Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011198.1 Corchorus olitorius cultivar O-4 contig11231, 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: 11193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33


Found at i:443 original size:29 final size:29

Alignment explanation


    Indices: 401--456  Score: 78
    Period size: 29  Copynumber: 1.9  Consensus size: 29

        391 TGTCCCTCTG

                            *            
        401 AAAAAAAACAAAAGAGTGTTAGTAACCTC
          1 AAAAAAAACAAAAGAGAGTTAGTAACCTC

                           *            
        430 AAAAGAAAA-AAAAGGGAGTTAGTAACC
          1 AAAA-AAAACAAAAGAGAGTTAGTAACC

        457 CCTAAATCAT


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

Matches are distributed among these distances:
  29   20  0.83
  30    4  0.17

ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14


Consensus pattern (29 bp):   
AAAAAAAACAAAAGAGAGTTAGTAACCTC

Found at i:6629 original size:51 final size:51

Alignment explanation


    Indices: 6527--6629  Score: 129
    Period size: 51  Copynumber: 2.0  Consensus size: 51

       6517 CATTCTTCAA

                 *                                    * **     
       6527 TATTTTCTTGTTTCAATCTTGTCTCCAGACAAAAGAACACTCTTTTAGTGT
          1 TATTTCCTTGTTTCAATCTTGTCTCCAGACAAAAGAACACTCGTACAGTGT

                                      *                          
       6578 TATTTCCTTGTTTCAATCTTGTCTCCGGACATAAA-AACACT-GTACACGTGT
          1 TATTTCCTTGTTTCAATCTTGTCTCCAGACA-AAAGAACACTCGTACA-GTGT

             
       6629 T
          1 T

       6630 TCTCTCTCAG


Statistics
Matches: 45,  Mismatches: 5, Indels: 4
        0.83            0.09        0.07

Matches are distributed among these distances:
  50    2  0.04
  51   40  0.89
  52    3  0.07

ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41


Consensus pattern (51 bp):   
TATTTCCTTGTTTCAATCTTGTCTCCAGACAAAAGAACACTCGTACAGTGT

Found at i:10093 original size:89 final size:83

Alignment explanation


    Indices: 9997--10162  Score: 208
    Period size: 85  Copynumber: 1.9  Consensus size: 83

       9987 AAATTATAAT

                                                           *                 
       9997 ATATATCTAAGTTATATAATTAA-AATATATAAGTAAAAATGGTAAATATAAAATAGTTATAAAA
          1 ATATATCTAAGTT-T-TAATTAATAA-A-AT-AGT-AAAATGGTAAACATAAAATAGTTATAAAA

                                     
      10061 AGATTAGATTTAATTAAAAATTCTA
         60 A-ATTAGATTTAATTAAAAATTCTA

                           **                          *               *     
      10086 ATATATCTAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAACGTAAAATAGTTATAAAGAATTA
          1 ATATATCTAAGTTTTAATTAA-TAAAATAGTAAAATGGTAAACATAAAATAGTTATAAAAAATTA

                        
      10151 GATTTAATTAAA
         65 GATTTAATTAAA

      10163 TAAAAATAGA


Statistics
Matches: 70,  Mismatches: 5, Indels: 9
        0.83            0.06        0.11

Matches are distributed among these distances:
  84   16  0.23
  85   27  0.39
  86    3  0.04
  87    7  0.10
  88    2  0.03
  89   15  0.21

ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37


Consensus pattern (83 bp):   
ATATATCTAAGTTTTAATTAATAAAATAGTAAAATGGTAAACATAAAATAGTTATAAAAAATTAG
ATTTAATTAAAAATTCTA
Done.