Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011404.1 Corchorus capsularis cultivar CVL-1 contig11425, 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: 34654
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:5671 original size:3 final size:3

Alignment explanation


    Indices: 5663--5703  Score: 73
    Period size: 3  Copynumber: 13.7  Consensus size: 3

       5653 CCCAGACAGC

                                                     *            
       5663 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TGT TCT TCT TC
          1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC

       5704 CTACTATTAC


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

Matches are distributed among these distances:
   3   36  1.00

ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66


Consensus pattern (3 bp):   
TCT

Found at i:12642 original size:24 final size:25

Alignment explanation


    Indices: 12608--12654  Score: 87
    Period size: 24  Copynumber: 1.9  Consensus size: 25

      12598 AGTCATTGCT

                                     
      12608 TCTTTCTAATTAAATGCATGTTTGA
          1 TCTTTCTAATTAAATGCATGTTTGA

                                   
      12633 TCTTT-TAATTAAATGCATGTTT
          1 TCTTTCTAATTAAATGCATGTTT

      12655 CAAGAAGGGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  24   17  0.77
  25    5  0.23

ACGTcount: A:0.28, C:0.11, G:0.11, T:0.51


Consensus pattern (25 bp):   
TCTTTCTAATTAAATGCATGTTTGA

Found at i:12708 original size:27 final size:27

Alignment explanation


    Indices: 12678--12732  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

      12668 TCTGAAAAAC

                                       
      12678 AAGAGAAATGGACAATTAAAAAGGAAT
          1 AAGAGAAATGGACAATTAAAAAGGAAT

                                       
      12705 AAGAGAAATGGACAATTAAAAAGGAAT
          1 AAGAGAAATGGACAATTAAAAAGGAAT

             
      12732 A
          1 A

      12733 GAAGAGTAAT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.60, C:0.04, G:0.22, T:0.15


Consensus pattern (27 bp):   
AAGAGAAATGGACAATTAAAAAGGAAT

Found at i:28833 original size:4 final size:4

Alignment explanation


    Indices: 28824--28850  Score: 54
    Period size: 4  Copynumber: 6.8  Consensus size: 4

      28814 CAGTATAGGT

                                             
      28824 TTTA TTTA TTTA TTTA TTTA TTTA TTT
          1 TTTA TTTA TTTA TTTA TTTA TTTA TTT

      28851 TTTGGTACCA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   23  1.00

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


Consensus pattern (4 bp):   
TTTA

Found at i:32543 original size:2 final size:2

Alignment explanation


    Indices: 32536--32573  Score: 67
    Period size: 2  Copynumber: 18.5  Consensus size: 2

      32526 TAATAGGTTA

                                                                    
      32536 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A

      32574 CTGATCAATC


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

Matches are distributed among these distances:
   2   33  0.94
   3    2  0.06

ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47


Consensus pattern (2 bp):   
AT

Found at i:34621 original size:2 final size:2

Alignment explanation


    Indices: 34614--34654  Score: 82
    Period size: 2  Copynumber: 20.5  Consensus size: 2

      34604 GGATAGATCC

                                                                         
      34614 AT AT AT AT AT AT 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 AT AT AT AT AT AT A


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   39  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.