C15 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011033085,0.074348218,0.012113716,0.158408284,0.000000000],[0.018262496,0.008870795,0.201792114,0.013691727,0.000000000],[0.012104519,0.181373891,0.002341722,0.095844836,0.000000000],[0.157531112,0.013758912,0.023639681,0.014884893,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair C8 - G14 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 truncationSequences of instances from IL_05684.1:
> IL_05684.1 IL_3BNP_003 C 5 G 18 CACC*GCAAG > IL_05684.1 IL_3BNP_002 C 6 G 17 CACC*GCAAG > IL_05684.1 IL_3BNQ_005 C 7 G 19 CACC*GCAAG > IL_05684.1 IL_2QBG_057 U 1468 G 1524 UAAG*UGAUG > IL_05684.1 IL_3V2F_043 U 1240 G 1206 UAAG*CGAUG