[Bioperl-l] writing genbank files
Hilmar Lapp
hlapp@gnf.org
Wed, 18 Sep 2002 09:42:07 -0700
I believe Jason fixed something yesterday in Species.pm in order to
allow spaces in certain places. Jason?
-hilmar
On Wednesday, September 18, 2002, at 01:48 AM, gert thijs wrote:
> Hilmar,
>
> I just installed the modules from the main trunk. I tried to test
> it but now I was unable to parse input sequences in genbank format.
> Now I have a problem uploading a genbank flat file. There seems to
> be a problem while parsing the species name. I guess not having an
> upper case starting letter stops the genbank parser. In attachment
> you can find a file on which the parser throws the expection.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Invalid name 'eurosids II' (Wrong case?)
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/Root/Root.pm:318
> STACK: Bio::Species::validate_name
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/Species.pm:283
> STACK: Bio::Species::classification
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/Species.pm:121
> STACK: Bio::SeqIO::genbank::_read_GenBank_Species
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/SeqIO/genbank.pm:884
> STACK: Bio::SeqIO::genbank::next_seq
> /users/sista/thijs/perl/lib/site_perl/5.6.0/Bio/SeqIO/genbank.pm:229
> STACK: AnnotatedSequence::new
> /users/sista/thijs/perl/lib//AnnotatedSequence.pm:66
> STACK: GeneIndex.pl:168
> -----------------------------------------------------------
>
> Gert
>
>
> Hilmar Lapp wrote:
>> It should be written as join(complement(...),complement(...),...).
>> This is main trunk only though. Do you have an example where this
>> is not true?
>> -hilmar
>> On Tuesday, September 17, 2002, at 02:06 AM, gert thijs wrote:
>>> Hello,
>>>
>>> I have a question about the current status of the genbank file
>>> parser/writer. I noticed that a CDS with a location of the type
>>> complement(join()) is written as a join() without the complement.
>>> I saw that this problem has been a major thread on the list a few
>>> weeks ago, but I could not find if the problem has been solved by
>>> now or if it was solved how it should be solved.
>>>
>>> Gert
>>>
>>>
>>>
>>> -- + Gert Thijs
>>> + K.U.Leuven
>>> + ESAT-SCD
>>> + Kasteelpark Arenberg 10
>>> + B-3001 Leuven-Heverlee
>>> + Belgium
>>> +
>>> + Tel : +32 16 32 85 88
>>> + Fax : +32 16 32 19 70
>>> + email: gert.thijs@esat.kuleuven.ac.be
>>> +
>>> + http://www.esat.kuleuven.ac.be/~thijs
>>> + http://www.esat.kuleuven.ac.be/~dna/BioI/
>>> +
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l@bioperl.org
>>> http://bioperl.org/mailman/listinfo/bioperl-l
>>>
>> -- -------------------------------------------------------------
>> Hilmar Lapp email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
>> -------------------------------------------------------------
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l@bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>
>
> -- + Gert Thijs
> + K.U.Leuven
> + ESAT-SCD
> + Kasteelpark Arenberg 10
> + B-3001 Leuven-Heverlee
> + Belgium
> +
> + Tel : +32 16 32 85 88
> + Fax : +32 16 32 19 70
> + email: gert.thijs@esat.kuleuven.ac.be
> +
> + http://www.esat.kuleuven.ac.be/~thijs
> + http://www.esat.kuleuven.ac.be/~dna/BioI/
> +
> LOCUS AB000094 15532 bp DNA linear PLN
> 13-JAN-1998
> DEFINITION Arabidopsis thaliana gene for inorganic phosphate
> transporter,
> protein phosphatase 1 catalytic subunit, complete cds.
> ACCESSION AB000094
> VERSION AB000094.1 GI:2780346
> KEYWORDS protein phosphatase 1 catalytic subunit inorganic phosphate
> SOURCE Arabidopsis thaliana (strain:Columbia) DNA.
> ORGANISM Arabidopsis thaliana
> Eukaryota; Viridiplantae; Streptophyta; Embryophyta;
> Tracheophyta;
> Spermatophyta; Magnoliophyta; eudicotyledons; core
> eudicots;
> Rosidae; eurosids II; Brassicales; Brassicaceae;
> Arabidopsis.
> REFERENCE 1 (bases 0 to 0)
> AUTHORS Mitsukawa,N., Okumura,S. and Shibata,D.
> TITLE High-affinity phosphate transporter genes of
> Arabidopsis thaliana
> JOURNAL Soil Sci. Plant Nutr. 43, 971-974 (1997)
> REFERENCE 2 (bases 0 to 0)
> AUTHORS Mitsukawa,N., Okumura,S. and Shibata,D.
> TITLE Isolation of a gene that encode a protein phosphatase 1
> catalytic
> subun it in Arabidopsis thaliana
> JOURNAL Unpublished (1996)
> REFERENCE 3 (bases 1 to 15532)
> AUTHORS Mitsukawa,N.
> TITLE Direct Submission
> JOURNAL Submitted (24-DEC-1996) to the DDBJ/EMBL/GenBank databases.
> Norihiro Mitsukawa, Mitsui Plant Biotech.Res.Inst.,
> Research
> Division; TCI-D21, Sengen 2-1-6, Tsukuba, Ibaraki 305,
> JAPAN
> (E-mail:tsu01129@koryu.statci.go.jp, Tel:0298-58-6252,
> Fax:0298-58-6234)
> COMMENT Sequence updated (08-Jan-1998).
> FEATURES Location/Qualifiers
> source 1..15532
> /chromosome=5
> /strain="Columbia"
> /organism="Arabidopsis thaliana"
> /db_xref="taxon:3702"
> gene join(2560..2960,3086..4250)
> /gene="PHT3"
> CDS join(2560..2960,3086..4250)
> /product="inorganic phosphate transporter"
> /gene="PHT3"
> /protein_id="BAA24281.1"
> /codon_start=1
>
> /translation="MADQQLGVLKALDVAKTQLYHFTAIVIAGMGFFTDAYDLFCVSL
>
> VTKLLGRLYYFNPTSAKPGSLPPHVAAAVNGVALCGTLAGQLFFGWLGDKLGRKKVYG
>
> ITLIMMILCSVASGLSLGNSAKGVMTTLCFFRFWLGFGIGGDYPLSATIMSEYANKKT
>
> RGAFIAAVFAMQGVGILAGGFVALAVSSIFDKKFPSPTYEQDRFLSTPPQADYIWRII
>
> VMFGALPAALTYYWRMKMPETARYTALVAKNIKQATADMSKVLQTDLELEERVEDDVK
>
> DPKKNYGLFSKEFLRRHGLHLLGTTSTWFLLDIAFYSQNLFQKDIFSAIGWIPKAATM
>
> NAIHEVFKIARAQTLIALCSTVPGYWFTVAFIDIIGRFAIQLMGFFMMTVFMFAIAFP
>
> YNHWILPDNRIGFVVMYSLTFFFANFGPNATTFIVPAEIFPARLRSTCHGISAATGKA
>
> GAIVGAFGFLYAAQPQDKTKTDAGYPPGIGVKNSLIMLGVINFVGMLFTFLVPEPKGK
> SLEELSGEAEVDK"
> /db_xref="GI:2780347"
> gene join(9110..9510,9661..10834)
> /gene="PHT2"
> CDS join(9110..9510,9661..10834)
> /product="inorganic phosphate transporter"
> /gene="PHT2"
> /protein_id="BAA24282.1"
> /codon_start=1
>
> /translation="MAEQQLGVLKALDVAKTQLYHFTAIVIAGMGFFTDAYDLFCVSL
>
> VTKLLGRIYYFNPESAKPGSLPPHVAAAVNGVALCGTLSGQLFFGWLGDKLGRKKVYG
>
> LTLIMMILCSVASGLSFGNEAKGVMTTLCFFRFWLGFGIGGDYPLSATIMSEYANKKT
>
> RGAFIAAVFAMQGVGILAGGFVALAVSSIFDKKFPAPTYAVNRALSTPPQVDYIWRII
>
> VMFGALPAALTYYWRMKMPETARYTALVAKNIKQATADMSKVLQTDIELEERVEDDVK
>
> DPRQNYGLFSKEFLRRHGLHLLGTTSTWFLLDIAFYSQNLFQKDIFSAIGWIPKAATM
>
> NATHEVFRIARAQTLIALCSTVPGYWFTVAFIDTIGRFKIQLNGFFMMTVFMFAIAFP
>
> YNHWIKPENRIGFVVMYSLTFFFANFGPNATTFIVPAEIFPARLRSTCHGISAAAGKA
>
> GAIIGAFGFLYAAQNQDKAKVDAGYPPGIGVKNSLIVLGVLNFIGMLFTFLVPEPKGK
> SLEELSGEAEVSHDEK"
> /db_xref="GI:2780348"
> CDS join(13719..13967,14046..14605,14688..14862)
> /product="protein phosphatase 1 catalytic subunit"
> /protein_id="BAA24283.1"
> /codon_start=1
>
> /translation="MDPGTLNSVINRLLEAREKPGKIVQLSETEIKQLCFVSRDIFLR
>
> QPNLLELEAPVKICGDIHGQYPDLLRLFEHGGYPPNSNYLFLGDYVDRGKQSLETICL
>
> LLAYKIKFPENFFLLRGNHESASINRIYGFYDECKRRFSVKIWRIFTDCFNCLPVAAL
>
> IDERIFCMHGGLSPELLSLRQIRDIRRPTDIPDRGLLCDLLWSDPDKDVRGWGPNDRG
>
> VSYTFGSDIVSGFLKRLDLDLICRAHQVVEDGFEFFANKQLVTIFSAPNYCGEFDNAG
>
> AMMSVSEDLTCSFQILKSNDKKSKFSFGSRGGAKTSFPYPKVKVCINHITF"
> /db_xref="GI:2780349"
> BASE COUNT 5197 a 2674 c 2593 g 5068 t
> ORIGIN
> 1 cttttaaaaa atttacaaag atttttaaaa gcattttttt ggctgggaaa
> aaaattttac
> 61 gagaaaacat ttttggcggg aaattttttt tttggcggga aaaaaagttt
> ggcggaaatt
> 121 ttttgtttgg cgggaaaaat aaattttggt acatgttatt attaaatgag
> ggtaatttgg
> 181 tcattctgtt caatagaagg gatattttta aaaataaaca atataaaatg
> gtattgttac
> 241 aaaagggtag taaaaaaagg gtagttttgc aaatctccct cgagaatttg
> caatttctct
> 301 ctcatagcat aacatgtctt ttttttagta aatttcaaga tgacaaaaag
> aaaaaaaaaa
> 361 cataaagaaa caaattgaaa gcaacatcta tttttctgac ttgtaaaaat
> gtggtgttac
> 421 tagcaaatat caaatttttg tatctataaa ctagatttta acccgcggta
> tactaggaga
> 481 acgatttatt ttttaaagtt aatatatata caagtttaca aattgaatat
> atttataaaa
> 541 aaaataaatt ttttagttta caattattat taggtaacat cccgccaaat
> ctgttccatc
> 601 aaaaagctta ttaattttat taatgttaac cttagttatg atatgattct
> aaatcattgt
> 661 ctagatattt tagccaatgt taggacgttg aacccacata gttttcgtca
> attgaataat
> 721 atatgttcgt tttataaatt tcgaatcaca atttatgcag aaaatgtttt
> gaaatttttc
> 781 ttaactttac atattataca ataaaaaatc aaacaaagat gataggaaat
> tcatagtttt
> 841 aaatcttaat caaatcttct aaatatcaat attgttaaat atagaagtaa
> tgagtataag
> 901 agttgggttt tatttgaacc aacccaacta agatttaatg aacatcataa
> actaatgggt
> 961 ctggtatcaa atgtaatcag atgcatttta acccacaatc aaaaggtgac
> tgcaaaaata
> 1021 ctatataaga ttcatagaag tagatcgtct atataggcct gaaaaatatc
> agttttaaat
> 1081 taaattattt agagatctta ttttgttggg cttaaatact ggagaataag
> actactttag
> 1141 taatcaaaat atttgggcca tgtaactaat gcaaaccaaa atcattattg
> acaaaagtca
> 1201 ttgcatcaaa tgattttctt accaaaatgt ctttaaaata tatatatata
> tatatatata
> 1261 tatatgtacc ttcgtacggt acggttgctt ttatataaaa aggtgttgta
> cggttgcatt
> 1321 gacttttgat cgtaaatact atatagtccg gagactcaaa tgcaaaccac
> tttctctatt
> 1381 tttttggacg gaagttatgt taacctaaat tatctaaaat attacacaaa
> taatttttaa
> 1441 acagtttaaa atggcatata attatgttaa tagaaatttg acttttagta
> cggagataca
> 1501 ttagctgaga agtttgacct caccttattt agtgggaacc ttgttacttt
> tgaattagtt
> 1561 tgaacaatat atctctaatt catataaagt attttgaaat ataaagcttt
> ataaatataa
> 1621 catatttttt ggtgggtaat gcttcttttt ttctgtggct tataactacg
> tggagatctt
> 1681 atcttctgtc cgcttatatt agtatttcac catagtgatt ttaataaaaa
> tcagattaaa
> 1741 caatatataa cagctatttt agtttacagg tttaaacttt tattttagtt
> ctttgatttt
> 1801 ttttttcttt cagaaaatgg tggacatctt ctaaagtttg ttttattaat
> ctaggtagaa
> 1861 actttcaaac aaaagacgaa aacagaaaag ttgactttag tacggaaata
> catgatatga
> 1921 gataactgat aagataactt gttagatggt ttccactctc ataaacaata
> taaaaaaatt
> 1981 attaacgata gtgaactcga tttttagtaa ctctatgaaa atcttcttgt
> gagatcataa
> 2041 cattttagaa gactaggctt ttcgtgtaat atgatctgta gaccattcca
> atgttatcat
> 2101 atgcagaaca gcaacacaat gaaataaatt aagagatgga aaataaatta
> agatcaaata
> 2161 aaatgtggat atacccttaa gattccggag acaatacttc tccagttctc
> ctctcgtcta
> 2221 taaatttctg ccgtctcagc caacataatc acaaccacca cctctctcaa
> taattctctc
> 2281 tcttgtcctt cacaacctgt tactacttag gtgaatatca tctacatgtt
> tattttgtct
> 2341 taatccaaat tcacatttaa ttttgttttc actcttttta tcatgtatac
> ttttttaatt
> 2401 agctagccga gattatatat gttaaaacta cctctatttc taacacaccc
> aagcaatata
> 2461 tcatctttcc aatatttacg aaagaagaaa tttctataca aatattaacc
> tttactttgt
> 2521 gcaaaatagg agagaagaaa aacaaaaaga ctgactgaga tggccgatca
> acagctagga
> 2581 gtgctaaagg cacttgatgt tgcgaagacg caactttacc atttcacggc
> tattgtcatt
> 2641 gccggtatgg gcttctttac ggacgcgtac gatctctttt gtgtgtcctt
> ggtgaccaag
> 2701 cttcttggcc gcctctacta cttcaatcca acgtcagcaa agcctggctc
> acttccccct
> 2761 catgttgcgg ctgcagtcaa cggtgtggcc ctttgtggaa cccttgccgg
> tcaactcttc
> 2821 ttcggatggc ttggtgacaa actcggacgg aaaaaggtgt acggtatcac
> tttgatcatg
> 2881 atgattctct gctcagttgc ttccggtctt tccttgggca attcggccaa
> gggtgtcatg
> 2941 acgactcttt gcttcttcag gtacaattta tttagccaca aacctaatat
> cacatacgtc
> 3001 acagatacaa gctcgagaga ttagtcacta tttcgaccta gattatggtt
> acttaagata
> 3061 ctgatatcta gacgattata tataggtttt ggctcgggtt tggcattgga
> ggtgactacc
> 3121 ctctatctgc caccatcatg tctgaatacg ctaacaagaa gactcgtggg
> gctttcatcg
> 3181 cggcagtgtt cgccatgcaa ggtgtaggta tcttggcggg aggttttgtg
> gcacttgcag
> 3241 tttcttccat atttgacaaa aagttcccat cgccgacgta tgagcaagac
> aggtttctat
> 3301 caacgcctcc tcaagctgat tacatttggc gaatcatcgt catgtttggt
> gctttacccg
> 3361 cagctttgac ttactattgg cgtatgaaga tgcctgaaac agcccgttac
> accgctttag
> 3421 ttgccaagaa catcaaacaa gccacagcag acatgtccaa ggtcttacaa
> acagatctcg
> 3481 agcttgagga aagggtggag gatgacgtca aggaccccaa aaaaaactat
> ggcttgttct
> 3541 ccaaggaatt ccttagacgc catgggcttc atctccttgg gactacctcc
> acttggtttt
> 3601 tgcttgacat cgccttctac agccaaaact tgttccaaaa ggatattttc
> tcggccattg
> 3661 gatggatccc aaaggcagcc actatgaacg ccatccatga ggttttcaag
> attgctaggg
> 3721 ctcagactct cattgccctc tgcagtacag tcccaggtta ctggttcaca
> gtagccttta
> 3781 ttgatatcat tggaaggttt gcgatccaac taatgggatt tttcatgatg
> accgttttta
> 3841 tgtttgctat tgccttccca tacaaccact ggattttacc agataatcgt
> atcggattcg
> 3901 tggttatgta ctcactcaca tttttcttcg ccaactttgg acccaatgca
> actactttca
> 3961 ttgtcccagc tgaaatcttt ccagcaaggc taaggtctac gtgccatgga
> atatcagccg
> 4021 caactggtaa ggctggagcc atcgttggag ccttcgggtt cctatatgct
> gctcaaccac
> 4081 aggataagac caagacagac gcaggatacc caccgggcat cggagtcaag
> aactcattga
> 4141 tcatgcttgg tgtcattaac tttgttggta tgctcttcac cttcctcgtc
> cctgagccca
> 4201 agggcaagtc ccttgaagaa ctctccggcg aggctgaggt tgataaatga
> ttatgccgtc
> 4261 atatatgttt gtcattggtt ttgcgatgtg tgaattatat ttgtaatggt
> gtactacttt
> 4321 tacgttttac gttctttgcg atgagtgaat tatatttgta acggtgtact
> actttcgctt
> 4381 tttgtttaaa tgtgtgtgca agtgcaactt gttaagatgt aaactcatgt
> tatggtcata
> 4441 tcctagtaat gctataagtt tggaagcaat aaagacatga acaatcaaac
> aaaaaatatg
> 4501 cttagtggaa agtttgaaat gaaagatata agggctagtg gatgtaattc
> tagggatcaa
> 4561 tattgataga actgataata caaaaaatca gcttgtactg gtatattagg
> ttgaaaagat
> 4621 aaatgagata ttttagaact actgaactat aaagattggt atattgttgt
> tcatgtaatc
> 4681 gaaagatttt ttttgtaaga ttgtagatga atttatcatc aaatgaacta
> caaagactag
> 4741 ggactcccaa gagtccaaga ccctactctt cacttgtcta aacatttaag
> tgaagcaatg
> 4801 tcaaattagg agtatgatgc aacagtctat ttgatatatt tgaccagttg
> tactagactc
> 4861 aatttgatgc tgccagtgtg ccgtagaagc cttccaaata gacattatag
> ctttagtcaa
> 4921 agcaaatgag gaagccgagt ggtttcagaa cttgaaaata tttcgatggg
> agaaaccagt
> 4981 gttggcacta cgtgtaaact aaactctgat agcaattatt tattgttcga
> gcattgcgct
> 5041 cttagtttaa tgttaaatct tgtctaatta gaagacaaca caaaaaccaa
> tagcaactaa
> 5101 tctcaaatag tgtaatctca cttgattata tcaaatcgga tgataaccta
> tgacctattt
> 5161 tactaaaagg tctgtcacaa aagtaagtta tatatattca aaacaaaaaa
> aatataagat
> 5221 aaaaaataaa acgaagaaaa actgggaatg tcaaatatga taaatgattt
> aaacaaatat
> 5281 gtcatgacaa gaaaaagaaa aaagaaaaaa aactgtcacc gttacaaaaa
> actgtcacca
> 5341 ttataagtgt tattatactt ataaaaatca gcaagaacaa caaattttgg
> tcatcataag
> 5401 aattcaaaat tacaaatata tcgtaacata aaacattata gtggtcattc
> catcaatttt
> 5461 gtttatcgtt taacaaatct gcgatcaaac gatatatttt agtaatataa
> tttcatctat
> 5521 cacaacataa ccaattatgt cataactaaa aatactatat tttaaaaaca
> aatatgttgt
> 5581 tacatgaaaa tattttggta acattataaa aatctgtcat aagatataac
> aaatctgcta
> 5641 tcattagagg tcattatatt tattagtttt ttgtacataa atttcttata
> acatgataga
> 5701 tgtttttaga aaattataaa tctaccgagt cattcaaaat aaaacagcca
> gacactacag
> 5761 taagtctgtt ataaactatg aaagtatgta gttgaataaa aaaatctgtc
> aaaaaaataa
> 5821 atatgtcaaa aaaataaatc agctacaatt gttttagtct attgtaacca
> tattctaaaa
> 5881 aatctgtcaa ccaaaaaagt ctgccaaaag aaatatttac ggacaaatag
> atctgtagta
> 5941 tataaattag atattaaact tttgtaaaat tattgctaga attaatttga
> aaggacattt
> 6001 ttctatttat ttttttacac atgagacaag tgtattttag acatgaaaat
> aatttaaccc
> 6061 aaattgtttt taaaataatc tagtaattaa actgataatt tatgttaatc
> tagtaacttt
> 6121 cccattatta taatgataaa ttgttgagaa aatttacttt attttagtgt
> tactttgttc
> 6181 tagagtaaaa tcgaagaata cttagggagg gacatagggt cagtgccggc
> ttaacatgga
> 6241 gaggagggag tgcaacaacg agtggcccat aaagcaaaag ggacacatac
> aattctttcc
> 6301 ttttgtaaac ataaaaagaa aaagaaaaaa atatgtgcaa atataacaga
> aaattgcaaa
> 6361 tttttactaa aaagctcata tatatttgca ttccttttaa atataaggta
> aaaaaaaatt
> 6421 ctaaatttat tgggcccaaa ttatatgttg atatatttta atccaacaac
> tctaatacaa
> 6481 atattgattt attgggccaa atctcttttg taaaatgaga ttgttgtttt
> attttatttt
> 6541 aaatgatgtt tactaagtgt tttacttttg tacgaaaaca atttccaata
> tattaagggt
> 6601 ccaatttttt ttttgcccta ggacctagaa taagcttgag ccggcactgc
> agagggtcct
> 6661 aggatttttg tattttttac tttgtaagtg aatgccatag caagccaagg
> actgaagaag
> 6721 aacaacggaa aatatagaga atatgaattt gtgtgatgcg aagacgaaaa
> gaaattatag
> 6781 aaaatcaact gaaattgatg acgtcgaatt tgattgagga gaaaaaatag
> ctacaaaata
> 6841 agaggaagaa aaaggaaaat aaagaaaaga acgaagagaa tgagaaggag
> aagccgaaaa
> 6901 gggtctagag aagaggggtg ttttttcatg aagacaagat actacgaaag
> aaggaagatg
> 6961 aagggctagt tataagtaga tgtagatctc tgaatatata tatatatata
> tatatataaa
> 7021 gtgtctccct aaaccggaaa aaacgatggg ttttgatatg ctgaacgggg
> gacaaaaccc
> 7081 gagaaccgaa atcaatttaa aagttcaccg atcactatac aactctgcac
> ttattgaaac
> 7141 cgaaaaccaa aattctccgt ttagacggtt ttggttcaat acggttctta
> ttgaacgtca
> 7201 atcactctat ctactactat acttgaaaaa caaaattaaa ttttttgcct
> tgacttgatc
> 7261 cagagagatg ttacgcggcg gcgatgcatt aatcgataaa atcaaacaac
> atgccacgca
> 7321 ttgacttttg caagaagcca gcaactttat ataaaacaat cgatgataat
> tgtgatcgtt
> 7381 acaactatgt aataatgcat atatataagc tatgtattaa ctgtaaactt
> gatttaaata
> 7441 atactgatgg ggagtatata ccttgatgca tagaataaaa atgtaaaata
> cgtatgaatt
> 7501 actagcttag tggtagcctt gttacttgga ttagtttagc aagcaaatat
> ctagctctaa
> 7561 ttcacaagct aaccctaaaa gttggttgga catatacatc gtcaaatata
> tcgaagctat
> 7621 atatatatat ttaacatatt tgtttttgtt acattaaaac aaacaaaaca
> aaagaaaaaa
> 7681 gttttttttg tgctcctcct ttttaatatc ttttatgaaa atggctgact
> gttatggaaa
> 7741 atgatgtttt tattaatcta agtagtgcct ttcaccaaag aaaaaaaaaa
> accaaatata
> 7801 gtagacttta gtacggagat acgtgaacat aacttgttag attggttttc
> aacaaaagag
> 7861 tatagaatgg aaaatcgtta catactgact ctcatgaaca aacatatttt
> gcttaatgaa
> 7921 aagtcaactc gatctttatt atttatgagg ataaaaatca aataggctct
> gtcgacaaaa
> 7981 cgaaacaatc agactaccct ttagaatata tttaaaatta ccaaaaatat
> taatctttta
> 8041 ggaaattaca catgatgata ttttagcata tggcggatat ttacctccaa
> ctccaaatga
> 8101 ggatatttta gcatatggcg gtctttattc gtacgtacta ttttgcaaat
> cattttatat
> 8161 gattgtatat accatagatt ataatcacta ctcttagtcc cataatttgt
> aaataatagt
> 8221 aattcgtaga catagatgat caaagttctt tgtaatctta ctacatacac
> aaaaagtaat
> 8281 aaaacacaac atttttgttg tattaaatgt gcttgtccgt tgacaaaaaa
> gataaaagaa
> 8341 tagctttgtt tgtcctttct cgacaagttt gtattataat cgtctcacgt
> tcatttcaag
> 8401 attacatgca gaatttgtca aatgaagtct aaatcatcaa aagtaatttt
> tccttatttg
> 8461 ttctcacttg aatataaatt aacgaaatat gattcaccat aaattacacg
> aactatagga
> 8521 tacgggtact tatttattcc cttgcggtaa tacgaatagg tccaagattg
> gaaatctcag
> 8581 agttgtcatg aatactaagt taaaatatgt gcagaccata caaaacatag
> acgagcatag
> 8641 aaagagaagt tgatcaagtg atggaaaaag attaaaataa aatataaata
> tggatatacc
> 8701 cttaagattc cggagactat gcttctccga tctcgtctat aaatttcagc
> cgtctcagcc
> 8761 aacacaatca caaccaccac ctccctccct ctctctctct taatctttct
> gcccccacca
> 8821 ttagcgcaca acggtgagat tcgttagatg tttattatct atgcatccaa
> attcacatat
> 8881 agatagatag tacatatata gttgtttata tcaatagaaa cttttgtttc
> taaattgtaa
> 8941 tcgcttaaat tatttgattt atgtataggt ttaattataa atgttattct
> gttggttgta
> 9001 ttggtactaa actaaaataa tttagtagca tctttccaat attattataa
> aattatagtt
> 9061 aagatattta tttttacttc atgaagcagg aaagacaaga gaggcttaga
> tggctgaaca
> 9121 acaactagga gtgctaaagg cactcgatgt tgcgaagacg caactttatc
> atttcacggc
> 9181 gattgtcatc gccggtatgg gtttctttac cgatgcgtac gatctttttt
> gcgtgtcctt
> 9241 ggtaacaaag ctccttggcc gcatctacta cttcaatccg gagtcagcga
> agcctggctc
> 9301 acttccccct catgttgcgg ccgctgtcaa tggtgtggcc ctttgtggaa
> ccctttctgg
> 9361 tcaactcttc ttcggttggc tcggtgacaa actcggacgg aaaaaagtgt
> acggtcttac
> 9421 tttgatcatg atgatcttat gctctgtcgc ttctggcctc tcttttggca
> acgaagccaa
> 9481 gggtgtcatg accacccttt gcttcttcag gtacagtttt catccaatta
> caatattata
> 9541 tacacacatg attaaccaat aatctaataa cgaatgcaag ttttaaaagt
> tagtcacgct
> 9601 tcgaactgat ttaggtattt ttctttgaga aagttttttt atatataaac
> cattacgtag
> 9661 gttttggttg ggatttggta ttggaggtga ctacccactt tctgccacca
> tcatgtctga
> 9721 atacgcaaac aagaagaccc gtggggcttt catcgcagct gtcttcgcca
> tgcaaggtgt
> 9781 cggtatcttg gctggaggtt tcgtggcact cgcagtatct tctatattcg
> acaaaaagtt
> 9841 cccagctcca acatatgcag taaacagggc cctctcaacg cctcctcaag
> ttgattacat
> 9901 ttggcgaatc atcgtcatgt ttggtgcttt acccgcagct ttgacttact
> actggcgtat
> 9961 gaagatgcct gaaactgccc gttacaccgc tttggttgcc aagaacatca
> aacaagccac
> 10021 agccgacatg tccaaggtct tacaaacaga tatcgagctt gaggaaaggg
> tggaggatga
> 10081 cgtcaaagac cccagacaaa actatggctt gttctccaag gaattcctta
> gacgccatgg
> 10141 acttcatctc cttggaacta cctccacttg gtttttgctt gacattgcct
> tctacagcca
> 10201 aaacttgttc cagaaggata ttttctcggc catcggatgg atcccaaagg
> cagccaccat
> 10261 gaacgccacc catgaggttt tcaggattgc tagggctcag actcttatcg
> ccctttgcag
> 10321 tacagtccca ggctactggt tcacagttgc gtttattgat accattggaa
> ggtttaagat
> 10381 ccaactaaat ggatttttca tgatgaccgt gtttatgttt gccattgcct
> tcccttacaa
> 10441 ccactggatc aaaccagaaa accgtatcgg atttgtggtt atgtactctc
> ttactttctt
> 10501 cttcgccaat tttggtccaa atgcaaccac ttttattgtc cctgctgaga
> tattcccggc
> 10561 caggctaagg tcaacatgtc atggaatatc agccgcggct ggtaaggctg
> gagccatcat
> 10621 tggagccttc gggttcttat atgcggctca aaatcaagac aaggctaagg
> tggatgcagg
> 10681 atacccacca ggtatcggag ttaagaactc attgatcgtg cttggtgttc
> ttaacttcat
> 10741 cggtatgctc ttcaccttcc ttgtcccaga gcccaagggc aagtccctcg
> aagaactctc
> 10801 tggtgaagct gaagttagcc atgacgagaa ataatttact ttgtgatcaa
> atgtggagtt
> 10861 gtttgtggtt tgtttgattt ttttgtttct ttccaaattt tttttttcct
> ttccttgatg
> 10921 cagtaagaaa tgtttgattg tgtggaatac ttcagtctta ctgccgtgag
> tgcaaatctt
> 10981 gtaatccact tttttgtgtt ctaattaaca ttgtcaaata aagtttctta
> aactttgatt
> 11041 ctaactttcc aaacactaac gaactctctg ttgtgcgttt atgtttatca
> atttgaagca
> 11101 tgaaaatttg attgttcata tgtttgctat atactgagaa acaccaaaga
> atagttttta
> 11161 tggatttcga ttatctgatc aacacattag ttggttatgg tgttcaatgt
> tcagtgtctt
> 11221 gtcatcacta acgttatctc tttgccttat atcgacacat tcaagtgggc
> gtagttgtag
> 11281 accattagtc ttgtgctctg tttgtaaata acgctattgg ttagttagct
> ttctttttgg
> 11341 ttggtgtata tattcttttt gggttgaagc tctgtgtagc gtttagaaat
> gttaaaagtt
> 11401 cgatcccaaa atgtagcaag atttgaaatt tctttttgga ttgatgtaat
> gtatttaact
> 11461 ggcttcttat gaatcacggt gcttattgtt tgattaatgt gaactgaatt
> gttctgtgct
> 11521 tgagattcaa aaagctcaag aggatctaat actaaatagt ctcactaatg
> catatgtttg
> 11581 atttgtttca aatattgatt gttctctctg acgcatttgt ttgattattg
> tgcactacct
> 11641 gtttgggatg ggcattctat tggtctcact ataccaaatt accaactttg
> tgaaactcac
> 11701 cataacttgt gtgatccata aaatcttaga ttaattactg ttaagtttca
> tgaaatttta
> 11761 actcaaaaca atttggcaat aaatagattg acattgtatg tccaaaaacc
> aaactgagta
> 11821 tttaacaaaa ccaactattt ccgaccaatg aatgcgtcta aaatgtttgt
> ttccaacaaa
> 11881 tttctgatca ttgatttcgt cggaactaac acaaataata attcgcataa
> tcataataat
> 11941 tctcctaatc agttcataaa cttgaatgac aagttaattt actcatttta
> ccatgaccat
> 12001 taattcataa attgagtcac aaattaatat caagatttga ccatgtccct
> tatgcaagag
> 12061 ggggttggaa agcgatgggt ctatagtgtt acaattaatt ctctagtatt
> catataacca
> 12121 aaacacaatt ataatatttt cacattaaag ataaattaaa aacatccata
> taatgtttca
> 12181 catttaataa tatacatatt ttaaatattt tgttaacatt taaaattatg
> atttttctat
> 12241 catttttttt attttttaaa ctactttgaa tcatcatata atacataaca
> ctaattaaaa
> 12301 tctaattttt tctggatata ttgtgattcg gatgtttgaa aacagccata
> tattactcac
> 12361 ataatgaaat aaaattattt gtgttcaaag tctcacatca gctaaaactt
> tgtgtccaaa
> 12421 atctcataaa taagaccaaa ttgaacccaa agaaatatga gtgagtagga
> atcctaactt
> 12481 aacaaacatc caaatttaaa tatttgttca gtttaattcg gttctttagt
> caaaccgttt
> 12541 aattatacca gatatcataa attctaaact ttttaaaaaa ttaaaatatt
> ataattgatc
> 12601 tatttaaagt gtataaaaac ttcaaaatat tatcaacgtt taacttataa
> aaagtttaaa
> 12661 atatcacggt atgggttata tggtttgacg agtttgaatc ttcattaata
> taaatttaaa
> 12721 tatcattaac tcggtggtac aacatgggta agtcatcatt ttaatatttt
> gttaacacta
> 12781 gcaatattat aatgatatgt caagttaaat tgattcaatt atgattatgt
> attaaaacaa
> 12841 gatatataag tattagtttt ctaggtatct gcaatattag aaaccagata
> tccaaaagtc
> 12901 acggatctgg attgttaaag cacagttctg aatacttttc aaattctagg
> atatccggat
> 12961 ccattctacc aattacaatc ctgcagaagc cttgttggcc acacaatcga
> cacaagagtt
> 13021 agctagccaa aaagtgcctt caacttaaga agatgcaaac cggaaagaaa
> aaaacatatc
> 13081 tttggtccga aggaaatcat gttttattat caaatttaac caccaacaac
> tacaaaccaa
> 13141 atttacaaca acaacaacca aaaataaaaa cacatacaca caagtgatag
> cagcagacaa
> 13201 cacaaaacat aacaaaaaca gaagcttccc aaaattccga aattcaaaat
> cctctttaat
> 13261 ttctcatcat atagtagtcg agttacgttg gcatggtttc taatagttat
> tatgcggagt
> 13321 tttaaatctt catcagttgt attctttcga attttgcgaa ctcagaatcg
> actgcaaata
> 13381 aacatgttta attagatcaa atggttagag attccgagct tgccttgtaa
> catgacatga
> 13441 caacaatgat ttggctataa attacttgta agttactagt gagaaacata
> gcaaaccaat
> 13501 tttcaagtat accacagtgt tagttttgac taacattagg tctaattcgg
> tgaagtcaat
> 13561 actaatccaa agtttcatct atcaatgcga atagatttaa aattattgag
> gagcacaaac
> 13621 agattcaaaa tgttaaatca ttcaaaaaca tttagtaata gagcaaatta
> ttatgcattt
> 13681 accatatttc attttttgtg ctacagtata tccacaaatt aaaaagtgat
> gtgattaata
> 13741 cataccttca ctttaggata agggaagcta gttttagcac cacctctgct
> tccgaaactg
> 13801 aactttgatt tcttgtcatt agattttaag atctgaaaag agcaggtcaa
> atcctcagac
> 13861 acactcatca tcgcacctgc attgtcaaat tccccacagt aattcggcgc
> agagaatatc
> 13921 gttacgagct gcttattcgc aaagaactcg aatccatctt caacaacctg
> ttacaaaatc
> 13981 gttgcttgtg tcaaaaggaa acacgttaaa aatgtttctt tgggcacaag
> gaacaataaa
> 14041 caaacctggt gagccctaca aatgaggtca agatcgagtc ttttaagaaa
> tccagaaact
> 14101 atatctgatc caaaagtgta agaaactccg cgatcgttag gcccccaacc
> tctaacatct
> 14161 ttatcaggat cagaccacaa gagatcacag agtaaaccac gatcaggaat
> atccgttgga
> 14221 cgacgaatat ccctaatctg cctcaagctt agcagctccg gggagagccc
> accatgcata
> 14281 caaaaaatcc gctcatcgat gagtgcagcg acggggagac agttgaagca
> atcagtgaag
> 14341 attcgccaaa tcttgacact gaatctacgt ttacactcgt catagaagcc
> gtaaatacga
> 14401 ttgattgatg cactttcatg gtttcctctg agaaggaaga agttttcagg
> gaacttaatc
> 14461 ttgtaagcaa gtaaaagaca aatcgtttcg aggctttgct tgccgcgatc
> gacataatct
> 14521 ccaagaaaca agtagtttga attaggaggg tatccgccat gttcgaatag
> tctcaagaga
> 14581 tccggatatt gtccatgaat gtcccctgtt tattatttgt ttaaccaaaa
> gattacatag
> 14641 gagcacaatc tcagaaaaga gtcagagaga aacagagaga aacgtaccac
> atattttaac
> 14701 aggagcttca agttccaaga gatttggttg tctcaagaag atatctctag
> agacgaaaca
> 14761 gagctgtttg atctctgttt cagacaactg aacaatcttt cctggttttt
> ctctagcttc
> 14821 aagcaaccta ttgatcaccg agtttaaagt accaggatcc atttataaaa
> cctcaagaaa
> 14881 cagagcaaca atgagacaaa acaacaacaa cgcctagaag ctttataata
> tacaaaagct
> 14941 attgacaata tggaataaat ttaaaaagta tggagctttt atgttctttt
> atgcttgctc
> 15001 tttgagaaaa agaatggtga ttgtcaaatt caagaagggc tttataaagc
> cgcgtttaag
> 15061 aatatattct tcataccttt ttagcaaaag tcacatgtgt tcatacctac
> ctacattgtt
> 15121 ctaacttcaa ctaaatcata taataatcag attctagcta atttagtaac
> acattgtttg
> 15181 tgtgtgtgtt aagcttcaca ggattgaatc ctgtccggta cgtcatgatt
> caaatttaag
> 15241 atctttccgc cggtactttg agtgcgaaaa acgctctttc ttcttcttct
> agtatcgatg
> 15301 tttttggatt cgtccgcgtc atattaagca acttggctat ttacaaaaaa
> catattcttc
> 15361 ttcctttgta gccaaaagcc atgggtaaaa acctacccta attgttctaa
> cttcaactac
> 15421 atctaataac caaaaatgtt agctatattt tctcttttat ggtcaaaaca
> tattagctag
> 15481 tttagacact ttctttgtgt tgagcttttt aggcttgaat ctaatcgaat tc
> 15541
> //
>
--
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Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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