Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1547

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, 943

Length: 1572
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29


Found at i:1415 original size:28 final size:27

Alignment explanation


    Indices: 1352--1503  Score: 241
    Period size: 27  Copynumber: 5.6  Consensus size: 27

       1342 ATATTAAGTC

                    *       *   *      
       1352 CGCACACTCAGTGCTATATAATCAACT
          1 CGCACACTTAGTGCTACATAGTCAACT

                                *       
       1379 CGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAGTC-AACT

                                       
       1407 CGCACACTTAGTGCTACATAGTCAACT
          1 CGCACACTTAGTGCTACATAGTCAACT

                                        
       1434 CGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTC-AACT

                                     * 
       1462 CGCACACTTAGTGCTACATAGTCAATT
          1 CGCACACTTAGTGCTACATAGTCAACT

                           
       1489 CGCACACTTAGTGCT
          1 CGCACACTTAGTGCT

       1504 GCACAATTTA


Statistics
Matches: 119,  Mismatches: 4, Indels: 4
        0.94            0.03        0.03

Matches are distributed among these distances:
  27   66  0.55
  28   53  0.45

ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26


Consensus pattern (27 bp):   
CGCACACTTAGTGCTACATAGTCAACT

Found at i:1436 original size:55 final size:55

Alignment explanation


    Indices: 1352--1503  Score: 259
    Period size: 55  Copynumber: 2.8  Consensus size: 55

       1342 ATATTAAGTC

                    *       *   *                                  
       1352 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
          1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT

                                                           *       
       1407 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
          1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT

                                     *                
       1462 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
          1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT

       1504 GCACAATTTA


Statistics
Matches: 92,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  55   92  1.00

ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26


Consensus pattern (55 bp):   
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Done.