Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017871.1 Corchorus olitorius cultivar O-4 contig17904, 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: 27807
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:12494 original size:18 final size:18

Alignment explanation


    Indices: 12471--12506  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

      12461 AAAACAAATT

                              
      12471 TTCTTTTATTTTCTTTTG
          1 TTCTTTTATTTTCTTTTG

                   *    *     
      12489 TTCTTTTCTTTTTTTTTG
          1 TTCTTTTATTTTCTTTTG

      12507 ATGAAGTGGA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   16  1.00

ACGTcount: A:0.03, C:0.11, G:0.06, T:0.81


Consensus pattern (18 bp):   
TTCTTTTATTTTCTTTTG

Found at i:12948 original size:3 final size:3

Alignment explanation


    Indices: 12931--12978  Score: 53
    Period size: 3  Copynumber: 15.7  Consensus size: 3

      12921 CACCGCCCTT

                                                       *   *             
      12931 TCC T-C TCC TTCC TCC TCC TCC TCC TCC TCC TCA TCT TCC TCTC TCC
          1 TCC TCC TCC -TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC-C TCC

              
      12977 TC
          1 TC

      12979 GCCTCCGACA


Statistics
Matches: 39,  Mismatches: 3, Indels: 6
        0.81            0.06        0.12

Matches are distributed among these distances:
   2    2  0.05
   3   31  0.79
   4    6  0.15

ACGTcount: A:0.02, C:0.58, G:0.00, T:0.40


Consensus pattern (3 bp):   
TCC

Found at i:22456 original size:21 final size:21

Alignment explanation


    Indices: 22432--22478  Score: 67
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      22422 CTCGTTAAGG

                 *               
      22432 AAGGGTTCGAGACGGCGGAGA
          1 AAGGGCTCGAGACGGCGGAGA

                   *        *    
      22453 AAGGGCTGGAGACGGCTGAGA
          1 AAGGGCTCGAGACGGCGGAGA

                 
      22474 AAGGG
          1 AAGGG

      22479 ATCATTACAG


Statistics
Matches: 23,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   23  1.00

ACGTcount: A:0.30, C:0.13, G:0.49, T:0.09


Consensus pattern (21 bp):   
AAGGGCTCGAGACGGCGGAGA
Done.