Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007815.1 Corchorus capsularis cultivar CVL-1 contig07836, 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: 8742
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29


Found at i:989 original size:22 final size:22

Alignment explanation


    Indices: 961--1005  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        951 CTAAAAACTA

                                  
        961 ATAAATTTTCAAATGCTCTTAC
          1 ATAAATTTTCAAATGCTCTTAC

                                  
        983 ATAAATTTTCAAATGCTCTTAC
          1 ATAAATTTTCAAATGCTCTTAC

             
       1005 A
          1 A

       1006 GTAGTGTAGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40


Consensus pattern (22 bp):   
ATAAATTTTCAAATGCTCTTAC

Found at i:2715 original size:121 final size:122

Alignment explanation


    Indices: 2503--2734  Score: 319
    Period size: 121  Copynumber: 1.9  Consensus size: 122

       2493 GCTACTGACA

                            *        *                   *           *  *    
       2503 AAGGGTAACACTTCTTTATATACCTCAAGTTTTCAACAAGAAGGATGCGTTTTTTACTAGGATCC
          1 AAGGGTAACACTTCTTCATATACCTAAAGTTTTCAACAAGAA-GAGGCGTTTTTTACAAGAATCC

             *                                                        
       2568 CTAAGTCCCTTGTCGATAAGCTTATACAAACATACACTAGAATTATCAGCTACTAGCT
         65 CCAAGTCCCTTGTCGATAAGCTTATACAAACATACACTAGAATTATCAGCTACTAGCT

                               *                *                            
       2626 AAGGGTAACACTTCTTCATGTACCTAAAG-TTTCAATAA-AA-AGGCGTTTTCTTTACAAGAATC
          1 AAGGGTAACACTTCTTCATATACCTAAAGTTTTCAACAAGAAGAGGCG-TTT-TTTACAAGAATC

                               *                            
       2688 CCCAAGTCCCTTGTACGA-CAGCTTATACAAACATACACTAGAATTAT
         64 CCCAAGTCCCTTGT-CGATAAGCTTATACAAACATACACTAGAATTAT

       2735 ATTAGCTTGG


Statistics
Matches: 97,  Mismatches: 9, Indels: 8
        0.85            0.08        0.07

Matches are distributed among these distances:
 119    4  0.04
 120    3  0.03
 121   53  0.55
 122   11  0.11
 123   26  0.27

ACGTcount: A:0.34, C:0.22, G:0.14, T:0.31


Consensus pattern (122 bp):   
AAGGGTAACACTTCTTCATATACCTAAAGTTTTCAACAAGAAGAGGCGTTTTTTACAAGAATCCC
CAAGTCCCTTGTCGATAAGCTTATACAAACATACACTAGAATTATCAGCTACTAGCT

Found at i:8037 original size:21 final size:21

Alignment explanation


    Indices: 8013--8061  Score: 62
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       8003 GCGTTGGGCG

                    *     * *    
       8013 CCCATGTGCTATGCTTGGCAC
          1 CCCATGTGATATGCCTCGCAC

                      *          
       8034 CCCATGTGATTTGCCTCGCAC
          1 CCCATGTGATATGCCTCGCAC

                   
       8055 CCCATGT
          1 CCCATGT

       8062 ACTCCAATGC


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.14, C:0.37, G:0.20, T:0.29


Consensus pattern (21 bp):   
CCCATGTGATATGCCTCGCAC
Done.