Tandem Repeats Finder Program written by: Gary Benson Program in Bioinformatics Boston University Version 4.09 Sequence: Scaffold321 Parameters: 2 7 7 80 10 50 1000 Pmatch=0.80,Pindel=0.10 tuple sizes 0,4,5,7 tuple distances 0, 29, 159, 1000 Length: 24601 ACGTcount: A:0.32, C:0.22, G:0.16, T:0.31 Found at i:6564 original size:93 final size:93 Alignment explanation
Indices: 6405--6575 Score: 308 Period size: 93 Copynumber: 1.8 Consensus size: 93 6395 GGATGGTTGA 6405 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT 6470 TGAGTCCGAGTTCGTGAGATGTAACTAG 66 TGAGTCCGAGTTCGTGAGATGTAACTAG * * 6498 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGAG 1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCC-GAACTCGTTGAG 6562 TTGAGTCCGAGTTC 65 TTGAGTCCGAGTTC 6576 ACTTAGGGGC Statistics Matches: 75, Mismatches: 2, Indels: 2 0.95 0.03 0.03 Matches are distributed among these distances: 92 2 0.03 93 73 0.97 ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29 Consensus pattern (93 bp): GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAGT TGAGTCCGAGTTCGTGAGATGTAACTAG Found at i:6578 original size:46 final size:45 Alignment explanation
Indices: 6409--6580 Score: 206 Period size: 46 Copynumber: 3.7 Consensus size: 45 6399 GGTTGAGCAT * 6409 CCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG 1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * * * * 6454 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAG-GCAT- 1 -CCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATG 6502 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG 1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG * 6547 CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA 1 CC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTA 6581 GGGGCGGGTT Statistics Matches: 107, Mismatches: 10, Indels: 18 0.79 0.07 0.13 Matches are distributed among these distances: 43 1 0.01 44 4 0.04 45 3 0.03 46 61 0.57 47 31 0.29 48 2 0.02 49 4 0.04 50 1 0.01 ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29 Consensus pattern (45 bp): CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG Found at i:15266 original size:27 final size:27 Alignment explanation
Indices: 15234--15438 Score: 214 Period size: 27 Copynumber: 7.6 Consensus size: 27 15224 ATATTGAGTC * * 15234 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAATCAACT * * * 15261 CACACACTTAGTGCTACGTAATCAAAT 1 CGCACACTTAGTGCTACATAATCAACT * 15288 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAATC-AACT ** ** * 15316 CGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAATCAACT * ** 15343 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAATCAACT * * * 15370 CGCACACTTAGTGCAACATAGTCAAAT 1 CGCACACTTAGTGCTACATAATCAACT * * 15397 CGCACACTTAGTGCTACATAGTCAAAT 1 CGCACACTTAGTGCTACATAATCAACT 15424 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 15439 GTACAATTTA Statistics Matches: 154, Mismatches: 21, Indels: 6 0.85 0.12 0.03 Matches are distributed among these distances: 27 130 0.84 28 24 0.16 ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAATCAACT Found at i:15394 original size:54 final size:54 Alignment explanation
Indices: 15234--15437 Score: 248 Period size: 54 Copynumber: 3.8 Consensus size: 54 15224 ATATTGAGTC * * * * * * * * 15234 CGCACACTCAGTGCTATATAATCAACTCACACACTTAGTGCTACGTAATCAAAT 1 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT ** * * 15288 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAGTCAAA-TCGCACACTTAGTGCAACATAGTCAAAT * ** 15343 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT 1 CGCACACTTAGTGCTA-CATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT 15397 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC 1 CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGC 15438 TGTACAATTT Statistics Matches: 126, Mismatches: 21, Indels: 6 0.82 0.14 0.04 Matches are distributed among these distances: 54 83 0.66 55 43 0.34 ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26 Consensus pattern (54 bp): CGCACACTTAGTGCTACATAGTCAAATCGCACACTTAGTGCAACATAGTCAAAT Found at i:23345 original size:27 final size:27 Alignment explanation
Indices: 23314--23518 Score: 259 Period size: 27 Copynumber: 7.6 Consensus size: 27 23304 TATATGAGTC * * * * 23314 CGCACACTCAGTGCTATATAATCAACT 1 CGCACACTTAGTGCTACATAGTCAAAT * * 23341 CGCACACTTAGTGCTACGTAATCAAAT 1 CGCACACTTAGTGCTACATAGTCAAAT 23368 CGCACACTTAGTGCTACATAGTCAAACT 1 CGCACACTTAGTGCTACATAGTCAAA-T ** * * 23396 CGCACACTTAGTGCCGCATGGTCAATT 1 CGCACACTTAGTGCTACATAGTCAAAT * ** 23423 CGCACACTTAGTGC-ATCATATTCATTT 1 CGCACACTTAGTGCTA-CATAGTCAAAT * 23450 CGCACACTTAGTGCAACATAGTCAAAT 1 CGCACACTTAGTGCTACATAGTCAAAT 23477 CGCACACTTAGTGCTACATAGTCAAAT 1 CGCACACTTAGTGCTACATAGTCAAAT 23504 CGCACACTTAGTGCT 1 CGCACACTTAGTGCT 23519 GTACAATTAC Statistics Matches: 157, Mismatches: 18, Indels: 6 0.87 0.10 0.03 Matches are distributed among these distances: 27 133 0.85 28 24 0.15 ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27 Consensus pattern (27 bp): CGCACACTTAGTGCTACATAGTCAAAT Found at i:23542 original size:109 final size:109 Alignment explanation
Indices: 23312--23517 Score: 290 Period size: 109 Copynumber: 1.9 Consensus size: 109 23302 GGTATATGAG * * ** * * 23312 TCCGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACT 1 TCCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACT *** 23376 TAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAA 65 TAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCACAATCAA * * 23421 TTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTT 1 TCCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACTT 23486 AGTGCTACATAGTCAAA-TCGCACACTTAGTGC 66 AGTGCTACATAGTCAAACTCGCACACTTAGTGC 23518 TGTACAATTA Statistics Matches: 88, Mismatches: 8, Indels: 3 0.89 0.08 0.03 Matches are distributed among these distances: 108 17 0.19 109 71 0.81 ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27 Consensus pattern (109 bp): TCCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAATCAAATCGCACACTT AGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCACAATCAA Done.