Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01017399.1 Corchorus olitorius cultivar O-4 contig17432, 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: 10369
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32


Found at i:96 original size:42 final size:42

Alignment explanation


    Indices: 37--137  Score: 184
    Period size: 42  Copynumber: 2.4  Consensus size: 42

         27 ATAGGCAAAA

                                                      
         37 TTGATATATTGTAAATTATTATCAAAGGATCTTATTAGTTGT
          1 TTGATATATTGTAAATTATTATCAAAGGATCTTATTAGTTGT

                                   *      *           
         79 TTGATATATTGTAAATTATTATCTAAGGATTTTATTAGTTGT
          1 TTGATATATTGTAAATTATTATCAAAGGATCTTATTAGTTGT

                             
        121 TTGATATATTGTAAATT
          1 TTGATATATTGTAAATT

        138 GGAATTTGAT


Statistics
Matches: 57,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  42   57  1.00

ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50


Consensus pattern (42 bp):   
TTGATATATTGTAAATTATTATCAAAGGATCTTATTAGTTGT

Found at i:155 original size:34 final size:34

Alignment explanation


    Indices: 107--172  Score: 123
    Period size: 34  Copynumber: 1.9  Consensus size: 34

         97 TTATCTAAGG

                *                             
        107 ATTTTATTAGTTGTTTGATATATTGTAAATTGGA
          1 ATTTGATTAGTTGTTTGATATATTGTAAATTGGA

                                            
        141 ATTTGATTAGTTGTTTGATATATTGTAAATTG
          1 ATTTGATTAGTTGTTTGATATATTGTAAATTG

        173 ATATATTGAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  34   31  1.00

ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53


Consensus pattern (34 bp):   
ATTTGATTAGTTGTTTGATATATTGTAAATTGGA

Found at i:6974 original size:15 final size:15

Alignment explanation


    Indices: 6937--6968  Score: 55
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       6927 GATAAAACTG

                           
       6937 AAAATTAAGTGCTGA
          1 AAAATTAAGTGCTGA

                       *   
       6952 AAAATTAAGTGTTGA
          1 AAAATTAAGTGCTGA

              
       6967 AA
          1 AA

       6969 TTTTAATACT


Statistics
Matches: 16,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.50, C:0.03, G:0.19, T:0.28


Consensus pattern (15 bp):   
AAAATTAAGTGCTGA

Found at i:7451 original size:17 final size:17

Alignment explanation


    Indices: 7429--7462  Score: 50
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       7419 TAATACTACT

                             
       7429 AATAAAAATCAAATTTG
          1 AATAAAAATCAAATTTG

                  *     *    
       7446 AATAAACATCAATTTTG
          1 AATAAAAATCAAATTTG

       7463 TTTTGTTGTC


Statistics
Matches: 15,  Mismatches: 2, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  17   15  1.00

ACGTcount: A:0.53, C:0.09, G:0.06, T:0.32


Consensus pattern (17 bp):   
AATAAAAATCAAATTTG
Done.