Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3745

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: 32192
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30


Found at i:3791 original size:46 final size:46

Alignment explanation


    Indices: 3724--3898  Score: 183
    Period size: 46  Copynumber: 3.8  Consensus size: 46

       3714 TGTAACCCGC

                                                          
       3724 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT

                                                     * *  * 
       3770 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATG-GCTAG-TT
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCGTTCGCAT

            *   ***                         * *  * *       
       3816 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCAT
          1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT

               *                       *   *    
       3863 CCACAAGTGAACTCGGACTCAACTCAATGAGTTCGG
          1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG

       3899 ATGCCCAAAT


Statistics
Matches: 103,  Mismatches: 21, Indels: 10
        0.77            0.16        0.07

Matches are distributed among these distances:
  46   69  0.67
  47   33  0.32
  48    1  0.01

ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22


Consensus pattern (46 bp):   
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT

Found at i:3844 original size:93 final size:93

Alignment explanation


    Indices: 3732--3901  Score: 277
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       3722 GCCCATAAGT

                                        * *          *                       
       3732 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAA

                                        
       3797 CGAGCTCGGATGGCTAGTTACATCTCTC
         66 CGAGCTCGGATGGCTAGTTACATCTCTC

                                   * *                                       
       3825 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAA
          1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAA

            *   *       
       3890 TGAGTTCGGATG
         66 CGAGCTCGGATG

       3902 CCCAAATATC


Statistics
Matches: 70,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  93   70  1.00

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


Consensus pattern (93 bp):   
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCACAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGGCTAGTTACATCTCTC

Found at i:4352 original size:30 final size:30

Alignment explanation


    Indices: 4318--4374  Score: 78
    Period size: 30  Copynumber: 1.9  Consensus size: 30

       4308 CCAAAATCAT

                                          
       4318 ATTTTGGCAAAATTACAATTTTGCCCCTAA
          1 ATTTTGGCAAAATTACAATTTTGCCCCTAA

                 *   * *     *         
       4348 ATTTTTGCATATTTACACTTTTGCCCC
          1 ATTTTGGCAAAATTACAATTTTGCCCC

       4375 AAAGCTCGTA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  30   23  1.00

ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42


Consensus pattern (30 bp):   
ATTTTGGCAAAATTACAATTTTGCCCCTAA

Found at i:26498 original size:40 final size:39

Alignment explanation


    Indices: 26389--26571  Score: 170
    Period size: 40  Copynumber: 4.6  Consensus size: 39

      26379 TTGAATGCTG

                  *              *       *   * *  * 
      26389 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
          1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA

                 *                 *         *       
      26429 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
          1 TCCGGGTTAAG-TCCCGAAGG-CATTGTGCGAGTTACTAAA

                                    *         **    
      26469 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAA

                     *                 *           
      26509 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA

            *     *  *              
      26548 ACCGGGCTATGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

      26572 TGAACGAGGA


Statistics
Matches: 119,  Mismatches: 20, Indels: 9
        0.80            0.14        0.06

Matches are distributed among these distances:
  39   37  0.31
  40   73  0.61
  41    9  0.08

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


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA

Done.