Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024907.1 Corchorus olitorius cultivar O-4 contig24940, 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: 22097
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33


Found at i:9004 original size:17 final size:18

Alignment explanation


    Indices: 8982--9016  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       8972 TGTTTCATGG

                              
       8982 AACT-AAATCATGTGTGA
          1 AACTAAAATCATGTGTGA

                     *        
       8999 AACTAAAATTATGTGTGA
          1 AACTAAAATCATGTGTGA

       9017 GAATTTAATT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  17    4  0.25
  18   12  0.75

ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31


Consensus pattern (18 bp):   
AACTAAAATCATGTGTGA

Found at i:11793 original size:33 final size:33

Alignment explanation


    Indices: 11756--11824  Score: 95
    Period size: 33  Copynumber: 2.1  Consensus size: 33

      11746 TGATGCTATC

                                              
      11756 TTATTTCTTAATGATC-AAAATTCATGATAAATT
          1 TTATTT-TTAATGATCAAAAATTCATGATAAATT

                    **  *                    
      11789 TTATTTTTTTTGTTCAAAAATTCATGATAAATT
          1 TTATTTTTAATGATCAAAAATTCATGATAAATT

               
      11822 TTA
          1 TTA

      11825 AGGGTAATTA


Statistics
Matches: 32,  Mismatches: 3, Indels: 2
        0.86            0.08        0.05

Matches are distributed among these distances:
  32    6  0.19
  33   26  0.81

ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51


Consensus pattern (33 bp):   
TTATTTTTAATGATCAAAAATTCATGATAAATT

Found at i:15257 original size:12 final size:12

Alignment explanation


    Indices: 15240--15281  Score: 52
    Period size: 12  Copynumber: 3.6  Consensus size: 12

      15230 AGGCCTTTGT

                        
      15240 AGTTAATTAAGA
          1 AGTTAATTAAGA

                     *  
      15252 AGTTAATTATG-
          1 AGTTAATTAAGA

                         
      15263 A-TTAATTAAGTA
          1 AGTTAATTAAG-A

                   
      15275 AGTTAAT
          1 AGTTAAT

      15282 GGCCGGTTAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 5
        0.78            0.06        0.16

Matches are distributed among these distances:
  10    8  0.32
  11    1  0.04
  12   11  0.44
  13    5  0.20

ACGTcount: A:0.45, C:0.00, G:0.14, T:0.40


Consensus pattern (12 bp):   
AGTTAATTAAGA

Found at i:20313 original size:29 final size:29

Alignment explanation


    Indices: 20279--20345  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

      20269 CCGAGTGCAT

                            * *          
      20279 ACCCACACTCAAACAATCCCAAGTGCACA
          1 ACCCACACTCAAACAAACACAAGTGCACA

                     **                  
      20308 ACCCACACTTGAACAAACACAAGTGCACA
          1 ACCCACACTCAAACAAACACAAGTGCACA

                *    
      20337 ACCCGCACT
          1 ACCCACACT

      20346 TGATACACCA


Statistics
Matches: 33,  Mismatches: 5, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  29   33  1.00

ACGTcount: A:0.40, C:0.40, G:0.09, T:0.10


Consensus pattern (29 bp):   
ACCCACACTCAAACAAACACAAGTGCACA

Found at i:21444 original size:37 final size:38

Alignment explanation


    Indices: 21403--21478  Score: 118
    Period size: 40  Copynumber: 2.0  Consensus size: 38

      21393 CATTATCTTA

                               *                  
      21403 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAC
          1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAC

                                                   
      21440 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAA
          1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAA

      21479 GCTAATATTA


Statistics
Matches: 35,  Mismatches: 1, Indels: 3
        0.90            0.03        0.08

Matches are distributed among these distances:
  37    6  0.17
  40   29  0.83

ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33


Consensus pattern (38 bp):   
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAC
Done.