Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01000979.1 Corchorus olitorius cultivar O-4 contig00979, 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: 4865
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31


Found at i:1641 original size:23 final size:23

Alignment explanation


    Indices: 1615--1659  Score: 81
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       1605 AGCCAAATTT

                *                  
       1615 CACCGCCTCCGCTCCAACAGCTC
          1 CACCACCTCCGCTCCAACAGCTC

                                  
       1638 CACCACCTCCGCTCCAACAGCT
          1 CACCACCTCCGCTCCAACAGCT

       1660 ATCAACGGCT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  23   21  1.00

ACGTcount: A:0.20, C:0.56, G:0.11, T:0.13


Consensus pattern (23 bp):   
CACCACCTCCGCTCCAACAGCTC

Found at i:1989 original size:33 final size:34

Alignment explanation


    Indices: 1906--2009  Score: 124
    Period size: 33  Copynumber: 3.1  Consensus size: 34

       1896 CTGCAAACTT

                 *                            
       1906 CACCTAAACGTCCTTCGCTCCAACAGTCATCATG
          1 CACCTCAACGTCCTTCGCTCCAACAGTCATCATG

             *                    *            
       1940 CTCCTCAACGTCCTTCGCTCCAGCAG-CAATC-TG
          1 CACCTCAACGTCCTTCGCTCCAACAGTC-ATCATG

                  *            *   *          
       1973 CACCTCTACGTCCTTCGCTTCAAAAGTCATCA-G
          1 CACCTCAACGTCCTTCGCTCCAACAGTCATCATG

                
       2006 CACC
          1 CACC

       2010 CTTACATTCT


Statistics
Matches: 59,  Mismatches: 8, Indels: 7
        0.80            0.11        0.09

Matches are distributed among these distances:
  33   32  0.54
  34   27  0.46

ACGTcount: A:0.23, C:0.40, G:0.12, T:0.24


Consensus pattern (34 bp):   
CACCTCAACGTCCTTCGCTCCAACAGTCATCATG

Found at i:2975 original size:33 final size:33

Alignment explanation


    Indices: 2931--3012  Score: 121
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       2921 CCTGATCAAG

                  *                           
       2931 TTCAGTGGGGATCTGCAGCC-GCAGTACCTGAGA
          1 TTCAGTCGGGATCTGCA-CCTGCAGTACCTGAGA

                  *                          
       2964 TTCAGTTGGGATCTGCACCTGCAGTACCTGAGA
          1 TTCAGTCGGGATCTGCACCTGCAGTACCTGAGA

                   *        
       2997 TTCAGTCAGGATCTGC
          1 TTCAGTCGGGATCTGC

       3013 CGGAGCACCA


Statistics
Matches: 45,  Mismatches: 3, Indels: 2
        0.90            0.06        0.04

Matches are distributed among these distances:
  32    2  0.04
  33   43  0.96

ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26


Consensus pattern (33 bp):   
TTCAGTCGGGATCTGCACCTGCAGTACCTGAGA

Found at i:4354 original size:2 final size:2

Alignment explanation


    Indices: 4341--4370  Score: 51
    Period size: 2  Copynumber: 15.0  Consensus size: 2

       4331 GGGTTAGCTT

                      *                                 
       4341 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       4371 CTTTTGTCAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   2   26  1.00

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (2 bp):   
TA

Done.