Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga05g03725.F1

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: 5223
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36


Found at i:1235 original size:59 final size:59

Alignment explanation


    Indices: 1104--1253  Score: 142
    Period size: 60  Copynumber: 2.5  Consensus size: 59

       1094 ACCCTAGTAC

                                         *   *             *           
       1104 TAGATTTAAAAAAACAATATTTTTTTAGTGTTGTGACATTAATTGCTGACATCTCAATA
          1 TAGATTTAAAAAAACAATATTTTTTTAGTATTGGGACATTAATTGCTAACATCTCAATA

               *    *                  *          *       **   *         
       1163 TCATATTTTAAAAAA-AATATTTTTTTGGTTATTGGGATATTAATTTTTAATATC-CAATA
          1 T-AGATTTAAAAAAACAATATTTTTTTAG-TATTGGGACATTAATTGCTAACATCTCAATA

                           *                
       1222 GTAGATTTAAAAAAATATATATATTTTTTAGT
          1 -TAGATTTAAAAAAACA-ATAT-TTTTTTAGT

       1254 TGTTAAGATA


Statistics
Matches: 72,  Mismatches: 13, Indels: 10
        0.76            0.14        0.11

Matches are distributed among these distances:
  59   29  0.40
  60   31  0.43
  61    5  0.07
  62    7  0.10

ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45


Consensus pattern (59 bp):   
TAGATTTAAAAAAACAATATTTTTTTAGTATTGGGACATTAATTGCTAACATCTCAATA

Found at i:4820 original size:104 final size:105

Alignment explanation


    Indices: 4553--4835  Score: 300
    Period size: 104  Copynumber: 2.7  Consensus size: 105

       4543 CTAGTCTGTT

                       **              *                                 *   
       4553 AATGGCCGGCATTAGAGTACGAGTTTAAAAAAAAACAATTGGTGCTGGCCTGTCAATGGCCAGCA
          1 AATGGCCGGCACCAGAGTACGAGTTT-TAAAAAAA-AATTGGTGCTGGCCTGTCAATGGCCGGCA

                                               *      
       4618 CTAAGTACAAAAAAAATCAAATTTTTTTGGTACTGGCCCATC
         64 CTAAGTACAAAAAAAATCAAATTTTTTTGGTACTGACCCATC

                          *              *******           * *       *   *   
       4660 AATGGCCGGCACCAAAGTACGAGTTTTAATTTTTTTTTGGTGCTGGCATATCAATGGTCGGTACT
          1 AATGGCCGGCACCAGAGTACGAGTTTTAAAAAAAAATTGGTGCTGGCCTGTCAATGGCCGGCACT

                                          *      *   
       4725 AAGTAC-AAAAAAATCAAAATTTTTTT-GTGCTGACCTATC
         66 AAGTACAAAAAAAATC-AAATTTTTTTGGTACTGACCCATC

                     *                                 ***     *             
       4764 AATGGCCGGTACCAGAGTACGAGTTTTAAAAAAAAATTGGTGCCAACCTGTAAATGGCCGGCACT
          1 AATGGCCGGCACCAGAGTACGAGTTTTAAAAAAAAATTGGTGCTGGCCTGTCAATGGCCGGCACT

                   
       4829 AGAGTAC
         66 A-AGTAC

       4836 CAGTATTTAA


Statistics
Matches: 138,  Mismatches: 36, Indels: 6
        0.77            0.20        0.03

Matches are distributed among these distances:
 104   68  0.49
 105   45  0.33
 106    2  0.01
 107   23  0.17

ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28


Consensus pattern (105 bp):   
AATGGCCGGCACCAGAGTACGAGTTTTAAAAAAAAATTGGTGCTGGCCTGTCAATGGCCGGCACT
AAGTACAAAAAAAATCAAATTTTTTTGGTACTGACCCATC
Done.