Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019893.1 Corchorus olitorius cultivar O-4 contig19926, 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: 6073
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:1524 original size:23 final size:25

Alignment explanation


    Indices: 1498--1549  Score: 72
    Period size: 25  Copynumber: 2.2  Consensus size: 25

       1488 CTGCTGGGCC

                             *       
       1498 GGCCTG-GCGCGGCCC-TGCGCGCG
          1 GGCCTGTGCGCGGCCCAGGCGCGCG

                      *              
       1521 GGCCTGTGCGTGGCCCAGGCGCGCG
          1 GGCCTGTGCGCGGCCCAGGCGCGCG

                
       1546 GGCC
          1 GGCC

       1550 AGGCCACCAG


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23    6  0.24
  24    8  0.32
  25   11  0.44

ACGTcount: A:0.02, C:0.40, G:0.48, T:0.10


Consensus pattern (25 bp):   
GGCCTGTGCGCGGCCCAGGCGCGCG

Found at i:1622 original size:5 final size:6

Alignment explanation


    Indices: 1572--1634  Score: 58
    Period size: 6  Copynumber: 10.5  Consensus size: 6

       1562 CCAAGCCAGG

                                          * *    * *                 
       1572 AAAAG- AAAA-A AAAAGA AAAAGGA ATAGGA AGAGGA AAAAGAA AAAAGA
          1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAG-A AAAAGA

                             
       1620 AAAAGA AAAAGA AAA
          1 AAAAGA AAAAGA AAA

       1635 TAAAATAAGT


Statistics
Matches: 49,  Mismatches: 5, Indels: 7
        0.80            0.08        0.11

Matches are distributed among these distances:
   5    8  0.16
   6   31  0.63
   7   10  0.20

ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02


Consensus pattern (6 bp):   
AAAAGA

Found at i:1623 original size:13 final size:12

Alignment explanation


    Indices: 1572--1634  Score: 58
    Period size: 13  Copynumber: 5.2  Consensus size: 12

       1562 CCAAGCCAGG

                        
       1572 AAAAG-AAAA-A
          1 AAAAGAAAAAGA

                         
       1582 AAAAGAAAAAGGA
          1 AAAAGAAAAA-GA

             * *   * *  
       1595 ATAGGAAGAGGA
          1 AAAAGAAAAAGA

                         
       1607 AAAAGAAAAAAGA
          1 AAAAG-AAAAAGA

                        
       1620 AAAAGAAAAAGA
          1 AAAAGAAAAAGA

               
       1632 AAA
          1 AAA

       1635 TAAAATAAGT


Statistics
Matches: 41,  Mismatches: 8, Indels: 6
        0.75            0.15        0.11

Matches are distributed among these distances:
  10    5  0.12
  11    4  0.10
  12   15  0.37
  13   17  0.41

ACGTcount: A:0.78, C:0.00, G:0.21, T:0.02


Consensus pattern (12 bp):   
AAAAGAAAAAGA
Done.