Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold635

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: 3108
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34


Found at i:1892 original size:40 final size:40

Alignment explanation


    Indices: 1758--1979  Score: 269
    Period size: 40  Copynumber: 5.5  Consensus size: 40

       1748 TATTCGGATG

                                            *   *   
       1758 ATATCC-GGCTAAGTCCCGAAGGCA-TTGTGCAAGTTACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                                                         
       1796 ATATCCGGGCTAAGTCCCGAAAGGCA-TTGTGCGAGTAGTTG-CT
          1 ATATCCGGGCTAAGTCCCG-AAGGCATTTGTGC---TAG-TGACT

                                                     
       1839 ATA-CTCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
          1 ATATC-CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                                       **           
       1879 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

                          *                 *        
       1919 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
          1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT

                         *        
       1959 ATATCC-GGCTAAATCCCGAAG
          1 ATATCCGGGCTAAGTCCCGAAG

       1980 ATACTTGGTT


Statistics
Matches: 163,  Mismatches: 10, Indels: 21
        0.84            0.05        0.11

Matches are distributed among these distances:
  38    6  0.04
  39   27  0.17
  40   92  0.56
  41    3  0.02
  42    7  0.04
  43   27  0.17
  44    1  0.01

ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25


Consensus pattern (40 bp):   
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT

Done.