Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024662.1 Corchorus olitorius cultivar O-4 contig24695, 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: 4438
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28


Found at i:2430 original size:42 final size:42

Alignment explanation


    Indices: 2384--2474  Score: 119
    Period size: 42  Copynumber: 2.2  Consensus size: 42

       2374 CGAGTATCAC

                           *          *       *   *   
       2384 GCCCGGCCATGCCCGGCACCACAAGCTTCAGCCGCGCCTCAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                              * *         *           
       2426 GCCCGGCCATGCCCGCCATCTCAAGCCTCATCCGAGCCACAT
          1 GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

                   
       2468 GCCCGGC
          1 GCCCGGC

       2475 TAGGACCGGC


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.16, C:0.48, G:0.23, T:0.12


Consensus pattern (42 bp):   
GCCCGGCCATGCCCGCCACCACAAGCCTCAGCCGAGCCACAT

Found at i:2608 original size:21 final size:21

Alignment explanation


    Indices: 2565--2619  Score: 65
    Period size: 21  Copynumber: 2.6  Consensus size: 21

       2555 CGCCCATTCA

                        *  **    
       2565 CCGTGCCACCACAGGTTAAGC
          1 CCGTGCCACCACCGGCCAAGC

                              *  
       2586 CCGTGCCACCACCGGCCATGC
          1 CCGTGCCACCACCGGCCAAGC

                    *    
       2607 CCGTGCCATCACC
          1 CCGTGCCACCACC

       2620 ATTCAGTGCC


Statistics
Matches: 29,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   29  1.00

ACGTcount: A:0.18, C:0.47, G:0.22, T:0.13


Consensus pattern (21 bp):   
CCGTGCCACCACCGGCCAAGC

Found at i:2994 original size:15 final size:14

Alignment explanation


    Indices: 2974--3003  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       2964 ATCTCTTTAA

                           
       2974 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       2989 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3003 T
          1 T

       3004 GCTTTGTTTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT
Done.