Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g02417.P1

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: 12529
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33


Found at i:5594 original size:41 final size:41

Alignment explanation


    Indices: 5548--5625  Score: 111
    Period size: 41  Copynumber: 1.9  Consensus size: 41

       5538 ATTATAATAG

                                                     
       5548 ATACAGAACATGCTTAACAGATAACAAATTATACACAACTT
          1 ATACAGAACATGCTTAACAGATAACAAATTATACACAACTT

                   **        *       **          
       5589 ATACAGATTATGCTTAATAGATAACTTATTATACACA
          1 ATACAGAACATGCTTAACAGATAACAAATTATACACA

       5626 TAGAGCTTGT


Statistics
Matches: 32,  Mismatches: 5, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  41   32  1.00

ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29


Consensus pattern (41 bp):   
ATACAGAACATGCTTAACAGATAACAAATTATACACAACTT

Found at i:7871 original size:23 final size:23

Alignment explanation


    Indices: 7829--7873  Score: 63
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       7819 CAAAGAACCA

                  *       **       
       7829 TATCGATAAGCTCATGAAGAGCT
          1 TATCGAAAAGCTCACAAAGAGCT

                                  
       7852 TATCGAAAAGCTCACAAAGAGC
          1 TATCGAAAAGCTCACAAAGAGC

       7874 CATGTAACGG


Statistics
Matches: 19,  Mismatches: 3, Indels: 0
        0.86            0.14        0.00

Matches are distributed among these distances:
  23   19  1.00

ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20


Consensus pattern (23 bp):   
TATCGAAAAGCTCACAAAGAGCT

Found at i:9091 original size:17 final size:16

Alignment explanation


    Indices: 9069--9102  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       9059 TTTGAATTCC

                   *         
       9069 ATAGCTATTAGATACTT
          1 ATAGCTACTAGA-ACTT

                            
       9086 ATAGCTACTAGAACTT
          1 ATAGCTACTAGAACTT

             
       9102 A
          1 A

       9103 ACTTTTTCAT


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  16    5  0.31
  17   11  0.69

ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35


Consensus pattern (16 bp):   
ATAGCTACTAGAACTT

Found at i:11161 original size:26 final size:27

Alignment explanation


    Indices: 11128--11238  Score: 131
    Period size: 26  Copynumber: 4.2  Consensus size: 27

      11118 TGATACAAAT

                                       
      11128 TGATAATGGGAT-AGGTAAATATTTCA
          1 TGATAATGGGATAAGGTAAATATTTCA

               *                        
      11154 TGACAAT-GGATTAAGGTAAATATTTCA
          1 TGATAATGGGA-TAAGGTAAATATTTCA

                        *        *   * 
      11181 TGATAATGGG-TTAGGTAAATGTTTAA
          1 TGATAATGGGATAAGGTAAATATTTCA

                        *        *     
      11207 TGATAATGGG-TGAGGTAAATGTTTCA
          1 TGATAATGGGATAAGGTAAATATTTCA

                  
      11233 TGATAA
          1 TGATAA

      11239 GAATTACATG


Statistics
Matches: 75,  Mismatches: 7, Indels: 6
        0.85            0.08        0.07

Matches are distributed among these distances:
  25    3  0.04
  26   50  0.67
  27   20  0.27
  28    2  0.03

ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35


Consensus pattern (27 bp):   
TGATAATGGGATAAGGTAAATATTTCA

Found at i:11196 original size:53 final size:52

Alignment explanation


    Indices: 11128--11238  Score: 150
    Period size: 53  Copynumber: 2.1  Consensus size: 52

      11118 TGATACAAAT

                                    *           *                
      11128 TGATAATGGGATAGGTAAATATTTCATGACAATGGATTAAGGTAAATATTTCA
          1 TGATAATGGGATAGGTAAATATTTAATGACAATGG-GTAAGGTAAATATTTCA

                      *         *        *       *        *     
      11181 TGATAATGGGTTAGGTAAATGTTTAATGATAATGGGTGAGGTAAATGTTTCA
          1 TGATAATGGGATAGGTAAATATTTAATGACAATGGGTAAGGTAAATATTTCA

                  
      11233 TGATAA
          1 TGATAA

      11239 GAATTACATG


Statistics
Matches: 51,  Mismatches: 7, Indels: 1
        0.86            0.12        0.02

Matches are distributed among these distances:
  52   20  0.39
  53   31  0.61

ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35


Consensus pattern (52 bp):   
TGATAATGGGATAGGTAAATATTTAATGACAATGGGTAAGGTAAATATTTCA
Done.