Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014807.1 Corchorus olitorius cultivar O-4 contig14840, 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: 23092
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31


Found at i:336 original size:61 final size:61

Alignment explanation


    Indices: 222--337  Score: 173
    Period size: 61  Copynumber: 1.9  Consensus size: 61

        212 AAATTTGATG

                        *                            **                  
        222 TTTTAGTTTGAATGTTTTAGAGGATTTGAAGTTAGAAAGTTTGAAGAAAATGAAGTAAAGA
          1 TTTTAGTTTGAAGGTTTTAGAGGATTTGAAGTTAGAAAGTTAAAAGAAAATGAAGTAAAGA

                                                                     
        283 TTTTAGTTTGAAGGTTTTA-ATGGATTTGAAGTTAGAAAG-TAAAAGAAATATGAAG
          1 TTTTAGTTTGAAGGTTTTAGA-GGATTTGAAGTTAGAAAGTTAAAAGAAA-ATGAAG

        338 CAAAAGGGCA


Statistics
Matches: 50,  Mismatches: 3, Indels: 4
        0.88            0.05        0.07

Matches are distributed among these distances:
  60    8  0.16
  61   42  0.84

ACGTcount: A:0.40, C:0.00, G:0.24, T:0.36


Consensus pattern (61 bp):   
TTTTAGTTTGAAGGTTTTAGAGGATTTGAAGTTAGAAAGTTAAAAGAAAATGAAGTAAAGA

Found at i:4839 original size:22 final size:22

Alignment explanation


    Indices: 4814--4867  Score: 90
    Period size: 22  Copynumber: 2.5  Consensus size: 22

       4804 GCTTATTGCT

                 *                
       4814 CAAAAAGGCCCCTAAACTTACA
          1 CAAAACGGCCCCTAAACTTACA

                         *        
       4836 CAAAACGGCCCCTGAACTTACA
          1 CAAAACGGCCCCTAAACTTACA

                      
       4858 CAAAACGGCC
          1 CAAAACGGCC

       4868 AAATAAGCCC


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

Matches are distributed among these distances:
  22   30  1.00

ACGTcount: A:0.41, C:0.35, G:0.13, T:0.11


Consensus pattern (22 bp):   
CAAAACGGCCCCTAAACTTACA

Found at i:10546 original size:21 final size:21

Alignment explanation


    Indices: 10504--10546  Score: 50
    Period size: 21  Copynumber: 2.0  Consensus size: 21

      10494 AACATCGCTT

                *           **   
      10504 GCCCGCGCGCGGCTTGGGTCA
          1 GCCCACGCGCGGCTTGCCTCA

                           *     
      10525 GCCCACGCGCGGCTTTCCTCA
          1 GCCCACGCGCGGCTTGCCTCA

             
      10546 G
          1 G

      10547 GCCCTTTAGG


Statistics
Matches: 18,  Mismatches: 4, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  21   18  1.00

ACGTcount: A:0.07, C:0.42, G:0.35, T:0.16


Consensus pattern (21 bp):   
GCCCACGCGCGGCTTGCCTCA

Found at i:22631 original size:17 final size:17

Alignment explanation


    Indices: 22609--22641  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

      22599 TTTTATGGAT

                              
      22609 ATTTAT-ATTATTAATTA
          1 ATTTATAATT-TTAATTA

                            
      22626 ATTTATAATTTTAATT
          1 ATTTATAATTTTAATT

      22642 GATGTAATGA


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  17   12  0.80
  18    3  0.20

ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61


Consensus pattern (17 bp):   
ATTTATAATTTTAATTA
Done.