Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2056

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: 6629
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37


Found at i:1042 original size:6 final size:6

Alignment explanation


    Indices: 1031--1059  Score: 58
    Period size: 6  Copynumber: 4.8  Consensus size: 6

       1021 AGGAACTGAA

                                             
       1031 AGTGGC AGTGGC AGTGGC AGTGGC AGTGG
          1 AGTGGC AGTGGC AGTGGC AGTGGC AGTGG

       1060 GTGGGGCCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   23  1.00

ACGTcount: A:0.17, C:0.14, G:0.52, T:0.17


Consensus pattern (6 bp):   
AGTGGC

Found at i:3401 original size:18 final size:17

Alignment explanation


    Indices: 3380--3414  Score: 52
    Period size: 17  Copynumber: 2.0  Consensus size: 17

       3370 AAAAAAAAAT

                              
       3380 AAGAAAAGATAAAATAAA
          1 AAGAAAAG-TAAAATAAA

                 *           
       3398 AAGAATAGTAAAATAAA
          1 AAGAAAAGTAAAATAAA

       3415 TCAATAAAAT


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

Matches are distributed among these distances:
  17    9  0.56
  18    7  0.44

ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14


Consensus pattern (17 bp):   
AAGAAAAGTAAAATAAA

Found at i:6050 original size:4 final size:4

Alignment explanation


    Indices: 6041--6070  Score: 51
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       6031 CAAATTAGTT

                                       *         
       6041 ATAC ATAC ATAC ATAC ATAC ATCC ATAC AT
          1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT

       6071 GTATATATAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
   4   24  1.00

ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27


Consensus pattern (4 bp):   
ATAC

Found at i:6079 original size:2 final size:2

Alignment explanation


    Indices: 6072--6108  Score: 65
    Period size: 2  Copynumber: 18.5  Consensus size: 2

       6062 TCCATACATG

                                                            *      
       6072 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       6109 CAGTGTTTGA


Statistics
Matches: 33,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   33  1.00

ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49


Consensus pattern (2 bp):   
TA

Done.