| 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 9 4 | 9 9 I | 10 10 | 11 9 I | 12 9 5 | 13 8 I | 14 7 6 | 15 2 I | 16 2 7 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_31531.3_Instance_1 IL_31531.3,IL_2ET8_002,G38_C8 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_1 IL_31531.32ET8_G38_C8 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_2 IL_31531.3,IL_2O3X_002,G39_C9 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_2 IL_31531.32O3X_G39_C9 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_3 IL_31531.3,IL_4ZC7_003,A16_U32 | A | A | A | G | C | G | U | |||||||||||||||
| IL_31531.3_Sequence_3 IL_31531.34ZC7_A16_U32 | A | A | A | G | * | C | G | U | true | 80 | 0 | 0 | 1.92 | |||||||||
| IL_31531.3_Instance_4 IL_31531.3,IL_4LFB_070,G1491_C1409 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_4 IL_31531.34LFB_G_1491_C_1409 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_5 IL_31531.3,IL_1ZZ5_001,G7_C28 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_5 IL_31531.31ZZ5_G7_C28 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_6 IL_31531.3,IL_4PDQ_002,G39_C9 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_6 IL_31531.34PDQ_G39_C9 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_7 IL_31531.3,IL_3C3Z_003,G7_C17 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_7 IL_31531.33C3Z_G7_C17 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_8 IL_31531.3,IL_1T0E_001,G7_C18 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_8 IL_31531.31T0E_G7_C18 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_9 IL_31531.3,IL_7A0S_100,G2846_C2820 | G | G | A | C | G | G | C | |||||||||||||||
| IL_31531.3_Sequence_9 IL_31531.37A0S_G_2846_C_2820 | G | G | A | C | * | G | G | C | true | 66 | 0 | 0 | 3.27 | |||||||||
| IL_31531.3_Instance_10 IL_31531.3,IL_1ZX7_005,G7_C28 | G | A | A | G | C | A | C | |||||||||||||||
| IL_31531.3_Sequence_10 IL_31531.31ZX7_G7_C28 | G | A | A | G | * | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_31531.3_Instance_11 IL_31531.3,IL_5J7L_065,U1445_G1457 | U | A | A | C | G | A | G | |||||||||||||||
| IL_31531.3_Sequence_11 IL_31531.35J7L_U_1445_G_1457 | U | A | A | C | * | G | A | G | true | 90 | 0 | 0 | 0.95 | |||||||||
| IL_31531.3_Instance_12 IL_31531.3,IL_4WF9_107,U2891_G2865 | U | G | A | C | G | A | G | |||||||||||||||
| IL_31531.3_Sequence_12 IL_31531.34WF9_U_2891_G_2865 | U | G | A | C | * | G | A | G | true | 74 | 0 | 0 | 2.47 | |||||||||
| IL_31531.3_Instance_13 IL_31531.3,IL_3NDB_006,U175_G154 | U | A | A | C | G | A | G | |||||||||||||||
| IL_31531.3_Sequence_13 IL_31531.33NDB_U175_G154 | U | A | A | C | * | G | A | G | true | 90 | 0 | 0 | 0.95 |
1 7 cWW 2 3 s35 4 5 cWW 4 6 s55 5 6 s35 6 7 s35JAR3D SCFG/MRF model for IL_31531.3:
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 [7] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009069917,0.017109380,0.010589104,0.156595115,0.000000000],[0.074921054,0.012452211,0.149178857,0.012360626,0.000000000],[0.010575950,0.231598327,0.002136037,0.023477106,0.000000000],[0.155763524,0.012439501,0.111676306,0.010056985,0.000000000],[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 [1] | Right Index [7] // Basepair G38 - C8 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.766666667,0.033333333,0.166666667,0.033333333,0.000000000] | Position [1] | Left Index [2] | Right Index [6] // Fixed node on left for 2ET8|1|A|A|7 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 [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.900000000,0.033333333,0.033333333,0.033333333,0.000000000] | Position [1] | Left Index [3] | Right Index [6] // Fixed node on left for 2ET8|1|A|C|8 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 [4] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.766666667,0.033333333,0.166666667,0.033333333,0.000000000] | Position [2] | Left Index [4] | Right Index [6] // Fixed node on right for 2ET8|1|B|A|40 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 [4] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008654733,0.017201161,0.009886421,0.179465948,0.000000000],[0.016254170,0.008594604,0.218921759,0.012042951,0.000000000],[0.009849698,0.272243793,0.001870455,0.022975640,0.000000000],[0.178697293,0.012193163,0.021989869,0.009158344,0.000000000],[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 G41 - C6 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_31531.3:
> IL_31531.3 2ET8 G 38 C 8 GAAG*CAC > IL_31531.3 2O3X G 39 C 9 GAAG*CAC > IL_31531.3 4ZC7 A 16 U 32 AAAG*CGU > IL_31531.3 4LFB G 1491 C 1409 GAAG*CAC > IL_31531.3 1ZZ5 G 7 C 28 GAAG*CAC > IL_31531.3 4PDQ G 39 C 9 GAAG*CAC > IL_31531.3 3C3Z G 7 C 17 GAAG*CAC > IL_31531.3 1T0E G 7 C 18 GAAG*CAC > IL_31531.3 7A0S G 2846 C 2820 GGAC*GGC > IL_31531.3 1ZX7 G 7 C 28 GAAG*CAC > IL_31531.3 5J7L U 1445 G 1457 UAAC*GAG > IL_31531.3 4WF9 U 2891 G 2865 UGAC*GAG > IL_31531.3 3NDB U 175 G 154 UAAC*GAG