Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01016021.1 Corchorus capsularis cultivar CVL-1 contig16042, 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: 27641
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34


Found at i:87 original size:32 final size:33

Alignment explanation


    Indices: 18--91  Score: 98
    Period size: 32  Copynumber: 2.3  Consensus size: 33

          8 AAAATAGCCT

                                      *      
         18 AGCCGCCCTAGTGGGGCGGCACAGCCGTGGCAA
          1 AGCCGCCCTAGTGGGGCGGCACAGCCCTGGCAA

                                   *         *
         51 AGCCGCCCTAG-GAGGGCGGC-CTGCCCTGGCAC
          1 AGCCGCCCTAGTG-GGGCGGCACAGCCCTGGCAA

                     
         83 AGCCGCCCT
          1 AGCCGCCCT

         92 CCTGCGGCGG


Statistics
Matches: 37,  Mismatches: 3, Indels: 3
        0.86            0.07        0.07

Matches are distributed among these distances:
  32   19  0.51
  33   18  0.49

ACGTcount: A:0.15, C:0.39, G:0.36, T:0.09


Consensus pattern (33 bp):   
AGCCGCCCTAGTGGGGCGGCACAGCCCTGGCAA

Found at i:8643 original size:31 final size:30

Alignment explanation


    Indices: 8602--8659  Score: 82
    Period size: 29  Copynumber: 1.9  Consensus size: 30

       8592 CAATTCACCA

                                 *          
       8602 ATTTTATAAGTACACATGGACTAAATTGATTG
          1 ATTTTATAAGT--ACATGGACGAAATTGATTG

                                       
       8634 ATTTT-TAAGTACATGGACGAAATTGA
          1 ATTTTATAAGTACATGGACGAAATTGA

       8660 ACATTTTTGT


Statistics
Matches: 25,  Mismatches: 1, Indels: 3
        0.86            0.03        0.10

Matches are distributed among these distances:
  29   15  0.60
  31    5  0.20
  32    5  0.20

ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36


Consensus pattern (30 bp):   
ATTTTATAAGTACATGGACGAAATTGATTG

Found at i:15124 original size:17 final size:19

Alignment explanation


    Indices: 15102--15144  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 19

      15092 TGGACATCTC

                               
      15102 AAGAAAGAC-T-GTCCGAA
          1 AAGAAAGACTTGGTCCGAA

                   *      *    
      15119 AAGAAAGGCTTGGTTCGAA
          1 AAGAAAGACTTGGTCCGAA

                   
      15138 AAGAAAG
          1 AAGAAAG

      15145 GTACATATAT


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  17    8  0.36
  18    1  0.05
  19   13  0.59

ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14


Consensus pattern (19 bp):   
AAGAAAGACTTGGTCCGAA

Found at i:25290 original size:75 final size:76

Alignment explanation


    Indices: 25207--25397  Score: 296
    Period size: 75  Copynumber: 2.5  Consensus size: 76

      25197 ATAATAATGG

                                                                             
      25207 GAATATTTTTTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAA-ATAAT
          1 GAATATTTTTTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATA-AAT

                    * * 
      25271 AATAAAG-TTGA
         65 AATAAAGAATAA

                                                                            *
      25282 GAATATTTTTTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAAATT
          1 GAATATTTTTTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAAATA

                       
      25347 ATAAAGAATAA
         66 ATAAAGAATAA

                      *            *      *         
      25358 GAATATTTCTCTAAATCTTGCCAGATTGTGAGAGATTTAG
          1 GAATATTT-TTTAAATCTTGCCAAATTGTGGGAGATTTAG

      25398 AAAATATCAA


Statistics
Matches: 107,  Mismatches: 6, Indels: 4
        0.91            0.05        0.03

Matches are distributed among these distances:
  75   68  0.64
  76   11  0.10
  77   28  0.26

ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36


Consensus pattern (76 bp):   
GAATATTTTTTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAATAAATAAATA
ATAAAGAATAA

Done.