Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3578

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: 15362
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30


Found at i:4394 original size:13 final size:13

Alignment explanation


    Indices: 4376--4400  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       4366 CATATGCCCA

                         
       4376 TCTACAATTTTTT
          1 TCTACAATTTTTT

                        
       4389 TCTACAATTTTT
          1 TCTACAATTTTT

       4401 GGTTGGGCCA


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60


Consensus pattern (13 bp):   
TCTACAATTTTTT

Found at i:5630 original size:39 final size:40

Alignment explanation


    Indices: 5556--5739  Score: 189
    Period size: 39  Copynumber: 4.7  Consensus size: 40

       5546 GCTACTCGTT

                                                     
       5556 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
          1 CAAATGCCTTCGGGACATAGCCCGGATT-TAGTAACTCGCA

                               *                 *  
       5596 CAAATGCCTTCGGGAC-TAACCCGGATTTAGTAACTCTCA
          1 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA

                            *         *      *      
       5635 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
          1 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA

                             *   *      * *  *    *   
       5674 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
          1 CAAATGCCTTCGGGA-CATAGCCCGGATTTAGTAAC-TCGCA

                        *   *         
       5715 CAAA-GCCTTCGAGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACATAGCCCGGA

       5740 CATCATTCAA


Statistics
Matches: 123,  Mismatches: 15, Indels: 12
        0.82            0.10        0.08

Matches are distributed among these distances:
  38    3  0.02
  39   62  0.50
  40   48  0.39
  41   10  0.08

ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24


Consensus pattern (40 bp):   
CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA

Found at i:13711 original size:79 final size:82

Alignment explanation


    Indices: 13600--13784  Score: 238
    Period size: 79  Copynumber: 2.3  Consensus size: 82

      13590 GCTACTCGTT

                            *         *                                      
      13600 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC

                *         *   
      13663 GGATTTAGTAAC-TCGCA
         65 GGATATAGTAACTTAGCA

                                              *                         **   
      13680 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG

                 *  *        
      13743 GATATGGTCACTTAGCA
         66 GATATAGTAACTTAGCA

                                      
      13760 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

      13785 CATCATTCAA


Statistics
Matches: 92,  Mismatches: 9, Indels: 8
        0.84            0.08        0.07

Matches are distributed among these distances:
  78    3  0.03
  79   55  0.60
  80   34  0.37

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


Consensus pattern (82 bp):   
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA

Found at i:13784 original size:40 final size:40

Alignment explanation


    Indices: 13581--13784  Score: 238
    Period size: 40  Copynumber: 5.1  Consensus size: 40

      13571 CGGAATTTAA

                              **                *    
      13581 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                                 * 
      13621 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *                                 
      13661 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                         *                           *
      13700 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
      13740 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
      13780 CCGGA
          1 CCGGA

      13785 CATCATTCAA


Statistics
Matches: 141,  Mismatches: 16, Indels: 14
        0.82            0.09        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   33  0.23
  40   94  0.67
  41   12  0.09

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.