Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024772.1 Corchorus olitorius cultivar O-4 contig24805, 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: 23370
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33


Found at i:2047 original size:12 final size:12

Alignment explanation


    Indices: 2032--2058  Score: 54
    Period size: 12  Copynumber: 2.2  Consensus size: 12

       2022 TTAAGAGCTT

                        
       2032 TCTTATATAGAA
          1 TCTTATATAGAA

                        
       2044 TCTTATATAGAA
          1 TCTTATATAGAA

               
       2056 TCT
          1 TCT

       2059 GACGCGGACT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   15  1.00

ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44


Consensus pattern (12 bp):   
TCTTATATAGAA

Found at i:6542 original size:9 final size:9

Alignment explanation


    Indices: 6528--6573  Score: 74
    Period size: 9  Copynumber: 5.1  Consensus size: 9

       6518 ACGCAGAGTT

                     
       6528 GGAAGAAGA
          1 GGAAGAAGA

                     
       6537 GGAAGAAGA
          1 GGAAGAAGA

                     
       6546 GGAAGAAGA
          1 GGAAGAAGA

            *        
       6555 TGAAGAAGA
          1 GGAAGAAGA

            *        
       6564 TGAAGAAGA
          1 GGAAGAAGA

             
       6573 G
          1 G

       6574 CATGGGCAAT


Statistics
Matches: 35,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   9   35  1.00

ACGTcount: A:0.54, C:0.00, G:0.41, T:0.04


Consensus pattern (9 bp):   
GGAAGAAGA

Found at i:6544 original size:3 final size:3

Alignment explanation


    Indices: 6529--6572  Score: 52
    Period size: 3  Copynumber: 14.7  Consensus size: 3

       6519 CGCAGAGTTG

                      *           *           *           *           
       6529 GAA GAA GAG GAA GAA GAG GAA GAA GAT GAA GAA GAT GAA GAA GA
          1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA

       6573 GCATGGGCAA


Statistics
Matches: 33,  Mismatches: 8, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   3   33  1.00

ACGTcount: A:0.57, C:0.00, G:0.39, T:0.05


Consensus pattern (3 bp):   
GAA

Found at i:10985 original size:31 final size:31

Alignment explanation


    Indices: 10948--11012  Score: 103
    Period size: 31  Copynumber: 2.1  Consensus size: 31

      10938 ATCTCATCTG

                             *             
      10948 TACAGTTGCTAAACAGTGTCAATCGCACCGT
          1 TACAGTTGCTAAACAGTATCAATCGCACCGT

                               *       *   
      10979 TACAGTTGCTAAACAGTATTAATCGCATCGT
          1 TACAGTTGCTAAACAGTATCAATCGCACCGT

               
      11010 TAC
          1 TAC

      11013 CACAACGCTC


Statistics
Matches: 31,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29


Consensus pattern (31 bp):   
TACAGTTGCTAAACAGTATCAATCGCACCGT

Found at i:23352 original size:16 final size:18

Alignment explanation


    Indices: 23331--23367  Score: 51
    Period size: 16  Copynumber: 2.2  Consensus size: 18

      23321 AATAAGGAAC

                              
      23331 AAAAAAAGAA-AAAA-AA
          1 AAAAAAAGAAGAAAACAA

                  *           
      23347 AAAAAACGAAGAAAACAA
          1 AAAAAAAGAAGAAAACAA

               
      23365 AAA
          1 AAA

      23368 GAC


Statistics
Matches: 18,  Mismatches: 1, Indels: 2
        0.86            0.05        0.10

Matches are distributed among these distances:
  16    9  0.50
  17    4  0.22
  18    5  0.28

ACGTcount: A:0.86, C:0.05, G:0.08, T:0.00


Consensus pattern (18 bp):   
AAAAAAAGAAGAAAACAA
Done.