Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01011614.1 Corchorus capsularis cultivar CVL-1 contig11635, 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: 11760
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30


Found at i:300 original size:2 final size:2

Alignment explanation


    Indices: 295--326  Score: 64
    Period size: 2  Copynumber: 16.0  Consensus size: 2

        285 TGTATATAAC

                                                           
        295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

        327 TCGCTAAAAT


Statistics
Matches: 30,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (2 bp):   
AT

Found at i:3450 original size:30 final size:30

Alignment explanation


    Indices: 3414--3526  Score: 217
    Period size: 30  Copynumber: 3.8  Consensus size: 30

       3404 GACATCTTAA

                                          
       3414 TGGCATCTCCATGAGGCTTTGCGATTCCAT
          1 TGGCATCTCCATGAGGCTTTGCGATTCCAT

                                          
       3444 TGGCATCTCCATGAGGCTTTGCGATTCCAT
          1 TGGCATCTCCATGAGGCTTTGCGATTCCAT

                                          
       3474 TGGCATCTCCATGAGGCTTTGCGATTCCAT
          1 TGGCATCTCCATGAGGCTTTGCGATTCCAT

                           *       
       3504 TGGCATCTCCATGAGACTTTGCG
          1 TGGCATCTCCATGAGGCTTTGCG

       3527 GTACCTTCCT


Statistics
Matches: 82,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  30   82  1.00

ACGTcount: A:0.17, C:0.27, G:0.24, T:0.33


Consensus pattern (30 bp):   
TGGCATCTCCATGAGGCTTTGCGATTCCAT

Found at i:7939 original size:33 final size:33

Alignment explanation


    Indices: 7849--7989  Score: 131
    Period size: 33  Copynumber: 4.3  Consensus size: 33

       7839 AGCACAAGTG

                    *          *     *     * 
       7849 ACCGGCCATGCGACTTGGAGATGCCTGGCCAAC
          1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC

                    *          *       *     
       7882 ACCGGCCATGCGACTTGGAGATGCCCGACCATC
          1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC

                          *   *              
       7915 ACCGGCCACGCGACATGGCCATGCCCGGCCA-C
          1 ACCGGCCACGCGACTTGGACATGCCCGGCCATC

                  *   **    *  *             *
       7947 GACCGGTCACATGACTCGGCCATGCCCGGCCATA
          1 -ACCGGCCACGCGACTTGGACATGCCCGGCCATC

                     
       7981 ACCGGCCAC
          1 ACCGGCCAC

       7990 ATGATCCTTT


Statistics
Matches: 91,  Mismatches: 15, Indels: 4
        0.83            0.14        0.04

Matches are distributed among these distances:
  32    1  0.01
  33   90  0.99

ACGTcount: A:0.21, C:0.40, G:0.28, T:0.12


Consensus pattern (33 bp):   
ACCGGCCACGCGACTTGGACATGCCCGGCCATC

Found at i:7952 original size:10 final size:10

Alignment explanation


    Indices: 7931--7988  Score: 53
    Period size: 10  Copynumber: 5.5  Consensus size: 10

       7921 CACGCGACAT

                   *  
       7931 GGCCATGCCC
          1 GGCCATGACC

                 *    
       7941 GGCCACGACC
          1 GGCCATGACC

                         
       7951 GGTCACATGACTC
          1 GG-C-CATGAC-C

                   *  
       7964 GGCCATGCCC
          1 GGCCATGACC

                  *   
       7974 GGCCATAACC
          1 GGCCATGACC

                 
       7984 GGCCA
          1 GGCCA

       7989 CATGATCCTT


Statistics
Matches: 39,  Mismatches: 6, Indels: 6
        0.76            0.12        0.12

Matches are distributed among these distances:
  10   24  0.62
  11    6  0.15
  12    6  0.15
  13    3  0.08

ACGTcount: A:0.19, C:0.43, G:0.28, T:0.10


Consensus pattern (10 bp):   
GGCCATGACC

Found at i:11628 original size:226 final size:230

Alignment explanation


    Indices: 11339--11760  Score: 782
    Period size: 227  Copynumber: 1.9  Consensus size: 230

      11329 GGAGTGAGGA

                                                                             
      11339 CCAAAAATTCGTACCCGAGTACATTTATTTGGGGCCCACCCGTCATTATAAAACAACTACTGTTT
          1 CCAAAAATTCGTACCCGAGTACATTTATTTGGGGCCCACCCGTCATTATAAAACAACTACTGTTT

                                                              *              
      11404 ACTGATTCTTA-CTTAGCTAACTCTCATGAATGACAATTAAAGTGCATGACAGATTGATCTTACT
         66 ACTGATTCTTATCTTAGCTAACTCTCATGAATGACAATTAAAGTGCATGAAAGATTGATCTTACT

                                                                             
      11468 TAC-ATGCATTAACACAAGTCTA-CCCAAAGTCAA-CTCCATAAACCTTTCCCACGCATTATGGG
        131 TACTATGCATTAACACAAGTCTATCCCAAAGTCAACCTCCATAAACCTTTCCCACGCATTATGGG

                                               
      11530 GGTATTTATGGAATGAACCAGTCTAGAAGGATCTC
        196 GGTATTTATGGAATGAACCAGTCTAGAAGGATCTC

                                                                             
      11565 CCAAAAATTCGTACCCGAGTACATTTATTT-GGGCCCACCCGTCATTATAAAACAACATACTGTT
          1 CCAAAAATTCGTACCCGAGTACATTTATTTGGGGCCCACCCGTCATTATAAAACAAC-TACTGTT

                                                                            *
      11629 TACTGATTCTTATCTTAGCTAACTCTCATGAATGACAATTAAAGTGCATGAAAGATTGATCTTAT
         65 TACTGATTCTTATCTTAGCTAACTCTCATGAATGACAATTAAAGTGCATGAAAGATTGATCTTAC

                                                                             
      11694 TTACTATGCATTAACACAAGTCTATCCCAAAGTCAACCTCCATAAACCTTTCCCACGCATTATGG
        130 TTACTATGCATTAACACAAGTCTATCCCAAAGTCAACCTCCATAAACCTTTCCCACGCATTATGG

              
      11759 GG
        195 GG


Statistics
Matches: 189,  Mismatches: 2, Indels: 6
        0.96            0.01        0.03

Matches are distributed among these distances:
 225   26  0.14
 226   49  0.26
 227   54  0.29
 228   19  0.10
 229   11  0.06
 230   30  0.16

ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30


Consensus pattern (230 bp):   
CCAAAAATTCGTACCCGAGTACATTTATTTGGGGCCCACCCGTCATTATAAAACAACTACTGTTT
ACTGATTCTTATCTTAGCTAACTCTCATGAATGACAATTAAAGTGCATGAAAGATTGATCTTACT
TACTATGCATTAACACAAGTCTATCCCAAAGTCAACCTCCATAAACCTTTCCCACGCATTATGGG
GGTATTTATGGAATGAACCAGTCTAGAAGGATCTC
Done.