Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g00269.F3

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: 3547
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36


Found at i:2484 original size:94 final size:95

Alignment explanation


    Indices: 2339--2523  Score: 318
    Period size: 94  Copynumber: 2.0  Consensus size: 95

       2329 TCACAGTTAG

                                                                             
       2339 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
          1 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG

                *                         
       2404 CTGCCCATCTCTTCGCTGTTGTATAGTTTT
         66 CTGCACATCTCTTCGCTGTTGTATAGTTTT

                    *   *                                 *                  
       2434 TTTTTTTTTTTTTAATAATCTAAACTTCT-GACATCCCTTTTGTTGTAATGCCATTTACTGGCTG
          1 TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG

                         *            
       2498 CTGCACATCTCTTTGCTGTTGTATAG
         66 CTGCACATCTCTTCGCTGTTGTATAG

       2524 AAATTAAACA


Statistics
Matches: 85,  Mismatches: 5, Indels: 1
        0.93            0.05        0.01

Matches are distributed among these distances:
  94   58  0.68
  95   27  0.32

ACGTcount: A:0.19, C:0.20, G:0.14, T:0.48


Consensus pattern (95 bp):   
TTTTTTTTATTTAAATAATCTAAACTTCTGGACATCCCTTTTGTTGCAATGCCATTTACTGGCTG
CTGCACATCTCTTCGCTGTTGTATAGTTTT

Found at i:3031 original size:15 final size:16

Alignment explanation


    Indices: 2997--3033  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       2987 AACAACCAGT

                         *  
       2997 TCAA-ACAATGGGTCA
          1 TCAATACAATGGGACA

                            
       3012 TCAATACAATGGGACA
          1 TCAATACAATGGGACA

                   
       3028 -CAATAC
          1 TCAATAC

       3034 GCTCCGGGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  15   10  0.50
  16   10  0.50

ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19


Consensus pattern (16 bp):   
TCAATACAATGGGACA

Found at i:3254 original size:4 final size:4

Alignment explanation


    Indices: 3245--3275  Score: 62
    Period size: 4  Copynumber: 7.8  Consensus size: 4

       3235 ATGTAATAGC

                                                  
       3245 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC
          1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATC

       3276 AAGTATGAAA


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   27  1.00

ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48


Consensus pattern (4 bp):   
ATCT

Done.