Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022654.1 Corchorus olitorius cultivar O-4 contig22687, 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: 5458
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Found at i:422 original size:35 final size:36

Alignment explanation


    Indices: 375--443  Score: 97
    Period size: 35  Copynumber: 1.9  Consensus size: 36

        365 GAGATTTTGG

                   *     *                       
        375 AGAAATATGATAATCAAAAT-TACAAAA-ATGTAATA
          1 AGAAATACGATAACCAAAATCT-CAAAAGATGTAATA

                                              
        410 AGAAATACGATAACCAAAATCTCAAAAGATGTAA
          1 AGAAATACGATAACCAAAATCTCAAAAGATGTAA

        444 GGTTATTGAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  35   23  0.77
  36    7  0.23

ACGTcount: A:0.58, C:0.10, G:0.10, T:0.22


Consensus pattern (36 bp):   
AGAAATACGATAACCAAAATCTCAAAAGATGTAATA

Found at i:3347 original size:30 final size:30

Alignment explanation


    Indices: 3311--3369  Score: 109
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       3301 ATTAGTCATG

                   *                      
       3311 GGTTGAATTAAATTGAAGAAAACTTGAATA
          1 GGTTGAAATAAATTGAAGAAAACTTGAATA

                                         
       3341 GGTTGAAATAAATTGAAGAAAACTTGAAT
          1 GGTTGAAATAAATTGAAGAAAACTTGAAT

       3370 CAAGGGAGCT


Statistics
Matches: 28,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   28  1.00

ACGTcount: A:0.47, C:0.03, G:0.20, T:0.29


Consensus pattern (30 bp):   
GGTTGAAATAAATTGAAGAAAACTTGAATA

Found at i:4857 original size:28 final size:28

Alignment explanation


    Indices: 4817--4912  Score: 165
    Period size: 28  Copynumber: 3.4  Consensus size: 28

       4807 TTTACTTCTT

                                        
       4817 ATTTTGGTCATTTTGCATGTCCAGGGGC
          1 ATTTTGGTCATTTTGCATGTCCAGGGGC

                           *       *    
       4845 ATTTTGGTCATTTTGTATGTCCAAGGGC
          1 ATTTTGGTCATTTTGCATGTCCAGGGGC

                                       *
       4873 ATTTTGGTCATTTTGCATGTCCAGGGGA
          1 ATTTTGGTCATTTTGCATGTCCAGGGGC

                        
       4901 ATTTTGGTCATT
          1 ATTTTGGTCATT

       4913 GCACAGGGGG


Statistics
Matches: 63,  Mismatches: 5, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  28   63  1.00

ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43


Consensus pattern (28 bp):   
ATTTTGGTCATTTTGCATGTCCAGGGGC
Done.