Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga06g00479.F6

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: 4150
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30


Found at i:1240 original size:15 final size:15

Alignment explanation


    Indices: 1222--1252  Score: 53
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       1212 ACTTAGTTGT

                           
       1222 CCTTCCAAACATGAA
          1 CCTTCCAAACATGAA

                *          
       1237 CCTTTCAAACATGAA
          1 CCTTCCAAACATGAA

             
       1252 C
          1 C

       1253 TGTTTAGCGA


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.39, C:0.32, G:0.06, T:0.23


Consensus pattern (15 bp):   
CCTTCCAAACATGAA

Found at i:1636 original size:93 final size:94

Alignment explanation


    Indices: 1418--1712  Score: 273
    Period size: 93  Copynumber: 3.1  Consensus size: 94

       1408 TTTTTAGTAC

                         * *                   **     *        *    *      * 
       1418 TTTCAAAGGATCAGTTGAGTCCAAAACAAAACCAAGTTGAAGTACTTCCTCGTG-ATC-T-ATTT
          1 TTTCAAAGGATCAATGGAGTCCAAAACAAAACCAAACTGAAGCACTTCCTCTTGAACCTTAATCT

                      *                     *
       1480 AGTGAAGATACTG-CG-ATGCGCCTTTT-ATGC
         66 AGTGAAGATAGTGACGTAT----CTTTTAATGA

                  *      ***                           *                 *   
       1510 TTTCAAGGGATCAGCAGAGTCCAAAACAAAACCAAACTGAAGCGCTTCCT-TATGAACCTTTATC
          1 TTTCAAAGGATCAATGGAGTCCAAAACAAAACCAAACTGAAGCACTTCCTCT-TGAACCTTAATC

                           *             *
       1574 TAGTGAAGAT-GTGATGTATCTTTTAATGT
         65 TAGTGAAGATAGTGACGTATCTTTTAATGA

                                       *                                   * 
       1603 TTTCAAAGGATCAATGGAGTCCAAAACCAAACCAAACTGAAGCACTTCCTCTTGAACCTTAATTT
          1 TTTCAAAGGATCAATGGAGTCCAAAACAAAACCAAACTGAAGCACTTCCTCTTGAACCTTAATCT

                               *           
       1668 AGTGAAGATGCAGTGACGTGTCTTTTAATGA
         66 AGTGAAGAT--AGTGACGTATCTTTTAATGA

                  *       
       1699 TTTCAATGGATCAA
          1 TTTCAAAGGATCAA

       1713 CAGGGTCCCA


Statistics
Matches: 167,  Mismatches: 25, Indels: 18
        0.80            0.12        0.09

Matches are distributed among these distances:
  92   50  0.30
  93   69  0.41
  94    4  0.02
  95   13  0.08
  96   31  0.19

ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30


Consensus pattern (94 bp):   
TTTCAAAGGATCAATGGAGTCCAAAACAAAACCAAACTGAAGCACTTCCTCTTGAACCTTAATCT
AGTGAAGATAGTGACGTATCTTTTAATGA
Done.