Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01022871.1 Corchorus olitorius cultivar O-4 contig22904, 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: 2740
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34


Found at i:38 original size:30 final size:30

Alignment explanation


    Indices: 2--336  Score: 496
    Period size: 30  Copynumber: 11.2  Consensus size: 30

          1 G

                      *                   
          2 AAATAAAGCACTGATCCTCAACCAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                 *        
         32 AAATAAAGCAATGATCCTCAAACAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                 *  *     
         62 AAATAAAGCAATGATCCTCAAACATGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                          
         92 AAATAAAGCAATGATCCTCAACCAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                              *           
        122 AAATAAAGCAATGATCCTAAACCAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

               * *               *        
        152 AAACAGAGCAATGATCCTCAAACAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                    *     
        182 AAATAAAGCAATGATCCTCAACCAAGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                          
        212 AAATAAAGCAATGATCCTCAACCAGGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                                 *  *     
        242 AAATAAAGCAATGATCCTCAAACAAGATTA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                     *            *        
        272 AAAT-AAGATAATGATCCTCAAACAGGATTA
          1 AAATAAAG-CAATGATCCTCAACCAGGATTA

                        *          *    * 
        302 AAATAAAGCAATAATCCT--ACCCGGATCA
          1 AAATAAAGCAATGATCCTCAACCAGGATTA

                   
        330 AAATAAA
          1 AAATAAA

        337 CTGACAAAGT


Statistics
Matches: 279,  Mismatches: 24, Indels: 6
        0.90            0.08        0.02

Matches are distributed among these distances:
  28   14  0.05
  29    3  0.01
  30  259  0.93
  31    3  0.01

ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20


Consensus pattern (30 bp):   
AAATAAAGCAATGATCCTCAACCAGGATTA

Found at i:699 original size:169 final size:169

Alignment explanation


    Indices: 375--828  Score: 695
    Period size: 169  Copynumber: 2.7  Consensus size: 169

        365 AACATGAGAA

                     *      *    *            *              *               
        375 GCCCGGAGGTCTTATCAAATGTAAACTCTG-AAATGAGACCTTAAACAAAGATTTT-AACTTAAA
          1 GCCCGGAGGACTTA-CCAATGCAAACTCTGAAAAGGA-ACCTTAAACAAGGATTTTAAACTTAAA

                                                 *          *    *        *  
        438 CATGAA-CTTT--TGAAAAACTTGATGAAATGAAATGGTACCCGGA-GCTTTACCAATTGCCTGG
         64 CATGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGG

                                                    *
        499 AGAACTTATCAGAATTAATACCCGAAGGTTTCTGAATTTGT
        129 AGAACTTATCAGAATTAATACCCGAAGGTTTCTGAATTTGC

                                                                             
        540 GCCCGGAGGACTTACCAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACA
          1 GCCCGGAGGACTTACCAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACA

                                     *    *                                  
        605 TGAATCTTTGATGAAAAACTTGATGGAATGGAATGATACCCGGAGGTTTTATCAATTGCCCGGAG
         66 TGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAG

            *                     *                
        670 GACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGC
        131 AACTTATCAGAATTAATACCCGAAGGTTTCTGAATTTGC

                                                                             
        709 GCCCGGAGGACTTACCAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACA
          1 GCCCGGAGGACTTACCAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACA

                 *                  *                      *       
        774 TGAATTTTTGATGAAAAACTTGATAAAATGAAATGATACCCGGAGGTCTTATCAA
         66 TGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAA

        829 ATGGAATAAG


Statistics
Matches: 264,  Mismatches: 19, Indels: 8
        0.91            0.07        0.03

Matches are distributed among these distances:
 164   30  0.11
 165   32  0.12
 166    4  0.02
 168   30  0.11
 169  168  0.64

ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27


Consensus pattern (169 bp):   
GCCCGGAGGACTTACCAATGCAAACTCTGAAAAGGAACCTTAAACAAGGATTTTAAACTTAAACA
TGAATCTTTGATGAAAAACTTGATGAAATGAAATGATACCCGGAGGTTTTATCAATTGCCCGGAG
AACTTATCAGAATTAATACCCGAAGGTTTCTGAATTTGC
Done.