Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00120.M1

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: 7758
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32


Found at i:2886 original size:78 final size:78

Alignment explanation


    Indices: 2797--3031  Score: 380
    Period size: 78  Copynumber: 3.0  Consensus size: 78

       2787 GTCAGGCAGA

                                    *    **                                  
       2797 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       2862 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

                                                              *              
       2875 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

                         
       2940 CGGCTTTCTGGAC
         66 CGGCTTTCTGGAC

            *                              *           *             *  *    
       2953 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
          1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC

             *           
       3018 CAGCTTTCTGGAC
         66 CGGCTTTCTGGAC

             
       3031 G
          1 G

       3032 GCATGTCCGT


Statistics
Matches: 145,  Mismatches: 12, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  78  145  1.00

ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23


Consensus pattern (78 bp):   
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC

Found at i:4814 original size:31 final size:31

Alignment explanation


    Indices: 4779--4850  Score: 92
    Period size: 31  Copynumber: 2.3  Consensus size: 31

       4769 TGCAAAATTT

                      *          *          
       4779 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
          1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA

                   *                      *
       4810 TTATTGAATTATTTGAAAGTTATATTTTAAG
          1 TTATTGAGTTATTTGAAAGTTATATTTTAAA

                      
       4841 TTATTGAGTT
          1 TTATTGAGTT

       4851 GTTAAGTTAT


Statistics
Matches: 35,  Mismatches: 5, Indels: 2
        0.83            0.12        0.05

Matches are distributed among these distances:
  30    1  0.03
  31   34  0.97

ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54


Consensus pattern (31 bp):   
TTATTGAGTTATTTGAAAGTTATATTTTAAA

Found at i:5240 original size:41 final size:41

Alignment explanation


    Indices: 5194--5319  Score: 185
    Period size: 35  Copynumber: 3.2  Consensus size: 41

       5184 ACTAAATCAT

                                               *     
       5194 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                                                     
       5235 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                                  *                  
       5270 AATATCTCATATAATACACTTATATTTGTATGCTTGT-ATA
          1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

                      
       5310 AATATCTCAT
          1 AATATCTCAT

       5320 TTAGTAAGAA


Statistics
Matches: 77,  Mismatches: 2, Indels: 13
        0.84            0.02        0.14

Matches are distributed among these distances:
  35   31  0.40
  36    3  0.04
  40   16  0.21
  41   27  0.35

ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43


Consensus pattern (41 bp):   
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA

Done.