| 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 7 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_45262.4_Instance_1 IL_45262.4_IL_4IOA_062_G1668_C1989 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_45262.4_Sequence_1 IL_45262.4_IL_4IOA_062_G_1668_C_1989 | G | A | G | A | A | C | * | G | A | C | ||||||||||||||||
| IL_45262.4_Instance_2 IL_45262.4_IL_3V2F_061_G1651_C2006 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_45262.4_Sequence_2 IL_45262.4_IL_3V2F_061_G_1651_C_2006 | G | A | G | A | A | C | * | G | A | C | ||||||||||||||||
| IL_45262.4_Instance_3 IL_45262.4_IL_2QBG_062_G1651_C2006 | G | A | G | A | A | C | G | A | C | |||||||||||||||||
| IL_45262.4_Sequence_3 IL_45262.4_IL_2QBG_062_G_1651_C_2006 | G | A | G | A | A | C | * | G | A | C | ||||||||||||||||
| IL_45262.4_Instance_4 IL_45262.4_IL_1S72_059_G1728_C2047 | G | A | G | C | A | A | C | G | G | C | ||||||||||||||||
| IL_45262.4_Sequence_4 IL_45262.4_IL_1S72_059_G_1728_C_2047 | G | A | G | C | A | A | C | * | G | G | C |
1 2 s35 1 9 cWW 2 3 s35 4 5 s35 4 8 s33 5 6 s35 5 8 tHS 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 6 5 7BPh 9 8 7BPh 5 8 6BRJAR3D SCFG/MRF model for IL_45262.4:
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 [9] // Initial node G1668 - C1989 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.003876703,0.055283349,0.004488645,0.073569181,0.000000000],[0.006541094,0.022376317,0.079237697,0.005043447,0.000000000],[0.004432143,0.610609112,0.000817354,0.010483940,0.000000000],[0.073144353,0.037059067,0.009043524,0.003994075,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G1668 - C1989 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left InitialNode | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.583333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [8] // Fixed node on left InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [5] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.173411245,0.141252118,0.139885603,0.137787579,0.000000000],[0.125873053,0.075536512,0.001501862,0.132650365,0.000000000],[0.001501862,0.001501862,0.011776213,0.001501862,0.000000000],[0.010844398,0.001501862,0.041971740,0.001501862,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A1672 - A1988 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003812320,0.006539138,0.004430817,0.073122478,0.000000000],[0.055266817,0.022793068,0.610438009,0.037047985,0.000000000],[0.004487303,0.079214000,0.000817109,0.009040820,0.000000000],[0.073547180,0.005041939,0.010480804,0.003920212,0.000000000],[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 [6] | Right Index [7] // Basepair C1673 - G1987 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 truncationSequences of instances from IL_45262.4:
> IL_45262.4 IL_4IOA_062 G 1668 C 1989 GAGAAC*GAC > IL_45262.4 IL_3V2F_061 G 1651 C 2006 GAGAAC*GAC > IL_45262.4 IL_2QBG_062 G 1651 C 2006 GAGAAC*GAC > IL_45262.4 IL_1S72_059 G 1728 C 2047 GAGCAAC*GGC