Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016675.1 Corchorus olitorius cultivar O-4 contig16708, 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: 10126
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32


Found at i:7 original size:2 final size:2

Alignment explanation


    Indices: 1--39  Score: 71
    Period size: 2  Copynumber: 20.0  Consensus size: 2

                                                                       
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

         40 TGTTGACAAT


Statistics
Matches: 36,  Mismatches: 0, Indels: 2
        0.95            0.00        0.05

Matches are distributed among these distances:
   1    1  0.03
   2   35  0.97

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (2 bp):   
AT

Found at i:1154 original size:18 final size:18

Alignment explanation


    Indices: 1131--1173  Score: 68
    Period size: 18  Copynumber: 2.4  Consensus size: 18

       1121 TAAACTGAGG

                              
       1131 GCAGCGGCTAGAAGAGAA
          1 GCAGCGGCTAGAAGAGAA

                     *       *
       1149 GCAGCGGCTTGAAGAGAT
          1 GCAGCGGCTAGAAGAGAA

                   
       1167 GCAGCGG
          1 GCAGCGG

       1174 GAAGAAGATA


Statistics
Matches: 23,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.30, C:0.19, G:0.42, T:0.09


Consensus pattern (18 bp):   
GCAGCGGCTAGAAGAGAA

Found at i:1180 original size:18 final size:18

Alignment explanation


    Indices: 1131--1181  Score: 57
    Period size: 18  Copynumber: 2.8  Consensus size: 18

       1121 TAAACTGAGG

                    *         
       1131 GCAGCGGCTAGAAGAGAA
          1 GCAGCGGCAAGAAGAGAA

                    **       *
       1149 GCAGCGGCTTGAAGAGAT
          1 GCAGCGGCAAGAAGAGAA

                   *       
       1167 GCAGCGGGAAGAAGA
          1 GCAGCGGCAAGAAGA

       1182 TAGACTGAAA


Statistics
Matches: 28,  Mismatches: 5, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  18   28  1.00

ACGTcount: A:0.35, C:0.16, G:0.41, T:0.08


Consensus pattern (18 bp):   
GCAGCGGCAAGAAGAGAA

Found at i:4839 original size:22 final size:22

Alignment explanation


    Indices: 4811--4859  Score: 80
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       4801 TTCCAGAATC

                                  
       4811 CGAAGCGACGTGCCTCGAAACT
          1 CGAAGCGACGTGCCTCGAAACT

                           *    * 
       4833 CGAAGCGACGTGCCTTGAAATT
          1 CGAAGCGACGTGCCTCGAAACT

                 
       4855 CGAAG
          1 CGAAG

       4860 TGTCGTTTCC


Statistics
Matches: 25,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  22   25  1.00

ACGTcount: A:0.29, C:0.27, G:0.29, T:0.16


Consensus pattern (22 bp):   
CGAAGCGACGTGCCTCGAAACT
Done.