Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017189.1 Corchorus olitorius cultivar O-4 contig17222, 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: 7792
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:256 original size:21 final size:21

Alignment explanation


    Indices: 217--265  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

        207 TCAATGCTTT

                         **       
        217 AGGAATGCAAGAGGGATTTCAA
          1 AGGAA-GCAAGAGCCATTTCAA

                               * 
        239 AGGAAGCAAGAGCCATTTCCA
          1 AGGAAGCAAGAGCCATTTCAA

                   
        260 A-GAAGC
          1 AGGAAGC

        266 TACAATTCTT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    5  0.21
  21   14  0.58
  22    5  0.21

ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14


Consensus pattern (21 bp):   
AGGAAGCAAGAGCCATTTCAA

Found at i:4286 original size:17 final size:19

Alignment explanation


    Indices: 4264--4298  Score: 56
    Period size: 19  Copynumber: 1.9  Consensus size: 19

       4254 ATTGCATGCA

                               
       4264 TTTTT-ATTT-TATTTGTG
          1 TTTTTAATTTGTATTTGTG

                              
       4281 TTTTTAATTTGTATTTGT
          1 TTTTTAATTTGTATTTGT

       4299 CTTATGTTTA


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

Matches are distributed among these distances:
  17    5  0.31
  18    4  0.25
  19    7  0.44

ACGTcount: A:0.14, C:0.00, G:0.11, T:0.74


Consensus pattern (19 bp):   
TTTTTAATTTGTATTTGTG

Found at i:5198 original size:26 final size:26

Alignment explanation


    Indices: 5164--5213  Score: 73
    Period size: 26  Copynumber: 1.9  Consensus size: 26

       5154 TGTCCCTCTG

                         *            
       5164 AAAAAAAAAAGAGTGTTAGTAACCTC
          1 AAAAAAAAAAGAGAGTTAGTAACCTC

                *      *            
       5190 AAAAGAAAAAGGGAGTTAGTAACC
          1 AAAAAAAAAAGAGAGTTAGTAACC

       5214 CCTAAATCAT


Statistics
Matches: 21,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  26   21  1.00

ACGTcount: A:0.54, C:0.10, G:0.20, T:0.16


Consensus pattern (26 bp):   
AAAAAAAAAAGAGAGTTAGTAACCTC
Done.