Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1207

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: 12936
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30


Found at i:710 original size:40 final size:40

Alignment explanation


    Indices: 514--696  Score: 205
    Period size: 40  Copynumber: 4.6  Consensus size: 40

        504 CGAATGATGT

                                        *   *  *   * 
        514 CGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAAC

               *                           *        * 
        554 CGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATTC
          1 CGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-AC

                                  *                  
        594 CGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AATC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-C

                *                                   
        633 CGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC
          1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC

                   *                
        673 CGGGCTATGTCCCGAAGGCATTTG
          1 CGGGCTAAGTCCCGAAGGCATTTG

        697 AACGAGTAGC


Statistics
Matches: 123,  Mismatches: 13, Indels: 14
        0.82            0.09        0.09

Matches are distributed among these distances:
  39   34  0.28
  40   79  0.64
  41   10  0.08

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


Consensus pattern (40 bp):   
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAC

Found at i:718 original size:79 final size:79

Alignment explanation


    Indices: 565--729  Score: 201
    Period size: 79  Copynumber: 2.1  Consensus size: 79

        555 GGACTAAGAT

                                       *                        **           
        565 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
          1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA

                       *  
        630 ATCCGGGTTAAGTC
         66 ATCCGGGTTAAATC

                               *                 *              *            
        644 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
          1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C

              *             *
        707 TATATCC-GGTTAAATT
         63 TAAATCCGGGTTAAATC

                   
        723 CCGAAGG
          1 CCGAAGG

        730 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   48  0.65
  80   24  0.32

ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25


Consensus pattern (79 bp):   
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC

Found at i:8774 original size:79 final size:81

Alignment explanation


    Indices: 8638--8820  Score: 223
    Period size: 79  Copynumber: 2.3  Consensus size: 81

       8628 TCGAATGATG

                                    *              *                         
       8638 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT

                            
       8702 TGTGCGAGATACTA-A
         66 TGTGCGAGATACTATA

                                           *   *  *        **                
       8717 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
          1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA

                      *       
       8779 TTTGTGCGAGTTACTATA
         64 TTTGTGCGAGATACTATA

            *        *              
       8797 ACCGGGCTATGTCCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATT

       8821 TGAACGAGTA


Statistics
Matches: 89,  Mismatches: 10, Indels: 8
        0.83            0.09        0.07

Matches are distributed among these distances:
  78    1  0.01
  79   58  0.65
  80   30  0.34

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


Consensus pattern (81 bp):   
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA

Found at i:8836 original size:40 final size:40

Alignment explanation


    Indices: 8639--8822  Score: 207
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       8629 CGAATGATGT

                                         *   *  *   *
       8639 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA

                *                           *        *
       8679 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
          1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A

                                   *                
       8719 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                  *                                  
       8757 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
          1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

                    *                
       8798 CCGGGCTATGTCCCGAAGGCATTTG
          1 CCGGGCTAAGTCCCGAAGGCATTTG

       8823 AACGAGTAGC


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

Matches are distributed among these distances:
  39   34  0.27
  40   80  0.65
  41   10  0.08

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


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA

Found at i:8844 original size:79 final size:79

Alignment explanation


    Indices: 8691--8855  Score: 201
    Period size: 79  Copynumber: 2.1  Consensus size: 79

       8681 GGACTAAGAT

                                       *                        **           
       8691 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
          1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA

                       *  
       8756 ATCCGGGTTAAGTC
         66 ATCCGGGTTAAATC

                               *                 *              *            
       8770 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
          1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C

              *             *
       8833 TATATCC-GGTTAAATT
         63 TAAATCCGGGTTAAATC

                   
       8849 CCGAAGG
          1 CCGAAGG

       8856 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   48  0.65
  80   24  0.32

ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25


Consensus pattern (79 bp):   
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Done.