eprimer3.txt

emboss的linux版本的源代码

  [Part of this file has been deleted for brevity]

FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   intron          857..950
FT                   /number=2
FT   exon            951..1095
FT                   /number=3
FT   intron          1096..1556
FT                   /number=3
FT   exon            1557..1612
FT                   /number=4
FT   intron          1613..1786
FT                   /number=4
FT   exon            1787..>1912
FT                   /number=5
FT   polyA_signal    1938..1943
XX
SQ   Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
     ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac        6
0
     ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       12
0
     tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       18
0
     agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       24
0
     gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       30
0
     tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       36
0
     gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       42
0
     cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       48
0
     gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       54
0
     tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       60
0
     tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       66
0
     cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       72
0
     ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       78
0
     tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       84
0
     ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       90
0
     tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       96
0
     cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      102
0
     aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      108
0
     gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      114
0
     tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      120
0
     tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      126
0
     tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      132
0
     ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      138
0
     agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      144
0
     ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      150
0
     ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      156
0
     agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      162
0
     gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      168
0
     ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      174
0
     gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      180
0
     gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      186
0
     caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      192
0
     taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      198
0
     tacttgcaag gcctcaggga gaggtgtgct tctcgg                                201
6
//

Output file format

  Output files for usage example

  File: hsfau.eprimer3


# EPRIMER3 RESULTS FOR HSFAU1

# FORWARD PRIMER STATISTICS:
# considered 16422
# GC content failed 156
# low tm 3616
# high tm 9306
# high any compl 9
# high end compl 26
# long poly-x seq 45
#high 3' stability 304
# ok 2960

# REVERSE PRIMER STATISTICS:
# considered 16330
# GC content failed 161
# low tm 3580
# high tm 9309
# high any compl 2
# high end compl 9
# long poly-x seq 66
#high 3' stability 301
# ok 2902

# PRIMER PAIR STATISTICS:
# considered 2652
# unacceptable product size 2444
# high any compl 2
# high end compl 20
# ok 186

#                      Start  Len   Tm     GC%   Sequence

   1 PRODUCT SIZE: 202
     FORWARD PRIMER     801   20  59.72  60.00  CCCAGGAGCTACACACCTTC

     REVERSE PRIMER     983   20  59.81  55.00  GGAGCACGACTTGATCTTCC


   2 PRODUCT SIZE: 203
     FORWARD PRIMER    1810   20  59.43  55.00  GAAGAAGACAGGTCGGGCTA

     REVERSE PRIMER    1993   20  59.99  60.00  GAAGCACACCTCTCCCTGAG


   3 PRODUCT SIZE: 204
     FORWARD PRIMER    1810   20  59.43  55.00  GAAGAAGACAGGTCGGGCTA

     REVERSE PRIMER    1994   20  59.99  55.00  AGAAGCACACCTCTCCCTGA


   4 PRODUCT SIZE: 196
     FORWARD PRIMER    1266   20  59.43  60.00  GGGAGACTGAGCCAGAGTGT

     REVERSE PRIMER    1442   20  60.06  50.00  GCGCCCAATAGGTAATGAGA


   5 PRODUCT SIZE: 205
     FORWARD PRIMER     801   20  59.72  60.00  CCCAGGAGCTACACACCTTC

     REVERSE PRIMER     986   20  60.41  55.00  CCAGGAGCACGACTTGATCT



   If the '-explain' flag has been used, as in the example, then
   statistics are output describing the number of primers that were
   considered and rejected for various reasons.

   Headers describing the input file name and the names of the output
   columns are displayed.

   The best 5 primer pairs are displayed with the product size.

   The reverse sequence is displayed as the reverse complement to the
   input forward sense sequence.

   The 'Start' positions are given counting from the start of the
   sequence for both the forward and reverse primer (and for the internal
   oligos).

   Note that if you compare the results to the output from the public
   Primer3 web site you will see a difference in the reverse primer
   positions - this is because the original Primer3 program reports the
   reverse primer positions as counted from the 3' end. The convention in
   EMBOSS is to report both forward and reverse features as counted from
   the 5' end, so the reverse primer positions are given counted from the
   5' start of the sequence.

Data files

   None.

Notes

   The Whitehead Institute's primer3 program is not part of this program,
   but it must be set up on your system and on your path.

   The Whitehead Institute program that is run by this program is
   available from:
   http://www-genome.wi.mit.edu/genome_software/other/primer3.html
   (Then see the link 'Get release 0.9')

   The version that is run by this program is 3.0.9 currently available
   from:
   http://www-genome.wi.mit.edu/ftp/distribution/software/primer3_0_9_tes
   t.tar.gz The Whitehead Institute's primer3 program is:
   Copyright (c) 1996,1997,1998
   Whitehead Institute for Biomedical Research. All rights reserved.

   The Whitehead Institute requests that use of this software be cited in
   publications as:

   Steve Rozen, Helen J. Skaletsky (1996,1997,1998)
   Primer3. Code available at
   http://www-genome.wi.mit.edu/genome_software/other/primer3.html

References

   None.

Warnings

   None.

Diagnostic Error Messages

   The message: "EMBOSS An error in eprimer3.c at line 315: The program
   'primer3_core' must be on the path. It is part of the 'primer3'
   package, available from the Whitehead Institute. See:
   http://www-genome.wi.mit.edu/" is output if you do not have the
   Whitehead Institute's primer3 program set up and on your path.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                         Description
   primersearch Searches DNA sequences for matches with primer pairs
   stssearch    Search a DNA database for matches with a set of STS primers

History

Author(s)

   Gary Williams (gwilliam