Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023561.1 Corchorus olitorius cultivar O-4 contig23594, 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: 13174
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:1002 original size:17 final size:17

Alignment explanation


    Indices: 980--1015  Score: 54
    Period size: 17  Copynumber: 2.1  Consensus size: 17

        970 ATACAAAGAG

                             
        980 CTATCTAGTATAACAAA
          1 CTATCTAGTATAACAAA

                  *  *       
        997 CTATCTGGTGTAACAAA
          1 CTATCTAGTATAACAAA

              
       1014 CT
          1 CT

       1016 TTACAAATCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  17   17  1.00

ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31


Consensus pattern (17 bp):   
CTATCTAGTATAACAAA

Found at i:2832 original size:18 final size:18

Alignment explanation


    Indices: 2769--2837  Score: 66
    Period size: 18  Copynumber: 3.8  Consensus size: 18

       2759 CAAAGGTTCT

                    *         
       2769 TGCGGCAGCGGAACATCC
          1 TGCGGCAGTGGAACATCC

              *    *  *     * 
       2787 TGTGGCAATGCAACATTC
          1 TGCGGCAGTGGAACATCC

               * *            
       2805 TGCAGTAGTGGAACATCC
          1 TGCGGCAGTGGAACATCC

                      *    
       2823 TGCGGCAGTGTAACA
          1 TGCGGCAGTGGAACA

       2838 ATATTTTGTA


Statistics
Matches: 37,  Mismatches: 14, Indels: 0
        0.73            0.27        0.00

Matches are distributed among these distances:
  18   37  1.00

ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20


Consensus pattern (18 bp):   
TGCGGCAGTGGAACATCC

Found at i:6181 original size:12 final size:12

Alignment explanation


    Indices: 6164--6191  Score: 56
    Period size: 12  Copynumber: 2.3  Consensus size: 12

       6154 AGGGCACCCA

                        
       6164 TTGGTTAAAAGC
          1 TTGGTTAAAAGC

                        
       6176 TTGGTTAAAAGC
          1 TTGGTTAAAAGC

                
       6188 TTGG
          1 TTGG

       6192 GATTTTTTGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   16  1.00

ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36


Consensus pattern (12 bp):   
TTGGTTAAAAGC

Found at i:6600 original size:31 final size:31

Alignment explanation


    Indices: 6551--6657  Score: 142
    Period size: 31  Copynumber: 3.5  Consensus size: 31

       6541 ACGGTGTCCG

                    *    *                 
       6551 ATGTGGCATGCCATGTGTACCAAAAAGCGAC
          1 ATGTGGCACGCCACGTGTACCAAAAAGCGAC

                 *                         
       6582 ATGTGACACGCCACGTGTACCAAAAAGCGAC
          1 ATGTGGCACGCCACGTGTACCAAAAAGCGAC

             *            *            *   
       6613 ACGTGGCACGCCACATGTACCAAAAAGTGAC
          1 ATGTGGCACGCCACGTGTACCAAAAAGCGAC

             **           
       6644 ACATGGCACGCCAC
          1 ATGTGGCACGCCAC

       6658 ATATACAAAA


Statistics
Matches: 68,  Mismatches: 8, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  31   68  1.00

ACGTcount: A:0.34, C:0.29, G:0.23, T:0.14


Consensus pattern (31 bp):   
ATGTGGCACGCCACGTGTACCAAAAAGCGAC

Found at i:6658 original size:31 final size:31

Alignment explanation


    Indices: 6566--6707  Score: 149
    Period size: 31  Copynumber: 4.6  Consensus size: 31

       6556 GCATGCCATG

                        *    *   *        *
       6566 TGTACCAAAAAGCGACATGTGACACGCCACG
          1 TGTACCAAAAAGTGACACGTGGCACGCCACA

                        *                  
       6597 TGTACCAAAAAGCGACACGTGGCACGCCACA
          1 TGTACCAAAAAGTGACACGTGGCACGCCACA

                              *            
       6628 TGTACCAAAAAGTGACACATGGCACGCCACA
          1 TGTACCAAAAAGTGACACGTGGCACGCCACA

             *   *       * *     **      **
       6659 TATACAAAAAAGTTAAACGTGTTACGCCATG
          1 TGTACCAAAAAGTGACACGTGGCACGCCACA

             *                
       6690 TATACCAAAAAGTGACAC
          1 TGTACCAAAAAGTGACAC

       6708 ATGACATGTC


Statistics
Matches: 94,  Mismatches: 17, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  31   94  1.00

ACGTcount: A:0.39, C:0.26, G:0.19, T:0.15


Consensus pattern (31 bp):   
TGTACCAAAAAGTGACACGTGGCACGCCACA
Done.