Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023714.1 Corchorus olitorius cultivar O-4 contig23747, 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: 6685
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35


Found at i:1928 original size:28 final size:28

Alignment explanation


    Indices: 1897--1951  Score: 110
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       1887 TTTCAATAAT

                                        
       1897 TACTTTACATAAATAAAGTGAAAATTAG
          1 TACTTTACATAAATAAAGTGAAAATTAG

                                       
       1925 TACTTTACATAAATAAAGTGAAAATTA
          1 TACTTTACATAAATAAAGTGAAAATTA

       1952 AAGCAATTGT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   27  1.00

ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33


Consensus pattern (28 bp):   
TACTTTACATAAATAAAGTGAAAATTAG

Found at i:3039 original size:6 final size:7

Alignment explanation


    Indices: 3023--3047  Score: 50
    Period size: 7  Copynumber: 3.6  Consensus size: 7

       3013 TTCTTCAACA

                   
       3023 TTTTTGT
          1 TTTTTGT

                   
       3030 TTTTTGT
          1 TTTTTGT

                   
       3037 TTTTTGT
          1 TTTTTGT

                
       3044 TTTT
          1 TTTT

       3048 ACATTTTACA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   7   18  1.00

ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88


Consensus pattern (7 bp):   
TTTTTGT

Found at i:3958 original size:30 final size:31

Alignment explanation


    Indices: 3924--3986  Score: 119
    Period size: 30  Copynumber: 2.1  Consensus size: 31

       3914 TAATAATAAT

                                           
       3924 TTCCTACATATAAATTAC-TTAAAAAAAACC
          1 TTCCTACATATAAATTACTTTAAAAAAAACC

                                           
       3954 TTCCTACATATAAATTACTTTAAAAAAAACC
          1 TTCCTACATATAAATTACTTTAAAAAAAACC

              
       3985 TT
          1 TT

       3987 TCCATTAACT


Statistics
Matches: 32,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  30   18  0.56
  31   14  0.44

ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33


Consensus pattern (31 bp):   
TTCCTACATATAAATTACTTTAAAAAAAACC

Found at i:6005 original size:13 final size:13

Alignment explanation


    Indices: 5969--6014  Score: 65
    Period size: 13  Copynumber: 3.5  Consensus size: 13

       5959 TAATGCACCC

                          
       5969 AAAACAATTTACAT
          1 AAAACAATTTA-AT

                 *       
       5983 AAAACCATTTAAT
          1 AAAACAATTTAAT

            *            
       5996 TAAACAATTTAAT
          1 AAAACAATTTAAT

                  
       6009 AAAACA
          1 AAAACA

       6015 GTAATAAAAT


Statistics
Matches: 28,  Mismatches: 4, Indels: 1
        0.85            0.12        0.03

Matches are distributed among these distances:
  13   18  0.64
  14   10  0.36

ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28


Consensus pattern (13 bp):   
AAAACAATTTAAT
Done.