Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3919

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, 375

Length: 626
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31


Found at i:381 original size:41 final size:41

Alignment explanation


    Indices: 336--603  Score: 403
    Period size: 41  Copynumber: 6.5  Consensus size: 41

        326 GACTTTAAGT

                       *                             
        336 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

                                            *        
        377 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGATTATGAAC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

                                        *        *   
        418 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

                       *                             
        459 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAAC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

               *  *                     *        *   
        500 CTATCAAGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

                       *     *          *             
        541 CTAGCAGGCTACGTGCCAGTGATCTGAATCAGGTTAT-AAGC
          1 CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAA-C

               *                  
        582 CTAACAGGCTAAGTGCCGGTGA
          1 CTAGCAGGCTAAGTGCCGGTGA

        604 ATATGTTAAA


Statistics
Matches: 206,  Mismatches: 20, Indels: 2
        0.90            0.09        0.01

Matches are distributed among these distances:
  40    2  0.01
  41  204  0.99

ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23


Consensus pattern (41 bp):   
CTAGCAGGCTAAGTGCCGGTGATCTGAACCAGGTTATGAAC

Found at i:513 original size:123 final size:123

Alignment explanation


    Indices: 336--603  Score: 446
    Period size: 123  Copynumber: 2.2  Consensus size: 123

        326 GACTTTAAGT

                                                           *                 
        336 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAGGCTAAGTGCCGGTGATC
          1 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC

                         *                    *                       
        401 TGAACCAGATTATGAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
         66 TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC

                                                        *                    
        459 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTATCAAGCTAAGTGCCGGTGATC
          1 CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC

                *   *                   *                           * 
        524 TGAATCAGGTTATAAACCTAGCAGGCTACGTGCCAGTGATCTGAATCAGGTTATAAGC
         66 TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC

               *       *          
        582 CTAACAGGCTAAGTGCCGGTGA
          1 CTAGCAGGCTACGTGCCGGTGA

        604 ATATGTTAAA


Statistics
Matches: 135,  Mismatches: 10, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
 123  135  1.00

ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23


Consensus pattern (123 bp):   
CTAGCAGGCTACGTGCCGGTGATCTGAACCAGGTTATGAACCTAGCAAGCTAAGTGCCGGTGATC
TGAACCAGATTATAAACCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAAAC
Done.