Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWWV01007944.1 Corchorus capsularis cultivar CVL-1 contig07965, 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: 17383
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33


Found at i:57 original size:33 final size:33

Alignment explanation


    Indices: 8--87  Score: 92
    Period size: 33  Copynumber: 2.5  Consensus size: 33

          1 CCTGGCT

                     * *           ***       
          8 AAGCCGCCCCAATGGGGCGACCTTTTCATGGTG
          1 AAGCCGCCCTAGTGGGGCGACCTGCCCATGGTG

                               *             
         41 AAGCCGCCCTAGTGGGGCGGCCTGCCCATGGTG
          1 AAGCCGCCCTAGTGGGGCGACCTGCCCATGGTG

                            
         74 AAGCCG--CTAGTGGG
          1 AAGCCGCCCTAGTGGG

         88 ACGGTTCCGC


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  31    8  0.20
  33   33  0.80

ACGTcount: A:0.16, C:0.30, G:0.36, T:0.17


Consensus pattern (33 bp):   
AAGCCGCCCTAGTGGGGCGACCTGCCCATGGTG

Found at i:4713 original size:28 final size:28

Alignment explanation


    Indices: 4673--4730  Score: 116
    Period size: 28  Copynumber: 2.1  Consensus size: 28

       4663 AAGAGCTGAT

                                        
       4673 CTCTCTGTGGGTTCGACCCCTACTTGCC
          1 CTCTCTGTGGGTTCGACCCCTACTTGCC

                                        
       4701 CTCTCTGTGGGTTCGACCCCTACTTGCC
          1 CTCTCTGTGGGTTCGACCCCTACTTGCC

              
       4729 CT
          1 CT

       4731 AGCTAGTTTA


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

Matches are distributed among these distances:
  28   30  1.00

ACGTcount: A:0.07, C:0.40, G:0.21, T:0.33


Consensus pattern (28 bp):   
CTCTCTGTGGGTTCGACCCCTACTTGCC

Found at i:15854 original size:31 final size:31

Alignment explanation


    Indices: 15816--15987  Score: 168
    Period size: 31  Copynumber: 5.5  Consensus size: 31

      15806 TCCTTTTGTG

                              *          * 
      15816 CACGTGGCATGCCACGTGCCACTTTTTGAAA
          1 CACGTGGCATGCCACGTGTCACTTTTTGATA

              *           *             *  
      15847 CATGTGGCATGCCATGTGTCACTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGATA

                    *  *  *                 
      15878 CACGTGGCGTGACATGTGTCACTTTTTTG-TA
          1 CACGTGGCATGCCACGTGTCAC-TTTTTGATA

            *       *  *  *                 
      15909 TACGTGGCGTGACATGTGTCACTTTTTTG-TA
          1 CACGTGGCATGCCACGTGTCAC-TTTTTGATA

              *     *      *            *  
      15940 CATGTGGCGTGCCACATGTCACTTTTTGGTA
          1 CACGTGGCATGCCACGTGTCACTTTTTGATA

                             
      15971 CACGTGGCATGCCACGT
          1 CACGTGGCATGCCACGT

      15988 CGAACACCGT


Statistics
Matches: 122,  Mismatches: 17, Indels: 4
        0.85            0.12        0.03

Matches are distributed among these distances:
  30    6  0.05
  31  110  0.90
  32    6  0.05

ACGTcount: A:0.17, C:0.23, G:0.26, T:0.34


Consensus pattern (31 bp):   
CACGTGGCATGCCACGTGTCACTTTTTGATA

Found at i:15901 original size:62 final size:61

Alignment explanation


    Indices: 15816--15984  Score: 196
    Period size: 62  Copynumber: 2.7  Consensus size: 61

      15806 TCCTTTTGTG

                    *         *          *                                
      15816 CACGTGGCATGCCACGTGCCACTTTTTGAAACATGTGGCATGCCATGTGTCACTTTTTGGTA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGATACA-GTGGCATGCCATGTGTCACTTTTTGGTA

                       *  *                         *  *               *   
      15878 CACGTGGCGTGACATGTGTCACTTTTTTGTATAC-GTGGCGTGACATGTGTCACTTTTTTGTA
          1 CACGTGGCGTGCCACGTGTCAC-TTTTTG-ATACAGTGGCATGCCATGTGTCACTTTTTGGTA

              *            *            *                
      15940 CATGTGGCGTGCCACATGTCACTTTTTGGTACACGTGGCATGCCA
          1 CACGTGGCGTGCCACGTGTCACTTTTTGATACA-GTGGCATGCCA

      15985 CGTCGAACAC


Statistics
Matches: 88,  Mismatches: 15, Indels: 8
        0.79            0.14        0.07

Matches are distributed among these distances:
  60    3  0.03
  61    6  0.07
  62   70  0.80
  63    6  0.07
  64    3  0.03

ACGTcount: A:0.18, C:0.22, G:0.25, T:0.34


Consensus pattern (61 bp):   
CACGTGGCGTGCCACGTGTCACTTTTTGATACAGTGGCATGCCATGTGTCACTTTTTGGTA

Found at i:17198 original size:20 final size:20

Alignment explanation


    Indices: 17160--17197  Score: 69
    Period size: 19  Copynumber: 1.9  Consensus size: 20

      17150 GAATTTATAA

                                
      17160 ATAACCTTATAATTGTTTTG
          1 ATAACCTTATAATTGTTTTG

                               
      17180 ATAACC-TATAATTGTTTT
          1 ATAACCTTATAATTGTTTT

      17198 TTAGTAATCA


Statistics
Matches: 18,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  19   12  0.67
  20    6  0.33

ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50


Consensus pattern (20 bp):   
ATAACCTTATAATTGTTTTG
Done.