Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021997.1 Corchorus olitorius cultivar O-4 contig22030, 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: 3270
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32


Found at i:1985 original size:31 final size:30

Alignment explanation


    Indices: 1941--2015  Score: 98
    Period size: 30  Copynumber: 2.5  Consensus size: 30

       1931 GAGAATAAAG

                           *             *  
       1941 AAAATATTTTTTTTTATA-AAAACGCAGACAC
          1 AAAAT-TTTTTTTTTTTAGAAAACGCA-AAAC

               *                          
       1972 AAATTTTTTTTTTTTTAGAAAACGCAAAAC
          1 AAAATTTTTTTTTTTTAGAAAACGCAAAAC

                          
       2002 AAAATTTTTTTTTT
          1 AAAATTTTTTTTTT

       2016 GAAAAACATA


Statistics
Matches: 39,  Mismatches: 4, Indels: 3
        0.85            0.09        0.07

Matches are distributed among these distances:
  30   27  0.69
  31   12  0.31

ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45


Consensus pattern (30 bp):   
AAAATTTTTTTTTTTTAGAAAACGCAAAAC

Found at i:2083 original size:22 final size:22

Alignment explanation


    Indices: 2055--2109  Score: 74
    Period size: 24  Copynumber: 2.4  Consensus size: 22

       2045 GCAAGAAAAC

                                    
       2055 TTTTTTTTTATGAAGCAGAAATTT
          1 TTTTTTTTTATGAAGCA-AAA-TT

                         *     *  
       2079 TTTTTTTTTATGACGCAAATTT
          1 TTTTTTTTTATGAAGCAAAATT

                     
       2101 TTTTTTTTT
          1 TTTTTTTTT

       2110 CGACGCAAAA


Statistics
Matches: 29,  Mismatches: 2, Indels: 2
        0.88            0.06        0.06

Matches are distributed among these distances:
  22   11  0.38
  23    2  0.07
  24   16  0.55

ACGTcount: A:0.22, C:0.05, G:0.09, T:0.64


Consensus pattern (22 bp):   
TTTTTTTTTATGAAGCAAAATT

Found at i:2101 original size:21 final size:22

Alignment explanation


    Indices: 2055--2118  Score: 85
    Period size: 22  Copynumber: 2.9  Consensus size: 22

       2045 GCAAGAAAAC

                         *          
       2055 TTTTTTTTTATGAAGCAGAAATTT
          1 TTTTTTTTTATGACGC--AAATTT

                                  
       2079 TTTTTTTTTATGACGCAAATTT
          1 TTTTTTTTTATGACGCAAATTT

                      *        
       2101 TTTTTTTTT-CGACGCAAA
          1 TTTTTTTTTATGACGCAAA

       2119 ACACAAAACA


Statistics
Matches: 38,  Mismatches: 2, Indels: 3
        0.88            0.05        0.07

Matches are distributed among these distances:
  21    8  0.21
  22   15  0.39
  24   15  0.39

ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55


Consensus pattern (22 bp):   
TTTTTTTTTATGACGCAAATTT

Found at i:2521 original size:16 final size:15

Alignment explanation


    Indices: 2483--2524  Score: 75
    Period size: 15  Copynumber: 2.7  Consensus size: 15

       2473 ACAGAGGTTG

                           
       2483 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                           
       2498 ACAGAAAACAATTAA
          1 ACAGAAAACAATTAA

                        
       2513 ACTAGAAAACAA
          1 AC-AGAAAACAA

       2525 AGCAAAGTAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  15   17  0.65
  16    9  0.35

ACGTcount: A:0.67, C:0.14, G:0.07, T:0.12


Consensus pattern (15 bp):   
ACAGAAAACAATTAA
Done.