Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1866

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: 34741
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:28576 original size:20 final size:20

Alignment explanation


    Indices: 28530--28576  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      28520 AGCTCGTTTC

                      *         
      28530 CAGCTCACTCGAGCTCAAGT
          1 CAGCTCACTCAAGCTCAAGT

              *               * 
      28550 CAACTCACTCAAGCTCAATT
          1 CAGCTCACTCAAGCTCAAGT

                   
      28570 CAGCTCA
          1 CAGCTCA

      28577 ATCTTAACCC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21


Consensus pattern (20 bp):   
CAGCTCACTCAAGCTCAAGT

Found at i:30108 original size:10 final size:10

Alignment explanation


    Indices: 30075--30100  Score: 52
    Period size: 10  Copynumber: 2.6  Consensus size: 10

      30065 AAAAAAAGAG

                      
      30075 AAAAATTCAA
          1 AAAAATTCAA

                      
      30085 AAAAATTCAA
          1 AAAAATTCAA

                  
      30095 AAAAAT
          1 AAAAAT

      30101 CGAAAAAAGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  10   16  1.00

ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19


Consensus pattern (10 bp):   
AAAAATTCAA

Found at i:31296 original size:48 final size:48

Alignment explanation


    Indices: 31238--31343  Score: 144
    Period size: 48  Copynumber: 2.2  Consensus size: 48

      31228 GAGTGTCATA

                                     *            *           
      31238 GAAAAAGAAATTGAGATTGAA-AAAGGATGTGAA-AAAGAGAAAGAAATC
          1 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAAGAAAAAGAAA-AAATC

                                                     *     *
      31286 GAAAAAGAAATTGAGATTGAACAAAAGTGTGAAGAAAAAGAGAAAATT
          1 GAAAAAGAAATTGAGATTGAACAAAAGTGTGAAGAAAAAGAAAAAATC

                      
      31334 GAAAAAGAAA
          1 GAAAAAGAAA

      31344 GAAAAGACAA


Statistics
Matches: 52,  Mismatches: 4, Indels: 4
        0.87            0.07        0.07

Matches are distributed among these distances:
  48   41  0.79
  49   11  0.21

ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14


Consensus pattern (48 bp):   
GAAAAAGAAATTGAGATTGAACAAAAGTGTGAAGAAAAAGAAAAAATC

Found at i:33057 original size:20 final size:20

Alignment explanation


    Indices: 33011--33057  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      33001 AGCTCGTTTC

                      *         
      33011 CAGCTCACTCGAGCTCAAGT
          1 CAGCTCACTCAAGCTCAAGT

              *               * 
      33031 CAACTCACTCAAGCTCAATT
          1 CAGCTCACTCAAGCTCAAGT

                   
      33051 CAGCTCA
          1 CAGCTCA

      33058 ATCTTAACCC


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21


Consensus pattern (20 bp):   
CAGCTCACTCAAGCTCAAGT
Done.