Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2413

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: 7771
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30


Found at i:690 original size:29 final size:28

Alignment explanation


    Indices: 654--724  Score: 99
    Period size: 29  Copynumber: 2.5  Consensus size: 28

        644 TCATGAGATT

                           *              
        654 GGCACTAAGTGTGCGGGTTTAAATTGTACA
          1 GGCACTAAGTGTGCGAGTTTAAA--GTACA

                                        
        684 -GCACTAAGTGTGCGAGTTTAAAGTACA
          1 GGCACTAAGTGTGCGAGTTTAAAGTACA

                          
        711 TGGCACTAAGTGTG
          1 -GGCACTAAGTGTG

        725 TGCGGTTGAT


Statistics
Matches: 38,  Mismatches: 1, Indels: 5
        0.86            0.02        0.11

Matches are distributed among these distances:
  27    5  0.13
  29   33  0.87

ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28


Consensus pattern (28 bp):   
GGCACTAAGTGTGCGAGTTTAAAGTACA

Found at i:992 original size:173 final size:174

Alignment explanation


    Indices: 685--1010  Score: 546
    Period size: 173  Copynumber: 1.9  Consensus size: 174

        675 AATTGTACAG

                                                    *           *   *       *
        685 CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGTGCGGTTGATTATTAAGCACTATGT
          1 CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC

                                                   *                      *  
        750 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGAT
         66 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT

                                                        
        815 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
        131 TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA

                       *           *                  *                *     
        859 CACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGTGGTTGATTACTAAACATTATGC
          1 CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC

                      *                                                      
        924 GTGC-AACCCTATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
         66 GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT

                                   
        988 TTTGGACAGCGGAAAAGGTAAGT
        131 TTTGGACAGCGGAAAAGGTAAGT

       1011 ACCTTGAGTT


Statistics
Matches: 141,  Mismatches: 11, Indels: 1
        0.92            0.07        0.01

Matches are distributed among these distances:
 173   80  0.57
 174   61  0.43

ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32


Consensus pattern (174 bp):   
CACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTACTAAACACTATGC
GTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAAT
TTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATGA
Done.