Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015245.1 Corchorus olitorius cultivar O-4 contig15278, 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: 3060
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Found at i:669 original size:19 final size:20

Alignment explanation


    Indices: 645--690  Score: 62
    Period size: 19  Copynumber: 2.5  Consensus size: 20

        635 AGAAAAAACA

                                
        645 AAACAAGAT-TCTTTTGAAC
          1 AAACAAGATGTCTTTTGAAC

                       *        
        664 AAACAAG-TGTGTTTTGAAC
          1 AAACAAGATGTCTTTTGAAC

                     
        683 AAA-AAGAT
          1 AAACAAGAT

        691 AAGATGAGAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  18    4  0.17
  19   20  0.83

ACGTcount: A:0.46, C:0.11, G:0.15, T:0.28


Consensus pattern (20 bp):   
AAACAAGATGTCTTTTGAAC

Found at i:1235 original size:14 final size:14

Alignment explanation


    Indices: 1206--1252  Score: 76
    Period size: 14  Copynumber: 3.3  Consensus size: 14

       1196 AAGGAAATTA

                           
       1206 TTTTCAAGAAAAAGG
          1 TTTTCAA-AAAAAGG

                      *   
       1221 TTTTCAAAAATAGG
          1 TTTTCAAAAAAAGG

                          
       1235 TTTTCAAAAAAAGG
          1 TTTTCAAAAAAAGG

                
       1249 TTTT
          1 TTTT

       1253 GAGTCTTTTA


Statistics
Matches: 30,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  14   23  0.77
  15    7  0.23

ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36


Consensus pattern (14 bp):   
TTTTCAAAAAAAGG

Found at i:1930 original size:17 final size:17

Alignment explanation


    Indices: 1908--1946  Score: 51
    Period size: 17  Copynumber: 2.3  Consensus size: 17

       1898 GCAACTAACC

                             
       1908 AAAAAAAAAAAGAAAAG
          1 AAAAAAAAAAAGAAAAG

                   * *     * 
       1925 AAAAAAAGAGAGAAATG
          1 AAAAAAAAAAAGAAAAG

                 
       1942 AAAAA
          1 AAAAA

       1947 TGAAATGAAA


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  17   19  1.00

ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03


Consensus pattern (17 bp):   
AAAAAAAAAAAGAAAAG
Done.