Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010451.1 Corchorus capsularis cultivar CVL-1 contig10472, 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: 7092
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38


Found at i:5655 original size:23 final size:23

Alignment explanation


    Indices: 5627--5711  Score: 102
    Period size: 23  Copynumber: 3.7  Consensus size: 23

       5617 CATAAGAAAG

                                   
       5627 TTATCAAAATTTTATAGGCAGGT
          1 TTATCAAAATTTTATAGGCAGGT

                           *  *  * 
       5650 TTATCAAAATTTTATTGGAAGAT
          1 TTATCAAAATTTTATAGGCAGGT

                                    
       5673 TTATCAAAATTTTATA-GCGAGG-
          1 TTATCAAAATTTTATAGGC-AGGT

                  *     *    
       5695 TTATCACAATTTCATAG
          1 TTATCAAAATTTTATAG

       5712 TGTGATTATC


Statistics
Matches: 52,  Mismatches: 8, Indels: 4
        0.81            0.12        0.06

Matches are distributed among these distances:
  22   15  0.29
  23   37  0.71

ACGTcount: A:0.36, C:0.09, G:0.14, T:0.40


Consensus pattern (23 bp):   
TTATCAAAATTTTATAGGCAGGT

Found at i:5809 original size:22 final size:22

Alignment explanation


    Indices: 5525--5905  Score: 132
    Period size: 22  Copynumber: 17.3  Consensus size: 22

       5515 TATGTAGATA

                     * *        * 
       5525 AAAATTTCACAGGGAGGTTAAC
          1 AAAATTTCATATGGAGGTTATC

                          *  *     
       5547 AAAATTTCATAAT-AAGATTATC
          1 AAAATTTCAT-ATGGAGGTTATC

                **     *          
       5569 AAAAAATCATAGGGAGGTTATC
          1 AAAATTTCATATGGAGGTTATC

                         *  *       
       5591 -AAA-TT--T-TGTAGTTATAATC
          1 AAAATTTCATATGGAGGT-T-ATC

              *        * * *      
       5610 AAGATTTCATAAGAAAGTTATC
          1 AAAATTTCATATGGAGGTTATC

                   *                
       5632 AAAATTTTATA-GGCAGGTTTATC
          1 AAAATTTCATATGG-AGG-TTATC

                   *          *     
       5655 AAAATTTTAT-TGGAAGATTTATC
          1 AAAATTTCATATGG-AG-GTTATC

                   *               
       5678 AAAATTTTATA-GCGAGGTTATC
          1 AAAATTTCATATG-GAGGTTATC

             *                      
       5700 ACAATTTCATAGTGTGA--TTATC
          1 AAAATTTCATA-TG-GAGGTTATC

                                  * 
       5722 AAAATTTCATAGTGTGA--TT-CC
          1 AAAATTTCATA-TG-GAGGTTATC

                                 * *
       5743 TAACAATTT-ATATGGAGGTTTTT
          1 -AA-AATTTCATATGGAGGTTATC

               *    *      *       
       5766 AAATTTTCGTAAT-GTGGTTATC
          1 AAAATTTCAT-ATGGAGGTTATC

              *  *                
       5788 AATATATCATATGGAGGTTATC
          1 AAAATTTCATATGGAGGTTATC

              *  *        **       
       5810 AACATCTCATAGTGTTGGTTATC
          1 AAAATTTCATA-TGGAGGTTATC

                            *      
       5833 AAAATTTCAT-TAGGAAGTTATC
          1 AAAATTTCATAT-GGAGGTTATC

                        *          
       5855 AAAATTTCATATTGAGGTCT-TC
          1 AAAATTTCATATGGAGGT-TATC

                  * *  *        **
       5877 AAAATTCCTTAGGGAGGTTAAA
          1 AAAATTTCATATGGAGGTTATC

                   
       5899 AAAATTT
          1 AAAATTT

       5906 ATAAAAAGGT


Statistics
Matches: 268,  Mismatches: 61, Indels: 60
        0.69            0.16        0.15

Matches are distributed among these distances:
  17    4  0.01
  18    2  0.01
  19    3  0.01
  20    5  0.02
  21   18  0.07
  22  163  0.61
  23   66  0.25
  24    7  0.03

ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37


Consensus pattern (22 bp):   
AAAATTTCATATGGAGGTTATC

Found at i:5853 original size:45 final size:45

Alignment explanation


    Indices: 5780--5865  Score: 111
    Period size: 45  Copynumber: 1.9  Consensus size: 45

       5770 TTTCGTAATG

                      *            *        *            
       5780 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
          1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT

                         *                      *     
       5825 TGGTTATCAAAATTTCAT-TAGGAAGTTATCAAAATTTCATA
          1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA

       5866 TTGAGGTCTT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  44    1  0.03
  45   34  0.97

ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38


Consensus pattern (45 bp):   
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Done.