Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01018127.1 Corchorus olitorius cultivar O-4 contig18160, 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: 7885
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30


Found at i:872 original size:32 final size:32

Alignment explanation


    Indices: 836--994  Score: 192
    Period size: 32  Copynumber: 5.0  Consensus size: 32

        826 TTACATAAAC

                   *   *                    
        836 GCGGCGTCTCGTAATTTAGACGCCGCTATTTA
          1 GCGGCGTTTCGAAATTTAGACGCCGCTATTTA

                        *     *         **  
        868 GCGGCGTTTCGATATTTAAACGCCGCTAAATA
          1 GCGGCGTTTCGAAATTTAGACGCCGCTATTTA

                           *            **  
        900 GCGGCGTTTCGAAATATAGACGCCGCTAAATA
          1 GCGGCGTTTCGAAATTTAGACGCCGCTATTTA

                           *                
        932 GCGGCGTTTCGAAATATAGACGCCGCTATTTA
          1 GCGGCGTTTCGAAATTTAGACGCCGCTATTTA

            *          *      *      *     
        964 ACGGCGTTTCGGAATTTAAACGCCGTTATTT
          1 GCGGCGTTTCGAAATTTAGACGCCGCTATTT

        995 TGACCTCTTA


Statistics
Matches: 111,  Mismatches: 16, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  32  111  1.00

ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29


Consensus pattern (32 bp):   
GCGGCGTTTCGAAATTTAGACGCCGCTATTTA

Found at i:2079 original size:3 final size:3

Alignment explanation


    Indices: 2071--2140  Score: 104
    Period size: 3  Copynumber: 23.0  Consensus size: 3

       2061 GTAAAGGAAG

                        *   *                                           
       2071 AAT AAT AAT GAT GAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT
          1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT

                                    *      
       2117 AAT AAT AAT AAT AAT AAT GAT AAT
          1 AAT AAT AAT AAT AAT AAT AAT AAT

       2141 GGAAGAAAAG


Statistics
Matches: 62,  Mismatches: 4, Indels: 2
        0.91            0.06        0.03

Matches are distributed among these distances:
   3   59  0.95
   4    3  0.05

ACGTcount: A:0.61, C:0.00, G:0.04, T:0.34


Consensus pattern (3 bp):   
AAT

Found at i:5056 original size:19 final size:19

Alignment explanation


    Indices: 5021--5062  Score: 59
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       5011 AAATATTATA

                  *            
       5021 TTTTAACATATAAAACTT-
          1 TTTTAAAATATAAAACTTG

                                
       5039 TTTTAAAATATAAAAACTTG
          1 TTTTAAAATAT-AAAACTTG

                
       5059 TTTT
          1 TTTT

       5063 TGGCTGAATT


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  18   10  0.48
  19    7  0.33
  20    4  0.19

ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48


Consensus pattern (19 bp):   
TTTTAAAATATAAAACTTG

Found at i:5266 original size:31 final size:32

Alignment explanation


    Indices: 5190--5287  Score: 103
    Period size: 31  Copynumber: 3.1  Consensus size: 32

       5180 TCCTTTAATT

                                            
       5190 CTAAATAGTGGCGTTTTCCTAAATAAACGCCA
          1 CTAAATAGTGGCGTTTTCCTAAATAAACGCCA

               **   *              *         
       5222 CTATTTAGGGGCG-TTTCTCT-ATTAAACGCCA
          1 CTAAATAGTGGCGTTTTC-CTAAATAAACGCCA

                              **   *        
       5253 CTAAATAGTGGCGTTTT-GAAAAGAAACGCCA
          1 CTAAATAGTGGCGTTTTCCTAAATAAACGCCA

                
       5284 CTAA
          1 CTAA

       5288 TTTTAGTCTT


Statistics
Matches: 52,  Mismatches: 11, Indels: 7
        0.74            0.16        0.10

Matches are distributed among these distances:
  31   37  0.71
  32   15  0.29

ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29


Consensus pattern (32 bp):   
CTAAATAGTGGCGTTTTCCTAAATAAACGCCA

Found at i:6839 original size:14 final size:14

Alignment explanation


    Indices: 6820--6851  Score: 55
    Period size: 14  Copynumber: 2.3  Consensus size: 14

       6810 ATTAAGTTAG

                          
       6820 AAATTAAAAATTTA
          1 AAATTAAAAATTTA

                   *      
       6834 AAATTAAGAATTTA
          1 AAATTAAAAATTTA

                
       6848 AAAT
          1 AAAT

       6852 AAATAGCAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  14   17  1.00

ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34


Consensus pattern (14 bp):   
AAATTAAAAATTTA
Done.