Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024804.1 Corchorus olitorius cultivar O-4 contig24837, 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: 13984
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:9597 original size:60 final size:60

Alignment explanation


    Indices: 9533--9675  Score: 205
    Period size: 60  Copynumber: 2.4  Consensus size: 60

       9523 AACGTTTGCC

                 *       *                               *              
       9533 AAAATACTCAAATTAGGGTCTGATATTTTAATTTGACCAAATAAGGGCCTAACATTATCG
          1 AAAATGCTCAAATAAGGGTCTGATATTTTAATTTGACCAAATAAGAGCCTAACATTATCG

                    *         * *   *          *                 *      
       9593 AAAATGCTTAAATAAGGGCCCGATTTTTTAATTTGGCCAAATAAGAGCCTAACGTTATCG
          1 AAAATGCTCAAATAAGGGTCTGATATTTTAATTTGACCAAATAAGAGCCTAACATTATCG

                                   
       9653 AAAATGCTCAAATAAGGGTCTGA
          1 AAAATGCTCAAATAAGGGTCTGA

       9676 CGTCAGTTTG


Statistics
Matches: 71,  Mismatches: 12, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  60   71  1.00

ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29


Consensus pattern (60 bp):   
AAAATGCTCAAATAAGGGTCTGATATTTTAATTTGACCAAATAAGAGCCTAACATTATCG

Found at i:9751 original size:31 final size:31

Alignment explanation


    Indices: 9713--9811  Score: 114
    Period size: 31  Copynumber: 3.3  Consensus size: 31

       9703 TTCGATGCAA

                                           
       9713 GCCCTTATTTGAGCATTTTGGCAAACATTAG
          1 GCCCTTATTTGAGCATTTTGGCAAACATTAG

                          * **    *   *     
       9744 GCCCTTATTTG-GTAAAATT--AAAAGATTAG
          1 GCCCTTATTTGAG-CATTTTGGCAAACATTAG

                                      *    
       9773 GCCCTTATTTGAGCATTTTGGCAAACGTTAG
          1 GCCCTTATTTGAGCATTTTGGCAAACATTAG

                    
       9804 GCCCTTAT
          1 GCCCTTAT

       9812 GGTCAAATTA


Statistics
Matches: 53,  Mismatches: 11, Indels: 8
        0.74            0.15        0.11

Matches are distributed among these distances:
  29   22  0.42
  30    2  0.04
  31   29  0.55

ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35


Consensus pattern (31 bp):   
GCCCTTATTTGAGCATTTTGGCAAACATTAG

Found at i:9806 original size:60 final size:60

Alignment explanation


    Indices: 9713--9931  Score: 263
    Period size: 60  Copynumber: 3.7  Consensus size: 60

       9703 TTCGATGCAA

                                                        *               
       9713 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTAAAATTAAAAGATTAG
          1 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATTAG

                                      *                              * *
       9773 GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTA--TGGTCAAATTAAAAGATCAA
          1 GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATTAG

            *           * *                                             * 
       9831 ACCCTTATATTTAAACATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGA-TCG
          1 GCCC-T-TATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATTAG

                           *            *               
       9892 G----TATTTGAGTATATTTTGGCAAACGTTAGGCCCTTATTTG
          1 GCCCTTATTTGAG--CATTTTGGCAAACATTAGGCCCTTATTTG

       9932 AGGAATTAGC


Statistics
Matches: 137,  Mismatches: 16, Indels: 15
        0.82            0.10        0.09

Matches are distributed among these distances:
  55    6  0.04
  57   27  0.20
  58   20  0.15
  59    1  0.01
  60   67  0.49
  62   16  0.12

ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35


Consensus pattern (60 bp):   
GCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTCAAATTAAAAGATTAG

Found at i:13744 original size:31 final size:31

Alignment explanation


    Indices: 13706--13767  Score: 97
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      13696 ATGTGAGGGT

                    *                      
      13706 ACATCCCATATCATGAAAAGATAGGTTGTTA
          1 ACATCCCACATCATGAAAAGATAGGTTGTTA

                             *    *        
      13737 ACATCCCACATCATGAAGAGATGGGTTGTTA
          1 ACATCCCACATCATGAAAAGATAGGTTGTTA

      13768 GAGTAGCTTA


Statistics
Matches: 28,  Mismatches: 3, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  31   28  1.00

ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27


Consensus pattern (31 bp):   
ACATCCCACATCATGAAAAGATAGGTTGTTA

Found at i:13943 original size:17 final size:17

Alignment explanation


    Indices: 13921--13956  Score: 72
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      13911 ACACAATGTC

                             
      13921 ATGAGATGTCCATGTTA
          1 ATGAGATGTCCATGTTA

                             
      13938 ATGAGATGTCCATGTTA
          1 ATGAGATGTCCATGTTA

              
      13955 AT
          1 AT

      13957 TAATTAAGAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   19  1.00

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


Consensus pattern (17 bp):   
ATGAGATGTCCATGTTA
Done.