Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g00809.M1

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: 3250
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28


Found at i:2573 original size:14 final size:14

Alignment explanation


    Indices: 2554--2583  Score: 60
    Period size: 14  Copynumber: 2.1  Consensus size: 14

       2544 CTCTACTTTT

                          
       2554 ATAGGAAGAAGGAG
          1 ATAGGAAGAAGGAG

                          
       2568 ATAGGAAGAAGGAG
          1 ATAGGAAGAAGGAG

              
       2582 AT
          1 AT

       2584 CTAGTTAGTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   16  1.00

ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10


Consensus pattern (14 bp):   
ATAGGAAGAAGGAG

Found at i:3185 original size:25 final size:25

Alignment explanation


    Indices: 3157--3216  Score: 88
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       3147 ACTCTTGTTT

                                      
       3157 TTCATTTATTTATTCAAAAAAA-TAG
          1 TTCATTTATTTATT-AAAAAAATTAG

                                     
       3182 TTCATTTA-TTATTAAAAAAATTAG
          1 TTCATTTATTTATTAAAAAAATTAG

                 *     
       3206 TTCATCTATTT
          1 TTCATTTATTT

       3217 GAAAAATATG


Statistics
Matches: 32,  Mismatches: 1, Indels: 4
        0.86            0.03        0.11

Matches are distributed among these distances:
  23    7  0.22
  24   15  0.47
  25   10  0.31

ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48


Consensus pattern (25 bp):   
TTCATTTATTTATTAAAAAAATTAG

Found at i:3221 original size:23 final size:23

Alignment explanation


    Indices: 3172--3222  Score: 68
    Period size: 23  Copynumber: 2.2  Consensus size: 23

       3162 TTATTTATTC

                           *      *
       3172 AAAAAAATAGTTCATTTATTATT
          1 AAAAAAATAGTTCATCTATTATG

                                    
       3195 AAAAAAATTAGTTCATCTATT-TG
          1 AAAAAAA-TAGTTCATCTATTATG

                 
       3218 AAAAA
          1 AAAAA

       3223 TATGGCTAAC


Statistics
Matches: 25,  Mismatches: 2, Indels: 2
        0.86            0.07        0.07

Matches are distributed among these distances:
  23   13  0.52
  24   12  0.48

ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37


Consensus pattern (23 bp):   
AAAAAAATAGTTCATCTATTATG
Done.