Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga03g00630.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: 11284
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:768 original size:3 final size:3

Alignment explanation


    Indices: 760--808  Score: 89
    Period size: 3  Copynumber: 16.3  Consensus size: 3

        750 CGTTGTTCTC

                                                *                          
        760 GAT GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT GAT GAT GAT
          1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT

             
        808 G
          1 G

        809 GGGTAAAAGG


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
   3   44  1.00

ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33


Consensus pattern (3 bp):   
GAT

Found at i:3513 original size:42 final size:42

Alignment explanation


    Indices: 3456--3543  Score: 158
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       3446 CCTAATTAGA

                                                      
       3456 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG
          1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG

                                              *      *
       3498 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAT
          1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG

                
       3540 AAAA
          1 AAAA

       3544 ATATTCCTAG


Statistics
Matches: 44,  Mismatches: 2, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  42   44  1.00

ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28


Consensus pattern (42 bp):   
AAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAG

Found at i:3564 original size:43 final size:42

Alignment explanation


    Indices: 3455--3565  Score: 109
    Period size: 42  Copynumber: 2.6  Consensus size: 42

       3445 TCCTAATTAG

                          * * *                       
       3455 AAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
          1 AAAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA

            *             * * *                *      
       3497 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
          1 AAAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA

                                         
       3539 TAAAAATA-TT-CCTAGAATATGAATAAA
          1 -AAAAATAGTTCCCT-GAATAT-AATAAA

       3566 ACTTATTTAA


Statistics
Matches: 60,  Mismatches: 6, Indels: 5
        0.85            0.08        0.07

Matches are distributed among these distances:
  41    3  0.05
  42   45  0.75
  43   12  0.20

ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29


Consensus pattern (42 bp):   
AAAAATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA

Found at i:3590 original size:19 final size:18

Alignment explanation


    Indices: 3568--3607  Score: 53
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       3558 TGAATAAAAC

                *              
       3568 TTATTTAACTAAATAAGAT
          1 TTATCTAACTAAATAA-AT

                   *          
       3587 TTATCTACCTAAATAAAT
          1 TTATCTAACTAAATAAAT

               
       3605 TTA
          1 TTA

       3608 AAATATATAC


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  18    5  0.26
  19   14  0.74

ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42


Consensus pattern (18 bp):   
TTATCTAACTAAATAAAT

Found at i:6746 original size:42 final size:43

Alignment explanation


    Indices: 6699--6789  Score: 148
    Period size: 42  Copynumber: 2.1  Consensus size: 43

       6689 CCTAATTAGG

                                        *     *        
       6699 AAAATAGTTCACTTATTCTAATAAACTATTAAAATATAAAA-A
          1 AAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAATA

                      *                                
       6741 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATA
          1 AAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAATA

                  
       6784 AAAATA
          1 AAAATA

       6790 TTCTTATAAT


Statistics
Matches: 45,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  42   38  0.84
  43    7  0.16

ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31


Consensus pattern (43 bp):   
AAAATAGTTCACTTATTCTAATAAACTACTAAAAGATAAAATA

Found at i:6833 original size:19 final size:18

Alignment explanation


    Indices: 6811--6850  Score: 71
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       6801 TGAATAAAAC

                               
       6811 TTATCTACCTAAATAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       6830 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

               
       6848 TTA
          1 TTA

       6851 AAATATATAC


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  18    5  0.24
  19   16  0.76

ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40


Consensus pattern (18 bp):   
TTATCTACCTAAATAAAT

Found at i:9007 original size:28 final size:28

Alignment explanation


    Indices: 8967--9023  Score: 114
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       8957 GAAGATTGAA

                                        
       8967 TCAACTTAAGGAAAGAATATTTCTTAAT
          1 TCAACTTAAGGAAAGAATATTTCTTAAT

                                        
       8995 TCAACTTAAGGAAAGAATATTTCTTAAT
          1 TCAACTTAAGGAAAGAATATTTCTTAAT

             
       9023 T
          1 T

       9024 AGAATATCTA


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  28   29  1.00

ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37


Consensus pattern (28 bp):   
TCAACTTAAGGAAAGAATATTTCTTAAT
Done.