Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01001960.1 Corchorus olitorius cultivar O-4 contig01960, 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, 664

Length: 1107
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30


Found at i:315 original size:37 final size:37

Alignment explanation


    Indices: 265--919  Score: 851
    Period size: 37  Copynumber: 17.5  Consensus size: 37

        255 GTCGAAGTTA

                                                   
        265 AAACTGAGGAAAGATGACCTGTTTCCAGTCAACTTTGAT
          1 AAACTGA--AAAGATGACCTGTTTCCAGTCAACTTTGAT

                                  *              
        304 AAACTGAAAAGATGACCTGTTTTCAGTCAACTTTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                          *        
        341 AAATGCTGAAAAGATGACCTGTTTCCAGTCGACTTTGAT
          1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                   *             
        380 AAACTGAAAAGATGACCTGTTTCTAGTCAACTTTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                             *                  *  
        417 AAATGCTGAAAAGATGATCTGTTTCCAGTCAACTTTAAT
          1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                      *         *  *             
        456 AAACTGAAAACATGACCTGTCTCTAGTCAACTTTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                                *  
        493 AAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTAAT
          1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                                  
        532 AAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT

                  * *                       *    
        568 AAACTGGAGAGATGACCTGTTTCCAGTCAACTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                          *      
        605 AAA-TGAAAAGATGACCTGTTTCCAGTCAATTTTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                    *                  *    *    
        641 AAACTGAAGAGATGACCTGTTTCCAGTAAACTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                                                  
        678 AAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT

                    *                       *    
        714 AAACTGAAGAGATGACCTGTTTCCAGTCAACTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                            *                     
        751 AAA-TGAAAAGATGACGTGTTTCCAGTCAA-TTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT

                * * *                       *    
        787 AAACCGGAGAGATGACCTGTTTCCAGTCAACTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                            *                     
        824 AAA-TGAAAAGATGACATGTTTCCAGTCAA-TTCTGAT
          1 AAACTGAAAAGATGACCTGTTTCCAGTCAACTT-TGAT

                            *          **          
        860 AAACGCTGAAAAGATGGCCTGTTTCCAACCAACTTTGAT
          1 AAA--CTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

                            *    
        899 AAACGCTGAAAAGATGGCCTG
          1 AAA--CTGAAAAGATGACCTG

        920 AAAGATAAAA


Statistics
Matches: 544,  Mismatches: 51, Indels: 42
        0.85            0.08        0.07

Matches are distributed among these distances:
  35    5  0.01
  36  155  0.28
  37  223  0.41
  38    3  0.01
  39  156  0.29
  40    2  0.00

ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29


Consensus pattern (37 bp):   
AAACTGAAAAGATGACCTGTTTCCAGTCAACTTTGAT

Found at i:607 original size:73 final size:74

Alignment explanation


    Indices: 274--919  Score: 874
    Period size: 73  Copynumber: 8.6  Consensus size: 74

        264 AAAACTGAGG

                                                                *            
        274 AAAGATGACCTGTTTCCAGTCAACTTTGATAAACTGAAAAGATGACCTGTTTTCAGTCAACTT-T
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCT

                        
        338 GATAAATGCTGA
         64 GATAAA-GCTGA

                                 *                               *           
        350 AAAGATGACCTGTTTCCAGTCGACTTTGATAAACTGAAAAGATGACCTGTTTCTAGTCAACTT-T
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCT

                        
        414 GATAAATGCTGA
         64 GATAAA-GCTGA

                    *                  *            *         *  *           
        426 AAAGATGATCTGTTTCCAGTCAACTTTAATAAACTGAAAACATGACCTGTCTCTAGTCAACTT-T
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAA-TGAAAAGATGACCTGTTTCCAGTCAA-TTCT

                        
        490 GATAAATGCTGA
         64 GATAAA-GCTGA

                                       *                                     
        502 AAAGATGACCTGTTTCCAGTCAACTTTAATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA

                    *
        567 TAAA-CTGG
         66 TAAAGCTGA

             *                       *                                   *   
        575 AGAGATGACCTGTTTCCAGTCAACTCTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTTTGA
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA

                     
        640 TAAA-CTGA
         66 TAAAGCTGA

             *                  *    *                                       
        648 AGAGATGACCTGTTTCCAGTAAACTCTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA

                     
        713 TAAA-CTGA
         66 TAAAGCTGA

             *                       *                   *                   
        721 AGAGATGACCTGTTTCCAGTCAACTCTGATAAATGAAAAGATGACGTGTTTCCAGTCAATTCTGA
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA

                  * *
        786 TAAA-CCGG
         66 TAAAGCTGA

             *                       *                   *                   
        794 AGAGATGACCTGTTTCCAGTCAACTCTGATAAATGAAAAGATGACATGTTTCCAGTCAATTCTGA
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA

                      
        859 TAAACGCTGA
         66 TAAA-GCTGA

                   *          **                          *    
        869 AAAGATGGCCTGTTTCCAACCAACTTTGATAAACGCTGAAAAGATGGCCTG
          1 AAAGATGACCTGTTTCCAGTCAACTTTGATAAA---TGAAAAGATGACCTG

        920 AAAGATAAAA


Statistics
Matches: 530,  Mismatches: 34, Indels: 10
        0.92            0.06        0.02

Matches are distributed among these distances:
  73  279  0.53
  74    2  0.00
  75   60  0.11
  76  176  0.33
  78   13  0.02

ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29


Consensus pattern (74 bp):   
AAAGATGACCTGTTTCCAGTCAACTTTGATAAATGAAAAGATGACCTGTTTCCAGTCAATTCTGA
TAAAGCTGA

Done.