Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01008519.1 Corchorus capsularis cultivar CVL-1 contig08540, 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: 27981
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.30


Found at i:2465 original size:19 final size:19

Alignment explanation


    Indices: 2429--2467  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       2419 TCGTAAACTT

                       *       
       2429 ACTTCATTTTTTGCTGTGC
          1 ACTTCATTTTTCGCTGTGC

                         *     
       2448 ACTTCATTTTTCGTTGTGC
          1 ACTTCATTTTTCGCTGTGC

             
       2467 A
          1 A

       2468 TGCCATTTAC


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51


Consensus pattern (19 bp):   
ACTTCATTTTTCGCTGTGC

Found at i:9530 original size:45 final size:45

Alignment explanation


    Indices: 9466--9557  Score: 175
    Period size: 45  Copynumber: 2.0  Consensus size: 45

       9456 CATTCAATAG

                                     *                   
       9466 ATAAATTAAATTCCAACTAAATTTCTACTACCACTAACAAGGGTA
          1 ATAAATTAAATTCCAACTAAATTTCCACTACCACTAACAAGGGTA

                                                         
       9511 ATAAATTAAATTCCAACTAAATTTCCACTACCACTAACAAGGGTA
          1 ATAAATTAAATTCCAACTAAATTTCCACTACCACTAACAAGGGTA

              
       9556 AT
          1 AT

       9558 TTAGTGGGTT


Statistics
Matches: 46,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  45   46  1.00

ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28


Consensus pattern (45 bp):   
ATAAATTAAATTCCAACTAAATTTCCACTACCACTAACAAGGGTA

Found at i:22144 original size:2 final size:2

Alignment explanation


    Indices: 22137--22165  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

      22127 TAGAATAGTC

                                                       
      22137 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      22166 CTCCCTCTGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Done.