Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001601.1 Corchorus olitorius cultivar O-4 contig01601, 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, 727

Length: 1212
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26


Found at i:128 original size:5 final size:6

Alignment explanation


    Indices: 104--135  Score: 55
    Period size: 6  Copynumber: 5.3  Consensus size: 6

         94 TCTTTGCACA

                                     *           
        104 TTTAAT TTTAAT TTTAAT TTTATT TTTAAT TT
          1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT

        136 ATACACTAAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   6   24  1.00

ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72


Consensus pattern (6 bp):   
TTTAAT

Found at i:455 original size:27 final size:27

Alignment explanation


    Indices: 425--549  Score: 229
    Period size: 27  Copynumber: 4.7  Consensus size: 27

        415 CGCTGATGCT

                                       
        425 GCGACATGCTGCTGCTGCGTTAAAGCA
          1 GCGACATGCTGCTGCTGCGTTAAAGCA

                                       
        452 GCGACATGCTGCTGCTGCGTTAAAGCA
          1 GCGACATGCTGCTGCTGCGTTAAAGCA

                                       
        479 GCGACA---TGCTGCTGCGTTAAAGCA
          1 GCGACATGCTGCTGCTGCGTTAAAGCA

                                       
        503 GCGACATGCTGCTGCTGCGTTAAAGCA
          1 GCGACATGCTGCTGCTGCGTTAAAGCA

                                
        530 GCGACATGCTGCTGCTGCGT
          1 GCGACATGCTGCTGCTGCGT

        550 AGGCAGCGCT


Statistics
Matches: 95,  Mismatches: 0, Indels: 6
        0.94            0.00        0.06

Matches are distributed among these distances:
  24   24  0.25
  27   71  0.75

ACGTcount: A:0.21, C:0.26, G:0.30, T:0.22


Consensus pattern (27 bp):   
GCGACATGCTGCTGCTGCGTTAAAGCA

Found at i:504 original size:51 final size:51

Alignment explanation


    Indices: 434--544  Score: 222
    Period size: 51  Copynumber: 2.2  Consensus size: 51

        424 TGCGACATGC

                                                               
        434 TGCTGCTGCGTTAAAGCAGCGACATGCTGCTGCTGCGTTAAAGCAGCGACA
          1 TGCTGCTGCGTTAAAGCAGCGACATGCTGCTGCTGCGTTAAAGCAGCGACA

                                                               
        485 TGCTGCTGCGTTAAAGCAGCGACATGCTGCTGCTGCGTTAAAGCAGCGACA
          1 TGCTGCTGCGTTAAAGCAGCGACATGCTGCTGCTGCGTTAAAGCAGCGACA

                     
        536 TGCTGCTGC
          1 TGCTGCTGC

        545 TGCGTAGGCA


Statistics
Matches: 60,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  51   60  1.00

ACGTcount: A:0.22, C:0.26, G:0.30, T:0.23


Consensus pattern (51 bp):   
TGCTGCTGCGTTAAAGCAGCGACATGCTGCTGCTGCGTTAAAGCAGCGACA
Done.