X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FJ03321.gb;fp=test%2Fjalview%2Fio%2FJ03321.gb;h=99729e45c40986cd94eaa39f1b9a96c2a6c43a13;hb=da62703518a88707b9144bc51e50d6af7093a7c7;hp=0000000000000000000000000000000000000000;hpb=8550acbddfcf94dbacaae9738a4b6d4f68b16b02;p=jalview.git diff --git a/test/jalview/io/J03321.gb b/test/jalview/io/J03321.gb new file mode 100644 index 0000000..99729e4 --- /dev/null +++ b/test/jalview/io/J03321.gb @@ -0,0 +1,258 @@ +LOCUS CH1L1CG 7502 bp DNA circular BCT 06-APR-2020 +DEFINITION Chlamydia trachomatis plasmid pCHL1, complete sequence. +ACCESSION J03321 +VERSION J03321.1 +DBLINK BioSample: SAMN14225621 +KEYWORDS . +SOURCE Chlamydia trachomatis + ORGANISM Chlamydia trachomatis + Bacteria; Chlamydiae; Chlamydiales; Chlamydiaceae; + Chlamydia/Chlamydophila group; Chlamydia. +REFERENCE 1 (bases 1 to 7502) + AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G. + TITLE Diversity of the Chlamydia trachomatis common plasmid in biovars + with different pathogenicity + JOURNAL Plasmid 23 (2), 149-154 (1990) + PUBMED 2194229 +REFERENCE 2 (bases 1 to 7502) + AUTHORS Comanducci,M., Ricci,S., Cevenini,R. and Ratti,G. + TITLE Direct Submission + JOURNAL Submitted (23-JUN-2010) Sclavo Research Centre, Siena, Italy +COMMENT Draft entry and computer-readable sequence kindly submitted by + G.Ratti, 28-MAR-1990. + ! CDS location split below (and this line added), for Jalview test purposes ! +FEATURES Location/Qualifiers + source 1..7502 + /organism="Chlamydia trachomatis" + /mol_type="genomic DNA" + /serotype="D" + /isolate="G0/86" + /isolation_source="trachoma" + /db_xref="taxon:813" + /plasmid="pCHL1" + CDS join(7022..7502, + 1..437) + /note="pGP7-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91567.1" + /translation="MGSMAFHKSRLFLTFGDASEIWLSTLSYLTRKNYASGINFLVSL + EILDLSETLIKAISLDHSESLFKIKSLDVFNGKVVSEASKQARAACYISFTKFLYRLT + KGYIKPAIPLKDFGNTTFFKIRDKIKTESISKQEWTVFFEALRIVNYRDYLIGKLIVQ + GIRKLDEILSLRTDDLFFASNQISFRIKKRQNKETKILITFPISLMEELQKYTCGRNG + RVFVSKIGIPVTTSQVAHNFRLAEFHSAMKIKITPRVLRASALIHLKQIGLKDEEIMR + ISCLSSRQSVCSYCSGEEVIPLVQTPTIL" + CDS complement(488..1480) + /note="pGP8-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91568.1" + /translation="MGKGILSLQQEMSLEYSEKSYQEVLKIRQESYWKRMKSFSLFEV + IMHWTASLNKHTCRSYRGSFLSLEKIGLLSLDMNLQEFSLLNHNLILDAIKKVSSAKT + SWTEGTKQVRAASYISLTRFLNRMTQGIVAIAQPSKQENSRTFFKTREIVKTDAMNSL + QTASFLKELKKINARDWLIAQTMLQGGKRSSEVLSLEISQICFQQATISFSQLKNRQT + EKRIIITYPQKFMHFLQEYIGQRRGFVFVTRSGKMVGLRQIARTFSQAGLQAAIPFKI + TPHVLRATAVTEYKRLGCSDSDIMKVTGHATAKMIFAYDKSSREDNASKKMALI" + CDS 1579..2934 + /note="pGP1-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91569.1" + /translation="MKTRSEIENRMQDIEYALLGKALIFEDSTEYILRQLANYEFKCS + HHKNIFIVFKHLKDNGLPITVDSAWEELLRRRIKDMDKSYLGLMLHDALSNDKLRSVS + HTVFLDDLSVCSAEENLSNFIFRSFNEYNENPLRRSPFLLLERIKGRLDSAIAKTFSI + RSARGRSIYDIFSQSEIGVLARIKKRRVAFSENQNSFFDGFPTGYKDIDDKGVILAKG + NFVIIAARPSIGKTALAIDMAINLAVTQQRRVGFLSLEMSAGQIVERIIANLTGISGE + KLQRGDLSKEELFRVEEAGETVRESHFYICSDSQYKLNLIANQIRLLRKEDRVDVIFI + DYLQLINSSVGENRQNEIADISRTLRGLASELNIPIVCLSQLSRKVEDRANKVPMLSD + LRDSGQIEQDADVILFINRKESSSNCEITVGKNRHGSVFSSVLHFDPKISKFSAIKKV + W" + CDS 2928..3992 + /note="pGP2-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91570.1" + /translation="MVNYSNCHFIKSPIHLENQKFGRRPGQSIKISPKLAQNGMVEVI + GLDFLSSHYHALAAIQRLLTATNYKGNTKGVVLSRESNSFQFEGWIPRIRFTKTEFLE + AYGVKRYKTSRNKYEFSGKEAETALEALYHLGHQPFLIVATRTRWTNGTQIVDRYQTL + SPIIRIYEGWEGLTDEENIDIDLTPFNSPPTRKHKGFVVEPCPILVDQIESYFVIKPA + NVYQEIKMRFPNASKYAYTFIDWVITAAAKKRRKLTKDNSWPENLLLNVNVKSLAYIL + RMNRYICTRNWKKIELAIDKCIEIAIQLGWLSRRKRIEFLDSSKLSKKEILYLNKERF + EEITKKSKEQMEQLEQESIN" + CDS 4054..4848 + /note="pGP3-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91571.1" + /translation="MGNSGFYLYNTENCVFADNIKVGQMTEPLKDQQIILGTTSTPVA + AKMTASDGISLTVSNNSSTNASITIGLDAEKAYQLILEKLGDQILDGIADTIVDSTVQ + DILDKIKTDPSLGLLKAFNNFPITNKIQCNGLFTPSNIETLLGGTEIGKFTVTPKSSG + SMFLVSADIIASRMEGGVVLALVREGDSKPCAISYGYSSGIPNLCSLRTSITNTGLTP + TTYSLRVGGLESGVVWVNALSNGNDILGITNTSNVSFLEVIPQTNA" + CDS 4918..5226 + /note="pGP4-D" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91572.1" + /translation="MQNKRKVRDDFIKIVKDVKKDFPELDLKIRVNKEKVTFLNSPLE + LYHKSVSLILGLLQQIENSLGLFPDSPVLEKLEDNSLKLKKALIMLILSRKDMFSKAE + " + CDS 5317..6048 + /note="pGP5-D (gtg start codon)" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91573.1" + /translation="MGCNLAQFLGKKVLLADLDPQSNLSSGLGASVRSDQKGLHDIVY + TSNDLKSIICETKKDSVDLIPASFSSEQFRELDIHRGPSNNLKLFLNEYCAPFYDICI + IDTPPSLGGLTKEAFVAGDKLIACLTPEPFSILGLQKIREFLSSVGKPEEEHILGIAL + SFWDDRNSTNQMYIDIIESIYKNKLFSTKIRRDISLSRSLLKEDSVANVYPNSRAAED + ILKLTHEIANILHIEYERDYSQRTT" + CDS 6045..6788 + /note="pGP6-D (gtg start codon)" + /codon_start=1 + /transl_table=11 + /product="hypothetical protein" + /protein_id="AAA91574.1" + /translation="MNKLKKEADVFFKKNQTAASLDFKKTLPSIELFSATLNSEESQS + LDRLFLSESQNYSDEEFYQEDILAVKLLTGQIKSIQKQHVLLLGEKIYNARKILSKDH + FSSTTFSSWIELVFRTKSSAYNALAYYELFINLPNQTLQKEFQSIPYKSAYILAARKG + DLKTKVDVIGKVCGMSNSSAIRVLDQFLPSSRNKDVRETIDKSDSEKNRQLSDFLIEI + LRIMCSGVSLSSYNENLLQQLFELFKQKS" + repeat_region 6857..6945 + /note="four tandem 22bp repeats" +ORIGIN + 1 ggatccgtaa gttagacgaa attttgtctt tgcgcacaga cgatctattt tttgcatcca + 61 atcagatttc ctttcgcatt aaaaaaagac agaataaaga aaccaaaatt ctaatcacat + 121 ttcctatcag cttaatggaa gagttgcaaa aatacacttg tgggagaaat gggagagtat + 181 ttgtttctaa aatagggatt cctgtaacaa caagtcaggt tgcgcataat tttaggcttg + 241 cagagttcca tagtgctatg aaaataaaaa ttactcccag agtacttcgt gcaagcgctt + 301 tgattcattt aaagcaaata ggattaaaag atgaggaaat catgcgtatt tcctgtcttt + 361 catcgagaca aagtgtgtgt tcttattgtt ctggggaaga ggtaattcct ctagtacaaa + 421 cacccacaat attgtgatat aattaaaatt atattcatat tctgttgcca gaaaaaacac + 481 ctttaggcta tattagagcc atcttctttg aagcgttgtc ttctcgagaa gatttatcgt + 541 acgcaaatat catctttgcg gttgcgtgtc ctgtgacctt cattatgtcg gagtctgagc + 601 accctaggcg tttgtactcc gtcacagcgg ttgctcgaag cacgtgcggg gttattttaa + 661 aagggattgc agcttgtagt cctgcttgag agaacgtgcg ggcgatttgc cttaacccca + 721 ccatttttcc ggagcgagtt acgaagacaa aacctcttcg ttgaccgatg tactcttgta + 781 gaaagtgcat aaacttctga ggataagtta taataatcct cttttctgtc tgacggttct + 841 taagctggga gaaagaaatg gtagcttgtt ggaaacaaat ctgactaatc tccaagctta + 901 agacttcaga ggagcgttta cctccttgga gcattgtctg ggcgatcaac caatcccggg + 961 cattgatttt ttttagctct tttaggaagg atgctgtttg caaactgttc atcgcatccg + 1021 tttttactat ttccctggtt ttaaaaaatg ttcgactatt ttcttgttta gaaggttgcg + 1081 ctatagcgac tattccttga gtcatcctgt ttaggaatct tgttaaggaa atatagcttg + 1141 ctgctcgaac ttgtttagta ccttcggtcc aagaagtctt ggcagaggaa acttttttaa + 1201 tcgcatctag gattagatta tgatttaaaa gggaaaactc ttgcagattc atatccaagg + 1261 acaatagacc aatcttttct aaagacaaaa aagatcctcg atatgatcta caagtatgtt + 1321 tgttgagtga tgcggtccaa tgcataataa cttcgaataa ggagaagctt ttcatgcgtt + 1381 tccaatagga ttcttggcga atttttaaaa cttcctgata agacttttca ctatattcta + 1441 acgacatttc ttgctgcaaa gataaaatcc ctttacccat gaaatccctc gtgatataac + 1501 ctatccgtaa aatgtcctga ttagtgaaat aatcaggttg ttaacaggat agcacgctcg + 1561 gtattttttt atataaacat gaaaactcgt tccgaaatag aaaatcgcat gcaagatatc + 1621 gagtatgcgt tgttaggtaa agctctgata tttgaagact ctactgagta tattctgagg + 1681 cagcttgcta attatgagtt taagtgttct catcataaaa acatattcat agtatttaaa + 1741 cacttaaaag acaatggatt acctataact gtagactcgg cttgggaaga gcttttgcgg + 1801 cgtcgtatca aagatatgga caaatcgtat ctcgggttaa tgttgcatga tgctttatca + 1861 aatgacaagc ttagatccgt ttctcatacg gttttcctcg atgatttgag cgtgtgtagc + 1921 gctgaagaaa atttgagtaa tttcattttc cgctcgttta atgagtacaa tgaaaatcca + 1981 ttgcgtagat ctccgtttct attgcttgag cgtataaagg gaaggcttga tagtgctata + 2041 gcaaagactt tttctattcg cagcgctaga ggccggtcta tttatgatat attctcacag + 2101 tcagaaattg gagtgctggc tcgtataaaa aaaagacgag tagcgttctc tgagaatcaa + 2161 aattctttct ttgatggctt cccaacagga tacaaggata ttgatgataa aggagttatc + 2221 ttagctaaag gtaatttcgt gattatagca gctagaccat ctatagggaa aacagcttta + 2281 gctatagaca tggcgataaa tcttgcggtt actcaacagc gtagagttgg tttcctatct + 2341 ctagaaatga gcgcaggtca aattgttgag cggattattg ctaatttaac aggaatatct + 2401 ggtgaaaaat tacaaagagg ggatctctct aaagaagaat tattccgagt agaagaagct + 2461 ggagaaacgg ttagagaatc acatttttat atctgcagtg atagtcagta taagcttaac + 2521 ttaatcgcga atcagatccg gttgctgaga aaagaagatc gagtagacgt aatatttatc + 2581 gattacttgc agttgatcaa ctcatcggtt ggagaaaatc gtcaaaatga aatagcagat + 2641 atatctagaa ccttaagagg tttagcctca gagctaaaca ttcctatagt ttgtttatcc + 2701 caactatcta gaaaagttga ggatagagca aataaagttc ccatgctttc agatttgcga + 2761 gacagcggtc aaatagagca agacgcagat gtgattttgt ttatcaatag gaaggaatcg + 2821 tcttctaatt gtgagataac tgttgggaaa aatagacatg gatcggtttt ctcttcggta + 2881 ttacatttcg atccaaaaat tagtaaattc tccgctatta aaaaagtatg gtaaattata + 2941 gtaactgcca cttcatcaaa agtcctatcc accttgaaaa tcagaagttt ggaagaagac + 3001 ctggtcaatc tattaagata tctcccaaat tggctcaaaa tgggatggta gaagttatag + 3061 gtcttgattt tctttcatct cattaccatg cattagcagc tatccaaaga ttactgaccg + 3121 caacgaatta caaggggaac acaaaagggg ttgttttatc cagagaatca aatagttttc + 3181 aatttgaagg atggatacca agaatccgtt ttacaaaaac tgaattctta gaggcttatg + 3241 gagttaagcg gtataaaaca tccagaaata agtatgagtt tagtggaaaa gaagctgaaa + 3301 ctgctttaga agccttatac catttaggac atcaaccgtt tttaatagtg gcaactagaa + 3361 ctcgatggac taatggaaca caaatagtag accgttacca aactctttct ccgatcatta + 3421 ggatttacga aggatgggaa ggtttaactg acgaagaaaa tatagatata gacttaacac + 3481 cttttaattc accacctaca cggaaacata aagggttcgt tgtagagcca tgtcctatct + 3541 tggtagatca aatagaatcc tactttgtaa tcaagcctgc aaatgtatac caagaaataa + 3601 aaatgcgttt cccaaatgca tcaaagtatg cttacacatt tatcgactgg gtgattacag + 3661 cagctgcgaa aaagagacga aaattaacta aggataattc ttggccagaa aacttgttat + 3721 taaacgttaa cgttaaaagt cttgcatata ttttaaggat gaatcggtac atctgtacaa + 3781 ggaactggaa aaaaatcgag ttagctatcg ataaatgtat agaaatcgcc attcagcttg + 3841 gctggttatc tagaagaaaa cgcattgaat ttctggattc ttctaaactc tctaaaaaag + 3901 aaattctata tctaaataaa gagcgctttg aagaaataac taagaaatct aaagaacaaa + 3961 tggaacaatt agaacaagaa tctattaatt aatagcaagc ttgaaactaa aaacctaatt + 4021 tatttaaagc tcaaaataaa aaagagtttt aaaatgggaa attctggttt ttatttgtat + 4081 aacactgaaa actgcgtctt tgctgataat atcaaagttg ggcaaatgac agagccgctc + 4141 aaggaccagc aaataatcct tgggacaaca tcaacacctg tcgcagccaa aatgacagct + 4201 tctgatggaa tatctttaac agtctccaat aattcatcaa ccaatgcttc tattacaatt + 4261 ggtttggatg cggaaaaagc ttaccagctt attctagaaa agttgggaga tcaaattctt + 4321 gatggaattg ctgatactat tgttgatagt acagtccaag atattttaga caaaatcaaa + 4381 acagaccctt ctctaggttt gttgaaagct tttaacaact ttccaatcac taataaaatt + 4441 caatgcaacg ggttattcac tcccagtaac attgaaactt tattaggagg aactgaaata + 4501 ggaaaattca cagtcacacc caaaagctct gggagcatgt tcttagtctc agcagatatt + 4561 attgcatcaa gaatggaagg cggcgttgtt ctagctttgg tacgagaagg tgattctaag + 4621 ccctgcgcga ttagttatgg atactcatca ggcattccta atttatgtag tctaagaacc + 4681 agtattacta atacaggatt gactccgaca acgtattcat tacgtgtagg cggtttagaa + 4741 agcggtgtgg tatgggttaa tgccctttct aatggcaatg atattttagg aataacaaat + 4801 acttctaatg tatctttttt agaggtaata cctcaaacaa acgcttaaac aatttttatt + 4861 ggatttttct tataggtttt atatttagag aaaacagttc gaattacggg gtttgttatg + 4921 caaaataaaa gaaaagtgag ggacgatttt attaaaattg ttaaagatgt gaaaaaagat + 4981 ttccccgaat tagacctaaa aatacgagta aacaaggaaa aagtaacttt cttaaattct + 5041 cccttagaac tctaccataa aagtgtctca ctaattctag gactgcttca acaaatagaa + 5101 aactctttag gattattccc agactctcct gttcttgaaa aattagagga taacagttta + 5161 aagctaaaaa aggctttgat tatgcttatc ttgtctagaa aagacatgtt ttccaaggct + 5221 gaatagacaa cttactctaa cgttggagtt gatttgcaca ccttagtttt ttgctctttt + 5281 aagggaggaa ctggaaaaac aacactttct ctaaacgtgg gatgcaactt ggcccaattt + 5341 ttagggaaaa aagtgttact tgctgaccta gacccgcaat ccaatttatc ttctggattg + 5401 ggggctagtg tcagaagtga ccaaaaaggc ttgcacgaca tagtatacac atcaaacgat + 5461 ttaaaatcaa tcatttgcga aacaaaaaaa gatagtgtgg acctaattcc tgcatcattt + 5521 tcatccgaac agtttagaga attggatatt catagaggac ctagtaacaa cttaaagtta + 5581 tttctgaatg agtactgcgc tcctttttat gacatctgca taatagacac tccacctagc + 5641 ctaggagggt taacgaaaga agcttttgtt gcaggagaca aattaattgc ttgtttaact + 5701 ccagaacctt tttctattct agggttacaa aagatacgtg aattcttaag ttcggtcgga + 5761 aaacctgaag aagaacacat tcttggaata gctttgtctt tttgggatga tcgtaactcg + 5821 actaaccaaa tgtatataga cattatcgag tctatttaca aaaacaagct tttttcaaca + 5881 aaaattcgtc gagatatttc tctcagccgt tctcttctta aagaagattc tgtagctaat + 5941 gtctatccaa attctagggc cgcagaagat attctgaagt taacgcatga aatagcaaat + 6001 attttgcata tcgaatatga acgagattac tctcagagga caacgtgaac aaactaaaaa + 6061 aagaagcgga tgtctttttt aaaaaaaatc aaactgccgc ttctctagat tttaagaaga + 6121 cgcttccctc cattgaacta ttctcagcaa ctttgaattc tgaggaaagt cagagtttgg + 6181 atcgattatt tttatcagag tcccaaaact attcggatga agaattttat caagaagaca + 6241 tcctagcggt aaaactgctt actggtcaga taaaatccat acagaagcaa cacgtacttc + 6301 ttttaggaga aaaaatctat aatgctagaa aaatcctgag taaggatcac ttctcctcaa + 6361 caactttttc atcttggata gagttagttt ttagaactaa gtcttctgct tacaatgctc + 6421 ttgcatatta cgagcttttt ataaacctcc ccaaccaaac tctacaaaaa gagtttcaat + 6481 cgatccccta taaatccgca tatattttgg ccgctagaaa aggcgattta aaaaccaagg + 6541 tcgatgtgat agggaaagta tgtggaatgt cgaactcatc ggcgataagg gtgttggatc + 6601 aatttcttcc ttcatctaga aacaaagacg ttagagaaac gatagataag tctgattcag + 6661 agaagaatcg ccaattatct gatttcttaa tagagatact tcgcatcatg tgttccggag + 6721 tttctttgtc ctcctataac gaaaatcttc tacaacagct ttttgaactt tttaagcaaa + 6781 agagctgatc ctccgtcagc tcatatatat atatctatta tatatatata tttagggatt + 6841 tgatttcacg agagagattt gcaactcttg gtggtagact ttgcaactct tggtggtaga + 6901 ctttgcaact cttggtggta gactttgcaa ctcttggtgg tagacttggt cataatggac + 6961 ttttgttaaa aaatttatta aaatcttaga gctccgattt tgaatagctt tggttaagaa + 7021 aatgggctcg atggctttcc ataaaagtag attgttttta acttttgggg acgcgtcgga + 7081 aatttggtta tctactttat cttatctaac tagaaaaaat tatgcgtctg ggattaactt + 7141 tcttgtttct ttagagattc tggatttatc ggaaaccttg ataaaggcta tttctcttga + 7201 ccacagcgaa tctttgttta aaatcaagtc tctagatgtt tttaatggaa aagttgtttc + 7261 agaggcatct aaacaggcta gagcggcatg ctacatatct ttcacaaagt ttttgtatag + 7321 attgaccaag ggatatatta aacccgctat tccattgaaa gattttggaa acactacatt + 7381 ttttaaaatc cgagacaaaa tcaaaacaga atcgatttct aagcaggaat ggacagtttt + 7441 ttttgaagcg ctccggatag tgaattatag agactattta atcggtaaat tgattgtaca + 7501 ag +// +