Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022062.1 Corchorus olitorius cultivar O-4 contig22095, 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: 2814
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32


Found at i:589 original size:12 final size:13

Alignment explanation


    Indices: 571--600  Score: 53
    Period size: 12  Copynumber: 2.4  Consensus size: 13

        561 GTTTTCTTTA

                         
        571 ATTTTCTTGATTG
          1 ATTTTCTTGATTG

                         
        584 -TTTTCTTGATTG
          1 ATTTTCTTGATTG

                 
        596 ATTTT
          1 ATTTT

        601 AATTGCTAGT


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  12   12  0.75
  13    4  0.25

ACGTcount: A:0.13, C:0.07, G:0.13, T:0.67


Consensus pattern (13 bp):   
ATTTTCTTGATTG

Found at i:1744 original size:58 final size:58

Alignment explanation


    Indices: 1655--2228  Score: 938
    Period size: 58  Copynumber: 9.9  Consensus size: 58

       1645 AATTCATCAG

                                                                     *
       1655 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAG
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                                       *                               
       1713 AGATGGATCTGAAGACAGTTTCC-AAAGGATTTTAAGATTGAGACTGAAGACAGCTCAC
          1 AGATGGATCTGAAGACAG-TTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                                                         *           *
       1771 AGATGGATCT-AAGACAGTTCCT-AAAGATTTTAAGATTGAGACTAAAGACAGCTCAT
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                                                         *           *
       1827 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTAAAGACAGCTCAA
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                             *                                        
       1885 AGATGGATCTGAAGACAATTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                    *      *                                          
       1943 AGATGGATATGAAGATAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                             *                          *     *       
       2001 AGATGGATCTGAAGACAATTCCTAAAAGATTTTAAGATTGAGACCGAAGATAGCTCAC
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                                                      * *           * 
       2059 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGCCCGAAGACAGCTCGC
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                                                       *              
       2117 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGAATGAAGACAGCTCAC
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

                *                                * *              
       2175 AGATTGATCTGAAGACAGTTCCTAAAAGATTTTAAGACTAAGACCTGAAGACAG
          1 AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGA-CTGAAGACAG

       2229 GTCAGAAGGA


Statistics
Matches: 482,  Mismatches: 29, Indels: 9
        0.93            0.06        0.02

Matches are distributed among these distances:
  56   45  0.09
  57   19  0.04
  58  405  0.84
  59   13  0.03

ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24


Consensus pattern (58 bp):   
AGATGGATCTGAAGACAGTTCCTAAAAGATTTTAAGATTGAGACTGAAGACAGCTCAC

Found at i:2711 original size:49 final size:49

Alignment explanation


    Indices: 2654--2752  Score: 180
    Period size: 49  Copynumber: 2.0  Consensus size: 49

       2644 AAGTCCGTTT

                        *                                    
       2654 GCTCATTTGGGATTTGCTTTTGGGCTTTGAGACTTGGAAAGCCCAAATA
          1 GCTCATTTGGGAGTTGCTTTTGGGCTTTGAGACTTGGAAAGCCCAAATA

                                         *                   
       2703 GCTCATTTGGGAGTTGCTTTTGGGCTTTGGGACTTGGAAAGCCCAAATA
          1 GCTCATTTGGGAGTTGCTTTTGGGCTTTGAGACTTGGAAAGCCCAAATA

             
       2752 G
          1 G

       2753 AGGCATGCAC


Statistics
Matches: 48,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  49   48  1.00

ACGTcount: A:0.21, C:0.16, G:0.29, T:0.33


Consensus pattern (49 bp):   
GCTCATTTGGGAGTTGCTTTTGGGCTTTGAGACTTGGAAAGCCCAAATA
Done.