Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01473.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: 3859
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32


Found at i:1373 original size:31 final size:30

Alignment explanation


    Indices: 1328--1433  Score: 123
    Period size: 29  Copynumber: 3.6  Consensus size: 30

       1318 GACCTAAGTA

                    *                       
       1328 TAAATAT-AGAAAAG-TTTGTGGCATAAATTG
          1 TAAATATGCGAAAAGTTTTGTGGCAT-AA-TG

                                          
       1358 TAAATATGCGAAAAGTTTTGTGGCATAA-G
          1 TAAATATGCGAAAAGTTTTGTGGCATAATG

                                           *
       1387 TAAATATGCGAAAAGTTTTGTGTG-ATAAGTA
          1 TAAATATGCGAAAAGTTTTGTG-GCATAA-TG

                             
       1418 TAAATATG-GAAAAGTT
          1 TAAATATGCGAAAAGTT

       1434 GAAGTGAAAG


Statistics
Matches: 69,  Mismatches: 2, Indels: 10
        0.85            0.02        0.12

Matches are distributed among these distances:
  29   27  0.39
  30   16  0.23
  31   16  0.23
  32   10  0.14

ACGTcount: A:0.42, C:0.04, G:0.22, T:0.33


Consensus pattern (30 bp):   
TAAATATGCGAAAAGTTTTGTGGCATAATG

Found at i:3075 original size:46 final size:46

Alignment explanation


    Indices: 3022--3290  Score: 300
    Period size: 46  Copynumber: 5.8  Consensus size: 46

       3012 TATTTGGGCA

                                                          
       3022 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                                           ***    *       *   
       3068 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG

                 *                                        
       3115 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                                           **     *       *   
       3161 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTAG-GCA--
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG

                 *                                        
       3208 TCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

                  *                               
       3254 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
          1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG

       3291 GCAGGTTACA


Statistics
Matches: 186,  Mismatches: 22, Indels: 30
        0.78            0.09        0.13

Matches are distributed among these distances:
  43    2  0.01
  44    6  0.03
  45    4  0.02
  46   99  0.53
  47   65  0.35
  48    2  0.01
  49    6  0.03
  50    2  0.01

ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30


Consensus pattern (46 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG

Found at i:3137 original size:47 final size:47

Alignment explanation


    Indices: 3018--3236  Score: 229
    Period size: 47  Copynumber: 4.7  Consensus size: 47

       3008 AGGATATTTG

                                               **     *    
       3018 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA

               *                                    *         
       3061 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTA
          1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA

                     *                         **     *    
       3111 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA

               *                                              
       3154 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA
          1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA

                     *                       
       3204 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTC
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTC

       3237 ACTTATGGAT


Statistics
Matches: 144,  Mismatches: 18, Indels: 24
        0.77            0.10        0.13

Matches are distributed among these distances:
  43    2  0.01
  44    5  0.03
  45    1  0.01
  46   61  0.42
  47   65  0.45
  48    2  0.01
  49    6  0.04
  50    2  0.01

ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29


Consensus pattern (47 bp):   
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGATATGTAACTA

Found at i:3177 original size:93 final size:93

Alignment explanation


    Indices: 3018--3282  Score: 478
    Period size: 93  Copynumber: 2.8  Consensus size: 93

       3008 AGGATATTTG

                                                                             
       3018 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG

                                        
       3083 TTGAGTCCGAGTTCGAGAGATGTAACTA
         66 TTGAGTCCGAGTTCGAGAGATGTAACTA

                     *                                                       
       3111 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG

                              *         
       3176 TTGAGTCCGAGTTCGAGATATGTAACTA
         66 TTGAGTCCGAGTTCGAGAGATGTAACTA

                     *                                              *        
       3204 GGCATCCGATCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-CCTGAGCTCGTTGA
          1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCC-GAACTCGTTGA

                           
       3268 GTTGAGTCCGAGTTC
         65 GTTGAGTCCGAGTTC

       3283 ACTTATGGGC


Statistics
Matches: 167,  Mismatches: 4, Indels: 2
        0.97            0.02        0.01

Matches are distributed among these distances:
  92    2  0.01
  93  165  0.99

ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29


Consensus pattern (93 bp):   
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Done.