Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016085.1 Corchorus olitorius cultivar O-4 contig16118, 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: 27004
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:16171 original size:6 final size:6

Alignment explanation


    Indices: 16147--16184  Score: 51
    Period size: 6  Copynumber: 6.3  Consensus size: 6

      16137 AAGGAGCCGC

                             *                           
      16147 TGCTGG TGGCT-G TGGTGG TGCTGG TGCTGG TGCTGG TG
          1 TGCTGG T-GCTGG TGCTGG TGCTGG TGCTGG TGCTGG TG

      16185 GTGACTGTGG


Statistics
Matches: 28,  Mismatches: 2, Indels: 4
        0.82            0.06        0.12

Matches are distributed among these distances:
   5    2  0.07
   6   23  0.82
   7    3  0.11

ACGTcount: A:0.00, C:0.13, G:0.53, T:0.34


Consensus pattern (6 bp):   
TGCTGG

Found at i:24103 original size:31 final size:30

Alignment explanation


    Indices: 24063--24125  Score: 108
    Period size: 31  Copynumber: 2.1  Consensus size: 30

      24053 AAGGCAAGGT

                              *           
      24063 CACTGCACACCAACCCTTGCACACTGCACA
          1 CACTGCACACCAACCCTTACACACTGCACA

                                           
      24093 CACTGTCACACCAACCCTTACACACTGCACA
          1 CACTG-CACACCAACCCTTACACACTGCACA

              
      24124 CA
          1 CA

      24126 ACAAACAAAC


Statistics
Matches: 31,  Mismatches: 1, Indels: 1
        0.94            0.03        0.03

Matches are distributed among these distances:
  30    5  0.16
  31   26  0.84

ACGTcount: A:0.32, C:0.46, G:0.08, T:0.14


Consensus pattern (30 bp):   
CACTGCACACCAACCCTTACACACTGCACA

Found at i:25632 original size:19 final size:20

Alignment explanation


    Indices: 25597--25636  Score: 73
    Period size: 19  Copynumber: 2.0  Consensus size: 20

      25587 GAGGCTTGGT

                                
      25597 TCTTTGTTTCGGTTTGGGCC
          1 TCTTTGTTTCGGTTTGGGCC

                                
      25617 TCTTTGTTTC-GTTTGGGCC
          1 TCTTTGTTTCGGTTTGGGCC

             
      25636 T
          1 T

      25637 AGTCTTTAAC


Statistics
Matches: 20,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   10  0.50
  20   10  0.50

ACGTcount: A:0.00, C:0.20, G:0.28, T:0.53


Consensus pattern (20 bp):   
TCTTTGTTTCGGTTTGGGCC

Found at i:26246 original size:12 final size:12

Alignment explanation


    Indices: 26229--26265  Score: 65
    Period size: 12  Copynumber: 3.0  Consensus size: 12

      26219 AGTCATTTCT

                        
      26229 AAAAAAAAAAGA
          1 AAAAAAAAAAGA

                        
      26241 AAAAAAAAAAGA
          1 AAAAAAAAAAGA

                         
      26253 AAAAAAGAAAAGA
          1 AAAAAA-AAAAGA

      26266 GGATATCAAC


Statistics
Matches: 24,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  12   18  0.75
  13    6  0.25

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (12 bp):   
AAAAAAAAAAGA

Found at i:26247 original size:13 final size:13

Alignment explanation


    Indices: 26229--26265  Score: 58
    Period size: 13  Copynumber: 2.9  Consensus size: 13

      26219 AGTCATTTCT

                         
      26229 AAAAAAAAAAG-A
          1 AAAAAAAAAAGAA

                         
      26241 AAAAAAAAAAGAA
          1 AAAAAAAAAAGAA

                 *      
      26254 AAAAAGAAAAGA
          1 AAAAAAAAAAGA

      26266 GGATATCAAC


Statistics
Matches: 23,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  12   11  0.48
  13   12  0.52

ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAAGAA
Done.