Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013181.1 Corchorus olitorius cultivar O-4 contig13214, 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: 2091
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27


Found at i:575 original size:54 final size:54

Alignment explanation


    Indices: 515--647  Score: 212
    Period size: 54  Copynumber: 2.5  Consensus size: 54

        505 CGGCCACGGC

                                          *                       
        515 CCGGCCACCCGAGCCATCTACCCGGTCATGTCAGACCTCATCCGCGCCATCCGA
          1 CCGGCCACCCGAGCCATCTACCCGGTCATGCCAGACCTCATCCGCGCCATCCGA

                            *                                     
        569 CCGGCCACCCGAGCCAGCTACCCGGTCATGCCAGACCTCATCCGCGCCATCCGA
          1 CCGGCCACCCGAGCCATCTACCCGGTCATGCCAGACCTCATCCGCGCCATCCGA

                   *   *   *   *     
        623 CCGGCCATCCGCGCCGTCTGCCCGG
          1 CCGGCCACCCGAGCCATCTACCCGG

        648 CTAGCCGTGC


Statistics
Matches: 72,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  54   72  1.00

ACGTcount: A:0.16, C:0.48, G:0.23, T:0.13


Consensus pattern (54 bp):   
CCGGCCACCCGAGCCATCTACCCGGTCATGCCAGACCTCATCCGCGCCATCCGA

Found at i:954 original size:21 final size:22

Alignment explanation


    Indices: 930--980  Score: 68
    Period size: 21  Copynumber: 2.4  Consensus size: 22

        920 CGGCCATTCA

                        *  *      
        930 CCGTGCCACCACTAGTTAA-GC
          1 CCGTGCCACCACCAGCTAATGC

                         *        
        951 CCGTGCCACCACCGGCTAATGC
          1 CCGTGCCACCACCAGCTAATGC

                    
        973 CCGTGCCA
          1 CCGTGCCA

        981 TCACAATTCA


Statistics
Matches: 26,  Mismatches: 3, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  21   16  0.62
  22   10  0.38

ACGTcount: A:0.20, C:0.43, G:0.22, T:0.16


Consensus pattern (22 bp):   
CCGTGCCACCACCAGCTAATGC

Found at i:1357 original size:15 final size:14

Alignment explanation


    Indices: 1337--1366  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       1327 ATCTTTTTAA

                           
       1337 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       1352 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       1366 T
          1 T

       1367 GCTTTGATTG


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.