Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017193.1 Corchorus olitorius cultivar O-4 contig17226, 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: 10795
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34


Found at i:3716 original size:15 final size:15

Alignment explanation


    Indices: 3696--3729  Score: 52
    Period size: 15  Copynumber: 2.3  Consensus size: 15

       3686 ATATCAAACA

                            
       3696 CAAAAACAT-TACCCT
          1 CAAAAACATCTA-CCT

                           
       3711 CAAAAACATCTACCT
          1 CAAAAACATCTACCT

                
       3726 CAAA
          1 CAAA

       3730 GGTTGTAAAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  15   16  0.89
  16    2  0.11

ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18


Consensus pattern (15 bp):   
CAAAAACATCTACCT

Found at i:3917 original size:23 final size:23

Alignment explanation


    Indices: 3887--3934  Score: 96
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       3877 ACGTCAGCAC

                                   
       3887 ATGACTCTGCAGTAAGCAATTTA
          1 ATGACTCTGCAGTAAGCAATTTA

                                   
       3910 ATGACTCTGCAGTAAGCAATTTA
          1 ATGACTCTGCAGTAAGCAATTTA

              
       3933 AT
          1 AT

       3935 TCCAAGGACA


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  23   25  1.00

ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31


Consensus pattern (23 bp):   
ATGACTCTGCAGTAAGCAATTTA

Found at i:4883 original size:2 final size:2

Alignment explanation


    Indices: 4866--4900  Score: 56
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       4856 TGTCACAAAT

                                                                   
       4866 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       4901 TATGAAGAAC


Statistics
Matches: 31,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
   1    2  0.06
   2   29  0.94

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (2 bp):   
TA

Found at i:6589 original size:22 final size:22

Alignment explanation


    Indices: 6561--6603  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       6551 ATTGTTATGG

                      *    *      
       6561 AAGAATGGAGGGAAGGAAGAGA
          1 AAGAATGGAGAGAAGAAAGAGA

                                 
       6583 AAGAATGGAGAGAAGAAAGAG
          1 AAGAATGGAGAGAAGAAAGAG

       6604 GAAGGGGCGG


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.53, C:0.00, G:0.42, T:0.05


Consensus pattern (22 bp):   
AAGAATGGAGAGAAGAAAGAGA
Done.