annotate test-data/CP008719.gbk @ 0:c917ef6807d7 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
author public-health-bioinformatics
date Tue, 12 Nov 2019 22:47:36 -0500
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c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
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1 LOCUS CP008719 2101 bp DNA circular BCT 05-JAN-2016
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2 DEFINITION Escherichia coli strain ST648 plasmid pEC648_5, complete sequence.
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3 ACCESSION CP008719
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4 VERSION CP008719.1
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5 DBLINK BioProject: PRJNA248607
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6 BioSample: SAMN02800875
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7 KEYWORDS .
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8 SOURCE Escherichia coli
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9 ORGANISM Escherichia coli
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10 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
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11 Enterobacteriaceae; Escherichia.
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12 REFERENCE 1 (bases 1 to 2101)
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13 AUTHORS Gao,Z.
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14 TITLE Complete Genome Sequence of Multiple Antibiotic Resistant
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15 Escherichia coli Isolated from Pleural Effusion of Patients with
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16 Empyema Thoracis
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17 JOURNAL Unpublished
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18 REFERENCE 2 (bases 1 to 2101)
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19 AUTHORS Gao,Z.
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20 TITLE Direct Submission
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21 JOURNAL Submitted (09-JUN-2014) Department of Respiratory and Critical care
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22 medicine, Peking University People's hospital, Xizhimen South
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23 Street, Beijing, Beijing 100101, China
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24 COMMENT Annotation was added by the NCBI Prokaryotic Genome Annotation
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25 Pipeline (released 2013). Information about the Pipeline can be
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26 found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
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27
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28 ##Genome-Assembly-Data-START##
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29 Assembly Method :: Newbler v. 2.3; Consed
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30 Genome Coverage :: 40x; 350x
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31 Sequencing Technology :: Roche 454 GS FLX; Illumina Hiseq 2000
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32 ##Genome-Assembly-Data-END##
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33
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34 ##Genome-Annotation-Data-START##
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35 Annotation Provider :: NCBI
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36 Annotation Date :: 06/13/2014 09:01:46
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37 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation
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38 Pipeline
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39 Annotation Method :: Best-placed reference protein set;
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40 GeneMarkS+
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41 Annotation Software revision :: 2.6 (rev. 437579)
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42 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;
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43 repeat_region
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44 Genes :: 4,807
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45 CDS :: 4,578
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46 Pseudo Genes :: 132
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47 CRISPR Arrays :: 2
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48 rRNAs :: 21 (5S, 16S, 23S)
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49 tRNAs :: 72
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50 ncRNA :: 4
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51 Frameshifted Genes :: 116
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52 ##Genome-Annotation-Data-END##
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53 FEATURES Location/Qualifiers
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54 source 1..2101
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55 /organism="Escherichia coli"
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56 /mol_type="genomic DNA"
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57 /strain="ST648"
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58 /db_xref="taxon:562"
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59 /plasmid="pEC648_5"
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60 gene join(1882..2101,1..47)
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61 /locus_tag="FH07_00765"
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62 CDS join(1882..2101,1..47)
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63 /locus_tag="FH07_00765"
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64 /inference="EXISTENCE: similar to AA
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65 sequence:RefSeq:WP_001024536.1"
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66 /note="Derived by automated computational analysis using
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67 gene prediction method: Protein Homology."
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68 /codon_start=1
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69 /transl_table=11
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70 /product="hypothetical protein"
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71 /protein_id="ALV71377.1"
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72 /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTF
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73 GFHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
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74 gene 913..1878
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75 /locus_tag="FH07_00775"
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76 CDS 913..1878
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77 /locus_tag="FH07_00775"
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78 /inference="EXISTENCE: similar to AA
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
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diff changeset
79 sequence:RefSeq:WP_012421200.1"
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
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diff changeset
80 /note="Derived by automated computational analysis using
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
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diff changeset
81 gene prediction method: Protein Homology."
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
82 /codon_start=1
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
83 /transl_table=11
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
84 /product="Replication protein"
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
85 /protein_id="ALV71376.1"
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
86 /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRM
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
87 ASCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIV
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
88 VDYPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRG
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
89 KDGSAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGE
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
90 VVANVAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQL
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
91 DRETNEDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
92 ORIGIN
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
93 1 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
94 61 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
95 121 cctgcattat cctcagcatt atcctcagca ttatcctcag ccttgccaac tcgacaccaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
96 181 tgcaggatag acaatccgat gtcaaatgtt aacactctgc gagtggtaca ttttccccgg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
97 241 attatcgtcc tgagcctgcc gctggctctc tttctaccgc ctcgctttgc tcgttgctca
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
98 301 acgcctcaca gacacggatt aaaatccgca tccgttcacc gttttttaaa gtccgttaaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
99 361 agcatgatgc catctccgag agttaatctc gtcaaatgct aaatcgtggg ggtccccttt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
100 421 ggggttccga tttagtgatt gacgacacca ccgattaaaa aacttatgcg gggtggatgg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
101 481 tttcacgaag tgaggccatc cacctgtaag acagggtttt gtttttattc cctgttttgg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
102 541 tgatcgggtg tgtggaaaag gttggggtaa gccgttcggg ggtgcttgtt ttggggggtt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
103 601 aaaattgtgg ttattttttg cgcaattctc gcgcgtgatc cttgtattta tacttaaggg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
104 661 ataaatggcg gatatgaaat agtggtttag cccagtaatg acgaggcttt gagtgggttt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
105 721 tgacaggtca aagaaaatgg agcagaattg aggcgttttt aatcggcgtt ggggagtgcg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
106 781 tcaacactcc ccaacatttc gaatgtgtca cctcagcggc aaactctggt gacatgtact
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
107 841 ggctcgcaat gcacaggtac gtgatgaata taccacatca aatcacagcc tgcccagatc
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
108 901 ggagcaggct taatgtcaga agataaattc ctttcggact acagcccccg tgatgcagtt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
109 961 tgggataccc agcgcacgct taccgattct gtcgggggta tctaccagac tgctgctgaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
110 1021 ttcgagcgct atgcactccg tatggcctcc tgtagcggtt tgttacgttt tggttggtct
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
111 1081 accatcatgg aaaccggaga aacgcgccta cggcttcgta gtgcgcaatt ttgccgtgtc
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
112 1141 cgtcattgcc ctgtctgcca gtggagaaga accctcatgt ggcaagcccg tttttatcag
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
113 1201 gctctaccga aaatcgttgt ggattacccg tcttcccgat ggttgtttct gacgttaact
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
114 1261 gtcaggaact gcgagatagg tgaacttgga acagtcctta cagcaatgaa tgcggcgttt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
115 1321 aagcgaatgg aaaagcgaaa ggagctatca cctgttcagg ggtggatcag ggctacggag
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
116 1381 gtgacgcgag gtaaggatgg cagcgcacat ccgcattttc actgtctgct gatggtgcaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
117 1441 ccttcttggt ttaaagggaa gaactacgtt aagcacgaac gttgggtaga actctggcgc
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
118 1501 gattgcttgc gggtgaacta tgagccgaat atcgatattc gggcagtaaa aactaagaca
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
119 1561 ggtgaggttg tggccaacgt tgccgagcaa ctgcaaagcg cggttgctga aacgctgaaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
120 1621 tactccgtta aaccggaaga tatggcaaac gatcctgagt ggtttcttga gctgacgcgg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
121 1681 cagcttcaca agcgccgttt tatctcgacc ggtggggcgc taaaaaacgt cctccagttg
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
122 1741 gatcgagaaa ccaatgagga tcttgtcatt gccgacgatg taggggatgg cactgatgac
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
123 1801 gggaagcgga cggcgtttgt ctgggattca ggtaaacggc gttacaaacg cgcccctgag
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
124 1861 aaggataaat cggattaacg tatgaatatt aatattgaat acctgaatgg aaataagact
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
125 1921 attggtttat tttttttaag aagtgaagcg gtgattcctg acaggtttaa aaaccttatt
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
126 1981 ttgcttattg atggattaag ttttggcaca tttggttttc atccgcacga aggttttgag
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
127 2041 gatgaattaa ttttatatat tcagaaaaca aacgagaggg taaaaactct ttttgtgaaa
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
128 2101 a
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
parents:
diff changeset
129 //
c917ef6807d7 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/match_plasmid_to_reference commit 0f3fff91eb329adf437224eb8f7449853083b01e"
public-health-bioinformatics
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diff changeset
130