Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold10464.1

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: 3604
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28


Found at i:2011 original size:37 final size:37

Alignment explanation

Indices: 1970--2042 Score: 137 Period size: 37 Copynumber: 2.0 Consensus size: 37 1960 ACCTTTGACA * 1970 AATCGTCGGTAATAACCGGCGAGTCCCAAAAAGCTCT 1 AATCGTCGGTAATAACCGGCGAGCCCCAAAAAGCTCT 2007 AATCGTCGGTAATAACCGGCGAGCCCCAAAAAGCTC 1 AATCGTCGGTAATAACCGGCGAGCCCCAAAAAGCTC 2043 CGAACCTCAG Statistics Matches: 35, Mismatches: 1, Indels: 0 0.97 0.03 0.00 Matches are distributed among these distances: 37 35 1.00 ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16 Consensus pattern (37 bp): AATCGTCGGTAATAACCGGCGAGCCCCAAAAAGCTCT Found at i:2056 original size:37 final size:37 Alignment explanation

Indices: 1978--2057 Score: 108 Period size: 37 Copynumber: 2.2 Consensus size: 37 1968 CAAATCGTCG * * * * 1978 GTAATAACCGGCGAGTCCCAAAAAGCTCTAATCGTCG 1 GTAATAACCGGCGAGCCCCAAAAAGCTCGAATCCTCA 2015 GTAATAACCGGCGAGCCCCAAAAAGCTCCGAA-CCTCA 1 GTAATAACCGGCGAGCCCCAAAAAGCT-CGAATCCTCA 2052 GTAATA 1 GTAATA 2058 TTTCTCGGAG Statistics Matches: 38, Mismatches: 4, Indels: 2 0.86 0.09 0.05 Matches are distributed among these distances: 37 35 0.92 38 3 0.08 ACGTcount: A:0.35, C:0.29, G:0.20, T:0.16 Consensus pattern (37 bp): GTAATAACCGGCGAGCCCCAAAAAGCTCGAATCCTCA Found at i:2414 original size:45 final size:45 Alignment explanation

Indices: 2363--2452 Score: 144 Period size: 45 Copynumber: 2.0 Consensus size: 45 2353 TAGTGAGCCC * 2363 AAACGGCATCACTAAGAACTCGTAGTGACCGTACCTCATTCTGAA 1 AAACGGCATCACTAAGAACTCGTAGTGACCATACCTCATTCTGAA * * * 2408 AAACGGCATCACTAAGAATTCGTAGTGACCATATCTCGTTCTGAA 1 AAACGGCATCACTAAGAACTCGTAGTGACCATACCTCATTCTGAA 2453 GGCAGTTTTG Statistics Matches: 41, Mismatches: 4, Indels: 0 0.91 0.09 0.00 Matches are distributed among these distances: 45 41 1.00 ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24 Consensus pattern (45 bp): AAACGGCATCACTAAGAACTCGTAGTGACCATACCTCATTCTGAA Found at i:2843 original size:235 final size:235 Alignment explanation

Indices: 2432--2900 Score: 920 Period size: 235 Copynumber: 2.0 Consensus size: 235 2422 AGAATTCGTA 2432 GTGACCATATCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTCGCAACTGATAAT 1 GTGACCATATCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTCGCAACTGATAAT 2497 AGCCCGATCTCAAATCTATTTTCGAGAACACTGTGGCTCCCTTCAGTTGGTCGAACAAATCATCG 66 AGCCCGATCTCAAATCTATTTTCGAGAACACTGTGGCTCCCTTCAGTTGGTCGAACAAATCATCG 2562 ATGCGCGGCAACGGATATTTGTTCTTTATCGTCACTTTATTCAGTTGACGATAGTCAATGCACAA 131 ATGCGCGGCAACGGATATTTGTTCTTTATCGTCACTTTATTCAGTTGACGATAGTCAATGCACAA * * 2627 CCTCATGGTTCTGTCCTTCTTTTTCACGAACAATACTGGG 196 CCTCATGGTTCCGTCCTTCTTTTTCACAAACAATACTGGG 2667 GTGACCATATCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTCGCAACTGATAAT 1 GTGACCATATCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTCGCAACTGATAAT 2732 AGCCCGATCTCAAATCTATTTTCGAGAACACTGTGGCTCCCTTCAGTTGGTCGAACAAATCATCG 66 AGCCCGATCTCAAATCTATTTTCGAGAACACTGTGGCTCCCTTCAGTTGGTCGAACAAATCATCG 2797 ATGCGCGGCAACGGATATTTGTTCTTTATCGTCACTTTATTCAGTTGACGATAGTCAATGCACAA 131 ATGCGCGGCAACGGATATTTGTTCTTTATCGTCACTTTATTCAGTTGACGATAGTCAATGCACAA 2862 CCTCATGGTTCCGTCCTTCTTTTTCACAAACAATACTGG 196 CCTCATGGTTCCGTCCTTCTTTTTCACAAACAATACTGG 2901 TGCACCCCAA Statistics Matches: 232, Mismatches: 2, Indels: 0 0.99 0.01 0.00 Matches are distributed among these distances: 235 232 1.00 ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32 Consensus pattern (235 bp): GTGACCATATCTCGTTCTGAAGGCAGTTTTGGGTATGTCCGAATCTCGAATTCGCAACTGATAAT AGCCCGATCTCAAATCTATTTTCGAGAACACTGTGGCTCCCTTCAGTTGGTCGAACAAATCATCG ATGCGCGGCAACGGATATTTGTTCTTTATCGTCACTTTATTCAGTTGACGATAGTCAATGCACAA CCTCATGGTTCCGTCCTTCTTTTTCACAAACAATACTGGG Done.