Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold788

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: 15469
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:6381 original size:2 final size:2

Alignment explanation


    Indices: 6362--6396  Score: 52
    Period size: 2  Copynumber: 17.5  Consensus size: 2

       6352 AATGGCAAGT

                      *        *                                
       6362 TA TA TA TG TA TA TG TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6397 TATTCTTGAT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51


Consensus pattern (2 bp):   
TA

Found at i:10267 original size:30 final size:30

Alignment explanation


    Indices: 10231--10291  Score: 113
    Period size: 30  Copynumber: 2.0  Consensus size: 30

      10221 ATACCAATAT

                           *              
      10231 AGTGTCAACCAGTTTTCCTTTCCCTTTATC
          1 AGTGTCAACCAGTTTCCCTTTCCCTTTATC

                                          
      10261 AGTGTCAACCAGTTTCCCTTTCCCTTTATC
          1 AGTGTCAACCAGTTTCCCTTTCCCTTTATC

             
      10291 A
          1 A

      10292 CTTCTGCTCA


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  30   30  1.00

ACGTcount: A:0.18, C:0.31, G:0.10, T:0.41


Consensus pattern (30 bp):   
AGTGTCAACCAGTTTCCCTTTCCCTTTATC

Found at i:15025 original size:15 final size:15

Alignment explanation


    Indices: 15005--15034  Score: 51
    Period size: 15  Copynumber: 2.0  Consensus size: 15

      14995 TAAATTTTTA

                           
      15005 TTATTTGTTTATAAT
          1 TTATTTGTTTATAAT

                  *        
      15020 TTATTTTTTTATAAT
          1 TTATTTGTTTATAAT

      15035 AATAATATAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  15   14  1.00

ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70


Consensus pattern (15 bp):   
TTATTTGTTTATAAT

Found at i:15156 original size:29 final size:28

Alignment explanation


    Indices: 15114--15172  Score: 68
    Period size: 27  Copynumber: 2.1  Consensus size: 28

      15104 TTTAAAACAT

                    *                      
      15114 ATCTACATTTTTATCAA-AATTATTTTTTAA
          1 ATCTACATATTTAT-AATAA-TA-TTTTTAA

                                        
      15144 ATCTA-ATATTTATAATAATATTTTTAA
          1 ATCTACATATTTATAATAATATTTTTAA

              
      15171 AT
          1 AT

      15173 ATCAAACAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 5
        0.82            0.03        0.15

Matches are distributed among these distances:
  27    9  0.33
  28    4  0.15
  29    9  0.33
  30    5  0.19

ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53


Consensus pattern (28 bp):   
ATCTACATATTTATAATAATATTTTTAA
Done.