Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01033.C1

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: 4005
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34


Found at i:977 original size:49 final size:50

Alignment explanation


    Indices: 911--1025  Score: 198
    Period size: 51  Copynumber: 2.3  Consensus size: 50

        901 AAATCATGTG

                                                      *       
        911 AAAA-TGAAAAAGAGAGTGAAAGAAAAG-AAAGAACTTGAACGAGAAAAT
          1 AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAGAACTTGAACAAGAAAAT

                                                               
        959 AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAAGAACTTGAACAAGAAAAT
          1 AAAATTGAAAAAGAGAGTGAAAGAAAAG-AAAAGAACTTGAACAAGAAAAT

                            
       1010 AAAATTGAAAAAGAGA
          1 AAAATTGAAAAAGAGA

       1026 TTGAGAGTGG


Statistics
Matches: 63,  Mismatches: 1, Indels: 3
        0.94            0.01        0.04

Matches are distributed among these distances:
  48    4  0.06
  49   23  0.37
  51   36  0.57

ACGTcount: A:0.64, C:0.03, G:0.21, T:0.11


Consensus pattern (50 bp):   
AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAGAACTTGAACAAGAAAAT

Found at i:1017 original size:18 final size:18

Alignment explanation


    Indices: 952--1023  Score: 62
    Period size: 18  Copynumber: 4.2  Consensus size: 18

        942 AACTTGAACG

                              
        952 AGAAAATAAAATTGAAAA
          1 AGAAAATAAAATTGAAAA

               * * *          
        970 AGAGAGTGAAA--G-AAA
          1 AGAAAATAAAATTGAAAA

                       *     * 
        985 AGAAAA-AGAACTTGAACA
          1 AGAAAATA-AAATTGAAAA

                              
       1003 AGAAAATAAAATTGAAAA
          1 AGAAAATAAAATTGAAAA

               
       1021 AGA
          1 AGA

       1024 GATTGAGAGT


Statistics
Matches: 39,  Mismatches: 10, Indels: 10
        0.66            0.17        0.17

Matches are distributed among these distances:
  15    9  0.23
  16    1  0.03
  17    1  0.03
  18   27  0.69
  19    1  0.03

ACGTcount: A:0.67, C:0.03, G:0.18, T:0.12


Consensus pattern (18 bp):   
AGAAAATAAAATTGAAAA
Done.