Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012663.1 Corchorus olitorius cultivar O-4 contig12696, 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: 21420
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:12934 original size:13 final size:14

Alignment explanation


    Indices: 12915--12960  Score: 56
    Period size: 16  Copynumber: 3.0  Consensus size: 14

      12905 ACAAGCAACA

                          
      12915 AAAAAGAGAAAAAG
          1 AAAAAGAGAAAAAG

                            
      12929 AAAAGAGGAGAAAAAG
          1 AAAA-A-GAGAAAAAG

                            
      12945 AAAAGAGAAGAAAAAG
          1 AAAA-AG-AGAAAAAG

      12961 GAGGAGTACC


Statistics
Matches: 29,  Mismatches: 0, Indels: 4
        0.88            0.00        0.12

Matches are distributed among these distances:
  14    4  0.14
  15    2  0.07
  16   23  0.79

ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00


Consensus pattern (14 bp):   
AAAAAGAGAAAAAG

Found at i:12941 original size:16 final size:16

Alignment explanation


    Indices: 12920--12960  Score: 73
    Period size: 16  Copynumber: 2.6  Consensus size: 16

      12910 CAACAAAAAA

                            
      12920 GAGAAAAAGAAAAGAG
          1 GAGAAAAAGAAAAGAG

                            
      12936 GAGAAAAAGAAAAGAG
          1 GAGAAAAAGAAAAGAG

            *        
      12952 AAGAAAAAG
          1 GAGAAAAAG

      12961 GAGGAGTACC


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   24  1.00

ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00


Consensus pattern (16 bp):   
GAGAAAAAGAAAAGAG

Found at i:13598 original size:18 final size:18

Alignment explanation


    Indices: 13572--13606  Score: 52
    Period size: 18  Copynumber: 1.9  Consensus size: 18

      13562 GGAGAGAGAA

                *             
      13572 AAAGCAAAAAAAAAAAGG
          1 AAAGAAAAAAAAAAAAGG

                     *       
      13590 AAAGAAAAACAAAAAAG
          1 AAAGAAAAAAAAAAAAG

      13607 ACACAGACAA


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  18   15  1.00

ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00


Consensus pattern (18 bp):   
AAAGAAAAAAAAAAAAGG

Found at i:16036 original size:26 final size:26

Alignment explanation


    Indices: 15985--16037  Score: 72
    Period size: 26  Copynumber: 2.0  Consensus size: 26

      15975 CTTACTATAC

                           *  *       
      15985 TATATATATTATATATAATATAGAAA
          1 TATATATATTATATAAAAAATAGAAA

                                       
      16011 TATATATATTATATAAAGAAAT-GAAA
          1 TATATATATTATATAAA-AAATAGAAA

             
      16037 T
          1 T

      16038 TAAACCATTT


Statistics
Matches: 24,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  26   21  0.88
  27    3  0.12

ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40


Consensus pattern (26 bp):   
TATATATATTATATAAAAAATAGAAA
Done.