Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020000.1 Corchorus olitorius cultivar O-4 contig20033, 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: 9163
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:2132 original size:73 final size:73

Alignment explanation


    Indices: 2007--2156  Score: 237
    Period size: 73  Copynumber: 2.1  Consensus size: 73

       1997 TATGTCACGT

                                                                             
       2007 GGGGAACCTATAACGACGTTCATTATTAATAAACACCGTTATAAAACATTTTCAGTGGATTTTCA
          1 GGGGAACCTATAACGACGTTCATTATTAATAAACACCGTTATAAAACATTTTCAGTGGATTTTCA

                    
       2072 CAATTTAA
         66 CAATTTAA

                           *            *     *        **  *                 
       2080 GGGGAACCTATAACGGCGTTCATTATTACTAAACGCCGTTATAGGACTTTTTCAGTGGATTTTCA
          1 GGGGAACCTATAACGACGTTCATTATTAATAAACACCGTTATAAAACATTTTCAGTGGATTTTCA

                   *
       2145 CAATTTAG
         66 CAATTTAA

                
       2153 GGGG
          1 GGGG

       2157 GAAAAAAGGG


Statistics
Matches: 70,  Mismatches: 7, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  73   70  1.00

ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33


Consensus pattern (73 bp):   
GGGGAACCTATAACGACGTTCATTATTAATAAACACCGTTATAAAACATTTTCAGTGGATTTTCA
CAATTTAA

Found at i:3877 original size:16 final size:16

Alignment explanation


    Indices: 3835--3877  Score: 77
    Period size: 16  Copynumber: 2.7  Consensus size: 16

       3825 GTCTGAATTG

                      *     
       3835 GATATGTGGCATGCAT
          1 GATATGTGGCGTGCAT

                            
       3851 GATATGTGGCGTGCAT
          1 GATATGTGGCGTGCAT

                       
       3867 GATATGTGGCG
          1 GATATGTGGCG

       3878 CAATATGGCT


Statistics
Matches: 26,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   26  1.00

ACGTcount: A:0.21, C:0.12, G:0.37, T:0.30


Consensus pattern (16 bp):   
GATATGTGGCGTGCAT

Found at i:6881 original size:78 final size:78

Alignment explanation


    Indices: 6735--6883  Score: 255
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       6725 TAGGGAGATT

                                     *    *                             *    
       6735 CTAACAAGATTGATCAAATCATTTCTATTTTGATCAAGTTAAAACAATGGCCAAATATTAGGACT
          1 CTAACAAGATTGATCAAATCATTTCAATTTAGATCAAGTTAAAACAATGGCCAAATATTAAGACT

                         
       6800 GTACATATATATG
         66 GTACATATATATG

                                                                             
       6813 CTAACAAGATTGATCAAATCATTTCAATTTAGATCAAGTTAAAAACAATGGCCAAATATTAAGA-
          1 CTAACAAGATTGATCAAATCATTTCAATTTAGATCAAGTT-AAAACAATGGCCAAATATTAAGAC

                   
       6877 TGTACAT
         65 TGTACAT

       6884 GTGTTAATTA


Statistics
Matches: 67,  Mismatches: 3, Indels: 2
        0.93            0.04        0.03

Matches are distributed among these distances:
  78   45  0.67
  79   22  0.33

ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32


Consensus pattern (78 bp):   
CTAACAAGATTGATCAAATCATTTCAATTTAGATCAAGTTAAAACAATGGCCAAATATTAAGACT
GTACATATATATG

Found at i:9005 original size:2 final size:2

Alignment explanation


    Indices: 8998--9042  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       8988 TCTTATTCTC

                                                                          
       8998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

                
       9040 AT A
          1 AT A

       9043 CTATTAATCA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Done.