Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01012577.1 Corchorus olitorius cultivar O-4 contig12610, 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: 7198
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33


Found at i:5480 original size:12 final size:13

Alignment explanation


    Indices: 5450--5482  Score: 50
    Period size: 12  Copynumber: 2.6  Consensus size: 13

       5440 GAAGTTCGTG

                        *
       5450 TTTGAAGACTTTT
          1 TTTGAAGACTTTA

                         
       5463 TTTGAAGA-TTTA
          1 TTTGAAGACTTTA

                    
       5475 TTTGAAGA
          1 TTTGAAGA

       5483 ATTGAAGATC


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  12   11  0.58
  13    8  0.42

ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48


Consensus pattern (13 bp):   
TTTGAAGACTTTA

Found at i:6254 original size:23 final size:24

Alignment explanation


    Indices: 6195--6268  Score: 77
    Period size: 23  Copynumber: 3.2  Consensus size: 24

       6185 ATGGTGAAAT

                      *              
       6195 TTATATCATGATGAGATTTTGTGA-
          1 TTATATCATGGTGAGATTTTGT-AC

                   *                
       6219 TT-T-T-GTGGTGAGATTTTG-AC
          1 TTATATCATGGTGAGATTTTGTAC

                                  * 
       6239 TTATATCATGGTGAGATTTTGTGC
          1 TTATATCATGGTGAGATTTTGTAC

                  
       6263 TTATAT
          1 TTATAT

       6269 ATGAAAATTG


Statistics
Matches: 41,  Mismatches: 4, Indels: 10
        0.75            0.07        0.18

Matches are distributed among these distances:
  19    1  0.02
  20    2  0.05
  21   13  0.32
  22    2  0.05
  23   14  0.34
  24    9  0.22

ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49


Consensus pattern (24 bp):   
TTATATCATGGTGAGATTTTGTAC
Done.