Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g00466.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: 8523
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32


Found at i:5366 original size:18 final size:18

Alignment explanation


    Indices: 5287--5380  Score: 131
    Period size: 18  Copynumber: 5.4  Consensus size: 18

       5277 CAAGGTCACG

                   *          
       5287 ATCAATAGCGTCACTATC
          1 ATCAATATCGTCACTATC

                   *        * 
       5305 ATCAATAGCGTCACTAGC
          1 ATCAATATCGTCACTATC

                            * 
       5323 ATCAATATCGTCACTAGC
          1 ATCAATATCGTCACTATC

                              
       5341 ATCAATATCGTCACTATC
          1 ATCAATATCGTCACTATC

                              
       5359 ATCAATATCG--A-TATC
          1 ATCAATATCGTCACTATC

                   
       5374 ATCAATA
          1 ATCAATA

       5381 AGAAAACCTT


Statistics
Matches: 73,  Mismatches: 3, Indels: 3
        0.92            0.04        0.04

Matches are distributed among these distances:
  15   11  0.15
  16    1  0.01
  18   61  0.84

ACGTcount: A:0.36, C:0.26, G:0.10, T:0.29


Consensus pattern (18 bp):   
ATCAATATCGTCACTATC

Found at i:5367 original size:9 final size:9

Alignment explanation


    Indices: 5287--5367  Score: 54
    Period size: 9  Copynumber: 9.0  Consensus size: 9

       5277 CAAGGTCACG

                   * 
       5287 ATCAATAGC
          1 ATCAATATC

            *   *    
       5296 GTCACTATC
          1 ATCAATATC

                   * 
       5305 ATCAATAGC
          1 ATCAATATC

            *   *  * 
       5314 GTCACTAGC
          1 ATCAATATC

                     
       5323 ATCAATATC
          1 ATCAATATC

            *   *  * 
       5332 GTCACTAGC
          1 ATCAATATC

                     
       5341 ATCAATATC
          1 ATCAATATC

            *   *    
       5350 GTCACTATC
          1 ATCAATATC

                     
       5359 ATCAATATC
          1 ATCAATATC

       5368 GATATCATCA


Statistics
Matches: 51,  Mismatches: 21, Indels: 0
        0.71            0.29        0.00

Matches are distributed among these distances:
   9   51  1.00

ACGTcount: A:0.35, C:0.27, G:0.10, T:0.28


Consensus pattern (9 bp):   
ATCAATATC

Found at i:7776 original size:21 final size:21

Alignment explanation


    Indices: 7746--7834  Score: 90
    Period size: 21  Copynumber: 4.1  Consensus size: 21

       7736 CTCACAAAGA

                        * *      
       7746 AAAAAG-GAAGTGAGTTAGAC
          1 AAAAAGAGAAGTAACTTAGAC

                       *     *   
       7766 AAAAAGAGAAGCAACTTGGAC
          1 AAAAAGAGAAGTAACTTAGAC

                             *   
       7787 AAAAAGAGAAGTAACTTGGAC
          1 AAAAAGAGAAGTAACTTAGAC

                           *        
       7808 AAAAAGAAACGAAGTGACTTAGAC
          1 AAAAAG--A-GAAGTAACTTAGAC

               
       7832 AAA
          1 AAA

       7835 TCTTTTTTGT


Statistics
Matches: 58,  Mismatches: 7, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  20    6  0.10
  21   36  0.62
  23    1  0.02
  24   15  0.26

ACGTcount: A:0.54, C:0.10, G:0.24, T:0.12


Consensus pattern (21 bp):   
AAAAAGAGAAGTAACTTAGAC

Found at i:7827 original size:24 final size:21

Alignment explanation


    Indices: 7746--7814  Score: 95
    Period size: 21  Copynumber: 3.3  Consensus size: 21

       7736 CTCACAAAGA

                        * *  *   
       7746 AAAAAG-GAAGTGAGTTAGAC
          1 AAAAAGAGAAGTAACTTGGAC

                       *         
       7766 AAAAAGAGAAGCAACTTGGAC
          1 AAAAAGAGAAGTAACTTGGAC

                                 
       7787 AAAAAGAGAAGTAACTTGGAC
          1 AAAAAGAGAAGTAACTTGGAC

                   
       7808 AAAAAGA
          1 AAAAAGA

       7815 AACGAAGTGA


Statistics
Matches: 43,  Mismatches: 5, Indels: 1
        0.88            0.10        0.02

Matches are distributed among these distances:
  20    6  0.14
  21   37  0.86

ACGTcount: A:0.55, C:0.09, G:0.25, T:0.12


Consensus pattern (21 bp):   
AAAAAGAGAAGTAACTTGGAC
Done.