Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2559

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, 544

Length: 908
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32


Found at i:96 original size:41 final size:41

Alignment explanation


    Indices: 66--235  Score: 241
    Period size: 41  Copynumber: 4.1  Consensus size: 41

         56 GCACTTAGCA

                    *                        *       
         66 TGCTAGACATAAAGTCTGAAATGTTTCACTGGCGTCAAGCC
          1 TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCCTCAAGCC

                             *               *       
        107 TGCTAGACTTAAAGTCTAAAATGTTTCACTGGCGTCAAGCC
          1 TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCCTCAAGCC

                                         *   **      
        148 TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGACAAGCC
          1 TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCCTCAAGCC

                                 ** *        *       
        189 TGCTAGACTTAAAGTCTGAAACATATCACTGGCATCAAGCC
          1 TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCCTCAAGCC

                  
        230 TGCTAG
          1 TGCTAG

        236 GCACCGAGCC


Statistics
Matches: 118,  Mismatches: 11, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  41  118  1.00

ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26


Consensus pattern (41 bp):   
TGCTAGACTTAAAGTCTGAAATGTTTCACTGGCCTCAAGCC

Found at i:152 original size:82 final size:82

Alignment explanation


    Indices: 66--235  Score: 268
    Period size: 82  Copynumber: 2.1  Consensus size: 82

         56 GCACTTAGCA

                                         *    *                           ** 
         66 TGCTAGACATAAAGTCTGAAATGTTTCACTGGCGTCAAGCCTGCTAGACTTAAAGTCTAAAATGT
          1 TGCTAGACATAAAGTCTGAAATGTTTCACCGGCGACAAGCCTGCTAGACTTAAAGTCTAAAACAT

            *        *       
        131 TTCACTGGCGTCAAGCC
         66 ATCACTGGCATCAAGCC

                    *                                                 *      
        148 TGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGACAAGCCTGCTAGACTTAAAGTCTGAAACAT
          1 TGCTAGACATAAAGTCTGAAATGTTTCACCGGCGACAAGCCTGCTAGACTTAAAGTCTAAAACAT

                             
        213 ATCACTGGCATCAAGCC
         66 ATCACTGGCATCAAGCC

                  
        230 TGCTAG
          1 TGCTAG

        236 GCACCGAGCC


Statistics
Matches: 80,  Mismatches: 8, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  82   80  1.00

ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26


Consensus pattern (82 bp):   
TGCTAGACATAAAGTCTGAAATGTTTCACCGGCGACAAGCCTGCTAGACTTAAAGTCTAAAACAT
ATCACTGGCATCAAGCC

Done.