Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019786.1 Corchorus olitorius cultivar O-4 contig19819, 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: 28534
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:3057 original size:24 final size:26

Alignment explanation


    Indices: 3012--3060  Score: 84
    Period size: 24  Copynumber: 2.0  Consensus size: 26

       3002 GGTCCTGAGG

                                      
       3012 AAAACAAGTTAATATACTCTTTTGGA
          1 AAAACAAGTTAATATACTCTTTTGGA

                                     
       3038 AAAACAAGTT-A-ATACTCTTTTGG
          1 AAAACAAGTTAATATACTCTTTTGG

       3061 TGGTTTAAGC


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
  24   12  0.52
  25    1  0.04
  26   10  0.43

ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35


Consensus pattern (26 bp):   
AAAACAAGTTAATATACTCTTTTGGA

Found at i:15206 original size:2 final size:2

Alignment explanation


    Indices: 15199--15237  Score: 78
    Period size: 2  Copynumber: 19.5  Consensus size: 2

      15189 GCAATCTCAA

                                                                      
      15199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A

      15238 AGATGCTAAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   37  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:21271 original size:13 final size:13

Alignment explanation


    Indices: 21253--21277  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

      21243 TTCAATGTTC

                         
      21253 TAAATATTATTTA
          1 TAAATATTATTTA

                        
      21266 TAAATATTATTT
          1 TAAATATTATTT

      21278 GGAATTCCAA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (13 bp):   
TAAATATTATTTA
Done.