Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017407.1 Corchorus olitorius cultivar O-4 contig17440, 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: 8086
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:3410 original size:17 final size:17

Alignment explanation


    Indices: 3367--3417  Score: 50
    Period size: 17  Copynumber: 2.9  Consensus size: 17

       3357 CCCAAGCCAG

                              
       3367 GAAAAGAGAAAAAAAAAC
          1 GAAAA-AGAAAAAAAAAC

              * *             
       3385 GAGAGAGAAAAGAAAAA-
          1 GAAAAAGAAAA-AAAAAC

                            
       3402 GAAAAAGAAAATAAAA
          1 GAAAAAGAAAA-AAAA

       3418 TAAAATAAAT


Statistics
Matches: 27,  Mismatches: 5, Indels: 3
        0.77            0.14        0.09

Matches are distributed among these distances:
  17   19  0.70
  18    8  0.30

ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02


Consensus pattern (17 bp):   
GAAAAAGAAAAAAAAAC

Found at i:4287 original size:28 final size:28

Alignment explanation


    Indices: 4218--4293  Score: 73
    Period size: 28  Copynumber: 2.7  Consensus size: 28

       4208 TATGGGCATA

                   *          *         
       4218 AAATTACTGTTTTACCCTAAGAATGAAT
          1 AAATTACAGTTTTACCCTTAGAATGAAT

                     *                ** 
       4246 AAATTACCATTTTTACCCTTAGAA-GGTT
          1 AAATTA-CAGTTTTACCCTTAGAATGAAT

                           *    
       4274 AAATTTACAGTTTTAACCTT
          1 AAA-TTACAGTTTTACCCTT

       4294 GTACTTTGAA


Statistics
Matches: 39,  Mismatches: 7, Indels: 4
        0.78            0.14        0.08

Matches are distributed among these distances:
  28   22  0.56
  29   17  0.44

ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39


Consensus pattern (28 bp):   
AAATTACAGTTTTACCCTTAGAATGAAT
Done.