Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023799.1 Corchorus olitorius cultivar O-4 contig23832, 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: 17258
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34


Found at i:11419 original size:16 final size:15

Alignment explanation


    Indices: 11387--11424  Score: 51
    Period size: 16  Copynumber: 2.5  Consensus size: 15

      11377 AGACCTTGCA

                           
      11387 AAAAAG-AGGAAAAT
          1 AAAAAGAAGGAAAAT

                     *      
      11401 AAAAAGAAGTAAAAGT
          1 AAAAAGAAGGAAAA-T

                    
      11417 AAAAAGAA
          1 AAAAAGAA

      11425 AACCTTTAAA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  14    6  0.29
  15    6  0.29
  16    9  0.43

ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08


Consensus pattern (15 bp):   
AAAAAGAAGGAAAAT

Found at i:13578 original size:7 final size:7

Alignment explanation


    Indices: 13566--13630  Score: 130
    Period size: 7  Copynumber: 9.3  Consensus size: 7

      13556 GAGCGATGTG

                   
      13566 ATGGGGA
          1 ATGGGGA

                   
      13573 ATGGGGA
          1 ATGGGGA

                   
      13580 ATGGGGA
          1 ATGGGGA

                   
      13587 ATGGGGA
          1 ATGGGGA

                   
      13594 ATGGGGA
          1 ATGGGGA

                   
      13601 ATGGGGA
          1 ATGGGGA

                   
      13608 ATGGGGA
          1 ATGGGGA

                   
      13615 ATGGGGA
          1 ATGGGGA

                   
      13622 ATGGGGA
          1 ATGGGGA

              
      13629 AT
          1 AT

      13631 TGGAAGACTT


Statistics
Matches: 58,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   58  1.00

ACGTcount: A:0.29, C:0.00, G:0.55, T:0.15


Consensus pattern (7 bp):   
ATGGGGA

Found at i:14631 original size:34 final size:34

Alignment explanation


    Indices: 14584--14685  Score: 177
    Period size: 34  Copynumber: 3.0  Consensus size: 34

      14574 AATAGCAGAT

                    *                  *      
      14584 CCCAAATTCCTTGAGACCCATGTAAACAATGAGA
          1 CCCAAATTTCTTGAGACCCATGTAAACGATGAGA

                                              
      14618 CCCAAATTTCTTGAGACCCATGTAAACGATGAGA
          1 CCCAAATTTCTTGAGACCCATGTAAACGATGAGA

                        *                     
      14652 CCCAAATTTCTTAAGACCCATGTAAACGATGAGA
          1 CCCAAATTTCTTGAGACCCATGTAAACGATGAGA

      14686 TTATAGGATT


Statistics
Matches: 65,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  34   65  1.00

ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23


Consensus pattern (34 bp):   
CCCAAATTTCTTGAGACCCATGTAAACGATGAGA

Found at i:16951 original size:2 final size:2

Alignment explanation


    Indices: 16940--16975  Score: 51
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      16930 CTTCAGTTTG

                                                                      
      16940 TA TA -A TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      16976 TGTTTTACAT


Statistics
Matches: 31,  Mismatches: 0, Indels: 6
        0.84            0.00        0.16

Matches are distributed among these distances:
   1    3  0.10
   2   28  0.90

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


Consensus pattern (2 bp):   
TA

Done.