Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01010886.1 Corchorus olitorius cultivar O-4 contig10918, 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: 7238
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29


Found at i:2042 original size:22 final size:22

Alignment explanation


    Indices: 2014--2057  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2004 CATTTTCCTT

                                  
       2014 TGCCTCTTAAGGCTCCCAATAG
          1 TGCCTCTTAAGGCTCCCAATAG

                                  
       2036 TGCCTCTTAAGGCTCCCAATAG
          1 TGCCTCTTAAGGCTCCCAATAG

       2058 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:2694 original size:22 final size:22

Alignment explanation


    Indices: 2666--2709  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       2656 ATACATCAAT

                                  
       2666 CAGGGGATGAAAGAGCTGATTA
          1 CAGGGGATGAAAGAGCTGATTA

                                  
       2688 CAGGGGATGAAAGAGCTGATTA
          1 CAGGGGATGAAAGAGCTGATTA

       2710 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:3891 original size:19 final size:19

Alignment explanation


    Indices: 3867--3923  Score: 114
    Period size: 19  Copynumber: 3.0  Consensus size: 19

       3857 CTAATTCTAA

                               
       3867 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

                               
       3886 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

                               
       3905 GTAAAGTCAGAAAGATAAC
          1 GTAAAGTCAGAAAGATAAC

       3924 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:4376 original size:22 final size:22

Alignment explanation


    Indices: 4348--4392  Score: 90
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4338 TTGCGAGTAG

                                  
       4348 TCCGTCTAGTATGCCTTCTTAC
          1 TCCGTCTAGTATGCCTTCTTAC

                                  
       4370 TCCGTCTAGTATGCCTTCTTAC
          1 TCCGTCTAGTATGCCTTCTTAC

             
       4392 T
          1 T

       4393 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

Found at i:5037 original size:14 final size:14

Alignment explanation


    Indices: 5018--5045  Score: 56
    Period size: 14  Copynumber: 2.0  Consensus size: 14

       5008 AAGGTACTTG

                          
       5018 TTAATAGGCTTAGA
          1 TTAATAGGCTTAGA

                          
       5032 TTAATAGGCTTAGA
          1 TTAATAGGCTTAGA

       5046 CCCTTGTTAC


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   14  1.00

ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36


Consensus pattern (14 bp):   
TTAATAGGCTTAGA

Found at i:6787 original size:20 final size:20

Alignment explanation


    Indices: 6764--6803  Score: 80
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       6754 CGTCAAAGCC

                                
       6764 TTTGCTATTGAATCAACCAT
          1 TTTGCTATTGAATCAACCAT

                                
       6784 TTTGCTATTGAATCAACCAT
          1 TTTGCTATTGAATCAACCAT

       6804 ATTGTATTAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   20  1.00

ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40


Consensus pattern (20 bp):   
TTTGCTATTGAATCAACCAT
Done.