Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01009544.1 Corchorus capsularis cultivar CVL-1 contig09565, 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: 23704
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31


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

Alignment explanation


    Indices: 1--45  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

                                                                          
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

                
         43 CT C
          1 CT C

         46 ATCATATGTA


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49


Consensus pattern (2 bp):   
CT

Found at i:2594 original size:40 final size:40

Alignment explanation


    Indices: 2539--2620  Score: 146
    Period size: 40  Copynumber: 2.0  Consensus size: 40

       2529 TCTCTCAAGC

                                  *                 
       2539 TTACCAAATTGAGAAAAATCAATATTATGGAGGGATAAAA
          1 TTACCAAATTGAGAAAAATCAACATTATGGAGGGATAAAA

                                   *                
       2579 TTACCAAATTGAGAAAAATCAACGTTATGGAGGGATAAAA
          1 TTACCAAATTGAGAAAAATCAACATTATGGAGGGATAAAA

              
       2619 TT
          1 TT

       2621 TTATTTTATG


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

Matches are distributed among these distances:
  40   40  1.00

ACGTcount: A:0.48, C:0.09, G:0.18, T:0.26


Consensus pattern (40 bp):   
TTACCAAATTGAGAAAAATCAACATTATGGAGGGATAAAA

Found at i:3096 original size:109 final size:109

Alignment explanation


    Indices: 2900--3195  Score: 459
    Period size: 109  Copynumber: 2.7  Consensus size: 109

       2890 ACTATTATAG

                         *                     *                             
       2900 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
          1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT

                                                             
       2965 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
         61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                                                                             
       3014 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT

                                 *                      
       3079 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
         66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA

                                                           *           **    
       3123 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAAATTTTTTTA
          1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TAT-AATTACTTTA

                     
       3187 TTTTTACCA
         63 TTTTTACCA

       3196 TTTTAATTTA


Statistics
Matches: 173,  Mismatches: 6, Indels: 9
        0.92            0.03        0.05

Matches are distributed among these distances:
 108    1  0.01
 109  126  0.73
 110    6  0.03
 111   19  0.11
 114   21  0.12

ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50


Consensus pattern (109 bp):   
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.