Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01005666.1 Corchorus capsularis cultivar CVL-1 contig05684, 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: 9306
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37


Found at i:2296 original size:58 final size:59

Alignment explanation


    Indices: 2184--2296  Score: 156
    Period size: 59  Copynumber: 1.9  Consensus size: 59

       2174 ATTAATCAAA

                                        *             *     *          
       2184 TATCAAGTAACATGTTTTTCTATTAGATGCATAATAAAAGACGTTTTATGACCGATGCT
          1 TATCAAGTAACATGTTTTTCTATTAGATCCATAATAAAAGACATTTTAGGACCGATGCT

                *   *          *          *                        
       2243 TATCGAGTGACATGTTTTTTTATTAGATCCCTAA-AAAAGACATTTTAGGACCGA
          1 TATCAAGTAACATGTTTTTCTATTAGATCCATAATAAAAGACATTTTAGGACCGA

       2297 GGCATGTTGC


Statistics
Matches: 47,  Mismatches: 7, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  58   18  0.38
  59   29  0.62

ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36


Consensus pattern (59 bp):   
TATCAAGTAACATGTTTTTCTATTAGATCCATAATAAAAGACATTTTAGGACCGATGCT

Found at i:3772 original size:8 final size:8

Alignment explanation


    Indices: 3759--3784  Score: 52
    Period size: 8  Copynumber: 3.2  Consensus size: 8

       3749 ATTAGGAGTT

                    
       3759 TTATTTTA
          1 TTATTTTA

                    
       3767 TTATTTTA
          1 TTATTTTA

                    
       3775 TTATTTTA
          1 TTATTTTA

              
       3783 TT
          1 TT

       3785 CTATGTGTAT


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   18  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (8 bp):   
TTATTTTA

Found at i:8003 original size:6 final size:6

Alignment explanation


    Indices: 7985--8026  Score: 66
    Period size: 6  Copynumber: 6.8  Consensus size: 6

       7975 GTTTAGACTT

                                            *               
       7985 ATATAG TATATAG ATATAG ATATAG ATACAG ATATAG ATATA
          1 ATATAG -ATATAG ATATAG ATATAG ATATAG ATATAG ATATA

       8027 AAAGAAAAGA


Statistics
Matches: 33,  Mismatches: 2, Indels: 1
        0.92            0.06        0.03

Matches are distributed among these distances:
   6   27  0.82
   7    6  0.18

ACGTcount: A:0.50, C:0.02, G:0.14, T:0.33


Consensus pattern (6 bp):   
ATATAG

Done.