Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gohir.D01G183500.1.v1.1

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: 5157
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30


Found at i:75 original size:6 final size:6

Alignment explanation


    Indices: 66--105  Score: 62
    Period size: 6  Copynumber: 6.3  Consensus size: 6

         56 AAATCAAAAT

                                                          
         66 AATAAA AATAAA AATAAA AATAAAA AATAAAA AATAAA AA
          1 AATAAA AATAAA AATAAA AAT-AAA AAT-AAA AATAAA AA

        106 AGGGAAGCGA


Statistics
Matches: 33,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   6   20  0.61
   7   13  0.39

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (6 bp):   
AATAAA

Found at i:83 original size:12 final size:12

Alignment explanation


    Indices: 66--105  Score: 62
    Period size: 13  Copynumber: 3.2  Consensus size: 12

         56 AAATCAAAAT

                        
         66 AATAAAAATAAA
          1 AATAAAAATAAA

                         
         78 AATAAAAATAAAA
          1 AATAAAAAT-AAA

                         
         91 AATAAAAAATAAA
          1 AAT-AAAAATAAA

              
        104 AA
          1 AA

        106 AGGGAAGCGA


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  12    9  0.35
  13   11  0.42
  14    6  0.23

ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15


Consensus pattern (12 bp):   
AATAAAAATAAA

Found at i:85 original size:7 final size:7

Alignment explanation


    Indices: 56--106  Score: 63
    Period size: 7  Copynumber: 7.4  Consensus size: 7

         46 ACGTAAGCAT

                    
         56 AAATCAAA
          1 AAAT-AAA

                    
         64 ATAAT-AA
          1 A-AATAAA

                   
         71 AAAT-AA
          1 AAATAAA

                   
         77 AAAT-AA
          1 AAATAAA

                   
         83 AAATAAA
          1 AAATAAA

                   
         90 AAATAAA
          1 AAATAAA

                   
         97 AAATAAA
          1 AAATAAA

               
        104 AAA
          1 AAA

        107 GGGAAGCGAA


Statistics
Matches: 41,  Mismatches: 0, Indels: 5
        0.89            0.00        0.11

Matches are distributed among these distances:
   6   15  0.37
   7   22  0.54
   8    1  0.02
   9    3  0.07

ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16


Consensus pattern (7 bp):   
AAATAAA

Found at i:92 original size:20 final size:21

Alignment explanation


    Indices: 56--105  Score: 68
    Period size: 20  Copynumber: 2.4  Consensus size: 21

         46 ACGTAAGCAT

                *                 
         56 AAATCAAAATAATAAAAAT-AA
          1 AAATAAAAAT-ATAAAAATAAA

                                 
         77 AAATAAAAATA-AAAAATAAA
          1 AAATAAAAATATAAAAATAAA

                     
         97 AAATAAAAA
          1 AAATAAAAA

        106 AGGGAAGCGA


Statistics
Matches: 27,  Mismatches: 1, Indels: 3
        0.87            0.03        0.10

Matches are distributed among these distances:
  19    6  0.22
  20   12  0.44
  21    9  0.33

ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16


Consensus pattern (21 bp):   
AAATAAAAATATAAAAATAAA

Found at i:524 original size:3 final size:3

Alignment explanation


    Indices: 516--569  Score: 108
    Period size: 3  Copynumber: 18.0  Consensus size: 3

        506 TCATCTTCCA

                                                                           
        516 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT
          1 ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT ACT

                   
        564 ACT ACT
          1 ACT ACT

        570 TCCGTTTCTT


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   51  1.00

ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33


Consensus pattern (3 bp):   
ACT

Done.