Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017285.1 Corchorus olitorius cultivar O-4 contig17318, 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: 5939
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30


Found at i:3674 original size:30 final size:28

Alignment explanation


    Indices: 3614--3674  Score: 79
    Period size: 30  Copynumber: 2.1  Consensus size: 28

       3604 GTGTGTGCTG

                                    *   
       3614 GAGAGAGTGAGGGTAGAGAAAAAGGAGA
          1 GAGAGAGTGAGGGTAGAGAAAAAGAAGA

                                           
       3642 GAGAGAAGATGAGGGTAGAGAAAAA-AATGA
          1 GAGAG-AG-TGAGGGTAGAGAAAAAGAA-GA

               
       3672 GAG
          1 GAG

       3675 GTTTTTGACA


Statistics
Matches: 29,  Mismatches: 1, Indels: 4
        0.85            0.03        0.12

Matches are distributed among these distances:
  28    5  0.17
  29    3  0.10
  30   21  0.72

ACGTcount: A:0.49, C:0.00, G:0.43, T:0.08


Consensus pattern (28 bp):   
GAGAGAGTGAGGGTAGAGAAAAAGAAGA

Found at i:5486 original size:21 final size:22

Alignment explanation


    Indices: 5456--5496  Score: 59
    Period size: 21  Copynumber: 1.9  Consensus size: 22

       5446 GCATAATTTC

                                   
       5456 TAAAATCAGGGA-CTAAATTGAA
          1 TAAAATCAGGGATC-AAATTGAA

                                
       5478 TAAAA-CAGGGATCAAATTG
          1 TAAAATCAGGGATCAAATTG

       5497 CATTTAAACA


Statistics
Matches: 18,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  21   12  0.67
  22    6  0.33

ACGTcount: A:0.49, C:0.10, G:0.20, T:0.22


Consensus pattern (22 bp):   
TAAAATCAGGGATCAAATTGAA
Done.