Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012445.1 Corchorus olitorius cultivar O-4 contig12478, 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: 6868
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28


Found at i:5556 original size:28 final size:28

Alignment explanation


    Indices: 5494--5554  Score: 81
    Period size: 27  Copynumber: 2.2  Consensus size: 28

       5484 GAGGCAACCC

                                        
       5494 AATTTTAATTCTTTTAATAATTAATTTT
          1 AATTTTAATTCTTTTAATAATTAATTTT

                               *    *    
       5522 AATTTTAATT-TTATT-ATTATTATTTTT
          1 AATTTTAATTCTT-TTAATAATTAATTTT

                  
       5549 AATTTT
          1 AATTTT

       5555 TACACTAATT


Statistics
Matches: 30,  Mismatches: 2, Indels: 3
        0.86            0.06        0.09

Matches are distributed among these distances:
  27   18  0.60
  28   12  0.40

ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66


Consensus pattern (28 bp):   
AATTTTAATTCTTTTAATAATTAATTTT

Found at i:6335 original size:22 final size:20

Alignment explanation


    Indices: 6307--6365  Score: 73
    Period size: 21  Copynumber: 2.8  Consensus size: 20

       6297 TCGACTAAGG

                                  
       6307 AATTGTCGACTTCAAGGAGAGA
          1 AATTGTCGAC-TCAAGGA-AGA

                       *         
       6329 AATTGTCGACTAAGAGGAAGA
          1 AATTGTCGACTCA-AGGAAGA

                *           
       6350 AATTTTCGACTCAAGG
          1 AATTGTCGACTCAAGG

       6366 TGAAGCAATT


Statistics
Matches: 33,  Mismatches: 3, Indels: 4
        0.82            0.08        0.10

Matches are distributed among these distances:
  20    3  0.09
  21   16  0.48
  22   14  0.42

ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24


Consensus pattern (20 bp):   
AATTGTCGACTCAAGGAAGA

Found at i:6352 original size:21 final size:21

Alignment explanation


    Indices: 6307--6391  Score: 68
    Period size: 22  Copynumber: 3.9  Consensus size: 21

       6297 TCGACTAAGG

                        *          
       6307 AATTGTCGACTTCA-AGGAGAGA
          1 AATTGTCGAC-TAAGAGGA-AGA

                                 
       6329 AATTGTCGACTAAGAGGAAGA
          1 AATTGTCGACTAAGAGGAAGA

                *                 *
       6350 AATTTTCGACTCAAG-GTGAAGC
          1 AATTGTCGACT-AAGAG-GAAGA

                                 
       6372 AATTCGTCGAC-AAGGAGGAA
          1 AATT-GTCGACTAA-GAGGAA

       6392 AGCAAGGAAT


Statistics
Matches: 53,  Mismatches: 4, Indels: 12
        0.77            0.06        0.17

Matches are distributed among these distances:
  21   18  0.34
  22   29  0.55
  23    6  0.11

ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21


Consensus pattern (21 bp):   
AATTGTCGACTAAGAGGAAGA

Found at i:6375 original size:22 final size:21

Alignment explanation


    Indices: 6307--6382  Score: 75
    Period size: 22  Copynumber: 3.5  Consensus size: 21

       6297 TCGACTAAGG

                                   
       6307 AATTGTCGACTTCAA-GGAGAGA
          1 AATTGTCGAC-TCAAGGGA-AGA

                                  
       6329 AATTGTCGACT-AAGAGGAAGA
          1 AATTGTCGACTCAAG-GGAAGA

                *                *
       6350 AATTTTCGACTCAAGGTGAAGC
          1 AATTGTCGACTCAAGG-GAAGA

                       
       6372 AATTCGTCGAC
          1 AATT-GTCGAC

       6383 AAGGAGGAAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 9
        0.79            0.05        0.16

Matches are distributed among these distances:
  20    2  0.04
  21   15  0.33
  22   24  0.52
  23    5  0.11

ACGTcount: A:0.36, C:0.16, G:0.25, T:0.24


Consensus pattern (21 bp):   
AATTGTCGACTCAAGGGAAGA
Done.