Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012633.1 Corchorus olitorius cultivar O-4 contig12666, 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: 16873
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28


Found at i:386 original size:29 final size:29

Alignment explanation


    Indices: 354--431  Score: 102
    Period size: 29  Copynumber: 2.7  Consensus size: 29

        344 CAGTGAACTT

                                         
        354 AAAATGACCAAAATGCCCCTGAATGTGCA
          1 AAAATGACCAAAATGCCCCTGAATGTGCA

                          *      ** * ** 
        383 AAAATGACCAAAATACCCCTGGGTTTTTA
          1 AAAATGACCAAAATGCCCCTGAATGTGCA

                                
        412 AAAATGACCAAAATGCCCCT
          1 AAAATGACCAAAATGCCCCT

        432 AGGTGATCCT


Statistics
Matches: 42,  Mismatches: 7, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  29   42  1.00

ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21


Consensus pattern (29 bp):   
AAAATGACCAAAATGCCCCTGAATGTGCA

Found at i:1978 original size:41 final size:40

Alignment explanation


    Indices: 1902--1993  Score: 139
    Period size: 41  Copynumber: 2.3  Consensus size: 40

       1892 TTTTTCAAAG

                        *                        *  
       1902 TGGGAAAGATCCGAACAAGTTTTTTCAAAGTTTTCAATTT
          1 TGGGAAAGATCCCAACAAGTTTTTTCAAAGTTTTCAACTT

                          *                          
       1942 TGGGAAAGATCCCATCAAGTTTTTTTCAAAGTTTTCAACTT
          1 TGGGAAAGATCCCAACAAG-TTTTTTCAAAGTTTTCAACTT

            *          
       1983 AGGGAAAGATC
          1 TGGGAAAGATC

       1994 TCGTCAGCTT


Statistics
Matches: 47,  Mismatches: 4, Indels: 1
        0.90            0.08        0.02

Matches are distributed among these distances:
  40   17  0.36
  41   30  0.64

ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35


Consensus pattern (40 bp):   
TGGGAAAGATCCCAACAAGTTTTTTCAAAGTTTTCAACTT
Done.