Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011579.1 Corchorus capsularis cultivar CVL-1 contig11600, 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: 20930
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35


Found at i:2544 original size:15 final size:16

Alignment explanation


    Indices: 2514--2549  Score: 63
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       2504 CCTCTCTTGC

                   *        
       2514 AAAAGAGTAAGAAAAA
          1 AAAAGAGCAAGAAAAA

                            
       2530 AAAAGAGCAAGAAAAA
          1 AAAAGAGCAAGAAAAA

                
       2546 AAAA
          1 AAAA

       2550 CAATTCAAAC


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03


Consensus pattern (16 bp):   
AAAAGAGCAAGAAAAA

Found at i:11622 original size:19 final size:20

Alignment explanation


    Indices: 11604--11639  Score: 58
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      11594 AATTAATTAT

                                
      11604 TTTA-ATATTA-ATTTTTTA
          1 TTTATATATTATATTTTTTA

                              
      11622 TTTATATATTATATTTTT
          1 TTTATATATTATATTTTT

      11640 ACTTAAAAAT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  18    4  0.25
  19    6  0.38
  20    6  0.38

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (20 bp):   
TTTATATATTATATTTTTTA

Found at i:12336 original size:2 final size:2

Alignment explanation


    Indices: 12331--12367  Score: 74
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      12321 TTTTATTACC

                                                                   
      12331 AT AT AT AT 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 AT AT AT AT A

      12368 GTAGATATTA


Statistics
Matches: 35,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   35  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.