Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024453.1 Corchorus olitorius cultivar O-4 contig24486, 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: 42395
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:9324 original size:16 final size:16

Alignment explanation


    Indices: 9303--9334  Score: 64
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       9293 AAATTATCCT

                            
       9303 TTAATATATATTTGGG
          1 TTAATATATATTTGGG

                            
       9319 TTAATATATATTTGGG
          1 TTAATATATATTTGGG

       9335 AAAAAAACAT


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


Consensus pattern (16 bp):   
TTAATATATATTTGGG

Found at i:14377 original size:24 final size:22

Alignment explanation


    Indices: 14341--14385  Score: 63
    Period size: 24  Copynumber: 2.0  Consensus size: 22

      14331 AAAATCAGCC

                                  
      14341 CAAAATATTTTTTTAAGAAAAA
          1 CAAAATATTTTTTTAAGAAAAA

                             *     
      14363 CAAAATATATATTTTTATGAAAA
          1 CAAAATAT-T-TTTTTAAGAAAA

      14386 TCATTTTTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    8  0.40
  23    1  0.05
  24   11  0.55

ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38


Consensus pattern (22 bp):   
CAAAATATTTTTTTAAGAAAAA

Found at i:19624 original size:2 final size:2

Alignment explanation


    Indices: 19612--19644  Score: 57
    Period size: 2  Copynumber: 16.5  Consensus size: 2

      19602 AAAGTTAACT

                  *                                          
      19612 TA TA AA 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 T

      19645 TCATAAGAAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
TA

Found at i:21705 original size:13 final size:13

Alignment explanation


    Indices: 21687--21712  Score: 52
    Period size: 13  Copynumber: 2.0  Consensus size: 13

      21677 TCAAAAGTAA

                         
      21687 AATTTATTACTTT
          1 AATTTATTACTTT

                         
      21700 AATTTATTACTTT
          1 AATTTATTACTTT

      21713 TTAGGGTGAG


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   13  1.00

ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62


Consensus pattern (13 bp):   
AATTTATTACTTT
Done.