Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01006358.1 Corchorus olitorius cultivar O-4 contig06383, 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, 970

Length: 1618
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.39

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:299 original size:24 final size:24

Alignment explanation


    Indices: 253--299  Score: 69
    Period size: 25  Copynumber: 2.0  Consensus size: 24

        243 ACTTAATTTG

                            *       
        253 TTAATATTGTCAAAGTTTGTTTTT
          1 TTAATATTGTCAAAGTATGTTTTT

                                    
        277 TTAATATTTGTCAAAGTAT-TTTT
          1 TTAATA-TTGTCAAAGTATGTTTT

        300 CTATAACATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  24   10  0.48
  25   11  0.52

ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57


Consensus pattern (24 bp):   
TTAATATTGTCAAAGTATGTTTTT

Found at i:310 original size:25 final size:25

Alignment explanation


    Indices: 259--311  Score: 63
    Period size: 25  Copynumber: 2.1  Consensus size: 25

        249 TTTGTTAATA

                            * *   *  
        259 TTGTCAAAGTTTGTTTTTTTAATAT
          1 TTGTCAAAGTTTGTTTCTATAACAT

                                      
        284 TTGTCAAAGTATT-TTTCTATAACAT
          1 TTGTCAAAGT-TTGTTTCTATAACAT

               
        309 TTG
          1 TTG

        312 ACCTTTATTA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  25   22  0.92
  26    2  0.08

ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55


Consensus pattern (25 bp):   
TTGTCAAAGTTTGTTTCTATAACAT

Found at i:656 original size:24 final size:25

Alignment explanation


    Indices: 629--678  Score: 77
    Period size: 24  Copynumber: 2.0  Consensus size: 25

        619 TTTTTATTCA

                                      
        629 TATATGATT-TATAAAA-TTAATTAT
          1 TATATG-TTATATAAAAGTTAATTAT

                                     
        653 TATATGTTATATAAAAGTTAATTAT
          1 TATATGTTATATAAAAGTTAATTAT

             
        678 T
          1 T

        679 CATCTTATAT


Statistics
Matches: 24,  Mismatches: 0, Indels: 3
        0.89            0.00        0.11

Matches are distributed among these distances:
  23    2  0.08
  24   13  0.54
  25    9  0.38

ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50


Consensus pattern (25 bp):   
TATATGTTATATAAAAGTTAATTAT

Found at i:686 original size:24 final size:24

Alignment explanation


    Indices: 638--689  Score: 70
    Period size: 24  Copynumber: 2.2  Consensus size: 24

        628 ATATATGATT

                             *  *   
        638 TATAAAATTAATTATTATATGTTA
          1 TATAAAATTAATTATTACATCTTA

                                     
        662 TATAAAAGTTAATTATT-CATCTTA
          1 TATAAAA-TTAATTATTACATCTTA

                
        686 TATA
          1 TATA

        690 TATTTCAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  24   16  0.64
  25    9  0.36

ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48


Consensus pattern (24 bp):   
TATAAAATTAATTATTACATCTTA
Done.