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.