Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022950.1 Corchorus olitorius cultivar O-4 contig22983, 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: 7380
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32


Found at i:5757 original size:21 final size:21

Alignment explanation


    Indices: 5724--5772  Score: 55
    Period size: 21  Copynumber: 2.3  Consensus size: 21

       5714 AAGAATAGTA

                          **     
       5724 GCTT-CTTGGAAATGGCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    *            
       5744 GCTTCCTTTGAAATCCCTCTT
          1 GCTTCCTTGGAAATCCCTCTT

                    
       5765 GCATTCCT
          1 GC-TTCCT

       5773 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:6323 original size:10 final size:9

Alignment explanation


    Indices: 6280--6337  Score: 50
    Period size: 10  Copynumber: 6.4  Consensus size: 9

       6270 TAAAAGTAAC

                     
       6280 TAAGAAAAA
          1 TAAGAAAAA

                *     
       6289 TAAACAAAAA
          1 T-AAGAAAAA

                      
       6299 TAA-AAGAAA
          1 TAAGAA-AAA

                     
       6308 -AAGAAAAA
          1 TAAGAAAAA

                      
       6316 TAACGAAAAA
          1 TAA-GAAAAA

                   * 
       6326 TAA-AAAGA
          1 TAAGAAAAA

                
       6334 TAAG
          1 TAAG

       6338 GGTAAGAAAT


Statistics
Matches: 41,  Mismatches: 2, Indels: 12
        0.75            0.04        0.22

Matches are distributed among these distances:
   8   14  0.34
   9   10  0.24
  10   17  0.41

ACGTcount: A:0.76, C:0.03, G:0.10, T:0.10


Consensus pattern (9 bp):   
TAAGAAAAA

Found at i:6323 original size:16 final size:17

Alignment explanation


    Indices: 6294--6331  Score: 51
    Period size: 16  Copynumber: 2.3  Consensus size: 17

       6284 AAAAATAAAC

                             
       6294 AAAAATAAAAGAAAAAG
          1 AAAAATAAAAGAAAAAG

                     *      *
       6311 AAAAAT-AACGAAAAAT
          1 AAAAATAAAAGAAAAAG

                 
       6327 AAAAA
          1 AAAAA

       6332 GATAAGGGTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  16   13  0.68
  17    6  0.32

ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08


Consensus pattern (17 bp):   
AAAAATAAAAGAAAAAG
Done.