Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2763

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: 11804
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30


Found at i:1689 original size:40 final size:40

Alignment explanation


    Indices: 1606--1867  Score: 316
    Period size: 40  Copynumber: 6.6  Consensus size: 40

       1596 TTGAATGCTG

                  *                 *     *   * *  * 
       1606 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
          1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA

                 *                *  *       *  *    
       1646 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
          1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA

                                                    
       1686 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA

                                                    
       1726 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA

                                              *     
       1766 TCCGGGTTAAGTCCCGAAGGCA-TCGTGCGAGTTGTTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA

                     *                  *      *    
       1805 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
          1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA

            *     *  *              
       1844 ACCGGGCTATGTCCCGAAGGCATT
          1 TCCGGGTTAAGTCCCGAAGGCATT

       1868 TGAACGAGGA


Statistics
Matches: 199,  Mismatches: 19, Indels: 9
        0.88            0.08        0.04

Matches are distributed among these distances:
  39   72  0.36
  40  119  0.60
  41    8  0.04

ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27


Consensus pattern (40 bp):   
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA

Found at i:1891 original size:78 final size:79

Alignment explanation


    Indices: 1607--1902  Score: 262
    Period size: 80  Copynumber: 3.7  Consensus size: 79

       1597 TGAATGCTGT

                                * *     *      *  *      *                *  
       1607 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGA-ATATATCCGGATTAAGAT-CCGAAGGCCTT
          1 CCGGGCTAAGTCCCGAAGGCATCGTGC-GAG-GAGCTAAATCCGGGTTAAG-TCCCGAAGGCATT

            *       *       *
       1670 TGTGCGAGATACTAAAT
         63 CGTGCGAGTTACTAAAA

                 *                          *  *                             
       1687 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TTAAATCCGGGTTAAGTCCCGAAGGCATTC
          1 CCGGGCTAAGTCCCGAAGGCA-TCGTGCGAG-GAGCTAAATCCGGGTTAAGTCCCGAAGGCATTC

                      *    *
       1751 GTGCGAGTTATTAAAT
         64 GTGCGAGTTACTAAAA

                 *                        ** *             *                 
       1767 CCGGGTTAAGTCCCGAAGGCATCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATT-GT
          1 CCGGGCTAAGTCCCGAAGGCATCGTGCGAGGAGCTAAATCCGGGTTAAGTCCCGAAGGCATTCGT

             *            
       1831 GTGAGTTACTAAAA
         66 GCGAGTTACTAAAA

                    *              *              *           *         
       1845 CCGGGCTATGTCCCGAAGGCAT-TTGAACGAGGAGCTATATCC-GGTTAAATCCCGAAGG
          1 CCGGGCTAAGTCCCGAAGGCATCGTG--CGAGGAGCTAAATCCGGGTTAAGTCCCGAAGG

       1903 TACGTGATTT


Statistics
Matches: 185,  Mismatches: 26, Indels: 12
        0.83            0.12        0.05

Matches are distributed among these distances:
  77    2  0.01
  78   48  0.26
  79   49  0.26
  80   81  0.44
  81    5  0.03

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


Consensus pattern (79 bp):   
CCGGGCTAAGTCCCGAAGGCATCGTGCGAGGAGCTAAATCCGGGTTAAGTCCCGAAGGCATTCGT
GCGAGTTACTAAAA

Found at i:9618 original size:40 final size:40

Alignment explanation


    Indices: 9534--9666  Score: 114
    Period size: 40  Copynumber: 3.4  Consensus size: 40

       9524 TTGAATGCTG

                 *                       *            
       9534 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACT-AT
          1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT

                                  *           *  *    
       9573 ATCCGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTATTAAT
          1 -TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT

                 **              *                  
       9614 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
          1 TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT

                  *       
       9654 TCCGG-GTAAGTCC
          1 TCCGGACTAAGTCC

       9667 GAAAGATTCC


Statistics
Matches: 76,  Mismatches: 12, Indels: 11
        0.77            0.12        0.11

Matches are distributed among these distances:
  39    8  0.11
  40   56  0.74
  41   12  0.16

ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29


Consensus pattern (40 bp):   
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT

Found at i:9718 original size:60 final size:61

Alignment explanation


    Indices: 9612--9727  Score: 164
    Period size: 60  Copynumber: 1.9  Consensus size: 61

       9602 CGAGTTATTA

                                   *  *              *                   
       9612 ATTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAATTCCGGG-TAAGTCCGAAAG
          1 ATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCGAAAG

                                                **                   
       9672 ATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG-TTTTAAAATCCGGGTTAAGTCC
          1 ATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACT-AAATCCGGGTTAAGTCC

       9728 CGAAGGCATT


Statistics
Matches: 49,  Mismatches: 5, Indels: 3
        0.86            0.09        0.05

Matches are distributed among these distances:
  59    2  0.04
  60   40  0.82
  61    7  0.14

ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27


Consensus pattern (61 bp):   
ATTCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTCCGAAAG

Found at i:9758 original size:39 final size:39

Alignment explanation


    Indices: 9674--9784  Score: 125
    Period size: 40  Copynumber: 2.8  Consensus size: 39

       9664 TCCGAAAGAT

                                      **      *     
       9674 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAAA
          1 TCCGGGTTAAGTCCCGAAGGCATT-GAACGAGTTCTAAAA

                                       *         *  
       9714 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
          1 TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTT-CTAAAA

                  *  *                      
       9754 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG
          1 TCCGGGTTAAGTCCCGAAGGCA-TTGAACGAG

       9785 GAGCTAAATC


Statistics
Matches: 61,  Mismatches: 8, Indels: 4
        0.84            0.11        0.05

Matches are distributed among these distances:
  39   25  0.41
  40   36  0.59

ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24


Consensus pattern (39 bp):   
TCCGGGTTAAGTCCCGAAGGCATTGAACGAGTTCTAAAA
Done.