Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005938.1 Corchorus capsularis cultivar CVL-1 contig05956, 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: 5439
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30


Found at i:1821 original size:27 final size:27

Alignment explanation


    Indices: 1791--1859  Score: 102
    Period size: 27  Copynumber: 2.6  Consensus size: 27

       1781 AGGTGAACAT

                     **     *          
       1791 AAAAATGACTGAAATGTCCCTGAGTGC
          1 AAAAATGACCAAAATGCCCCTGAGTGC

                                  *    
       1818 AAAAATGACCAAAATGCCCCTGGGTGC
          1 AAAAATGACCAAAATGCCCCTGAGTGC

                           
       1845 AAAAATGACCAAAAT
          1 AAAAATGACCAAAAT

       1860 ACCCTTGGGC


Statistics
Matches: 38,  Mismatches: 4, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  27   38  1.00

ACGTcount: A:0.43, C:0.20, G:0.19, T:0.17


Consensus pattern (27 bp):   
AAAAATGACCAAAATGCCCCTGAGTGC

Found at i:1868 original size:27 final size:27

Alignment explanation


    Indices: 1808--1868  Score: 95
    Period size: 27  Copynumber: 2.3  Consensus size: 27

       1798 ACTGAAATGT

                 *                   * 
       1808 CCCTGAGTGCAAAAATGACCAAAATGC
          1 CCCTGGGTGCAAAAATGACCAAAATAC

                                       
       1835 CCCTGGGTGCAAAAATGACCAAAATAC
          1 CCCTGGGTGCAAAAATGACCAAAATAC

              *    
       1862 CCTTGGG
          1 CCCTGGG

       1869 CGGCCCTAAT


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   31  1.00

ACGTcount: A:0.36, C:0.26, G:0.21, T:0.16


Consensus pattern (27 bp):   
CCCTGGGTGCAAAAATGACCAAAATAC

Found at i:4657 original size:14 final size:14

Alignment explanation


    Indices: 4638--4671  Score: 59
    Period size: 14  Copynumber: 2.4  Consensus size: 14

       4628 GCATATTAAC

                          
       4638 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

                          
       4652 TTTAGTCCATTTAG
          1 TTTAGTCCATTTAG

            *     
       4666 ATTAGT
          1 TTTAGT

       4672 ATCATAGTTA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50


Consensus pattern (14 bp):   
TTTAGTCCATTTAG
Done.