Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008935.1 Corchorus olitorius cultivar O-4 contig08962, 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, 616

Length: 1027
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37


Found at i:161 original size:24 final size:24

Alignment explanation


    Indices: 123--415  Score: 353
    Period size: 24  Copynumber: 12.2  Consensus size: 24

        113 GACTCCTTGC

                                 *   
        123 ATCATTATCAGAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                    * *          *   
        147 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        171 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        195 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        219 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        243 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        267 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                              *  *   
        291 ATCATTATCAGAACTTT-TTGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        315 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *             
        339 ATCATTATAATAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                    * *          *   
        363 ATCATTATAATAACTTTC-TGATAA
          1 ATCATTATCAGAACTTTCAT-CTAA

                                    
        387 ATCATTATCAGAACTTTCATCTAA
          1 ATCATTATCAGAACTTTCATCTAA

                 
        411 ATCAT
          1 ATCAT

        416 AACCACTTGT


Statistics
Matches: 235,  Mismatches: 27, Indels: 14
        0.85            0.10        0.05

Matches are distributed among these distances:
  23    3  0.01
  24  228  0.97
  25    4  0.02

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


Consensus pattern (24 bp):   
ATCATTATCAGAACTTTCATCTAA

Found at i:241 original size:72 final size:72

Alignment explanation


    Indices: 144--415  Score: 490
    Period size: 72  Copynumber: 3.8  Consensus size: 72

        134 AACTTTCTGA

                         *                                                   
        144 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        209 TTTCATC
         66 TTTCATC

                       *        *                                            
        216 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        281 TTTCATC
         66 TTTCATC

                       *        *                                            
        288 TAAATCATTATCAGAACTTTTTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC

                   
        353 TTTCATC
         66 TTTCATC

                         *                                          
        360 TAAATCATTATAATAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT
          1 TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCAT

        416 AACCACTTGT


Statistics
Matches: 194,  Mismatches: 6, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  72  194  1.00

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


Consensus pattern (72 bp):   
TAAATCATTATAAGAACTTTCTGATAAATCATTATCAGAACTTTCATCTAAATCATTATAATAAC
TTTCATC
Done.