Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013633.1 Corchorus olitorius cultivar O-4 contig13666, 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: 10883
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31


Found at i:3575 original size:17 final size:16

Alignment explanation


    Indices: 3537--3575  Score: 53
    Period size: 17  Copynumber: 2.4  Consensus size: 16

       3527 CCCTTTCCTA

                            
       3537 TTTTTTTTTCTCCTTT
          1 TTTTTTTTTCTCCTTT

                              
       3553 TCTTTTCTTTT-TCCTTT
          1 T-TTTT-TTTTCTCCTTT

                  
       3570 TTTTTT
          1 TTTTTT

       3576 GGCTGTTTGG


Statistics
Matches: 21,  Mismatches: 0, Indels: 5
        0.81            0.00        0.19

Matches are distributed among these distances:
  15    1  0.05
  16    5  0.24
  17   11  0.52
  18    4  0.19

ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82


Consensus pattern (16 bp):   
TTTTTTTTTCTCCTTT

Found at i:5568 original size:83 final size:84

Alignment explanation


    Indices: 5429--5596  Score: 266
    Period size: 83  Copynumber: 2.0  Consensus size: 84

       5419 ATTTGTTAAA

                         *              **                                   
       5429 ACTTGAAAATAAATAAGGTATAATAATAGGGACACGTGGCATAATTTGGTGAAT-GGGCATGGAG
          1 ACTTGAAAATAAACAAGGTATAATAATACAGACACGTGGCATAATTTGGTGAATGGGGCATGGAG

                               
       5493 TGGGACACAAAAATGGGGT
         66 TGGGACACAAAAATGGGGT

                   *                          *   *                          
       5512 ACTTGAAGATAAACAAGGTATAATAATACAGACATGTGTCATAATTTGGTGAATGGGGCATGGAG
          1 ACTTGAAAATAAACAAGGTATAATAATACAGACACGTGGCATAATTTGGTGAATGGGGCATGGAG

                 *             
       5577 TGGGATACAAAAATGGGGT
         66 TGGGACACAAAAATGGGGT

             
       5596 A
          1 A

       5597 GGTGATTTCC


Statistics
Matches: 77,  Mismatches: 7, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  83   48  0.62
  84   29  0.38

ACGTcount: A:0.39, C:0.08, G:0.29, T:0.24


Consensus pattern (84 bp):   
ACTTGAAAATAAACAAGGTATAATAATACAGACACGTGGCATAATTTGGTGAATGGGGCATGGAG
TGGGACACAAAAATGGGGT
Done.