Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01000026.1 Corchorus capsularis cultivar CVL-1 contig00026, 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, 631

Length: 1053
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30


Found at i:482 original size:3 final size:3

Alignment explanation


    Indices: 476--528  Score: 88
    Period size: 3  Copynumber: 17.3  Consensus size: 3

        466 TTTTAATCAT

                      *                                                 
        476 ATA ATA ATC ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
          1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA

                     
        522 ATA ATA A
          1 ATA ATA A

        529 GGGTTAGACT


Statistics
Matches: 47,  Mismatches: 2, Indels: 2
        0.92            0.04        0.04

Matches are distributed among these distances:
   3   44  0.94
   4    3  0.06

ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34


Consensus pattern (3 bp):   
ATA

Found at i:708 original size:15 final size:15

Alignment explanation


    Indices: 688--717  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

        678 CATCCAATAC

                      *    
        688 AAATACTCACTTGGT
          1 AAATACTCACCTGGT

                           
        703 AAATACTCACCTGGT
          1 AAATACTCACCTGGT

        718 GAGATACTTA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.33, C:0.23, G:0.13, T:0.30


Consensus pattern (15 bp):   
AAATACTCACCTGGT

Found at i:765 original size:16 final size:16

Alignment explanation


    Indices: 746--792  Score: 85
    Period size: 16  Copynumber: 2.9  Consensus size: 16

        736 CACCCAGTAC

                            
        746 AATACTCACCTGGTGT
          1 AATACTCACCTGGTGT

                            
        762 AATACTCACCTGGTGT
          1 AATACTCACCTGGTGT

                    *      
        778 AATACTCATCTGGTG
          1 AATACTCACCTGGTG

        793 AGATATTCAC


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  16   30  1.00

ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32


Consensus pattern (16 bp):   
AATACTCACCTGGTGT

Found at i:795 original size:74 final size:73

Alignment explanation


    Indices: 689--834  Score: 222
    Period size: 74  Copynumber: 2.0  Consensus size: 73

        679 ATCCAATACA

                     *                              *                        
        689 AATACTCACTTGGTAAATACTCACCTGGTGAGATACTT-ATCCACACTCACCCAGTACAATACTC
          1 AATACTCACCTGGTAAATACTCACCTGGTGAGATA-TTCACCCACACTCACCCAGTACAATACTC

                     
        753 ACCTGGTGT
         65 ACCTGGTGT

                           *        *                        *               
        762 AATACTCACCTGGTGTAATACTCATCTGGTGAGATATTCACCCACACTCTCCCAGTACAATACTC
          1 AATACTCACCTGGT-AAATACTCACCTGGTGAGATATTCACCCACACTCACCCAGTACAATACTC

                    
        827 ACCTGGTG
         65 ACCTGGTG

        835 AGGCCATGCT


Statistics
Matches: 66,  Mismatches: 5, Indels: 3
        0.89            0.07        0.04

Matches are distributed among these distances:
  73   15  0.23
  74   51  0.77

ACGTcount: A:0.29, C:0.29, G:0.14, T:0.27


Consensus pattern (73 bp):   
AATACTCACCTGGTAAATACTCACCTGGTGAGATATTCACCCACACTCACCCAGTACAATACTCA
CCTGGTGT
Done.