Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga10g00295.C3

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: 5183
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27


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:4804 original size:183 final size:181

Alignment explanation


    Indices: 4448--5003  Score: 844
    Period size: 183  Copynumber: 3.0  Consensus size: 181

       4438 GTATTTTCCG

                       *        *        *           *                       
       4448 ACTTGATTAGTTGGTTAAGGTTTTTGAGACTGAAACAGATCAGTGTTTCCCTTGTTGATGTGGCT
          1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTT-CCTTGTTGATGTGGCT

                              *          *                    *              
       4513 CCTCCACAAACAGTGAATGTTGACCA-ACTGGACTGGTCGAGTTTTTCTGAGACAAAAAGTAAAA
         65 CCTCCACAAACAGTGAA-CTTGA-CAGACCGGACTGGTCGAGTTTTTCTGGGACAAAAAGTAAAA

                       *                                           
       4577 GGTTTGTATGACCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
        128 GGTTTGTAT-AGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA

                                                                  *          
       4632 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCTTTGCTGATGTGGCT
          1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCC-TTGTTGATGTGGCT

                                               *                       **    
       4697 CCTCCACAAACAGTGAACTTGACAGACCGGACTGGCCGAGTTTTTCTGGGACAAAAAGTGGAAGG
         65 CCTCCACAAACAGTGAACTTGACAGACCGGACTGGTCGAGTTTTTCTGGGACAAAAAGTAAAAGG

                                                                 
       4762 TTTGTATAAGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
        130 TTTGTAT-AGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA

                                          *                    *             
       4815 ACTTGATTAGTCGGTTAAGGGTTTTGAGATAGAAACAGATCTGTGTTTGCCCTGTTGATGTGGCT
          1 ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTT-CCTTGTTGATGTGGCT

                          *         *            *    *            *         
       4880 CCTCCACAAACAGTAAACGTTGACTGACCGGACTGGTTGAGTCTTTCTGGGACAATAAGTAAAAG
         65 CCTCCACAAACAGTGAAC-TTGACAGACCGGACTGGTCGAGTTTTTCTGGGACAAAAAGTAAAAG

                        *                                         
       4945 GTTTGTATAGTCTATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
        129 GTTTGTATAG-CAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA

                 
       4999 ACTTG
          1 ACTTG

       5004 TGGTATACTC


Statistics
Matches: 342,  Mismatches: 25, Indels: 10
        0.91            0.07        0.03

Matches are distributed among these distances:
 182    2  0.01
 183  170  0.50
 184  170  0.50

ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31


Consensus pattern (181 bp):   
ACTTGATTAGTCGGTTAAGGGTTTTGAGATTGAAACAGATCTGTGTTTCCTTGTTGATGTGGCTC
CTCCACAAACAGTGAACTTGACAGACCGGACTGGTCGAGTTTTTCTGGGACAAAAAGTAAAAGGT
TTGTATAGCAATCAGAATAATATTTGAGGGAAAATATGAAGTCCATATGCA
Done.