Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2871

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: 34032
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31


Found at i:2401 original size:40 final size:40

Alignment explanation


    Indices: 2346--2612  Score: 480
    Period size: 40  Copynumber: 6.7  Consensus size: 40

       2336 AACATTGGAT

                                                    
       2346 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
       2386 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
       2426 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

            *                                       
       2466 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                         *                    * *   
       2506 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
       2546 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

               *      *                
       2586 TATGTCCGGGTTAAGACCCGAAGGCAA
          1 TATATCCGGGCTAAGACCCGAAGGCAA

       2613 ATGTGTTTGC


Statistics
Matches: 217,  Mismatches: 10, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40  217  1.00

ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22


Consensus pattern (40 bp):   
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

Found at i:11215 original size:40 final size:40

Alignment explanation


    Indices: 11160--11426  Score: 480
    Period size: 40  Copynumber: 6.7  Consensus size: 40

      11150 AACATTGGAT

                                                    
      11160 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
      11200 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
      11240 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

            *                                       
      11280 CATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                         *                    * *   
      11320 TATATCCGGGCTATGACCCGAAGGCAATTATGCGGGATGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

                                                    
      11360 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA
          1 TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

               *      *                
      11400 TATGTCCGGGTTAAGACCCGAAGGCAA
          1 TATATCCGGGCTAAGACCCGAAGGCAA

      11427 ATGTGTTTGC


Statistics
Matches: 217,  Mismatches: 10, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  40  217  1.00

ACGTcount: A:0.30, C:0.21, G:0.28, T:0.22


Consensus pattern (40 bp):   
TATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTGA

Found at i:14724 original size:46 final size:46

Alignment explanation


    Indices: 14657--14782  Score: 180
    Period size: 46  Copynumber: 2.7  Consensus size: 46

      14647 AACCCACCCC

                                        *    ***          
      14657 TAAGTGAACTCGAACTCAACTCAACGAGCTCGGGTGTTCGCATCCA
          1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCA

                        *                         * *     
      14703 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGTATCCA
          1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCA

              *                               
      14749 TAGGTGAACTCGAACTCAACTCAACGAGTTCGGA
          1 TAAGTGAACTCGAACTCAACTCAACGAGTTCGGA

      14783 TGCTCAACCA


Statistics
Matches: 71,  Mismatches: 9, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  46   71  1.00

ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23


Consensus pattern (46 bp):   
TAAGTGAACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCA

Found at i:15239 original size:30 final size:30

Alignment explanation


    Indices: 15205--15264  Score: 84
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      15195 ATTTAAGATG

                                   *      
      15205 AACTTTGGAAAAATTACACTTTTTCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

                  * * *                   
      15235 AACTTTTGCATAATTACACTTTTGCCCCTA
          1 AACTTTGGAAAAATTACACTTTTGCCCCTA

      15265 GGCTCAGGAA


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:0.25, G:0.07, T:0.38


Consensus pattern (30 bp):   
AACTTTGGAAAAATTACACTTTTGCCCCTA

Found at i:19625 original size:55 final size:55

Alignment explanation


    Indices: 19510--19627  Score: 130
    Period size: 55  Copynumber: 2.1  Consensus size: 55

      19500 CCTGCCAAAA

                         *    *          *    *              *     
      19510 TAACACGGGCGTGCGACATGCCCGTGCCTTGAAATCGTGGCCAAACCTATCTAAT
          1 TAACACGGGCGTGAGACACGCCCGTGCCTAGAAACCGTGGCCAAACCTAGCTAAT

            *                         *    * *      *               
      19565 CAACACGGGCGTGAGACACGCCCGTGTCTAGCACCCGTGGTCAAACCT-GCTAGAT
          1 TAACACGGGCGTGAGACACGCCCGTGCCTAGAAACCGTGGCCAAACCTAGCTA-AT

                    
      19620 TAACACGG
          1 TAACACGG

      19628 ATGTGGGTCT


Statistics
Matches: 51,  Mismatches: 11, Indels: 2
        0.80            0.17        0.03

Matches are distributed among these distances:
  54    3  0.06
  55   48  0.94

ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19


Consensus pattern (55 bp):   
TAACACGGGCGTGAGACACGCCCGTGCCTAGAAACCGTGGCCAAACCTAGCTAAT
Done.