Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000666.1 Corchorus olitorius cultivar O-4 contig00666, 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, 663

Length: 1106
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30


Found at i:401 original size:23 final size:21

Alignment explanation


    Indices: 370--414  Score: 63
    Period size: 21  Copynumber: 2.0  Consensus size: 21

        360 GAAGGAGAAA

                                   
        370 GGAAATTGGCATCCTTGCGGGCT
          1 GGAAATTGGCA--CTTGCGGGCT

                *                
        393 GGAACTTGGCACTTGCGGGCT
          1 GGAAATTGGCACTTGCGGGCT

             
        414 G
          1 G

        415 CCCTAGTGTC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   11  0.52
  23   10  0.48

ACGTcount: A:0.16, C:0.22, G:0.38, T:0.24


Consensus pattern (21 bp):   
GGAAATTGGCACTTGCGGGCT

Found at i:603 original size:27 final size:27

Alignment explanation


    Indices: 572--633  Score: 97
    Period size: 27  Copynumber: 2.3  Consensus size: 27

        562 GCTGCTGTTA

                       **              
        572 GCGGCCTTGCGGGCTGCAGGTGCTGGG
          1 GCGGCCTTGCGAACTGCAGGTGCTGGG

                             *         
        599 GCGGCCTTGCGAACTGCTGGTGCTGGG
          1 GCGGCCTTGCGAACTGCAGGTGCTGGG

                    
        626 GCGGCCTT
          1 GCGGCCTT

        634 ACGGAGCAGC


Statistics
Matches: 32,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  27   32  1.00

ACGTcount: A:0.05, C:0.27, G:0.47, T:0.21


Consensus pattern (27 bp):   
GCGGCCTTGCGAACTGCAGGTGCTGGG

Found at i:888 original size:3 final size:3

Alignment explanation


    Indices: 880--917  Score: 76
    Period size: 3  Copynumber: 12.7  Consensus size: 3

        870 TTAGTGTAAA

                                                              
        880 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
          1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA

        918 ATGTAAAATT


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

Matches are distributed among these distances:
   3   35  1.00

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (3 bp):   
AAT

Done.