Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01015779.1 Corchorus olitorius cultivar O-4 contig15812, 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: 17709
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34


Found at i:2183 original size:20 final size:21

Alignment explanation


    Indices: 2155--2194  Score: 64
    Period size: 20  Copynumber: 2.0  Consensus size: 21

       2145 ACGATTAATG

                                 
       2155 TTAGCTTTATTTTGA-GAATA
          1 TTAGCTTTATTTTGATGAATA

                *               
       2175 TTAGTTTTATTTTGATGAAT
          1 TTAGCTTTATTTTGATGAAT

       2195 TACCTAGAAA


Statistics
Matches: 18,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20   14  0.78
  21    4  0.22

ACGTcount: A:0.28, C:0.03, G:0.15, T:0.55


Consensus pattern (21 bp):   
TTAGCTTTATTTTGATGAATA

Found at i:14689 original size:12 final size:12

Alignment explanation


    Indices: 14669--14722  Score: 72
    Period size: 12  Copynumber: 4.5  Consensus size: 12

      14659 CAAGCAACGG

                *     * 
      14669 CAGCGGCAGCCA
          1 CAGCAGCAGCAA

                        
      14681 CAGCAGCAGCAA
          1 CAGCAGCAGCAA

                        
      14693 CAGCAGCAGCAA
          1 CAGCAGCAGCAA

                 *     *
      14705 CAGCAACAGCAG
          1 CAGCAGCAGCAA

                  
      14717 CAGCAG
          1 CAGCAG

      14723 TTTCAGCAGT


Statistics
Matches: 37,  Mismatches: 5, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  12   37  1.00

ACGTcount: A:0.37, C:0.35, G:0.28, T:0.00


Consensus pattern (12 bp):   
CAGCAGCAGCAA

Found at i:14696 original size:18 final size:19

Alignment explanation


    Indices: 14675--14721  Score: 64
    Period size: 18  Copynumber: 2.6  Consensus size: 19

      14665 ACGGCAGCGG

                        *      
      14675 CAGCCA-CAGCAGCAGCAA
          1 CAGCCAGCAGCAACAGCAA

                               
      14693 CAG-CAGCAGCAACAGCAA
          1 CAGCCAGCAGCAACAGCAA

                        
      14711 CAG-CAGCAGCA
          1 CAGCCAGCAGCA

      14722 GTTTCAGCAG


Statistics
Matches: 27,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  17    2  0.07
  18   25  0.93

ACGTcount: A:0.40, C:0.36, G:0.23, T:0.00


Consensus pattern (19 bp):   
CAGCCAGCAGCAACAGCAA

Found at i:14722 original size:6 final size:6

Alignment explanation


    Indices: 14668--14722  Score: 58
    Period size: 6  Copynumber: 9.2  Consensus size: 6

      14658 GCAAGCAACG

                 *                       *             *      *     
      14668 GCAGCG GCAGCCA -CAGCA GCAGCA ACAGCA GCAGCA ACAGCA ACAGCA
          1 GCAGCA GCAG-CA GCAGCA GCAGCA GCAGCA GCAGCA GCAGCA GCAGCA

                    
      14716 GCAGCA G
          1 GCAGCA G

      14723 TTTCAGCAGT


Statistics
Matches: 42,  Mismatches: 5, Indels: 4
        0.82            0.10        0.08

Matches are distributed among these distances:
   5    2  0.05
   6   39  0.93
   7    1  0.02

ACGTcount: A:0.36, C:0.35, G:0.29, T:0.00


Consensus pattern (6 bp):   
GCAGCA

Found at i:15320 original size:15 final size:14

Alignment explanation


    Indices: 15300--15329  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

      15290 CACAGCAAGT

                           
      15300 CTCAAGCTGAGCCAG
          1 CTCAAGCTGA-CCAG

                          
      15315 CTCAAGCTGACCAG
          1 CTCAAGCTGACCAG

             
      15329 C
          1 C

      15330 AGCCCGGGAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    5  0.33
  15   10  0.67

ACGTcount: A:0.27, C:0.37, G:0.23, T:0.13


Consensus pattern (14 bp):   
CTCAAGCTGACCAG
Done.