| 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 2 2 | 5 2 I | 6 2 3 | 7 2 I | 8 2 4 | 9 2 I | 10 2 5 | 11 3 I | 12 4 6 | 13 4 I | 14 5 7 | 15 5 I | 16 6 | 17 5 I | 18 5 8 | 19 4 I | 20 4 9 | 21 3 I | 22 2 10 | 23 2 I | 24 2 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_65553.8_Instance_1 IL_65553.8_IL_3GX5_002_C31_G21 | C | G | A | C | G | A | A | A | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_1 IL_65553.8_IL_3GX5_002_C31_G21 | C | G | A | C | G | A | A | A | * | U | G | G | A | G | true | 95 | 0 | 0 | 0.94 | |||||||||||||
| IL_65553.8_Instance_2 IL_65553.8_IL_3V7E_006_C231_G221 | C | G | A | U | G | A | A | A | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_2 IL_65553.8_IL_3V7E_006_C231_G221 | C | G | A | U | G | A | A | A | * | U | G | G | A | G | true | 97 | 0 | 0 | 0.46 | |||||||||||||
| IL_65553.8_Instance_3 IL_65553.8_IL_3V2F_044_C1208_G1238 | C | G | A | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_3 IL_65553.8_IL_3V2F_044_C_1208_G_1238 | C | G | A | U | G | A | A | G | * | U | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_65553.8_Instance_4 IL_65553.8_IL_3U5H_064_U1388_A1419 | U | G | A | C | G | A | A | G | U | C | G | A | A | |||||||||||||||||||
| IL_65553.8_Sequence_4 IL_65553.8_IL_3U5H_064_U_1388_A_1419 | U | G | A | C | G | A | A | G | * | U | C | G | A | A | true | 78 | 0 | 0 | 3.69 | |||||||||||||
| IL_65553.8_Instance_5 IL_65553.8_IL_4KQY_002_C31_G21 | C | G | A | C | G | A | A | G | C | A | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_5 IL_65553.8_IL_4KQY_002_C31_G21 | C | G | A | C | G | A | A | G | * | C | A | G | A | G | true | 84 | 0 | 0 | 2.69 | |||||||||||||
| IL_65553.8_Instance_6 IL_65553.8_IL_4C4W_001_U26_G7 | U | G | A | U | G | A | C | C | G | C | A | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_6 IL_65553.8_IL_4C4W_001_U26_G7 | U | G | A | U | G | A | C | C | * | G | C | A | A | G | true | 73 | 0 | 0 | 4.61 | |||||||||||||
| IL_65553.8_Instance_7 IL_65553.8_IL_1S72_048_G1312_C1342 | G | A | U | G | G | A | A | G | U | G | G | A | C | |||||||||||||||||||
| IL_65553.8_Sequence_7 IL_65553.8_IL_1S72_048_G_1312_C_1342 | G | A | U | G | G | A | A | G | * | U | G | G | A | C | true | 78 | 0 | 0 | 3.70 | |||||||||||||
| IL_65553.8_Instance_8 IL_65553.8_IL_4IOA_045_C1221_G1251 | C | G | G | A | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_8 IL_65553.8_IL_4IOA_045_C_1221_G_1251 | C | G | G | A | G | A | A | G | * | U | G | G | A | G | true | 89 | 0 | 0 | 1.87 | |||||||||||||
| IL_65553.8_Instance_9 IL_65553.8_IL_2QBG_047_C1208_G1238 | C | U | G | C | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_9 IL_65553.8_IL_2QBG_047_C_1208_G_1238 | C | U | G | C | G | A | A | G | * | U | G | G | A | G | true | 79 | 0 | 0 | 3.50 | |||||||||||||
| IL_65553.8_Instance_10 IL_65553.8_IL_4A1B_062_C1414_G1445 | C | C | U | A | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_10 IL_65553.8_IL_4A1B_062_C_1414_G_1445 | C | C | U | A | G | A | A | G | * | U | G | G | A | G | true | 77 | 0 | 0 | 3.97 | |||||||||||||
| IL_65553.8_Instance_11 IL_65553.8_IL_4AOB_002_U31_G21 | U | G | A | U | G | A | C | C | G | C | A | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_11 IL_65553.8_IL_4AOB_002_U31_G21 | U | G | A | U | G | A | C | C | * | G | C | A | A | G | true | 73 | 0 | 0 | 4.61 | |||||||||||||
| IL_65553.8_Instance_12 IL_65553.8_IL_1T0K_001_C54_G13 | C | A | G | A | G | A | U | G | C | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_12 IL_65553.8_IL_1T0K_001_C54_G13 | C | A | G | A | G | A | U | G | * | C | G | G | A | G | true | 79 | 0 | 0 | 3.53 | |||||||||||||
| IL_65553.8_Instance_13 IL_65553.8_IL_1S72_004_C93_G81 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_13 IL_65553.8_IL_1S72_004_C93_G81 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 94 | 0 | 0 | 1.06 | |||||||||||||
| IL_65553.8_Instance_14 IL_65553.8_IL_4GXY_005_C139_G86 | C | G | A | G | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_14 IL_65553.8_IL_4GXY_005_C139_G86 | C | G | A | G | G | A | U | C | * | G | G | G | A | G | true | 92 | 0 | 0 | 1.33 | |||||||||||||
| IL_65553.8_Instance_15 IL_65553.8_IL_3V2F_004_C97_G85 | C | G | U | G | G | A | U | C | G | G | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_15 IL_65553.8_IL_3V2F_004_C97_G85 | C | G | U | G | G | A | U | C | * | G | G | G | A | G | true | 89 | 0 | 0 | 1.85 | |||||||||||||
| IL_65553.8_Instance_16 IL_65553.8_IL_4IOA_004_C96_G84 | C | U | U | U | G | A | C | U | A | C | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_16 IL_65553.8_IL_4IOA_004_C96_G84 | C | U | U | U | G | A | C | U | * | A | C | G | A | G | true | 75 | 0 | 0 | 4.23 | |||||||||||||
| IL_65553.8_Instance_17 IL_65553.8_IL_4GMA_003_G143_C97 | G | G | A | U | G | A | G | U | A | G | G | A | C | |||||||||||||||||||
| IL_65553.8_Sequence_17 IL_65553.8_IL_4GMA_003_G143_C97 | G | G | A | U | G | A | G | U | * | A | G | G | A | C | true | 80 | 0 | 0 | 3.39 | |||||||||||||
| IL_65553.8_Instance_18 IL_65553.8_IL_3U5F_051_C910_G899 | C | U | U | G | G | A | U | U | G | U | C | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_18 IL_65553.8_IL_3U5F_051_C910_G899 | C | U | U | G | G | A | U | U | * | G | U | C | A | G | true | 45 | 0 | 0 | 9.46 | |||||||||||||
| IL_65553.8_Instance_19 IL_65553.8_IL_1S72_032_C1026_G940 | C | G | U | UU | G | A | C | G | C | C | G | A | G | |||||||||||||||||||
| IL_65553.8_Sequence_19 IL_65553.8_IL_1S72_032_C_1026_G940 | C | G | U | UU | G | A | C | G | * | C | C | G | A | G | true | 64 | 0 | 0 | 6.08 | |||||||||||||
| IL_65553.8_Instance_20 IL_65553.8_IL_3RW6_002_C43_G18 | C | A | A | U | G | A | C | G | U | A | AGA | C | A | G | ||||||||||||||||||
| IL_65553.8_Sequence_20 IL_65553.8_IL_3RW6_002_C43_G18 | C | A | A | U | G | A | C | G | * | U | A | AGA | C | A | G | true | 38 | 0 | 0 | 10.53 | ||||||||||||
| IL_65553.8_Instance_21 IL_65553.8_IL_2AW7_014_C277_G247 | C | G | A | C | G | A | U | C | G | A | U | U | A | G | ||||||||||||||||||
| IL_65553.8_Sequence_21 IL_65553.8_IL_2AW7_014_C277_G247 | C | G | A | C | G | A | U | C | * | G | A | U | U | A | G | true | 53 | 0 | 0 | 7.96 | ||||||||||||
| IL_65553.8_Instance_22 IL_65553.8_IL_3U5F_019_U348_A316 | U | U | U | C | A | A | C | G | U | A | U | C | A | A | ||||||||||||||||||
| IL_65553.8_Sequence_22 IL_65553.8_IL_3U5F_019_U348_A316 | U | U | U | C | A | A | C | G | * | U | A | U | C | A | A | true | 39 | 0 | 0 | 10.40 | ||||||||||||
| IL_65553.8_Instance_23 IL_65553.8_IL_4BPP_017_C339_G307 | C | A | G | U | C | A | C | G | U | A | U | C | A | G | ||||||||||||||||||
| IL_65553.8_Sequence_23 IL_65553.8_IL_4BPP_017_C339_G307 | C | A | G | U | C | A | C | G | * | U | A | U | C | A | G | true | 53 | 0 | 0 | 8.02 |
1 2 s35 1 12 cWW 2 11 tSS 2 12 s55 3 4 s35 3 11 s33 4 10 s33 4 11 tSH 5 6 s35 5 10 tHS 5 11 s55 5 12 tSS 6 7 s35 6 9 tHS 7 8 cWW 8 9 s35 9 10 s35 10 11 s35 9 5 6BPh 10 5 6BPh 11 2 6BR 10 4 6BR 11 4 6BRJAR3D SCFG/MRF model for IL_65553.8:
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 [12] // Initial node C31 - G21 from junction ClusterNode | Deletion Probability [0.000000000000000000001549484556559301900000000000000000000000] | Num Left Bases [5] | Num Right Bases [3] | Left Index [1] | Right Index [12] | Norm Constant [0.094806833173160] // Cluster node C31:A36 and G19:G21 Interaction | Interacting Bases [5,6] | Pair Probability [[0.081378496,0.098546092,0.388749317,0.053999063,0.000000000],[0.063189619,0.045680214,0.002558985,0.039956944,0.000000000],[0.000713427,0.000588948,0.012712851,0.000457180,0.000000000],[0.004459938,0.000588948,0.205962796,0.000457180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G19 tHS Interaction | Interacting Bases [2,7] | Pair Probability [[0.165813762,0.027446076,0.026469528,0.026092728,0.000000000],[0.033494723,0.007176489,0.007176489,0.007176489,0.000000000],[0.456888233,0.071193943,0.071937937,0.015714203,0.000000000],[0.061889933,0.007176489,0.007176489,0.007176489,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G32 - A20 tSS Interaction | Interacting Bases [4,7] | Pair Probability [[0.167477241,0.036008291,0.000377768,0.001878311,0.000000000],[0.168744503,0.032054522,0.000377768,0.000377768,0.000000000],[0.356845819,0.000377768,0.001929297,0.029052875,0.000000000],[0.170826576,0.032915957,0.000377768,0.000377768,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G35 - A20 tSH Interaction | Interacting Bases [1,8] | Pair Probability [[0.008479529,0.014561897,0.009826657,0.149620471,0.000000000],[0.038597518,0.007703173,0.302258354,0.011499664,0.000000000],[0.009933633,0.176224842,0.001882503,0.019390841,0.000000000],[0.167564853,0.011015113,0.062328090,0.009112862,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C31 - G21 cWW Interaction | Interacting Bases [5,8] | Pair Probability [[0.161548555,0.169966367,0.372406758,0.139858546,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.008609318,0.009842421,0.014904474,0.110113490,0.000000000],[0.001593759,0.001593759,0.001593759,0.001593759,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A36 - G21 tSS Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.020000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.180000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A33 Insertion | Location [3] | Length Distribution [0.002070169,0.952371991,0.045355528,0.000197607,0.000004705] | Letter Distribution [0.173076923,0.250000000,0.173076923,0.403846154,0.000000000]// Insertion after nucleotide 3, position 3 in cluster node 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 [0.824177637,0.131879734,0.000466622,0.043377026,0.000094267,0.000004713] | Right Letter Distribution [0.312500000,0.062500000,0.187500000,0.437500000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.047811319,0.050466058,0.302105938,0.047561334,0.000000000],[0.090847252,0.086472653,0.002900073,0.043001204,0.000000000],[0.000629921,0.000629921,0.061099075,0.000629921,0.000000000],[0.021682211,0.000629921,0.229627575,0.013905624,0.000000000],[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 [6] | Right Index [9] // Basepair A37 - G18 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010420873,0.110403380,0.010827885,0.125139785,0.000000000],[0.025695383,0.008447915,0.159702672,0.011573885,0.000000000],[0.010744835,0.136352265,0.002255713,0.197636037,0.000000000],[0.123320488,0.011981439,0.038018641,0.017478805,0.000000000],[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 A38 - U17 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_65553.8:
> IL_65553.8 IL_3GX5_002 C 31 G 21 CGACGAAA*UGGAG > IL_65553.8 IL_3V7E_006 C 231 G 221 CGAUGAAA*UGGAG > IL_65553.8 IL_3V2F_044 C 1208 G 1238 CGAUGAAG*UGGAG > IL_65553.8 IL_3U5H_064 U 1388 A 1419 UGACGAAG*UCGAA > IL_65553.8 IL_4KQY_002 C 31 G 21 CGACGAAG*CAGAG > IL_65553.8 IL_4C4W_001 U 26 G 7 UGAUGACC*GCAAG > IL_65553.8 IL_1S72_048 G 1312 C 1342 GAUGGAAG*UGGAC > IL_65553.8 IL_4IOA_045 C 1221 G 1251 CGGAGAAG*UGGAG > IL_65553.8 IL_2QBG_047 C 1208 G 1238 CUGCGAAG*UGGAG > IL_65553.8 IL_4A1B_062 C 1414 G 1445 CCUAGAAG*UGGAG > IL_65553.8 IL_4AOB_002 U 31 G 21 UGAUGACC*GCAAG > IL_65553.8 IL_1T0K_001 C 54 G 13 CAGAGAUG*CGGAG > IL_65553.8 IL_1S72_004 C 93 G 81 CGAAGAAC*GGGAG > IL_65553.8 IL_4GXY_005 C 139 G 86 CGAGGAUC*GGGAG > IL_65553.8 IL_3V2F_004 C 97 G 85 CGUGGAUC*GGGAG > IL_65553.8 IL_4IOA_004 C 96 G 84 CUUUGACU*ACGAG > IL_65553.8 IL_4GMA_003 G 143 C 97 GGAUGAGU*AGGAC > IL_65553.8 IL_3U5F_051 C 910 G 899 CUUGGAUU*GUCAG > IL_65553.8 IL_1S72_032 C 1026 G 940 CGUUUGACG*CCGAG > IL_65553.8 IL_3RW6_002 C 43 G 18 CAAUGACG*UAAGACAG > IL_65553.8 IL_2AW7_014 C 277 G 247 CGACGAUC*GAUUAG > IL_65553.8 IL_3U5F_019 U 348 A 316 UUUCAACG*UAUCAA > IL_65553.8 IL_4BPP_017 C 339 G 307 CAGUCACG*UAUCAG