--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ARBH01000003.1.final	Wed Feb 07 06:22:58 2018 -0500
@@ -0,0 +1,339 @@
+LOCUS       ARBH01000003            3500 bp    DNA     linear   BCT 22-APR-2013
+DEFINITION  Amycolatopsis balhimycina FH 1894 strain DSM 44591
+            A3CEDRAFT_scaffold1.1_C3, whole genome shotgun sequence.
+ACCESSION   ARBH01000003
+VERSION     ARBH01000003.1
+DBLINK      BioProject:PRJNA165347
+            BioSample:SAMN02256403
+KEYWORDS    WGS; GSC:MIGS:2.1; IMPROVED_HIGH_QUALITY_DRAFT.
+SOURCE      Amycolatopsis balhimycina FH 1894
+  ORGANISM  Amycolatopsis balhimycina FH 1894
+            Bacteria; Actinobacteria; Pseudonocardiales; Pseudonocardiaceae;
+            Amycolatopsis.
+REFERENCE   1  (bases 1 to 3500)
+  AUTHORS   Klenk,H.-P., Huntemann,M., Han,J., Chen,A., Kyrpides,N.,
+            Mavromatis,K., Markowitz,V., Palaniappan,K., Ivanova,N.,
+            Schaumberg,A., Pati,A., Liolios,K., Nordberg,H.P., Cantor,M.N.,
+            Hua,S.X. and Woyke,T.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (16-APR-2013) DOE Joint Genome Institute, 2800 Mitchell
+            Drive, Walnut Creek, CA 94598-1698, USA
+COMMENT     URL -- http://www.jgi.doe.gov
+            JGI Project ID: 404843
+            Source DNA and Organism available from Hans-Peter  Klenk
+            (hpk@dsmz.de)
+            Source DNA available from Hans-Peter  Klenk (hpk@dsmz.de)
+            Organism available from Hans-Peter  Klenk (hpk@dsmz.de)
+            Contacts: Hans-Peter  Klenk (hpk@dsmz.de)
+            Tanja Woyke (microbe@cuba.jgi-psf.org)
+            Whole genome sequencing and draft assembly at JGI-PGF
+            Annotation by JGI-ORNL
+            The JGI and collaborators endorse the principles for the
+            distribution and use of large scale sequencing data adopted by the
+            larger genome sequencing community and urge users of this data to
+            follow them. It is our intention to publish the work of this
+            project in a timely fashion and we welcome collaborative
+            interaction on the project and analysis.
+            (http://www.genome.gov/page.cfm?pageID=10506376)
+            Full annotations are available from IMG.
+            v. 4.24
+            Phrap v. 4.24
+FEATURES             Location/Qualifiers
+     source          1..3500
+                     /culture_collection="DSM:44591"
+                     /db_xref="taxon:1089545"
+                     /mol_type="genomic DNA"
+                     /organism="Amycolatopsis balhimycina FH 1894"
+                     /strain="DSM 44591"
+     cluster         1..3500
+                     /contig_edge="True"
+                     /cutoff=20000
+                     /extension=20000
+                     /note="Cluster number: 1"
+                     /note="Detection rule(s) for this cluster type: t1pks:
+                     ((PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS &
+                     PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or
+                     (tra_KS & PKS_AT));"
+                     /note="Monomers prediction: (mal)"
+                     /note="Structure image: structures/genecluster1.png"
+                     /product="t1pks"
+     CDS             3..3500
+                     /aSProdPred="mal"
+                     /locus_tag="ctg1_1"
+                     /note="smCOG:
+                     SMCOG1001:short-chain_dehydrogenase/reductase_SDR (Score:
+                     64.2; E-value: 2.2e-19);"
+                     /sec_met="Type: t1pks"
+                     /sec_met="Domains detected: PP-binding (E-value: 1.3e-15,
+                     bitscore: 44.0, seeds: 164); PKS_AT (E-value: 8.7e-82,
+                     bitscore: 260.9, seeds: 1682); mod_KS (E-value: 9.4e-224,
+                     bitscore: 729.0, seeds: 217); adh_short (E-value: 7.1e-52,
+                     bitscore: 162.1, seeds: 230)"
+                     /sec_met="Kind: biosynthetic"
+                     /sec_met="NRPS/PKS subtype: Type I Modular PKS"
+                     /sec_met="NRPS/PKS Domain: PKS_KR (60-237). E-value:
+                     1.4e-53. Score: 173.1; Predicted KR activity: active;
+                     Predicted KR stereochemistry: A2;"
+                     /sec_met="NRPS/PKS Domain: ACP (341-412). E-value: 7.8e-31.
+                     Score: 97.8;"
+                     /sec_met="NRPS/PKS Domain: PKS_KS (434-858). E-value:
+                     3e-179. Score: 587.9;"
+                     /sec_met="NRPS/PKS Domain: PKS_AT (958-1166). E-value:
+                     4e-80. Score: 260.9; Substrate specificity predictions: mal
+                     (PKS signature), mal (Minowa), mal (consensus);"
+                     /translation="GGVLALPAELDRRGGDRLAAVLSGATGEDQLAIRAAGVFGRRVVR
+                     APAGDRAPARTWTPRGTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQL
+                     LAELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFS
+                     RTVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRA
+                     RGLRATALSWGIWADDRELGRVDPEQIVRSGLVFMAPELALEGLRRALDDDETALAVAD
+                     LDWERYYPVYTAVRPTLLFDELPEVRRLTEAAAATAATGAGGEFAARLRTLPEAERAHL
+                     LLELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISAGTGLTLPATMVFD
+                     HPTPRRLAGFLAATITGSGAVEQAPAVAGVDTGEPVAIIGMACRYPGGANTPERLWDLV
+                     VGGVDAISGFPADRNWPTDALYDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREAL
+                     SMDPQQRLLLETAWEAFERAGIDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMI
+                     TGSLGSILSGRLSYLFGLEGPAVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVM
+                     ATPGAFVGFSRQRALATDGRCKAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVV
+                     RGSATNQDGASNGMTAPSGPSQQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQ
+                     ALLATYGQDRERPLLLGSVKSNIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTH
+                     VDWSTGSIELPSGSVPWPESGRPRRAGISSFGLSGTNVHTILEQAPEPAAEAGPEPEPG
+                     LVPVPLSGRTEAALRAQAATVLDTLDDGVSPAVLGYSLASTRSAFEHRAVLLAEDHDEL
+                     RRGLAALAGDQPDGGVVRGTVTRGRTAFLFAGQGSQRAGMGRELYERHPVFADALDAVL
+                     GHFDLPRALRDVMWDDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGE
+                     IAAAHVAGVLSLADACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVN
+                     GPESVVLAGTEDAVLQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH
+                     "
+     aSDomain        183..713
+                     /asDomain_id="nrpspksdomains_ctg1_1_KR1"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
+                     /domain="PKS_KR"
+                     /evalue="1.40E-53"
+                     /label="ctg1_1_KR1"
+                     /locus_tag="ctg1_1"
+                     /score="173.1"
+                     /specificity="KR activity: active"
+                     /specificity="KR stereochemistry: A2"
+                     /translation="GTTLITGGTGTLAPHLARWLAEQGAEHIVLTSRTGAEAPKARQLL
+                     AELGETVEAVACDVTDKAALAALLARLRAEGRTVRNVVHTAAVIELHTLAETDLAAFSR
+                     TVHAKVVGARNLDELLDTDELDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRRAR
+                     GLRATALSWGIWAD"
+     CDS_motif       192..284
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0001"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="3.80E-15"
+                     /label="PKSI-KR_m1"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KR_m1"
+                     /note="NRPS/PKS Motif: PKSI-KR_m1 (e-value: 3.8e-15,
+                     bit-score: 48.4)"
+                     /score="48.4"
+                     /translation="LITGGTGTLAPHLARWLAEQGAEHIVLTSRT"
+     CDS_motif       555..665
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0002"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="1.60E-14"
+                     /label="PKSI-KR_m4"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KR_m4"
+                     /note="NRPS/PKS Motif: PKSI-KR_m4 (e-value: 1.6e-14,
+                     bit-score: 46.4)"
+                     /score="46.4"
+                     /translation="LDAFVLYSSTAGLWGTGAHAAYVAGNAYLHALAAHRR"
+     aSDomain        1026..1238
+                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom01"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
+                     /domain="ACP"
+                     /evalue="7.80E-31"
+                     /locus_tag="ctg1_1"
+                     /score="97.8"
+                     /translation="LELVRAEAAAVLGHASADALPEDRAFRDVGFDSVTAVDLRNRISA
+                     GTGLTLPATMVFDHPTPRRLAGFLAA"
+     aSDomain        1305..2576
+                     /asDomain_id="nrpspksdomains_ctg1_1_Xdom02"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
+                     /domain="PKS_KS"
+                     /evalue="3.00E-179"
+                     /locus_tag="ctg1_1"
+                     /score="587.9"
+                     /translation="VAIIGMACRYPGGANTPERLWDLVVGGVDAISGFPADRNWPTDAL
+                     YDPDPDAGGKTYSVQGGFLHEAAEFDPGFFGISPREALSMDPQQRLLLETAWEAFERAG
+                     IDPHTLRGSGTGTFIGASYQDYTAAVSGAVDNADGHMITGSLGSILSGRLSYLFGLEGP
+                     AVTLDTACSSSLVAIHLAAQSLRSGESSLALAGGVSVMATPGAFVGFSRQRALATDGRC
+                     KAYSDRADGMTLGEGVGLVLLEKLSDAQRNGHRILAVVRGSATNQDGASNGMTAPSGPS
+                     QQRVIRQALANARLSASEVDVIEGHGTGTALGDPIEAQALLATYGQDRERPLLLGSVKS
+                     NIGHTQMASGVAGVIKVVQALRHGLVPKTLHVDEPSTHVDWSTGSIELPSGSVPWPESG
+                     RPRRAGISSFGLSGTNVHTILEQAP"
+     CDS_motif       1788..1835
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0003"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="2.00E-06"
+                     /label="PKSI-KS_m3"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KS_m3"
+                     /note="NRPS/PKS Motif: PKSI-KS_m3 (e-value: 2e-06,
+                     bit-score: 19.7)"
+                     /score="19.7"
+                     /translation="GPAVTLDTACSSSLVA"
+     CDS_motif       2211..2255
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0004"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="1.90E-03"
+                     /label="PKSI-KS_m5"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KS_m5"
+                     /note="NRPS/PKS Motif: PKSI-KS_m5 (e-value: 0.0019,
+                     bit-score: 10.8)"
+                     /score="10.8"
+                     /translation="IEGHGTGTALGDPIE"
+     CDS_motif       2310..2354
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0005"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="1.10E-03"
+                     /label="PKSI-KS_m6"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-KS_m6"
+                     /note="NRPS/PKS Motif: PKSI-KS_m6 (e-value: 0.0011,
+                     bit-score: 11.5)"
+                     /score="11.5"
+                     /translation="GSVKSNIGHTQMASG"
+     CDS_motif       2874..2927
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0006"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="2.30E-06"
+                     /label="PKSI-AT-mM_m1"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-mM_m1"
+                     /note="NRPS/PKS Motif: PKSI-AT-mM_m1 (e-value: 2.3e-06,
+                     bit-score: 19.8)"
+                     /score="19.8"
+                     /translation="FLFAGQGSQRAGMGRELY"
+     aSDomain        2877..3500
+                     /asDomain_id="nrpspksdomains_ctg1_1_AT1"
+                     /database="nrpspksdomains.hmm"
+                     /detection="hmmscan"
+                     /domain="PKS_AT"
+                     /evalue="4.00E-80"
+                     /label="ctg1_1_AT1"
+                     /locus_tag="ctg1_1"
+                     /score="260.9"
+                     /specificity="PKS signature: mal"
+                     /specificity="Minowa: mal"
+                     /specificity="consensus: mal"
+                     /translation="LFAGQGSQRAGMGRELYERHPVFADALDAVLGHFDLPRALRDVMW
+                     DDDSTALDETGYTQPALFAFEVALFRLLESWGVTPDYLAGHSIGEIAAAHVAGVLSLAD
+                     ACALVAARGALMQALPSGGAMVSVRGSEADVAGHLGEDVAVAAVNGPESVVLAGTEDAV
+                     LQAAGRLEAAGHKVRRLRVSHAFHSPLMDPVLAEFATVAQGLTYH"
+     CDS_motif       3033..3095
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0007"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="3.20E-03"
+                     /label="PKSI-AT-mM_m2"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-mM_m2"
+                     /note="NRPS/PKS Motif: PKSI-AT-mM_m2 (e-value: 0.0032,
+                     bit-score: 10.9)"
+                     /score="10.9"
+                     /translation="DETGYTQPALFAFEVALFRLL"
+     CDS_motif       3105..3227
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0008"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="2.30E-22"
+                     /label="PKSI-AT-M_m3"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-M_m3"
+                     /note="NRPS/PKS Motif: PKSI-AT-M_m3 (e-value: 2.3e-22,
+                     bit-score: 71.3)"
+                     /score="71.3"
+                     /translation="GVTPDYLAGHSIGEIAAAHVAGVLSLADACALVAARGALMQ"
+     CDS_motif       3312..3350
+                     /aSTool="pksnrpsmotif"
+                     /asDomain_id="nrpspksmotif_ctg1_1_0009"
+                     /database="abmotifs"
+                     /detection="hmmscan"
+                     /evalue="4.70E-04"
+                     /label="PKSI-AT-M_m5"
+                     /locus_tag="ctg1_1"
+                     /motif="PKSI-AT-M_m5"
+                     /note="NRPS/PKS Motif: PKSI-AT-M_m5 (e-value: 0.00047,
+                     bit-score: 13.4)"
+                     /score="13.4"
+                     /translation="AAVNGPESVVLAG"
+ORIGIN
+        1 ggggcggcgt gctcgccctg cccgccgagc tggaccgccg cggcggcgac cggctggcgg
+       61 ctgtgctgtc cggcgccacc ggcgaagacc agctggccat ccgcgccgcc ggcgtgttcg
+      121 gccgccgcgt ggtgcgggcc ccggccggcg accgcgcgcc ggcgcggacc tggaccccgc
+      181 gcggcaccac gctgatcacc ggcggcaccg gcaccctggc cccgcacctg gcccgctggc
+      241 tggccgagca gggcgccgag cacatcgtgc tgaccagccg caccggcgcc gaggccccga
+      301 aggcccggca gctgctggcg gagctgggcg agaccgtcga ggcggtggcc tgcgacgtca
+      361 ccgacaaggc ggcgctggcc gccctgctgg cgcggttgcg ggccgagggc cggaccgtgc
+      421 ggaacgtggt gcacacggcc gccgtgatcg agctgcacac gctggccgag accgacctgg
+      481 ccgcgttctc ccggaccgtg cacgccaagg tggtgggcgc gcgcaacctg gacgagctgc
+      541 tcgacaccga cgagctcgat gcgttcgtgc tgtactcctc caccgccggc ctgtggggca
+      601 ccggcgcgca cgccgcctac gtggccggca acgcgtactt gcacgcgctg gcagcccacc
+      661 ggcgcgcccg ggggctgcgg gccaccgcgc tgtcgtgggg catctgggcc gacgaccgcg
+      721 aactcggccg ggtcgacccg gagcagatcg tgcgcagcgg cctggtgttc atggcgccgg
+      781 agctggcgct ggagggtctg cgccgggccc tggacgacga cgagaccgcg ctggccgtgg
+      841 ccgatctgga ctgggagcgg tactacccgg tctacaccgc cgtccggccg acgctgctgt
+      901 tcgacgagct gccggaggtg cggcggctca ccgaggccgc cgccgccacg gccgccaccg
+      961 gcgccggcgg cgagttcgcc gcccggctgc gcacgctgcc cgaggccgag cgcgcccacc
+     1021 tgctcctgga actggtccgg gccgaggccg cggccgtgct gggccacgcg tcggccgacg
+     1081 cgctgcccga ggaccgcgcc ttccgcgacg tcggcttcga ctcggtcacc gcggtcgacc
+     1141 tgcgcaaccg gatctccgcc ggcaccggcc tgaccctgcc cgccaccatg gtgttcgacc
+     1201 acccgacgcc gaggcggctg gccgggttcc tggccgccac gatcaccggc tcgggtgccg
+     1261 tcgagcaggc accggccgtg gccggcgtgg acaccggcga gcccgtcgcc atcatcggga
+     1321 tggcctgccg ctacccgggt ggcgcgaaca ccccggaacg gttgtgggac ctggtcgtgg
+     1381 gcggcgtgga cgccatctcc ggcttcccgg ccgaccgcaa ctggccgacc gacgcgctct
+     1441 acgacccgga cccggacgcc ggcggcaaga cctattcggt gcagggcggc ttcctgcacg
+     1501 aggcggccga gttcgacccg ggcttcttcg gcatctcgcc gcgggaggca ctgtccatgg
+     1561 atccgcagca gcgcctgctg ctggagacgg cgtgggaggc gttcgagcgg gccgggatcg
+     1621 acccgcacac gctgcggggc agcggcaccg gcaccttcat cggggccagc taccaggact
+     1681 acaccgcggc cgtgtccggc gcggtggaca acgccgacgg ccacatgatc accggctcgc
+     1741 tgggcagcat cctgtccggc cggctctcct acctgttcgg gctggagggc ccggcggtca
+     1801 ccctggacac cgcctgctcg tcgtcgctgg tcgccatcca cctggccgcg cagtcgctgc
+     1861 ggtcggggga gagcagcctg gcgctggccg gcggggtgag cgtgatggcg acgccggggg
+     1921 cgttcgtcgg cttctcgcgc cagcgcgcac tggccacgga cggccgttgc aaggcctact
+     1981 cggaccgggc cgacggcatg accctcggcg agggcgtcgg cctggtgctg ctggagaagc
+     2041 tgtccgacgc gcagcgcaac gggcaccgga tcctggcggt ggtccggggt tcggccacga
+     2101 accaggacgg cgcgtccaac ggcatgaccg cgcccagcgg cccgtcccag cagcgggtga
+     2161 tccggcaggc gctggccaac gcgcggctct cggcgtccga ggtggacgtg atcgagggcc
+     2221 acggcaccgg caccgcgctg ggcgacccga tcgaggccca ggccctgctg gccacctacg
+     2281 gccaggaccg ggaacggccg ctgctgctcg gctcggtgaa gtccaacatc ggccacaccc
+     2341 agatggcctc cggcgtggcc ggcgtgatca aggtggtgca ggcgctgcgg cacgggctgg
+     2401 tacccaagac gctgcacgtg gacgagccct ccacgcacgt cgactggagc accggctcga
+     2461 tcgagctgcc gtccggcagc gtgccgtggc cggagagcgg ccggccgcgc cgggccggta
+     2521 tctcgtcctt cgggctgagc ggcacgaacg tgcacaccat cctcgagcag gccccggaac
+     2581 cggccgccga agccggcccc gagccggagc ccggcctggt gccggtcccg ctgtccggcc
+     2641 ggacggaagc agcgctgcgc gctcaggccg ccaccgtgct ggacaccctg gacgacggcg
+     2701 tgtcgccggc cgtgctcggg tactcgctgg cctccacccg gtcggccttc gaacaccgtg
+     2761 cggtgctgct ggccgaggac cacgacgaac tgcggcgcgg cctggccgca ctggccggcg
+     2821 accagccgga cggcggcgtg gtgcggggca ccgtgacgcg gggccgcacg gcgttcctgt
+     2881 tcgccggcca gggcagccag cgggccggga tgggccgcga gctgtacgag cgccacccgg
+     2941 tgttcgccga cgcgctggac gcggtgctgg ggcacttcga cctgccccgt gcgctgcggg
+     3001 acgtgatgtg ggacgacgat tccacggccc tcgacgagac ggggtacacc cagccggcgt
+     3061 tgttcgcctt cgaggtggcg ttgttccggt tgctggagtc gtggggtgtg acgccggatt
+     3121 acctggccgg gcattcgatc ggtgagatcg ccgcggcgca cgtggccgga gtgttgtcgc
+     3181 tggccgatgc ctgtgcgttg gtcgctgcgc ggggtgcgct gatgcaggcg ctgccgtccg
+     3241 gcggggccat ggtttcggtg cgcggctccg aggccgacgt cgccgggcac ctcggcgagg
+     3301 acgtcgccgt cgcggcggtc aacgggcccg agtcggtggt gctggccggg accgaggacg
+     3361 cggtgctcca ggcggccggc cgcctggagg ccgccggcca caaggtccgc cgcctgcggg
+     3421 tcagccacgc cttccactcg cccttgatgg atcccgtgct ggccgagttc gcgacggtgg
+     3481 ctcagggcct gacctaccac
+//