Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01011194.1 Corchorus olitorius cultivar O-4 contig11227, 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: 9215
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33


Found at i:1709 original size:55 final size:56

Alignment explanation


    Indices: 1603--1712  Score: 186
    Period size: 55  Copynumber: 2.0  Consensus size: 56

       1593 TTTATTTTGT

                                    *    *                           
       1603 AGAATAATTAAGTAGAGATAGGGGGGATATGATTTATTATAACATTTATTGTGTGGA
          1 AGAATAATTAAGTAGAGATA-GGGAGATAAGATTTATTATAACATTTATTGTGTGGA

                                                                  
       1660 AGAATAATTAAGTAGAGATA-GGAGATAAGATTTATTATAACATTTATTGTGTG
          1 AGAATAATTAAGTAGAGATAGGGAGATAAGATTTATTATAACATTTATTGTGTG

       1713 AAAGGAAAAG


Statistics
Matches: 51,  Mismatches: 2, Indels: 2
        0.93            0.04        0.04

Matches are distributed among these distances:
  55   31  0.61
  57   20  0.39

ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35


Consensus pattern (56 bp):   
AGAATAATTAAGTAGAGATAGGGAGATAAGATTTATTATAACATTTATTGTGTGGA

Found at i:5352 original size:19 final size:19

Alignment explanation


    Indices: 5302--5352  Score: 61
    Period size: 19  Copynumber: 2.7  Consensus size: 19

       5292 CATAAAATTT

                               
       5302 TTAATAA-TAATTATTCAA
          1 TTAATAATTAATTATTCAA

              *              *  
       5320 TAAAATAATT-ATTATTTAA
          1 T-TAATAATTAATTATTCAA

                          
       5339 TTAATAATTAATTA
          1 TTAATAATTAATTA

       5353 ATTTCAGCCC


Statistics
Matches: 27,  Mismatches: 3, Indels: 5
        0.77            0.09        0.14

Matches are distributed among these distances:
  18    8  0.30
  19   18  0.67
  20    1  0.04

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (19 bp):   
TTAATAATTAATTATTCAA

Found at i:7311 original size:22 final size:22

Alignment explanation


    Indices: 7262--7312  Score: 59
    Period size: 22  Copynumber: 2.3  Consensus size: 22

       7252 AAATATTACC

                         *   **   
       7262 ATAATTATTTTTGGCAGCCATA
          1 ATAATTATTTTTGCCAGAAATA

                                   
       7284 ATAATTATTTTTGCCAAGAAATA
          1 ATAATTATTTTTGCC-AGAAATA

                   
       7307 A-AATTA
          1 ATAATTA

       7313 GGGAATAATT


Statistics
Matches: 25,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  22   19  0.76
  23    6  0.24

ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39


Consensus pattern (22 bp):   
ATAATTATTTTTGCCAGAAATA
Done.