Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01002231.1 Corchorus olitorius cultivar O-4 contig02231, 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: 4995
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--31  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

                                                          
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C

         32 CTGAGAGTTT


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48


Consensus pattern (2 bp):   
CT

Found at i:780 original size:14 final size:14

Alignment explanation


    Indices: 761--791  Score: 62
    Period size: 14  Copynumber: 2.2  Consensus size: 14

        751 TATTTTTATT

                          
        761 AAAACTTCATTTGC
          1 AAAACTTCATTTGC

                          
        775 AAAACTTCATTTGC
          1 AAAACTTCATTTGC

               
        789 AAA
          1 AAA

        792 TCCGTAACTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32


Consensus pattern (14 bp):   
AAAACTTCATTTGC

Found at i:1556 original size:13 final size:13

Alignment explanation


    Indices: 1538--1568  Score: 53
    Period size: 13  Copynumber: 2.4  Consensus size: 13

       1528 AGCAAACAAC

                         
       1538 AAATAAACTAAAT
          1 AAATAAACTAAAT

                      *  
       1551 AAATAAACTAGAT
          1 AAATAAACTAAAT

                 
       1564 AAATA
          1 AAATA

       1569 TAGAATTTCT


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  13   17  1.00

ACGTcount: A:0.68, C:0.06, G:0.03, T:0.23


Consensus pattern (13 bp):   
AAATAAACTAAAT

Found at i:2308 original size:4 final size:4

Alignment explanation


    Indices: 2301--2342  Score: 52
    Period size: 4  Copynumber: 10.5  Consensus size: 4

       2291 CAAGGATTAA

                                                                  
       2301 TTAT TTAT TTAT TGTAT TTAT TTA- TTA- TTACT TTAT TTAT TT
          1 TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTA-T TTAT TTAT TT

       2343 TCATTAAGTT


Statistics
Matches: 35,  Mismatches: 0, Indels: 6
        0.85            0.00        0.15

Matches are distributed among these distances:
   3    6  0.17
   4   22  0.63
   5    7  0.20

ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71


Consensus pattern (4 bp):   
TTAT

Done.