Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01004056.1 Corchorus capsularis cultivar CVL-1 contig04064, 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, 656

Length: 1094
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42


Found at i:60 original size:6 final size:6

Alignment explanation


    Indices: 49--114  Score: 109
    Period size: 6  Copynumber: 11.3  Consensus size: 6

         39 ATTAGATTTA

                            *                                      
         49 ATCTAT ATCTAT ATATAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT
          1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT

                                   
         97 A-CTAT ATCTAT A-CTAT AT
          1 ATCTAT ATCTAT ATCTAT AT

        115 TAAAAAAGTC


Statistics
Matches: 56,  Mismatches: 2, Indels: 4
        0.90            0.03        0.06

Matches are distributed among these distances:
   5   10  0.18
   6   46  0.82

ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48


Consensus pattern (6 bp):   
ATCTAT

Found at i:361 original size:78 final size:70

Alignment explanation


    Indices: 201--355  Score: 222
    Period size: 70  Copynumber: 2.2  Consensus size: 70

        191 TTGTTTAGGT

                            *            *        *                          
        201 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
          1 TTTTACTA-TTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATT

                  
        265 ATTTTA
         65 ATTTTA

                                                           *       *      *  
        271 TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
          1 TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATTA

              *  
        336 TTATA
         66 TTTTA

                  *        
        341 TTTTACCATTTTACT
          1 TTTTACTATTTTACT

        356 ATTTTAATTA


Statistics
Matches: 76,  Mismatches: 8, Indels: 2
        0.88            0.09        0.02

Matches are distributed among these distances:
  70   74  0.97
  71    2  0.03

ACGTcount: A:0.37, C:0.12, G:0.01, T:0.51


Consensus pattern (70 bp):   
TTTTACTATTTTACTTAACTAAAAACTCAATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Done.