Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023701.1 Corchorus olitorius cultivar O-4 contig23734, 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: 10665
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31


Found at i:2107 original size:2 final size:2

Alignment explanation


    Indices: 2100--2135  Score: 72
    Period size: 2  Copynumber: 18.0  Consensus size: 2

       2090 AATCAATCGA

                                                                 
       2100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

       2136 TCCTTTATTT


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   34  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:9656 original size:36 final size:36

Alignment explanation


    Indices: 9589--9657  Score: 93
    Period size: 36  Copynumber: 1.9  Consensus size: 36

       9579 AATCGACGAA

                *     *      *       *          
       9589 ACGCGATCCATCAAGTAGTTCATCAGATGGTCGACG
          1 ACGCAATCCAACAAGTACTTCATCACATGGTCGACG

                                      *      
       9625 ACGCAATCCAACAAGTACTTCATCACCTGGTCG
          1 ACGCAATCCAACAAGTACTTCATCACATGGTCG

       9658 TGGGCGCAGC


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  36   28  1.00

ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22


Consensus pattern (36 bp):   
ACGCAATCCAACAAGTACTTCATCACATGGTCGACG

Found at i:10647 original size:25 final size:24

Alignment explanation


    Indices: 10584--10658  Score: 89
    Period size: 24  Copynumber: 3.1  Consensus size: 24

      10574 TTGAGCAATT

                   *                 
      10584 AAAAATAAAGA-AGATATTTTAAAG
          1 AAAAATAGAGAGA-ATATTTTAAAG

                                  * 
      10608 AAAAATAGAGAGAATATTTTAATG
          1 AAAAATAGAGAGAATATTTTAAAG

                 *              *    
      10632 AAAATTTAGAGAGAATATTTGAAAG
          1 AAAA-ATAGAGAGAATATTTTAAAG

              
      10657 AA
          1 AA

      10659 TTATAAT


Statistics
Matches: 44,  Mismatches: 5, Indels: 3
        0.85            0.10        0.06

Matches are distributed among these distances:
  24   24  0.55
  25   20  0.45

ACGTcount: A:0.57, C:0.00, G:0.16, T:0.27


Consensus pattern (24 bp):   
AAAAATAGAGAGAATATTTTAAAG
Done.