Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018308.1 Corchorus olitorius cultivar O-4 contig18341, 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: 25491
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:1680 original size:76 final size:76

Alignment explanation


    Indices: 1530--1673  Score: 168
    Period size: 76  Copynumber: 1.9  Consensus size: 76

       1520 ACAAGGACCC

                  *       *                                    *           * 
       1530 CGACTCTACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
          1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT

                       
       1595 GGGCAGTGTCA
         66 GGGCAGTGTCA

                    *                    *                            **     
       1606 CGACTCCAGCTGGGCGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
          1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA

                  
       1668 GATGGG
         63 GATGGG

       1674 TTGTGTCTTA


Statistics
Matches: 57,  Mismatches: 8, Indels: 6
        0.80            0.11        0.08

Matches are distributed among these distances:
  75    4  0.07
  76   47  0.82
  77    6  0.11

ACGTcount: A:0.17, C:0.29, G:0.29, T:0.24


Consensus pattern (76 bp):   
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA

Found at i:8329 original size:22 final size:22

Alignment explanation


    Indices: 8288--8330  Score: 61
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       8278 CCAAACCATA

                           *      
       8288 TTTGTGACAAAATCTCCAAATC
          1 TTTGTGACAAAATCTACAAATC

                                  
       8310 TTTGTGACAAAAGTC-ACAAAT
          1 TTTGTGACAAAA-TCTACAAAT

       8331 GCTAAGTCCA


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  22   17  0.89
  23    2  0.11

ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30


Consensus pattern (22 bp):   
TTTGTGACAAAATCTACAAATC

Found at i:14391 original size:2 final size:2

Alignment explanation


    Indices: 14386--14413  Score: 56
    Period size: 2  Copynumber: 14.0  Consensus size: 2

      14376 GCTCTGCCAC

                                                     
      14386 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG

      14414 TAATAAAATA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
AG

Found at i:24659 original size:39 final size:39

Alignment explanation


    Indices: 24616--24694  Score: 158
    Period size: 39  Copynumber: 2.0  Consensus size: 39

      24606 TCACTTTGAA

                                                   
      24616 AAACAAAACAAAATAAAGGCTCTATATCGAGATATATAT
          1 AAACAAAACAAAATAAAGGCTCTATATCGAGATATATAT

                                                   
      24655 AAACAAAACAAAATAAAGGCTCTATATCGAGATATATAT
          1 AAACAAAACAAAATAAAGGCTCTATATCGAGATATATAT

             
      24694 A
          1 A

      24695 TATATATGTA


Statistics
Matches: 40,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  39   40  1.00

ACGTcount: A:0.54, C:0.13, G:0.10, T:0.23


Consensus pattern (39 bp):   
AAACAAAACAAAATAAAGGCTCTATATCGAGATATATAT

Found at i:24724 original size:6 final size:6

Alignment explanation


    Indices: 24686--24727  Score: 52
    Period size: 6  Copynumber: 7.3  Consensus size: 6

      24676 CTATATCGAG

                *      *                                       
      24686 ATATAT ATATAT ATATGT ATATG- -TATGT ATATGT ATATGT AT
          1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT AT

      24728 GTATTCTTGA


Statistics
Matches: 33,  Mismatches: 1, Indels: 4
        0.87            0.03        0.11

Matches are distributed among these distances:
   4    4  0.12
   6   29  0.88

ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50


Consensus pattern (6 bp):   
ATATGT

Found at i:24724 original size:16 final size:16

Alignment explanation


    Indices: 24687--24731  Score: 72
    Period size: 16  Copynumber: 2.8  Consensus size: 16

      24677 TATATCGAGA

                 *   *      
      24687 TATATATATATATATG
          1 TATATGTATGTATATG

                            
      24703 TATATGTATGTATATG
          1 TATATGTATGTATATG

                         
      24719 TATATGTATGTAT
          1 TATATGTATGTAT

      24732 TCTTGACTCC


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   27  1.00

ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51


Consensus pattern (16 bp):   
TATATGTATGTATATG

Found at i:24728 original size:10 final size:10

Alignment explanation


    Indices: 24693--24731  Score: 51
    Period size: 10  Copynumber: 3.9  Consensus size: 10

      24683 GAGATATATA

                 *    
      24693 TATATATATG
          1 TATATGTATG

                      
      24703 TATATGTATG
          1 TATATGTATG

                     *
      24713 TATATGTATA
          1 TATATGTATG

             *       
      24723 TGTATGTAT
          1 TATATGTAT

      24732 TCTTGACTCC


Statistics
Matches: 26,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  10   26  1.00

ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51


Consensus pattern (10 bp):   
TATATGTATG
Done.