Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01013355.1 Corchorus olitorius cultivar O-4 contig13388, 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: 19758
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31


Found at i:4766 original size:21 final size:21

Alignment explanation


    Indices: 4733--4781  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       4723 AAGAATTGTA

                          **     
       4733 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       4753 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       4774 GCATTCCT
          1 GC-TTCCT

       4782 AAAGCATTGA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  20    4  0.17
  21   15  0.62
  22    5  0.21

ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41


Consensus pattern (21 bp):   
GCTTCCTTGGAAATCCCTCTT

Found at i:9640 original size:6 final size:6

Alignment explanation


    Indices: 9629--9657  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       9619 GATAACTAAT

                                             
       9629 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG
          1 ATTTGG ATTTGG ATTTGG ATTTGG ATTTG

       9658 AGGATTTGAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52


Consensus pattern (6 bp):   
ATTTGG

Found at i:17277 original size:12 final size:11

Alignment explanation


    Indices: 17259--17298  Score: 55
    Period size: 12  Copynumber: 3.6  Consensus size: 11

      17249 TGCTCATTTT

                       
      17259 AGAAGAAGAAA
          1 AGAAGAAGAAA

                        
      17270 ATGAAGAAGAAA
          1 A-GAAGAAGAAA

                     * 
      17282 AGAAGAAG-GA
          1 AGAAGAAGAAA

                   
      17292 AGAAGAA
          1 AGAAGAA

      17299 AGTAGACATA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  10    8  0.30
  11    8  0.30
  12   11  0.41

ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03


Consensus pattern (11 bp):   
AGAAGAAGAAA

Found at i:17293 original size:18 final size:17

Alignment explanation


    Indices: 17259--17299  Score: 55
    Period size: 18  Copynumber: 2.3  Consensus size: 17

      17249 TGCTCATTTT

                        *     
      17259 AGAAGAAGAAAATGAAGA
          1 AGAA-AAGAAAAGGAAGA

                              
      17277 AGAAAAGAAGAAGGAAGA
          1 AGAAAAGAA-AAGGAAGA

                 
      17295 AGAAA
          1 AGAAA

      17300 GTAGACATAC


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  17    5  0.24
  18   16  0.76

ACGTcount: A:0.68, C:0.00, G:0.29, T:0.02


Consensus pattern (17 bp):   
AGAAAAGAAAAGGAAGA
Done.