Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3510

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, 440

Length: 734
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29


Found at i:446 original size:22 final size:21

Alignment explanation


    Indices: 405--453  Score: 64
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        395 TGCACTAATG

                                 
        405 AACAGAGAGCACTAAAGTGCT
          1 AACAGAGAGCACTAAAGTGCT

                             *     
        426 ATACAGAGAGCAC-AGATGTGCT
          1 A-ACAGAGAGCACTA-AAGTGCT

                  
        448 AACAGA
          1 AACAGA

        454 TGTGCTAAAC


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  21    7  0.28
  22   18  0.72

ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14


Consensus pattern (21 bp):   
AACAGAGAGCACTAAAGTGCT

Found at i:454 original size:12 final size:13

Alignment explanation


    Indices: 437--466  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        427 TACAGAGAGC

                         
        437 ACAGATGTGCT-A
          1 ACAGATGTGCTAA

                         
        449 ACAGATGTGCTAA
          1 ACAGATGTGCTAA

                 
        462 ACAGA
          1 ACAGA

        467 GAGCACTGAC


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  12   11  0.65
  13    6  0.35

ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20


Consensus pattern (13 bp):   
ACAGATGTGCTAA

Found at i:543 original size:25 final size:25

Alignment explanation


    Indices: 463--544  Score: 103
    Period size: 25  Copynumber: 3.3  Consensus size: 25

        453 ATGTGCTAAA

                       *             
        463 CAGAGAGCACTGACGTGCTAA-AAT
          1 CAGAGAGCACTAACGTGCTAATAAT

                      *     *   *  * 
        487 CAGAGAGCACCAACGTTCTAGTAGT
          1 CAGAGAGCACTAACGTGCTAATAAT

                                     
        512 CAGAGAGCACTAACGTGCTAATAAT
          1 CAGAGAGCACTAACGTGCTAATAAT

              *     
        537 CAAAGAGC
          1 CAGAGAGC

        545 GCGCTAAAGT


Statistics
Matches: 47,  Mismatches: 10, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  24   17  0.36
  25   30  0.64

ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17


Consensus pattern (25 bp):   
CAGAGAGCACTAACGTGCTAATAAT
Done.