Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01010375.1 Corchorus capsularis cultivar CVL-1 contig10396, 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: 50857
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:9 original size:4 final size:4

Alignment explanation


    Indices: 1--39  Score: 57
    Period size: 4  Copynumber: 10.5  Consensus size: 4

                                                                
          1 GAAA GAAA GAAA GAAA GAAA GAAA G-AA G-AA G-AA GAAA GA
          1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA

         40 TTGCTCTATA


Statistics
Matches: 34,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   3    9  0.26
   4   25  0.74

ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00


Consensus pattern (4 bp):   
GAAA

Found at i:24907 original size:3 final size:3

Alignment explanation


    Indices: 24899--24930  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

      24889 ATCATCGTCA

                                                      
      24899 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC

      24931 AGCTTTTACT


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

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66


Consensus pattern (3 bp):   
TCT

Found at i:28139 original size:6 final size:6

Alignment explanation


    Indices: 28105--28135  Score: 53
    Period size: 6  Copynumber: 5.2  Consensus size: 6

      28095 TTTCCTGTTT

                                         *      
      28105 GAATTA GAATTA GAATTA GAATTA GTATTA G
          1 GAATTA GAATTA GAATTA GAATTA GAATTA G

      28136 TATTCTCACA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35


Consensus pattern (6 bp):   
GAATTA

Found at i:50644 original size:2 final size:2

Alignment explanation


    Indices: 50637--50668  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      50627 ATATGAGGAC

                                                           
      50637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      50669 TAGAATGAAA


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

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:50684 original size:6 final size:6

Alignment explanation


    Indices: 50675--50703  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

      50665 ATATTAGAAT

                                             
      50675 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA
          1 GAAAAG GAAAAG GAAAAG GAAAAG GAAAA

      50704 AAAGGGAGGG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

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


Consensus pattern (6 bp):   
GAAAAG

Done.