Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007146.1 Corchorus capsularis cultivar CVL-1 contig07167, 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: 18910
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:2031 original size:30 final size:31

Alignment explanation


    Indices: 1974--2032  Score: 84
    Period size: 31  Copynumber: 1.9  Consensus size: 31

       1964 AGATTTTTGG

                                  *        
       1974 AGAAATTTAATTATTATTTTATTTAAAAAAT
          1 AGAAATTTAATTATTATTTTATGTAAAAAAT

                *   *                    
       2005 AGAAGTTTTATTATTA-TTTATGTAAAAA
          1 AGAAATTTAATTATTATTTTATGTAAAAA

       2033 GGTCTAAACA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  30   11  0.44
  31   14  0.56

ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47


Consensus pattern (31 bp):   
AGAAATTTAATTATTATTTTATGTAAAAAAT

Found at i:3322 original size:6 final size:6

Alignment explanation


    Indices: 3311--3341  Score: 62
    Period size: 6  Copynumber: 5.2  Consensus size: 6

       3301 CAACATTATT

                                                
       3311 ATATAC ATATAC ATATAC ATATAC ATATAC A
          1 ATATAC ATATAC ATATAC ATATAC ATATAC A

       3342 CATGAAATGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   25  1.00

ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32


Consensus pattern (6 bp):   
ATATAC

Found at i:12301 original size:7 final size:7

Alignment explanation


    Indices: 12289--12314  Score: 52
    Period size: 7  Copynumber: 3.7  Consensus size: 7

      12279 CACAACAACC

                   
      12289 TAATCAG
          1 TAATCAG

                   
      12296 TAATCAG
          1 TAATCAG

                   
      12303 TAATCAG
          1 TAATCAG

                 
      12310 TAATC
          1 TAATC

      12315 CCATCCAAGA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   19  1.00

ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31


Consensus pattern (7 bp):   
TAATCAG
Done.