Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold7134.1

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: 8118
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29


Found at i:3533 original size:66 final size:66

Alignment explanation


    Indices: 3450--3581  Score: 255
    Period size: 66  Copynumber: 2.0  Consensus size: 66

       3440 AACTAAATCG

                                                            *                
       3450 ACACTACCTAAATTCGATCGGGAATATAATACGACTCGTCACATCATCTGAATCGAGCTCGTATC
          1 ACACTACCTAAATTCGATCGGGAATATAATACGACTCGTCACATCATCCGAATCGAGCTCGTATC

             
       3515 A
         66 A

                                                                             
       3516 ACACTACCTAAATTCGATCGGGAATATAATACGACTCGTCACATCATCCGAATCGAGCTCGTATC
          1 ACACTACCTAAATTCGATCGGGAATATAATACGACTCGTCACATCATCCGAATCGAGCTCGTATC

             
       3581 A
         66 A

       3582 GTTGGTATCA


Statistics
Matches: 65,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  66   65  1.00

ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25


Consensus pattern (66 bp):   
ACACTACCTAAATTCGATCGGGAATATAATACGACTCGTCACATCATCCGAATCGAGCTCGTATC
A

Found at i:3645 original size:13 final size:12

Alignment explanation


    Indices: 3627--3685  Score: 93
    Period size: 12  Copynumber: 4.9  Consensus size: 12

       3617 TTGTATATTC

                        
       3627 AAAAAAAATTGA
          1 AAAAAAAATTGA

                     *  
       3639 AAAAAAAATCG-
          1 AAAAAAAATTGA

                         
       3650 AAAAAAAATTGAA
          1 AAAAAAAATTG-A

                        
       3663 AAAAAAAATTGA
          1 AAAAAAAATTGA

                       
       3675 AAAAAAAATTG
          1 AAAAAAAATTG

       3686 CATACGGTCT


Statistics
Matches: 43,  Mismatches: 2, Indels: 4
        0.88            0.04        0.08

Matches are distributed among these distances:
  11   10  0.23
  12   22  0.51
  13   11  0.26

ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15


Consensus pattern (12 bp):   
AAAAAAAATTGA

Found at i:3763 original size:20 final size:20

Alignment explanation


    Indices: 3738--3782  Score: 90
    Period size: 20  Copynumber: 2.2  Consensus size: 20

       3728 TTTAATGAAT

                                
       3738 TTTCACGCTATTAAAAAAAA
          1 TTTCACGCTATTAAAAAAAA

                                
       3758 TTTCACGCTATTAAAAAAAA
          1 TTTCACGCTATTAAAAAAAA

                 
       3778 TTTCA
          1 TTTCA

       3783 ATTAGTGAAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  20   25  1.00

ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33


Consensus pattern (20 bp):   
TTTCACGCTATTAAAAAAAA
Done.