Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01012437.1 Corchorus capsularis cultivar CVL-1 contig12458, 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: 30706
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


Found at i:16851 original size:12 final size:12

Alignment explanation


    Indices: 16807--16849  Score: 68
    Period size: 12  Copynumber: 3.5  Consensus size: 12

      16797 TTAATACAGG

                        
      16807 TATCGACGGATA
          1 TATCGACGGATA

                         
      16819 TATCGAACGGATA
          1 TATCG-ACGGATA

                  *     
      16832 TATCGATGGATA
          1 TATCGACGGATA

                  
      16844 TATCGA
          1 TATCGA

      16850 TGAAATTCAA


Statistics
Matches: 29,  Mismatches: 1, Indels: 2
        0.91            0.03        0.06

Matches are distributed among these distances:
  12   17  0.59
  13   12  0.41

ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28


Consensus pattern (12 bp):   
TATCGACGGATA

Found at i:30500 original size:78 final size:78

Alignment explanation


    Indices: 30402--30648  Score: 388
    Period size: 78  Copynumber: 3.2  Consensus size: 78

      30392 TTGTTTAGGT

                            *                     *                 *        
      30402 TTTTA-TAGTTTTACTGAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAACT
          1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT

               *          
      30466 ATTTTATTTTACCA
         65 ATTATATTTTACCA

                                                                             
      30480 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA

                         
      30545 TTATATTTTACCA
         66 TTATATTTTACCA

                                                           *  *  *           
      30558 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTATTAACCTTATAACTA
          1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA

                      ** 
      30623 TTATATTTTAATA
         66 TTATATTTTACCA

                  *      
      30636 TTTTACCATTTTA
          1 TTTTACTATTTTA

      30649 ATTAAAAAAA


Statistics
Matches: 158,  Mismatches: 10, Indels: 2
        0.93            0.06        0.01

Matches are distributed among these distances:
  78  156  0.99
  79    2  0.01

ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50


Consensus pattern (78 bp):   
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACCA

Found at i:30513 original size:38 final size:38

Alignment explanation


    Indices: 30470--30591  Score: 90
    Period size: 38  Copynumber: 3.2  Consensus size: 38

      30460 ATAACTATTT

                                                  
      30470 TATTTTACCATTTTACTATTTTACTCAACTAAAAACTC
          1 TATTTTACCATTTTACTATTTTACTCAACTAAAAACTC

                     *      * *   **               * * *
      30508 TATTTTTA-TATAATTAAATATAATA-TC--CTTATAACTATTA
          1 TA-TTTTACCAT--TTTACTATTTTACTCAAC-TA-AA-AACTC

                                                  
      30548 TATTTTACCATTTTACTATTTTACTCAACTAAAAACTC
          1 TATTTTACCATTTTACTATTTTACTCAACTAAAAACTC

                  
      30586 TATTTT
          1 TATTTT

      30592 TATATAATTA


Statistics
Matches: 58,  Mismatches: 16, Indels: 20
        0.62            0.17        0.21

Matches are distributed among these distances:
  37    1  0.02
  38   22  0.38
  39   18  0.31
  40   16  0.28
  41    1  0.02

ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48


Consensus pattern (38 bp):   
TATTTTACCATTTTACTATTTTACTCAACTAAAAACTC
Done.