Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga08g00585.F4

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: 3910
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32


Found at i:1991 original size:16 final size:16

Alignment explanation


    Indices: 1954--1984  Score: 62
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       1944 AAGGTCTATG

                            
       1954 ATATGATTGCATGATA
          1 ATATGATTGCATGATA

                           
       1970 ATATGATTGCATGAT
          1 ATATGATTGCATGAT

       1985 TGTATGAAAA


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.35, C:0.06, G:0.19, T:0.39


Consensus pattern (16 bp):   
ATATGATTGCATGATA

Found at i:3225 original size:46 final size:45

Alignment explanation


    Indices: 3169--3344  Score: 169
    Period size: 46  Copynumber: 3.8  Consensus size: 45

       3159 TGGTTGAGCA

                                                          
       3169 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAA-G

                                 *          **    *       *  
       3215 TCCGAACTCGTTGAGTTGAGTTCGAGTTCGAGAGATGTAACTAG-GCA-
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-AGTTATG-GA-T-GCGAAG

                 **            *          *               
       3262 TCCGAGTTCGTTGAGTTGATTCCGAGTTCACTTATGGATGCGAACG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAA-G

            *    *                                
       3308 CCCGAGCTCGTTGAGTTGAGTCCGAGTTC-GCTTATGG
          1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAG-TTATGG

       3345 GCGGGTTACA


Statistics
Matches: 104,  Mismatches: 18, Indels: 16
        0.75            0.13        0.12

Matches are distributed among these distances:
  43    1  0.01
  44    3  0.03
  45    1  0.01
  46   64  0.62
  47   30  0.29
  48    1  0.01
  49    3  0.03
  50    1  0.01

ACGTcount: A:0.20, C:0.19, G:0.30, T:0.30


Consensus pattern (45 bp):   
TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAAG

Found at i:3325 original size:93 final size:93

Alignment explanation


    Indices: 3166--3337  Score: 272
    Period size: 93  Copynumber: 1.8  Consensus size: 93

       3156 GGATGGTTGA

                                             *             * *               
       3166 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATGTCCGAACTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT

                 *                      
       3231 TGAGTTCGAGTTCGAGAGATGTAACTAG
         66 TGAGTCCGAGTTCGAGAGATGTAACTAG

                    **            *                               *          
       3259 GCATCCGAGTTCGTTGAGTTGATTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
          1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT

                          
       3324 TGAGTCCGAGTTCG
         66 TGAGTCCGAGTTCG

       3338 CTTATGGGCG


Statistics
Matches: 71,  Mismatches: 8, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  93   71  1.00

ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29


Consensus pattern (93 bp):   
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Done.