Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022379.1 Corchorus olitorius cultivar O-4 contig22412, 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: 20765
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31


Found at i:7323 original size:29 final size:29

Alignment explanation


    Indices: 7287--7345  Score: 118
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       7277 TGTAATGAAA

                                         
       7287 CTAAACTCACATTCCGTGAGAATTGAACC
          1 CTAAACTCACATTCCGTGAGAATTGAACC

                                         
       7316 CTAAACTCACATTCCGTGAGAATTGAACC
          1 CTAAACTCACATTCCGTGAGAATTGAACC

             
       7345 C
          1 C

       7346 AACACCTCAT


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

Matches are distributed among these distances:
  29   30  1.00

ACGTcount: A:0.34, C:0.29, G:0.14, T:0.24


Consensus pattern (29 bp):   
CTAAACTCACATTCCGTGAGAATTGAACC

Found at i:18541 original size:32 final size:32

Alignment explanation


    Indices: 18514--18635  Score: 226
    Period size: 32  Copynumber: 3.8  Consensus size: 32

      18504 TTTTGTATTG

                                            
      18514 TAGACGCCGCTAAATAAGGGCGTTTTGTTCTA
          1 TAGACGCCGCTAAATAAGGGCGTTTTGTTCTA

                                           *
      18546 TAGACGCCGCTAAATAAGGGCGTTTTGTTCTG
          1 TAGACGCCGCTAAATAAGGGCGTTTTGTTCTA

                              *             
      18578 TAGACGCCGCTAAATAAGAGCGTTTTGTTCTA
          1 TAGACGCCGCTAAATAAGGGCGTTTTGTTCTA

                                      
      18610 TAGACGCCGCTAAATAAGGGCGTTTT
          1 TAGACGCCGCTAAATAAGGGCGTTTT

      18636 CTTTTCGCGC


Statistics
Matches: 86,  Mismatches: 4, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  32   86  1.00

ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30


Consensus pattern (32 bp):   
TAGACGCCGCTAAATAAGGGCGTTTTGTTCTA

Found at i:18605 original size:64 final size:64

Alignment explanation


    Indices: 18490--18635  Score: 240
    Period size: 64  Copynumber: 2.2  Consensus size: 64

      18480 TTAAAGCAAT

                         *                            *                      
      18490 TAAATATAGCGGCATTTTGTATTGTAGACGCCGCTAAATAAGGGCGTTTTGTTCTATAGACGCCG
          1 TAAATA-AG-GGCGTTTTGTATTGTAGACGCCGCTAAATAAGAGCGTTTTGTTCTATAGACGCCG

             
      18555 C
         64 C

                                                                             
      18556 TAAATAAGGGCGTTTTGT-TCTGTAGACGCCGCTAAATAAGAGCGTTTTGTTCTATAGACGCCGC
          1 TAAATAAGGGCGTTTTGTAT-TGTAGACGCCGCTAAATAAGAGCGTTTTGTTCTATAGACGCCGC

                            
      18620 TAAATAAGGGCGTTTT
          1 TAAATAAGGGCGTTTT

      18636 CTTTTCGCGC


Statistics
Matches: 77,  Mismatches: 2, Indels: 4
        0.93            0.02        0.05

Matches are distributed among these distances:
  63    1  0.01
  64   68  0.88
  65    2  0.03
  66    6  0.08

ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32


Consensus pattern (64 bp):   
TAAATAAGGGCGTTTTGTATTGTAGACGCCGCTAAATAAGAGCGTTTTGTTCTATAGACGCCGC
Done.