Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014988.1 Corchorus olitorius cultivar O-4 contig15021, 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: 7644
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34


Found at i:530 original size:33 final size:33

Alignment explanation


    Indices: 493--586  Score: 163
    Period size: 33  Copynumber: 2.8  Consensus size: 33

        483 GGACAAGCAT

                           *                  
        493 CGGCATCAG-CAGGCTAGCCCGCGCGCCAGCACG
          1 CGGCATC-GCCAGGCCAGCCCGCGCGCCAGCACG

                                             
        526 CGGCATCGCCAGGCCAGCCCGCGCGCCAGCACG
          1 CGGCATCGCCAGGCCAGCCCGCGCGCCAGCACG

                                        
        559 CGGCATCGCCAGGCCAGCCCGCGCGCCA
          1 CGGCATCGCCAGGCCAGCCCGCGCGCCA

        587 AGCAGCAGGC


Statistics
Matches: 59,  Mismatches: 1, Indels: 2
        0.95            0.02        0.03

Matches are distributed among these distances:
  32    1  0.02
  33   58  0.98

ACGTcount: A:0.16, C:0.47, G:0.33, T:0.04


Consensus pattern (33 bp):   
CGGCATCGCCAGGCCAGCCCGCGCGCCAGCACG

Found at i:537 original size:16 final size:16

Alignment explanation


    Indices: 516--570  Score: 51
    Period size: 16  Copynumber: 3.4  Consensus size: 16

        506 CTAGCCCGCG

                            
        516 CGCCAGCACGCGGCAT
          1 CGCCAGCACGCGGCAT

                          *   *
        532 CGCCAGGC-CAGCCCGC-G
          1 CGCCA-GCAC-G-CGGCAT

                            
        549 CGCCAGCACGCGGCAT
          1 CGCCAGCACGCGGCAT

                  
        565 CGCCAG
          1 CGCCAG

        571 GCCAGCCCGC


Statistics
Matches: 30,  Mismatches: 4, Indels: 10
        0.68            0.09        0.23

Matches are distributed among these distances:
  15    3  0.10
  16   15  0.50
  17    9  0.30
  18    3  0.10

ACGTcount: A:0.16, C:0.47, G:0.33, T:0.04


Consensus pattern (16 bp):   
CGCCAGCACGCGGCAT

Found at i:554 original size:17 final size:17

Alignment explanation


    Indices: 532--586  Score: 53
    Period size: 17  Copynumber: 3.3  Consensus size: 17

        522 CACGCGGCAT

                             
        532 CGCCAGGCCAGCCCGCG
          1 CGCCAGGCCAGCCCGCG

                          *   *
        549 CGCCA-G-CA-CGCGGCAT
          1 CGCCAGGCCAGC-CCGC-G

                             
        565 CGCCAGGCCAGCCCGCG
          1 CGCCAGGCCAGCCCGCG

                 
        582 CGCCA
          1 CGCCA

        587 AGCAGCAGGC


Statistics
Matches: 29,  Mismatches: 4, Indels: 10
        0.67            0.09        0.23

Matches are distributed among these distances:
  14    1  0.03
  15    5  0.17
  16    6  0.21
  17   11  0.38
  18    5  0.17
  19    1  0.03

ACGTcount: A:0.15, C:0.51, G:0.33, T:0.02


Consensus pattern (17 bp):   
CGCCAGGCCAGCCCGCG

Found at i:1858 original size:12 final size:11

Alignment explanation


    Indices: 1829--1858  Score: 51
    Period size: 11  Copynumber: 2.7  Consensus size: 11

       1819 AGAAAATTGT

                       
       1829 TTGTTTTTGGA
          1 TTGTTTTTGGA

                       
       1840 TTGTTTTTGGA
          1 TTGTTTTTGGA

               *    
       1851 TTGATTTT
          1 TTGTTTTT

       1859 CGACTTAAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   18  1.00

ACGTcount: A:0.10, C:0.00, G:0.23, T:0.67


Consensus pattern (11 bp):   
TTGTTTTTGGA
Done.