[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
> //
>
--
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------