Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012727.1 Corchorus capsularis cultivar CVL-1 contig12748, 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: 3253
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26


Found at i:1613 original size:23 final size:24

Alignment explanation


    Indices: 1554--1626  Score: 75
    Period size: 22  Copynumber: 3.2  Consensus size: 24

       1544 TCCCAAAAGG

                   *                
       1554 AAAGAAACGAGAAGAAAAAA-G-A
          1 AAAGAAAAGAGAAGAAAAAAGGAA

            *                        
       1576 TAA-AAAAGATGAAGAAAAAAGGAA
          1 AAAGAAAAGA-GAAGAAAAAAGGAA

                                     
       1600 AAAGAAAAGA-AAG-AAAAAGAGAA
          1 AAAGAAAAGAGAAGAAAAAAG-GAA

                
       1623 AAAG
          1 AAAG

       1627 CAAATATGGT


Statistics
Matches: 43,  Mismatches: 3, Indels: 9
        0.78            0.05        0.16

Matches are distributed among these distances:
  21    5  0.12
  22   18  0.42
  23   11  0.26
  24    3  0.07
  25    6  0.14

ACGTcount: A:0.74, C:0.01, G:0.22, T:0.03


Consensus pattern (24 bp):   
AAAGAAAAGAGAAGAAAAAAGGAA

Found at i:1619 original size:29 final size:30

Alignment explanation


    Indices: 1569--1626  Score: 75
    Period size: 29  Copynumber: 2.0  Consensus size: 30

       1559 AACGAGAAGA

                            **            
       1569 AAAAAGATAAAAAAGATGAAGA-AAAAAGG
          1 AAAAAGATAAAAAAGAAAAAGAGAAAAAGG

                                          
       1598 AAAAAGA-AAAGAAAGAAAAAGAGAAAAAG
          1 AAAAAGATAAA-AAAGAAAAAGAGAAAAAG

       1627 CAAATATGGT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  28    3  0.12
  29   16  0.64
  30    6  0.24

ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03


Consensus pattern (30 bp):   
AAAAAGATAAAAAAGAAAAAGAGAAAAAGG

Found at i:1683 original size:45 final size:45

Alignment explanation


    Indices: 1632--1754  Score: 178
    Period size: 44  Copynumber: 2.8  Consensus size: 45

       1622 AAAAGCAAAT

                                              *          
       1632 ATGGTTTTCAAAAAAGAGTCATGGTTTTCAAAAGGTTTTGATAAA
          1 ATGGTTTTCAAAAAAGAGTCATGGTTTTCAAAAGATTTTGATAAA

                                        *                
       1677 ATGGTTTT-AAAAAAGAGTCATGGTTTTTAAAAGATTTTGATAAA
          1 ATGGTTTTCAAAAAAGAGTCATGGTTTTCAAAAGATTTTGATAAA

                *                *        *    
       1721 ATGCTTTTTC-AAAAAGAGTCTTGGTTTTCCAAAG
          1 ATG-GTTTTCAAAAAAGAGTCATGGTTTTCAAAAG

       1755 TGGTGTTTTC


Statistics
Matches: 70,  Mismatches: 6, Indels: 4
        0.88            0.08        0.05

Matches are distributed among these distances:
  44   37  0.53
  45   33  0.47

ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37


Consensus pattern (45 bp):   
ATGGTTTTCAAAAAAGAGTCATGGTTTTCAAAAGATTTTGATAAA

Done.