Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019920.1 Corchorus olitorius cultivar O-4 contig19953, 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: 2785
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:1633 original size:6 final size:6

Alignment explanation


    Indices: 1622--1667  Score: 71
    Period size: 6  Copynumber: 8.2  Consensus size: 6

       1612 TATATTATCA

                                                                   
       1622 ATCTAT ATCTAT ATC--T ATCTAT ATCTAT ATCTAT ATCTAT A-CTAT
          1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT

             
       1667 A
          1 A

       1668 CTAAAAAGTA


Statistics
Matches: 38,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
   4    4  0.11
   5    5  0.13
   6   29  0.76

ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48


Consensus pattern (6 bp):   
ATCTAT

Found at i:1640 original size:10 final size:10

Alignment explanation


    Indices: 1627--1667  Score: 55
    Period size: 10  Copynumber: 3.8  Consensus size: 10

       1617 TATCAATCTA

                      
       1627 TATCTATATC
          1 TATCTATATC

                      
       1637 TATCTATATC
          1 TATCTATATC

                        
       1647 TATATCTATATC
          1 --TATCTATATC

                     
       1659 TATACTATA
          1 TAT-CTATA

       1668 CTAAAAAGTA


Statistics
Matches: 28,  Mismatches: 0, Indels: 5
        0.85            0.00        0.15

Matches are distributed among these distances:
  10   13  0.46
  11    5  0.18
  12   10  0.36

ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49


Consensus pattern (10 bp):   
TATCTATATC

Found at i:1641 original size:16 final size:16

Alignment explanation


    Indices: 1617--1655  Score: 69
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       1607 AGCTGTATAT

                *           
       1617 TATCAATCTATATCTA
          1 TATCTATCTATATCTA

                            
       1633 TATCTATCTATATCTA
          1 TATCTATCTATATCTA

                   
       1649 TATCTAT
          1 TATCTAT

       1656 ATCTATACTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  16   22  1.00

ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49


Consensus pattern (16 bp):   
TATCTATCTATATCTA
Done.