Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01001030.1 Corchorus capsularis cultivar CVL-1 contig01030, 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: 16319
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30


Found at i:1634 original size:17 final size:18

Alignment explanation


    Indices: 1593--1639  Score: 62
    Period size: 18  Copynumber: 2.7  Consensus size: 18

       1583 GAGAAAGAAA

                   *          
       1593 AAGAAAATAAAAGGAGAG
          1 AAGAAAAGAAAAGGAGAG

                               
       1611 AAGAAAAGAAAATGGAGAG
          1 AAGAAAAGAAAA-GGAGAG

                        
       1630 -A-AAAAGAAAA
          1 AAGAAAAGAAAA

       1640 AAATAGATTT


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  17    9  0.33
  18   12  0.44
  19    6  0.22

ACGTcount: A:0.70, C:0.00, G:0.26, T:0.04


Consensus pattern (18 bp):   
AAGAAAAGAAAAGGAGAG

Found at i:1641 original size:19 final size:19

Alignment explanation


    Indices: 1588--1642  Score: 58
    Period size: 19  Copynumber: 2.8  Consensus size: 19

       1578 GAAACGAGAA

                                 
       1588 AGAAAAAGAAAATAAAAGGAG
          1 AGAAAAAG-AAA-AAAAGGAG

                      *    *    
       1609 AGAAGAAA-AGAAAATGGAG
          1 AGAA-AAAGAAAAAAAGGAG

                           
       1628 AGAAAAAGAAAAAAA
          1 AGAAAAAGAAAAAAA

       1643 TAGATTTTTA


Statistics
Matches: 28,  Mismatches: 4, Indels: 6
        0.74            0.11        0.16

Matches are distributed among these distances:
  18    3  0.11
  19   16  0.57
  20    2  0.07
  21    4  0.14
  22    3  0.11

ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04


Consensus pattern (19 bp):   
AGAAAAAGAAAAAAAGGAG

Found at i:16281 original size:2 final size:2

Alignment explanation


    Indices: 16274--16319  Score: 92
    Period size: 2  Copynumber: 23.0  Consensus size: 2

      16264 GTTTTCAAAA

                                                                          
      16274 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
          1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG

                 
      16316 AG AG
          1 AG AG


Statistics
Matches: 44,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   44  1.00

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


Consensus pattern (2 bp):   
AG

Done.