Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011365.1 Corchorus olitorius cultivar O-4 contig11398, 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: 19772
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33


Found at i:673 original size:16 final size:16

Alignment explanation


    Indices: 652--683  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

        642 TTGAGGATTT

                            
        652 GTTGAAGAAAATGAAG
          1 GTTGAAGAAAATGAAG

                            
        668 GTTGAAGAAAATGAAG
          1 GTTGAAGAAAATGAAG

        684 TGAAGATTAA


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

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19


Consensus pattern (16 bp):   
GTTGAAGAAAATGAAG

Found at i:5259 original size:23 final size:23

Alignment explanation


    Indices: 5233--5289  Score: 114
    Period size: 23  Copynumber: 2.5  Consensus size: 23

       5223 TTATATGGGT

                                   
       5233 GCCCACCCCAAATAATTATGAGC
          1 GCCCACCCCAAATAATTATGAGC

                                   
       5256 GCCCACCCCAAATAATTATGAGC
          1 GCCCACCCCAAATAATTATGAGC

                       
       5279 GCCCACCCCAA
          1 GCCCACCCCAA

       5290 TTAGATTAAA


Statistics
Matches: 34,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   34  1.00

ACGTcount: A:0.33, C:0.40, G:0.12, T:0.14


Consensus pattern (23 bp):   
GCCCACCCCAAATAATTATGAGC

Found at i:17508 original size:15 final size:16

Alignment explanation


    Indices: 17484--17523  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

      17474 AGAGGTTGAA

                 *          
      17484 AGAAAGCAATTA-AAT
          1 AGAAAACAATTATAAT

                          * 
      17499 AGAAAACAATTATACT
          1 AGAAAACAATTATAAT

                     
      17515 AGAAAACAA
          1 AGAAAACAA

      17524 AGCAAAGTAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 1
        0.88            0.08        0.04

Matches are distributed among these distances:
  15   11  0.50
  16   11  0.50

ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17


Consensus pattern (16 bp):   
AGAAAACAATTATAAT

Found at i:18496 original size:13 final size:14

Alignment explanation


    Indices: 18471--18499  Score: 51
    Period size: 13  Copynumber: 2.1  Consensus size: 14

      18461 CTAGAGTAAA

                          
      18471 ATCCAAGTTAAAAT
          1 ATCCAAGTTAAAAT

                          
      18485 ATCCAA-TTAAAAT
          1 ATCCAAGTTAAAAT

              
      18498 AT
          1 AT

      18500 TTCCTTTGAT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  13    9  0.60
  14    6  0.40

ACGTcount: A:0.52, C:0.14, G:0.03, T:0.31


Consensus pattern (14 bp):   
ATCCAAGTTAAAAT
Done.