Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g00609.F2

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: 4566
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32


Found at i:3035 original size:107 final size:103

Alignment explanation


    Indices: 2894--3100  Score: 272
    Period size: 103  Copynumber: 2.0  Consensus size: 103

       2884 ATTTGATATC

                                         *                      *    *  *    
       2894 AATTAGTTCTATTGTTAATTACTTGATCTTTGATTTCAG-ACATGGCTATTTGGCTAGATTAAGT
          1 AATTAGTTCTATTGTTAATTACTTGATCTATGATTT-AGCACAT-G--A-TTAGCTAAATCAAGT

                           *  *                        
       2958 CTATGTTTAACTGTGTGGCGTACCTACTAGATTAATATGTATA
         61 CTATGTTTAACTGTGAGGAGTACCTACTAGATTAATATGTATA

                            *                   *                            
       3001 AATTAGTTCTATTGTTGATTACTTGATCTATGATTTTGCACATGATTAGCTAAATCAAGTCTATG
          1 AATTAGTTCTATTGTTAATTACTTGATCTATGATTTAGCACATGATTAGCTAAATCAAGTCTATG

                          * *                  
       3066 TTTAACTGTGAGGATTTCCTACTAGATTAATATGT
         66 TTTAACTGTGAGGAGTACCTACTAGATTAATATGT

       3101 TGTATTTATA


Statistics
Matches: 89,  Mismatches: 10, Indels: 6
        0.85            0.10        0.06

Matches are distributed among these distances:
 103   48  0.54
 104    1  0.01
 106    2  0.02
 107   38  0.43

ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43


Consensus pattern (103 bp):   
AATTAGTTCTATTGTTAATTACTTGATCTATGATTTAGCACATGATTAGCTAAATCAAGTCTATG
TTTAACTGTGAGGAGTACCTACTAGATTAATATGTATA

Found at i:4141 original size:12 final size:12

Alignment explanation


    Indices: 4124--4158  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

       4114 ATCAAGTAAG

                        
       4124 TGATTCTGATTA
          1 TGATTCTGATTA

                      * 
       4136 TGATTCTGATGA
          1 TGATTCTGATTA

                 *     
       4148 TGATTTTGATT
          1 TGATTCTGATT

       4159 TCAGCATTTT


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  12   20  1.00

ACGTcount: A:0.23, C:0.06, G:0.20, T:0.51


Consensus pattern (12 bp):   
TGATTCTGATTA
Done.