Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021240.1 Corchorus olitorius cultivar O-4 contig21273, 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: 36889
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31


Found at i:1011 original size:118 final size:118

Alignment explanation


    Indices: 802--1034  Score: 412
    Period size: 118  Copynumber: 2.0  Consensus size: 118

        792 TGTTAACGCG

                                                           *               * 
        802 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAGAGTTGGTTTGAAGTGGA
          1 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAAAGTTGGTTTGAAGTGAA

                                 *                  *            
        867 AAATTCAAGGACTTGAAATTCTTCAAAACAATATTCATGGTTGTGGTGGAGCA
         66 AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGCTGTGGTGGAGCA

                 *                                                           
        920 TTTGGGATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAAAGTTGGTTTGAAGTGAA
          1 TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAAAGTTGGTTTGAAGTGAA

                 *                                            
        985 AAATTTAAGGACTTGAAATTCCTCAAAACAATATTCATGGCTGTGGTGGA
         66 AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGCTGTGGTGGA

       1035 TGTTCTTCCA


Statistics
Matches: 109,  Mismatches: 6, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 118  109  1.00

ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36


Consensus pattern (118 bp):   
TTTGGAATCTAAGAATTAAGGAGTAATTTATACTATTTTTATTGGAAAAGTTGGTTTGAAGTGAA
AAATTCAAGGACTTGAAATTCCTCAAAACAATATTCATGGCTGTGGTGGAGCA

Found at i:2718 original size:13 final size:13

Alignment explanation


    Indices: 2696--2720  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       2686 ATTGCAAGTA

                         
       2696 CAATTTGCTTAGT
          1 CAATTTGCTTAGT

                        
       2709 CAATTTGCTTAG
          1 CAATTTGCTTAG

       2721 GCATGGATCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44


Consensus pattern (13 bp):   
CAATTTGCTTAGT

Found at i:15097 original size:28 final size:28

Alignment explanation


    Indices: 15065--15126  Score: 81
    Period size: 28  Copynumber: 2.2  Consensus size: 28

      15055 TTACAATTTT

                                         
      15065 ACCCTT-GAATGGGTAAAATTACTAAATC
          1 ACCCTTAGAAT-GGTAAAATTACTAAATC

                    *   *              *
      15093 ACCCTTAGGATGTTAAAATTACTAAATT
          1 ACCCTTAGAATGGTAAAATTACTAAATC

                  
      15121 ACCCTT
          1 ACCCTT

      15127 TAAAGAGGAA


Statistics
Matches: 30,  Mismatches: 3, Indels: 2
        0.86            0.09        0.06

Matches are distributed among these distances:
  28   27  0.90
  29    3  0.10

ACGTcount: A:0.37, C:0.19, G:0.11, T:0.32


Consensus pattern (28 bp):   
ACCCTTAGAATGGTAAAATTACTAAATC

Found at i:20085 original size:2 final size:2

Alignment explanation


    Indices: 20080--20104  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      20070 ACTACTTTGG

                                                 
      20080 AT AT AT AT AT AT AT AT AT AT AT AT A
          1 AT AT AT AT AT AT AT AT AT AT AT AT A

      20105 GAATACTTTG


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (2 bp):   
AT

Found at i:20993 original size:2 final size:2

Alignment explanation


    Indices: 20986--21019  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

      20976 AAAGTTAAAA

                                                       *      
      20986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
          1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT

      21020 GTAAGAAGAA


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

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


Consensus pattern (2 bp):   
AT

Found at i:24297 original size:14 final size:14

Alignment explanation


    Indices: 24276--24316  Score: 55
    Period size: 14  Copynumber: 2.9  Consensus size: 14

      24266 GCCACAATAT

                          
      24276 ACATATACATATAC
          1 ACATATACATATAC

             *         *  
      24290 ATATATACATACAC
          1 ACATATACATATAC

               *         
      24304 ACACATACATATA
          1 ACATATACATATA

      24317 TACAAATCAT


Statistics
Matches: 22,  Mismatches: 5, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  14   22  1.00

ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27


Consensus pattern (14 bp):   
ACATATACATATAC
Done.