Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g02734.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: 6316
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28


Found at i:516 original size:12 final size:12

Alignment explanation


    Indices: 495--571  Score: 82
    Period size: 12  Copynumber: 6.2  Consensus size: 12

        485 GAGATAGGAA

                 *      
        495 GGATAAGGATAG
          1 GGATAGGGATAG

                           
        507 GGATAGGGATAAGAG
          1 GGATAGGGAT---AG

               *  *     
        522 GGACAGAGATAG
          1 GGATAGGGATAG

            *           
        534 AGATAGGGATAG
          1 GGATAGGGATAG

                        
        546 GGATAGGGATAG
          1 GGATAGGGATAG

                  *     
        558 GGATAGAGATAG
          1 GGATAGGGATAG

              
        570 GG
          1 GG

        572 GCAGAGATAG


Statistics
Matches: 54,  Mismatches: 8, Indels: 6
        0.79            0.12        0.09

Matches are distributed among these distances:
  12   44  0.81
  15   10  0.19

ACGTcount: A:0.39, C:0.01, G:0.45, T:0.14


Consensus pattern (12 bp):   
GGATAGGGATAG

Found at i:535 original size:6 final size:6

Alignment explanation


    Indices: 526--600  Score: 55
    Period size: 6  Copynumber: 12.5  Consensus size: 6

        516 TAAGAGGGAC

                            *      *      *      *             * **
        526 AGAGAT AGAGAT AGGGAT AGGGAT AGGGAT AGGGAT AGAGAT AGGGGC
          1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT

                                             
        574 AGAGAT AG-GAGT AG-GCAT AGAGAT AGA
          1 AGAGAT AGAGA-T AGAG-AT AGAGAT AGA

        601 TATAAGGAGG


Statistics
Matches: 58,  Mismatches: 8, Indels: 6
        0.81            0.11        0.08

Matches are distributed among these distances:
   5    2  0.03
   6   54  0.93
   7    2  0.03

ACGTcount: A:0.40, C:0.03, G:0.43, T:0.15


Consensus pattern (6 bp):   
AGAGAT

Found at i:569 original size:18 final size:18

Alignment explanation


    Indices: 495--571  Score: 82
    Period size: 18  Copynumber: 4.1  Consensus size: 18

        485 GAGATAGGAA

                 *      *     
        495 GGATAAGGATAGGGATAG
          1 GGATAGGGATAGAGATAG

                        *        
        513 GGATAAGAGGGACAGAGATAG
          1 GGAT---AGGGATAGAGATAG

            *           *     
        534 AGATAGGGATAGGGATAG
          1 GGATAGGGATAGAGATAG

                              
        552 GGATAGGGATAGAGATAG
          1 GGATAGGGATAGAGATAG

              
        570 GG
          1 GG

        572 GCAGAGATAG


Statistics
Matches: 48,  Mismatches: 8, Indels: 6
        0.77            0.13        0.10

Matches are distributed among these distances:
  18   34  0.71
  21   14  0.29

ACGTcount: A:0.39, C:0.01, G:0.45, T:0.14


Consensus pattern (18 bp):   
GGATAGGGATAGAGATAG

Found at i:4143 original size:3 final size:3

Alignment explanation


    Indices: 4135--4161  Score: 54
    Period size: 3  Copynumber: 9.0  Consensus size: 3

       4125 CAAAATAGAA

                                               
       4135 ATC ATC ATC ATC ATC ATC ATC ATC ATC
          1 ATC ATC ATC ATC ATC ATC ATC ATC ATC

       4162 TCGAGAAGTG


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   24  1.00

ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33


Consensus pattern (3 bp):   
ATC

Done.