Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006095.1 Corchorus olitorius cultivar O-4 contig06120, 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, 853

Length: 1423
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32


Found at i:400 original size:22 final size:22

Alignment explanation


    Indices: 375--421  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

        365 GTTTTAGTTG

                            *      
        375 AGTAAAACT-ATAAAAGTAAAAT
          1 AGTAAAA-TGATAAAAATAAAAT

                     *            
        397 AGTAAAATGGTAAAAATAAAAT
          1 AGTAAAATGATAAAAATAAAAT

               
        419 AGT
          1 AGT

        422 TATAAGGATA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    1  0.05
  22   21  0.95

ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23


Consensus pattern (22 bp):   
AGTAAAATGATAAAAATAAAAT

Found at i:420 original size:92 final size:93

Alignment explanation


    Indices: 299--482  Score: 298
    Period size: 92  Copynumber: 2.0  Consensus size: 93

        289 TCTTTTTAAT

                *      *                                                     
        299 TAAATTAGTAATATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
          1 TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG

                         *              
        364 AG-TTTTAGTTGAGTAAAACTATAAAAG
         66 AGTTTTTAGTTGACTAAAACTATAAAAG

                          *       *       *                     *            
        391 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
          1 TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG

                                       
        456 AGTTTTTAGTTGACTAAAACTATAAAA
         66 AGTTTTTAGTTGACTAAAACTATAAAA

        483 ATTTAAAGAA


Statistics
Matches: 84,  Mismatches: 7, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  92   61  0.73
  93   23  0.27

ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32


Consensus pattern (93 bp):   
TAAAATAGTAAAATCGTAAAAACAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG

Found at i:554 original size:31 final size:31

Alignment explanation


    Indices: 519--580  Score: 106
    Period size: 31  Copynumber: 2.0  Consensus size: 31

        509 TATTCGAAAA

                   *   *                   
        519 AATAAGGGTATGATAGGCGATTCAAAAGTTT
          1 AATAAGGATATAATAGGCGATTCAAAAGTTT

                                           
        550 AATAAGGATATAATAGGCGATTCAAAAGTTT
          1 AATAAGGATATAATAGGCGATTCAAAAGTTT

        581 TACAAAACTC


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   29  1.00

ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29


Consensus pattern (31 bp):   
AATAAGGATATAATAGGCGATTCAAAAGTTT
Done.