Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold11370.1

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: 2867
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30


Found at i:456 original size:40 final size:40

Alignment explanation


    Indices: 411--569  Score: 165
    Period size: 40  Copynumber: 4.0  Consensus size: 40

        401 CGAATACACG

                     *  *          *  *             
        411 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

            *                   *  ***     *        
        451 ACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATATA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

                *               **        *       * 
        491 TCACTAGCACGAATGCTCTTTAGAACTTAGTCCGGATACA
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

                *                         *        
        531 TCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATAT
          1 TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATAT

        570 GGTCACTTAG


Statistics
Matches: 99,  Mismatches: 20, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  40   99  1.00

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


Consensus pattern (40 bp):   
TCACCAGCACGAATGCTCTTCGGAACTTAGCCCGGATATA

Found at i:599 original size:40 final size:40

Alignment explanation


    Indices: 425--606  Score: 129
    Period size: 40  Copynumber: 4.5  Consensus size: 40

        415 CAGCATGATT

                     *  *   *       * *   *        *
        425 GCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAAT
          1 GCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAAA

                  *  ***             *              *
        465 GCTCTTTGGGGTTTAG-CACGGATATATCACTAGCACGAAT
          1 GCTCTTCGGAACTTAGTC-CGGATACATCACTAGCACGAAA

                  **                               *
        505 GCTCTTTAGAACTTAGTCCGGATACATCACTAGCACGAAT
          1 GCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAAA

                                     **               
        545 GCTCTTCGGAACTTAGTCCGGATATGGTCACTTAGCAC-AAA
          1 GCTCTTCGGAACTTAGTCCGGATA-CATCAC-TAGCACGAAA

                             *     
        586 GC-CTTCAGG-ACTTAGCCCGGA
          1 GCTCTTC-GGAACTTAGTCCGGA

        607 CATCATTCAA


Statistics
Matches: 120,  Mismatches: 17, Indels: 10
        0.82            0.12        0.07

Matches are distributed among these distances:
  39    1  0.01
  40  102  0.85
  41   11  0.09
  42    6  0.05

ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25


Consensus pattern (40 bp):   
GCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAAA

Found at i:599 original size:80 final size:80

Alignment explanation


    Indices: 425--606  Score: 190
    Period size: 80  Copynumber: 2.3  Consensus size: 80

        415 CAGCATGATT

                   *    *           *                     *  ***             
        425 GCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTTGGGGTTTAGCACGGATAT
          1 GCTCTTCAGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAGCACGGATAT

                          *
        490 ATCACTAGCACGAAT
         66 ATCACTAGCACGAAA

                  *  *      *         *   *                                  
        505 GCTCTTTAGAACTTAGTCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTC-CGGATA
          1 GCTCTTCAGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAG-CACGGATA

              *               
        569 TGGTCACTTAGCAC-AAA
         65 T-ATCAC-TAGCACGAAA

                                  
        586 GC-CTTCAGGACTTAGCCCGGA
          1 GCTCTTCAGGACTTAGCCCGGA

        607 CATCATTCAA


Statistics
Matches: 82,  Mismatches: 17, Indels: 6
        0.78            0.16        0.06

Matches are distributed among these distances:
  80   67  0.82
  81    9  0.11
  82    6  0.07

ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25


Consensus pattern (80 bp):   
GCTCTTCAGGACTTAGCCCGGATACAACACCAGCACGAATGCTCTTCGGAACTTAGCACGGATAT
ATCACTAGCACGAAA

Found at i:953 original size:29 final size:29

Alignment explanation


    Indices: 914--992  Score: 106
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        904 CTTAATAATC

                                   *       
        914 AACCACGCACACTTAGTGCCATGTACTTT-A
          1 AACC-CGCACACTTAGTGCCATGCA-TTTCA

               *                         
        944 AACTCGCACACTTAGTGCCATGCATTTCA
          1 AACCCGCACACTTAGTGCCATGCATTTCA

             *                  
        973 AGCCCGCACACTTAGTGCCA
          1 AACCCGCACACTTAGTGCCA

        993 ATCTCACAAC


Statistics
Matches: 44,  Mismatches: 4, Indels: 3
        0.86            0.08        0.06

Matches are distributed among these distances:
  28    3  0.07
  29   38  0.86
  30    3  0.07

ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24


Consensus pattern (29 bp):   
AACCCGCACACTTAGTGCCATGCATTTCA
Done.