Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000217.1 Corchorus capsularis cultivar CVL-1 contig00217, 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: 2085
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38


Found at i:119 original size:54 final size:55

Alignment explanation


    Indices: 1--236  Score: 359
    Period size: 54  Copynumber: 4.3  Consensus size: 55

                        *                      *                  *
          1 GACCGCACTGGACCACTTGAAGATAAACTTAATACCACTGGAAACTTTCTTGACG
          1 GACCGCACTGGATCACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGACT

              *              *                      *              
         56 GATCGCACTGGATCACTCGAAGATAAACTTAA-ACAACTGTAAACTTTCTTGACT
          1 GACCGCACTGGATCACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGACT

              *          *                          *              
        110 GATCGCACTGGATTACTTGAAGATAAACTTAA-ACAACTGTAAACTTTCTTGACT
          1 GACCGCACTGGATCACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGACT

                                               *                 * 
        164 GACCGCACTGGATCACTTGAAGATAAACTTAATACCACTGGAAACTTTCTTGATT
          1 GACCGCACTGGATCACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGACT

                              
        219 GACCGCACTGGATCACTT
          1 GACCGCACTGGATCACTT

        237 TGAAATTCGG


Statistics
Matches: 167,  Mismatches: 13, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
  54  101  0.60
  55   66  0.40

ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28


Consensus pattern (55 bp):   
GACCGCACTGGATCACTTGAAGATAAACTTAATACAACTGGAAACTTTCTTGACT

Found at i:1796 original size:16 final size:16

Alignment explanation


    Indices: 1758--1797  Score: 53
    Period size: 16  Copynumber: 2.5  Consensus size: 16

       1748 ATTTGGCGAC

                  *         
       1758 TTCTTCATTCCATCTT
          1 TTCTTCTTTCCATCTT

                     *   *  
       1774 TTCTTCTTTTCATTTT
          1 TTCTTCTTTCCATCTT

                    
       1790 TTCTTCTT
          1 TTCTTCTT

       1798 GCTTCTTTCT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  16   21  1.00

ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68


Consensus pattern (16 bp):   
TTCTTCTTTCCATCTT
Done.