Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019346.1 Corchorus olitorius cultivar O-4 contig19379, 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: 3810
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36


Found at i:2018 original size:59 final size:60

Alignment explanation


    Indices: 1946--2088  Score: 168
    Period size: 59  Copynumber: 2.4  Consensus size: 60

       1936 TTTTTTCCAT

                            *            *                *    *         
       1946 CGTTTGCGAAAATGCTTAAATAAGGG-CTTAAAG-AAAAAAATGCTTAAATCAGGGCTCAA
          1 CGTTTGCGAAAATGCTCAAATAAGGGTC-AAAAGAAAAAAAATGCTCAAATAAGGGCTCAA

                                    *                                    
       2005 CGTTTGCGAAAATGCTCAAATAAGTGTCAAAAGAAAAAAAATGCTCAAATAAGGG-TCCAA
          1 CGTTTGCGAAAATGCTCAAATAAGGGTCAAAAGAAAAAAAATGCTCAAATAAGGGCT-CAA

                 **                  
       2065 C-TTTTAGAAAATTGCTCAAATAAG
          1 CGTTTGCGAAAA-TGCTCAAATAAG

       2089 TCTCTGCTGT


Statistics
Matches: 73,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  59   37  0.51
  60   36  0.49

ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24


Consensus pattern (60 bp):   
CGTTTGCGAAAATGCTCAAATAAGGGTCAAAAGAAAAAAAATGCTCAAATAAGGGCTCAA

Found at i:2084 original size:60 final size:59

Alignment explanation


    Indices: 1946--2089  Score: 159
    Period size: 60  Copynumber: 2.4  Consensus size: 59

       1936 TTTTTTCCAT

                  *         *         *  *               *    *         
       1946 CGTTTGCGAAAATGCTTAAATAAG-GGCTTAAAGAAAAAAATGCTTAAATCAGGGCTCAA
          1 CGTTTGAGAAAATGCTCAAATAAGTGTC-AAAAGAAAAAAATGCTCAAATAAGGGCTCAA

                  *                                                      
       2005 CGTTTGCGAAAATGCTCAAATAAGTGTCAAAAGAAAAAAAATGCTCAAATAAGGG-TCCAA
          1 CGTTTGAGAAAATGCTCAAATAAGTGTCAAAAG-AAAAAAATGCTCAAATAAGGGCT-CAA

                 *                    
       2065 C-TTTTAGAAAATTGCTCAAATAAGT
          1 CGTTTGAGAAAA-TGCTCAAATAAGT

       2090 CTCTGCTGTC


Statistics
Matches: 74,  Mismatches: 7, Indels: 7
        0.84            0.08        0.08

Matches are distributed among these distances:
  59   36  0.49
  60   38  0.51

ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24


Consensus pattern (59 bp):   
CGTTTGAGAAAATGCTCAAATAAGTGTCAAAAGAAAAAAATGCTCAAATAAGGGCTCAA

Found at i:2139 original size:23 final size:23

Alignment explanation


    Indices: 2109--2161  Score: 74
    Period size: 22  Copynumber: 2.3  Consensus size: 23

       2099 CACTGTGTGG

                                    
       2109 TTATCAAAAATTCCATAAT-AAGA
          1 TTATCAAAAATTCCAT-ATGAAGA

                        *          
       2132 TTATC-AAAATTTCATATGAAGA
          1 TTATCAAAAATTCCATATGAAGA

                    
       2154 TTATCAAA
          1 TTATCAAA

       2162 TTTTCCTTGT


Statistics
Matches: 27,  Mismatches: 1, Indels: 4
        0.84            0.03        0.12

Matches are distributed among these distances:
  21    2  0.07
  22   18  0.67
  23    7  0.26

ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34


Consensus pattern (23 bp):   
TTATCAAAAATTCCATATGAAGA

Done.