Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020119.1 Corchorus olitorius cultivar O-4 contig20152, 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: 15477
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:594 original size:13 final size:13

Alignment explanation


    Indices: 562--595  Score: 59
    Period size: 13  Copynumber: 2.6  Consensus size: 13

        552 TTACTGATCC

                  *      
        562 TCCAAAAAAATTA
          1 TCCAAATAAATTA

                         
        575 TCCAAATAAATTA
          1 TCCAAATAAATTA

                    
        588 TCCAAATA
          1 TCCAAATA

        596 CACTGTTAGG


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  13   20  1.00

ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26


Consensus pattern (13 bp):   
TCCAAATAAATTA

Found at i:853 original size:40 final size:40

Alignment explanation


    Indices: 798--900  Score: 206
    Period size: 40  Copynumber: 2.6  Consensus size: 40

        788 TAGAAGCCTG

                                                    
        798 AATAGTGAAGCATAATAATAATTGGCTTTGTTCTCATTCC
          1 AATAGTGAAGCATAATAATAATTGGCTTTGTTCTCATTCC

                                                    
        838 AATAGTGAAGCATAATAATAATTGGCTTTGTTCTCATTCC
          1 AATAGTGAAGCATAATAATAATTGGCTTTGTTCTCATTCC

                                   
        878 AATAGTGAAGCATAATAATAATT
          1 AATAGTGAAGCATAATAATAATT

        901 TTGATAATAA


Statistics
Matches: 63,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  40   63  1.00

ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36


Consensus pattern (40 bp):   
AATAGTGAAGCATAATAATAATTGGCTTTGTTCTCATTCC

Found at i:15412 original size:52 final size:52

Alignment explanation


    Indices: 15334--15452  Score: 220
    Period size: 52  Copynumber: 2.3  Consensus size: 52

      15324 GAACATATAT

                                                                
      15334 ATATATATATATATACACTTATCCAGGAGCAAATGAACAGAGAAACAAATTA
          1 ATATATATATATATACACTTATCCAGGAGCAAATGAACAGAGAAACAAATTA

                     *                                          
      15386 ATATATATAAATATACACTTATCCAGGAGCAAATGAACAGAGAAACAAATTA
          1 ATATATATATATATACACTTATCCAGGAGCAAATGAACAGAGAAACAAATTA

                           
      15438 ATTATATATATATAT
          1 A-TATATATATATAT

      15453 TATATATATA


Statistics
Matches: 64,  Mismatches: 2, Indels: 1
        0.96            0.03        0.01

Matches are distributed among these distances:
  52   52  0.81
  53   12  0.19

ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28


Consensus pattern (52 bp):   
ATATATATATATATACACTTATCCAGGAGCAAATGAACAGAGAAACAAATTA

Found at i:15447 original size:2 final size:2

Alignment explanation


    Indices: 15440--15470  Score: 55
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      15430 ACAAATTAAT

                                                           
      15440 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      15471 CACACAC


Statistics
Matches: 28,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   1    1  0.04
   2   27  0.96

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


Consensus pattern (2 bp):   
TA

Done.