Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold682

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: 11390
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31


Found at i:6693 original size:79 final size:81

Alignment explanation


    Indices: 6557--6741  Score: 227
    Period size: 79  Copynumber: 2.3  Consensus size: 81

       6547 TTGAATGATG

                                                   *                       * 
       6557 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT

                            
       6621 TGTGCGAGATACTA-A
         66 TGTGCGAGATACTATA

                                           *   *  *        **                
       6636 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
          1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA

                      *       
       6698 ATTGTGCGAGTTACTATA
         64 ATTGTGCGAGATACTATA

            *        *                
       6716 ACCGGGCTATGTCCCGAAGGCATTTG
          1 TCCGGGCTAAGTCCCGAAGGCATTTG

       6742 AACGAGTAGC


Statistics
Matches: 91,  Mismatches: 10, Indels: 8
        0.83            0.09        0.07

Matches are distributed among these distances:
  78    1  0.01
  79   57  0.63
  80   33  0.36

ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25


Consensus pattern (81 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA

Found at i:6755 original size:40 final size:40

Alignment explanation


    Indices: 6558--6741  Score: 207
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       6548 TGAATGATGT

                                         *   *  *   *
       6558 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA

                *                           *        *
       6598 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
          1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A

                                                    
       6638 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                  *               *                  
       6676 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
          1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                    *                
       6717 CCGGGCTATGTCCCGAAGGCATTTG
          1 CCGGGCTAAGTCCCGAAGGCATTTG

       6742 AACGAGTAGC


Statistics
Matches: 124,  Mismatches: 13, Indels: 14
        0.82            0.09        0.09

Matches are distributed among these distances:
  39   35  0.28
  40   79  0.64
  41   10  0.08

ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

Found at i:6763 original size:79 final size:79

Alignment explanation


    Indices: 6610--6774  Score: 201
    Period size: 79  Copynumber: 2.1  Consensus size: 79

       6600 GGACTAAGAT

                     *                 *                        **           
       6610 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
          1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA

                       *  
       6675 ATCCGGGTTAAGTC
         66 ATCCGGGTTAAATC

                               *                 *                           
       6689 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
          1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C

              *             *
       6752 TATATCC-GGTTAAATT
         63 TAAATCCGGGTTAAATC

                   
       6768 CCGAAGG
          1 CCGAAGG

       6775 TACGTGATTT


Statistics
Matches: 74,  Mismatches: 9, Indels: 6
        0.83            0.10        0.07

Matches are distributed among these distances:
  78    2  0.03
  79   47  0.64
  80   25  0.34

ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25


Consensus pattern (79 bp):   
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.