| 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 4 3 | 7 4 I | 8 7 4 | 9 7 I | 10 7 5 | 11 8 I | 12 9 6 | 13 9 I | 14 10 7 | 15 10 I | 16 11 | 17 10 I | 18 10 8 | 19 9 I | 20 9 9 | 21 8 I | 22 7 10 | 23 6 I | 24 5 11 | 25 4 I | 26 4 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_29198.2_Instance_1 IL_29198.2,IL_8P9A_266,G991_U1058 | G | A | G | G | U | A | A | U | A | A | A | U | A | U | ||||||||||||||||||||||
| IL_29198.2_Sequence_1 IL_29198.28P9A_G991_U_1058 | G | A | G | G | U | A | A | * | U | A | A | A | U | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_29198.2_Instance_2 IL_29198.2,IL_8CRE_041,G987_U1054 | G | A | G | G | U | A | A | U | A | A | A | U | A | U | ||||||||||||||||||||||
| IL_29198.2_Sequence_2 IL_29198.28CRE_G987_U_1054 | G | A | G | G | U | A | A | * | U | A | A | A | U | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_29198.2_Instance_3 IL_29198.2,IL_4WF9_031,G901_C966 | G | A | G | G | U | A | G | C | G | A | A | U | G | C | ||||||||||||||||||||||
| IL_29198.2_Sequence_3 IL_29198.24WF9_G901_C966 | G | A | G | G | U | A | G | * | C | G | A | A | U | G | C | true | 95 | 0 | 0 | 0.99 | ||||||||||||||||
| IL_29198.2_Instance_4 IL_29198.2,IL_5J7L_270,G856_C921 | G | G | G | G | U | A | G | C | G | A | A | U | A | C | ||||||||||||||||||||||
| IL_29198.2_Sequence_4 IL_29198.25J7L_G856_C921 | G | G | G | G | U | A | G | * | C | G | A | A | U | A | C | true | 95 | 0 | 0 | 1.01 |
1 2 s35 1 14 cWW 2 3 s35 2 13 cWW 3 12 bif 3 13 s55 4 5 cSH 4 9 s33 5 6 s35 5 9 s33 5 10 tWH 6 7 s35 6 9 tHS 6 10 s55 7 8 cWW 7 9 s55 8 9 s35 10 11 s35 11 12 s35 12 13 s35 13 14 s35 4 10 6BPh 9 4 6BR 6 9 6BRJAR3D SCFG/MRF model for IL_29198.2:
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 [14] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.012540860,0.155529775,0.012456608,0.140202703,0.000000000],[0.015113779,0.010952378,0.117426741,0.013578237,0.000000000],[0.012245828,0.142067698,0.002615550,0.191455955,0.000000000],[0.115398566,0.014477202,0.018565386,0.025372734,0.000000000],[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 [14] // Basepair G991 - U1058 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.324258723,0.020669487,0.207340113,0.021874517,0.000000000],[0.016183108,0.009938791,0.022669555,0.034351847,0.000000000],[0.201673460,0.022947797,0.004691252,0.021989185,0.000000000],[0.021499233,0.035975684,0.017664835,0.016272412,0.000000000],[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 [2] | Right Index [13] // Basepair A992 - A1057 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.045965469,0.300684085,0.003676754,0.003676754,0.000000000],[0.023538170,0.014096579,0.003676754,0.003676754,0.000000000],[0.003676754,0.003676754,0.172811225,0.406136932,0.000000000],[0.003676754,0.003676754,0.003676754,0.003676754,0.000000000],[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 [3] | Right Index [12] // Basepair G993 - U1056 bif FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [4] | Right Index [11] // Fixed node on right for 8P9A|1|AR|A|1055 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [10] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [4] | Right Index [10] | Norm Constant [0.269832767432214] // Cluster node 8P9A|1|AR|G|994:8P9A|1|AR|U|995 and 8P9A|1|AR|A|1054:8P9A|1|AR|A|1054 Interaction | Interacting Bases [2,3] | Pair Probability [[0.018414538,0.004075167,0.019126511,0.004075167,0.000000000],[0.040981170,0.328380556,0.004075167,0.004075167,0.000000000],[0.004075167,0.009768444,0.030991298,0.018124938,0.000000000],[0.445978203,0.004075167,0.023643628,0.040139714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|U|995 - 8P9A|1|AR|A|1054 tWH Interaction | Interacting Bases [1,2] | Pair Probability [[0.030507812,0.031086061,0.001709208,0.030379978,0.000000000],[0.022776075,0.034323944,0.000378448,0.030443666,0.000000000],[0.186583170,0.002649134,0.227599663,0.303374889,0.000000000],[0.030981169,0.030795185,0.000378448,0.036033152,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|AR|G|994 - 8P9A|1|AR|U|995 cSH 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 [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.279711057,0.072417813,0.219753102,0.072117434,0.000000000],[0.055760800,0.046991416,0.002083215,0.070257469,0.000000000],[0.002658770,0.000790331,0.011958295,0.000790331,0.000000000],[0.015765394,0.000790331,0.147363911,0.000790331,0.000000000],[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 [6] | Right Index [9] // Basepair A996 - A1053 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009325457,0.020734609,0.010297314,0.218050308,0.000000000],[0.016974989,0.009378665,0.194777146,0.011594085,0.000000000],[0.010227486,0.218136243,0.002025500,0.039220448,0.000000000],[0.193588082,0.012169223,0.022789886,0.010710558,0.000000000],[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 [7] | Right Index [8] // Basepair A997 - U1052 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 IL_29198.2:
> IL_29198.2 8P9A G 991 U 1058 GAGGUAA*UAAAUAU > IL_29198.2 8CRE G 987 U 1054 GAGGUAA*UAAAUAU > IL_29198.2 4WF9 G 901 C 966 GAGGUAG*CGAAUGC > IL_29198.2 5J7L G 856 C 921 GGGGUAG*CGAAUAC