Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005641.1 Corchorus olitorius cultivar O-4 contig05665, 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, 747

Length: 1246
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:521 original size:50 final size:49

Alignment explanation


    Indices: 467--565  Score: 189
    Period size: 50  Copynumber: 2.0  Consensus size: 49

        457 GGAATAGGTT

                                                              
        467 TACATAGTTATGGTTCATTTACATTAACATCTAATTGAATTTGAATAAAA
          1 TACATAGTTATGGTTCATTTACATTAACATCTAATTGAA-TTGAATAAAA

                                                             
        517 TACATAGTTATGGTTCATTTACATTAACATCTAATTGAATTGAATAAAA
          1 TACATAGTTATGGTTCATTTACATTAACATCTAATTGAATTGAATAAAA

        566 AAATGGCTAA


Statistics
Matches: 49,  Mismatches: 0, Indels: 1
        0.98            0.00        0.02

Matches are distributed among these distances:
  49   10  0.20
  50   39  0.80

ACGTcount: A:0.40, C:0.10, G:0.10, T:0.39


Consensus pattern (49 bp):   
TACATAGTTATGGTTCATTTACATTAACATCTAATTGAATTGAATAAAA

Found at i:635 original size:22 final size:22

Alignment explanation


    Indices: 607--650  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

        597 GACAGCATAT

                                  
        607 ATATAAGAAAACTTATTGTAAG
          1 ATATAAGAAAACTTATTGTAAG

                                  
        629 ATATAAGAAAACTTATTGTAAG
          1 ATATAAGAAAACTTATTGTAAG

        651 CTGTCAAGAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.50, C:0.05, G:0.14, T:0.32


Consensus pattern (22 bp):   
ATATAAGAAAACTTATTGTAAG

Found at i:798 original size:12 final size:12

Alignment explanation


    Indices: 781--809  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

        771 GGACTTCTTT

                        
        781 CTTTTTTTTTCA
          1 CTTTTTTTTTCA

                        
        793 CTTTTTTTTTCA
          1 CTTTTTTTTTCA

                  
        805 -TTTTT
          1 CTTTTT

        810 CAATTGTACA


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

Matches are distributed among these distances:
  11    5  0.29
  12   12  0.71

ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79


Consensus pattern (12 bp):   
CTTTTTTTTTCA
Done.