| 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_87904.5_Instance_1 IL_87904.5_IL_3V2F_072_G1856_C1886 | G | G | G | A | G | C | G | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_1 IL_87904.5_IL_3V2F_072_G_1856_C_1886 | G | G | G | A | G | * | C | G | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_87904.5_Instance_2 IL_87904.5_IL_4IOA_070_U1848_A1869 | U | G | G | A | G | C | G | A | A | A | ||||||||||||||||||
| IL_87904.5_Sequence_2 IL_87904.5_IL_4IOA_070_U_1848_A_1869 | U | G | G | A | G | * | C | G | A | A | A | true | 96 | 0 | 0 | 0.36 | ||||||||||||
| IL_87904.5_Instance_3 IL_87904.5_IL_3U5H_075_A1806_U1649 | A | G | G | A | A | U | G | A | A | U | ||||||||||||||||||
| IL_87904.5_Sequence_3 IL_87904.5_IL_3U5H_075_A_1806_U_1649 | A | G | G | A | A | * | U | G | A | A | U | true | 90 | 0 | 0 | 0.96 | ||||||||||||
| IL_87904.5_Instance_4 IL_87904.5_IL_2A64_006_C347_G382 | C | G | G | A | G | C | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_4 IL_87904.5_IL_2A64_006_C347_G382 | C | G | G | A | G | * | C | G | A | A | G | true | 100 | 0 | 0 | 0.03 | ||||||||||||
| IL_87904.5_Instance_5 IL_87904.5_IL_4BPP_090_U1649_A1676 | U | G | G | A | C | G | A | A | A | A | ||||||||||||||||||
| IL_87904.5_Sequence_5 IL_87904.5_IL_4BPP_090_U_1649_A_1676 | U | G | G | A | C | * | G | A | A | A | A | true | 82 | 0 | 0 | 1.72 | ||||||||||||
| IL_87904.5_Instance_6 IL_87904.5_IL_4FAW_002_G113_C74 | G | G | A | C | G | C | U | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_6 IL_87904.5_IL_4FAW_002_G113_C74 | G | G | A | C | G | * | C | U | A | A | C | true | 88 | 0 | 0 | 1.10 | ||||||||||||
| IL_87904.5_Instance_7 IL_87904.5_IL_2A64_005_C297_G288 | C | G | G | A | G | C | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_7 IL_87904.5_IL_2A64_005_C297_G288 | C | G | G | A | G | * | C | G | A | A | G | true | 100 | 0 | 0 | 0.03 | ||||||||||||
| IL_87904.5_Instance_8 IL_87904.5_IL_3DHS_004_C297_G288 | C | G | G | A | G | C | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_8 IL_87904.5_IL_3DHS_004_C297_G288 | C | G | G | A | G | * | C | G | A | A | G | true | 100 | 0 | 0 | 0.03 | ||||||||||||
| IL_87904.5_Instance_9 IL_87904.5_IL_3IWN_002_G31_C16 | G | G | A | C | G | C | A | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_9 IL_87904.5_IL_3IWN_002_G31_C16 | G | G | A | C | G | * | C | A | A | A | C | true | 88 | 0 | 0 | 1.13 | ||||||||||||
| IL_87904.5_Instance_10 IL_87904.5_IL_2QBG_068_U1736_G1724 | U | G | G | A | G | U | G | A | G | G | ||||||||||||||||||
| IL_87904.5_Sequence_10 IL_87904.5_IL_2QBG_068_U_1736_G_1724 | U | G | G | A | G | * | U | G | A | G | G | true | 62 | 0 | 0 | 3.62 | ||||||||||||
| IL_87904.5_Instance_11 IL_87904.5_IL_4A1B_125_G3189_C3221 | G | A | G | C | G | U | U | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_11 IL_87904.5_IL_4A1B_125_G_3189_C_3221 | G | A | G | C | G | * | U | U | A | A | C | true | 76 | 0 | 0 | 2.32 | ||||||||||||
| IL_87904.5_Instance_12 IL_87904.5_IL_1S72_083_G2501_C2519 | G | C | A | A | G | C | G | A | C | C | ||||||||||||||||||
| IL_87904.5_Sequence_12 IL_87904.5_IL_1S72_083_G_2501_C_2519 | G | C | A | A | G | * | C | G | A | C | C | true | 92 | 0 | 0 | 0.79 | ||||||||||||
| IL_87904.5_Instance_13 IL_87904.5_IL_1S72_028_U815_G798 | U | G | G | A | A | U | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_13 IL_87904.5_IL_1S72_028_U815_G798 | U | G | G | A | A | * | U | G | A | A | G | true | 86 | 0 | 0 | 1.36 | ||||||||||||
| IL_87904.5_Instance_14 IL_87904.5_IL_2QBG_024_U724_G707 | U | G | G | A | G | U | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_14 IL_87904.5_IL_2QBG_024_U724_G707 | U | G | G | A | G | * | U | G | A | A | G | true | 86 | 0 | 0 | 1.36 | ||||||||||||
| IL_87904.5_Instance_15 IL_87904.5_IL_1U6B_002_G84_C60 | G | C | A | A | C | G | A | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_15 IL_87904.5_IL_1U6B_002_G84_C60 | G | C | A | A | C | * | G | A | A | A | C | true | 72 | 0 | 0 | 2.68 | ||||||||||||
| IL_87904.5_Instance_16 IL_87904.5_IL_3UCZ_001_G41_C26 | G | G | A | C | G | C | A | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_16 IL_87904.5_IL_3UCZ_001_G41_C26 | G | G | A | C | G | * | C | A | A | A | C | true | 88 | 0 | 0 | 1.13 | ||||||||||||
| IL_87904.5_Instance_17 IL_87904.5_IL_3U5F_091_A1678_U1723 | A | G | G | A | U | A | G | A | A | U | ||||||||||||||||||
| IL_87904.5_Sequence_17 IL_87904.5_IL_3U5F_091_A_1678_U_1723 | A | G | G | A | U | * | A | G | A | A | U | true | 89 | 0 | 0 | 1.03 | ||||||||||||
| IL_87904.5_Instance_18 IL_87904.5_IL_3V2F_021_U724_G707 | U | G | G | A | G | U | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_18 IL_87904.5_IL_3V2F_021_U724_G707 | U | G | G | A | G | * | U | G | A | A | G | true | 86 | 0 | 0 | 1.36 | ||||||||||||
| IL_87904.5_Instance_19 IL_87904.5_IL_4A1B_110_C2823_G2841 | C | C | A | A | G | C | G | A | C | G | ||||||||||||||||||
| IL_87904.5_Sequence_19 IL_87904.5_IL_4A1B_110_C_2823_G_2841 | C | C | A | A | G | * | C | G | A | C | G | true | 91 | 0 | 0 | 0.82 | ||||||||||||
| IL_87904.5_Instance_20 IL_87904.5_IL_3U5H_032_U855_G838 | U | G | G | A | G | U | G | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_20 IL_87904.5_IL_3U5H_032_U855_G838 | U | G | G | A | G | * | U | G | A | A | G | true | 86 | 0 | 0 | 1.36 | ||||||||||||
| IL_87904.5_Instance_21 IL_87904.5_IL_2QBG_094_C2466_G2484 | C | C | A | A | G | C | G | A | C | G | ||||||||||||||||||
| IL_87904.5_Sequence_21 IL_87904.5_IL_2QBG_094_C_2466_G_2484 | C | C | A | A | G | * | C | G | A | C | G | true | 91 | 0 | 0 | 0.82 | ||||||||||||
| IL_87904.5_Instance_22 IL_87904.5_IL_3V2F_092_C2466_G2484 | C | C | G | A | G | C | G | G | C | G | ||||||||||||||||||
| IL_87904.5_Sequence_22 IL_87904.5_IL_3V2F_092_C_2466_G_2484 | C | C | G | A | G | * | C | G | G | C | G | true | 77 | 0 | 0 | 2.14 | ||||||||||||
| IL_87904.5_Instance_23 IL_87904.5_IL_4IOA_089_C2445_G2463 | C | C | G | A | G | C | G | G | C | G | ||||||||||||||||||
| IL_87904.5_Sequence_23 IL_87904.5_IL_4IOA_089_C_2445_G_2463 | C | C | G | A | G | * | C | G | G | C | G | true | 77 | 0 | 0 | 2.14 | ||||||||||||
| IL_87904.5_Instance_24 IL_87904.5_IL_2AW7_058_G1272_C1263 | G | C | A | A | G | C | G | A | C | C | ||||||||||||||||||
| IL_87904.5_Sequence_24 IL_87904.5_IL_2AW7_058_G_1272_C_1263 | G | C | A | A | G | * | C | G | A | C | C | true | 92 | 0 | 0 | 0.79 | ||||||||||||
| IL_87904.5_Instance_25 IL_87904.5_IL_3U5H_112_U2835_A2853 | U | C | A | A | G | C | G | A | C | A | ||||||||||||||||||
| IL_87904.5_Sequence_25 IL_87904.5_IL_3U5H_112_U_2835_A_2853 | U | C | A | A | G | * | C | G | A | C | A | true | 88 | 0 | 0 | 1.15 | ||||||||||||
| IL_87904.5_Instance_26 IL_87904.5_IL_2QBG_019_G618_C610 | G | G | G | A | G | U | U | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_26 IL_87904.5_IL_2QBG_019_G618_C610 | G | G | G | A | G | * | U | U | A | A | C | true | 88 | 0 | 0 | 1.14 | ||||||||||||
| IL_87904.5_Instance_27 IL_87904.5_IL_1S72_021_G679_C667 | G | G | G | A | G | C | U | A | A | C | ||||||||||||||||||
| IL_87904.5_Sequence_27 IL_87904.5_IL_1S72_021_G679_C667 | G | G | G | A | G | * | C | U | A | A | C | true | 94 | 0 | 0 | 0.59 | ||||||||||||
| IL_87904.5_Instance_28 IL_87904.5_IL_4BPP_028_G509_C529 | G | A | A | C | A | U | U | A | G | C | ||||||||||||||||||
| IL_87904.5_Sequence_28 IL_87904.5_IL_4BPP_028_G509_C529 | G | A | A | C | A | * | U | U | A | G | C | true | 51 | 0 | 0 | 4.68 | ||||||||||||
| IL_87904.5_Instance_29 IL_87904.5_IL_3V2F_016_C618_G610 | C | G | G | A | G | U | U | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_29 IL_87904.5_IL_3V2F_016_C618_G610 | C | G | G | A | G | * | U | U | A | A | G | true | 88 | 0 | 0 | 1.17 | ||||||||||||
| IL_87904.5_Instance_30 IL_87904.5_IL_2QWY_001_C16_G50 | C | G | U | A | U | A | A | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_30 IL_87904.5_IL_2QWY_001_C16_G50 | C | G | U | A | U | * | A | A | A | A | G | true | 76 | 0 | 0 | 2.28 | ||||||||||||
| IL_87904.5_Instance_31 IL_87904.5_IL_4IOA_012_C629_G620 | C | G | G | A | G | U | U | A | A | G | ||||||||||||||||||
| IL_87904.5_Sequence_31 IL_87904.5_IL_4IOA_012_C629_G620 | C | G | G | A | G | * | U | U | A | A | G | true | 88 | 0 | 0 | 1.17 |
1 2 s35 1 10 cWW 2 3 s35 2 8 s33 2 9 tSH 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 9 2 6BRJAR3D SCFG/MRF model for IL_87904.5:
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 [10] // Initial node G1856 - C1886 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008122691,0.014661627,0.009375677,0.148321841,0.000000000],[0.052633032,0.007677310,0.217856305,0.010653760,0.000000000],[0.009416586,0.224845442,0.001847153,0.018715187,0.000000000],[0.156997400,0.010454861,0.099256991,0.009164136,0.000000000],[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 G1856 - C1886 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.090319003,0.093678642,0.012073407,0.017424652,0.000000000],[0.093928424,0.159982766,0.001106375,0.001106375,0.000000000],[0.249506271,0.001106375,0.026084151,0.077828330,0.000000000],[0.088479441,0.085163037,0.001106375,0.001106375,0.000000000],[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 [2] | Right Index [9] // Basepair G1857 - A1885 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.172658120,0.091625881,0.001252191,0.028779862,0.000000000],[0.092017248,0.068763516,0.001252191,0.001252191,0.000000000],[0.244092294,0.001252191,0.046055822,0.054742799,0.000000000],[0.103973853,0.089777455,0.001252191,0.001252191,0.000000000],[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 G1858 - A1884 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.114226799,0.091684732,0.250077615,0.138459354,0.000000000],[0.114669271,0.086616634,0.001065282,0.117277227,0.000000000],[0.001065282,0.001065282,0.005710459,0.001065282,0.000000000],[0.005519222,0.001065282,0.069366997,0.001065282,0.000000000],[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 A1859 - G1883 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009071527,0.074411793,0.009690705,0.145893352,0.000000000],[0.013609116,0.007309360,0.141711403,0.010426233,0.000000000],[0.009568793,0.252142141,0.001935840,0.146021452,0.000000000],[0.136309275,0.010994406,0.017166296,0.013738307,0.000000000],[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 G1860 - C1882 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_87904.5:
> IL_87904.5 IL_3V2F_072 G 1856 C 1886 GGGAG*CGAAC > IL_87904.5 IL_4IOA_070 U 1848 A 1869 UGGAG*CGAAA > IL_87904.5 IL_3U5H_075 A 1806 U 1649 AGGAA*UGAAU > IL_87904.5 IL_2A64_006 C 347 G 382 CGGAG*CGAAG > IL_87904.5 IL_4BPP_090 U 1649 A 1676 UGGAC*GAAAA > IL_87904.5 IL_4FAW_002 G 113 C 74 GGACG*CUAAC > IL_87904.5 IL_2A64_005 C 297 G 288 CGGAG*CGAAG > IL_87904.5 IL_3DHS_004 C 297 G 288 CGGAG*CGAAG > IL_87904.5 IL_3IWN_002 G 31 C 16 GGACG*CAAAC > IL_87904.5 IL_2QBG_068 U 1736 G 1724 UGGAG*UGAGG > IL_87904.5 IL_4A1B_125 G 3189 C 3221 GAGCG*UUAAC > IL_87904.5 IL_1S72_083 G 2501 C 2519 GCAAG*CGACC > IL_87904.5 IL_1S72_028 U 815 G 798 UGGAA*UGAAG > IL_87904.5 IL_2QBG_024 U 724 G 707 UGGAG*UGAAG > IL_87904.5 IL_1U6B_002 G 84 C 60 GCAAC*GAAAC > IL_87904.5 IL_3UCZ_001 G 41 C 26 GGACG*CAAAC > IL_87904.5 IL_3U5F_091 A 1678 U 1723 AGGAU*AGAAU > IL_87904.5 IL_3V2F_021 U 724 G 707 UGGAG*UGAAG > IL_87904.5 IL_4A1B_110 C 2823 G 2841 CCAAG*CGACG > IL_87904.5 IL_3U5H_032 U 855 G 838 UGGAG*UGAAG > IL_87904.5 IL_2QBG_094 C 2466 G 2484 CCAAG*CGACG > IL_87904.5 IL_3V2F_092 C 2466 G 2484 CCGAG*CGGCG > IL_87904.5 IL_4IOA_089 C 2445 G 2463 CCGAG*CGGCG > IL_87904.5 IL_2AW7_058 G 1272 C 1263 GCAAG*CGACC > IL_87904.5 IL_3U5H_112 U 2835 A 2853 UCAAG*CGACA > IL_87904.5 IL_2QBG_019 G 618 C 610 GGGAG*UUAAC > IL_87904.5 IL_1S72_021 G 679 C 667 GGGAG*CUAAC > IL_87904.5 IL_4BPP_028 G 509 C 529 GAACA*UUAGC > IL_87904.5 IL_3V2F_016 C 618 G 610 CGGAG*UUAAG > IL_87904.5 IL_2QWY_001 C 16 G 50 CGUAU*AAAAG > IL_87904.5 IL_4IOA_012 C 629 G 620 CGGAG*UUAAG