Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023204.1 Corchorus olitorius cultivar O-4 contig23237, 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: 16679
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26


Found at i:15112 original size:2 final size:2

Alignment explanation


    Indices: 15105--15136  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

      15095 CTGATACTCC

                                                           
      15105 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

      15137 CACATATTTA


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:15821 original size:50 final size:49

Alignment explanation


    Indices: 15765--15902  Score: 190
    Period size: 50  Copynumber: 2.8  Consensus size: 49

      15755 GAAGAATCAG

                       *                   *          *       
      15765 TTGGAAGACAGCTCAAAGGATAAGCGGAAGATGGTCCTTTTAGGATGGAA
          1 TTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATGG-A

                     *     *    *                         *  
      15815 TTGGAAGACCGTTCATAGGAAAAGCGGAAGACGGTCCTTTTAAGATTGA
          1 TTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGA

                                                     
      15864 --GGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
          1 TTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT

      15903 TATATTCGAG


Statistics
Matches: 78,  Mismatches: 10, Indels: 3
        0.86            0.11        0.03

Matches are distributed among these distances:
  47   36  0.46
  49    1  0.01
  50   41  0.53

ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22


Consensus pattern (49 bp):   
TTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATGGA

Found at i:16231 original size:28 final size:27

Alignment explanation


    Indices: 16191--16260  Score: 97
    Period size: 28  Copynumber: 2.5  Consensus size: 27

      16181 ATTTATTTCT

                                         
      16191 CATTTTGGTCATTTTG-CATGACCAGGGG
          1 CATTTTGGTCATTTTGACAT--CCAGGGG

                                        
      16219 CATTTTGGTCATTTTGTACATCCAGGGG
          1 CATTTTGGTCATTTTG-ACATCCAGGGG

                  *       
      16247 CATTTTAGTCATTT
          1 CATTTTGGTCATTT

      16261 CAAGAACCTT


Statistics
Matches: 39,  Mismatches: 1, Indels: 4
        0.89            0.02        0.09

Matches are distributed among these distances:
  28   36  0.92
  30    3  0.08

ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41


Consensus pattern (27 bp):   
CATTTTGGTCATTTTGACATCCAGGGG
Done.