Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016710.1 Corchorus olitorius cultivar O-4 contig16743, 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: 10666
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32


Found at i:729 original size:18 final size:19

Alignment explanation


    Indices: 706--741  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

        696 TCCATAGAGT

                   *           
        706 TATTAATGAAGA-AAAAAA
          1 TATTAATAAAGATAAAAAA

                              
        724 TATTAATAAAGATAAAAA
          1 TATTAATAAAGATAAAAA

        742 GAAATAAAGT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18   11  0.69
  19    5  0.31

ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25


Consensus pattern (19 bp):   
TATTAATAAAGATAAAAAA

Found at i:2347 original size:3 final size:3

Alignment explanation


    Indices: 2321--2373  Score: 67
    Period size: 3  Copynumber: 18.7  Consensus size: 3

       2311 ACATTAGGGT

                                 *      *                                  
       2321 TTC TTC TT- TT- TTC TCC TTC CTC TTC TT- TTC TTC TTC TTC TTC TTC
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC

                      
       2366 TTC TTC TT
          1 TTC TTC TT

       2374 TAGCAAAGCA


Statistics
Matches: 44,  Mismatches: 4, Indels: 4
        0.85            0.08        0.08

Matches are distributed among these distances:
   2    6  0.14
   3   38  0.86

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:3011 original size:24 final size:24

Alignment explanation


    Indices: 2979--3028  Score: 64
    Period size: 24  Copynumber: 2.1  Consensus size: 24

       2969 GGCATTGCCA

                        *           
       2979 TGAGATTTAAGCTTGCTCTGTTTC
          1 TGAGATTTAAGCATGCTCTGTTTC

                *    *       *      
       3003 TGAGTTTTATGCATGCTTTGTTTC
          1 TGAGATTTAAGCATGCTCTGTTTC

              
       3027 TG
          1 TG

       3029 TTAATTGTAT


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.14, C:0.14, G:0.22, T:0.50


Consensus pattern (24 bp):   
TGAGATTTAAGCATGCTCTGTTTC

Found at i:8623 original size:27 final size:27

Alignment explanation


    Indices: 8593--8666  Score: 103
    Period size: 27  Copynumber: 2.7  Consensus size: 27

       8583 TGTGAACTTA

                                  *    
       8593 AAATGACCAAAATGCCCCTAAATGTGC
          1 AAATGACCAAAATGCCCCTAAACGTGC

                               ***     
       8620 AAATGACCAAAATGCCCCTGGGCGTGC
          1 AAATGACCAAAATGCCCCTAAACGTGC

                   *            
       8647 AAATGACTAAAATGCCCCTA
          1 AAATGACCAAAATGCCCCTA

       8667 GGTGACCCTA


Statistics
Matches: 41,  Mismatches: 6, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  27   41  1.00

ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18


Consensus pattern (27 bp):   
AAATGACCAAAATGCCCCTAAACGTGC
Done.