Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga02g00592.N1

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: 1669
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29


Found at i:251 original size:3 final size:3

Alignment explanation


    Indices: 243--312  Score: 76
    Period size: 3  Copynumber: 24.7  Consensus size: 3

        233 TGGGCAGTAT

                              *                         * *                
        243 AAG AAG AAG -AG AAA AAG AAG AAG AAG AA- AAG TAT AAG AAG AAG -AG
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG

              *                               
        288 AAA AAG AAG AAG AAG AA- AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AA

        313 ATAGAGATGT


Statistics
Matches: 55,  Mismatches: 8, Indels: 8
        0.77            0.11        0.11

Matches are distributed among these distances:
   2    8  0.15
   3   47  0.85

ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03


Consensus pattern (3 bp):   
AAG

Found at i:262 original size:14 final size:14

Alignment explanation


    Indices: 243--312  Score: 70
    Period size: 14  Copynumber: 4.6  Consensus size: 14

        233 TGGGCAGTAT

                          
        243 AAGAAGAAGAGAAA
          1 AAGAAGAAGAGAAA

                               
        257 AAGAAGAAGAAGAAAAGTA
          1 AAGAAGAAG-AG--AA--A

                           
        276 TAAGAAGAAGAGAAA
          1 -AAGAAGAAGAGAAA

                           
        291 AAGAAGAAGA-AGAA
          1 AAGAAGAAGAGA-AA

                    
        305 AAGAAGAA
          1 AAGAAGAA

        313 ATAGAGATGT


Statistics
Matches: 49,  Mismatches: 0, Indels: 14
        0.78            0.00        0.22

Matches are distributed among these distances:
  13    1  0.02
  14   29  0.59
  15    3  0.06
  17    4  0.08
  19    3  0.06
  20    9  0.18

ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03


Consensus pattern (14 bp):   
AAGAAGAAGAGAAA

Found at i:276 original size:34 final size:34

Alignment explanation


    Indices: 238--307  Score: 140
    Period size: 34  Copynumber: 2.1  Consensus size: 34

        228 TTGGCTGGGC

                                              
        238 AGTATAAGAAGAAGAGAAAAAGAAGAAGAAGAAA
          1 AGTATAAGAAGAAGAGAAAAAGAAGAAGAAGAAA

                                              
        272 AGTATAAGAAGAAGAGAAAAAGAAGAAGAAGAAA
          1 AGTATAAGAAGAAGAGAAAAAGAAGAAGAAGAAA

              
        306 AG
          1 AG

        308 AAGAAATAGA


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  34   36  1.00

ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06


Consensus pattern (34 bp):   
AGTATAAGAAGAAGAGAAAAAGAAGAAGAAGAAA

Found at i:673 original size:47 final size:46

Alignment explanation


    Indices: 582--693  Score: 120
    Period size: 47  Copynumber: 2.5  Consensus size: 46

        572 TTTGTAATGT

                      *     *                      *      
        582 TGTTGTTGTTTAAATGAAAAACCAACTTATATGATAACTGGTATTG
          1 TGTTGTTGTTGAAATGGAAAACCAACTTATATGATAACTAGTATTG

                                     *     *    ***        
        628 CTGTTGTTGTTGAAATGGAAAACCAGCTTATGTGATTGTTAGTATTG
          1 -TGTTGTTGTTGAAATGGAAAACCAACTTATATGATAACTAGTATTG

            *                    
        675 AG--GTTGTTGAAATGGAAAA
          1 TGTTGTTGTTGAAATGGAAAA

        694 TAGTATTGGT


Statistics
Matches: 56,  Mismatches: 9, Indels: 3
        0.82            0.13        0.04

Matches are distributed among these distances:
  44   17  0.30
  46    1  0.02
  47   38  0.68

ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38


Consensus pattern (46 bp):   
TGTTGTTGTTGAAATGGAAAACCAACTTATATGATAACTAGTATTG
Done.