| 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 3 3 | 7 3 I | 8 3 4 | 9 4 I | 10 5 5 | 11 5 I | 12 6 6 | 13 6 I | 14 7 7 | 15 7 I | 16 8 | 17 7 I | 18 7 8 | 19 6 I | 20 6 9 | 21 5 I | 22 5 10 | 23 4 I | 24 3 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_70923.9_Instance_1 IL_70923.9,IL_5G4T_002,C3_G17 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_1 IL_70923.95G4T_C3_G17 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_2 IL_70923.9,IL_6Q8V_001,C3_G17 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_2 IL_70923.96Q8V_C3_G17 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_3 IL_70923.9,IL_5FJC_002,C31_G21 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_3 IL_70923.95FJC_C31_G21 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_4 IL_70923.9,IL_6Q8U_002,C4_G18 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_4 IL_70923.96Q8U_C4_G18 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_5 IL_70923.9,IL_5J7L_288,C1208_G1238 | C | U | G | C | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_5 IL_70923.95J7L_C_1208_G_1238 | C | U | G | C | G | A | A | G | * | U | G | G | A | G | true | 73 | 0 | 0 | 4.94 | |||||||||||||
| IL_70923.9_Instance_6 IL_70923.9,IL_3U4M_004,C2129_G2159 | C | U | G | U | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_6 IL_70923.93U4M_C_2129_G_2159 | C | U | G | U | G | A | A | C | * | G | G | G | A | G | true | 76 | 0 | 0 | 4.28 | |||||||||||||
| IL_70923.9_Instance_7 IL_70923.9,IL_6Q8U_001,C4_G18 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_7 IL_70923.96Q8U_C4_G18 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_8 IL_70923.9,IL_9DFE_046,C1208_G1238 | C | G | A | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_8 IL_70923.99DFE_C_1208_G_1238 | C | G | A | U | G | A | A | G | * | U | G | G | A | G | true | 96 | 0 | 0 | 0.68 | |||||||||||||
| IL_70923.9_Instance_9 IL_70923.9,IL_7JRS_002,C77_G59 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_9 IL_70923.97JRS_C77_G59 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_10 IL_70923.9,IL_7JRR_001,C23_G9 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_10 IL_70923.97JRR_C23_G9 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_11 IL_70923.9,IL_5FJ4_002,C26_G7 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_11 IL_70923.95FJ4_C26_G7 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_12 IL_70923.9,IL_4V9F_048,G1312_C1342 | G | A | U | G | G | A | A | G | U | G | G | A | C | |||||||||||||||||||
| IL_70923.9_Sequence_12 IL_70923.94V9F_G_1312_C_1342 | G | A | U | G | G | A | A | G | * | U | G | G | A | C | true | 58 | 0 | 0 | 7.73 | |||||||||||||
| IL_70923.9_Instance_13 IL_70923.9,IL_7EAG_003,C3_G17 | C | U | A | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_13 IL_70923.97EAG_C3_G17 | C | U | A | U | G | A | A | G | * | U | G | G | A | G | true | 85 | 0 | 0 | 2.69 | |||||||||||||
| IL_70923.9_Instance_14 IL_70923.9,IL_7JRS_007,C12_G124 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_14 IL_70923.97JRS_C12_G124 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_15 IL_70923.9,IL_3V7E_002,C31_G21 | C | G | A | U | G | A | A | A | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_15 IL_70923.93V7E_C31_G21 | C | G | A | U | G | A | A | A | * | U | G | G | A | G | true | 94 | 0 | 0 | 1.02 | |||||||||||||
| IL_70923.9_Instance_16 IL_70923.9,IL_5Y7M_008,A17_U33 | A | G | A | C | G | A | U | C | G | G | G | A | U | |||||||||||||||||||
| IL_70923.9_Sequence_16 IL_70923.95Y7M_A17_U33 | A | G | A | C | G | A | U | C | * | G | G | G | A | U | true | 82 | 0 | 0 | 3.27 | |||||||||||||
| IL_70923.9_Instance_17 IL_70923.9,IL_7JRS_006,C77_G59 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_17 IL_70923.97JRS_C77_G59 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_18 IL_70923.9,IL_7EAG_002,C3_G17 | C | U | A | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_18 IL_70923.97EAG_C3_G17 | C | U | A | U | G | A | A | G | * | U | G | G | A | G | true | 85 | 0 | 0 | 2.69 | |||||||||||||
| IL_70923.9_Instance_19 IL_70923.9,IL_4BW0_001,C16_G7 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_19 IL_70923.94BW0_C16_G7 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_20 IL_70923.9,IL_7A0S_043,C1221_G1251 | C | G | G | A | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_20 IL_70923.97A0S_C_1221_G_1251 | C | G | G | A | G | A | A | G | * | U | G | G | A | G | true | 89 | 0 | 0 | 2.03 | |||||||||||||
| IL_70923.9_Instance_21 IL_70923.9,IL_4WF9_046,C1246_G1276 | C | G | U | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_21 IL_70923.94WF9_C_1246_G_1276 | C | G | U | U | G | A | A | G | * | U | G | G | A | G | true | 86 | 0 | 0 | 2.50 | |||||||||||||
| IL_70923.9_Instance_22 IL_70923.9,IL_7JRS_003,C12_G124 | C | G | A | A | G | A | A | C | G | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_22 IL_70923.97JRS_C12_G124 | C | G | A | A | G | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_70923.9_Instance_23 IL_70923.9,IL_4KQY_002,C31_G21 | C | G | A | C | G | A | A | G | C | A | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_23 IL_70923.94KQY_C31_G21 | C | G | A | C | G | A | A | G | * | C | A | G | A | G | true | 82 | 0 | 0 | 3.35 | |||||||||||||
| IL_70923.9_Instance_24 IL_70923.9,IL_4C4W_002,U26_G7 | U | G | A | U | G | A | C | C | G | C | A | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_24 IL_70923.94C4W_U26_G7 | U | G | A | U | G | A | C | C | * | G | C | A | A | G | true | 65 | 0 | 0 | 6.42 | |||||||||||||
| IL_70923.9_Instance_25 IL_70923.9,IL_8P9A_287,U1388_A1419 | U | G | A | C | G | A | A | G | U | C | G | A | A | |||||||||||||||||||
| IL_70923.9_Sequence_25 IL_70923.98P9A_U_1388_A_1419 | U | G | A | C | G | A | A | G | * | U | C | G | A | A | true | 77 | 0 | 0 | 4.12 | |||||||||||||
| IL_70923.9_Instance_26 IL_70923.9,IL_8CRE_063,U1384_A1415 | U | G | A | C | G | A | A | G | U | C | G | A | A | |||||||||||||||||||
| IL_70923.9_Sequence_26 IL_70923.98CRE_U_1384_A_1415 | U | G | A | C | G | A | A | G | * | U | C | G | A | A | true | 77 | 0 | 0 | 4.12 | |||||||||||||
| IL_70923.9_Instance_27 IL_70923.9,IL_5J7L_330,C2129_G2159 | C | U | U | U | G | A | A | G | U | G | G | A | G | |||||||||||||||||||
| IL_70923.9_Sequence_27 IL_70923.95J7L_C_2129_G_2159 | C | U | U | U | G | A | A | G | * | U | G | G | A | G | true | 75 | 0 | 0 | 4.50 |
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 perp 6 7 s35 6 9 tHS 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 10 11 s35 9 5 6BPh 10 5 6BPh 10 4 6BR 11 4 6BR 12 5 2BR 6 9 6BR 4 10 6BRJAR3D SCFG/MRF model for IL_70923.9:
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 [12] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.005563209,0.008262228,0.018091094,0.099692097,0.000000000],[0.015272512,0.004772643,0.505034903,0.006314058,0.000000000],[0.006362373,0.101223902,0.003490307,0.011908173,0.000000000],[0.133310474,0.006127283,0.069732920,0.004841823,0.000000000],[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 [12] // Basepair C3 - G17 cWW ClusterNode | Deletion Probability [0.0000000000031219] | Num Left Bases [3] | Num Right Bases [1] | Left Index [2] | Right Index [11] | Norm Constant [0.470662777498451] // Cluster node 5G4T|1|A|G|4:5G4T|1|A|G|7 and 5G4T|1|B|A|16:5G4T|1|B|A|16 Interaction | Interacting Bases [1,4] | Pair Probability [[0.082176660,0.014316284,0.015160030,0.012850929,0.000000000],[0.029418362,0.005971669,0.068285341,0.005971669,0.000000000],[0.542438928,0.005971669,0.075555523,0.051013339,0.000000000],[0.072954587,0.005971669,0.005971669,0.005971669,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5G4T|1|A|G|4 - 5G4T|1|B|A|16 tSS Interaction | Interacting Bases [3,4] | Pair Probability [[0.052965220,0.056070824,0.000635812,0.002996585,0.000000000],[0.053358714,0.055940987,0.000635812,0.000635812,0.000000000],[0.450482841,0.002316352,0.011323909,0.196603197,0.000000000],[0.059123331,0.055638979,0.000635812,0.000635812,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 5G4T|1|A|G|7 - 5G4T|1|B|A|16 tSH Interaction | Interacting Bases [2,2] | Pair Probability [[0.741379310,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.017241379,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.120689655,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.120689655,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 5G4T|1|A|A|5 Insertion | Location [2] | Length Distribution [0.001844848,0.996218061,0.001844848,0.000092242] | Letter Distribution [0.465517241,0.189655172,0.051724138,0.293103448,0.000000000]// Insertion after nucleotide 3, position 2 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [10] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.057192438,0.037336519,0.491973135,0.040842178,0.000000000],[0.037912459,0.037263122,0.002815064,0.038590543,0.000000000],[0.000561611,0.000440177,0.013877256,0.000440177,0.000000000],[0.002857096,0.000440177,0.237017871,0.000440177,0.000000000],[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 [5] | Right Index [10] // Basepair A8 - G15 tHS BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.066028364,0.075214628,0.402100985,0.068377018,0.000000000],[0.049792264,0.064504005,0.002302054,0.062709036,0.000000000],[0.000752428,0.000752428,0.011821040,0.000752428,0.000000000],[0.003722356,0.000752428,0.189666110,0.000752428,0.000000000],[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 A9 - G14 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009532599,0.097201109,0.009775427,0.133793126,0.000000000],[0.014158910,0.008707036,0.234005991,0.011141529,0.000000000],[0.009734887,0.122912757,0.002020387,0.188098296,0.000000000],[0.112472120,0.011347231,0.017610445,0.017488151,0.000000000],[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 C10 - G13 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_70923.9:
> IL_70923.9 5G4T C 3 G 17 CGAAGAAC*GGGAG > IL_70923.9 6Q8V C 3 G 17 CGAAGAAC*GGGAG > IL_70923.9 5FJC C 31 G 21 CGAAGAAC*GGGAG > IL_70923.9 6Q8U C 4 G 18 CGAAGAAC*GGGAG > IL_70923.9 5J7L C 1208 G 1238 CUGCGAAG*UGGAG > IL_70923.9 3U4M C 2129 G 2159 CUGUGAAC*GGGAG > IL_70923.9 6Q8U C 4 G 18 CGAAGAAC*GGGAG > IL_70923.9 9DFE C 1208 G 1238 CGAUGAAG*UGGAG > IL_70923.9 7JRS C 77 G 59 CGAAGAAC*GGGAG > IL_70923.9 7JRR C 23 G 9 CGAAGAAC*GGGAG > IL_70923.9 5FJ4 C 26 G 7 CGAAGAAC*GGGAG > IL_70923.9 4V9F G 1312 C 1342 GAUGGAAG*UGGAC > IL_70923.9 7EAG C 3 G 17 CUAUGAAG*UGGAG > IL_70923.9 7JRS C 12 G 124 CGAAGAAC*GGGAG > IL_70923.9 3V7E C 31 G 21 CGAUGAAA*UGGAG > IL_70923.9 5Y7M A 17 U 33 AGACGAUC*GGGAU > IL_70923.9 7JRS C 77 G 59 CGAAGAAC*GGGAG > IL_70923.9 7EAG C 3 G 17 CUAUGAAG*UGGAG > IL_70923.9 4BW0 C 16 G 7 CGAAGAAC*GGGAG > IL_70923.9 7A0S C 1221 G 1251 CGGAGAAG*UGGAG > IL_70923.9 4WF9 C 1246 G 1276 CGUUGAAG*UGGAG > IL_70923.9 7JRS C 12 G 124 CGAAGAAC*GGGAG > IL_70923.9 4KQY C 31 G 21 CGACGAAG*CAGAG > IL_70923.9 4C4W U 26 G 7 UGAUGACC*GCAAG > IL_70923.9 8P9A U 1388 A 1419 UGACGAAG*UCGAA > IL_70923.9 8CRE U 1384 A 1415 UGACGAAG*UCGAA > IL_70923.9 5J7L C 2129 G 2159 CUUUGAAG*UGGAG