Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016795.1 Corchorus olitorius cultivar O-4 contig16828, 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: 10967
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32


Found at i:7609 original size:21 final size:21

Alignment explanation


    Indices: 7580--7619  Score: 62
    Period size: 21  Copynumber: 1.9  Consensus size: 21

       7570 AATTATAAAT

                *        *       
       7580 AAATTATTATTATTATTTTTG
          1 AAATAATTATTATCATTTTTG

                               
       7601 AAATAATTATTATCATTTT
          1 AAATAATTATTATCATTTT

       7620 CCATATATGC


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57


Consensus pattern (21 bp):   
AAATAATTATTATCATTTTTG

Found at i:9564 original size:22 final size:22

Alignment explanation


    Indices: 9514--9571  Score: 71
    Period size: 22  Copynumber: 2.6  Consensus size: 22

       9504 GAATTTTTTT

                            *    *
       9514 ATGAAATTTTGATAACTAACCT
          1 ATGAAATTTTGATAACCAACCA

              *           *   *   
       9536 ATTAAATTTTGATAGCCACCCA
          1 ATGAAATTTTGATAACCAACCA

                          
       9558 ATGAAATTTTGATA
          1 ATGAAATTTTGATA

       9572 TTTACCTAAG


Statistics
Matches: 30,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36


Consensus pattern (22 bp):   
ATGAAATTTTGATAACCAACCA

Found at i:9683 original size:42 final size:43

Alignment explanation


    Indices: 9637--9719  Score: 98
    Period size: 43  Copynumber: 2.0  Consensus size: 43

       9627 AATTTTAATA

                 *                            *         
       9637 AACCTTCCTATGAAATTTCG-TAATCT-TCCTATGATTTTTTAT
          1 AACCTCCCTATGAAATTTCGTTAATCTCT-CTATAATTTTTTAT

                     *   *    *                      
       9679 AACCTCCCTGTGAGATTTTGTTAATCTCTCTATAATTTTTT
          1 AACCTCCCTATGAAATTTCGTTAATCTCTCTATAATTTTTT

       9720 GATACTATAT


Statistics
Matches: 34,  Mismatches: 5, Indels: 3
        0.81            0.12        0.07

Matches are distributed among these distances:
  42   16  0.47
  43   17  0.50
  44    1  0.03

ACGTcount: A:0.24, C:0.19, G:0.08, T:0.48


Consensus pattern (43 bp):   
AACCTCCCTATGAAATTTCGTTAATCTCTCTATAATTTTTTAT
Done.