Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024851.1 Corchorus olitorius cultivar O-4 contig24884, 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: 11054
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32


Found at i:666 original size:44 final size:45

Alignment explanation


    Indices: 611--695  Score: 145
    Period size: 44  Copynumber: 1.9  Consensus size: 45

        601 CTGGCCAAAC

                        *     *                          
        611 TGGCCAGCAGACTAGCCAGCCAGGCCTTGGC-GGGCCTGCTGTTT
          1 TGGCCAGCAGACCAGCCAACCAGGCCTTGGCGGGGCCTGCTGTTT

                                                     
        655 TGGCCAGCAGACCAGCCAACCAGGCCTTGGCGGGGCCTGCT
          1 TGGCCAGCAGACCAGCCAACCAGGCCTTGGCGGGGCCTGCT

        696 TGTGATACTA


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  44   29  0.76
  45    9  0.24

ACGTcount: A:0.15, C:0.34, G:0.34, T:0.16


Consensus pattern (45 bp):   
TGGCCAGCAGACCAGCCAACCAGGCCTTGGCGGGGCCTGCTGTTT

Found at i:5521 original size:11 final size:13

Alignment explanation


    Indices: 5494--5537  Score: 65
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       5484 ATTTTATTAC

                         
       5494 TGTTTTATTAAAT
          1 TGTTTTATTAAAT

                         
       5507 TGTTTTA-TAAA-
          1 TGTTTTATTAAAT

                          
       5518 TGTTTTAATTAAAT
          1 TGTTTT-ATTAAAT

                  
       5532 TGTTTT
          1 TGTTTT

       5538 GGGTGCATGA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  11    6  0.21
  12    5  0.18
  13   11  0.39
  14    6  0.21

ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61


Consensus pattern (13 bp):   
TGTTTTATTAAAT

Found at i:5521 original size:24 final size:25

Alignment explanation


    Indices: 5485--5537  Score: 81
    Period size: 24  Copynumber: 2.2  Consensus size: 25

       5475 TGAGGAACTA

                  * *                
       5485 TTTTATTACTGTTTT-ATTAAATTG
          1 TTTTATAAATGTTTTAATTAAATTG

                                     
       5509 TTTTATAAATGTTTTAATTAAATTG
          1 TTTTATAAATGTTTTAATTAAATTG

                
       5534 TTTT
          1 TTTT

       5538 GGGTGCATGA


Statistics
Matches: 26,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
  24   13  0.50
  25   13  0.50

ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62


Consensus pattern (25 bp):   
TTTTATAAATGTTTTAATTAAATTG

Found at i:6687 original size:6 final size:6

Alignment explanation


    Indices: 6670--6730  Score: 70
    Period size: 6  Copynumber: 10.2  Consensus size: 6

       6660 ACATTTTGTT

                      *      *      *           *                  
       6670 TAAAAA -AATAA TAATAA TAATAA TAAAAA TTAAAA TAAAAA TAAAAA
          1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA

                            
       6717 TAAAAA CTAAAAA T
          1 TAAAAA -TAAAAA T

       6731 TCCAGTCTTC


Statistics
Matches: 49,  Mismatches: 4, Indels: 4
        0.86            0.07        0.07

Matches are distributed among these distances:
   5    4  0.08
   6   39  0.80
   7    6  0.12

ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23


Consensus pattern (6 bp):   
TAAAAA

Done.