Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2898

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: 8707
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31


Found at i:2455 original size:40 final size:40

Alignment explanation


    Indices: 2398--2655  Score: 355
    Period size: 40  Copynumber: 6.5  Consensus size: 40

       2388 CGGATGATAA

                                        *   *        
       2398 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T

             *                                        
       2438 CTGGGCTAAGTCCCGAAGGCA-TTGTTGCGAGTTACTA-ATT
          1 CCGGGCTAAGTCCCGAAGGCATTTG-TGCGAGTTACTATA-T

                                                    
       2478 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                                    
       2518 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                          **        
       2558 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

              *                    * *               
       2598 CCAGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT

                 *   *         
       2638 CC-GGTTAAATCCCGAAGG
          1 CCGGGCTAAGTCCCGAAGG

       2656 TACTTGGTTT


Statistics
Matches: 202,  Mismatches: 12, Indels: 9
        0.91            0.05        0.04

Matches are distributed among these distances:
  39   19  0.09
  40  179  0.89
  41    4  0.02

ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

Done.