Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024650.1 Corchorus olitorius cultivar O-4 contig24683, 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: 8609
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:57 original size:33 final size:34

Alignment explanation


    Indices: 20--87  Score: 111
    Period size: 33  Copynumber: 2.0  Consensus size: 34

         10 CGTCCTTCGG

                              **              
         20 GGACGGCACGACCATGGGTGTGCCGCCCT-GTGA
          1 GGACGGCACGACCATGGGCATGCCGCCCTGGTGA

                                              
         53 GGACGGCACGACCATGGGCATGCCGCCCTGGTGA
          1 GGACGGCACGACCATGGGCATGCCGCCCTGGTGA

             
         87 G
          1 G

         88 TGCCGCCCTA


Statistics
Matches: 32,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  33   27  0.84
  34    5  0.16

ACGTcount: A:0.16, C:0.31, G:0.40, T:0.13


Consensus pattern (34 bp):   
GGACGGCACGACCATGGGCATGCCGCCCTGGTGA

Found at i:128 original size:33 final size:33

Alignment explanation


    Indices: 85--168  Score: 105
    Period size: 33  Copynumber: 2.5  Consensus size: 33

         75 CCGCCCTGGT

                                             
         85 GAGTGCCGCCCTAGGAGGGCGGCATGCCATGGA
          1 GAGTGCCGCCCTAGGAGGGCGGCATGCCATGGA

                 *      ***            *    *
        118 GAGTGTCGCCCTCCTAGGGCGGCATGCTATGGC
          1 GAGTGCCGCCCTAGGAGGGCGGCATGCCATGGA

                        *     
        151 GAGTGCCGCCCTTGGAGG
          1 GAGTGCCGCCCTAGGAGG

        169 AGGGCACCGC


Statistics
Matches: 41,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  33   41  1.00

ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17


Consensus pattern (33 bp):   
GAGTGCCGCCCTAGGAGGGCGGCATGCCATGGA

Found at i:5591 original size:6 final size:6

Alignment explanation


    Indices: 5574--5613  Score: 53
    Period size: 6  Copynumber: 6.7  Consensus size: 6

       5564 GGCTCTGCAC

                *          *       *                      
       5574 TGCCAG TGCCTG TTCCTG TGTCTG TGCCTG TGCCTG TGCC
          1 TGCCTG TGCCTG TGCCTG TGCCTG TGCCTG TGCCTG TGCC

       5614 ACCACAAGTG


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.03, C:0.33, G:0.30, T:0.35


Consensus pattern (6 bp):   
TGCCTG

Found at i:8213 original size:30 final size:29

Alignment explanation


    Indices: 8117--8217  Score: 102
    Period size: 27  Copynumber: 3.5  Consensus size: 29

       8107 ATCTAAGGGA

                               *           
       8117 ATTTTGGGTCATTTT-CAAAATCC-AGGGGC
          1 ATTTT-GGTCATTTTGC-ACATCCGAGGGGC

                         *      *       *
       8146 ATTTTGGTCA-TTAGCACATTCG-GGGGT
          1 ATTTTGGTCATTTTGCACATCCGAGGGGC

                 *                        
       8173 ATTTTAGTCATTTTGCACATCCAGAGGGGC
          1 ATTTTGGTCATTTTGCACATCC-GAGGGGC

                           
       8203 ATTTTGGTCATTTTG
          1 ATTTTGGTCATTTTG

       8218 AGCTCACTTT


Statistics
Matches: 58,  Mismatches: 9, Indels: 9
        0.76            0.12        0.12

Matches are distributed among these distances:
  27   19  0.33
  28   15  0.26
  29    6  0.10
  30   18  0.31

ACGTcount: A:0.21, C:0.16, G:0.25, T:0.39


Consensus pattern (29 bp):   
ATTTTGGTCATTTTGCACATCCGAGGGGC
Done.