Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g01032.F1

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: 4140
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34


Found at i:963 original size:13 final size:12

Alignment explanation


    Indices: 945--977  Score: 66
    Period size: 12  Copynumber: 2.8  Consensus size: 12

        935 TTCGAAGTTG

                        
        945 AAAAAAAAATTC
          1 AAAAAAAAATTC

                        
        957 AAAAAAAAATTC
          1 AAAAAAAAATTC

                     
        969 AAAAAAAAA
          1 AAAAAAAAA

        978 GGTTCTGTTG


Statistics
Matches: 21,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   21  1.00

ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12


Consensus pattern (12 bp):   
AAAAAAAAATTC

Found at i:2104 original size:49 final size:50

Alignment explanation


    Indices: 2038--2152  Score: 198
    Period size: 51  Copynumber: 2.3  Consensus size: 50

       2028 AAATCATGTG

                                                      *       
       2038 AAAA-TGAAAAAGAGAGTGAAAGAAAAG-AAAGAACTTGAACGAGAAAAT
          1 AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAGAACTTGAACAAGAAAAT

                                                               
       2086 AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAAGAACTTGAACAAGAAAAT
          1 AAAATTGAAAAAGAGAGTGAAAGAAAAG-AAAAGAACTTGAACAAGAAAAT

                            
       2137 AAAATTGAAAAAGAGA
          1 AAAATTGAAAAAGAGA

       2153 TTGAGAGTGG


Statistics
Matches: 63,  Mismatches: 1, Indels: 3
        0.94            0.01        0.04

Matches are distributed among these distances:
  48    4  0.06
  49   23  0.37
  51   36  0.57

ACGTcount: A:0.64, C:0.03, G:0.21, T:0.11


Consensus pattern (50 bp):   
AAAATTGAAAAAGAGAGTGAAAGAAAAGAAAAGAACTTGAACAAGAAAAT

Found at i:2144 original size:18 final size:18

Alignment explanation


    Indices: 2079--2150  Score: 62
    Period size: 18  Copynumber: 4.2  Consensus size: 18

       2069 AACTTGAACG

                              
       2079 AGAAAATAAAATTGAAAA
          1 AGAAAATAAAATTGAAAA

               * * *          
       2097 AGAGAGTGAAA--G-AAA
          1 AGAAAATAAAATTGAAAA

                       *     * 
       2112 AGAAAA-AGAACTTGAACA
          1 AGAAAATA-AAATTGAAAA

                              
       2130 AGAAAATAAAATTGAAAA
          1 AGAAAATAAAATTGAAAA

               
       2148 AGA
          1 AGA

       2151 GATTGAGAGT


Statistics
Matches: 39,  Mismatches: 10, Indels: 10
        0.66            0.17        0.17

Matches are distributed among these distances:
  15    9  0.23
  16    1  0.03
  17    1  0.03
  18   27  0.69
  19    1  0.03

ACGTcount: A:0.67, C:0.03, G:0.18, T:0.12


Consensus pattern (18 bp):   
AGAAAATAAAATTGAAAA
Done.