Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021800.1 Corchorus olitorius cultivar O-4 contig21833, 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: 5991
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31


Found at i:723 original size:5 final size:5

Alignment explanation


    Indices: 713--745  Score: 66
    Period size: 5  Copynumber: 6.6  Consensus size: 5

        703 TTTCAAATGA

                                                   
        713 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
          1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA

        746 GAAAGAAAGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   5   28  1.00

ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18


Consensus pattern (5 bp):   
AAAAT

Found at i:2068 original size:33 final size:33

Alignment explanation


    Indices: 2003--2075  Score: 103
    Period size: 33  Copynumber: 2.2  Consensus size: 33

       1993 CTTCTTCTTC

                                  *  *       
       2003 TCATGATCAAACTCAAACAAGTTCTTCTCATGA
          1 TCATGATCAAACTCAAACAAGTGCTGCTCATGA

                                              
       2036 TCATGATCAAACTCAAACAAAGTGCTGC-CATGA
          1 TCATGATCAAACTCAAAC-AAGTGCTGCTCATGA

             *     
       2069 TGATGAT
          1 TCATGAT

       2076 ACTGATGATC


Statistics
Matches: 36,  Mismatches: 3, Indels: 2
        0.88            0.07        0.05

Matches are distributed among these distances:
  33   29  0.81
  34    7  0.19

ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27


Consensus pattern (33 bp):   
TCATGATCAAACTCAAACAAGTGCTGCTCATGA

Found at i:5952 original size:2 final size:2

Alignment explanation


    Indices: 5945--5989  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       5935 TTAAGTAACA

                                                                          
       5945 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

                
       5987 AG A
          1 AG A

       5990 AA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

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


Consensus pattern (2 bp):   
AG

Done.