Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2658

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, 531

Length: 885
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.22

Warning! 85 characters in sequence are not A, C, G, or T


Found at i:659 original size:52 final size:45

Alignment explanation


    Indices: 549--688  Score: 149
    Period size: 52  Copynumber: 2.9  Consensus size: 45

        539 AAAGGTGGGA

                 *     *                                  
        549 CCAAGATGAAAGCCTACAAAGGGCGCTTTGAGT-AAAAAAAAAGGG
          1 CCAAGGTGAAACCCTACAAAGGGC-CTTTGAGTAAAAAAAAAAGGG

                                                               
        594 CCAAGGTGAAACCCTACAAATGGGCTCTTTGAGTCAAAAAAAAAGAGAGAG
          1 CCAAGGTGAAACCCTACAAA-GGGC-CTTTGAGT-AAAAAAAAA-AG-G-G

                *                                        
        645 ACCAGGGTGAAACCCTACAAAGGGAGCC-TTGAGTAAAAAAAAAA
          1 -CCAAGGTGAAACCCTACAAA-GG-GCCTTTGAGTAAAAAAAAAA

        689 TGGAGAGGCT


Statistics
Matches: 82,  Mismatches: 5, Indels: 12
        0.83            0.05        0.12

Matches are distributed among these distances:
  45   18  0.22
  46   12  0.15
  48    8  0.10
  49    3  0.04
  50   10  0.12
  51    7  0.09
  52   22  0.27
  53    2  0.02

ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14


Consensus pattern (45 bp):   
CCAAGGTGAAACCCTACAAAGGGCCTTTGAGTAAAAAAAAAAGGG

Found at i:711 original size:52 final size:48

Alignment explanation


    Indices: 549--707  Score: 155
    Period size: 51  Copynumber: 3.2  Consensus size: 48

        539 AAAGGTGGGA

                 *     *              *                      
        549 CCAAGATGAAAGCCTACAAAGGGCGCTTTGAGT-AAAAAAAA--AG-GG
          1 CCAAGGTGAAACCCTACAAAGGG-GCCTTGAGTAAAAAAAAAGGAGAGG

                                *                              *
        594 CCAAGGTGAAACCCTACAAATGGGCTCTTTGAGTCAAAAAAAAAGAGAGAGA
          1 CCAAGGTGAAACCCTACAAAGGGGC-C-TTGAGT-AAAAAAAAAG-GAGAGG

               *                                               
        646 CCAGGGTGAAACCCTACAAAGGGAGCCTTGAGTAAAAAAAAAATGGAGAGG
          1 CCAAGGTGAAACCCTACAAAGGG-GCCTTGAGT-AAAAAAAAA-GGAGAGG

             *         
        697 CTAAGGTGAAA
          1 CCAAGGTGAAA

        708 ACCCGCAAAT


Statistics
Matches: 93,  Mismatches: 11, Indels: 14
        0.79            0.09        0.12

Matches are distributed among these distances:
  44    2  0.02
  45   20  0.22
  46    6  0.06
  48    8  0.09
  51   31  0.33
  52   24  0.26
  53    2  0.02

ACGTcount: A:0.44, C:0.16, G:0.26, T:0.14


Consensus pattern (48 bp):   
CCAAGGTGAAACCCTACAAAGGGGCCTTGAGTAAAAAAAAAGGAGAGG
Done.