Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g01180.N1

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: 5334
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33


Found at i:3844 original size:21 final size:21

Alignment explanation


    Indices: 3820--3863  Score: 63
    Period size: 21  Copynumber: 2.1  Consensus size: 21

       3810 TCTCCGCTCA

                          *       
       3820 TGTTTC-AAATTTTGAGCATGC
          1 TGTTTCTAAATTTTAAG-ATGC

                                 
       3841 TGTTTCTAAATTTTAAGATGC
          1 TGTTTCTAAATTTTAAGATGC

              
       3862 TG
          1 TG

       3864 GGGACACACA


Statistics
Matches: 21,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  21   12  0.57
  22    9  0.43

ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45


Consensus pattern (21 bp):   
TGTTTCTAAATTTTAAGATGC

Found at i:4925 original size:24 final size:24

Alignment explanation


    Indices: 4898--4952  Score: 58
    Period size: 24  Copynumber: 2.3  Consensus size: 24

       4888 TATATAACGG

                     *    *          
       4898 GAAGCTCA-TAAGAGCCATAATCGA
          1 GAAGCTCACAAAGAACCAT-ATCGA

                *                  *
       4922 GAAGTTCACAAAGAACCATATCGG
          1 GAAGCTCACAAAGAACCATATCGA

                   
       4946 GAAGCTC
          1 GAAGCTC

       4953 TGGAGAGCCA


Statistics
Matches: 25,  Mismatches: 5, Indels: 2
        0.78            0.16        0.06

Matches are distributed among these distances:
  24   17  0.68
  25    8  0.32

ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16


Consensus pattern (24 bp):   
GAAGCTCACAAAGAACCATATCGA

Found at i:4947 original size:48 final size:48

Alignment explanation


    Indices: 4895--5000  Score: 121
    Period size: 48  Copynumber: 2.2  Consensus size: 48

       4885 GGCTATATAA

                                                               
       4895 CGGGAAGCTCAT-AAGAGCC-ATAATCGAGAAGTTCACAAAGAACCA-TAT
          1 CGGGAAGCTCATGAAGAGCCAAT-ATCGAGAAGTTCA-AAAGAA-CATTAT

                         *           *           **         
       4943 CGGGAAGCTC-TGGAGAGCCAATATTGAGAAGTTCAAGCGAACATTAT
          1 CGGGAAGCTCATGAAGAGCCAATATCGAGAAGTTCAAAAGAACATTAT

                       
       4990 CGGGAAGCTCA
          1 CGGGAAGCTCA

       5001 CAAAGAGTCA


Statistics
Matches: 50,  Mismatches: 4, Indels: 8
        0.81            0.06        0.13

Matches are distributed among these distances:
  46    2  0.04
  47   18  0.36
  48   28  0.56
  49    2  0.04

ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18


Consensus pattern (48 bp):   
CGGGAAGCTCATGAAGAGCCAATATCGAGAAGTTCAAAAGAACATTAT
Done.