Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01008234.1 Corchorus olitorius cultivar O-4 contig08261, 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: 2308
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35


Found at i:1980 original size:23 final size:23

Alignment explanation


    Indices: 1948--2094  Score: 143
    Period size: 23  Copynumber: 6.7  Consensus size: 23

       1938 CACAATTGCT

                 *                 
       1948 TGGCGCCCGACCACTTCCAAACC
          1 TGGCGACCGACCACTTCCAAACC

                                   
       1971 TGGCGACCGACCACTTCC--A--
          1 TGGCGACCGACCACTTCCAAACC

             *   *                 
       1990 TAGCGCCCGACCACTTCCAAACC
          1 TGGCGACCGACCACTTCCAAACC

                                   
       2013 TGGCGACCGACCACTTCC--A--
          1 TGGCGACCGACCACTTCCAAACC

             *   *                 
       2032 TAGCGCCCGACCACTTCCAAACC
          1 TGGCGACCGACCACTTCCAAACC

              *                      
       2055 TGACGACCGACCACTTCCATAACGC
          1 TGGCGACCGACCACTTCCA-AAC-C

                             
       2080 -GGCG-CTCGACCACTT
          1 TGGCGAC-CGACCACTT

       2095 GTGACCATAA


Statistics
Matches: 102,  Mismatches: 11, Indels: 21
        0.76            0.08        0.16

Matches are distributed among these distances:
  19   32  0.31
  21    4  0.04
  23   50  0.49
  24   15  0.15
  25    1  0.01

ACGTcount: A:0.23, C:0.44, G:0.18, T:0.15


Consensus pattern (23 bp):   
TGGCGACCGACCACTTCCAAACC

Found at i:2001 original size:19 final size:19

Alignment explanation


    Indices: 1977--2050  Score: 94
    Period size: 19  Copynumber: 3.7  Consensus size: 19

       1967 AACCTGGCGA

                               
       1977 CCGACCACTTCCATAGCGC
          1 CCGACCACTTCCATAGCGC

                              *   *
       1996 CCGACCACTTCCAAACCTGGCGA
          1 CCGACCACTTCC--A--TAGCGC

                               
       2019 CCGACCACTTCCATAGCGC
          1 CCGACCACTTCCATAGCGC

                         
       2038 CCGACCACTTCCA
          1 CCGACCACTTCCA

       2051 AACCTGACGA


Statistics
Matches: 47,  Mismatches: 4, Indels: 8
        0.80            0.07        0.14

Matches are distributed among these distances:
  19   29  0.62
  21    2  0.04
  23   16  0.34

ACGTcount: A:0.23, C:0.47, G:0.15, T:0.15


Consensus pattern (19 bp):   
CCGACCACTTCCATAGCGC

Found at i:2009 original size:42 final size:42

Alignment explanation


    Indices: 1950--2075  Score: 243
    Period size: 42  Copynumber: 3.0  Consensus size: 42

       1940 CAATTGCTTG

                                                      
       1950 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

                                                      
       1992 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

                                   *                  
       2034 GCGCCCGACCACTTCCAAACCTGACGACCGACCACTTCCATA
          1 GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

       2076 ACGCGGCGCT


Statistics
Matches: 83,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  42   83  1.00

ACGTcount: A:0.25, C:0.45, G:0.16, T:0.14


Consensus pattern (42 bp):   
GCGCCCGACCACTTCCAAACCTGGCGACCGACCACTTCCATA

Found at i:2061 original size:19 final size:19

Alignment explanation


    Indices: 1955--2062  Score: 58
    Period size: 19  Copynumber: 5.3  Consensus size: 19

       1945 GCTTGGCGCC

                                  
       1955 CGACCACTTCCAAACCTGGCGA
          1 CGACCACTTCCAAACCT---GA

                         * *    *
       1977 CCGACCACTTCCATAGC-GCC
          1 -CGACCACTTCCAAACCTG-A

                                  
       1997 CGACCACTTCCAAACCTGGCGA
          1 CGACCACTTCCAAACCT---GA

                         * *    *
       2019 CCGACCACTTCCATAGC-GCC
          1 -CGACCACTTCCAAACCTG-A

                               
       2039 CGACCACTTCCAAACCTGA
          1 CGACCACTTCCAAACCTGA

                 
       2058 CGACC
          1 CGACC

       2063 GACCACTTCC


Statistics
Matches: 65,  Mismatches: 12, Indels: 20
        0.67            0.12        0.21

Matches are distributed among these distances:
  19   35  0.54
  20    1  0.02
  23   29  0.45

ACGTcount: A:0.25, C:0.45, G:0.16, T:0.14


Consensus pattern (19 bp):   
CGACCACTTCCAAACCTGA
Done.