Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016432.1 Corchorus capsularis cultivar CVL-1 contig16453, 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: 5823
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31


Found at i:290 original size:32 final size:32

Alignment explanation


    Indices: 254--335  Score: 92
    Period size: 32  Copynumber: 2.6  Consensus size: 32

        244 AGTGGCTGTG

                             *              
        254 CCGCCCCAGGGGTGCGGTTTGCCGTGGCAAAC
          1 CCGCCCCAGGGGTGCGGCTTGCCGTGGCAAAC

                     **          *         *
        286 CCGCCCCAGCTGTGCGGCTTGTCGTGGCAAAG
          1 CCGCCCCAGGGGTGCGGCTTGCCGTGGCAAAC

              *   *     *     
        318 CCTCCCTAGGGGGGCGGC
          1 CCGCCCCAGGGGTGCGGC

        336 AAGGCCCTGC


Statistics
Matches: 40,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
  32   40  1.00

ACGTcount: A:0.11, C:0.35, G:0.38, T:0.16


Consensus pattern (32 bp):   
CCGCCCCAGGGGTGCGGCTTGCCGTGGCAAAC

Found at i:969 original size:27 final size:27

Alignment explanation


    Indices: 939--1051  Score: 165
    Period size: 27  Copynumber: 4.2  Consensus size: 27

        929 TTGATGAGTT

                *                      
        939 TGAGCGTGCTCAGCCGGGTTACTATGA
          1 TGAGGGTGCTCAGCCGGGTTACTATGA

                    *      *           
        966 TGAGGGTGTTCAGCCAGGTTACTATGA
          1 TGAGGGTGCTCAGCCGGGTTACTATGA

                           *           
        993 TGAGGGTGCTCAGCCCGGTTACTATGA
          1 TGAGGGTGCTCAGCCGGGTTACTATGA

                   *                    
       1020 T-AGGGCAGCTCAGCCGGGTTACTATGA
          1 TGAGGG-TGCTCAGCCGGGTTACTATGA

                 
       1047 TGAGG
          1 TGAGG

       1052 CCGAGGATTA


Statistics
Matches: 77,  Mismatches: 7, Indels: 3
        0.89            0.08        0.03

Matches are distributed among these distances:
  26    4  0.05
  27   70  0.91
  28    3  0.04

ACGTcount: A:0.20, C:0.19, G:0.35, T:0.26


Consensus pattern (27 bp):   
TGAGGGTGCTCAGCCGGGTTACTATGA

Found at i:5643 original size:8 final size:8

Alignment explanation


    Indices: 5630--5663  Score: 50
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       5620 CACCTTCTTG

                    
       5630 AAAAATTC
          1 AAAAATTC

                    
       5638 AAAAATTC
          1 AAAAATTC

                 *   
       5646 AGAAACTTC
          1 A-AAAATTC

                    
       5655 AAAAATTC
          1 AAAAATTC

             
       5663 A
          1 A

       5664 TAGCCGATTC


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
   8   16  0.70
   9    7  0.30

ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24


Consensus pattern (8 bp):   
AAAAATTC
Done.