Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011969.1 Corchorus olitorius cultivar O-4 contig12002, 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: 13050
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:5301 original size:34 final size:32

Alignment explanation


    Indices: 5261--5387  Score: 132
    Period size: 34  Copynumber: 3.8  Consensus size: 32

       5251 TTTTGTAATA

                     *                        
       5261 AAAACGCCGGAATATAGGGGCGTTTGGTTCATAT
          1 AAAACGCCGCAATATAGGGGCGTTT-GTTCA-AT

                            *                 
       5295 AAAACGCCGGC-ATATCGGGGCGTTTGTGTCAAT
          1 AAAACGCC-GCAATATAGGGGCGTTTGT-TCAAT

                    *                   *     
       5328 ATAAACGCTGCAATATAGGGGCGTTT-TACAACT
          1 A-AAACGCCGCAATATAGGGGCGTTTGTTCAA-T

                                       
       5361 CAAAAACGCCGCAATATAGGGGCGTTT
          1 --AAAACGCCGCAATATAGGGGCGTTT

       5388 TCCATCTCAA


Statistics
Matches: 80,  Mismatches: 6, Indels: 14
        0.80            0.06        0.14

Matches are distributed among these distances:
  32    3  0.04
  33    9  0.11
  34   66  0.82
  35    2  0.03

ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24


Consensus pattern (32 bp):   
AAAACGCCGCAATATAGGGGCGTTTGTTCAAT

Found at i:5388 original size:34 final size:34

Alignment explanation


    Indices: 5330--5421  Score: 148
    Period size: 34  Copynumber: 2.7  Consensus size: 34

       5320 GTGTCAATAT

                                              
       5330 AAACGCTGCAATATAGGGGCGTTTTACAACTCAA
          1 AAACGCTGCAATATAGGGGCGTTTTACAACTCAA

                  *                  *  *     
       5364 AAACGCCGCAATATAGGGGCGTTTTCCATCTCAA
          1 AAACGCTGCAATATAGGGGCGTTTTACAACTCAA

                              *     
       5398 AAACGCTGCAATATAGGGTCGTTT
          1 AAACGCTGCAATATAGGGGCGTTT

       5422 CATGAGTCAT


Statistics
Matches: 53,  Mismatches: 5, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   53  1.00

ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25


Consensus pattern (34 bp):   
AAACGCTGCAATATAGGGGCGTTTTACAACTCAA
Done.