Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014766.1 Corchorus olitorius cultivar O-4 contig14799, 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: 51218
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32


Found at i:8499 original size:3 final size:3

Alignment explanation


    Indices: 8493--8589  Score: 185
    Period size: 3  Copynumber: 32.3  Consensus size: 3

       8483 TATAATACTC

                                                            *              
       8493 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

                                                                           
       8541 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
          1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA

             
       8589 T
          1 T

       8590 GTTAGTAAAT


Statistics
Matches: 92,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
   3   92  1.00

ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33


Consensus pattern (3 bp):   
TAA

Found at i:25742 original size:15 final size:14

Alignment explanation


    Indices: 25723--25752  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

      25713 TTAATACTCC

                          
      25723 ATTTTTTTGGTGAA
          1 ATTTTTTTGGTGAA

                          
      25737 ATTTTTTTGGTGAA
          1 ATTTTTTTGGTGAA

              
      25751 AT
          1 AT

      25753 AAAATAGTAG


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.23, C:0.00, G:0.20, T:0.57


Consensus pattern (14 bp):   
ATTTTTTTGGTGAA

Found at i:27514 original size:14 final size:15

Alignment explanation


    Indices: 27495--27536  Score: 50
    Period size: 15  Copynumber: 2.9  Consensus size: 15

      27485 TCTATCTCTC

                           
      27495 TTTGCTTT-TTTTTT
          1 TTTGCTTTCTTTTTT

                     **    
      27509 TTTGCTTTCCATTTT
          1 TTTGCTTTCTTTTTT

                    *    
      27524 TTTGCTTTGTTTT
          1 TTTGCTTTCTTTT

      27537 GGGACCTCAA


Statistics
Matches: 22,  Mismatches: 5, Indels: 1
        0.79            0.18        0.04

Matches are distributed among these distances:
  14    8  0.36
  15   14  0.64

ACGTcount: A:0.02, C:0.12, G:0.10, T:0.76


Consensus pattern (15 bp):   
TTTGCTTTCTTTTTT

Found at i:36111 original size:18 final size:18

Alignment explanation


    Indices: 36088--36124  Score: 74
    Period size: 18  Copynumber: 2.1  Consensus size: 18

      36078 TTAACTTTAC

                              
      36088 AAGTTGAAATATTTAAAG
          1 AAGTTGAAATATTTAAAG

                              
      36106 AAGTTGAAATATTTAAAG
          1 AAGTTGAAATATTTAAAG

             
      36124 A
          1 A

      36125 GTAGTATTAA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  18   19  1.00

ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32


Consensus pattern (18 bp):   
AAGTTGAAATATTTAAAG

Found at i:48226 original size:44 final size:44

Alignment explanation


    Indices: 48163--48294  Score: 255
    Period size: 44  Copynumber: 3.0  Consensus size: 44

      48153 TAGGAGTGTC

                      *                                 
      48163 ATTACAACCTCCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT
          1 ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT

                                                        
      48207 ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT
          1 ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT

                                                        
      48251 ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT
          1 ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT

      48295 CCTAGTAAAT


Statistics
Matches: 87,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
  44   87  1.00

ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45


Consensus pattern (44 bp):   
ATTACAACCTTCTCCTTAGTAATTTTTAAAAGTTCCATTTCCTT

Found at i:48456 original size:15 final size:15

Alignment explanation


    Indices: 48436--48465  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      48426 TTTTTATTTT

                           
      48436 ATTCAAAAATAAGTA
          1 ATTCAAAAATAAGTA

                  *        
      48451 ATTCAATAATAAGTA
          1 ATTCAAAAATAAGTA

      48466 CTTATAATAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30


Consensus pattern (15 bp):   
ATTCAAAAATAAGTA

Found at i:50306 original size:15 final size:15

Alignment explanation


    Indices: 50286--50315  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      50276 TTCTCATCTC

                           
      50286 TAAGAAACTTGGGTT
          1 TAAGAAACTTGGGTT

                           
      50301 TAAGAAACTTGGGTT
          1 TAAGAAACTTGGGTT

      50316 GTCAATTTCT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33


Consensus pattern (15 bp):   
TAAGAAACTTGGGTT
Done.