Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016857.1 Corchorus olitorius cultivar O-4 contig16890, 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: 5678
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32


Found at i:2502 original size:22 final size:22

Alignment explanation


    Indices: 2425--2505  Score: 94
    Period size: 22  Copynumber: 3.7  Consensus size: 22

       2415 GAAAGAGAGA

                      *           
       2425 TTATCAAAA-ATCATAGGAAGG
          1 TTATCAAAATTTCATAGGAAGG

                                  
       2446 TTA-CAAAATTTCATAGGAAGG
          1 TTATCAAAATTTCATAGGAAGG

                 *            **   
       2467 TTTATTAAAATTTCATAGTTAGG
          1 -TTATCAAAATTTCATAGGAAGG

                    *       
       2490 TTATCAAAGTTTCATA
          1 TTATCAAAATTTCATA

       2506 TTTCATAGGT


Statistics
Matches: 51,  Mismatches: 6, Indels: 5
        0.82            0.10        0.08

Matches are distributed among these distances:
  20    5  0.10
  21   14  0.27
  22   17  0.33
  23   15  0.29

ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36


Consensus pattern (22 bp):   
TTATCAAAATTTCATAGGAAGG

Found at i:2534 original size:29 final size:29

Alignment explanation


    Indices: 2476--2534  Score: 73
    Period size: 29  Copynumber: 2.0  Consensus size: 29

       2466 GTTTATTAAA

                     *  **        *  *   
       2476 ATTTCATAGTTAGGTTATCAAAGTTTCAT
          1 ATTTCATAGGTAAATTATCAAAATTCCAT

                                         
       2505 ATTTCATAGGTAAATTATCAAAATTCCAT
          1 ATTTCATAGGTAAATTATCAAAATTCCAT

             
       2534 A
          1 A

       2535 ACGTGGTTAT


Statistics
Matches: 25,  Mismatches: 5, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  29   25  1.00

ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41


Consensus pattern (29 bp):   
ATTTCATAGGTAAATTATCAAAATTCCAT

Found at i:2544 original size:22 final size:22

Alignment explanation


    Indices: 2519--2579  Score: 79
    Period size: 22  Copynumber: 2.8  Consensus size: 22

       2509 CATAGGTAAA

                       *         * 
       2519 TTATCAAAATTCCATAACG-TGG
          1 TTATCAAAATTTCATAA-GATAG

                        *         
       2541 TTATCAAAATTTAATAAGATAG
          1 TTATCAAAATTTCATAAGATAG

                             
       2563 TTATCAAAATTTCATAA
          1 TTATCAAAATTTCATAA

       2580 AATATTCAAT


Statistics
Matches: 34,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  21    1  0.03
  22   33  0.97

ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36


Consensus pattern (22 bp):   
TTATCAAAATTTCATAAGATAG

Found at i:3766 original size:26 final size:26

Alignment explanation


    Indices: 3737--3787  Score: 86
    Period size: 26  Copynumber: 2.0  Consensus size: 26

       3727 ATTATTAAAA

                                       
       3737 TATTTTATTTAGAAAAA-ATCAATTTT
          1 TATTTTATTTAGAAAAATA-CAATTTT

                                     
       3763 TATTTTATTTAGAAAAATACAATTT
          1 TATTTTATTTAGAAAAATACAATTT

       3788 CTACAATACC


Statistics
Matches: 24,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  26   23  0.96
  27    1  0.04

ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49


Consensus pattern (26 bp):   
TATTTTATTTAGAAAAATACAATTTT
Done.