| 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 5 4 | 9 5 I | 10 6 5 | 11 6 I | 12 7 | 13 6 I | 14 6 6 | 15 5 I | 16 5 7 | 17 4 I | 18 4 8 | 19 3 I | 20 3 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_17948.2_Instance_1 IL_17948.2,IL_5J7L_338,C2466_G2484 | C | C | A | A | G | C | G | A | C | G | ||||||||||||||||||
| IL_17948.2_Sequence_1 IL_17948.25J7L_C_2466_G_2484 | C | C | A | A | G | * | C | G | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_17948.2_Instance_2 IL_17948.2,IL_8P9A_333,U2835_A2853 | U | C | A | A | G | C | G | A | C | A | ||||||||||||||||||
| IL_17948.2_Sequence_2 IL_17948.28P9A_U_2835_A_2853 | U | C | A | A | G | * | C | G | A | C | A | true | 99 | 0 | 0 | 0.09 | ||||||||||||
| IL_17948.2_Instance_3 IL_17948.2,IL_8CRE_114,U2807_A2825 | U | C | A | A | G | C | G | A | C | A | ||||||||||||||||||
| IL_17948.2_Sequence_3 IL_17948.28CRE_U_2807_A_2825 | U | C | A | A | G | * | C | G | A | C | A | true | 99 | 0 | 0 | 0.09 | ||||||||||||
| IL_17948.2_Instance_4 IL_17948.2,IL_4WF9_093,C2493_G2511 | C | C | A | A | G | C | G | A | C | G | ||||||||||||||||||
| IL_17948.2_Sequence_4 IL_17948.24WF9_C_2493_G_2511 | C | C | A | A | G | * | C | G | A | C | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_17948.2_Instance_5 IL_17948.2,IL_7A0S_087,C2445_G2463 | C | C | G | A | G | C | G | G | C | G | ||||||||||||||||||
| IL_17948.2_Sequence_5 IL_17948.27A0S_C_2445_G_2463 | C | C | G | A | G | * | C | G | G | C | G | true | 93 | 0 | 0 | 0.83 | ||||||||||||
| IL_17948.2_Instance_6 IL_17948.2,IL_9DFE_095,C2466_G2484 | C | C | G | A | G | C | G | G | C | G | ||||||||||||||||||
| IL_17948.2_Sequence_6 IL_17948.29DFE_C_2466_G_2484 | C | C | G | A | G | * | C | G | G | C | G | true | 93 | 0 | 0 | 0.83 | ||||||||||||
| IL_17948.2_Instance_7 IL_17948.2,IL_4WFL_001,U72_A95 | U | C | G | A | G | C | G | A | C | A | ||||||||||||||||||
| IL_17948.2_Sequence_7 IL_17948.24WFL_U72_A95 | U | C | G | A | G | * | C | G | A | C | A | true | 95 | 0 | 0 | 0.61 | ||||||||||||
| IL_17948.2_Instance_8 IL_17948.2,IL_4V9F_085,G2501_C2519 | G | C | A | A | G | C | G | A | C | C | ||||||||||||||||||
| IL_17948.2_Sequence_8 IL_17948.24V9F_G_2501_C_2519 | G | C | A | A | G | * | C | G | A | C | C | true | 100 | 0 | 0 | 0.04 | ||||||||||||
| IL_17948.2_Instance_9 IL_17948.2,IL_5J7L_274,G875_C902 | G | C | A | A | G | C | A | A | C | C | ||||||||||||||||||
| IL_17948.2_Sequence_9 IL_17948.25J7L_G875_C902 | G | C | A | A | G | * | C | A | A | C | C | true | 97 | 0 | 0 | 0.40 | ||||||||||||
| IL_17948.2_Instance_10 IL_17948.2,IL_1U6B_002,G84_C60 | G | C | A | A | C | G | A | A | A | C | ||||||||||||||||||
| IL_17948.2_Sequence_10 IL_17948.21U6B_G84_C60 | G | C | A | A | C | * | G | A | A | A | C | true | 81 | 0 | 0 | 2.31 | ||||||||||||
| IL_17948.2_Instance_11 IL_17948.2,IL_5J7L_056,G1272_C1263 | G | C | A | A | G | C | G | A | C | C | ||||||||||||||||||
| IL_17948.2_Sequence_11 IL_17948.25J7L_G_1272_C_1263 | G | C | A | A | G | * | C | G | A | C | C | true | 100 | 0 | 0 | 0.04 | ||||||||||||
| IL_17948.2_Instance_12 IL_17948.2,IL_7A0S_056,C1529_G1495 | C | U | C | A | G | C | A | A | G | G | ||||||||||||||||||
| IL_17948.2_Sequence_12 IL_17948.27A0S_C_1529_G_1495 | C | U | C | A | G | * | C | A | A | G | G | true | 66 | 0 | 0 | 4.07 | ||||||||||||
| IL_17948.2_Instance_13 IL_17948.2,IL_6ZDP_003,A1298_U1318 | A | C | U | U | C | G | U | U | U | G | U | |||||||||||||||||
| IL_17948.2_Sequence_13 IL_17948.26ZDP_A_1298_U_1318 | A | C | U | U | C | * | G | U | U | U | G | U | true | 1 | 0 | 0 | 11.85 |
1 2 s35 1 10 cWW 2 3 s35 2 9 bif 2 10 s55 3 7 s33 3 8 tSH 4 5 s35 4 7 tHS 4 8 s55 5 6 cWW 5 7 s55 6 7 s35 8 9 s35 9 10 s35 4 7 6BRJAR3D SCFG/MRF model for IL_17948.2:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008540753,0.016750420,0.009637458,0.188846467,0.000000000],[0.017596354,0.008736198,0.227701616,0.011497236,0.000000000],[0.009648701,0.218091476,0.001873342,0.024076453,0.000000000],[0.207850918,0.011369075,0.028509731,0.009273802,0.000000000],[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 [10] // Basepair C2466 - G2484 cWW BasepairNode | Deletion Probability [0.0000160934329480] | Pair Probability [[0.018353837,0.021527808,0.006264372,0.006264372,0.000000000],[0.141158342,0.674817136,0.024528352,0.006264372,0.000000000],[0.006264372,0.006264372,0.019239330,0.025731867,0.000000000],[0.006264372,0.006264372,0.024528352,0.006264372,0.000000000],[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 [0.919387860,0.080126081,0.000471330,0.000014729] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair C2467 - C2483 bif BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.202312140,0.025397059,0.001883290,0.061653735,0.000000000],[0.136559293,0.062339506,0.001883290,0.001883290,0.000000000],[0.120489081,0.001883290,0.088195101,0.037516830,0.000000000],[0.119647549,0.118426721,0.001883290,0.018046532,0.000000000],[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 [8] // Basepair A2468 - A2482 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.141838453,0.114649756,0.203497326,0.120149935,0.000000000],[0.084756172,0.095675957,0.001304620,0.115095002,0.000000000],[0.001304620,0.001304620,0.007881631,0.001304620,0.000000000],[0.006697014,0.001304620,0.085767793,0.017467861,0.000000000],[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 [4] | Right Index [7] // Basepair A2469 - G2481 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008758791,0.017858159,0.009988348,0.181371622,0.000000000],[0.015874591,0.008639028,0.201788209,0.012061225,0.000000000],[0.009911428,0.285121904,0.001885965,0.023701586,0.000000000],[0.179761598,0.012375860,0.021636788,0.009264898,0.000000000],[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 [5] | Right Index [6] // Basepair G2470 - C2480 cWW 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_17948.2:
> IL_17948.2 5J7L C 2466 G 2484 CCAAG*CGACG > IL_17948.2 8P9A U 2835 A 2853 UCAAG*CGACA > IL_17948.2 8CRE U 2807 A 2825 UCAAG*CGACA > IL_17948.2 4WF9 C 2493 G 2511 CCAAG*CGACG > IL_17948.2 7A0S C 2445 G 2463 CCGAG*CGGCG > IL_17948.2 9DFE C 2466 G 2484 CCGAG*CGGCG > IL_17948.2 4WFL U 72 A 95 UCGAG*CGACA > IL_17948.2 4V9F G 2501 C 2519 GCAAG*CGACC > IL_17948.2 5J7L G 875 C 902 GCAAG*CAACC > IL_17948.2 1U6B G 84 C 60 GCAAC*GAAAC > IL_17948.2 5J7L G 1272 C 1263 GCAAG*CGACC > IL_17948.2 7A0S C 1529 G 1495 CUCAG*CAAGG > IL_17948.2 6ZDP A 1298 U 1318 ACUUC*GUUUGU