Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016550.1 Corchorus olitorius cultivar O-4 contig16583, 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: 26830
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34


Found at i:12458 original size:66 final size:66

Alignment explanation


    Indices: 12351--12483  Score: 212
    Period size: 66  Copynumber: 2.0  Consensus size: 66

      12341 CTTACAGATC

                           *          *                                      
      12351 ACCCACCAATGAGGATCACTGGCACGGCTCGAACCCCAAGCAGAGATCCGAAACCTTACCAACTC
          1 ACCCACCAATGAGGACCACTGGCACGACTCGAACCCCAAGCAGAGATCCGAAACCTTACCAACTC

             
      12416 A
         66 A

                             *                  *               **           
      12417 ACCCACCAATGAGGACCGCTGGCACGACTCGAACCCTAAGCAGAGATCCGAAGTCTTACCAACTC
          1 ACCCACCAATGAGGACCACTGGCACGACTCGAACCCCAAGCAGAGATCCGAAACCTTACCAACTC

             
      12482 A
         66 A

             
      12483 A
          1 A

      12484 TCAACCTCAA


Statistics
Matches: 61,  Mismatches: 6, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  66   61  1.00

ACGTcount: A:0.33, C:0.35, G:0.19, T:0.13


Consensus pattern (66 bp):   
ACCCACCAATGAGGACCACTGGCACGACTCGAACCCCAAGCAGAGATCCGAAACCTTACCAACTC
A

Found at i:23412 original size:28 final size:30

Alignment explanation


    Indices: 23364--23430  Score: 75
    Period size: 29  Copynumber: 2.2  Consensus size: 30

      23354 GGACTAATTT

                      *             *    * 
      23364 TCTTGAATTTGAAGATTCAGG-GGTAAAATG
          1 TCTTG-ATTTAAAGATTCAGGAGGCAAAACG

                                          
      23394 TCTTGATTTAAAG-TTCAGGAGGCAAAACG
          1 TCTTGATTTAAAGATTCAGGAGGCAAAACG

                    
      23423 TCCTTGAT
          1 T-CTTGAT

      23431 GCAATAGTTC


Statistics
Matches: 32,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  28    6  0.19
  29   15  0.47
  30   11  0.34

ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33


Consensus pattern (30 bp):   
TCTTGATTTAAAGATTCAGGAGGCAAAACG

Done.