Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012254.1 Corchorus olitorius cultivar O-4 contig12287, 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: 62202
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:25360 original size:8 final size:8

Alignment explanation


    Indices: 25349--25376  Score: 56
    Period size: 8  Copynumber: 3.5  Consensus size: 8

      25339 AAAGCACAGT

                    
      25349 GGAAACTG
          1 GGAAACTG

                    
      25357 GGAAACTG
          1 GGAAACTG

                    
      25365 GGAAACTG
          1 GGAAACTG

                
      25373 GGAA
          1 GGAA

      25377 TTAATTAAGA


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   8   20  1.00

ACGTcount: A:0.39, C:0.11, G:0.39, T:0.11


Consensus pattern (8 bp):   
GGAAACTG

Found at i:30638 original size:16 final size:18

Alignment explanation


    Indices: 30612--30650  Score: 55
    Period size: 16  Copynumber: 2.3  Consensus size: 18

      30602 ATAAAACAGC

                  *           
      30612 AGAAAAGGAGGAA-CCAT
          1 AGAAAAAGAGGAAGCCAT

                              
      30629 -GAAAAAGAGGAAGCCAT
          1 AGAAAAAGAGGAAGCCAT

                 
      30646 AGAAA
          1 AGAAA

      30651 TGAACTTCAT


Statistics
Matches: 19,  Mismatches: 1, Indels: 3
        0.83            0.04        0.13

Matches are distributed among these distances:
  16   11  0.58
  17    4  0.21
  18    4  0.21

ACGTcount: A:0.56, C:0.10, G:0.28, T:0.05


Consensus pattern (18 bp):   
AGAAAAAGAGGAAGCCAT

Found at i:52408 original size:12 final size:11

Alignment explanation


    Indices: 52381--52407  Score: 54
    Period size: 11  Copynumber: 2.5  Consensus size: 11

      52371 GGACTATTAC

                       
      52381 TTTTTGTTTTT
          1 TTTTTGTTTTT

                       
      52392 TTTTTGTTTTT
          1 TTTTTGTTTTT

                 
      52403 TTTTT
          1 TTTTT

      52408 TTTCATCAGA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  11   16  1.00

ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93


Consensus pattern (11 bp):   
TTTTTGTTTTT

Found at i:52549 original size:29 final size:28

Alignment explanation


    Indices: 52507--52566  Score: 111
    Period size: 29  Copynumber: 2.1  Consensus size: 28

      52497 ATGTGAGTTT

                                        
      52507 GTTTATAATTTGTTTGTTTATTTGGTAG
          1 GTTTATAATTTGTTTGTTTATTTGGTAG

                                         
      52535 GTTTATAAATTTGTTTGTTTATTTGGTAG
          1 GTTTAT-AATTTGTTTGTTTATTTGGTAG

               
      52564 GTT
          1 GTT

      52567 CCGTGAGATT


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  28    6  0.19
  29   25  0.81

ACGTcount: A:0.18, C:0.00, G:0.22, T:0.60


Consensus pattern (28 bp):   
GTTTATAATTTGTTTGTTTATTTGGTAG

Found at i:53050 original size:20 final size:20

Alignment explanation


    Indices: 53027--53064  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      53017 ATCCCCTAAA

                  *             
      53027 ATTTAAGAACAAATTTAAGT
          1 ATTTAACAACAAATTTAAGT

                        *     
      53047 ATTTAACAACAAGTTTAA
          1 ATTTAACAACAAATTTAA

      53065 CCCTCAATTA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34


Consensus pattern (20 bp):   
ATTTAACAACAAATTTAAGT
Done.