Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold623

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: 9859
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28


Found at i:1908 original size:27 final size:27

Alignment explanation


    Indices: 1858--1968  Score: 136
    Period size: 27  Copynumber: 4.1  Consensus size: 27

       1848 AGCGTGGCTG

                      *       *        
       1858 CCAGAACAGATA-ATGTGACAGAGCCA
          1 CCAGAACAGAAATATGTGGCAGAGCCA

                             *         
       1884 CCAGAACAGAAATATGTAGCAGAGCCA
          1 CCAGAACAGAAATATGTGGCAGAGCCA

                                   *   
       1911 CCAGAACAGAAATATGTGGCAGATCCA
          1 CCAGAACAGAAATATGTGGCAGAGCCA

                 *    *           *     
       1938 CCAGATCAGTTAAT-TGTGGCATAGCCA
          1 CCAGAACAG-AAATATGTGGCAGAGCCA

                
       1965 CCAG
          1 CCAG

       1969 GACGCTTCCT


Statistics
Matches: 74,  Mismatches: 9, Indels: 3
        0.86            0.10        0.03

Matches are distributed among these distances:
  26   11  0.15
  27   60  0.81
  28    3  0.04

ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15


Consensus pattern (27 bp):   
CCAGAACAGAAATATGTGGCAGAGCCA

Found at i:9758 original size:26 final size:26

Alignment explanation


    Indices: 9679--9772  Score: 109
    Period size: 26  Copynumber: 3.5  Consensus size: 26

       9669 AGCATGGCTG

                              *     *  
       9679 CCAGAAACAGATAATGTGACAGAGTCA
          1 CCAG-AACAGATAATGTGGCAGAGCCA

                            *           
       9706 CCAGATACAGATAATCATGGCAGAGCCA
          1 CCAGA-ACAGATAAT-GTGGCAGAGCCA

                                       
       9734 CCAGAACAGA-ATATGTGGCAGAGCCA
          1 CCAGAACAGATA-ATGTGGCAGAGCCA

                 *       
       9760 CCAGATCAGATAA
          1 CCAGAACAGATAA

       9773 AGGACGCTTC


Statistics
Matches: 58,  Mismatches: 5, Indels: 9
        0.81            0.07        0.12

Matches are distributed among these distances:
  26   23  0.40
  27   21  0.36
  28   14  0.24

ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14


Consensus pattern (26 bp):   
CCAGAACAGATAATGTGGCAGAGCCA
Done.