Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga14g00972.P2

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: 4082
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35


Found at i:448 original size:28 final size:26

Alignment explanation


    Indices: 406--480  Score: 78
    Period size: 26  Copynumber: 2.8  Consensus size: 26

        396 AAAAGTAGCT

                    * *      *        * 
        406 AAATTACTATAATACCCGTATGAATGGA
          1 AAATTACTGTTATACCCCTA-G-ATGCA

                                 *    
        434 AAATTACTGTTATACCCCTAGGTGCA
          1 AAATTACTGTTATACCCCTAGATGCA

                   *             
        460 AAATTACCGTTATACCCCTAG
          1 AAATTACTGTTATACCCCTAG

        481 GGTTAATTTT


Statistics
Matches: 41,  Mismatches: 6, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  26   23  0.56
  27    1  0.02
  28   17  0.41

ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29


Consensus pattern (26 bp):   
AAATTACTGTTATACCCCTAGATGCA

Found at i:625 original size:27 final size:27

Alignment explanation


    Indices: 584--723  Score: 156
    Period size: 27  Copynumber: 5.2  Consensus size: 27

        574 GAGGAAGCGT

                      *                
        584 TCTGGTGGCTATGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                                       
        611 TCTGGTGGCTCTGCCACAAATATCTGA
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                              *       *
        638 TCTGGTGGCTCTGCCACATATATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

               *     *       * *        
        665 TCTAGTGGCCCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACAAATATCTG-A

               *   *     *     *      *
        693 TCTAGTGACTCTGTCAC-ATTATCTGT
          1 TCTGGTGGCTCTGCCACAAATATCTGA

                 
        719 TCTGG
          1 TCTGG

        724 CAGCCATGCT


Statistics
Matches: 98,  Mismatches: 14, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  26    4  0.04
  27   80  0.82
  28   14  0.14

ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34


Consensus pattern (27 bp):   
TCTGGTGGCTCTGCCACAAATATCTGA

Found at i:673 original size:54 final size:55

Alignment explanation


    Indices: 584--721  Score: 172
    Period size: 54  Copynumber: 2.5  Consensus size: 55

        574 GAGGAAGCGT

                      *       *       *   *     *                  
        584 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCCCTGCCACAAATATCTGTA

                                                        * *        
        638 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCCCTGCCACGATTATCTGTA
          1 TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCCCTGCCACAAATATCTGTA

               *   *     *                
        693 TCTAGTGACTCTGTCACAT-TATCTGTTCT
          1 TCTGGTGGCTCTGCCACATATATCTGTTCT

        722 GGCAGCCATG


Statistics
Matches: 73,  Mismatches: 10, Indels: 2
        0.86            0.12        0.02

Matches are distributed among these distances:
  54   56  0.77
  55   17  0.23

ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35


Consensus pattern (55 bp):   
TCTGGTGGCTCTGCCACATATATCTGTTCTAGTGGCCCTGCCACAAATATCTGTA
Done.