Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014927.1 Corchorus olitorius cultivar O-4 contig14960, 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: 8701
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32


Found at i:624 original size:5 final size:5

Alignment explanation


    Indices: 614--654  Score: 55
    Period size: 5  Copynumber: 7.8  Consensus size: 5

        604 TACCTAATGA

                                  *                         
        614 AAAAG AAAAG AAAAG AAAAA ATAAAG AAAAG AAAAAG AAAA
          1 AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG -AAAAG AAAA

        655 CCAAAAACAA


Statistics
Matches: 32,  Mismatches: 2, Indels: 4
        0.84            0.05        0.11

Matches are distributed among these distances:
   5   23  0.72
   6    9  0.28

ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02


Consensus pattern (5 bp):   
AAAAG

Found at i:633 original size:11 final size:11

Alignment explanation


    Indices: 612--654  Score: 63
    Period size: 11  Copynumber: 4.0  Consensus size: 11

        602 TTTACCTAAT

                       
        612 GAAAAAGAAAA
          1 GAAAAAGAAAA

                       
        623 G-AAAAGAAAA
          1 GAAAAAGAAAA

                        
        633 -AATAAAGAAAA
          1 GAA-AAAGAAAA

                       
        644 GAAAAAGAAAA
          1 GAAAAAGAAAA

        655 CCAAAAACAA


Statistics
Matches: 29,  Mismatches: 0, Indels: 6
        0.83            0.00        0.17

Matches are distributed among these distances:
  10   10  0.34
  11   17  0.59
  12    2  0.07

ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02


Consensus pattern (11 bp):   
GAAAAAGAAAA

Found at i:633 original size:16 final size:16

Alignment explanation


    Indices: 612--654  Score: 70
    Period size: 16  Copynumber: 2.7  Consensus size: 16

        602 TTTACCTAAT

                            
        612 GAAAAAGAAAAGAAAA
          1 GAAAAAGAAAAGAAAA

                             
        628 GAAAAA-ATAAAGAAAA
          1 GAAAAAGA-AAAGAAAA

                       
        644 GAAAAAGAAAA
          1 GAAAAAGAAAA

        655 CCAAAAACAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  15    1  0.04
  16   23  0.92
  17    1  0.04

ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02


Consensus pattern (16 bp):   
GAAAAAGAAAAGAAAA

Found at i:8633 original size:2 final size:2

Alignment explanation


    Indices: 8626--8701  Score: 152
    Period size: 2  Copynumber: 38.0  Consensus size: 2

       8616 TTCTCTTTGT

                                                                          
       8626 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

                                                              
       8668 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA


Statistics
Matches: 74,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   74  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
GA

Done.