Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024337.1 Corchorus olitorius cultivar O-4 contig24370, 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: 16455
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34


Found at i:1082 original size:33 final size:33

Alignment explanation


    Indices: 994--1085  Score: 112
    Period size: 33  Copynumber: 2.8  Consensus size: 33

        984 CGACGGGATT

                   **         *   *    *   * 
        994 GCGCCTCGTCATATGGCGGGGCATCCCTAGGGG
          1 GCGCCTCACCATATGGCGAGGCGTCCCCAGGAG

                  *         *                
       1027 GCGCCTGACCATATGGGGAGGCGTCCCCAGGAG
          1 GCGCCTCACCATATGGCGAGGCGTCCCCAGGAG

                                      
       1060 GCGCCTCACCATATGGCGAGGCGTCC
          1 GCGCCTCACCATATGGCGAGGCGTCC

       1086 ACTATGGTCA


Statistics
Matches: 49,  Mismatches: 10, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  33   49  1.00

ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15


Consensus pattern (33 bp):   
GCGCCTCACCATATGGCGAGGCGTCCCCAGGAG

Found at i:1255 original size:18 final size:19

Alignment explanation


    Indices: 1206--1255  Score: 59
    Period size: 18  Copynumber: 2.7  Consensus size: 19

       1196 AAATATAATA

                     *         
       1206 ATTATTAGTGTTA-TTATT
          1 ATTATTAGTATTATTTATT

             *                 
       1224 AATATTAGTATTATTTATT
          1 ATTATTAGTATTATTTATT

                *         
       1243 ATTACTAGT-TTAT
          1 ATTATTAGTATTAT

       1256 ATTTCTAAAT


Statistics
Matches: 27,  Mismatches: 4, Indels: 2
        0.82            0.12        0.06

Matches are distributed among these distances:
  18   15  0.56
  19   12  0.44

ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58


Consensus pattern (19 bp):   
ATTATTAGTATTATTTATT

Found at i:2456 original size:18 final size:18

Alignment explanation


    Indices: 2411--2457  Score: 58
    Period size: 18  Copynumber: 2.6  Consensus size: 18

       2401 GGAAAAAATA

                          * * 
       2411 TTTTAAAAAAATATGTTT
          1 TTTTAAAAAAATATATAT

                **            
       2429 TTTTTGAAAAATATATAT
          1 TTTTAAAAAAATATATAT

                       
       2447 TTTTAAAAAAA
          1 TTTTAAAAAAA

       2458 CTTGAGACGA


Statistics
Matches: 23,  Mismatches: 6, Indels: 0
        0.79            0.21        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47


Consensus pattern (18 bp):   
TTTTAAAAAAATATATAT
Done.