Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g00001.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: 9452
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34


Found at i:1394 original size:78 final size:78

Alignment explanation


    Indices: 1248--1396  Score: 228
    Period size: 78  Copynumber: 1.9  Consensus size: 78

       1238 CTCATATTCT

                                              *                         *  * 
       1248 ACCATTAAACCATGATCCCTTGATCTCACCAGCTGGGAGAGTCGGTGATCATGTTGATAATGATC
          1 ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACC

                         
       1313 ACCATGGAGTTCG
         66 ACCATGGAGTTCG

                       *                               *                *    
       1326 ACCATTAAACCCTGATCCCTTGATCTCATCC-GCTAGGAGAGTTGGTGATCATGTTGATAGCGAC
          1 ACCATTAAACCATGATCCCTTGATCTCA-CCAGCTAGGAGAGTCGGTGATCATGTTGATAACGAC

                   
       1390 CACCATG
         65 CACCATG

       1397 ACGTTGTGCA


Statistics
Matches: 64,  Mismatches: 6, Indels: 2
        0.89            0.08        0.03

Matches are distributed among these distances:
  78   62  0.97
  79    2  0.03

ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27


Consensus pattern (78 bp):   
ACCATTAAACCATGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGACC
ACCATGGAGTTCG

Found at i:6368 original size:15 final size:15

Alignment explanation


    Indices: 6348--6386  Score: 60
    Period size: 16  Copynumber: 2.5  Consensus size: 15

       6338 CTGTCATACT

                           
       6348 TATCCCGGCCAGGGA
          1 TATCCCGGCCAGGGA

                    *       
       6363 TATCCCGTTCCAGGGA
          1 TATCCCG-GCCAGGGA

                    
       6379 TATCCCGG
          1 TATCCCGG

       6387 TTCGTTGTTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  15    7  0.33
  16   14  0.67

ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21


Consensus pattern (15 bp):   
TATCCCGGCCAGGGA
Done.