Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01009996.1 Corchorus olitorius cultivar O-4 contig10028, 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, 765

Length: 1275
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29


Found at i:53 original size:13 final size:13

Alignment explanation


    Indices: 35--73  Score: 53
    Period size: 13  Copynumber: 3.0  Consensus size: 13

         25 AACCCAAAAG

                          
         35 AAAAGAAA-AATGA
          1 AAAAGAAAGAA-GA

                         
         48 AAAAGAAAGAAGA
          1 AAAAGAAAGAAGA

                 *       
         61 AAAAGGAAGAAGA
          1 AAAAGAAAGAAGA

         74 CCAAATGCAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  13   22  0.92
  14    2  0.08

ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03


Consensus pattern (13 bp):   
AAAAGAAAGAAGA

Found at i:501 original size:39 final size:39

Alignment explanation


    Indices: 452--1143  Score: 1125
    Period size: 39  Copynumber: 18.0  Consensus size: 39

        442 CAACATAAAA

                 *                                 
        452 CTGAAGAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                      *     *      
        491 CTGAAAAGATGACCTGTTTCCAGTCATCTTTGGTAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                 *              *                  
        530 CTGAAGAGATGACCTGTTTCTAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                 *                          *      
        569 CTGAAGAGATGACCTGTTTCCAGTCAACTTTGGTAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                            *                      
        608 CTGAAAAGATGACCTGCTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                        **         
        647 CTGAAAAGATGACCTGTTTCCAGTCAACCCTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                *                  
        686 CTGAAAAGATGACCTGTTTCTAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                                   
        725 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

              *    *       *                       
        764 CTAAAAATATGACCTATTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                         *                         
        803 CTGAAAAGATGACTTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

            *                                      
        842 ATGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                                   
        881 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                                   
        920 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAA--
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                                   
        957 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                         *    *                    
        996 CT-AAAAGATGACTTGTTCCCAGTCAACTTTGATAAA--
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                         *   *                     
       1032 -TGAAAAGATGACGTGTCTCCAGTCAACTTTGATAAA--
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

                                                    
       1068 -TGAAAAGATGACCTGTTTCCAGTCAA-TTATGATAAATG
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTT-TGATAAATG

                                                  
       1106 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT
          1 CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAAT

       1144 TAACCTGTTT


Statistics
Matches: 609,  Mismatches: 36, Indels: 16
        0.92            0.05        0.02

Matches are distributed among these distances:
  35    3  0.00
  36   62  0.10
  37   37  0.06
  38   32  0.05
  39  473  0.78
  40    2  0.00

ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31


Consensus pattern (39 bp):   
CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATG

Done.