Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga11g01239.M2

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: 5925
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.31


Found at i:4065 original size:271 final size:271

Alignment explanation


    Indices: 3517--4020  Score: 834
    Period size: 271  Copynumber: 1.9  Consensus size: 271

       3507 TGAGATTGAA

                *                        *                                  *
       3517 AAAATATGGCATGATGATCAACTTCTTACTGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCT
          1 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA

                  ***     *    *                                             
       3582 AGTGTGGGGATGCCGTAAGTTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC
         66 AGTGTGCCAATGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC

                        *              *                                     
       3647 TGAAAACACTTAGAGGTCAGAAATTGTTATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG
        131 TGAAAACACTTAAAGGTCAGAAATTGTAATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG

                                                                             
       3712 GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC
        196 GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC

                       
       3777 TTCTAAATCTC
        261 TTCTAAATCTC

                                                                           * 
       3788 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGGA
          1 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA

                         *                                                   
       3853 AGTGT-CCAATTGTCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAAC
         66 AGTGTGCCAA-TGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAAC

                              *   *                                          
       3917 CTGAAAACACTTAAAGGTTAGACATTGTAAT-GAAATGGAAGACATAATAGAAGGAATACTAGGT
        130 CTGAAAACACTTAAAGGTCAGAAATTGTAATGGAAA-GGAAGACATAATAGAAGGAATACTAGGT

                                                     
       3981 GGGGAAGAAAGGATTAACAACAGCATTAAG-GTGTTCCCTA
        194 GGGGAAGAAAGGATTAACAACAGC-TTAAGCGTGTTCCCTA

       4021 CTCTTACCGT


Statistics
Matches: 216,  Mismatches: 14, Indels: 6
        0.92            0.06        0.03

Matches are distributed among these distances:
 270    5  0.02
 271  206  0.95
 272    5  0.02

ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30


Consensus pattern (271 bp):   
AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA
AGTGTGCCAATGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC
TGAAAACACTTAAAGGTCAGAAATTGTAATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG
GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC
TTCTAAATCTC

Found at i:4760 original size:21 final size:21

Alignment explanation


    Indices: 4736--4782  Score: 78
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       4726 TAGTATGGTA

                                  
       4736 GAAGAATCTGAAAATTCTTG-G
          1 GAAGAATCTGAAAATTC-TGAG

                                 
       4757 GAAGAATCTGAAAATTCTGAG
          1 GAAGAATCTGAAAATTCTGAG

                 
       4778 GAAGA
          1 GAAGA

       4783 TCTAAGCGAT


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20    2  0.08
  21   23  0.92

ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23


Consensus pattern (21 bp):   
GAAGAATCTGAAAATTCTGAG

Found at i:5787 original size:2 final size:2

Alignment explanation


    Indices: 5780--5810  Score: 62
    Period size: 2  Copynumber: 15.5  Consensus size: 2

       5770 ATTCTTCGTG

                                                          
       5780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T

       5811 GCGCAGAATG


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   29  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.