Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3321

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: 17137
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31


Found at i:3586 original size:19 final size:20

Alignment explanation


    Indices: 3549--3586  Score: 53
    Period size: 19  Copynumber: 1.9  Consensus size: 20

       3539 ATAAGGTGGT

                                
       3549 AAGATGATGAATGATGTTTA
          1 AAGATGATGAATGATGTTTA

                                
       3569 AAGATG-TGATAT-ATGTTT
          1 AAGATGATGA-ATGATGTTT

       3587 TGGTGGTACC


Statistics
Matches: 17,  Mismatches: 0, Indels: 3
        0.85            0.00        0.15

Matches are distributed among these distances:
  19    9  0.53
  20    8  0.47

ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39


Consensus pattern (20 bp):   
AAGATGATGAATGATGTTTA

Found at i:15643 original size:40 final size:40

Alignment explanation


    Indices: 15588--15798  Score: 221
    Period size: 40  Copynumber: 5.3  Consensus size: 40

      15578 ATTTGAATGA

                         *                          
      15588 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
          1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT

                         *                          
      15628 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
          1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT

                                       * * *        *
      15668 TATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGA-TA
          1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT

               *                       *   *      * *
      15708 TATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
          1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT

              *     *               *  *    *   *  *
      15748 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
          1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT

                        
      15788 TATCC-GGCTAA
          1 TATCCGGGCTAA

      15799 ATTCCGAAGA


Statistics
Matches: 152,  Mismatches: 16, Indels: 7
        0.87            0.09        0.04

Matches are distributed among these distances:
  39    7  0.05
  40  142  0.93
  41    3  0.02

ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29


Consensus pattern (40 bp):   
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT

Done.