Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g02904.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: 3410
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Found at i:1401 original size:12 final size:12

Alignment explanation


    Indices: 1380--1409  Score: 51
    Period size: 12  Copynumber: 2.5  Consensus size: 12

       1370 TTTTCAAAAT

                 *      
       1380 TAAAAGAAATTA
          1 TAAAAAAAATTA

                        
       1392 TAAAAAAAATTA
          1 TAAAAAAAATTA

                  
       1404 TAAAAA
          1 TAAAAA

       1410 TTAGCATTAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  12   17  1.00

ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23


Consensus pattern (12 bp):   
TAAAAAAAATTA

Found at i:3015 original size:114 final size:113

Alignment explanation


    Indices: 2816--3025  Score: 253
    Period size: 114  Copynumber: 1.8  Consensus size: 113

       2806 AAGGTTGAGC

                            *      *     *             *                    *
       2816 ATTAGCGGCGCTTCCCTAAAACGTCGCAATAGATCAAGCATTAGCGATGTTTTAAAGAAAGCGCT
          1 ATTAGCGGCGCTTCCCAAAAACGCCGCAAAAGATCAAGCATTAACGATGTTTTAAAGAAAGCGCC

                       *         *                          
       2881 GCTAAAAGATTCAGCAGAACGGCGTCGTTTACATTGAGTTTCCACGGA
         66 GCTAAAAGATTAAGCAGAACGACGTCGTTTACATTGAGTTTCCACGGA

                          **                    *                   *        
       2929 ATTAGCGGCGCTTAGGCAAAAACGCCGCAAAAGATCGAGCATTAAC-AGTGTTTT-TAGAAAAGC
          1 ATTAGCGGCGCTT-CCCAAAAACGCCGCAAAAGATCAAGCATTAACGA-TGTTTTAAAG-AAAGC

                      *      **               
       2992 GCCGCTAAAATATTAAGGTGAACGACGTCGTTTA
         63 GCCGCTAAAAGATTAAGCAGAACGACGTCGTTTA

       3026 GATTAAGCTT


Statistics
Matches: 80,  Mismatches: 14, Indels: 5
        0.81            0.14        0.05

Matches are distributed among these distances:
 113   16  0.20
 114   64  0.80

ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24


Consensus pattern (113 bp):   
ATTAGCGGCGCTTCCCAAAAACGCCGCAAAAGATCAAGCATTAACGATGTTTTAAAGAAAGCGCC
GCTAAAAGATTAAGCAGAACGACGTCGTTTACATTGAGTTTCCACGGA

Found at i:3044 original size:114 final size:113

Alignment explanation


    Indices: 2816--3055  Score: 250
    Period size: 114  Copynumber: 2.1  Consensus size: 113

       2806 AAGGTTGAGC

                            *      *     *             *                    *
       2816 ATTAGCGGCGCTTCCCTAAAACGTCGCAATAGATCAAGCATTAGCGATGTTTTAAAGAAAGCGCT
          1 ATTAGCGGCGCTTCCCAAAAACGCCGCAAAAGATCAAGCATTAACGATGTTTTAAAGAAAGCGCC

                       *         *             *  *  *      
       2881 GCTAAAAGATTCAGCAGAACGGCGTCGTTTACATTGAGTTTCCACGGA
         66 GCTAAAAGATTAAGCAGAACGACGTCGTTTACATTAAGCTTACACGGA

                          **                    *                   *        
       2929 ATTAGCGGCGCTTAGGCAAAAACGCCGCAAAAGATCGAGCATTAAC-AGTGTTTT-TAGAAAAGC
          1 ATTAGCGGCGCTT-CCCAAAAACGCCGCAAAAGATCAAGCATTAACGA-TGTTTTAAAG-AAAGC

                      *      **               *           **   
       2992 GCCGCTAAAATATTAAGGTGAACGACGTCGTTTAGATTAAGCTTACGTGGA
         63 GCCGCTAAAAGATTAAGCAGAACGACGTCGTTTACATTAAGCTTACACGGA

                 *       
       3043 ATTAGTGGCGCTT
          1 ATTAGCGGCGCTT

       3056 TCAGGAAAAC


Statistics
Matches: 103,  Mismatches: 21, Indels: 5
        0.80            0.16        0.04

Matches are distributed among these distances:
 113   16  0.16
 114   87  0.84

ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Consensus pattern (113 bp):   
ATTAGCGGCGCTTCCCAAAAACGCCGCAAAAGATCAAGCATTAACGATGTTTTAAAGAAAGCGCC
GCTAAAAGATTAAGCAGAACGACGTCGTTTACATTAAGCTTACACGGA

Done.