Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015059.1 Corchorus olitorius cultivar O-4 contig15092, 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: 6446
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29


Found at i:5385 original size:17 final size:17

Alignment explanation


    Indices: 5342--5388  Score: 58
    Period size: 18  Copynumber: 2.7  Consensus size: 17

       5332 TCCCAATAAA

                   *         
       5342 AAAAAATCAAAAAAATC
          1 AAAAAATGAAAAAAATC

                       *     *
       5359 AAAGAAATGAATAAAATG
          1 AAA-AAATGAAAAAAATC

                        
       5377 AAAAAATGAAAA
          1 AAAAAATGAAAA

       5389 GTGAAAAAAG


Statistics
Matches: 25,  Mismatches: 4, Indels: 2
        0.81            0.13        0.06

Matches are distributed among these distances:
  17   11  0.44
  18   14  0.56

ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13


Consensus pattern (17 bp):   
AAAAAATGAAAAAAATC

Found at i:5397 original size:9 final size:8

Alignment explanation


    Indices: 5351--5397  Score: 51
    Period size: 8  Copynumber: 5.8  Consensus size: 8

       5341 AAAAAAATCA

                   *
       5351 AAAAAATC
          1 AAAAAATG

                     
       5359 AAAGAAATG
          1 AAA-AAATG

                     
       5368 AATAAAATG
          1 AA-AAAATG

                    
       5377 AAAAAATG
          1 AAAAAATG

                 *  
       5385 -AAAAGTG
          1 AAAAAATG

                  
       5392 AAAAAA
          1 AAAAAA

       5398 GCACTTGGAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
   7    6  0.18
   8   13  0.39
   9   13  0.39
  10    1  0.03

ACGTcount: A:0.72, C:0.02, G:0.13, T:0.13


Consensus pattern (8 bp):   
AAAAAATG

Found at i:5835 original size:6 final size:6

Alignment explanation


    Indices: 5819--5864  Score: 60
    Period size: 6  Copynumber: 7.7  Consensus size: 6

       5809 TCAATAAAAA

                                                                   
       5819 AAAATTC AAAATC AAAATC AAAAATC -AAATC -AAATC AAAATC AAAA
          1 AAAA-TC AAAATC AAAATC -AAAATC AAAATC AAAATC AAAATC AAAA

       5865 GAGGATTGAT


Statistics
Matches: 37,  Mismatches: 0, Indels: 5
        0.88            0.00        0.12

Matches are distributed among these distances:
   5   10  0.27
   6   17  0.46
   7   10  0.27

ACGTcount: A:0.67, C:0.15, G:0.00, T:0.17


Consensus pattern (6 bp):   
AAAATC
Done.