Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008487.1 Corchorus olitorius cultivar O-4 contig08514, 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: 1787
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30


Found at i:523 original size:2 final size:2

Alignment explanation


    Indices: 516--544  Score: 58
    Period size: 2  Copynumber: 14.5  Consensus size: 2

        506 AAATAATAAA

                                                       
        516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

        545 ATAGGGCCAG


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   27  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:636 original size:12 final size:12

Alignment explanation


    Indices: 614--681  Score: 61
    Period size: 12  Copynumber: 5.6  Consensus size: 12

        604 CCCAAGCCAG

                         
        614 AAAGAGAAAAGAA
          1 AAAG-GAAAAGAA

                      * 
        627 AAAGGAAAAGGA
          1 AAAGGAAAAGAA

                        
        639 AAAGG-AAA-AA
          1 AAAGGAAAAGAA

                     *  
        649 AAA-GAAAAAAA
          1 AAAGGAAAAGAA

                          
        660 AAAGAGAAAAGGAA
          1 AAAG-GAAAA-GAA

                    
        674 ATAAGGAA
          1 A-AAGGAA

        682 TTAAAAAGAA


Statistics
Matches: 46,  Mismatches: 3, Indels: 11
        0.77            0.05        0.18

Matches are distributed among these distances:
   9    1  0.02
  10    7  0.15
  11    8  0.17
  12   12  0.26
  13    9  0.20
  14    6  0.13
  15    3  0.07

ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01


Consensus pattern (12 bp):   
AAAGGAAAAGAA

Found at i:655 original size:28 final size:28

Alignment explanation


    Indices: 620--674  Score: 85
    Period size: 28  Copynumber: 2.0  Consensus size: 28

        610 CCAGAAAGAG

                       *                 
        620 AAAAGAAAAAGGAAAAG-GAAAAGGAAAA
          1 AAAAGAAAAA-AAAAAGAGAAAAGGAAAA

                                       
        648 AAAAGAAAAAAAAAAGAGAAAAGGAAA
          1 AAAAGAAAAAAAAAAGAGAAAAGGAAA

        675 TAAGGAATTA


Statistics
Matches: 25,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  27    5  0.20
  28   20  0.80

ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00


Consensus pattern (28 bp):   
AAAAGAAAAAAAAAAGAGAAAAGGAAAA

Found at i:674 original size:6 final size:6

Alignment explanation


    Indices: 614--674  Score: 56
    Period size: 6  Copynumber: 10.3  Consensus size: 6

        604 CCCAAGCCAG

                        *                                        ** 
        614 AAAGAGA AAAGAA AAAGGA AAAGGA AAAGGA AAA--A AAA-GA AAAAAA
          1 AAAG-GA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA

                             
        660 AAAGAGA AAAGGA AA
          1 AAAG-GA AAAGGA AA

        675 TAAGGAATTA


Statistics
Matches: 46,  Mismatches: 5, Indels: 7
        0.79            0.09        0.12

Matches are distributed among these distances:
   4    4  0.09
   5    4  0.09
   6   29  0.63
   7    9  0.20

ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00


Consensus pattern (6 bp):   
AAAGGA
Done.