Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013640.1 Corchorus olitorius cultivar O-4 contig13673, 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: 16702
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:13399 original size:31 final size:30

Alignment explanation


    Indices: 13325--13456  Score: 111
    Period size: 31  Copynumber: 4.2  Consensus size: 30

      13315 CCGACGATGG

                                 *  * *    
      13325 CATGCCATGTGTACCAAAAAGCGATATGTGA
          1 CATGCCATGTGTACCAAAAAGTGACACGT-A

              *    *                   *  
      13356 CACGCCACGTGTACCAAAAAGTGACACATA
          1 CATGCCATGTGTACCAAAAAGTGACACGTA

                                        *   *
      13386 TCATGCCATGTGTACCAAAAAAGTGACATGTGG
          1 -CATGCCATGTGTACC-AAAAAGTGACACGT-A

                *       **                *
      13419 CATGTCATGTGTTTCAAAAAGTGACACGTGG
          1 CATGCCATGTGTACCAAAAAGTGACACGT-A

                   
      13450 CATGCCA
          1 CATGCCA

      13457 CGTGCACAAA


Statistics
Matches: 82,  Mismatches: 16, Indels: 6
        0.79            0.15        0.06

Matches are distributed among these distances:
  30    1  0.01
  31   57  0.70
  32   24  0.29

ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22


Consensus pattern (30 bp):   
CATGCCATGTGTACCAAAAAGTGACACGTA

Found at i:13454 original size:63 final size:62

Alignment explanation


    Indices: 13321--13456  Score: 164
    Period size: 63  Copynumber: 2.2  Consensus size: 62

      13311 GTATCCGACG

                                        *                                 
      13321 ATGGCATGCCATGTGTACCAAAAAGCGATATGTGACACGCCACGTGTACCAAAAAGTGACAC
          1 ATGGCATGCCATGTGTACCAAAAAGCGACATGTGACACGCCACGTGTACCAAAAAGTGACAC

              **                      *        *  * *  *    **             
      13383 ATATCATGCCATGTGTACCAAAAAAGTGACATGTGGCATGTCATGTGTTTCAAAAAGTGACAC
          1 ATGGCATGCCATGTGTACC-AAAAAGCGACATGTGACACGCCACGTGTACCAAAAAGTGACAC

            *          
      13446 GTGGCATGCCA
          1 ATGGCATGCCA

      13457 CGTGCACAAA


Statistics
Matches: 60,  Mismatches: 13, Indels: 1
        0.81            0.18        0.01

Matches are distributed among these distances:
  62   17  0.28
  63   43  0.72

ACGTcount: A:0.34, C:0.21, G:0.23, T:0.22


Consensus pattern (62 bp):   
ATGGCATGCCATGTGTACCAAAAAGCGACATGTGACACGCCACGTGTACCAAAAAGTGACAC

Found at i:13836 original size:58 final size:58

Alignment explanation


    Indices: 13774--13888  Score: 230
    Period size: 58  Copynumber: 2.0  Consensus size: 58

      13764 AATTTCTACA

                                                                      
      13774 AAAAAAGTATTATTTTGAGTTGTCATTGATATAATATGTTTAGATAAGTTATTAATTC
          1 AAAAAAGTATTATTTTGAGTTGTCATTGATATAATATGTTTAGATAAGTTATTAATTC

                                                                     
      13832 AAAAAAGTATTATTTTGAGTTGTCATTGATATAATATGTTTAGATAAGTTATTAATT
          1 AAAAAAGTATTATTTTGAGTTGTCATTGATATAATATGTTTAGATAAGTTATTAATT

      13889 GCATCGGTTA


Statistics
Matches: 57,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  58   57  1.00

ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45


Consensus pattern (58 bp):   
AAAAAAGTATTATTTTGAGTTGTCATTGATATAATATGTTTAGATAAGTTATTAATTC
Done.