Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1352

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: 5651
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37


Found at i:932 original size:17 final size:18

Alignment explanation


    Indices: 888--933  Score: 51
    Period size: 17  Copynumber: 2.6  Consensus size: 18

        878 TTGATTTGAT

                        *      
        888 ATTTATATAAATTTTTAAA
          1 ATTTATA-AAATATTTAAA

             *                
        907 AATTA-AAAATATTT-AA
          1 ATTTATAAAATATTTAAA

                       
        923 ATTTATAAAAT
          1 ATTTATAAAAT

        934 GCCCCCACGA


Statistics
Matches: 23,  Mismatches: 3, Indels: 4
        0.77            0.10        0.13

Matches are distributed among these distances:
  16    6  0.26
  17   12  0.52
  18    1  0.04
  19    4  0.17

ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46


Consensus pattern (18 bp):   
ATTTATAAAATATTTAAA

Found at i:2064 original size:32 final size:33

Alignment explanation


    Indices: 2004--2075  Score: 85
    Period size: 32  Copynumber: 2.2  Consensus size: 33

       1994 ACGATTATAT

                          *               *   
       2004 AAATA-TATATATATTTTAAAATTATATAATAAA
          1 AAATATTA-ATATAATTTAAAATTATATAAAAAA

              *                    *         
       2037 AATTATTAATATAATTT-AAATTTTATAAAAAA
          1 AAATATTAATATAATTTAAAATTATATAAAAAA

                   
       2069 AAATATT
          1 AAATATT

       2076 TTAAATTCAA


Statistics
Matches: 33,  Mismatches: 5, Indels: 3
        0.80            0.12        0.07

Matches are distributed among these distances:
  32   19  0.58
  33   12  0.36
  34    2  0.06

ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43


Consensus pattern (33 bp):   
AAATATTAATATAATTTAAAATTATATAAAAAA

Found at i:3087 original size:17 final size:17

Alignment explanation


    Indices: 3067--3120  Score: 54
    Period size: 17  Copynumber: 3.1  Consensus size: 17

       3057 GTGAAAATAA

                             
       3067 TTTATTTTTTAAAAAAT
          1 TTTATTTTTTAAAAAAT

                *  * *    *  
       3084 TTTAATTATGAAAATAT
          1 TTTATTTTTTAAAAAAT

                               
       3101 TTTAATTTTTTTAAAAAAT
          1 TTT-A-TTTTTTAAAAAAT

             
       3120 T
          1 T

       3121 AAATTAAAAT


Statistics
Matches: 27,  Mismatches: 8, Indels: 2
        0.73            0.22        0.05

Matches are distributed among these distances:
  17   16  0.59
  18    1  0.04
  19   10  0.37

ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56


Consensus pattern (17 bp):   
TTTATTTTTTAAAAAAT

Found at i:3353 original size:15 final size:15

Alignment explanation


    Indices: 3321--3358  Score: 62
    Period size: 14  Copynumber: 2.7  Consensus size: 15

       3311 TATGATCTAT

                           
       3321 TTTTA-TTAAATTTA
          1 TTTTATTTAAATTTA

                           
       3335 -TTTATTTAAATTTA
          1 TTTTATTTAAATTTA

                      
       3349 TTTTATTTAA
          1 TTTTATTTAA

       3359 TCATATTAAA


Statistics
Matches: 22,  Mismatches: 0, Indels: 3
        0.88            0.00        0.12

Matches are distributed among these distances:
  13    4  0.18
  14    9  0.41
  15    9  0.41

ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66


Consensus pattern (15 bp):   
TTTTATTTAAATTTA

Found at i:3405 original size:17 final size:18

Alignment explanation


    Indices: 3363--3405  Score: 63
    Period size: 17  Copynumber: 2.5  Consensus size: 18

       3353 ATTTAATCAT

                              
       3363 ATTAAA-TTAATTTTAAA
          1 ATTAAATTTAATTTTAAA

             *                
       3380 AGTAAATTTAA-TTTAAA
          1 ATTAAATTTAATTTTAAA

                     
       3397 ATTAAATTT
          1 ATTAAATTT

       3406 TAAAAATATT


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  17   19  0.83
  18    4  0.17

ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47


Consensus pattern (18 bp):   
ATTAAATTTAATTTTAAA

Done.