Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008393.1 Corchorus olitorius cultivar O-4 contig08420, 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, 834

Length: 1391
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38


Found at i:188 original size:22 final size:22

Alignment explanation


    Indices: 163--274  Score: 70
    Period size: 22  Copynumber: 5.2  Consensus size: 22

        153 TTCCTCAGGG

                                  
        163 AGGTTAATAAAATTTCATAAGA
          1 AGGTTAATAAAATTTCATAAGA

                        *       * 
        185 AGGTTAA-AAAAATT-ATAAAA
          1 AGGTTAATAAAATTTCATAAGA

             **   * *     *        
        205 ATATTATTGAAATTCCAT-AGTA
          1 AGGTTAATAAAATTTCATAAG-A

            **    *            *  
        227 TCGTTATTAAAATTTCATAGGA
          1 AGGTTAATAAAATTTCATAAGA

                                  *
        249 AGGTT-ATCAAAATTTCATAAGG
          1 AGGTTAAT-AAAATTTCATAAGA

                
        271 AGGT
          1 AGGT

        275 CATCAAAAAT


Statistics
Matches: 65,  Mismatches: 20, Indels: 10
        0.68            0.21        0.11

Matches are distributed among these distances:
  20    9  0.14
  21   12  0.18
  22   43  0.66
  23    1  0.02

ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34


Consensus pattern (22 bp):   
AGGTTAATAAAATTTCATAAGA

Found at i:284 original size:23 final size:22

Alignment explanation


    Indices: 235--282  Score: 71
    Period size: 22  Copynumber: 2.2  Consensus size: 22

        225 TATCGTTATT

                              *   
        235 AAAATTTCATAGGAAGGTTATC
          1 AAAATTTCATAGGAAGGTCATC

                                   
        257 AAAATTTCATAAGG-AGGTCATC
          1 AAAATTTCAT-AGGAAGGTCATC

                
        279 AAAA
          1 AAAA

        283 ATAGTGTAAT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  22   21  0.88
  23    3  0.12

ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27


Consensus pattern (22 bp):   
AAAATTTCATAGGAAGGTCATC

Found at i:395 original size:2 final size:2

Alignment explanation


    Indices: 388--425  Score: 76
    Period size: 2  Copynumber: 19.0  Consensus size: 2

        378 CTAAAACTAG

                                                                    
        388 TA TA TA 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 TA TA TA

        426 AAAGGACTTT


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   36  1.00

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


Consensus pattern (2 bp):   
TA

Done.