Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014484.1 Corchorus capsularis cultivar CVL-1 contig14505, 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: 20423
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


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

Alignment explanation


    Indices: 1--34  Score: 68
    Period size: 2  Copynumber: 17.0  Consensus size: 2

                                                              
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

         35 AAATAGTATG


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   32  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
TA

Found at i:9136 original size:7 final size:7

Alignment explanation


    Indices: 9124--9150  Score: 54
    Period size: 7  Copynumber: 3.9  Consensus size: 7

       9114 GAAAATTCAA

                   
       9124 TTGGCAT
          1 TTGGCAT

                   
       9131 TTGGCAT
          1 TTGGCAT

                   
       9138 TTGGCAT
          1 TTGGCAT

                  
       9145 TTGGCA
          1 TTGGCA

       9151 ACCCTTTCTT


Statistics
Matches: 20,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   20  1.00

ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41


Consensus pattern (7 bp):   
TTGGCAT

Found at i:10609 original size:27 final size:27

Alignment explanation


    Indices: 10549--10610  Score: 79
    Period size: 27  Copynumber: 2.3  Consensus size: 27

      10539 AGTAGCGGCG

                                * *   *
      10549 GGAGGAGAGCTCACTGGAACTGGAGCT
          1 GGAGGAGAGCTCACTGGAACAGCAGCA

              *        *               
      10576 GGTGGAGAGCTTACTGGAACAGCAGCA
          1 GGAGGAGAGCTCACTGGAACAGCAGCA

                    
      10603 GGAGGAGA
          1 GGAGGAGA

      10611 AGAAGCCGGA


Statistics
Matches: 29,  Mismatches: 6, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  27   29  1.00

ACGTcount: A:0.29, C:0.16, G:0.42, T:0.13


Consensus pattern (27 bp):   
GGAGGAGAGCTCACTGGAACAGCAGCA

Found at i:10623 original size:15 final size:15

Alignment explanation


    Indices: 10603--10636  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      10593 AACAGCAGCA

                        *  
      10603 GGAGGAGAAGAAGCC
          1 GGAGGAGAAGAAACC

                    *      
      10618 GGAGGAGAGGAAACC
          1 GGAGGAGAAGAAACC

                
      10633 GGAG
          1 GGAG

      10637 CAGATTTAGA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.38, C:0.12, G:0.50, T:0.00


Consensus pattern (15 bp):   
GGAGGAGAAGAAACC

Found at i:12473 original size:15 final size:15

Alignment explanation


    Indices: 12443--12510  Score: 62
    Period size: 15  Copynumber: 5.1  Consensus size: 15

      12433 TTCCTTCATT

                           
      12443 TTAATCATAAACTAA
          1 TTAATCATAAACTAA

                           
      12458 TTAA--AT--ACTAA
          1 TTAATCATAAACTAA

                           
      12469 TTAATCATAAACTAA
          1 TTAATCATAAACTAA

                 *         
      12484 TT-A-GAT--ACTAA
          1 TTAATCATAAACTAA

                *          
      12495 TTAAACATAAACTAA
          1 TTAATCATAAACTAA

             
      12510 T
          1 T

      12511 AAACTAAGTA


Statistics
Matches: 43,  Mismatches: 2, Indels: 16
        0.70            0.03        0.26

Matches are distributed among these distances:
  11   16  0.37
  12    1  0.02
  13    8  0.19
  14    1  0.02
  15   17  0.40

ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34


Consensus pattern (15 bp):   
TTAATCATAAACTAA

Found at i:12479 original size:26 final size:26

Alignment explanation


    Indices: 12443--12510  Score: 118
    Period size: 26  Copynumber: 2.6  Consensus size: 26

      12433 TTCCTTCATT

                                      
      12443 TTAATCATAAACTAATTAAATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                              *       
      12469 TTAATCATAAACTAATTAGATACTAA
          1 TTAATCATAAACTAATTAAATACTAA

                *           
      12495 TTAAACATAAACTAAT
          1 TTAATCATAAACTAAT

      12511 AAACTAAGTA


Statistics
Matches: 40,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  26   40  1.00

ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34


Consensus pattern (26 bp):   
TTAATCATAAACTAATTAAATACTAA
Done.