Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011984.1 Corchorus capsularis cultivar CVL-1 contig12005, 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: 13451
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37


Found at i:2149 original size:12 final size:12

Alignment explanation


    Indices: 2132--2156  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       2122 GACTTAAGAA

                        
       2132 TCTCACAAGTTT
          1 TCTCACAAGTTT

                        
       2144 TCTCACAAGTTT
          1 TCTCACAAGTTT

             
       2156 T
          1 T

       2157 GTTGCTGCTA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44


Consensus pattern (12 bp):   
TCTCACAAGTTT

Found at i:3754 original size:19 final size:18

Alignment explanation


    Indices: 3732--3771  Score: 62
    Period size: 18  Copynumber: 2.2  Consensus size: 18

       3722 ACCTTCTTAC

                               
       3732 TTTTTGATAACATTCTAAA
          1 TTTTT-ATAACATTCTAAA

                 *            
       3751 TTTTTTTAACATTCTAAA
          1 TTTTTATAACATTCTAAA

               
       3769 TTT
          1 TTT

       3772 AATTTCTACC


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18   15  0.75
  19    5  0.25

ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55


Consensus pattern (18 bp):   
TTTTTATAACATTCTAAA

Found at i:10952 original size:50 final size:50

Alignment explanation


    Indices: 10869--11239  Score: 634
    Period size: 50  Copynumber: 7.4  Consensus size: 50

      10859 TTAAAAAGTT

                                    *                  *     *
      10869 TAAAAAATTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCAAACATA
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

                                        *                     
      10919 TAAAAAATTTAGTAATTAGGAGACGGATAGGAGCTGACTCCCCGAACATC
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

                                                       *      
      10969 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCAAACATC
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

                                     *                 *       
      11019 TAAAAAATTTAGTAATTAGGAGACGAATGGGAGCTGACTCCCCAAACAATC
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAAC-ATC

                                                              
      11070 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

                                     *                        
      11120 TAAAAAATTTAGTAATTAGGAGACGAATGGGAGCTGACTCCCCGAACATC
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

                                                          *   *
      11170 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAAGATTT
          1 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACA-TC

                               
      11221 TAAAAAATTTAGTAATTAG
          1 TAAAAAATTTAGTAATTAG

      11240 CATACTGACA


Statistics
Matches: 306,  Mismatches: 13, Indels: 3
        0.95            0.04        0.01

Matches are distributed among these distances:
  50  238  0.78
  51   68  0.22

ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23


Consensus pattern (50 bp):   
TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAACATC

Found at i:11142 original size:151 final size:150

Alignment explanation


    Indices: 10869--11239  Score: 636
    Period size: 151  Copynumber: 2.5  Consensus size: 150

      10859 TTAAAAAGTT

                                                                             
      10869 TAAAAAATTTAGTAATTAGGAGACTGATGGGAGCTGACTCCCCAAAC-ATATAAAAAATTTAGTA
          1 TAAAAAATTTAGTAATTAGGAGAC-GATGGGAGCTGACTCCCCAAACAATATAAAAAATTTAGTA

                                                                         *   
      10933 ATTAGGAGACGGATAGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACGGATG
         65 ATTAGGAGACGGATAGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACGAATG

                                 
      10998 GGAGCTGACTCCCCAAACATC
        130 GGAGCTGACTCCCCAAACATC

                                                              *              
      11019 TAAAAAATTTAGTAATTAGGAGACGAATGGGAGCTGACTCCCCAAACAATCTAAAAAATTTAGTA
          1 TAAAAAATTTAGTAATTAGGAGACG-ATGGGAGCTGACTCCCCAAACAATATAAAAAATTTAGTA

                          *                                                  
      11084 ATTAGGAGACGGATGGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACGAATG
         65 ATTAGGAGACGGATAGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACGAATG

                          *      
      11149 GGAGCTGACTCCCCGAACATC
        130 GGAGCTGACTCCCCAAACATC

                                                       *  * * *              
      11170 TAAAAAATTTAGTAATTAGGAGACGGATGGGAGCTGACTCCCCGAAGATTTTAAAAAATTTAGTA
          1 TAAAAAATTTAGTAATTAGGAGAC-GATGGGAGCTGACTCCCCAAACAATATAAAAAATTTAGTA

                 
      11235 ATTAG
         65 ATTAG

      11240 CATACTGACA


Statistics
Matches: 210,  Mismatches: 8, Indels: 5
        0.94            0.04        0.02

Matches are distributed among these distances:
 149    1  0.00
 150   45  0.21
 151  163  0.78
 152    1  0.00

ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23


Consensus pattern (150 bp):   
TAAAAAATTTAGTAATTAGGAGACGATGGGAGCTGACTCCCCAAACAATATAAAAAATTTAGTAA
TTAGGAGACGGATAGGAGCTGACTCCCCGAACATCTAAAAAATTTAGTAATTAGGAGACGAATGG
GAGCTGACTCCCCAAACATC
Done.