Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold298

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: 32394
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31


Found at i:3457 original size:40 final size:40

Alignment explanation


    Indices: 3409--3633  Score: 393
    Period size: 40  Copynumber: 5.7  Consensus size: 40

       3399 GCAAACACAT

                            *      *         *      
       3409 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
       3449 TTGCCTTCGGGTCTTAGCCCGGATATAT---CTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *                          
       3486 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
       3526 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
       3566 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                        
       3606 TTGCCTTCGGGTCTTAGCCCGGATATAT
          1 TTGCCTTCGGGTCTTAGCCCGGATATAT

       3634 TCCAATGCTC


Statistics
Matches: 177,  Mismatches: 5, Indels: 6
        0.94            0.03        0.03

Matches are distributed among these distances:
  37   35  0.20
  40  142  0.80

ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

Found at i:12131 original size:40 final size:40

Alignment explanation


    Indices: 12083--12310  Score: 411
    Period size: 40  Copynumber: 5.7  Consensus size: 40

      12073 GCAAACACAT

                            *      *         *      
      12083 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                          *         
      12123 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                         *                          
      12163 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
      12203 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                                    
      12243 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
          1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

                                        
      12283 TTGCCTTCGGGTCTTAGCCCGGATATAT
          1 TTGCCTTCGGGTCTTAGCCCGGATATAT

      12311 TCCAATGCTC


Statistics
Matches: 181,  Mismatches: 7, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40  181  1.00

ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31


Consensus pattern (40 bp):   
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA

Found at i:23422 original size:40 final size:39

Alignment explanation


    Indices: 23359--23624  Score: 329
    Period size: 40  Copynumber: 6.7  Consensus size: 39

      23349 GCTACTCGCT

                   *        *           *           
      23359 CAAATGCGTTCGGGACATAGCCCGGTTAGAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAGCCCGGTT-TAGTAACTCACA

               *                                *   
      23399 CAATTGCCTTCGGGACTTAGCCCGGATTTAGTAACTTACA
          1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCACA

                                                    
      23439 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACA
          1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCACA

                                     *       *   *  
      23479 CAAATGCCTTCGGGACTTAGCCCGAATTTAGTAGCTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCG-GTTTAGTAACTCACA

                                                 *  
      23519 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
          1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCACA

                                      **    *       *
      23559 CAAATGCCTTCGGGACTT-GCCCGGAACTAGTCACT-AGCG
          1 CAAATGCCTTCGGGACTTAGCCCGG-TTTAGTAACTCA-CA

              *                        
      23598 CAGATGCCTTCGGGACTTAGCCCGGTT
          1 CAAATGCCTTCGGGACTTAGCCCGGTT

      23625 ATCATCCAAA


Statistics
Matches: 201,  Mismatches: 20, Indels: 11
        0.87            0.09        0.05

Matches are distributed among these distances:
  39   32  0.16
  40  167  0.83
  41    2  0.01

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.24


Consensus pattern (39 bp):   
CAAATGCCTTCGGGACTTAGCCCGGTTTAGTAACTCACA

Found at i:23473 original size:80 final size:80

Alignment explanation


    Indices: 23359--23622  Score: 363
    Period size: 80  Copynumber: 3.3  Consensus size: 80

      23349 GCTACTCGCT

                   *        *            *              *                    
      23359 CAAATGCGTTCGGGACATAGCCCGG-TTAGAGTAACTCACACAATTGCCTTCGGGACTTAGCCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCACACAAATGCCTTCGGGACTTAGCCCG

                            
      23423 GATTTAGTAACTTACA
         65 GATTTAGTAACTTACA

                                                                            *
      23439 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGA
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGG

                    *  **  
      23504 ATTTAGTAGCTCGCA
         66 ATTTAGTAACTTACA

                                                 *                           
      23519 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTT-GCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGG

             **    *       *
      23583 AACTAGTCAC-TAGCG
         66 ATTTAGTAACTTA-CA

              *                      
      23598 CAGATGCCTTCGGGACTTAGCCCGG
          1 CAAATGCCTTCGGGACTTAGCCCGG

      23623 TTATCATCCA


Statistics
Matches: 164,  Mismatches: 18, Indels: 5
        0.88            0.10        0.03

Matches are distributed among these distances:
  79   36  0.22
  80  126  0.77
  81    2  0.01

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


Consensus pattern (80 bp):   
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTTACA

Found at i:26942 original size:11 final size:11

Alignment explanation


    Indices: 26923--26954  Score: 55
    Period size: 11  Copynumber: 2.9  Consensus size: 11

      26913 ATTCAGGGGT

                *      
      26923 TTTAGGTTTTC
          1 TTTATGTTTTC

                       
      26934 TTTATGTTTTC
          1 TTTATGTTTTC

                      
      26945 TTTATGTTTT
          1 TTTATGTTTT

      26955 GTAATCATTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   20  1.00

ACGTcount: A:0.09, C:0.06, G:0.12, T:0.72


Consensus pattern (11 bp):   
TTTATGTTTTC
Done.