Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017777.1 Corchorus olitorius cultivar O-4 contig17810, 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: 2368
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33


Found at i:1805 original size:29 final size:28

Alignment explanation


    Indices: 1773--1992  Score: 188
    Period size: 29  Copynumber: 7.6  Consensus size: 28

       1763 ATGTGTAAAG

                  *         **           
       1773 ATGACCGAAATGCCCCTGGATATGCAAGA
          1 ATGACCAAAATGCCCCCAGATATGCAA-A

                         * ** *  *       
       1802 ATGACCAAAATGCTCTTATATGTGCATAA
          1 ATGACCAAAATGCCCCCAGATATGCA-AA

            *                *           
       1831 TTGACCAAAATGCCCCCGGATATGCGAAA
          1 ATGACCAAAATGCCCCCAGATATGC-AAA

                   *                 *   
       1860 ATGACCAGAATGCCCCCAGATATGTGAAA
          1 ATGACCAAAATGCCCCCAGATATG-CAAA

                   *                 **  
       1889 ATGACCAGAATGCCCCCAGATATGTGGAA
          1 ATGACCAAAATGCCCCCAGATATG-CAAA

                        *     *   *       
       1918 ATGACCAAAATACCCCCCGGATGTGCAAAA
          1 ATGACCAAAAT-GCCCCCAGATATGC-AAA

                              *          
       1948 ATGACCAAAATGCCCCCATATATGCAAAA
          1 ATGACCAAAATGCCCCCAGATATGC-AAA

                       *    
       1977 ATGACCAAAATTCCCC
          1 ATGACCAAAATGCCCC

       1993 TGAGCGTGCG


Statistics
Matches: 157,  Mismatches: 29, Indels: 10
        0.80            0.15        0.05

Matches are distributed among these distances:
  29  132  0.84
  30   25  0.16

ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19


Consensus pattern (28 bp):   
ATGACCAAAATGCCCCCAGATATGCAAA

Found at i:1963 original size:59 final size:60

Alignment explanation


    Indices: 1735--1992  Score: 208
    Period size: 58  Copynumber: 4.4  Consensus size: 60

       1725 GAACCTAGAG

                       *      *  *   *         *   *      *         **  
       1735 TATGCGAAAATAACCAAACT-GCCCTAGA-ATGTGTAAAGATGACCGAAATGCCCCTGGA
          1 TATGCGAAAATGACCAAAATACCCCCAGAGATGTGCAAAAATGACCAAAATGCCCCCAGA

                                   * * ** *       *  *                *  
       1793 TATGC-AAGAATGACCAAAAT--GCTCTTATATGTGCATAATTGACCAAAATGCCCCCGGA
          1 TATGCGAA-AATGACCAAAATACCCCCAGAGATGTGCAAAAATGACCAAAATGCCCCCAGA

                            *   *        *                 *            
       1851 TATGCGAAAATGACCAGAATGCCCCCAGATATGTG--AAAATGACCAGAATGCCCCCAGA
          1 TATGCGAAAATGACCAAAATACCCCCAGAGATGTGCAAAAATGACCAAAATGCCCCCAGA

                * *                   *                               * 
       1909 TATGTGGAAATGACCAAAATACCCCCCG-GATGTGCAAAAATGACCAAAATGCCCCCATA
          1 TATGCGAAAATGACCAAAATACCCCCAGAGATGTGCAAAAATGACCAAAATGCCCCCAGA

                 *              *    
       1968 TATGCAAAAATGACCAAAATTCCCC
          1 TATGCGAAAATGACCAAAATACCCC

       1993 TGAGCGTGCG


Statistics
Matches: 159,  Mismatches: 34, Indels: 13
        0.77            0.17        0.06

Matches are distributed among these distances:
  57    9  0.06
  58   97  0.61
  59   44  0.28
  60    9  0.06

ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19


Consensus pattern (60 bp):   
TATGCGAAAATGACCAAAATACCCCCAGAGATGTGCAAAAATGACCAAAATGCCCCCAGA

Found at i:1971 original size:88 final size:87

Alignment explanation


    Indices: 1773--1992  Score: 246
    Period size: 88  Copynumber: 2.5  Consensus size: 87

       1763 ATGTGTAAAG

                  *         **         *                * **       *         
       1773 ATGACCGAAATGCCCCTGGATATGCAAGAATGACCAAAATG--CTCTTATATGTGCATAATTGAC
          1 ATGACCAAAATGCCCCCAGATATGCAAAAATGACCAAAATGCCCCCAGATATGTGGA-AA-TGAC

                  *             *   
       1836 CAAAATGCCCCCGGATATGCGAAA
         64 CAAAATCCCCCCGGATATGCAAAA

                   *                **          *                            
       1860 ATGACCAGAATGCCCCCAGATATGTGAAAATGACCAGAATGCCCCCAGATATGTGGAAATGACCA
          1 ATGACCAAAATGCCCCCAGATATGCAAAAATGACCAAAATGCCCCCAGATATGTGGAAATGACCA

                           *       
       1925 AAATACCCCCCGGATGTGCAAAA
         66 AAAT-CCCCCCGGATATGCAAAA

                              *                     *    
       1948 ATGACCAAAATGCCCCCATATATGCAAAAATGACCAAAATTCCCC
          1 ATGACCAAAATGCCCCCAGATATGCAAAAATGACCAAAATGCCCC

       1993 TGAGCGTGCG


Statistics
Matches: 109,  Mismatches: 21, Indels: 5
        0.81            0.16        0.04

Matches are distributed among these distances:
  87   43  0.39
  88   56  0.51
  89   10  0.09

ACGTcount: A:0.38, C:0.26, G:0.18, T:0.19


Consensus pattern (87 bp):   
ATGACCAAAATGCCCCCAGATATGCAAAAATGACCAAAATGCCCCCAGATATGTGGAAATGACCA
AAATCCCCCCGGATATGCAAAA
Done.