Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024023.1 Corchorus olitorius cultivar O-4 contig24056, 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: 3574
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28


Found at i:402 original size:81 final size:81

Alignment explanation


    Indices: 267--429  Score: 326
    Period size: 81  Copynumber: 2.0  Consensus size: 81

        257 ACAGAAAATT

                                                                             
        267 GGAAATCAAATAGATTATGGTTTTAGTGGAATACCTGTGACGGTCGTCATATAATATGAATGAAC
          1 GGAAATCAAATAGATTATGGTTTTAGTGGAATACCTGTGACGGTCGTCATATAATATGAATGAAC

                            
        332 CGGCTCAGACTGCACA
         66 CGGCTCAGACTGCACA

                                                                             
        348 GGAAATCAAATAGATTATGGTTTTAGTGGAATACCTGTGACGGTCGTCATATAATATGAATGAAC
          1 GGAAATCAAATAGATTATGGTTTTAGTGGAATACCTGTGACGGTCGTCATATAATATGAATGAAC

                            
        413 CGGCTCAGACTGCACA
         66 CGGCTCAGACTGCACA

             
        429 G
          1 G

        430 AAGTGGCATC


Statistics
Matches: 82,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  81   82  1.00

ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27


Consensus pattern (81 bp):   
GGAAATCAAATAGATTATGGTTTTAGTGGAATACCTGTGACGGTCGTCATATAATATGAATGAAC
CGGCTCAGACTGCACA

Found at i:552 original size:27 final size:27

Alignment explanation


    Indices: 522--640  Score: 202
    Period size: 27  Copynumber: 4.4  Consensus size: 27

        512 CGAAATAACT

                                    *  
        522 GGATCCACTGCTGGGGTCGAAGTGTGA
          1 GGATCCACTGCTGGGGTCGAAGTGGGA

                                       
        549 GGATCCACTGCTGGGGTCGAAGTGGGA
          1 GGATCCACTGCTGGGGTCGAAGTGGGA

                                       
        576 GGATCCACTGCTGGGGTCGAAGTGGGA
          1 GGATCCACTGCTGGGGTCGAAGTGGGA

                     *            *  * 
        603 GGATCCACTACTGGGGTCGAAGCGGAA
          1 GGATCCACTGCTGGGGTCGAAGTGGGA

                       
        630 GGATCCACTGC
          1 GGATCCACTGC

        641 GGTAACAGTC


Statistics
Matches: 87,  Mismatches: 5, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  27   87  1.00

ACGTcount: A:0.20, C:0.21, G:0.40, T:0.18


Consensus pattern (27 bp):   
GGATCCACTGCTGGGGTCGAAGTGGGA

Found at i:3149 original size:18 final size:18

Alignment explanation


    Indices: 3128--3166  Score: 78
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3118 TACTATATGA

                              
       3128 CATAACAACACAAATATT
          1 CATAACAACACAAATATT

                              
       3146 CATAACAACACAAATATT
          1 CATAACAACACAAATATT

               
       3164 CAT
          1 CAT

       3167 GGTCTCTCTA


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   21  1.00

ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23


Consensus pattern (18 bp):   
CATAACAACACAAATATT
Done.