Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013570.1 Corchorus olitorius cultivar O-4 contig13603, 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: 24895
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:548 original size:2 final size:2

Alignment explanation


    Indices: 541--578  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

        531 TGAAGACTAG

                                                                    
        541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

        579 CAGCTTGCAC


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:10620 original size:22 final size:19

Alignment explanation


    Indices: 10605--10640  Score: 65
    Period size: 19  Copynumber: 1.9  Consensus size: 19

      10595 TGAAGATTCA

                               
      10605 TTGAAGATAATTTGAAGAT
          1 TTGAAGATAATTTGAAGAT

                              
      10624 TTGAAGATAA-TTGAAGA
          1 TTGAAGATAATTTGAAGA

      10641 ATTATTTCAA


Statistics
Matches: 17,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  18    7  0.41
  19   10  0.59

ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33


Consensus pattern (19 bp):   
TTGAAGATAATTTGAAGAT

Found at i:21761 original size:9 final size:9

Alignment explanation


    Indices: 21747--21772  Score: 52
    Period size: 9  Copynumber: 2.9  Consensus size: 9

      21737 AATAAACACT

                     
      21747 AAAACAAAC
          1 AAAACAAAC

                     
      21756 AAAACAAAC
          1 AAAACAAAC

                    
      21765 AAAACAAA
          1 AAAACAAA

      21773 GCAACTGTTT


Statistics
Matches: 17,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   17  1.00

ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00


Consensus pattern (9 bp):   
AAAACAAAC
Done.