Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01014312.1 Corchorus capsularis cultivar CVL-1 contig14333, 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: 5833
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27


Found at i:3371 original size:64 final size:64

Alignment explanation


    Indices: 3198--3477  Score: 303
    Period size: 64  Copynumber: 4.3  Consensus size: 64

       3188 TTAAGAATTA

                             *              *     *         ***        *     
       3198 ATCGGAAGACGATCTTGGTAAGAAGCTA-ACCGGAAGACGGTCTGCTAGGGAGAGTTTTTAGAAG
          1 ATCGGAAGACGATCTTGTTAAGAAG-TACACCAGAAGATGGT-T--TATCAAGAGTTTTCAGAAG

             * 
       3262 TGG
         62 TTG

                     *           *        *       *                         
       3265 ATCGGAAG-TGATCTTGTTAAAAAGTACACTAGAAGATAGTTTATCAAGAGTTTTCAGAAGTTG
          1 ATCGGAAGACGATCTTGTTAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGTTG

                 *             *     *                        *             
       3328 ATCGGGAGACGATCTTGTTTAGAAGCACACCAGAAGATGGTTTATCAAGAATTTTCAGAAGTTG
          1 ATCGGAAGACGATCTTGTTAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGTTG

                           *  * *                   *                     * 
       3392 ATCGGAAGACGATCTCGTCATGAAGTACACCAGAAGATGGGTTATCAAGAGTTTTCAGAAGTCG
          1 ATCGGAAGACGATCTTGTTAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGTTG

               *                  
       3456 ATGGGGAAGACGATCTTGTTAA
          1 AT-CGGAAGACGATCTTGTTAA

       3478 AAGATGCACT


Statistics
Matches: 177,  Mismatches: 33, Indels: 8
        0.81            0.15        0.04

Matches are distributed among these distances:
  63   24  0.14
  64  105  0.59
  65   18  0.10
  66   22  0.12
  67    8  0.05

ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26


Consensus pattern (64 bp):   
ATCGGAAGACGATCTTGTTAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGTTG

Found at i:3747 original size:50 final size:50

Alignment explanation


    Indices: 3693--4163  Score: 825
    Period size: 50  Copynumber: 9.4  Consensus size: 50

       3683 CTAAAGAATG

                          *                                   
       3693 GAATTGGAAGACAGCTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                                                              
       3743 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                             *                  *             
       3793 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                                               *              
       3843 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                             *                  *             
       3893 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                                         *                    
       3943 GAATTGGAAGACAGTTCAAAGGATAAGCGAAAGACGGTCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                                               *              
       3993 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACTGTCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                             *                  *             
       4043 GAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGATCCTTTTAAGATT
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                                               *             *
       4093 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACAGTCCTTTTAAGATG
          1 GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

                         *       
       4143 GAATTGGAAGACAATTCAAAG
          1 GAATTGGAAGACAGTTCAAAG

       4164 AAGTTGATTC


Statistics
Matches: 399,  Mismatches: 22, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  50  399  1.00

ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24


Consensus pattern (50 bp):   
GAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATT

Found at i:4517 original size:27 final size:27

Alignment explanation


    Indices: 4456--4523  Score: 84
    Period size: 27  Copynumber: 2.5  Consensus size: 27

       4446 GTCATCCAGC

                             *    *     
       4456 GGCA-TTTAGGTCATTTTTACATTAAGG
          1 GGCATTTTA-GTCATTTGTACACTAAGG

                    *                  
       4483 GGCATTTTCGTCATTTGTACACTAAGG
          1 GGCATTTTAGTCATTTGTACACTAAGG

              *           
       4510 GGGATTTTAGTCAT
          1 GGCATTTTAGTCAT

       4524 CTTTAAATCC


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  27   32  0.91
  28    3  0.09

ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40


Consensus pattern (27 bp):   
GGCATTTTAGTCATTTGTACACTAAGG
Done.