Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016924.1 Corchorus olitorius cultivar O-4 contig16957, 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: 40937
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:11597 original size:29 final size:29

Alignment explanation


    Indices: 11542--11598  Score: 89
    Period size: 29  Copynumber: 2.0  Consensus size: 29

      11532 GAGTTTTTGA

                                         
      11542 CCAAACCATTGTGATTTATAAAATAATTT
          1 CCAAACCATTGTGATTTATAAAATAATTT

                             *           
      11571 CCAAACCATTGT-ATTTTTAAAACTAATT
          1 CCAAACCATTGTGATTTATAAAA-TAATT

      11599 CTCATTCCCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  28    9  0.35
  29   17  0.65

ACGTcount: A:0.40, C:0.16, G:0.05, T:0.39


Consensus pattern (29 bp):   
CCAAACCATTGTGATTTATAAAATAATTT

Found at i:17120 original size:2 final size:2

Alignment explanation


    Indices: 17108--17142  Score: 61
    Period size: 2  Copynumber: 17.5  Consensus size: 2

      17098 TTTATAAACT

                  *                                             
      17108 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

      17143 GTAGAATCAT


Statistics
Matches: 31,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   31  1.00

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


Consensus pattern (2 bp):   
TA

Found at i:19972 original size:22 final size:22

Alignment explanation


    Indices: 19947--19993  Score: 60
    Period size: 22  Copynumber: 2.1  Consensus size: 22

      19937 TTTTTACTTG

                            *      
      19947 AGTAAAACT-ATAAAAGTAAAAT
          1 AGTAAAA-TGATAAAAATAAAAT

                     *            
      19969 AGTAAAATGGTAAAAATAAAAT
          1 AGTAAAATGATAAAAATAAAAT

               
      19991 AGT
          1 AGT

      19994 TACAAGGATA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  21    1  0.05
  22   21  0.95

ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23


Consensus pattern (22 bp):   
AGTAAAATGATAAAAATAAAAT

Found at i:20128 original size:31 final size:31

Alignment explanation


    Indices: 20093--20154  Score: 115
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      20083 ATATTCGAAA

                       *                   
      20093 AATAAGGATATGATAGGCGATTCAAAAGTTT
          1 AATAAGGATATAATAGGCGATTCAAAAGTTT

                                           
      20124 AATAAGGATATAATAGGCGATTCAAAAGTTT
          1 AATAAGGATATAATAGGCGATTCAAAAGTTT

      20155 TACAAAACTC


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   30  1.00

ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29


Consensus pattern (31 bp):   
AATAAGGATATAATAGGCGATTCAAAAGTTT

Found at i:22541 original size:26 final size:26

Alignment explanation


    Indices: 22505--22556  Score: 104
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      22495 CAGAATGAAG

                                      
      22505 GAACATGAATGGAAATGTGTGATTGT
          1 GAACATGAATGGAAATGTGTGATTGT

                                      
      22531 GAACATGAATGGAAATGTGTGATTGT
          1 GAACATGAATGGAAATGTGTGATTGT

      22557 CTATGGTGTA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   26  1.00

ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31


Consensus pattern (26 bp):   
GAACATGAATGGAAATGTGTGATTGT
Done.