Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00295.M5

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: 5621
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28


Found at i:329 original size:6 final size:6

Alignment explanation


    Indices: 318--418  Score: 112
    Period size: 6  Copynumber: 15.8  Consensus size: 6

        308 CTAGGGAGAA

                                                                      
        318 GGAAAG GGAAAG GGAAAAG CGTGAAAG GGAAAG GGAAAG GGAAAG GGAAAG
          1 GGAAAG GGAAAG GG-AAAG -G-GAAAG GGAAAG GGAAAG GGAAAG GGAAAG

            *                       *      *      *                  
        369 AGAAAGG GAGAAGAG GGAAAG AGAAAG AGAAAG AGAAAG GGAAAG GGAAA
          1 GGAAA-G G-GAA-AG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAA

        419 AAGAGAGGGA


Statistics
Matches: 85,  Mismatches: 4, Indels: 12
        0.84            0.04        0.12

Matches are distributed among these distances:
   6   64  0.75
   7    9  0.11
   8   10  0.12
   9    2  0.02

ACGTcount: A:0.53, C:0.01, G:0.45, T:0.01


Consensus pattern (6 bp):   
GGAAAG

Found at i:349 original size:45 final size:45

Alignment explanation


    Indices: 298--418  Score: 136
    Period size: 45  Copynumber: 2.7  Consensus size: 45

        288 GGAAAAGGAG

                      **               *            * *   
        298 AGGGAAAGAGCTAGGGAGAA-GGAAAGGGAAAGGGAAAAGCGTGAA
          1 AGGGAAAGAGAAAGGGA-AAGGGAAAGAGAAAGGGAAAAGAGGGAA

                    *                          *         
        343 AGGGAAAGGGAAAGGGAAAGGGAAAGAGAAAGGGAGAAGAGGGAA
          1 AGGGAAAGAGAAAGGGAAAGGGAAAGAGAAAGGGAAAAGAGGGAA

              *           *           *    
        388 AGAGAAAGAGAAAGAGAAAGGGAAAGGGAAA
          1 AGGGAAAGAGAAAGGGAAAGGGAAAGAGAAA

        419 AAGAGAGGGA


Statistics
Matches: 64,  Mismatches: 11, Indels: 2
        0.83            0.14        0.03

Matches are distributed among these distances:
  44    2  0.03
  45   62  0.97

ACGTcount: A:0.52, C:0.02, G:0.45, T:0.02


Consensus pattern (45 bp):   
AGGGAAAGAGAAAGGGAAAGGGAAAGAGAAAGGGAAAAGAGGGAA

Found at i:413 original size:39 final size:38

Alignment explanation


    Indices: 319--421  Score: 125
    Period size: 39  Copynumber: 2.7  Consensus size: 38

        309 TAGGGAGAAG

                              * *           *     *
        319 GAAAGGGAAAGGGAAAAGCGTGAAAGGGAAAGGGAAAGG
          1 GAAAGGGAAAGGG-AAAGGGAGAAAGGGAAAGAGAAAGA

                       *                           
        358 GAAAGGGAAAGAGAAAGGGAGAAGAGGGAAAGAGAAAGA
          1 GAAAGGGAAAGGGAAAGGGAGAA-AGGGAAAGAGAAAGA

                 *              *    
        397 GAAAGAGAAAGGGAAAGGGAAAAAG
          1 GAAAGGGAAAGGGAAAGGGAGAAAG

        422 AGAGGGAGAG


Statistics
Matches: 55,  Mismatches: 8, Indels: 3
        0.83            0.12        0.05

Matches are distributed among these distances:
  38   10  0.18
  39   45  0.82

ACGTcount: A:0.54, C:0.01, G:0.44, T:0.01


Consensus pattern (38 bp):   
GAAAGGGAAAGGGAAAGGGAGAAAGGGAAAGAGAAAGA

Found at i:5414 original size:184 final size:183

Alignment explanation


    Indices: 5106--5441  Score: 532
    Period size: 184  Copynumber: 1.8  Consensus size: 183

       5096 AAAAAGTAAA

                           *                           *                     
       5106 AGATCTGTGTTTCCTTTGCTGATGTGGCTCCTCCACAAACAGTGAACTTGACAGACCGGACTGGC
          1 AGATCTGTGTTTCCTCTGCTGATGTGGCTCCTCCACAAACAGTAAACTTGACAGACCGGACTGGC

                 *                 **                                        
       5171 CGAGTTTTTCTGGGACAAAAAGTGGAAGGTTTGTATAAGCAATCAGAATAATATTTGAGGGAAAA
         66 CGAGTCTTTCTGGGACAAAAAGTAAAAGGTTTGTATAAGCAATCAGAATAATATTTGAGGGAAAA

                                                                 
       5236 TATGAAGTCCATATGCAACTTGATTAGTCGGTTAAGGGTTTTGAGATAGAAAC
        131 TATGAAGTCCATATGCAACTTGATTAGTCGGTTAAGGGTTTTGAGATAGAAAC

                               *                                  *          
       5289 AGATCTGTGTTTGCC-CTGTTGATGTGGCTCCTCCACAAACAGTAAACGTTGACTGACCGGACTG
          1 AGATCTGTGTTT-CCTCTGCTGATGTGGCTCCTCCACAAACAGTAAAC-TTGACAGACCGGACTG

             **                 *                      *                     
       5353 GTTGAGTCTTTCTGGGACAATAAGTAAAAGGTTTGTAT-AGTCTATCAGAATAATATTTGAGGGA
         64 GCCGAGTCTTTCTGGGACAAAAAGTAAAAGGTTTGTATAAG-CAATCAGAATAATATTTGAGGGA

                                     
       5417 AAATATGAAGTCCATATGCAACTTG
        128 AAATATGAAGTCCATATGCAACTTG

       5442 TGGTATACTC


Statistics
Matches: 139,  Mismatches: 11, Indels: 5
        0.90            0.07        0.03

Matches are distributed among these distances:
 183   43  0.31
 184   96  0.69

ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30


Consensus pattern (183 bp):   
AGATCTGTGTTTCCTCTGCTGATGTGGCTCCTCCACAAACAGTAAACTTGACAGACCGGACTGGC
CGAGTCTTTCTGGGACAAAAAGTAAAAGGTTTGTATAAGCAATCAGAATAATATTTGAGGGAAAA
TATGAAGTCCATATGCAACTTGATTAGTCGGTTAAGGGTTTTGAGATAGAAAC
Done.