% getorf -minsize 300 
Finds and extracts open reading frames (ORFs)
Input sequence(s): tembl:eclaci
Output sequence [eclaci.orf]: 

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA

   Additional (Optional) qualifiers:
   -table              menu       Code to use
   -minsize            integer    Minimum nucleotide size of ORF to report
   -maxsize            integer    Maximum nucleotide size of ORF to report
   -find               menu       This is a small menu of possible output
                                  options. The first four options are to
                                  select either the protein translation or the
                                  original nucleic acid sequence of the open
                                  reading frame. There are two possible
                                  definitions of an open reading frame: it can
                                  either be a region that is free of STOP
                                  codons or a region that begins with a START
                                  codon and ends with a STOP codon. The last
                                  three options are probably only of interest
                                  to people who wish to investigate the
                                  statistical properties of the regions around
                                  potential START or STOP codons. The last
                                  option assumes that ORF lengths are
                                  calculated between two STOP codons.

   Advanced (Unprompted) qualifiers:
   -[no]methionine     boolean    START codons at the beginning of protein
                                  products will usually code for Methionine,
                                  despite what the codon will code for when it
                                  is internal to a protein. This qualifier
                                  sets all such START codons to code for
                                  Methionine by default.
   -circular           boolean    Is the sequence circular
   -[no]reverse        boolean    Set this to be false if you do not wish to
                                  find ORFs in the reverse complement of the
                                  sequence.
   -flanking           integer    If you have chosen one of the options of the
                                  type of sequence to find that gives the
                                  flanking sequence around a STOP or START
                                  codon, this allows you to set the number of
                                  nucleotides either side of that codon to
                                  output. If the region of flanking
                                  nucleotides crosses the start or end of the
                                  sequence, no output is given for this codon.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outseq" associated qualifiers
   -osformat2           string     Output seq format
   -osextension2        string     File name extension
   -osname2             string     Base file name
   -osdirectory2        string     Output directory
   -osdbname2           string     Database name to add
   -ossingle2           boolean    Separate file for each entry
   -oufo2               string     UFO features
   -offormat2           string     Features format
   -ofname2             string     Features file name
   -ofdirectory2        string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths

ID   ECLACI     standard; DNA; PRO; 1113 BP.
XX
AC   V00294;
XX
SV   V00294.1
XX
DT   09-JUN-1982 (Rel. 01, Created)
DT   10-FEB-1999 (Rel. 58, Last updated, Version 2)
XX
DE   E. coli laci gene (codes for the lac repressor).
XX
KW   DNA binding protein; repressor.
XX
OS   Escherichia coli
OC   Bacteria; Proteobacteria; gamma subdivision; Enterobacteriaceae;
OC   Escherichia.
XX
RN   [1]
RP   1-1113
RX   MEDLINE; 78246991.
RA   Farabaugh P.J.;
RT   "Sequence of the lacI gene";
RL   Nature 274:765-769(1978).
XX
DR   SWISS-PROT; P03023; LACI_ECOLI.
XX
CC   KST ECO.LACI
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1113
FT                   /db_xref="taxon:562"
FT                   /organism="Escherichia coli"
FT   CDS             31..1113
FT                   /db_xref="SWISS-PROT:P03023"
FT                   /note="reading frame"
FT                   /transl_table=11
FT                   /protein_id="CAA23569.1"
FT                   /translation="MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAEL
FT                   NYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGV
FT                   EACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSH
FT                   EDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSA
FT                   MSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSC
FT                   YIPPSTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPR
FT                   ALADSLMQLARQVSRLESGQ"
XX
SQ   Sequence 1113 BP; 249 A; 304 C; 322 G; 238 T; 0 other;
     ccggaagaga gtcaattcag ggtggtgaat gtgaaaccag taacgttata cgatgtcgca        60
     gagtatgccg gtgtctctta tcagaccgtt tcccgcgtgg tgaaccaggc cagccacgtt       120
     tctgcgaaaa cgcgggaaaa agtggaagcg gcgatggcgg agctgaatta cattcccaac       180
     cgcgtggcac aacaactggc gggcaaacag tcgttgctga ttggcgttgc cacctccagt       240
     ctggccctgc acgcgccgtc gcaaattgtc gcggcgatta aatctcgcgc cgatcaactg       300
     ggtgccagcg tggtggtgtc gatggtagaa cgaagcggcg tcgaagcctg taaagcggcg       360
     gtgcacaatc ttctcgcgca acgcgtcagt gggctgatca ttaactatcc gctggatgac       420
     caggatgcca ttgctgtgga agctgcctgc actaatgttc cggcgttatt tcttgatgtc       480
     tctgaccaga cacccatcaa cagtattatt ttctcccatg aagacggtac gcgactgggc       540
     gtggagcatc tggtcgcatt gggtcaccag caaatcgcgc tgttagcggg cccattaagt       600
     tctgtctcgg cgcgtctgcg tctggctggc tggcataaat atctcactcg caatcaaatt       660
     cagccgatag cggaacggga aggcgactgg agtgccatgt ccggttttca acaaaccatg       720
     caaatgctga atgagggcat cgttcccact gcgatgctgg ttgccaacga tcagatggcg       780
     ctgggcgcaa tgcgcgccat taccgagtcc gggctgcgcg ttggtgcgga tatctcggta       840
     gtgggatacg acgataccga agacagctca tgttatatcc cgccgtcaac caccatcaaa       900
     caggattttc gcctgctggg gcaaaccagc gtggaccgct tgctgcaact ctctcagggc       960
     caggcggtga agggcaatca gctgttgccc gtctcactgg tgaaaagaaa aaccaccctg      1020
     gcgcccaata cgcaaaccgc ctctccccgc gcgttggccg attcattaat gcagctggca      1080
     cgacaggttt cccgactgga aagcgggcag tga                                   1113
//

>ECLACI_1 [735 - 1112] E. coli laci gene (codes for the lac repressor).
GHRSHCDAGCQRSDGAGRNARHYRVRAARWCGYLGSGIRRYRRQLMLYPAVNHHQTGFSP
AGANQRGPLAATLSGPGGEGQSAVARLTGEKKNHPGAQYANRLSPRVGRFINAAGTTGFP
TGKRAV
>ECLACI_2 [1 - 1110] E. coli laci gene (codes for the lac repressor).
PEESQFRVVNVKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN
RVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAA
VHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLG
VEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTM
QMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPSTTIK
QDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLA
RQVSRLESGQ*
>ECLACI_3 [465 - 49] (REVERSE SENSE) E. coli laci gene (codes for the lac repressor).
RRNISAGSFHSNGILVIQRIVNDQPTDALREKIVHRRFTGFDAASFYHRHHHAGTQLIGA
RFNRRDNLRRRVQGQTGGGNANQQRLFARQLLCHAVGNVIQLRHRRFHFFPRFRRNVAGL
VHHAGNGLIRDTGILCDIV