Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012311.1 Corchorus olitorius cultivar O-4 contig12344, 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: 10430
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38


Found at i:1815 original size:2 final size:2

Alignment explanation


    Indices: 1808--1833  Score: 52
    Period size: 2  Copynumber: 13.0  Consensus size: 2

       1798 CTTTTGCTAG

                                                  
       1808 TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA

       1834 AAAGTAGGAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   24  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:2916 original size:20 final size:20

Alignment explanation


    Indices: 2879--2917  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       2869 TACTATTATT

                                
       2879 TTTTGAATTTAATATTTTAC
          1 TTTTGAATTTAATATTTTAC

                          *     
       2899 TTTT-AATTTCAATTTTTTA
          1 TTTTGAATTT-AATATTTTA

       2918 AATGTCAATA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19    5  0.29
  20   12  0.71

ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64


Consensus pattern (20 bp):   
TTTTGAATTTAATATTTTAC

Found at i:3940 original size:12 final size:13

Alignment explanation


    Indices: 3911--3952  Score: 66
    Period size: 13  Copynumber: 3.2  Consensus size: 13

       3901 CCCAAAGAAA

                         
       3911 AAAAAATGAAATG
          1 AAAAAATGAAATG

                         
       3924 AAAAAATGAAATG
          1 AAAAAATGAAATG

                  *    * 
       3937 AAAAAAAGAAAAG
          1 AAAAAATGAAATG

               
       3950 AAA
          1 AAA

       3953 GAAGAATAAG


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  13   27  1.00

ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10


Consensus pattern (13 bp):   
AAAAAATGAAATG
Done.