Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013771.1 Corchorus olitorius cultivar O-4 contig13804, 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: 4639
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31


Found at i:3574 original size:22 final size:22

Alignment explanation


    Indices: 3549--3595  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       3539 TTTTTAGTTG

                            *      
       3549 AGTAAAACT-ATAAAAGTAAAAT
          1 AGTAAAA-TGATAAAAATAAAAT

                     *            
       3571 AGTAAAATGGTAAAAATAAAAT
          1 AGTAAAATGATAAAAATAAAAT

               
       3593 AGT
          1 AGT

       3596 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:3681 original size:93 final size:93

Alignment explanation


    Indices: 3472--3656  Score: 316
    Period size: 93  Copynumber: 2.0  Consensus size: 93

       3462 ACTTTTTAAT

                *      *  *                                *                 
       3472 TAAATTAGTAATATTGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
          1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATGTAATTAAATAAAAATAG

                         *              
       3537 AGTTTTTAGTTGAGTAAAACTATAAAAG
         66 AGTTTTTAGTTGACTAAAACTATAAAAG

                                          *                                  
       3565 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATGTAATTAAATAAAAATAG
          1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATGTAATTAAATAAAAATAG

                                       
       3630 AGTTTTTAGTTGACTAAAACTATAAAA
         66 AGTTTTTAGTTGACTAAAACTATAAAA

       3657 TTTAAATTAT


Statistics
Matches: 86,  Mismatches: 6, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  93   86  1.00

ACGTcount: A:0.52, C:0.02, G:0.14, T:0.33


Consensus pattern (93 bp):   
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATGTAATTAAATAAAAATAG
AGTTTTTAGTTGACTAAAACTATAAAAG
Done.