Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000083.1 Corchorus capsularis cultivar CVL-1 contig00083, 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: 2654
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31


Found at i:277 original size:29 final size:29

Alignment explanation


    Indices: 237--295  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

        227 AATTACTTAC

                                         
        237 TTTTGGATTAATATTTGATGAGCTGGGTT
          1 TTTTGGATTAATATTTGATGAGCTGGGTT

                                         
        266 TTTTGGATTAATATTTGATGAGCTGGGTT
          1 TTTTGGATTAATATTTGATGAGCTGGGTT

             
        295 T
          1 T

        296 CTTTATCTGA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.20, C:0.03, G:0.27, T:0.49


Consensus pattern (29 bp):   
TTTTGGATTAATATTTGATGAGCTGGGTT

Found at i:1761 original size:51 final size:51

Alignment explanation


    Indices: 1685--1797  Score: 217
    Period size: 51  Copynumber: 2.2  Consensus size: 51

       1675 AGACCCTGTA

                                                               
       1685 AGTACATTAAGGTACATAGTTAAGGTTCTATCCATAGGTCGAGTGAAAAGC
          1 AGTACATTAAGGTACATAGTTAAGGTTCTATCCATAGGTCGAGTGAAAAGC

                                                   *           
       1736 AGTACATTAAGGTACATAGTTAAGGTTCTATCCATAGGTTGAGTGAAAAGC
          1 AGTACATTAAGGTACATAGTTAAGGTTCTATCCATAGGTCGAGTGAAAAGC

                       
       1787 AGTACATTAAG
          1 AGTACATTAAG

       1798 TCATTCTTGC


Statistics
Matches: 61,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  51   61  1.00

ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28


Consensus pattern (51 bp):   
AGTACATTAAGGTACATAGTTAAGGTTCTATCCATAGGTCGAGTGAAAAGC

Found at i:2519 original size:2 final size:2

Alignment explanation


    Indices: 2514--2562  Score: 98
    Period size: 2  Copynumber: 24.5  Consensus size: 2

       2504 AAAGACAAGT

                                                                          
       2514 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
          1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC

                      
       2556 AC AC AC A
          1 AC AC AC A

       2563 TATATATATA


Statistics
Matches: 47,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   47  1.00

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


Consensus pattern (2 bp):   
AC

Found at i:2567 original size:2 final size:2

Alignment explanation


    Indices: 2562--2592  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       2552 ACACACACAC

                                                          
       2562 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 A

       2593 GAGAGAGAGA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:2597 original size:2 final size:2

Alignment explanation


    Indices: 2592--2650  Score: 118
    Period size: 2  Copynumber: 29.5  Consensus size: 2

       2582 ATATATATAT

                                                                          
       2592 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                                     
       2634 AG AG AG AG AG AG AG AG A
          1 AG AG AG AG AG AG AG AG A

       2651 TGAT


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   57  1.00

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


Consensus pattern (2 bp):   
AG

Done.