Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3667

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: 9549
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29


Found at i:1830 original size:27 final size:27

Alignment explanation


    Indices: 1800--1977  Score: 205
    Period size: 27  Copynumber: 6.6  Consensus size: 27

       1790 ATATTAAGTC

                    *       *   *      
       1800 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAACT

                          *     *       
       1827 CGCACACTTAGTGCCACATAATCAAACT
          1 CGCACACTTAGTGCTACATAGTC-AACT

                                       
       1855 CGCACACTTAGTGCTACATAGTCAACT
          1 CGCACACTTAGTGCTACATAGTCAACT

                          **   *     * 
       1882 CGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAACT

                                 *   ** 
       1909 CGCACACTTAGTGC-ATCATATTCATTT
          1 CGCACACTTAGTGCTA-CATAGTCAACT

                          *          * 
       1936 CGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTACATAGTCAACT

                           
       1963 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       1978 GTACAATTTA


Statistics
Matches: 131,  Mismatches: 17, Indels: 6
        0.85            0.11        0.04

Matches are distributed among these distances:
  27  105  0.80
  28   26  0.20

ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAACT

Found at i:1868 original size:55 final size:54

Alignment explanation


    Indices: 1800--1977  Score: 232
    Period size: 54  Copynumber: 3.3  Consensus size: 54

       1790 ATATTAAGTC

                    *                                      *       
       1800 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
          1 CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T

                            *   *                     *   *     * 
       1855 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
          1 CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT

                                 *   **               *            
       1909 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
          1 CGCACACTTAGTGCTAT-ATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT

                           
       1963 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       1978 GTACAATTTA


Statistics
Matches: 106,  Mismatches: 15, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  53    1  0.01
  54   59  0.56
  55   46  0.43

ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26


Consensus pattern (54 bp):   
CGCACACTTAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT

Found at i:1966 original size:81 final size:82

Alignment explanation


    Indices: 1821--1976  Score: 235
    Period size: 81  Copynumber: 1.9  Consensus size: 82

       1811 TGCTATATAA

                                                            *          *     
       1821 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
          1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA

                             
       1886 CACTTAGTGCCGCATGG
         66 CACTTAGTGCCGCATGG

                *                      *    **                               
       1903 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
          1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC

                       
       1966 ACACTTAGTGC
         65 ACACTTAGTGC

       1977 TGTACAATTT


Statistics
Matches: 67,  Mismatches: 6, Indels: 3
        0.88            0.08        0.04

Matches are distributed among these distances:
  81   43  0.64
  82   24  0.36

ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26


Consensus pattern (82 bp):   
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Done.