Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012094.1 Corchorus olitorius cultivar O-4 contig12127, 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: 4606
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37


Found at i:1729 original size:2 final size:2

Alignment explanation


    Indices: 1722--1760  Score: 69
    Period size: 2  Copynumber: 19.0  Consensus size: 2

       1712 CCTTAACTAG

                                                                     
       1722 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA

       1761 AAAGTACGAA


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   2   34  0.94
   3    2  0.06

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Found at i:4493 original size:21 final size:22

Alignment explanation


    Indices: 4467--4519  Score: 72
    Period size: 21  Copynumber: 2.5  Consensus size: 22

       4457 CTTATGGAGT

                  *     *      *  
       4467 TTATCACAATTTTATAGG-TAG
          1 TTATCAAAATTTAATAGGACAG

                                  
       4488 TTATCAAAATTTAATAGGACAG
          1 TTATCAAAATTTAATAGGACAG

                      
       4510 TTATCAAAAT
          1 TTATCAAAAT

       4520 CAAAACATGT


Statistics
Matches: 28,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  21   16  0.57
  22   12  0.43

ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38


Consensus pattern (22 bp):   
TTATCAAAATTTAATAGGACAG

Found at i:4570 original size:2 final size:2

Alignment explanation


    Indices: 4563--4606  Score: 88
    Period size: 2  Copynumber: 22.0  Consensus size: 2

       4553 AAGTTAATAG

                                                                          
       4563 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA

              
       4605 TA
          1 TA


Statistics
Matches: 42,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   42  1.00

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


Consensus pattern (2 bp):   
TA

Done.