Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021524.1 Corchorus olitorius cultivar O-4 contig21557, 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: 15508
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:780 original size:14 final size:14

Alignment explanation


    Indices: 761--795  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

        751 CCTTTTAAAT

                          
        761 TAAAATAGTAAAAA
          1 TAAAATAGTAAAAA

                  *       
        775 TAAAATGGTAAAAA
          1 TAAAATAGTAAAAA

                   
        789 TAAAATA
          1 TAAAATA

        796 ATTATAAAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  14   19  1.00

ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23


Consensus pattern (14 bp):   
TAAAATAGTAAAAA

Found at i:6758 original size:27 final size:27

Alignment explanation


    Indices: 6720--6774  Score: 110
    Period size: 27  Copynumber: 2.0  Consensus size: 27

       6710 TCTCTTACTT

                                       
       6720 TTTTGTAATTCATAATGGGTAACTATG
          1 TTTTGTAATTCATAATGGGTAACTATG

                                       
       6747 TTTTGTAATTCATAATGGGTAACTATG
          1 TTTTGTAATTCATAATGGGTAACTATG

             
       6774 T
          1 T

       6775 AAGCCTGCAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  27   28  1.00

ACGTcount: A:0.29, C:0.07, G:0.18, T:0.45


Consensus pattern (27 bp):   
TTTTGTAATTCATAATGGGTAACTATG

Found at i:10616 original size:6 final size:6

Alignment explanation


    Indices: 10607--10641  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

      10597 AACAGCAGAA

                                                    
      10607 GCAATG GCAATG GCAATG GCAATG GCAATG GCAAT
          1 GCAATG GCAATG GCAATG GCAATG GCAATG GCAAT

      10642 CGCAGGCTTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17


Consensus pattern (6 bp):   
GCAATG

Found at i:12477 original size:31 final size:31

Alignment explanation


    Indices: 12439--12542  Score: 101
    Period size: 31  Copynumber: 3.4  Consensus size: 31

      12429 AACTGACGCC

                    *                      
      12439 AGGCCCTTTTTTGAGCATTTTCGATAACGTT
          1 AGGCCCTTATTTGAGCATTTTCGATAACGTT

                              **        *    
      12470 AGGCCCTTATTTG-GTCAAATT--A-AAAGATT
          1 AGGCCCTTATTTGAG-CATTTTCGATAACG-TT

                                            
      12499 -GGACCCTTATTTGAGCATTTTCGATAACGTT
          1 AGG-CCCTTATTTGAGCATTTTCGATAACGTT

                  *      
      12530 AGGCCCGTATTTG
          1 AGGCCCTTATTTG

      12543 TCCTAATTAA


Statistics
Matches: 57,  Mismatches: 8, Indels: 16
        0.70            0.10        0.20

Matches are distributed among these distances:
  28    5  0.09
  29   17  0.30
  30    2  0.04
  31   28  0.49
  32    5  0.09

ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38


Consensus pattern (31 bp):   
AGGCCCTTATTTGAGCATTTTCGATAACGTT

Found at i:12535 original size:60 final size:61

Alignment explanation


    Indices: 12442--12602  Score: 213
    Period size: 60  Copynumber: 2.7  Consensus size: 61

      12432 TGACGCCAGG

                 *                                                   *   
      12442 CCCTTTTTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGT-CAAATTAAAAGATTGGA
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCCAAATTAAAAGATCGGA

                                              *          *              *
      12502 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCGTATTT-GTCCTAATTAAAAGATCGGG
          1 CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCCAAATTAAAAGATCGGA

                       *                    *          
      12562 CCCTTATTTGAACATTTTAAC-A-AACGTTAGACCCTTATTTG
          1 CCCTTATTTGAGCATTTT--CGATAACGTTAGGCCCTTATTTG

      12603 AGCAATTAGC


Statistics
Matches: 89,  Mismatches: 8, Indels: 7
        0.86            0.08        0.07

Matches are distributed among these distances:
  59    2  0.02
  60   85  0.96
  61    1  0.01
  62    1  0.01

ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37


Consensus pattern (61 bp):   
CCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGTCCAAATTAAAAGATCGGA
Done.