Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01005265.1 Corchorus olitorius cultivar O-4 contig05288, 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, 655

Length: 1092
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.34


Found at i:847 original size:24 final size:24

Alignment explanation


    Indices: 804--1092  Score: 336
    Period size: 24  Copynumber: 12.0  Consensus size: 24

        794 GACTCCTTGC

                                  *   
        804 ATCATTATCAGAAACTTTC-TGATAA
          1 ATCATTATCAG-AACTTTCAT-CTAA

                    * *          *   
        829 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        853 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        877 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        901 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        925 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        949 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        973 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        997 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
       1021 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *          *   
       1045 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
       1069 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA


Statistics
Matches: 230,  Mismatches: 27, Indels: 15
        0.85            0.10        0.06

Matches are distributed among these distances:
  23    3  0.01
  24  214  0.93
  25   13  0.06

ACGTcount: A:0.39, C:0.17, G:0.04, T:0.40


Consensus pattern (24 bp):   
ATCATTATCAGAACTTTCATCTAA

Found at i:923 original size:72 final size:72

Alignment explanation


    Indices: 826--1092  Score: 480
    Period size: 72  Copynumber: 3.7  Consensus size: 72

        816 AACTTTCTGA

                         *                                                   
        826 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        891 TTTCATC
         66 TTTCATC

                       *        *                                            
        898 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        963 TTTCATC
         66 TTTCATC

                       *        *                                            
        970 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
       1035 TTTCATC
         66 TTTCATC

                         *                                     
       1042 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAA
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAA


Statistics
Matches: 189,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  72  189  1.00

ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40


Consensus pattern (72 bp):   
TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
TTTCATC
Done.