Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013717.1 Corchorus olitorius cultivar O-4 contig13750, whole genome shotgun sequence

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: 22489
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32


Found at i:7369 original size:31 final size:31

Alignment explanation


    Indices: 7207--7353  Score: 150
    Period size: 31  Copynumber: 4.7  Consensus size: 31

       7197 GACGCGGCAT

                              *       *   *
       7207 GCCACGTGTACCAAAAAGCGACATGTGGCAT
          1 GCCACGTGTACCAAAAAGTGACATGTAGCAC

                 *            *       *    
       7238 GCCACATGTACCAAAAAGCGACATGTGGCAC
          1 GCCACGTGTACCAAAAAGTGACATGTAGCAC

                   *               *   *   
       7269 GCCACGTATACCAAAAAGTGACACGTATCAC
          1 GCCACGTGTACCAAAAAGTGACATGTAGCAC

                *  *    *              *   
       7300 GCCATGTATACCCAAAAGTGACATGTATCAC
          1 GCCACGTGTACCAAAAAGTGACATGTAGCAC

            *   *       *          
       7331 ACCATGTGTACCCAAAAGTGACA
          1 GCCACGTGTACCAAAAAGTGACA

       7354 CTTAGCATGC


Statistics
Matches: 103,  Mismatches: 13, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31  103  1.00

ACGTcount: A:0.36, C:0.27, G:0.20, T:0.17


Consensus pattern (31 bp):   
GCCACGTGTACCAAAAAGTGACATGTAGCAC

Found at i:7702 original size:54 final size:54

Alignment explanation


    Indices: 7610--7776  Score: 196
    Period size: 54  Copynumber: 3.1  Consensus size: 54

       7600 TATGCAGATG

                      *           *                                
       7610 TGAGC-TATAAATGCAAATATAGTTGCTTTAAAAGGGTTCTATAATTGAAGCAAT
          1 TGAGCGTATAGATGCAAATATAATTGCTTTAAAA-GGTTCTATAATTGAAGCAAT

                            *                                      
       7664 TGAGCGT-TAGATGCATATATAATTGCTTATAAAAGGTTCTATAATTGAAGCAAT
          1 TGAGCGTATAGATGCAAATATAATTGCTT-TAAAAGGTTCTATAATTGAAGCAAT

                 *          *  *     *   *         * *             
       7718 TGAG-TTATAGATGCAGATGTAATTCCATGTAAAAGGTTATGTAATTGAAGCAAT
          1 TGAGCGTATAGATGCAAATATAATTGC-TTTAAAAGGTTCTATAATTGAAGCAAT

                 
       7772 TGAGC
          1 TGAGC

       7777 TATTAATGCA


Statistics
Matches: 98,  Mismatches: 10, Indels: 9
        0.84            0.09        0.08

Matches are distributed among these distances:
  53    1  0.01
  54   90  0.92
  55    7  0.07

ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34


Consensus pattern (54 bp):   
TGAGCGTATAGATGCAAATATAATTGCTTTAAAAGGTTCTATAATTGAAGCAAT

Found at i:17109 original size:13 final size:13

Alignment explanation


    Indices: 17091--17115  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      17081 TTTGCCAAAA

                         
      17091 AATAATTTTAAGC
          1 AATAATTTTAAGC

                        
      17104 AATAATTTTAAG
          1 AATAATTTTAAG

      17116 GTGGTTAAAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40


Consensus pattern (13 bp):   
AATAATTTTAAGC
Done.