Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016630.1 Corchorus olitorius cultivar O-4 contig16663, 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: 10485
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33


Found at i:5806 original size:20 final size:20

Alignment explanation


    Indices: 5783--5820  Score: 76
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       5773 TTTATCCTTC

                                
       5783 AATGGGTAGTTTTATTTTCA
          1 AATGGGTAGTTTTATTTTCA

                              
       5803 AATGGGTAGTTTTATTTT
          1 AATGGGTAGTTTTATTTT

       5821 TGATTTTTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   18  1.00

ACGTcount: A:0.24, C:0.03, G:0.21, T:0.53


Consensus pattern (20 bp):   
AATGGGTAGTTTTATTTTCA

Found at i:6732 original size:42 final size:43

Alignment explanation


    Indices: 6681--6774  Score: 120
    Period size: 45  Copynumber: 2.2  Consensus size: 43

       6671 AGTGCATTAC

                              *     *     *           *
       6681 CTAA-ATTCTA-CTCCATTTCTAGGTAATTCATCAAAATAAAG
          1 CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAA

                                                         
       6722 CTAATATTCTACTCCTCCATCTCTAGATAATTAATCAAAATAAAA
          1 CTAATATTCTA--CCTCCATCTCTAGATAATTAATCAAAATAAAA

                    
       6767 CTAATATT
          1 CTAATATT

       6775 AATTGTCGCT


Statistics
Matches: 45,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
  41    4  0.09
  42    6  0.13
  45   35  0.78

ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35


Consensus pattern (43 bp):   
CTAATATTCTACCTCCATCTCTAGATAATTAATCAAAATAAAA

Found at i:9368 original size:31 final size:31

Alignment explanation


    Indices: 9348--9429  Score: 146
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       9338 TCCAGCAGAC

                *                          
       9348 CCGAGACCCGAATGATCTGAATCTAGATGAG
          1 CCGAAACCCGAATGATCTGAATCTAGATGAG

                                           
       9379 CCGAAACCCGAATGATCTGAATCTAGATGAG
          1 CCGAAACCCGAATGATCTGAATCTAGATGAG

                     *          
       9410 CCGAAACCCAAATGATCTGA
          1 CCGAAACCCGAATGATCTGA

       9430 GAAAAGTACC


Statistics
Matches: 49,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  31   49  1.00

ACGTcount: A:0.35, C:0.24, G:0.22, T:0.18


Consensus pattern (31 bp):   
CCGAAACCCGAATGATCTGAATCTAGATGAG
Done.