Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011515.1 Corchorus olitorius cultivar O-4 contig11548, 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: 4999
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29


Found at i:2045 original size:22 final size:22

Alignment explanation


    Indices: 2017--2060  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2007 CATTTTCCTT

                                  
       2017 TGCCTCTTAAGGCTCCCAATAG
          1 TGCCTCTTAAGGCTCCCAATAG

                                  
       2039 TGCCTCTTAAGGCTCCCAATAG
          1 TGCCTCTTAAGGCTCCCAATAG

       2061 CCTAGGGATG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27


Consensus pattern (22 bp):   
TGCCTCTTAAGGCTCCCAATAG

Found at i:2693 original size:22 final size:22

Alignment explanation


    Indices: 2665--2708  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2655 ATACATCAAT

                                  
       2665 CAGGGGATGAAAGAGCTGATTA
          1 CAGGGGATGAAAGAGCTGATTA

                                  
       2687 CAGGGGATGAAAGAGCTGATTA
          1 CAGGGGATGAAAGAGCTGATTA

       2709 TTGCCGATAG


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18


Consensus pattern (22 bp):   
CAGGGGATGAAAGAGCTGATTA

Found at i:3890 original size:19 final size:19

Alignment explanation


    Indices: 3866--3922  Score: 114
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       3856 CTAATTCTAA

                               
       3866 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

                               
       3885 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

                               
       3904 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

       3923 TTCTGCTCGA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   38  1.00

ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16


Consensus pattern (19 bp):   
GTAAAGTCAGAAAGATAAC

Found at i:4375 original size:22 final size:22

Alignment explanation


    Indices: 4347--4391  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4337 TTGCGAGTAG

                                  
       4347 TCCGTCTAGTATGCCTTCTTAC
          1 TCCGTCTAGTATGCCTTCTTAC

                                  
       4369 TCCGTCTAGTATGCCTTCTTAC
          1 TCCGTCTAGTATGCCTTCTTAC

             
       4391 T
          1 T

       4392 TCTTAGTTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.13, C:0.31, G:0.13, T:0.42


Consensus pattern (22 bp):   
TCCGTCTAGTATGCCTTCTTAC
Done.