Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011860.1 Corchorus capsularis cultivar CVL-1 contig11881, 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: 4607
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29


Found at i:1306 original size:33 final size:32

Alignment explanation


    Indices: 1223--1330  Score: 108
    Period size: 33  Copynumber: 3.2  Consensus size: 32

       1213 GACTTGGAAA

                 *   *    *                *  
       1223 ACCGGGCACACGACTTGGAGATGCCCCGCGCAAC
          1 ACCGGCCACGCGACATGGAGATG-CCCG-GCCAC

                    *  *                     
       1257 ACCGGCCATGCCACATGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACATGGAGATGCCCGGCCA-C

                               *   *        
       1290 ACCGGCCACGCGACATGGACATGTCCGGCCAC
          1 ACCGGCCACGCGACATGGAGATGCCCGGCCAC

                     
       1322 AACCGGCCA
          1 -ACCGGCCA

       1331 TCGCTTGGCG


Statistics
Matches: 62,  Mismatches: 10, Indels: 5
        0.81            0.13        0.06

Matches are distributed among these distances:
  32    4  0.06
  33   40  0.65
  34   18  0.29

ACGTcount: A:0.23, C:0.40, G:0.28, T:0.09


Consensus pattern (32 bp):   
ACCGGCCACGCGACATGGAGATGCCCGGCCAC

Found at i:4091 original size:33 final size:33

Alignment explanation


    Indices: 4051--4143  Score: 132
    Period size: 33  Copynumber: 2.8  Consensus size: 33

       4041 AGCACTTGTG

                    *              *         
       4051 ACCGGCCATGCGACTTGGAGATGTCCGACCATC
          1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC

                       *               *     
       4084 ACCGGCCACGCCACTTGGAGATGCCCGCCCATC
          1 ACCGGCCACGCGACTTGGAGATGCCCGACCATC

                          *    *       
       4117 ACCGGCCACGCGACATGGACATGCCCG
          1 ACCGGCCACGCGACTTGGAGATGCCCG

       4144 GCAACAACAG


Statistics
Matches: 53,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   53  1.00

ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGATGCCCGACCATC

Found at i:4348 original size:33 final size:33

Alignment explanation


    Indices: 4310--4394  Score: 125
    Period size: 33  Copynumber: 2.6  Consensus size: 33

       4300 GGCGCGCGTG

                    *                        
       4310 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                           *     *         * 
       4343 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

                          *    
       4376 ACCGGCCACGCGACATGGA
          1 ACCGGCCACGCGACTTGGA

       4395 CATGTCCAGC


Statistics
Matches: 46,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  33   46  1.00

ACGTcount: A:0.22, C:0.39, G:0.31, T:0.08


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGAGAAGCCCGGCCAAC

Found at i:4413 original size:33 final size:33

Alignment explanation


    Indices: 4310--4416  Score: 101
    Period size: 33  Copynumber: 3.2  Consensus size: 33

       4300 GGCGCGCGTG

                    *      *   * *    *    * 
       4310 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
          1 ACCGGCCACGCGACTCGGACATGCCCAGCCATC

                               *      *      
       4343 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
          1 ACCGGCCACGCGACTCGGACATGCCCAGCCATC

                                    *         
       4376 ACCGGCCACGCGACAT-GGACATGTCCAGCCA-C
          1 ACCGGCCACGCGAC-TCGGACATGCCCAGCCATC

                     
       4408 AACCGGCCA
          1 -ACCGGCCA

       4417 TCGCTTGGCG


Statistics
Matches: 65,  Mismatches: 7, Indels: 4
        0.86            0.09        0.05

Matches are distributed among these distances:
  32    1  0.02
  33   63  0.97
  34    1  0.02

ACGTcount: A:0.23, C:0.40, G:0.28, T:0.08


Consensus pattern (33 bp):   
ACCGGCCACGCGACTCGGACATGCCCAGCCATC

Found at i:4449 original size:259 final size:258

Alignment explanation


    Indices: 3941--4416  Score: 718
    Period size: 259  Copynumber: 1.8  Consensus size: 258

       3931 CAATACTCAC

                                            * *                      *    *  
       3941 TGATGCGCCAAGGGCTTATCATGGCTTAAAAGGAGACATTGGAGCCAATGAAGATCATGGAGTTG
          1 TGATGCGCCAAGGGCTTATCATGGCTTAAAAGAACACATTGGAGCCAATGAAGATCAAGGAGATG

                                                    **                       
       4006 TCATCGATGCTAGCTTGGAGGAGCATGGAGATGGAAGCACTTGTGACCGGCCATGCGACTTGGAG
         66 TCATCGATGCTAGCTTGGAGGAGCATGGAGATGGAAGCACGCGTGACCGGCCATGCGACTTGGAG

             * *       *                *                                    
       4071 ATGTCCGACCATCACCGGCCACGCCACTTGGAGATGCCCGCCCATCACCGGCCACGCGACATGGA
        131 AAGCCCGACCAACACCGGCCACGCCACTCGGAGATGCCCGCCCATCACCGGCCACGCGACATGGA

                   *                          ***     *                     
       4136 CATGCCCGGCAACAACAGGCCACATGATTCGGCCTTGCCTAGTCACAACCGGCCACATGATCCT
        196 CATGCCCAGCAACAACAGGCCACA-GATTCGGCCCAACCTAGCCACAACCGGCCACATGATCCT

                                        *                                    
       4200 TGATGCGCCAAGGGCTTATCATGGCTTACAAGAACACATTGGAGCCAATGAAGATCAAGGAGATG
          1 TGATGCGCCAAGGGCTTATCATGGCTTAAAAGAACACATTGGAGCCAATGAAGATCAAGGAGATG

                                          *    *  *                          
       4265 TCATCGATGCTAGCTTGGAGGAGCATGGAGTTGGAGGCGCGCGTGACCGGCCATGCGACTTGGAG
         66 TCATCGATGCTAGCTTGGAGGAGCATGGAGATGGAAGCACGCGTGACCGGCCATGCGACTTGGAG

                   *                *               *                        
       4330 AAGCCCGGCCAACACCGGCCACGCGACTCGGAGATGCCCGGCCATCACCGGCCACGCGACATGGA
        131 AAGCCCGACCAACACCGGCCACGCCACTCGGAGATGCCCGCCCATCACCGGCCACGCGACATGGA

                *     *     *     
       4395 CATGTCCAGCCACAACCGGCCA
        196 CATGCCCAGCAACAACAGGCCA

       4417 TCGCTTGGCG


Statistics
Matches: 196,  Mismatches: 21, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
 259  196  1.00

ACGTcount: A:0.25, C:0.29, G:0.29, T:0.17


Consensus pattern (258 bp):   
TGATGCGCCAAGGGCTTATCATGGCTTAAAAGAACACATTGGAGCCAATGAAGATCAAGGAGATG
TCATCGATGCTAGCTTGGAGGAGCATGGAGATGGAAGCACGCGTGACCGGCCATGCGACTTGGAG
AAGCCCGACCAACACCGGCCACGCCACTCGGAGATGCCCGCCCATCACCGGCCACGCGACATGGA
CATGCCCAGCAACAACAGGCCACAGATTCGGCCCAACCTAGCCACAACCGGCCACATGATCCT
Done.