Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024305.1 Corchorus olitorius cultivar O-4 contig24338, 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: 12296
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27


Found at i:3400 original size:35 final size:35

Alignment explanation


    Indices: 3361--3438  Score: 104
    Period size: 34  Copynumber: 2.3  Consensus size: 35

       3351 GAGAATATCA

                      * *  *                   
       3361 TTAAGTTTTTTTTATTGGAAAAGTTCCCACCAGTT
          1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

                              *            *   
       3396 TTAAG-TTTTGTAATCGGGAAAGTTCCCACCGGTT
          1 TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

                     
       3430 TTAAGTTTT
          1 TTAAGTTTT

       3439 CAAATTGGGA


Statistics
Matches: 37,  Mismatches: 5, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  34   29  0.78
  35    8  0.22

ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44


Consensus pattern (35 bp):   
TTAAGTTTTTGTAATCGGAAAAGTTCCCACCAGTT

Found at i:3423 original size:34 final size:34

Alignment explanation


    Indices: 3380--3457  Score: 120
    Period size: 34  Copynumber: 2.3  Consensus size: 34

       3370 TTTTATTGGA

                                     **       
       3380 AAAGTTCCCACCAGTTTTAAGTTTTGTAATCGGG
          1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

                        *                 *   
       3414 AAAGTTCCCACCGGTTTTAAGTTTTCAAATTGGG
          1 AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

                      
       3448 AAAGTTCCCA
          1 AAAGTTCCCA

       3458 TTCAATTTTT


Statistics
Matches: 40,  Mismatches: 4, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  34   40  1.00

ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33


Consensus pattern (34 bp):   
AAAGTTCCCACCAGTTTTAAGTTTTCAAATCGGG

Found at i:6173 original size:31 final size:31

Alignment explanation


    Indices: 6108--6186  Score: 110
    Period size: 31  Copynumber: 2.6  Consensus size: 31

       6098 AGACCTGAAA

                               *           
       6108 TAGGACCAAATTGAGCA--GGTCTAAAGATT
          1 TAGGACCAAATTGAGCATTCGTCTAAAGATT

                                         *  
       6137 TAGGACCAAATTGAGCATTCCGTC-AAAGGTT
          1 TAGGACCAAATTGAGCATT-CGTCTAAAGATT

                               
       6168 TAGGACCAAATTGAGCATT
          1 TAGGACCAAATTGAGCATT

       6187 TAGCCGAGTG


Statistics
Matches: 45,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  29   17  0.38
  31   25  0.56
  32    3  0.07

ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25


Consensus pattern (31 bp):   
TAGGACCAAATTGAGCATTCGTCTAAAGATT
Done.