Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga07g01403.F3

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: 3667
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33


Found at i:1616 original size:25 final size:25

Alignment explanation


    Indices: 1588--1639  Score: 104
    Period size: 25  Copynumber: 2.1  Consensus size: 25

       1578 TATTAACTAA

                                     
       1588 AGAACTGAACTTAAATAGAGAAAAG
          1 AGAACTGAACTTAAATAGAGAAAAG

                                     
       1613 AGAACTGAACTTAAATAGAGAAAAG
          1 AGAACTGAACTTAAATAGAGAAAAG

              
       1638 AG
          1 AG

       1640 TCCTAATCCT


Statistics
Matches: 27,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  25   27  1.00

ACGTcount: A:0.56, C:0.08, G:0.21, T:0.15


Consensus pattern (25 bp):   
AGAACTGAACTTAAATAGAGAAAAG

Found at i:1718 original size:42 final size:42

Alignment explanation


    Indices: 1654--1744  Score: 155
    Period size: 42  Copynumber: 2.1  Consensus size: 42

       1644 AATCCTAATT

                                                       
       1654 AGAACAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA
          1 AGAA-AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA

                                                *     
       1697 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAA
          1 AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA

             *    
       1739 ATAAAA
          1 AGAAAA

       1745 ATATTCCTAG


Statistics
Matches: 46,  Mismatches: 2, Indels: 1
        0.94            0.04        0.02

Matches are distributed among these distances:
  42   42  0.91
  43    4  0.09

ACGTcount: A:0.52, C:0.15, G:0.05, T:0.27


Consensus pattern (42 bp):   
AGAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAA

Found at i:1765 original size:43 final size:42

Alignment explanation


    Indices: 1659--1766  Score: 103
    Period size: 42  Copynumber: 2.5  Consensus size: 42

       1649 TAATTAGAAC

                       * * *                       *  
       1659 AATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAGAA
          1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA

                       * * *                *          
       1701 AATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAATAAA
          1 AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAA-AAA

                                     
       1744 AATA-TT-CCTAGAATATGAATAAA
          1 AATAGTTCCCT-GAATAT-AATAAA

       1767 ACTTATTTAC


Statistics
Matches: 58,  Mismatches: 5, Indels: 5
        0.85            0.07        0.07

Matches are distributed among these distances:
  41    3  0.05
  42   43  0.74
  43   12  0.21

ACGTcount: A:0.51, C:0.14, G:0.06, T:0.30


Consensus pattern (42 bp):   
AATAGTTCCCTGAATATAATAAACTACTAAAACATAAAAAAA

Found at i:1791 original size:19 final size:18

Alignment explanation


    Indices: 1769--1808  Score: 62
    Period size: 19  Copynumber: 2.2  Consensus size: 18

       1759 TGAATAAAAC

                *              
       1769 TTATTTACCTAAATAAGAT
          1 TTATCTACCTAAATAA-AT

                              
       1788 TTATCTACCTAAATAAAT
          1 TTATCTACCTAAATAAAT

               
       1806 TTA
          1 TTA

       1809 AAATATTTAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  18    5  0.25
  19   15  0.75

ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42


Consensus pattern (18 bp):   
TTATCTACCTAAATAAAT
Done.