Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2572

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: 5489
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30


Found at i:4111 original size:40 final size:40

Alignment explanation


    Indices: 3886--4104  Score: 253
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       3876 TTGAATGATG

                                          *   *  * * 
       3886 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA

                 *                                   
       3926 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT-AA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

                                                     
       3965 TCC-GGCTAAGAT-CCGAAGG--TTTGTGCGAG-TACT-AA
          1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA

             *                                      
       4000 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

                  *                                  
       4039 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA

                     *                
       4080 -CCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       4105 AACGAGTAGC


Statistics
Matches: 158,  Mismatches: 11, Indels: 20
        0.84            0.06        0.11

Matches are distributed among these distances:
  35   15  0.09
  36   17  0.11
  37   10  0.06
  38   19  0.12
  39   15  0.09
  40   72  0.46
  41   10  0.06

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA

Done.