Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018871.1 Corchorus olitorius cultivar O-4 contig18904, 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: 4250
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32


Found at i:2738 original size:19 final size:18

Alignment explanation


    Indices: 2714--2763  Score: 64
    Period size: 19  Copynumber: 2.7  Consensus size: 18

       2704 TTTGCATTAT

                               
       2714 AATTAAATATTAATAAATA
          1 AATTAAA-ATTAATAAATA

                          *    
       2733 AATTAAAATTAAATGAATA
          1 AATTAAAATT-AATAAATA

             *          
       2752 ACTTAAAATTAA
          1 AATTAAAATTAA

       2764 CTTGTATTAT


Statistics
Matches: 28,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  18    5  0.18
  19   23  0.82

ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34


Consensus pattern (18 bp):   
AATTAAAATTAATAAATA

Found at i:2869 original size:19 final size:18

Alignment explanation


    Indices: 2846--2887  Score: 50
    Period size: 19  Copynumber: 2.3  Consensus size: 18

       2836 TGAGTAATTT

                               
       2846 TTAAAT-AAGAATATAATA
          1 TTAAATGAA-AATATAATA

                         *     
       2864 TATAAATGAAAATTTAATA
          1 T-TAAATGAAAATATAATA

                 
       2883 TTAAA
          1 TTAAA

       2888 ATAATCAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 4
        0.81            0.04        0.15

Matches are distributed among these distances:
  18    5  0.24
  19   14  0.67
  20    2  0.10

ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36


Consensus pattern (18 bp):   
TTAAATGAAAATATAATA

Found at i:3961 original size:23 final size:26

Alignment explanation


    Indices: 3912--3961  Score: 70
    Period size: 23  Copynumber: 2.0  Consensus size: 26

       3902 TAGATTGAAT

                                  *   
       3912 AATTAAGACATTAAATAAAATTTAAG
          1 AATTAAGACATTAAATAAAATTCAAG

                                      
       3938 AATTAAG-CATT-AA-AAAATTCAAG
          1 AATTAAGACATTAAATAAAATTCAAG

             
       3961 A
          1 A

       3962 CTGACCCAAT


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  23   10  0.43
  24    2  0.09
  25    4  0.17
  26    7  0.30

ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28


Consensus pattern (26 bp):   
AATTAAGACATTAAATAAAATTCAAG
Done.