Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019771.1 Corchorus olitorius cultivar O-4 contig19804, 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: 5835
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32


Found at i:4364 original size:4 final size:4

Alignment explanation


    Indices: 4355--4386  Score: 64
    Period size: 4  Copynumber: 8.0  Consensus size: 4

       4345 TGGGCCTGGC

                                                   
       4355 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA
          1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA

       4387 GAAGAGAAAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   28  1.00

ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00


Consensus pattern (4 bp):   
CAAA

Found at i:4497 original size:5 final size:6

Alignment explanation


    Indices: 4464--4511  Score: 71
    Period size: 6  Copynumber: 8.2  Consensus size: 6

       4454 CCCAAGCCAG

                       *                *                          
       4464 GAAAAA -AAAGA GAAAAA GAAAAA TAAAAA GAAAAA GAAAAA GAAAAA
          1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA

             
       4511 G
          1 G

       4512 GAAATAAAAT


Statistics
Matches: 37,  Mismatches: 4, Indels: 2
        0.86            0.09        0.05

Matches are distributed among these distances:
   5    4  0.11
   6   33  0.89

ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02


Consensus pattern (6 bp):   
GAAAAA

Found at i:4525 original size:22 final size:22

Alignment explanation


    Indices: 4495--4538  Score: 54
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       4485 AATAAAAAGA

                                   
       4495 AAAAGAAAA-AGAAAAAGGAAAT
          1 AAAAGAAAATA-AAAAAGGAAAT

                *        *        
       4517 AAAATAAAATAAATAAGGAAAT
          1 AAAAGAAAATAAAAAAGGAAAT

       4539 TAAGTTGAAA


Statistics
Matches: 19,  Mismatches: 2, Indels: 2
        0.83            0.09        0.09

Matches are distributed among these distances:
  22   18  0.95
  23    1  0.05

ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11


Consensus pattern (22 bp):   
AAAAGAAAATAAAAAAGGAAAT
Done.