Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011635.1 Corchorus capsularis cultivar CVL-1 contig11656, 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: 16533
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30


Found at i:300 original size:31 final size:31

Alignment explanation


    Indices: 242--300  Score: 82
    Period size: 31  Copynumber: 1.9  Consensus size: 31

        232 TTGGACGAAA

                           *  *   *        
        242 TAAAAGGTTTGATACTAAGTTGTGATTTTCT
          1 TAAAAGGTTTGATACCAAATTGAGATTTTCT

                       *                
        273 TAAAAGGTTTGGTACCAAATTGAGATTT
          1 TAAAAGGTTTGATACCAAATTGAGATTT

        301 CAGCCTATAA


Statistics
Matches: 24,  Mismatches: 4, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  31   24  1.00

ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41


Consensus pattern (31 bp):   
TAAAAGGTTTGATACCAAATTGAGATTTTCT

Found at i:1716 original size:2 final size:2

Alignment explanation


    Indices: 1709--1742  Score: 50
    Period size: 2  Copynumber: 16.5  Consensus size: 2

       1699 TTAATTTCAT

                                                *             
       1709 TA TA TA TA TA TA TA TA TA TA TA TA CA CTA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T

       1743 TATTTTTGTC


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
   2   28  0.97
   3    1  0.03

ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:2861 original size:70 final size:68

Alignment explanation


    Indices: 2750--2880  Score: 226
    Period size: 70  Copynumber: 1.9  Consensus size: 68

       2740 CTTTCTGTAA

                           *                                                 
       2750 TTGTTTATAAAAGATGCATCAAATAAATAAAAATATCTCACATAAAAACATGCATGTAGCGCAAG
          1 TTGTTTATAAAAGATACATCAAATAAATAAAAATATCTCACATAAAAACATGCATGTAGCGCAAG

               
       2815 CGC
         66 CGC

                              *                                            
       2818 TTGTTTATAAAACAGATATATCAAATAAATAAAAATATCTCACATAAAAACATGCATGTAGCG
          1 TTGTTTAT-AAA-AGATACATCAAATAAATAAAAATATCTCACATAAAAACATGCATGTAGCG

       2881 TAAACGCAGA


Statistics
Matches: 59,  Mismatches: 2, Indels: 2
        0.94            0.03        0.03

Matches are distributed among these distances:
  68    8  0.14
  69    3  0.05
  70   48  0.81

ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27


Consensus pattern (68 bp):   
TTGTTTATAAAAGATACATCAAATAAATAAAAATATCTCACATAAAAACATGCATGTAGCGCAAG
CGC

Found at i:7491 original size:26 final size:27

Alignment explanation


    Indices: 7460--7524  Score: 73
    Period size: 26  Copynumber: 2.4  Consensus size: 27

       7450 ATAATTTTAG

                                        
       7460 TTTTAATTTATAAT-TTATAT-ATAAGT
          1 TTTTAATTTATAATGTTATATAATAA-T

                             *         
       7486 TTTTAATTT-TAATGTTTTATAATAAT
          1 TTTTAATTTATAATGTTATATAATAAT

              *          
       7512 TTATATATTTATA
          1 TTTTA-ATTTATA

       7525 TTCAACATTT


Statistics
Matches: 33,  Mismatches: 2, Indels: 6
        0.80            0.05        0.15

Matches are distributed among these distances:
  25    4  0.12
  26   19  0.58
  27    8  0.24
  28    2  0.06

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60


Consensus pattern (27 bp):   
TTTTAATTTATAATGTTATATAATAAT

Found at i:8443 original size:19 final size:19

Alignment explanation


    Indices: 8421--8459  Score: 60
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       8411 TAAAGTGAAA

                         *     
       8421 AGGATAAATATAATTAACT
          1 AGGATAAATATAAGTAACT

                 *             
       8440 AGGATCAATATAAGTAACT
          1 AGGATAAATATAAGTAACT

             
       8459 A
          1 A

       8460 TTAACAATTA


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  19   18  1.00

ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28


Consensus pattern (19 bp):   
AGGATAAATATAAGTAACT
Done.