Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007657.1 Corchorus capsularis cultivar CVL-1 contig07678, 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: 8299
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32


Found at i:2790 original size:24 final size:23

Alignment explanation


    Indices: 2760--2819  Score: 70
    Period size: 21  Copynumber: 2.7  Consensus size: 23

       2750 TCAGCAAGTC

                            *      
       2760 CTTCTTCTTCCTCTTTTTCACTT
          1 CTTCTTCTTCCTCTTTCTCACTT

                         *          
       2783 C--CTTCTTCCTCGTTCTCACTTT
          1 CTTCTTCTTCCTCTTTCTCAC-TT

                  *        
       2805 CTTCTTTTTCCTCTT
          1 CTTCTTCTTCCTCTT

       2820 CCCTAGAGAC


Statistics
Matches: 30,  Mismatches: 4, Indels: 5
        0.77            0.10        0.13

Matches are distributed among these distances:
  21   16  0.53
  22    3  0.10
  23    1  0.03
  24   10  0.33

ACGTcount: A:0.03, C:0.37, G:0.02, T:0.58


Consensus pattern (23 bp):   
CTTCTTCTTCCTCTTTCTCACTT

Found at i:7908 original size:24 final size:24

Alignment explanation


    Indices: 7872--7941  Score: 122
    Period size: 24  Copynumber: 2.9  Consensus size: 24

       7862 ACCTGATAAC

                 *  *               
       7872 GGCGTCTAAACGCCGTCATATAGA
          1 GGCGTTTAGACGCCGTCATATAGA

                                    
       7896 GGCGTTTAGACGCCGTCATATAGA
          1 GGCGTTTAGACGCCGTCATATAGA

                                  
       7920 GGCGTTTAGACGCCGTCATATA
          1 GGCGTTTAGACGCCGTCATATA

       7942 TTCTTTCCAA


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   44  1.00

ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24


Consensus pattern (24 bp):   
GGCGTTTAGACGCCGTCATATAGA

Found at i:8137 original size:24 final size:24

Alignment explanation


    Indices: 8046--8138  Score: 114
    Period size: 24  Copynumber: 3.9  Consensus size: 24

       8036 TAGAATGCAT

                *      *       *    
       8046 ATAGCGGCGTCCAGACGCCCCCAA
          1 ATAGGGGCGTCTAGACGCCACCAA

                *              *    
       8070 ATAGTGGCGTCTAGACGCCGCCAA
          1 ATAGGGGCGTCTAGACGCCACCAA

                                   *
       8094 ATAGGGGCGTCTAGACGCCACCAT
          1 ATAGGGGCGTCTAGACGCCACCAA

            *              *     
       8118 TTAGGGGCGTCTAGATGCCAC
          1 ATAGGGGCGTCTAGACGCCAC

       8139 TATATTCAAT


Statistics
Matches: 61,  Mismatches: 8, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  24   61  1.00

ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16


Consensus pattern (24 bp):   
ATAGGGGCGTCTAGACGCCACCAA
Done.