Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014273.1 Corchorus olitorius cultivar O-4 contig14306, 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: 16971
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33


Found at i:6504 original size:3 final size:3

Alignment explanation


    Indices: 6496--6644  Score: 171
    Period size: 3  Copynumber: 50.0  Consensus size: 3

       6486 GATGAGTTAA

                             *       *   *               *        *        
       6496 AAG AAG AAG AAG AGG AAG AGG ATG AAG AAG AAG ACG AAG AAA AAG AAG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

                            *                                    *      
       6544 AAG AAG AAG AAG TAG -AG AAAG AAG AAG AAG AAG AAG AAG TAG -AG
          1 AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG

                                         *                               
       6588 AAAG AAG AAG AAG AAG AAG AAG TAG -AG AAAG AAG AAG AAG AAG AAG
          1 -AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG

                           
       6634 AAG AAG -AG AAG
          1 AAG AAG AAG AAG

       6645 GTTGAAGAGA


Statistics
Matches: 127,  Mismatches: 12, Indels: 14
        0.83            0.08        0.09

Matches are distributed among these distances:
   2    8  0.06
   3  113  0.89
   4    6  0.05

ACGTcount: A:0.62, C:0.01, G:0.34, T:0.03


Consensus pattern (3 bp):   
AAG

Found at i:6652 original size:27 final size:27

Alignment explanation


    Indices: 6496--6643  Score: 212
    Period size: 27  Copynumber: 5.6  Consensus size: 27

       6486 GATGAGTTAA

                          *    *  *    
       6496 AAGAAGAAGAAGAGGAAGAGGATGAAG
          1 AAGAAGAAGAAGAGAAAGAAGAAGAAG

                   *                   
       6523 AAGAAGACG-A-AGAAA-AAGAAGAAG
          1 AAGAAGAAGAAGAGAAAGAAGAAGAAG

                     *                 
       6547 AAGAAGAAGTAGAGAAAGAAGAAGAAG
          1 AAGAAGAAGAAGAGAAAGAAGAAGAAG

                     *                 
       6574 AAGAAGAAGTAGAGAAAGAAGAAGAAG
          1 AAGAAGAAGAAGAGAAAGAAGAAGAAG

                     *                 
       6601 AAGAAGAAGTAGAGAAAGAAGAAGAAG
          1 AAGAAGAAGAAGAGAAAGAAGAAGAAG

                            
       6628 AAGAAGAAGAAGAGAA
          1 AAGAAGAAGAAGAGAA

       6644 GGTTGAAGAG


Statistics
Matches: 112,  Mismatches: 6, Indels: 6
        0.90            0.05        0.05

Matches are distributed among these distances:
  24   15  0.13
  25    5  0.04
  26    6  0.05
  27   86  0.77

ACGTcount: A:0.63, C:0.01, G:0.34, T:0.03


Consensus pattern (27 bp):   
AAGAAGAAGAAGAGAAAGAAGAAGAAG

Found at i:12408 original size:16 final size:17

Alignment explanation


    Indices: 12387--12420  Score: 52
    Period size: 17  Copynumber: 2.1  Consensus size: 17

      12377 GTACGTATAC

                        *    
      12387 ATTATAT-TTAATAAAT
          1 ATTATATATTAACAAAT

                             
      12403 ATTATATATTAACAAAT
          1 ATTATATATTAACAAAT

             
      12420 A
          1 A

      12421 CAAAATAAAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    7  0.44
  17    9  0.56

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44


Consensus pattern (17 bp):   
ATTATATATTAACAAAT

Done.