Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01024753.1 Corchorus olitorius cultivar O-4 contig24786, 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: 11783
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31


Found at i:10531 original size:29 final size:30

Alignment explanation


    Indices: 10471--10550  Score: 99
    Period size: 29  Copynumber: 2.7  Consensus size: 30

      10461 GCTAAATACC

                 *   *                *    
      10471 CAAAAAAATTCCTTATGTTTTGCTTTTGGGA
          1 CAAAATAATCCCTTATGTTTT-CTTTCGGGA

                                          
      10502 CAAAATAATCCCTTATGTTTT-TTTCGGGA
          1 CAAAATAATCCCTTATGTTTTCTTTCGGGA

                *          *    
      10531 CAAATTAATCCCTTACGTTT
          1 CAAAATAATCCCTTATGTTT

      10551 CAAAAATGAG


Statistics
Matches: 44,  Mismatches: 5, Indels: 2
        0.86            0.10        0.04

Matches are distributed among these distances:
  29   25  0.57
  31   19  0.43

ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41


Consensus pattern (30 bp):   
CAAAATAATCCCTTATGTTTTCTTTCGGGA

Found at i:10668 original size:31 final size:31

Alignment explanation


    Indices: 10633--10729  Score: 167
    Period size: 31  Copynumber: 3.1  Consensus size: 31

      10623 AAGGGACTGA

                                           
      10633 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                                           
      10664 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
          1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT

                              *       *     
      10695 TTTGTCCCAAAAGAAAAATATAAGAGAATTTT
          1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT

               
      10727 TTT
          1 TTT

      10730 AGTATTTAGT


Statistics
Matches: 63,  Mismatches: 2, Indels: 1
        0.95            0.03        0.02

Matches are distributed among these distances:
  31   54  0.86
  32    9  0.14

ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32


Consensus pattern (31 bp):   
TTTGTCCCAAAAGAAAAACATAAGGGATTTT

Found at i:11474 original size:126 final size:125

Alignment explanation


    Indices: 11342--11581  Score: 319
    Period size: 126  Copynumber: 1.9  Consensus size: 125

      11332 CTTATTTTTC

                      *                                                      
      11342 AAATATATTTTTTAAAT-ACCATT-TTTAAACTTTTACAATTTTACTCAATTA-AAAAC-TCTAT
          1 AAATATATTTCTTAAATGA-CATTATTTAAACTTTTACAATTTTA-T--ATTACAAAACTTCTAT

                   *                      *           *                      
      11403 TTTTATTTAATCAAA-TCTAATATATTTTATAACTATTTTATTTTTACCATTTTACTATTTTAAT
         62 TTTTATTCAATCAAATTC-AATAT-TTTTACAACTATTTTATCTTTACCATTTTACTATTTTAAT

             
      11467 T
        125 T

                                                  *      *                   
      11468 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTTACCAAAACTTCTATTTT
          1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATATTA-CAAAACTTCTATTTT

                    *                                        
      11533 TATTCAATTAAATTCAATATTTTTACAACTATTTTATCTTTACCATTTT
         65 TATTCAATCAAATTCAATATTTTTACAACTATTTTATCTTTACCATTTT

      11582 TTTAGGGAAT


Statistics
Matches: 101,  Mismatches: 7, Indels: 12
        0.84            0.06        0.10

Matches are distributed among these distances:
 124    3  0.03
 126   53  0.52
 127   43  0.43
 128    2  0.02

ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52


Consensus pattern (125 bp):   
AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATATTACAAAACTTCTATTTTT
ATTCAATCAAATTCAATATTTTTACAACTATTTTATCTTTACCATTTTACTATTTTAATT

Done.