Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01006605.1 Corchorus capsularis cultivar CVL-1 contig06626, 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, 636

Length: 1061
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29


Found at i:803 original size:428 final size:427

Alignment explanation


    Indices: 1--1061  Score: 1933
    Period size: 428  Copynumber: 2.5  Consensus size: 427

                                                                             
          1 GTATGCAACACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA
          1 GTATGCAACACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA

                                                                             
         66 GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTT
         66 GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTT

                                                                             
        131 TAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATT
        131 TAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATT

                                                                          *  
        196 GCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAAGTT
        196 GCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTT

                                             *        *        *             
        261 TGCACATTTTTGTGCTAAACATAGTTCTTAGCAGAACTCTTTTTGGATGCGTTTTTTCGCGAAAC
        261 TGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGAAAC

            *                                         *                      
        326 TAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAGACAGCGCTACACACAAACAAAG
        326 GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACAGCGCTACACACAAACAAAG

                          *                      
        391 CTCTCCTCGAAGTCTAAAGCATCAACTTCGCGAGTTT
        391 CTCTCCTCGAAGTCCAAAGCATCAACTTCGCGAGTTT

                       *                                                     
        428 GTATGCAACACTTCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA
          1 GTATGCAACACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA

                                *                                            
        493 GAAACAAAGCTTTCCTAGATTCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACAGTCATTT
         66 GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACA-TCATTT

                *                         *                                  
        558 TTAGTGAAAGGCTCATTCCAGATGCTTTTTCTGCGCAACGAGTACTCAAATGTCGTGCGTCGAAT
        130 TTAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAAT

                                                                             
        623 TGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACT
        195 TGCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACT

                * *           **                                          *  
        688 TTGCGCGTTTTTGTGCTATTCATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGCAA
        260 TTGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGAAA

                                                                 **          
        753 CGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACAGCGCTATGCACAAACAAA
        325 CGAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACAGCGCTACACACAAACAAA

                                         *        
        818 GCTCTCCTCGAAGTCCAAAGCATCAACTTTGCGAGTTT
        390 GCTCTCCTCGAAGTCCAAAGCATCAACTTCGCGAGTTT

                                        *                                    
        856 GTATGCAACACATCGTTCTTAGAGGTTTATCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA
          1 GTATGCAACACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA

                                                                             
        921 GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTT
         66 GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTT

                                                                             
        986 TAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATT
        131 TAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATT

                       
       1051 GCGATGAGATT
        196 GCGATGAGATT


Statistics
Matches: 609,  Mismatches: 24, Indels: 2
        0.96            0.04        0.00

Matches are distributed among these distances:
 427  202  0.33
 428  407  0.67

ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29


Consensus pattern (427 bp):   
GTATGCAACACATCGTTCTTAGAGGTTTGTCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCA
GAAACAAAGCTTTCCTAGATGCCCAAAACCTCAACTTTGAGCGGTTGTATGCAAAACATCATTTT
TAGCGAAAGGCTCATTCCAGATGCTTTTTTTGCGCAACGAGTACTCAAATGTCGTGCGTCGAATT
GCGATGAGATTGTTGGACAGCCCTGTGCACAAACAAAGCTTTCACGAAGTCCAAAGCCTCAACTT
TGCACATTTTTGTGCTAAACATAGTTCTTAGCAAAACTCTTTCTGGATGCGCTTTTTCGCGAAAC
GAGTGCTCAAAAGTCGTGTGTCGGAATGAGATGAGCTTGTTAAACAGCGCTACACACAAACAAAG
CTCTCCTCGAAGTCCAAAGCATCAACTTCGCGAGTTT

Found at i:955 original size:111 final size:111

Alignment explanation


    Indices: 774--980  Score: 252
    Period size: 111  Copynumber: 1.9  Consensus size: 111

        764 AAGTCGTGTG

                          *             *                       *    *     * 
        774 TCGGAATGAGATGAGCTTGTTAAACAGCGCTATGCACAAACAAAGCTCTCCTCGAAGTCCAAAGC
          1 TCGGAATGAGATGAACTTGTTAAACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAAC

                      *   *          *                    
        839 ATCAACTTTGCGAGTTTGTATGCAACACATCGTTCTTAGAGGTTTA
         66 ATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGAGGTTTA

                 *            *  **        *    *          *       *         
        885 TCGGAGTGAGATGAACTTTTTGGACAGCCCTGTGCAGAAACAAAGCTTTCCTAGATGCCCAAAAC
          1 TCGGAATGAGATGAACTTGTTAAACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAAC

            *           *                  
        950 CTCAACTTTGAGCGGTTGTATGCAAAACATC
         66 ATCAACTTTGAGAGGTTGTATGCAAAACATC

        981 ATTTTTAGCG


Statistics
Matches: 78,  Mismatches: 18, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
 111   78  1.00

ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26


Consensus pattern (111 bp):   
TCGGAATGAGATGAACTTGTTAAACAGCCCTATGCACAAACAAAGCTCTCCTAGAAGCCCAAAAC
ATCAACTTTGAGAGGTTGTATGCAAAACATCGTTCTTAGAGGTTTA
Done.