Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023067.1 Corchorus olitorius cultivar O-4 contig23100, 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: 9516
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34


Found at i:7882 original size:2 final size:2

Alignment explanation


    Indices: 7877--7901  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

       7867 TTATATAAGT

                                                 
       7877 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

       7902 TAGTTTATCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:8630 original size:32 final size:32

Alignment explanation


    Indices: 8590--8658  Score: 138
    Period size: 32  Copynumber: 2.2  Consensus size: 32

       8580 GCACCACCTT

                                            
       8590 GGCGGTGTCGCCCCACGGCGTCGCCCTGTTGG
          1 GGCGGTGTCGCCCCACGGCGTCGCCCTGTTGG

                                            
       8622 GGCGGTGTCGCCCCACGGCGTCGCCCTGTTGG
          1 GGCGGTGTCGCCCCACGGCGTCGCCCTGTTGG

                 
       8654 GGCGG
          1 GGCGG

       8659 CACCGCCGGA


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  32   37  1.00

ACGTcount: A:0.03, C:0.36, G:0.43, T:0.17


Consensus pattern (32 bp):   
GGCGGTGTCGCCCCACGGCGTCGCCCTGTTGG

Found at i:8902 original size:13 final size:13

Alignment explanation


    Indices: 8884--8908  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       8874 TTTATTGTAA

                         
       8884 TTACTATAATTAT
          1 TTACTATAATTAT

                        
       8897 TTACTATAATTA
          1 TTACTATAATTA

       8909 CTTAGAATTA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52


Consensus pattern (13 bp):   
TTACTATAATTAT

Found at i:8906 original size:22 final size:21

Alignment explanation


    Indices: 8865--8910  Score: 65
    Period size: 22  Copynumber: 2.1  Consensus size: 21

       8855 TTATTATTTG

                         * *     
       8865 ACTATAATTTTTATTGTAATT
          1 ACTATAATTTTTACTATAATT

                                  
       8886 ACTATAATTATTTACTATAATT
          1 ACTATAATT-TTTACTATAATT

               
       8908 ACT
          1 ACT

       8911 TAGAATTAAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  21    9  0.41
  22   13  0.59

ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52


Consensus pattern (21 bp):   
ACTATAATTTTTACTATAATT
Done.