Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2495

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: 29118
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31


Found at i:17503 original size:39 final size:38

Alignment explanation


    Indices: 17363--17496  Score: 178
    Period size: 39  Copynumber: 3.4  Consensus size: 38

      17353 TAACTCATTC

                                    *             *
      17363 AATGCCTTCGGACTTAACCCGGATTTTAAAACTCGCACG
          1 AATGCCTTCGGACTTAACCCGGA-ATTAAAACTCGCACA

                                         * *        
      17402 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
          1 AATGCCTTC-GGACTTAACCCGGAATTA-AAACTCGCACA

              *                                   
      17442 AAGGCCTTCGGACTTAACCCGGAATTAAAACTCGCACA
          1 AATGCCTTCGGACTTAACCCGGAATTAAAACTCGCACA

               *             
      17480 AATACCTTCGGATCTTA
          1 AATGCCTTCGGA-CTTA

      17497 GTCCGGATAT


Statistics
Matches: 83,  Mismatches: 9, Indels: 6
        0.85            0.09        0.06

Matches are distributed among these distances:
  38   19  0.23
  39   34  0.41
  40   30  0.36

ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25


Consensus pattern (38 bp):   
AATGCCTTCGGACTTAACCCGGAATTAAAACTCGCACA

Found at i:17519 original size:78 final size:78

Alignment explanation


    Indices: 17366--17542  Score: 202
    Period size: 78  Copynumber: 2.3  Consensus size: 78

      17356 CTCATTCAAT

                                 *             *   *                         
      17366 GCCTTCGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGAATTAG
          1 GCCTTCGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTAG

                 *       
      17431 TATCTCGCACAAA
         66 TATCTAGCACAAA

                                                                   **        
      17444 GGCCTTCGGACTTAACCCGGA-ATTAAAACTCGCACAAATACCTTC-GGATCTTAGTCCGG-A-T
          1 -GCCTTCGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGA-CTTAACCCGGAATT

                              
      17505 A-TATCACTTAGCACAAA
         64 AGTAT--C-TAGCACAAA

                          *      
      17522 GCCTTCGGGACTTAGCCCGGA
          1 GCCTTC-GGACTTAACCCGGA

      17543 CAGCATTCAA


Statistics
Matches: 86,  Mismatches: 7, Indels: 11
        0.83            0.07        0.11

Matches are distributed among these distances:
  75    3  0.03
  76    2  0.02
  77   11  0.13
  78   50  0.58
  79   20  0.23

ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24


Consensus pattern (78 bp):   
GCCTTCGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGAATTAG
TATCTAGCACAAA

Found at i:25301 original size:80 final size:80

Alignment explanation


    Indices: 25190--25370  Score: 219
    Period size: 80  Copynumber: 2.3  Consensus size: 80

      25180 CTCATTCAAT

                                  *             *   *                        
      25190 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
          1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-

                      *       
      25253 TAGT-A-TCTCGCACAAA
         64 TAGTCACT-TAGCACAAA

                                                                    **       
      25269 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
          1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA

                             
      25333 TAGTCACTTAGCACAAA
         64 TAGTCACTTAGCACAAA

                          *      
      25350 GCCTTCGGGACTTAGCCCGGA
          1 GCCTTCGGGACTTAACCCGGA

      25371 CAGCATTCAA


Statistics
Matches: 89,  Mismatches: 7, Indels: 10
        0.84            0.07        0.09

Matches are distributed among these distances:
  79    7  0.08
  80   71  0.80
  81   10  0.11
  82    1  0.01

ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24


Consensus pattern (80 bp):   
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA

Found at i:25330 original size:40 final size:40

Alignment explanation


    Indices: 25187--25370  Score: 196
    Period size: 40  Copynumber: 4.6  Consensus size: 40

      25177 TAACTCATTC

                                     *              *
      25187 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
          1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA

                                        *  *        
      25227 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

              *                                     
      25267 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
          1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

               *              **          * *    *     
      25307 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
          1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA

                             *      
      25348 AA-GCCTTCGGGACTTAGCCCGGA
          1 AATGCCTTCGGGACTTAACCCGGA

      25371 CAGCATTCAA


Statistics
Matches: 122,  Mismatches: 16, Indels: 11
        0.82            0.11        0.07

Matches are distributed among these distances:
  39    8  0.07
  40  103  0.84
  41   11  0.09

ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24


Consensus pattern (40 bp):   
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA

Found at i:27452 original size:19 final size:18

Alignment explanation


    Indices: 27428--27463  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      27418 AAAGTTTTTT

                               
      27428 ATTATTTAAATATTAATTA
          1 ATTATTTAAA-ATTAATTA

                   *         
      27447 ATTATTTTAAATTAATT
          1 ATTATTTAAAATTAATT

      27464 TATATTTCAA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56


Consensus pattern (18 bp):   
ATTATTTAAAATTAATTA
Done.