Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2847

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: 30243
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32


Found at i:26729 original size:39 final size:40

Alignment explanation


    Indices: 26605--26825  Score: 206
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      26595 GCTCCTCGTT

                            *  *                 *  
      26605 CAAATGCCTTC-GGACATAGCCC-G-TTTAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                            *             *         
      26642 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

             *          *                           
      26681 CGAATGCCTTCGAGACTTAACCCGGATTTAGT-ACTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

                *         *                   *      
      26720 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
          1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA

                                **       * * *    *   
      26760 CAAATGCCTTC-GGATCTTAGTCCGGATTAATTCACTTAGCA
          1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA

                               *      
      26801 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAACCCGGA

      26826 CAGCATTCAA


Statistics
Matches: 153,  Mismatches: 21, Indels: 17
        0.80            0.11        0.09

Matches are distributed among these distances:
  36    9  0.06
  37   11  0.07
  38    1  0.01
  39   48  0.31
  40   73  0.48
  41   11  0.07

ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA

Found at i:26732 original size:79 final size:77

Alignment explanation


    Indices: 26605--26825  Score: 232
    Period size: 79  Copynumber: 2.8  Consensus size: 77

      26595 GCTCCTCGTT

                           *                    *     *           *          
      26605 CAAATGCCTTCGGACATAGCCC-G-TTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGAT
          1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAAGCCTTCGGGACTTAACCCGGAT

                         
      26668 TTAATAACTCGCA
         66 TT-ATAACTCGCA

             *                 *                                  *          
      26681 CGAATGCCTTCGAGACTTAACCCGGATTTAGT-ACTCGCACAAAGGCCTTCGGGGCTTAACCCGG
          1 CAAATGCCTTCG-GACTTAGCCCGGATTTAGTAACTCGCACAAA-GCCTTCGGGACTTAACCCGG

                 *  *      
      26745 AATTTGTATCTCGCA
         64 -ATTTATAACTCGCA

                                *       * * *    *                     *     
      26760 CAAATGCCTTCGGATCTTAGTCCGGATTAATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAAGCCTTCGGGACTTAACCCGG

             
      26825 A
         64 A

      26826 CAGCATTCAA


Statistics
Matches: 120,  Mismatches: 17, Indels: 13
        0.80            0.11        0.09

Matches are distributed among these distances:
  76   11  0.09
  77    8  0.07
  78   12  0.10
  79   57  0.47
  80   24  0.20
  81    8  0.07

ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25


Consensus pattern (77 bp):   
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAAGCCTTCGGGACTTAACCCGGAT
TTATAACTCGCA

Done.