Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold2111

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, 657

Length: 1096
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40


Found at i:612 original size:24 final size:24

Alignment explanation


    Indices: 585--669  Score: 80
    Period size: 24  Copynumber: 3.5  Consensus size: 24

        575 ATGTATTTAC

                  *   *             
        585 ATTTGTGTCTATATTTGTATCTGT
          1 ATTTGTATCTGTATTTGTATCTGT

                 *           * *    
        609 ATTTGCATCTGTATTTGCACCTGT
          1 ATTTGTATCTGTATTTGTATCTGT

              *           *     *   
        633 ATCTGTATCTGTATATGTATATGT
          1 ATTTGTATCTGTATTTGTATCTGT

                **       
        657 ATTTACATCTGTA
          1 ATTTGTATCTGTA

        670 ACTGCATCTG


Statistics
Matches: 47,  Mismatches: 14, Indels: 0
        0.77            0.23        0.00

Matches are distributed among these distances:
  24   47  1.00

ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51


Consensus pattern (24 bp):   
ATTTGTATCTGTATTTGTATCTGT

Found at i:626 original size:12 final size:12

Alignment explanation


    Indices: 596--682  Score: 84
    Period size: 12  Copynumber: 7.2  Consensus size: 12

        586 TTTGTGTCTA

                  *     
        596 TATTTGTATCTG
          1 TATTTGCATCTG

                        
        608 TATTTGCATCTG
          1 TATTTGCATCTG

                    *   
        620 TATTTGCACCTG
          1 TATTTGCATCTG

               *  *     
        632 TATCTGTATCTG
          1 TATTTGCATCTG

               *  *  *  
        644 TATATGTATATG
          1 TATTTGCATCTG

                 *      
        656 TATTTACATCTG
          1 TATTTGCATCTG

              **        
        668 TAACTGCATCTG
          1 TATTTGCATCTG

               
        680 TAT
          1 TAT

        683 CTAAAATTTT


Statistics
Matches: 60,  Mismatches: 15, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  12   60  1.00

ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48


Consensus pattern (12 bp):   
TATTTGCATCTG

Found at i:640 original size:6 final size:6

Alignment explanation


    Indices: 600--684  Score: 62
    Period size: 6  Copynumber: 14.2  Consensus size: 6

        590 TGTCTATATT

                        *   *         *   * *                     *
        600 TGTATC TGTATT TGCATC TGTATT TGCACC TGTATC TGTATC TGTATA
          1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC

                 *      *  **        *    *            
        648 TGTATA TGTATT TACATC TGTAAC TGCATC TGTATC T
          1 TGTATC TGTATC TGTATC TGTATC TGTATC TGTATC T

        685 AAAATTTTCA


Statistics
Matches: 58,  Mismatches: 21, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
   6   58  1.00

ACGTcount: A:0.21, C:0.16, G:0.15, T:0.47


Consensus pattern (6 bp):   
TGTATC

Found at i:640 original size:36 final size:36

Alignment explanation


    Indices: 600--682  Score: 103
    Period size: 36  Copynumber: 2.3  Consensus size: 36

        590 TGTCTATATT

                       *     *       *        * 
        600 TGTATCTGTATTTGCATCTGTATTTGCACCTGTATC
          1 TGTATCTGTATATGCATATGTATTTACACCTGTAAC

                          *             *       
        636 TGTATCTGTATATGTATATGTATTTACATCTGTAAC
          1 TGTATCTGTATATGCATATGTATTTACACCTGTAAC

              *        
        672 TGCATCTGTAT
          1 TGTATCTGTAT

        683 CTAAAATTTT


Statistics
Matches: 40,  Mismatches: 7, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  36   40  1.00

ACGTcount: A:0.22, C:0.16, G:0.16, T:0.47


Consensus pattern (36 bp):   
TGTATCTGTATATGCATATGTATTTACACCTGTAAC

Done.