Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold957

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: 12280
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30


Found at i:1766 original size:40 final size:40

Alignment explanation


    Indices: 1682--1863  Score: 180
    Period size: 40  Copynumber: 4.6  Consensus size: 40

       1672 TCGAATGATG

                                          *   *      
       1682 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTG-TGAGTTACTAAT

                  *                                   
       1721 ATCCGGACTAAGAT-CCGAAGGCATTTGTGTGAGTTACTAAT
          1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGTGAGTTACTAAT

                                    *   *           *
       1762 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAAA
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT-AAT

                  *                     *           
       1802 TCCGGGTTAAGTCCCGAAGGCATTT-TGCGA-TTACT-AT
          1 TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAT

             *        *              
       1839 AACCGGGCTATGTCCCGAAGGCATT
          1 -TCCGGGCTAAGTCCCGAAGGCATT

       1864 GAACGAGTAG


Statistics
Matches: 122,  Mismatches: 13, Indels: 16
        0.81            0.09        0.11

Matches are distributed among these distances:
  37    1  0.01
  38   21  0.17
  39   27  0.22
  40   52  0.43
  41   21  0.17

ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26


Consensus pattern (40 bp):   
TCCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACTAAT

Found at i:1819 original size:80 final size:79

Alignment explanation


    Indices: 1682--1864  Score: 205
    Period size: 80  Copynumber: 2.3  Consensus size: 79

       1672 TCGAATGATG

                                    *              *                         
       1682 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
          1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT

                *           
       1746 TGTGTGAGTTACTA-A
         66 T-TGCGA-TTACTATA

                                           *   *            **               
       1761 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAAATCCGGGTTAAG-TCCCGAAGGC
          1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACT-AAATCCGGACTAAGAT-CCGAAGGC

                             
       1823 ATTTTGCGATTACTATA
         63 ATTTTGCGATTACTATA

            *        *               
       1840 ACCGGGCTATGTCCCGAAGGCATTG
          1 TCCGGGCTAAGTCCCGAAGGCATTG

       1865 AACGAGTAGC


Statistics
Matches: 89,  Mismatches: 9, Indels: 11
        0.82            0.08        0.10

Matches are distributed among these distances:
  78   15  0.17
  79   34  0.38
  80   40  0.45

ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26


Consensus pattern (79 bp):   
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATT
TTGCGATTACTATA
Done.