Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga12g01089.F5

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: 3593
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30


Found at i:416 original size:47 final size:47

Alignment explanation


    Indices: 354--587  Score: 245
    Period size: 47  Copynumber: 4.9  Consensus size: 47

        344 TTGCAACATA

                      *                                     
        354 TGATATGTGATTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG
          1 TGATATGTG-CTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG

                                       *    *                   
        402 TGATATGTGCTTCCGTATAAGACCATAACTGGACTATGGCATCAGTGTGATG
          1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCA----G-TG

                                 *      *     *   *      *  
        454 TGATTATGTGCTTCCGTATAATACCATATCTGGGATATAGCATCAATG
          1 TGA-TATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG

                         ** *          **    *             
        502 TGATATGTGCTTCTATGTAAGACCATATTTGGGATATGGCATCAGTG
          1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG

                      *     *         *             
        549 TGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGC
          1 TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGC

        588 TTCGGTGTAT


Statistics
Matches: 157,  Mismatches: 23, Indels: 14
        0.81            0.12        0.07

Matches are distributed among these distances:
  46   23  0.15
  47   78  0.50
  48   14  0.09
  51    1  0.01
  52    5  0.03
  53   36  0.23

ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32


Consensus pattern (47 bp):   
TGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTG

Found at i:480 original size:100 final size:100

Alignment explanation


    Indices: 365--552  Score: 270
    Period size: 100  Copynumber: 1.9  Consensus size: 100

        355 GATATGTGAT

                                   *   *      *                *             
        365 TTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGTGATATGTGCTTCCGTATAAGACCATAA
          1 TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA

                                                
        430 CT-GGACTATGGCATCAGTGTGATGTGATTATGTGC
         66 CTGGGA-TATGGCATCAGTGTGATGTGATTATGTGC

                      *      *                                *  *          *
        465 TTCCGTATAATACCATATCTGGGATATAGCATCAATGTGATATGTGCTTCTATGTAAGACCATAT
          1 TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA

            *                      
        530 TTGGGATATGGCATCAGTGTGAT
         66 CTGGGATATGGCATCAGTGTGAT

        553 ATGTGATCCG


Statistics
Matches: 77,  Mismatches: 10, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
 100   74  0.96
 101    3  0.04

ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33


Consensus pattern (100 bp):   
TTCCGTATAAGACCATAGCTGGGATATAGCATCAATGTGATATGTGCTTCCATATAAGACCATAA
CTGGGATATGGCATCAGTGTGATGTGATTATGTGC
Done.