plotorf.txt

emboss的linux版本的源代码

  File: mito.seq

>gi|5819095|ref|NC_001321.1| Balaenoptera physalus mitochondrion, complete geno
me
GTTAATTACTAATCAGCCCATGATCATAACATAACTGAGGTTTCATACATTTGGTATTTTTTTATTTTTTTTGGGGGGC
T
TGCACGGACTCCCCTATGACCCTAAAGGGTCTCGTCGCAGTCAGATAAATTGTAGCTGGGCCTGGATGTATTTGTTATT
T
GACTAGCACAACCAACATGTGCAGTTAAATTAATGGTTACAGGACATAGTACTCCACTATTCCCCCCGGGCTCAAAAAA
C
TGTATGTCTTAGAGGACCAAACCCCCCTCCTTCCATACAATACTAACCCTCTGCTTAGATATTCACCACCCCCCTAGAC
A
GGCTCGTCCCTAGATTTAAAAGCCATTTTATTTATAAATCAATACTAAATCTGACACAAGCCCAATAATGAAAATACAT
G
AACGCCATCCCTATCCAATACGTTGATGTAGCTTAAACACTTACAAAGCAAGACACTGAAAATGTCTAGATGGGTCTAG
C
CAACCCCATTGACATTAAAGGTTTGGTCCCAGCCTTTCTATTAGTTCTTAACAGACTTACACATGCAAGTATCCACATC
C
CAGTGAGAACGCCCTCTAAATCATAAAGATTAAAAGGAGCGGGTATCAAGCACGCTAGCACTAGCAGCTCACAACGCCT
C
GCTTAGCCACGCCCCCACGGGACACAGCAGTGATAAAAATTAAGCTATAAACGAAAGTTCGACTAAGTCATGTTAATTT
A
AGGGTTGGTAAACTTCGTGCCAGCCACCGCGGTCATACGATCGACCCAAATTAATAGAAGCACGGCGTAAAGAGTGTTA
A
GGAGCCACATGAAATAAAGTCAAACCTTAATTAAGCTGTAAAAAGCCCTAATTAAAATTAAGCCAAACTACGAAAGTGA
C
TTTAATATAATCTGATCACACGACAGCTAAGATCCAAACTGGGATTAGATACCCCACTATGCTTAGTCGTAAACCCCAA
T
AGTCACAAAACAAGACTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTTGGCGGTGCCTCATACCC
A
TCTAGAGGAGCCTGTTCTGTAACCGATAAACCCCGATCAACCTCACCAACCCTTGCTACTTCAGTCTATATACCGCCAT
C
TTCAGCAAACCCTAAAGGGAGAAAAGTAAGCATAACCATCCTACATAAAAACGTTAGGTCAAGGTGTAACCCATGGGTT
G
GGAAGTAATGGGCTACATTTTCTAAGCTAAGAACATCCCCTATACTCACACGAAAGTTTTTATGAAACTTAAAAACTAA
A
GGAGGATTTAGTAGTAAATCAAGAGCAGAGTGCTTGATTGAATAAGGCCATGAGGGCACGCACACACCGCCCGTCACCC
T
CCTCAAGTACCCCAGCTATAAACCCCAGTTCGTTAACTCAGGCCAAGCAATTATACGAGAGGAGACAAGTCGTAACAAG
G
TAAGCATACCGGAAGGTGTGCTTGGACAAAACAAGATATAGCTTAAACAAAGCATGTAGTTTACACCTAGAAGATTCCA
C
AGCCCGTGTATATCTTGAACTAGCCCTAGCCCACACCCTCCCCACCTCTACTACCACAAATCAATCAAATAAAACATTT
A
CCATCCCTTCAAAGTATAGGAGATAGAAATTTAAATATCAGTGGCGCTATAGAGATAGTACCGTAAGGAAAGATGAAAG
A
AAAACCTAAAAGTAATAAAAAGCAAAGCTTACCACTTGTACCTTTTGCATAATGACTTAACTAGTAATAAATTAGCAAA
G
AGACCTTAAGTTAAATTACCCGAAACCAGACGAGCTACTTATGAGCAGCACCTAGAACGAACTCATCTATGTGGCAAAA
T
AGTGAGAAGACTTATAAGTAGAGGTGAAAAGCCTAACGAGCCTGGTGATAGCTGGTTGTCCCTGAAAAGAATCTCAGTT
C
AACATTAAATAATACTAAAAGCCCATGCCAAGCCTTAACGTATATTTAACTGTTAATCTAAAAAGGTACAGCTTTTTAG
A
AATGGGTACAACCTTGACTAGAGAGTAAAATCAAACATAAACATAGTTGGCCTAAAAGCAGCCATCAATTAAGAAAGCG
T
TCAAGCTCGACAACAAAATAATGTTTTAATTCCAACATTAAGTAAATCAACTCCTAGCCTGACTATTGGACTAATCTAT
A
CAAATATAGAAGCAATACTGTTAATATGAGTAACAAGAAATTTTTCTCCTAGCACAAGCTTACACCAGTAACTGATAAT
A
TACTGATAATTAACAGCAAATAAATAAAACCCAACACTAAATTATTTATTAAAATACTGTTAACCCAACACAGGCGTGC
A
TTAAGGAAAGATTAAAAAAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTTACCAAAAACATCACCTCTAGCA
T
AACCAGTATTAGAGCACTGCCTGCCCGGTGACTAATCGTTAAACGGCCGCGGTATCCTGACCGTGCAAAGGTAGCATAA
T
CACTTGTTCTCTAATTAGGGACTTGTATGAATGGCCACACGAGGGTTTTACTGTCTCTTACTTTTAATCAGTGAAATTG
A
CCTCTCCGTGAAGAGGCGGAGATAACAAAATAAGACGAGAAGACCCTATGGAGCTTCAATTAATCAACCCAAAAACCAT
A
ACCTTAAACCACCAAGGGATAACAAAACCTTATATGGGCTGACAATTTCGGTTGGGGTGACCTCGGAGTACAAAAAACC
C
TCCGAGTGATTAAAACTTAGGCCCACTAGCCAAAGTACAATATCACTTATTGATCCAATCCTTTGATCAACGGAACAAG
T
TACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCGACAATAGGGTTTACGACCTCGATGTTGGATCAGGA
C
ATCCTAATGGTGCAGCTGCTATTAAGGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGT
A
ATCCAGGTCGGTTTCTATCTATTACGCATTTCTCCCAGTACGAAAGGACAAGAGAAATAAGGCCAACTTCAAACAAGCG
C
CTTCAAACAATTAATGACCTAGTCTCAACTTAATAATTAAGCGCAAACAAACCTGCCCAAGACCAGGGCCTTGTTGAGG
T
GGCAGAGTTCGGTAATTGCATAAAACTTAAACTTTTACACCCAGAGGTTCAAATCCTCTCCCCAACAAAATGTTTATAA
T
TAACATTCTAACACTCATTCTCCCCATCCTCCTAGCCGTAGCATTCCTAACGCTAGTAGAACGCAAAATTCTAGGCTAT
A
TGCAGTTCCGAAAGGGGCCAAACATCGTAGGCCCACATGGCTTACTCCAACCCTTTGCCGATGCAATTAAATTATTCAC
T
AAAGAACCCCTACGGCCAGCTACATCCTCAACTACTATGTTTATCATTGCACCAGTACTAGCCCTAACCCTGGCCCTCA
C
TATATGAAGCCCCCTACCCATACCATACCCCCTCATTAACATAAACCTAGGAGTATTATTCATATTAGCAATATCCAGC
C
TAGCCGTCTACTCCATCCTATGATCAGGCTGAGCCTCCAACTCAAAATACGCACTAATTGGAGCCCTACGAGCAGTAGC
A
CAAACAATCTCATATGAGGTAACACTAGCCATTATCCTCCTATCAGTACTCCTAATAAACGGCTCCTACACCTTATCAA
C
ATTAGCCACAACACAAGAACAACTATGATTACTATTCCCATCATGACCCTTAGCCATAATGTGATTCATCTCCACCCTA
G
CAGAAACTAATCGAGCTCCTTTTGATCTAACAGAGGGAGAATCAGAACTCGTATCAGGCTTCAACGTAGAATATGCAGC
A
GGCCCTTTCGCCCTATTCTTCCTGGCAGAATACGCCAACATCATTATAATGAATATACTCACAGCCATTTTATTCCTAG
G


  [Part of this file has been deleted for brevity]

CATTGTCTTCTGCGCCTTCATCACTAGTCTAGTTCCCGCAATAGTATATCTTCACACAAACCAAGAAACACTCATCTCA
A
ACTGACACTGAATCACAATCCAAACCCTCAAACTAACACTTAGCTTTAAAATAGATTACTTTTCACTTATATTTATACC
A
GTAGCACTATTCATTACATGATCCATCATAGAATTCTCAATATGATATATGCACTCCGACCCCTACATCAACCAATTTT
T
TAAATACTTACTCCTCTTCCTCATCACCATACTAATCCTTGTTACAGCTAACAATCTCTTCCAACTTTTCATCGGATGA
G
AAGGAGTAGGAATTATATCCTTCTTACTAATTGGCTGATGATTCGGACGAACAGATGCAAATACAGCCGCCCTCCAAGC
A
ATCCTATACAATCGTATCGGAGACATTGGACTCCTTGCATCAATAGCATGATTTCTCTCTAATATAAACACATGAGACC
T
AGAACAAATCTTTATACTCAACCAAAACCCCTTAAATTTCCCCCTCATAGGACTCGTACTAGCCGCAGCAGGAAAATCG
G
CTCAATTCGGACTCCACCCTTGACTCCCATCAGCAATAGAAGGTCCTACCCCAGTCTCAGCCCTACTCCACTCAAGCAC
A
ATAGTTGTAGCAGGAATCTTCTTGCTTGTCCGCTTCTACCCATTAATAGAAAATAACAAGCTAATCCAAACAGTAACCC
T
CTGCTTAGGCGCTATCACAACTCTATTTACAGCCATCTGTGCCCTCACCCAAAACGACATCAAAAAAATTATTGCTTTC
T
CCACCTCCAGCCAGCTAGGCCTAATAATAGTAACAATCGGCCTTAACCAACCTTACCTAGCATTCCTACACATTTGCAC
A
CACGCCTTCTTTAAAGCTATACTATTCCTATGTTCTGGCTCCATCATCCATAACCTAAACAACGAACAAGATATCCGAA
A
AATAGGAGGGCTATTTAAGGCCCTCCCATTCACCACAACCGCCCTTATCATCGGATGTCTTGCACTAACAGGAATGCCA
T
TCCTGACCGGATTCTACTCCAAAGATCCCATTATTGAAGCCGCCACTTCGTCTTATACCAACGCCTGAGCCCTATTACT
G
ACCTTAATCGCCACCTCCCTTACGGCCGTCTATAGCACCCGCATCATTTTCTTTGCACTACTAGGACAACCCCGCTTCC
C
TCCCTCCACAACCATTAACGAAAATAATCCACTGTTAATCAACCCTATCAAACGACTACTCGTCGGAAGTATCTTCGCT
G
GCTTCATCCTATCCAACAGTATTCCCCCAATAACTACACCTTTAATAACCATACCCCTGCACTTAAAATTAACCGCCCT
T
GCAATAACAACCCTAGGCTTCATCATCGCATTCGAAATTAACCTTGACACACAAAATCTAAAGCACAAGCACCCATCAA
A
CTCCTTTAAATTCTCCACCTTACTAGGTTATTTCCCCACAATCATACATCGCCTACCCCCTCACCTTGACCTGTTAATA
A
GCCAAAAACTAGCAACTTCCCTACTAGATCTAACTTGACTAGAAACTATTTTACCAAAAACCACAGCCCTTATCCAACT
A
AAAGCCTCTACACTAACCTCTAACCAACAAGGCCTCATCAAACTCTACTTCTTATCTTTCCTCATCACCATCACCCTCA
G
CATAATCTTATTTAACTACCCCGAGTAATCTCCATAATAATTACAACACTAATAAATAAAGACCAACCCGTAACAATCA
C
CAACCAAACACCATAACTATATAATGCCGCAATCCCTGTAGCCTCCTCACTAAAAACCCCAGAACCCCCAGTATCATAA
A
CAACCCAGTCCCCTAGTCCATCAAACTCAAACATAATCTTCACCTCCCCACTCTTCAAAGCATAAATCACAATTAAAAA
C
TCCACCACCAACCCTAAAACAAATGCTCCTAGTACAACTTTATTAGAAACCCAAACCTCAGGATACTGTTCAGTAGCCA
T
AGCTGTTGTATAACCAAATACTACCAGCATTCCCCCCAAATAAATCAAAAACACCATTAACCCCAAAAACGAACCACCA
A
AACTCAAAATAACTCCACATCCAACACCACCACCCACAATCAACCCTAAACCCCCATAAATAGGTGAAGGCTTTGAAGA
A
ACCCCCACAAAACTAATTACAAAAATAATACTTAAAATGAAAACAATATACATTATCATTATTCTCACATGGACTTCAA
C
CATGACCAATGACATGAAAAATCATCGTTGTTATTCAACTACAAGAACACCAATGACCAACATCCGAAAAACACACCCA
C
TAATAAAAATCGTCAACGACGCATTCGTCGATCTCCCCACCCCATCAAATATCTCTTCATGATGGAACTTCGGCTCCCT
A
CTCGGCCTCTGCTTAATTATACAAATCCTAACAGGCCTATTCCTAGCAATACACTACACACCAGACACAACAACCGCCT
T
CTCATCAGTCACACACATCTGCCGAGACGTGAATTACGGCTGAATTATCCGATACCTACATGCAAATGGGGCTTCTATA
T
TCTTCATCTGCCTCTACGCTCACATAGGACGAGGCCTATACTACGGCTCCTACGCCTTCCGAGAAACATGAAATATTGG
A
GTTATTCTACTATTCACAGTTATAGCCACCGCATTCGTAGGCTACGTCCTGCCCTGAGGACAAATATCATTCTGAGGCG
C
AACTGTAATCACTAACCTCCTATCAGCAATCCCATACATTGGTACCACCCTAGTCGAATGAATCTGAGGCGGTTTCTCT
G
TAGATAAAGCAACACTAACACGCTTTTTTGCCTTTCACTTTATCCTCCCCTTCATCATCCTAGCATTAGCAATTGTCCA
C
CTTATTTTCCTTCACGAAACAGGATCCAACAACCCCACAGGCATCCCATCCGACATAGATAAAATCCCATTCCACCCCT
A
CCACACAATTAAAGACATTCTAGGTGCCCTATTACTAATCCTAATCCTACTAATACTAACCCTATTCGCACCCGACCTA
C
TTGGAGACCCAGACAACTATACCCCAGCAAACCCACTCAGTACCCCAGCACACATTAAACCAGAATGGTATTTTCTATT
C
GCATACGCAATCCTACGATCAATCCCCAACAAACTAGGCGGAGTCTTAGCCCTACTACTCTCAATCCTAATCCTAGCCT
T
CATCCCAATACTCCACACATCCAATCAACGAAGCATAATATTTCGACCCTTTAGCCAGTTCTTGTTCTGAGTCCTAGTC
G
CAGATCTACTAACCCTAACATGGATCGGCGGCCAACCAGTAGAACACCCCTACATAATTGTAGGCCAACTCGCATCCAT
C
CTCTATTTCCTCTTAATTCTAGTATTAATACCAGTAACTAGTCTTATCGAGAACAAACTTATAAAATGAAGAGTCTTTG
T
AGTATAATTAAATACCCCGGTTTTGTAAACCGGAAAAGGAGACAAGACACACCTCCCTAAGACTCAAGGAAGAAGTATT
A
CACTCCACCATCAGCACCCAAAGCTGAAGTTCTACATAAACTATTCCCTGAAAAAGTATATTGTACAATAACCACAGGA
C
CACAGTACTATGTCCGTATTGAAAATAACTTGCCTTATTAGATATTATTATGTAACTCGTGCATGCATGTACTTCCACA
T
AATTAATAGCGTCTTTCCATGGGTATGAACAGATATACATGCTATGTATAATTGTGCATTCAATTATTTTCACCACGAG
C
AGTTGAAGCTCGTATTAAATTTTATTAATTTTACATATTACATAATATGTATTAATAGTACAATAGCGCATGTTCTTAT
G
CATCCCCAGATCTATTTAAATCAAATGATTCCTATGGCCGCTCCATTAGATCACGAGCTTAGTCAGCATGCCGCGTGAA
A
CCAGCAACCCGCTTGGCAGGGATCCCTCTTCTCGCACCGGGCCCATCACTCGTGGGGGTAGCTATTTAATGATCTTTAT
A
AGACATCTGGTTCTTACTTCAGGACCATATTAACTTAAAATCGCCCACTCGTTCCCCTTAAATAAGACATCTCGATGG

Output file format

  Output files for usage example

  Graphics File: plotorf.ps

   [plotorf results]

  Output files for usage example 2

  Graphics File: plotorf.ps

   [plotorf results]

Data files

   None.

Notes

   ORFs in this program are defined as being regions between START and
   STOP codons.

   Note that this definition of an ORF would miss those exons in
   eukaryotic genomic sequences which do not contain a START codon.
   plotorf is only really useful when dealing with prokaryotic or mRNA
   eukaryotic sequences.

References

   None.

Warnings

   See the Notes section.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                         Description
   backtranambig Back translate a protein sequence to ambiguous codons
   backtranseq   Back translate a protein sequence
   coderet       Extract CDS, mRNA and translations from feature tables
   getorf        Finds and extracts open reading frames (ORFs)
   marscan       Finds MAR/SAR sites in nucleic sequences
   prettyseq     Output sequence with translated ranges
   remap         Display sequence with restriction sites, translation etc
   showorf       Pretty output of DNA translations
   showseq       Display a sequence with features, translation etc
   sixpack       Display a DNA sequence with 6-frame translation and ORFs
   syco          Synonymous codon usage Gribskov statistic plot
   tcode         Fickett TESTCODE statistic to identify protein-coding DNA
   transeq       Translate nucleic acid sequences
   wobble        Wobble base plot

Author(s)

   Alan Bleasby (ajb