Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1454

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: 26004
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31


Found at i:1791 original size:30 final size:30

Alignment explanation


    Indices: 1757--1816  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

       1747 ATTTAATACG

                              *           
       1757 AACTTTGGAAAAATTACATTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                   
       1787 AACTTTTGCATAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

       1817 GGCTCGGGAA


Statistics
Matches: 26,  Mismatches: 4, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  30   26  1.00

ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACACTTTTGCCCCTA

Found at i:7061 original size:21 final size:21

Alignment explanation


    Indices: 7037--7077  Score: 55
    Period size: 21  Copynumber: 2.0  Consensus size: 21

       7027 TCATCAGATC

                        *        
       7037 TACACCTTGAGGCATCGGGGG
          1 TACACCTTGAGGAATCGGGGG

                **              
       7058 TACAGGTTGAGGAATCGGGG
          1 TACACCTTGAGGAATCGGGG

       7078 AGGTGGGGGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  21   17  1.00

ACGTcount: A:0.22, C:0.17, G:0.41, T:0.20


Consensus pattern (21 bp):   
TACACCTTGAGGAATCGGGGG

Found at i:9080 original size:38 final size:39

Alignment explanation


    Indices: 8968--9090  Score: 176
    Period size: 39  Copynumber: 3.2  Consensus size: 39

       8958 TATATGTCCA

                *              *     *             
       8968 GCATGTAGCCTGCGGACCTAAAGTCTGGATATAATTCTC
          1 GCATATAGCCTGCGGACCTGAAGTCCGGATATAATTCTC

                             *   *                 
       9007 GCATATAGCCTGCGGACATGACGTCCGGATATAATTCTC
          1 GCATATAGCCTGCGGACCTGAAGTCCGGATATAATTCTC

              *                                    
       9046 GCTTATAGCCTGC-GACCTGAAGTCCGGATATAATTCTC
          1 GCATATAGCCTGCGGACCTGAAGTCCGGATATAATTCTC

              *    
       9084 GCGTATA
          1 GCATATA

       9091 TATATTCACA


Statistics
Matches: 75,  Mismatches: 9, Indels: 1
        0.88            0.11        0.01

Matches are distributed among these distances:
  38   29  0.39
  39   46  0.61

ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28


Consensus pattern (39 bp):   
GCATATAGCCTGCGGACCTGAAGTCCGGATATAATTCTC

Found at i:16188 original size:39 final size:39

Alignment explanation


    Indices: 16162--16280  Score: 193
    Period size: 39  Copynumber: 3.1  Consensus size: 39

      16152 GTCCAGCACG

                    *     *                        
      16162 TAGCCTGCAGACCTAAAGTCCGGATATAATTCTCGCATA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

                        *                       *  
      16201 TAGCCTGCGGACATGAAGTCCGGATATAATTCTCGCTTA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

                                                *  
      16240 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCGTA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

              
      16279 TA
          1 TA

      16281 TATATTCACA


Statistics
Matches: 74,  Mismatches: 6, Indels: 0
        0.93            0.08        0.00

Matches are distributed among these distances:
  39   74  1.00

ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27


Consensus pattern (39 bp):   
TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

Found at i:24374 original size:39 final size:39

Alignment explanation


    Indices: 24281--24397  Score: 175
    Period size: 39  Copynumber: 3.1  Consensus size: 39

      24271 GTCCAGCACG

                          *     *                  
      24281 TAGCCTGCGGACCTAAAGTCAGGATATAATTCT--CATA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

                        *                       *  
      24318 TAGCCTGCGGACATGAAGTCCGGATATAATTCTCGCTTA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

                                                *  
      24357 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCGTA
          1 TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA

              
      24396 TA
          1 TA

      24398 TATATTCACA


Statistics
Matches: 72,  Mismatches: 6, Indels: 2
        0.90            0.08        0.03

Matches are distributed among these distances:
  37   30  0.42
  39   42  0.58

ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27


Consensus pattern (39 bp):   
TAGCCTGCGGACCTGAAGTCCGGATATAATTCTCGCATA
Done.