Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1825

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: 20369
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Found at i:8117 original size:39 final size:39

Alignment explanation


    Indices: 8033--8143  Score: 116
    Period size: 40  Copynumber: 2.8  Consensus size: 39

       8023 AGATACTAAT

                                      **      *     
       8033 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA

                                       *         ** 
       8073 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATGA
          1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA

                  *  *                      
       8113 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

       8144 GAGCTATATC


Statistics
Matches: 60,  Mismatches: 9, Indels: 4
        0.82            0.12        0.05

Matches are distributed among these distances:
  39   25  0.42
  40   35  0.58

ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA

Found at i:10366 original size:20 final size:20

Alignment explanation


    Indices: 10341--10395  Score: 83
    Period size: 20  Copynumber: 2.8  Consensus size: 20

      10331 TGTGGTTCAA

                             *  
      10341 CTCATTCGAGCTCAAGTTAG
          1 CTCATTCGAGCTCAAGTCAG

                    *           
      10361 CTCATTCGTGCTCAAGTCAG
          1 CTCATTCGAGCTCAAGTCAG

                   *       
      10381 CTCATTCAAGCTCAA
          1 CTCATTCGAGCTCAA

      10396 TTTAACTCGT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   31  1.00

ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29


Consensus pattern (20 bp):   
CTCATTCGAGCTCAAGTCAG

Found at i:14818 original size:40 final size:40

Alignment explanation


    Indices: 14734--14917  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      14724 TTGAATGCTG

                  *                       *   * *    
      14734 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT

                  **              *                   
      14773 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT

                                 *          *  *    
      14814 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

                                    *               *
      14854 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT

                                    
      14894 TCCGGGTTAAGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

      14918 GAATGAGTTA


Statistics
Matches: 123,  Mismatches: 16, Indels: 10
        0.83            0.11        0.07

Matches are distributed among these distances:
  39    2  0.02
  40  111  0.90
  41   10  0.08

ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28


Consensus pattern (40 bp):   
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT

Found at i:14871 original size:80 final size:81

Alignment explanation


    Indices: 14734--14914  Score: 221
    Period size: 80  Copynumber: 2.3  Consensus size: 81

      14724 TTGAATGCTG

                  *                      *                               *   
      14734 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGTATT
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT

            *               *
      14798 TGTGCGAGTTATT-AAT
         66 CGTGCGAGTT-TTAAAA

                                                            **               
      14814 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC

                               
      14875 ATTCGTGCGAGTTTTAAAA
         63 ATTCGTGCGAGTTTTAAAA

                                 
      14894 TCCGGGTTAAGTCCCGAAGGC
          1 TCCGGGTTAAGTCCCGAAGGC

      14915 ATTGAATGAG


Statistics
Matches: 89,  Mismatches: 7, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  79    4  0.04
  80   76  0.85
  81    9  0.10

ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28


Consensus pattern (81 bp):   
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA

Found at i:14938 original size:39 final size:38

Alignment explanation


    Indices: 14815--14964  Score: 131
    Period size: 40  Copynumber: 3.8  Consensus size: 38

      14805 GTTATTAATT

                                 *   **    *       *
      14815 CCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATT
          1 CCGGGTTAAGTCCCGAAGG-CATTGAACGAGTTACTAA-A

                                     **       *     
      14855 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
          1 CCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTACT-AAA

                                       *            
      14894 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
          1 -CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTA-AA

                 *  *                      
      14934 CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 CCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

      14965 GAGCTAAATC


Statistics
Matches: 93,  Mismatches: 11, Indels: 12
        0.80            0.09        0.10

Matches are distributed among these distances:
  39   30  0.32
  40   63  0.68

ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25


Consensus pattern (38 bp):   
CCGGGTTAAGTCCCGAAGGCATTGAACGAGTTACTAAA
Done.