Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020262.1 Corchorus olitorius cultivar O-4 contig20295, 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: 11124
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32


Found at i:4907 original size:15 final size:15

Alignment explanation


    Indices: 4887--4916  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       4877 TACATCAGTT

                           
       4887 TGGCCAAAAGTAAAA
          1 TGGCCAAAAGTAAAA

                           
       4902 TGGCCAAAAGTAAAA
          1 TGGCCAAAAGTAAAA

       4917 GGCAATGCTA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13


Consensus pattern (15 bp):   
TGGCCAAAAGTAAAA

Found at i:9496 original size:146 final size:146

Alignment explanation


    Indices: 9232--9525  Score: 579
    Period size: 146  Copynumber: 2.0  Consensus size: 146

       9222 GCAATGATGG

                                                           *                 
       9232 CAGCCTAACTTCAGAGCCTCTGAAAATAGGCTCCCTACAACTATGGCTATCTGGATTCAACTCCC
          1 CAGCCTAACTTCAGAGCCTCTGAAAATAGGCTCCCTACAACTATGGCCATCTGGATTCAACTCCC

                                                                             
       9297 AGAATTGCCTGTTGAATTTTATGATGTGAATATACTCCAAGAAATCGCTTTATTGGTGGGCACTC
         66 AGAATTGCCTGTTGAATTTTATGATGTGAATATACTCCAAGAAATCGCTTTATTGGTGGGCACTC

                            
       9362 CGATTAAGATTGACGC
        131 CGATTAAGATTGACGC

                                                                             
       9378 CAGCCTAACTTCAGAGCCTCTGAAAATAGGCTCCCTACAACTATGGCCATCTGGATTCAACTCCC
          1 CAGCCTAACTTCAGAGCCTCTGAAAATAGGCTCCCTACAACTATGGCCATCTGGATTCAACTCCC

                                                                             
       9443 AGAATTGCCTGTTGAATTTTATGATGTGAATATACTCCAAGAAATCGCTTTATTGGTGGGCACTC
         66 AGAATTGCCTGTTGAATTTTATGATGTGAATATACTCCAAGAAATCGCTTTATTGGTGGGCACTC

                            
       9508 CGATTAAGATTGACGC
        131 CGATTAAGATTGACGC

              
       9524 CA
          1 CA

       9526 ACACCAGCAT


Statistics
Matches: 147,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
 146  147  1.00

ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29


Consensus pattern (146 bp):   
CAGCCTAACTTCAGAGCCTCTGAAAATAGGCTCCCTACAACTATGGCCATCTGGATTCAACTCCC
AGAATTGCCTGTTGAATTTTATGATGTGAATATACTCCAAGAAATCGCTTTATTGGTGGGCACTC
CGATTAAGATTGACGC

Found at i:10934 original size:52 final size:53

Alignment explanation


    Indices: 10865--11122  Score: 372
    Period size: 52  Copynumber: 5.0  Consensus size: 53

      10855 ATTGAAAACT

                    *                                      *      
      10865 AAAATCTGGTGGGAACTTTCCCAATTT-AAAAACCAGCTAAATTGAACACTTTG
          1 AAAAT-TGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

                *                                                
      10918 AAAACTGATGGGAACTTTCCCAATTTG-AAAACCAGCTAAATTGAATACTTTG
          1 AAAATTGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

                     *                       *                *  
      10970 AAAATTGATTGGAACTTTCCCAATTTGAAAAA-GAGCTAAATTGAATACTCTG
          1 AAAATTGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

                                                *                
      11022 AAAATTGATGGGAACTTTCCCAATTTGAAAAA-C--TTAAATTGAATACTTTG
          1 AAAATTGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

                                                *                
      11072 AAAATTGATGGGAACTTTCCCAATTTGAAAAA-C--TTAAATTGAATACTTTG
          1 AAAATTGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

             
      11122 A
          1 A

      11123 TG


Statistics
Matches: 192,  Mismatches: 11, Indels: 7
        0.91            0.05        0.03

Matches are distributed among these distances:
  50   66  0.34
  52  118  0.61
  53    8  0.04

ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31


Consensus pattern (53 bp):   
AAAATTGATGGGAACTTTCCCAATTTGAAAAACCAGCTAAATTGAATACTTTG

Done.