Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024289.1 Corchorus olitorius cultivar O-4 contig24322, 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: 22998
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:13785 original size:46 final size:46

Alignment explanation


    Indices: 13718--13871  Score: 254
    Period size: 46  Copynumber: 3.3  Consensus size: 46

      13708 CTTTGCAAGA

                           *              *        *      
      13718 AGCTACCGTATAGAGAATTCTTTCTGAAGATGGGTGCTCGCATAAG
          1 AGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG

                                            *  *          
      13764 AGCTACCGTATAGAGTATTCTTTCTGAAGAAGTGTCCTCACATAAG
          1 AGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG

                  *                                       
      13810 AGCTACTGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG
          1 AGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG

                            
      13856 AGCTACCGTATAGAGT
          1 AGCTACCGTATAGAGT

      13872 TCAAAATGTA


Statistics
Matches: 99,  Mismatches: 9, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  46   99  1.00

ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29


Consensus pattern (46 bp):   
AGCTACCGTATAGAGTATTCTTTCTGAAGAAGGGTGCTCACATAAG

Found at i:17181 original size:19 final size:18

Alignment explanation


    Indices: 17144--17183  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 18

      17134 TTCTTGAAAT

                        *     
      17144 AATTCTTCAATGGTCTTC
          1 AATTCTTCAATGATCTTC

                        *      
      17162 AATTCTTCAAATTATCTTC
          1 AATTCTTC-AATGATCTTC

               
      17181 AAT
          1 AAT

      17184 AAATCTTCAA


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

Matches are distributed among these distances:
  18    8  0.42
  19   11  0.58

ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45


Consensus pattern (18 bp):   
AATTCTTCAATGATCTTC

Found at i:17591 original size:44 final size:44

Alignment explanation


    Indices: 17525--17671  Score: 204
    Period size: 44  Copynumber: 3.3  Consensus size: 44

      17515 AACACCATAA

                   *     *   *              *        *  
      17525 TGAAAGAAGGTGATAGTCTCGCAAACACCATAAGCCTTTGATAT
          1 TGAAAGAGGGTGAAAGTTTCGCAAACACCATATGCCTTTGACAT

                                                        
      17569 TGAAAGAGGGTGAAAGTTTCGCAAACACCATATGCCTTTGACAT
          1 TGAAAGAGGGTGAAAGTTTCGCAAACACCATATGCCTTTGACAT

                         *    *  **                     
      17613 TGAAAGAGGGTGATAGTTCCGTGAACACCATATGCCTTTGACAT
          1 TGAAAGAGGGTGAAAGTTTCGCAAACACCATATGCCTTTGACAT

                           
      17657 TGAAAGAGGCGTGAA
          1 TGAAAGAGG-GTGAA

      17672 CTCCATATGT


Statistics
Matches: 92,  Mismatches: 10, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  44   88  0.96
  45    4  0.04

ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24


Consensus pattern (44 bp):   
TGAAAGAGGGTGAAAGTTTCGCAAACACCATATGCCTTTGACAT

Found at i:21702 original size:23 final size:25

Alignment explanation


    Indices: 21676--21739  Score: 78
    Period size: 25  Copynumber: 2.6  Consensus size: 25

      21666 GCCCTGTTGT

                             *       
      21676 GCAGCAACAGGC-TGCGTCGCGGA-
          1 GCAGCAACAGGCTTGCGCCGCGGAG

                                 *   
      21699 GCAGCAACAGGCTTGCGCCGCTGAG
          1 GCAGCAACAGGCTTGCGCCGCGGAG

                  *  *      
      21724 GCAGCAGCAAGCTTGC
          1 GCAGCAACAGGCTTGC

      21740 TGTTGCTCGC


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  23   12  0.34
  24    9  0.26
  25   14  0.40

ACGTcount: A:0.22, C:0.31, G:0.36, T:0.11


Consensus pattern (25 bp):   
GCAGCAACAGGCTTGCGCCGCGGAG
Done.