Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016936.1 Corchorus olitorius cultivar O-4 contig16969, 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: 2076
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:1073 original size:16 final size:17

Alignment explanation


    Indices: 1047--1078  Score: 57
    Period size: 16  Copynumber: 1.9  Consensus size: 17

       1037 AGTGCAAATT

                             
       1047 AAAATAGAAAAATAAAG
          1 AAAATAGAAAAATAAAG

                            
       1064 AAAA-AGAAAAATAAA
          1 AAAATAGAAAAATAAA

       1079 ACGCAATTTC


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16   11  0.73
  17    4  0.27

ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09


Consensus pattern (17 bp):   
AAAATAGAAAAATAAAG

Found at i:1371 original size:19 final size:18

Alignment explanation


    Indices: 1316--1371  Score: 55
    Period size: 19  Copynumber: 3.1  Consensus size: 18

       1306 CAATCAAGAA

                               
       1316 AATTAAAGAAAACAAT--T
          1 AATT-AAGAAAACAATGAT

                         *     
       1333 AA-TAAGAAAACAGTGAAT
          1 AATTAAGAAAACAATG-AT

                               
       1351 AATTAAGAAAACAATTGAT
          1 AATTAAGAAAACAA-TGAT

              
       1370 AA
          1 AA

       1372 AAACCTCCAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 8
        0.76            0.05        0.19

Matches are distributed among these distances:
  15   10  0.31
  16    1  0.03
  17    2  0.06
  18    3  0.09
  19   14  0.44
  20    2  0.06

ACGTcount: A:0.62, C:0.05, G:0.11, T:0.21


Consensus pattern (18 bp):   
AATTAAGAAAACAATGAT
Done.