Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023656.1 Corchorus olitorius cultivar O-4 contig23689, 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: 6797
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34


Found at i:5425 original size:22 final size:21

Alignment explanation


    Indices: 5397--5450  Score: 60
    Period size: 19  Copynumber: 2.6  Consensus size: 21

       5387 AAAGCTGGTG

                                  
       5397 TTTGAAGACTTATTGAAGATAA
          1 TTTGAAGA-TTATTGAAGATAA

                               * 
       5419 TTTGAAGA-T-TTGAAGATCA
          1 TTTGAAGATTATTGAAGATAA

                          
       5438 -TTGAAGAATTATT
          1 TTTGAAG-ATTATT

       5451 TCAAGAAGCA


Statistics
Matches: 28,  Mismatches: 1, Indels: 7
        0.78            0.03        0.19

Matches are distributed among these distances:
  18    6  0.21
  19   10  0.36
  20    2  0.07
  21    2  0.07
  22    8  0.29

ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39


Consensus pattern (21 bp):   
TTTGAAGATTATTGAAGATAA

Found at i:5986 original size:236 final size:235

Alignment explanation


    Indices: 5572--6041  Score: 796
    Period size: 236  Copynumber: 2.0  Consensus size: 235

       5562 GCCCATATAA

                                       *                                 *   
       5572 GCCCACAATTGGAGTTAAAATCCCAAATTGTGCCGCCTATATCAAAAGAAATATCCAATTGTCGC
          1 GCCCACAATTGGAGTTAAAATCCCAAAATGTGCCGCCTATATCAAAAGAAATATCCAATTGCCGC

                           *          *    *       *                        *
       5637 TTTTTCCGCATACTAGTCCTAATAGGTTTAGGATTTAGCGCAGTCTCAGTAAAAAGGTCATAACT
         66 TTTTTCCGCATACTACTCCTAATAGGATTAGAATTTAGCACAGTCTCAGTAAAAAGGTCATAACA

            *        *                           *   *           *           
       5702 CTCTGCTCAGATCTCCGTTTTAGGCCCGTGAGTAGGCGTTGGAAAGCTAATTTTGAGATCTACAA
        131 ATCTGCTCAAATCTCCGTTTTAGGCCCGTGAGTAGGCATTGAAAAGCTAATTTCGAGATCTACAA

                *                                   
       5767 CTTTTGTTCGAAGCCCAAAGCCCAGATCTGCCGTTTTCAG
        196 CTTTCGTTCGAAGCCCAAAGCCCAGATCTGCCGTTTTCAG

                                                       *                     
       5807 GCCCACAATTGGAGTTAAAATCCCAAAATGTGCCGCCTATATCCAAAGAAATATCCAATTGCCGC
          1 GCCCACAATTGGAGTTAAAATCCCAAAATGTGCCGCCTATATCAAAAGAAATATCCAATTGCCGC

                                                                             
       5872 TTATTTCCGCATACTACTCCTAATAGGATTAGAATTTAGCACAGTCTCAGTAAAAAGGTCATAAC
         66 TT-TTTCCGCATACTACTCCTAATAGGATTAGAATTTAGCACAGTCTCAGTAAAAAGGTCATAAC

                                                                             
       5937 AATCTGCTCAAATCTCCGTTTTAGGCCCGTGAGTAGGCATTGAAAAGCTAATTTCGAGATCTACA
        130 AATCTGCTCAAATCTCCGTTTTAGGCCCGTGAGTAGGCATTGAAAAGCTAATTTCGAGATCTACA

                                           *        
       6002 ACTTTCGTTCGAAGCCCAAAGCCCAGATCTGTCGTTTTCA
        195 ACTTTCGTTCGAAGCCCAAAGCCCAGATCTGCCGTTTTCA

       6042 AGCTCGAAAT


Statistics
Matches: 219,  Mismatches: 15, Indels: 1
        0.93            0.06        0.00

Matches are distributed among these distances:
 235   64  0.29
 236  155  0.71

ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29


Consensus pattern (235 bp):   
GCCCACAATTGGAGTTAAAATCCCAAAATGTGCCGCCTATATCAAAAGAAATATCCAATTGCCGC
TTTTTCCGCATACTACTCCTAATAGGATTAGAATTTAGCACAGTCTCAGTAAAAAGGTCATAACA
ATCTGCTCAAATCTCCGTTTTAGGCCCGTGAGTAGGCATTGAAAAGCTAATTTCGAGATCTACAA
CTTTCGTTCGAAGCCCAAAGCCCAGATCTGCCGTTTTCAG
Done.