Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01019429.1 Corchorus olitorius cultivar O-4 contig19462, 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: 4013
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.28


Found at i:3269 original size:54 final size:54

Alignment explanation


    Indices: 3187--3349  Score: 281
    Period size: 54  Copynumber: 3.0  Consensus size: 54

       3177 GAAACAGGTT

                      *                                           
       3187 TTCAGATGATTTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
          1 TTCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC

                             *                                    
       3241 TTCAGATGATCTAGTGCAGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC
          1 TTCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC

                       *                         *   *            
       3295 TTCAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TTCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC

             
       3349 T
          1 T

       3350 CGTTTCAAGA


Statistics
Matches: 103,  Mismatches: 6, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  54  103  1.00

ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34


Consensus pattern (54 bp):   
TTCAGATGATCTAGTGCGGTCATTCCAAGAAGTTTTCAATGGTCAGAGTTGATC

Found at i:3497 original size:140 final size:141

Alignment explanation


    Indices: 3337--3702  Score: 594
    Period size: 140  Copynumber: 2.6  Consensus size: 141

       3327 TTTTCGATGA

                          *                                                  
       3337 TCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTC
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTC

                         *                                                   
       3402 GGTGATCAGAGTTAATCTCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATCTCATTTTCAAG-A
         66 GGTGATCAGAGTTGATCTCCTTTCAGGAAG-TTTTTATGATCAGAGTTGATCTCA-TTTCAAGAA

                         
       3466 -TGTTTT-TATGG
        129 GTGTTTTATATGG

                                                                             
       3477 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTC
          1 TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTC

                                                                             
       3542 GGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGT
         66 GGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGT

            *          
       3607 TTTTTATATGG
        131 GTTTTATATGG

                          *                **                 **             
       3618 TCAGAGTTGATCTCCTTTCAAGAAGTTTTTTTTATGATCAGAGTTGATCTTATTTCAAGAAGTTT
          1 TCAGAGTTGATCTCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTT

               *                
       3683 TCGATGATCAGAGTTGATCT
         64 TCGGTGATCAGAGTTGATCT

       3703 TCACATTGAT


Statistics
Matches: 212,  Mismatches: 9, Indels: 7
        0.93            0.04        0.03

Matches are distributed among these distances:
 138    7  0.03
 139   25  0.12
 140   98  0.46
 141   29  0.14
 143   53  0.25

ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41


Consensus pattern (141 bp):   
TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTC
GGTGATCAGAGTTGATCTCCTTTCAGGAAGTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGT
GTTTTATATGG

Found at i:3703 original size:35 final size:35

Alignment explanation


    Indices: 3314--3702  Score: 503
    Period size: 35  Copynumber: 11.0  Consensus size: 35

       3304 TCCAGTGCGG

                 *                             
       3314 TCATTCCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *                                
       3349 TCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *                *           *   
       3384 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTAATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *     *        **                
       3419 TCCTTTCAGGAAGTTTTTTATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                        *      *   *            
       3454 TCATTTTCAAGATGTTTT-TATGGTCAGAGTTGATC
          1 TCA-TTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                                               
       3489 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *                *               
       3524 TCGTTTCAAGAAGTTTTCGGTGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

              *     *         *                
       3559 TCCTTTCAGGAAGTTTT-TATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

                               **   *            
       3593 TCATTTCAAGAAGTTTTTTATATGGTCAGAGTTGATC
          1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC

              *                **                
       3630 TCCTTTCAAGAAGTTTTTTTTATGATCAGAGTTGATC
          1 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATC

             *                                 
       3667 TTATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
          1 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC

             
       3702 T
          1 T

       3703 TCACATTGAT


Statistics
Matches: 316,  Mismatches: 33, Indels: 10
        0.88            0.09        0.03

Matches are distributed among these distances:
  34   39  0.12
  35  200  0.63
  36   16  0.05
  37   61  0.19

ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40


Consensus pattern (35 bp):   
TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
Done.