Mercurial > repos > cstrittmatter > ss2v110
changeset 10:e6437d423693 draft
planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty
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--- a/LICENSE Thu Apr 30 21:47:42 2020 -0400 +++ b/LICENSE Fri May 01 13:30:43 2020 -0400 @@ -1,21 +1,339 @@ -MIT License +GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., <http://fsf.org/> + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Lesser General Public License instead.) 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--- a/README.md Thu Apr 30 21:47:42 2020 -0400 +++ b/README.md Fri May 01 13:30:43 2020 -0400 @@ -1,51 +1,117 @@ -[](https://zenodo.org/badge/latestdoi/97020646) +# SeqSero2 v1.1.1 +Salmonella serotype prediction from genome sequencing data. + +Online version: http://www.denglab.info/SeqSero2 + +# Introduction +SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies -# SalmID -Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia). +# Dependencies +SeqSero2 has three workflows: + +(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). -## Requirements: -Python 3 +Allele micro-assembly workflow depends on: + +1. Python 3; + +2. Biopython 1.73; + +3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); -## Installation: -The easy way with homebrew ([Linux](http://linuxbrew.sh/) or [MacOS](https://brew.sh/)): -``` -brew install brewsci/bio/salmid -``` -Big thanks to [Torsten Seemann](https://tseemann.github.io/) for including this in homebrew! +4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + +5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + +6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + +7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + +8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); -Alternatively download from GitHub: +9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + +(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. -```bash -git clone https://github.com/hcdenbakker/SalmID.git -``` +Raw reads k-mer workflow (originally SeqSeroK) depends on: -build a wheel using [poetry](https://poetry.eustace.io/): +1. Python 3; +2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + +(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow -```bash -cd SalmID -poetry build +# Installation +### Conda +To install the latest SeqSero2 Conda package (recommended): +``` +conda install -c bioconda seqsero2=1.1.1 ``` - -and install using `pip` - -```bash -pip install dist/salmid*.whl +### Git +To install the SeqSero2 git repository locally: ``` - -To execute: +git clone https://github.com/denglab/SeqSero2.git +cd SeqSero2 +python3 -m pip install --user . ``` -SalmID.py -e .fastq.gz -``` -This will perform a SalmID run on all fastq.gz files in the current directory. -``` -SalmID.py -i your_fastq_gz.fastq.gz -``` -This will perform a SalmID run on an individual file (i.e., your_fastq_gz.fastq.gz) -``` -SalmID.py -d directory_with_data -e _1.fastq.gz -``` -This will perform a SalmID run on all files in directory 'directory_with_data' with extension '_1.fastq.gz' +### Other options +Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ +https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ +https://github.com/denglab/SeqSero2/issues/13 + + +# Executing the code +Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i <file> (/path/to/input/file) + + -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) -## Todo's and thoughts for future releases: -- Provide coverage estimates for genomes in sample based on kmer frequencies -- Write code to use SalmID on long read (minion, pacbio) platforms + -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n <string> (optional, to specify a sample name in the report output) + + -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check <flag> (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + +# Examples +Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + +K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + +# Output +Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + +# Citation +Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. +SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. +**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/PKG-INFO Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,132 @@ +Metadata-Version: 1.1 +Name: SeqSero2 +Version: 1.1.1 +Summary: Salmonella serotyping +Home-page: https://github.com/denglab/SeqSero2/ +Author: Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng +Author-email: zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu +License: GPLv2 +Description: # SeqSero2 v1.1.1 + Salmonella serotype prediction from genome sequencing data. + + Online version: http://www.denglab.info/SeqSero2 + + # Introduction + SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + + # Dependencies + SeqSero2 has three workflows: + + (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + + Allele micro-assembly workflow depends on: + + 1. Python 3; + + 2. Biopython 1.73; + + 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + + 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + + 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + + 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + + 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + + 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + + 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + + (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + + Raw reads k-mer workflow (originally SeqSeroK) depends on: + + 1. Python 3; + 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + + (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + + # Installation + ### Conda + To install the latest SeqSero2 Conda package (recommended): + ``` + conda install -c bioconda seqsero2=1.1.1 + ``` + ### Git + To install the SeqSero2 git repository locally: + ``` + git clone https://github.com/denglab/SeqSero2.git + cd SeqSero2 + python3 -m pip install --user . + ``` + ### Other options + Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ + https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ + https://github.com/denglab/SeqSero2/issues/13 + + + # Executing the code + Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i <file> (/path/to/input/file) + + -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n <string> (optional, to specify a sample name in the report output) + + -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check <flag> (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + + # Examples + Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + + K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + + # Output + Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + + # Citation + Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. + SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. + **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + + Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. + Salmonella serotype determination utilizing high-throughput genome sequencing data. + **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) + +Keywords: Salmonella serotyping bioinformatics WGS +Platform: UNKNOWN +Classifier: Development Status :: 3 - Alpha +Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) +Classifier: Programming Language :: Python :: 3 +Classifier: Topic :: Text Processing :: Linguistic
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/SOURCES.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,19 @@ +LICENSE +MANIFEST.in +README.md +setup.py +version.py +SeqSero2.egg-info/PKG-INFO +SeqSero2.egg-info/SOURCES.txt +SeqSero2.egg-info/dependency_links.txt +SeqSero2.egg-info/not-zip-safe +SeqSero2.egg-info/requires.txt +SeqSero2.egg-info/top_level.txt +bin/Initial_Conditions.py +bin/SeqSero2_package.py +bin/SeqSero2_update_kmer_database.py +bin/deinterleave_fastq.sh +seqsero2_db/H_and_O_and_specific_genes.fasta +seqsero2_db/antigens.pickle +seqsero2_db/invA_mers_dict +seqsero2_db/special.pickle \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/dependency_links.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/not-zip-safe Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/requires.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +biopython==1.73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SeqSero2.egg-info/top_level.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- a/SeqSero2_package.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1473 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import time -import random -import os -import subprocess -import gzip -import io -import pickle -import argparse -import itertools -import math -from distutils.version import LooseVersion -from distutils.spawn import find_executable - -try: - from .version import SeqSero2_version -except Exception: #ImportError - from version import SeqSero2_version - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.0.2')#add "-m <data_type>" in future - parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### ed_SL_05282019: add 'type=os.path.abspath' to generate absolute path of input data. - parser.add_argument("-t",choices=['1','2','3','4','5','6'],help="<int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") - parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") - parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") - parser.add_argument("-m",choices=['k','a'],default="a",help="<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") - parser.add_argument("-d",help="<string>: output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") - parser.add_argument("-c",action="store_true",help="<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") - parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies") - parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) - return parser.parse_args() - -### ed_SL_05282019: check paths of dependencies -check_dependencies = parse_args().check -dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] -if check_dependencies: - for item in dependencies: - ext_path = find_executable(item) - if ext_path is not None: - print ("Using "+item+" - "+ext_path) - else: - print ("ERROR: can not find "+item+" in PATH") - sys.exit() -### end of --check - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - - -def multifasta_single_string(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') - if (len(line.strip()) > 0) and (line.strip()[0] != '>') - ] - return ''.join(multifasta_list) - - -def chunk_a_long_sequence(long_sequence, chunk_size=60): - chunk_list = [] - steps = len(long_sequence) // 60 #how many chunks - for i in range(steps): - chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) - chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) - return chunk_list - - -def target_multifasta_kmerizer(multifasta, k, kmerDict): - forward_length = 300 #if find the target, put forward 300 bases - reverse_length = 2200 #if find the target, put backward 2200 bases - chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences - target_mers = [] - long_single_string = multifasta_single_string(multifasta) - multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) - unit_length = len(multifasta_list[0]) - forward_lines = int(forward_length / unit_length) + 1 - reverse_lines = int(forward_length / unit_length) + 1 - start_num = 0 - end_num = 0 - for i in range(len(multifasta_list)): - if i not in range(start_num, end_num): #avoid computational repetition - line = multifasta_list[i] - start = int((len(line) - k) // 2) - s1 = line[start:k + start] - if s1 in kmerDict: #detect it is a potential read or not (use the middle part) - if i - forward_lines >= 0: - start_num = i - forward_lines - else: - start_num = 0 - if i + reverse_lines <= len(multifasta_list) - 1: - end_num = i + reverse_lines - else: - end_num = len(multifasta_list) - 1 - target_list = [ - x.strip() for x in multifasta_list[start_num:end_num] - ] - target_line = "".join(target_list) - target_mers += [ - k1 for k1 in createKmerDict_reads([str(target_line)], k) - ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) - else: - pass - return set(target_mers) - - -def target_read_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = [] - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - start = int((len(line) - k) // 2) - if i % 4 == 2: - if file.endswith(".gz"): - s1 = line[start:k + start].decode() - line = line.decode() - else: - s1 = line[start:k + start] - if s1 in kmerDict: #detect it is a potential read or not (use the middle part) - n_reads += 1 - total_coverage += len(line) - target_mers += [ - k1 for k1 in createKmerDict_reads([str(line)], k) - ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) - i += 1 - if total_coverage >= 4000000: - break - return set(target_mers) - - -def minion_fasta_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = {} - for line in open(file): - if i % 2 == 0: - for kmer, rc_kmer in kmers(line.strip().upper(), k): - if (kmer in kmerDict) or (rc_kmer in kmerDict): - if kmer in target_mers: - target_mers[kmer] += 1 - else: - target_mers[kmer] = 1 - if rc_kmer in target_mers: - target_mers[rc_kmer] += 1 - else: - target_mers[rc_kmer] = 1 - i += 1 - return set([h for h in target_mers]) - - -def minion_fastq_kmerizer(file, k, kmerDict): - i = 1 - n_reads = 0 - total_coverage = 0 - target_mers = {} - for line in open(file): - if i % 4 == 2: - for kmer, rc_kmer in kmers(line.strip().upper(), k): - if (kmer in kmerDict) or (rc_kmer in kmerDict): - if kmer in target_mers: - target_mers[kmer] += 1 - else: - target_mers[kmer] = 1 - if rc_kmer in target_mers: - target_mers[rc_kmer] += 1 - else: - target_mers[rc_kmer] = 1 - i += 1 - return set([h for h in target_mers]) - - -def multifasta_single_string2(multifasta): - single_string = '' - with open(multifasta, 'r') as f: - for line in f: - if line.strip()[0] == '>': - pass - else: - single_string += line.strip() - return single_string - - -def kmers(seq, k): - rev_comp = reverse_complement(seq) - for start in range(1, len(seq) - k + 1): - yield seq[start:start + k], rev_comp[-(start + k):-start] - - -def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) - return lib_dict - - -def Combine(b, c): - fliC_combinations = [] - fliC_combinations.append(",".join(c)) - temp_combinations = [] - for i in range(len(b)): - for x in itertools.combinations(b, i + 1): - temp_combinations.append(",".join(x)) - for x in temp_combinations: - temp = [] - for y in c: - temp.append(y) - temp.append(x) - temp = ",".join(temp) - temp = temp.split(",") - temp.sort() - temp = ",".join(temp) - fliC_combinations.append(temp) - return fliC_combinations - - -def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): - #like test_output_06012017.txt - #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) - from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict - rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] - rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to - seronames = [] - seronames_none_subspecies=[] - for i in range(len(phase1)): - fliC_combine = [] - fljB_combine = [] - if phaseO[i] == Otype: # no VII in KW, but it's there - ### for fliC, detect every possible combinations to avoid the effect of "[" - if phase1[i].count("[") == 0: - fliC_combine.append(phase1[i]) - elif phase1[i].count("[") >= 1: - c = [] - b = [] - if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( - "[") == 1: - content = phase1[i].replace("[", "").replace("]", "") - fliC_combine.append(content) - fliC_combine.append("-") - else: - for x in phase1[i].split(","): - if "[" in x: - b.append(x.replace("[", "").replace("]", "")) - else: - c.append(x) - fliC_combine = Combine( - b, c - ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t - ### end of fliC "[" detect - ### for fljB, detect every possible combinations to avoid the effect of "[" - if phase2[i].count("[") == 0: - fljB_combine.append(phase2[i]) - elif phase2[i].count("[") >= 1: - d = [] - e = [] - if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( - "[") == 1: - content = phase2[i].replace("[", "").replace("]", "") - fljB_combine.append(content) - fljB_combine.append("-") - else: - for x in phase2[i].split(","): - if "[" in x: - d.append(x.replace("[", "").replace("]", "")) - else: - e.append(x) - fljB_combine = Combine(d, e) - ### end of fljB "[" detect - new_fliC = fliC.split( - "," - ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings - new_fliC.sort() - new_fliC = ",".join(new_fliC) - new_fljB = fljB.split(",") - new_fljB.sort() - new_fljB = ",".join(new_fljB) - if (new_fliC in fliC_combine - or fliC in fliC_combine) and (new_fljB in fljB_combine - or fljB in fljB_combine): - ######start, remove_list,rename_dict, added on 11/11/2018 - if sero[i] not in remove_list: - temp_sero=sero[i] - if temp_sero in rename_dict: - temp_sero=rename_dict[temp_sero] #rename if in the rename list - if temp_sero not in seronames:#the new sero may already included, if yes, then not consider - if subs[i] == subspecies: - seronames.append(temp_sero) - seronames_none_subspecies.append(temp_sero) - else: - pass - else: - pass - ######end, added on 11/11/2018 - #analyze seronames - subspecies_pointer="" - if len(seronames) == 0 and len(seronames_none_subspecies)!=0: - seronames=seronames_none_subspecies - subspecies_pointer="1" - if len(seronames) == 0: - seronames = [ - "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" - ] - star = "" - star_line = "" - if len(seronames) > 1: #there are two possible predictions for serotypes - star = "*" - #changed 04072019 - #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" - if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: - star="*" - star_line=" The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme." + star_line - #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line - if Otype=="": - Otype="-" - predict_form = Otype + ":" + fliC + ":" + fljB - predict_sero = (" or ").join(seronames) - ###special test for Enteritidis - if predict_form == "9:g,m:-": - sdf = "-" - for x in special_gene_list: - if x.startswith("sdf"): - sdf = "+" - #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" - star_line=" sdf gene detected." # ed_SL_04152019: new output format - #predict_form = predict_form + " Sdf prediction:" + sdf - predict_form = predict_form #changed 04072019 - if sdf == "-": - star = "*" - #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" - star_line=" sdf gene not detected." # ed_SL_04152019: new output format - #changed in 04072019, for new output - #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" - #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement - predict_sero = "Gallinarum or Enteritidis" # ed_SL_04152019: new output format - ###end of special test for Enteritidis - elif predict_form == "4:i:-": - predict_sero = "I 4,[5],12:i:-" # ed_SL_09242019: change serotype name - elif predict_form == "4:r:-": - predict_sero = "4:r:-" - elif predict_form == "4:b:-": # ed_SL_09272019: change for new output format - predict_sero = "N/A (4:b:-)" - #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo - #predict_sero = "Newport" - #star = "*" - #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." - claim = " The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" - if "N/A" in predict_sero: - claim = "" - #special test for Typhimurium - if "Typhimurium" in predict_sero or predict_form == "4:i:-": - normal = 0 - mutation = 0 - for x in special_gene_list: - if "oafA-O-4_full" in x: - normal = float(special_gene_list[x]) - elif "oafA-O-4_5-" in x: - mutation = float(special_gene_list[x]) - if normal > mutation: - pass - elif normal < mutation: - #predict_sero = predict_sero.strip() + "(O5-)" - predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 - star = "*" - #star_line = "Detected the deletion of O5-." - star_line = " Detected a deletion that causes O5- variant of Typhimurium." # ed_SL_04152019: new output format - else: - pass - #special test for Paratyphi B - if "Paratyphi B" in predict_sero or predict_form == "4:b:-": - normal = 0 - mutation = 0 - for x in special_gene_list: - if "gntR-family-regulatory-protein_dt-positive" in x: - normal = float(special_gene_list[x]) - elif "gntR-family-regulatory-protein_dt-negative" in x: - mutation = float(special_gene_list[x]) - #print(normal,mutation) - if normal > mutation: - #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 - predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() # ed_SL_04152019: new output format - star = "*" - #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." - star_line = " The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " # ed_SL_04152019: new output format - elif normal < mutation: - #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 - predict_sero = predict_sero.strip() - star = "*" - #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." - star_line = " Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B." # ed_SL_04152019: new output format - else: - star = "*" - #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." - star_line = " " ## ed_SL_05152019: do not report this situation. - #special test for O13,22 and O13,23 - if Otype=="13": - #ex_dir = os.path.dirname(os.path.realpath(__file__)) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 - f = open(ex_dir + '/special.pickle', 'rb') - special = pickle.load(f) - O22_O23=special['O22_O23'] - if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze - O22_score=0 - O23_score=0 - for x in special_gene_list: - if "O:22" in x: - O22_score = O22_score+float(special_gene_list[x]) - elif "O:23" in x: - O23_score = O23_score+float(special_gene_list[x]) - #print(O22_score,O23_score) - for z in O22_O23[0]: - if predict_sero.split(" or ")[0] in z: - if O22_score > O23_score: - star = "*" - #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 - predict_sero = z[0] - elif O22_score < O23_score: - star = "*" - #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 - predict_sero = z[1] - else: - star = "*" - #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 - if " or " in predict_sero: - star_line = star_line + " The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" - #special test for O6,8 - #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list - #for x in merge_O68_list: - # if x in predict_sero: - # predict_sero=x - # star="" - # star_line="" - #special test for Montevideo; most of them are monophasic - #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list - #star="*" - #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." - return predict_form, predict_sero, star, star_line, claim -### End of SeqSero Kmer part - -### Begin of SeqSero2 allele prediction and output -def xml_parse_score_comparision_seqsero(xmlfile): - #used to do seqsero xml analysis - from Bio.Blast import NCBIXML - handle=open(xmlfile) - handle=NCBIXML.parse(handle) - handle=list(handle) - List=[] - List_score=[] - List_ids=[] - List_query_region=[] - for i in range(len(handle)): - if len(handle[i].alignments)>0: - for j in range(len(handle[i].alignments)): - score=0 - ids=0 - cover_region=set() #fixed problem that repeated calculation leading percentage > 1 - List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) - for z in range(len(handle[i].alignments[j].hsps)): - hsp=handle[i].alignments[j].hsps[z] - temp=set(range(hsp.query_start,hsp.query_end)) - est_bit=(handle[i].ka_params[0]*hsp.score-math.log(handle[i].ka_params[1]))/(math.log(2)) - if len(cover_region)==0: - cover_region=cover_region|temp - fraction=1 - else: - fraction=1-len(cover_region&temp)/float(len(temp)) - cover_region=cover_region|temp - if "last" in handle[i].query or "first" in handle[i].query: - #score+=hsp.bits*fraction - score+=est_bit*fraction - ids+=float(hsp.identities)/handle[i].query_length*fraction - else: - #score+=hsp.bits*fraction - score+=est_bit*fraction - ids+=float(hsp.identities)/handle[i].query_length*fraction - List_score.append(score) - List_ids.append(ids) - List_query_region.append(cover_region) - temp=zip(List,List_score,List_ids,List_query_region) - Final_list=sorted(temp, key=lambda d:d[1], reverse = True) - return Final_list - - -def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number - Old=L - L.sort() - L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] - count=[] - for j in range(len(L)): - y=0 - for x in Old: - if L[j]==x: - y+=1 - count.append(y) - if sort_on_fre!="none": - d=zip(*sorted(zip(count, L))) - L=d[1] - count=d[0] - return (L,count) - -def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): - #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test - #this is mainly used for - a=nodes_vs_score_list - fliC_score=0 - fljB_score=0 - for z in a: - if "fliC" in z[0]: - fliC_score+=z[1] - elif "fljB" in z[0]: - fljB_score+=z[1] - if fliC_score>=fljB_score: - role="fliC" - else: - role="fljB" - return (role,abs(fliC_score-fljB_score)) - -def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): - #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) - #also used when no head or tail got blasted score for the contig - role="" - for z in Final_list_passed: - if node_name in z[0]: - role=z[0].split("_")[0] - break - return role - -def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): - #nodes_list is the c created by c,d=Uniq(nodes) in below function - first_target="" - role_list=[] - for x in nodes_list: - a=[] - role="" - for y in tail_head_list: - if x in y[0]: - a.append(y) - if len(a)==4: - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - elif len(a)==3: - ###however, if the one with highest score is the fewer one, compare their accumulation score - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - ###end of above score comparison - elif len(a)==2: - #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) - temp=[] - for z in a: - temp.append(z[0].split("_")[0]) - m,n=Uniq(temp)#should only have one choice, but weird situation might occur too - if len(m)==1: - pass - else: - pass - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation - elif len(a)==1: - #that one - role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) - if diff<20: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" - else:#a==0 - #use Final_list_passed best match - for z in Final_list_passed: - if x in z[0]: - role=z[0].split("_")[0] - break - #print x,role,len(a) - role_list.append((role,x)) - if len(role_list)==2: - if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase - #just use score to do a final test - role_list=[] - for x in nodes_list: - role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) - role_list.append((role,x)) - return role_list - -def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): - #used to decide which contig is FliC and which one is fljB - contigs=[] - nodes=[] - for x in Final_list_passed: - if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: - nodes.append(x[0].split("___")[1].strip()) - c,d=Uniq(nodes)#c is node_list - #print c - tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] - roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) - return roles - -def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): - #decide O based on Final_list - O_choice="?" - O_list=[] - special_genes={} - nodes=[] - for x in Final_list_passed: - if x[0].startswith("O-"): - nodes.append(x[0].split("___")[1].strip()) - elif not x[0].startswith("fl"): - special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] - #print "special_genes:",special_genes - c,d=Uniq(nodes) - #print "potential O antigen contig",c - final_O=[] - O_nodes_list=[] - for x in c:#c is the list for contigs - temp=0 - for y in Final_list_passed: - if x in y[0] and y[0].startswith("O-"): - final_O.append(y) - break - ### O contig has the problem of two genes on same contig, so do additional test - potenial_new_gene="" - for x in final_O: - pointer=0 #for genes merged or not - #not consider O-1,3,19_not_in_3,10, too short compared with others - if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region - pointer=x[0].split("___")[1].strip()#store the contig name - print(pointer) - if pointer!=0:#it has potential merge event - for y in Final_list: - if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O - potenial_new_gene=y - #print(potenial_new_gene) - break - if potenial_new_gene!="": - print("two differnt genes in same contig, fix it for O antigen") - print(potenial_new_gene[:3]) - pointer=0 - for y in final_O: - if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: - pointer=1 - if pointer!=0: #changed to consider two genes in same contig - final_O.append(potenial_new_gene) - ### end of the two genes on same contig test - final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted - if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): - #print "$$$No Otype, due to no hit"#may need to be changed - O_choice="-" - else: - highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) - O_list=[] - O_list_less_contamination=[] - for x in final_O: - if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off - O_list.append(x[0].split("__")[0]) - O_nodes_list.append(x[0].split("___")[1]) - if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: - O_list_less_contamination.append(x[0].split("__")[0]) - ### special test for O9,46 and O3,10 family - if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 - O_choice="O-9,46" - #print "$$$Most possilble Otype: O-9,46" - elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 - O_choice="O-9,46,27" - #print "$$$Most possilble Otype: O-9,46,27" - else: - O_choice="O-9"#next, detect O9 vs O2? - O2=0 - O9=0 - for z in special_genes: - if "tyr-O-9" in z: - O9=special_genes[z] - elif "tyr-O-2" in z: - O2=special_genes[z] - if O2>O9: - O_choice="O-2" - elif O2<O9: - pass - else: - pass - #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility." - elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 - O_choice="O-3,10" - #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" - else: - O_choice="O-1,3,19" - #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" - ### end of special test for O9,46 and O3,10 family - else: - try: - max_score=0 - for x in final_O: - if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold - max_score=x[2]#change from x[-1] to x[2],08172018 - O_choice=x[0].split("_")[0] - if O_choice=="O-1,3,19": - O_choice=final_O[1][0].split("_")[0] - #print "$$$Most possilble Otype: ",O_choice - except: - pass - #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" - #print "O:",O_choice,O_nodes_list - Otypes=[] - for x in O_list: - if x!="O-1,3,19_not_in_3,10": - if "O-9,46_" not in x: - Otypes.append(x.split("_")[0]) - else: - Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 - #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] - Otypes_uniq,Otypes_fre=Uniq(Otypes) - contamination_O="" - if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": - if len(Otypes_uniq)>2: - contamination_O="potential contamination from O antigen signals" - else: - if len(Otypes_uniq)>1: - if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - else: - contamination_O="potential contamination from O antigen signals" - return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq -### End of SeqSero2 allele prediction and output - -def get_input_files(make_dir,input_file,data_type,dirpath): - #tell input files from datatype - #"<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" - for_fq="" - rev_fq="" - os.chdir(make_dir) - if data_type=="1": - input_file=input_file[0].split("/")[-1] - if input_file.endswith(".sra"): - subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) - for_fq=input_file.replace(".sra","_1.fastq") - rev_fq=input_file.replace(".sra","_2.fastq") - else: - core_id=input_file.split(".fastq")[0].split(".fq")[0] - for_fq=core_id+"_1.fastq" - rev_fq=core_id+"_2.fastq" - if input_file.endswith(".gz"): - subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) - else: - subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) - elif data_type=="2": - for_fq=input_file[0].split("/")[-1] - rev_fq=input_file[1].split("/")[-1] - elif data_type=="3": - input_file=input_file[0].split("/")[-1] - if input_file.endswith(".sra"): - subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) - for_fq=input_file.replace(".sra","_1.fastq") - else: - for_fq=input_file - elif data_type in ["4","5","6"]: - for_fq=input_file[0].split("/")[-1] - os.chdir("..") - return for_fq,rev_fq - -def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): - #get O and H types from Final_list from blast parsing; allele mode - from Bio import SeqIO - fliC_choice="-" - fljB_choice="-" - fliC_contig="NA" - fljB_contig="NA" - fliC_region=set([0]) - fljB_region=set([0,]) - fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length - fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length - O_choice="-"#no need to decide O contig for now, should be only one - O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification - O_choice=O_choice.split("-")[-1].strip() - if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": - O_choice="-" - H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB - #add alignment locations, used for further selection, 03312019 - for i in range(len(H_contig_roles)): - x=H_contig_roles[i] - for y in Final_list_passed: - if x[1] in y[0] and y[0].startswith(x[0]): - H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) - break - log_file=open("SeqSero_log.txt","a") - extract_file=open("Extracted_antigen_alleles.fasta","a") - handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) - - #print("O_contigs:") - log_file.write("O_contigs:\n") - extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") - extract_file.write("#O_contigs:\n") - for x in O_nodes_roles: - if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker - #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) - log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") - title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" - seqs="" - for z in handle_fasta: - if x[0].split("___")[-1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - if len(H_contig_roles)!=0: - highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output - else: - highest_H_coverage=0 - for x in H_contig_roles: - #if multiple choices, temporately select the one with longest length for now, will revise in further change - if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list - fliC_contig=x[1] - fliC_length=len(x[-1]) - elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: - fljB_contig=x[1] - fljB_length=len(x[-1]) - for x in Final_list_passed: - if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: - fliC_choice=x[0].split("_")[1] - elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: - fljB_choice=x[0].split("_")[1] - elif fliC_choice!="-" and fljB_choice!="-": - break - #now remove contigs not in middle core part - first_allele="NA" - first_allele_percentage=0 - for x in Final_list: - if x[0].startswith("fliC") or x[0].startswith("fljB"): - first_allele=x[0].split("__")[0] #used to filter those un-middle contigs - first_allele_percentage=x[2] - break - additional_contigs=[] - for x in Final_list: - if first_allele in x[0]: - if (fliC_contig == x[0].split("___")[-1]): - fliC_region=x[3] - elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): - fljB_region=x[3] - else: - if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 - additional_contigs.append(x) - #else: - #print x[:3] - #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off - if first_allele_percentage>0.9: - if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: - target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) - elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000: - target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) - else: - target_region=set()#doesn't do anything - else: - target_region=set()#doesn't do anything - #print(target_region) - #print(additional_contigs) - target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best - target_region=target_region2|target_region - for x in additional_contigs: - removal=0 - contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) - if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5<len(x[3])<contig_length*1.5: #consider length and alignment length for now, but very loose,0.5 and 1.5 as cut-off - removal=1 - else: - if first_allele_percentage > 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) - removal=1 - else: - pass - if removal==1: - for y in H_contig_roles: - if y[1] in x[0]: - H_contig_roles.remove(y) - else: - pass - #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) - #end of removing none-middle contigs - #print("H_contigs:") - log_file.write("H_contigs:\n") - extract_file.write("#H_contigs:\n") - H_contig_stat=[] - H1_cont_stat={} - H2_cont_stat={} - for i in range(len(H_contig_roles)): - x=H_contig_roles[i] - a=0 - for y in Final_list_passed: - if x[1] in y[0] and y[0].startswith(x[0]): - if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide - for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it - if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB - #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) - log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") - H_contig_roles[i]="can't decide fliC or fljB, may be third phase" - title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" - seqs="" - for z in handle_fasta: - if x[1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - break - else: - #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) - log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") - title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" - seqs="" - for z in handle_fasta: - if x[1]==z.description: - seqs=str(z.seq) - extract_file.write(title+seqs+"\n") - if x[0]=="fliC": - if y[0].split("_")[1] not in H1_cont_stat: - H1_cont_stat[y[0].split("_")[1]]=y[2] - else: - H1_cont_stat[y[0].split("_")[1]]+=y[2] - if x[0]=="fljB": - if y[0].split("_")[1] not in H2_cont_stat: - H2_cont_stat[y[0].split("_")[1]]=y[2] - else: - H2_cont_stat[y[0].split("_")[1]]+=y[2] - break - #detect contaminations - #print(H1_cont_stat) - #print(H2_cont_stat) - H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] - H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] - contamination_H="" - if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: - contamination_H="potential contamination from H antigen signals" - elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": - contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" - #get additional antigens - """ - if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 - O_choice="O-9,46" - #print "$$$Most possilble Otype: O-9,46" - elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 - O_choice="O-9,46,27" - #print "$$$Most possilble Otype: O-9,46,27" - elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 - O_choice="O-3,10" - #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" - else: - O_choice="O-1,3,19" - #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" - ### end of special test for O9,46 and O3,10 family - - if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": - if len(Otypes_uniq)>2: - contamination_O="potential contamination from O antigen signals" - else: - if len(Otypes_uniq)>1: - if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund - contamination_O="" - """ - additonal_antigents=[] - #print(contamination_O) - #print(contamination_H) - log_file.write(contamination_O+"\n") - log_file.write(contamination_H+"\n") - log_file.close() - return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list - -def get_input_K(input_file,lib_dict,data_type,k_size): - #kmer mode; get input_Ks from dict and data_type - kmers = [] - for h in lib_dict: - kmers += lib_dict[h] - if data_type == '4': - input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) - elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later - input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) - elif data_type == '5':#minion_2d_fasta - input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) - if data_type == '6':#minion_2d_fastq - input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) - return input_Ks - -def get_kmer_dict(lib_dict,input_Ks): - #kmer mode; get predicted types - O_dict = {} - H_dict = {} - Special_dict = {} - for h in lib_dict: - score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 - if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases - if h.startswith('O-') and score > 25: - O_dict[h] = score - if h.startswith('fl') and score > 40: - H_dict[h] = score - if (h[:2] != 'fl') and (h[:2] != 'O-'): - Special_dict[h] = score - return O_dict,H_dict,Special_dict - -def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): - log_file=open("SeqSero_log.txt","a") - log_file.write("O_scores:\n") - #call O: - highest_O = '-' - if len(O_dict) == 0: - pass - else: - for x in O_dict: - log_file.write(x+"\t"+str(O_dict[x])+"\n") - if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 - if 'O-9,46_wzy__1191' in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 - highest_O = "O-9,46" - elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 - highest_O = "O-9,46,27" - else: - highest_O = "O-9" # next, detect O9 vs O2? - O2 = 0 - O9 = 0 - for z in Special_dict: - if "tyr-O-9" in z: - O9 = float(Special_dict[z]) - if "tyr-O-2" in z: - O2 = float(Special_dict[z]) - if O2 > O9: - highest_O = "O-2" - elif ("O-3,10_wzx__1539" in O_dict) and ( - "O-9,46_wzy__1191" in O_dict - ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 - if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 - highest_O = "O-3,10" - else: - highest_O = "O-1,3,19" - ### end of special test for O9,46 and O3,10 family - else: - try: - max_score = 0 - for x in O_dict: - if float(O_dict[x]) >= max_score: - max_score = float(O_dict[x]) - highest_O = x.split("_")[0] - if highest_O == "O-1,3,19": - highest_O = '-' - max_score = 0 - for x in O_dict: - if x == 'O-1,3,19_not_in_3,10__130': - pass - else: - if float(O_dict[x]) >= max_score: - max_score = float(O_dict[x]) - highest_O = x.split("_")[0] - except: - pass - #call_fliC: - if len(H_dict)!=0: - highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not - else: - highest_H_score_both_BC=0 - highest_fliC = '-' - highest_fliC_raw = '-' - highest_Score = 0 - log_file.write("\nH_scores:\n") - for s in H_dict: - log_file.write(s+"\t"+str(H_dict[s])+"\n") - if s.startswith('fliC'): - if float(H_dict[s]) > highest_Score: - highest_fliC = s.split('_')[1] - highest_fliC_raw = s - highest_Score = float(H_dict[s]) - #call_fljB - highest_fljB = '-' - highest_fljB_raw = '-' - highest_Score = 0 - for s in H_dict: - if s.startswith('fljB'): - if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other - highest_fljB = s.split('_')[1] - highest_fljB_raw = s - highest_Score = float(H_dict[s]) - log_file.write("\nSpecial_scores:\n") - for s in Special_dict: - log_file.write(s+"\t"+str(Special_dict[s])+"\n") - log_file.close() - return highest_O,highest_fliC,highest_fljB - -def get_temp_file_names(for_fq,rev_fq): - #seqsero2 -a; get temp file names - sam=for_fq+".sam" - bam=for_fq+".bam" - sorted_bam=for_fq+"_sorted.bam" - mapped_fq1=for_fq+"_mapped.fq" - mapped_fq2=rev_fq+"_mapped.fq" - combined_fq=for_fq+"_combined.fq" - for_sai=for_fq+".sai" - rev_sai=rev_fq+".sai" - return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai - -def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): - #seqsero2 -a; do mapping and sort - print("building database...") - subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) - print("mapping...") - if mapping_mode=="mem": - subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) - elif mapping_mode=="sam": - if fnameB!="": - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) - else: - subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) - subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) - subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) - ### check the version of samtools then use differnt commands - samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) - out, err = samtools_version.communicate() - version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() - print("check samtools version:",version) - ### end of samtools version check and its analysis - if LooseVersion(version)<=LooseVersion("1.2"): - subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) - else: - subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) - -def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): - #seqsero2 -a; extract, assembly and blast - subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) - #print("fnameA:",fnameA) - #print("fnameB:",fnameB) - if fnameB!="": - subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output - else: - pass - outdir=current_time+"_temp" - print("assembling...") - if int(threads)>4: - t="4" - else: - t=threads - if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" - if fnameB!="": - subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) - else: - subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) - #new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" - new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # ed_SL_09152019: change path to databse for packaging - subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) - #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta - subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) - print("blasting...","\n") - xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" - subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 - subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" - else: - xmlfile="NA" - return xmlfile,new_fasta - -def judge_subspecies(fnameA,dirpath): - #seqsero2 -a; judge subspecies on just forward raw reads fastq - salmID_output=subprocess.Popen("python " + dirpath + "/SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) - out, err = salmID_output.communicate() - out=out.decode("utf-8") - file=open("data_log.txt","a") - file.write(out) - file.close() - salm_species_scores=out.split("\n")[1].split("\t")[6:] - salm_species_results=out.split("\n")[0].split("\t")[6:] - max_score=0 - max_score_index=1 #default is 1, means "I" - for i in range(len(salm_species_scores)): - if max_score<float(salm_species_scores[i]): - max_score=float(salm_species_scores[i]) - max_score_index=i - prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0] - if float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare - prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part - if max_score<10: - prediction="-" - return prediction - -def judge_subspecies_Kmer(Special_dict): - #seqsero2 -k; - max_score=0 - prediction="-" #default should be I - for x in Special_dict: - if "mer" in x: - if max_score<float(Special_dict[x]): - max_score=float(Special_dict[x]) - prediction=x.split("_")[-1].strip() - if x.split("_")[-1].strip()=="bongori" and float(Special_dict[x])>95:#if bongori already, then no need to test enterica - prediction="bongori" - break - return prediction - -def main(): - #combine SeqSeroK and SeqSero2, also with SalmID - args = parse_args() - input_file = args.i - data_type = args.t - analysis_mode = args.m - mapping_mode=args.b - threads=args.p - make_dir=args.d - clean_mode=args.c - k_size=27 #will change for bug fixing - #database="H_and_O_and_specific_genes.fasta" - dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging - #database=ex_dir+"/seqsero2_db/H_and_O_and_specific_genes.fasta" # ed_SL_09152019: change path to database for packaging - database="H_and_O_and_specific_genes.fasta" - note="Note:" - NA_note=" This predicted serotype is not in the Kauffman-White scheme." # ed_SL_09272019: add for new output format - if len(sys.argv)==1: - subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file - else: - request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) - request_id += str(random.randint(1, 10000000)) - if make_dir is None: - make_dir="SeqSero_result_"+request_id - if os.path.isdir(make_dir): - pass - else: - subprocess.check_call(["mkdir",make_dir]) - #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) - #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) - #subprocess.check_call("ln -f -s "+database+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_09152019: change path to database for packaging - subprocess.check_call("ln -f -s "+dirpath+"/seqsero2_db/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### ed_SL_05282019: use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). - ############################begin the real analysis - if analysis_mode=="a": - if data_type in ["1","2","3"]:#use allele mode - for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) - os.chdir(make_dir) - ###add a function to tell input files - fnameA=for_fq.split("/")[-1] - fnameB=rev_fq.split("/")[-1] - current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) - sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id - map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort - xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast - if xmlfile=="NA": - O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") - else: - Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results - file=open("data_log.txt","a") - for x in Final_list: - file.write("\t".join(str(y) for y in x)+"\n") - file.close() - Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] - O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB - subspecies=judge_subspecies(fnameA,dirpath) #predict subspecies - ###output - predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) - claim="" #04132019, disable claim for new report requirement - contamination_report="" - H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] - if contamination_O!="" and contamination_H=="": - contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." - elif contamination_O=="" and contamination_H!="": - contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." - elif contamination_O!="" and contamination_H!="": - contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." - if contamination_report!="": - #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 - contamination_report=" Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles." - #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version - ## ed_SL_09272019: change for new output format - #if contamination_report+star_line+claim=="": #0413, new output style - # note="" - #else: - # note="Note:" - if clean_mode: - subprocess.check_call("rm -rf ../"+make_dir,shell=True) - make_dir="none-output-directory due to '-c' flag" - else: - new_file=open("SeqSero_result.txt","w") - if O_choice=="": - O_choice="-" - if "N/A" not in predict_sero: - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+contamination_report+star_line+claim+"\n")#+## - else: - #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" - star_line="" #04132019, for new output requirement, diable star_line if "NA" in output - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+contamination_report+star_line+claim+"\n")#+## - new_file.close() - print("\n") - #subprocess.check_call("cat Seqsero_result.txt",shell=True) - #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) - subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) - if "N/A" not in predict_sero: - #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+contamination_report+star_line+claim+"\n")#+## - else: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+"\t".join(input_file)+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ - "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+contamination_report+star_line+claim+"\n") - else: - print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") - elif analysis_mode=="k": - #ex_dir = os.path.dirname(os.path.realpath(__file__)) - ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging - #output_mode = args.mode - for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) - input_file = for_fq #-k will just use forward because not all reads were used - os.chdir(make_dir) - f = open(dirpath + '/seqsero2_db/antigens.pickle', 'rb') - lib_dict = pickle.load(f) - f.close - input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) - O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) - highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) - subspecies=judge_subspecies_Kmer(Special_dict) - if subspecies=="IIb" or subspecies=="IIa": - subspecies="II" - predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( - highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) - claim="" #no claim any more based on new output requirement - ## ed_SL_09272019: change for new output format - #if star_line+claim=="": #0413, new output style - # note="" - #else: - # note="Note:" - if clean_mode: - subprocess.check_call("rm -rf ../"+make_dir,shell=True) - make_dir="none-output-directory due to '-c' flag" - ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" - if highest_O.split('-')[-1]=="": - O_choice="-" - else: - O_choice=highest_O.split('-')[-1] - ### - else: - if highest_O.split('-')[-1]=="": - O_choice="-" - else: - O_choice=highest_O.split('-')[-1] - #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) - new_file=open("SeqSero_result.txt","w") - #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## - if "N/A" not in predict_sero: - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+star_line+claim+"\n")#+## - else: - #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" - star_line = "" #changed for new output requirement, 04132019 - new_file.write("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+star_line+claim+"\n")#+## - new_file.close() - subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) - if "N/A" not in predict_sero: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_sero+"\n"+ # ed_SL_04152019: change serotype(s) to serotype - note+star_line+claim+"\n")#+## - else: - print("Output_directory:\t"+make_dir+"\n"+ - "Input files:\t"+input_file+"\n"+ - "O antigen prediction:\t"+O_choice+"\n"+ - "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ - "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ - "Predicted subspecies:\t"+subspecies+"\n"+ - "Predicted antigenic profile:\t"+predict_form+"\n"+ - "Predicted serotype:\t"+predict_form+"\n"+ # ed_SL_09242019: add serotype output for "N/A" prediction - note+NA_note+star_line+claim+"\n")#+## - -if __name__ == '__main__': - main()
--- a/SeqSero2_update_kmer_database.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os,subprocess -import pickle - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') - return parser.parse_args() - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - -def multifasta_to_kmers_dict(multifasta): - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) - return lib_dict - -def get_salmid_invA_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/invA_mers_dict', 'rb') - invA_dict = pickle.load(a) - try: - del invA_dict['version'] - except: - pass - return invA_dict - -def get_salmid_rpoB_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/rpoB_mers_dict', 'rb') - rpoB_dict = pickle.load(a) - try: - del rpoB_dict['version'] - except: - pass - return rpoB_dict - -def main(): - args = parse_args() - ex_dir = os.path.dirname(os.path.realpath(__file__)) - lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') - invA_dict=get_salmid_invA_database(ex_dir) - #rpoB_dict=get_salmid_rpoB_database(ex_dir) - lib_dict_new = lib_dict.copy() - #print(len(lib_dict_new)) - lib_dict_new.update(invA_dict) - #print(len(lib_dict_new)) - #lib_dict_new.update(rpoB_dict) - #print(len(lib_dict_new)) - f = open(ex_dir + '/antigens.pickle', "wb") - pickle.dump(lib_dict_new, f) - f.close() - -if __name__ == '__main__': - main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bin/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/usr/bin/env python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 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u'Ivory', u'Shoreditch', u'Sokode', u'IIIb 50:r:1,5,(7)', u'IIIb 50:r:e,n,x,z15', u'IIIb 50:r:z', u'IIIb 50:r:z35', u'IIIb 50:r:z53', u'Fairfield', u'Massakory', u'IIIb 58:r:z', u'IIIb 47:r:e,n,x,z15', u'IIIb 58:r:e,n,x,z15', u'Brunflo', u'Lehrte', u'Bassadji', u'Sipane', u'IIIb 53:r:z', u'IIIb 53:r:z35', u'IIIb 53:r:z68', u'Czernyring', u'Deckstein', u'Kibusi', u'Camberwell', u'Yellowknife', u'IIIb (6),14:r:z', u'Heidelberg', u'Bradford', u'Winneba', u'Remo', u'Goldcoast', u'IIIb 8:r:z', u'44:r:-', u'IIIb 35:r:z', u'Albertbanjul', u'IIIb 47:r:1,5,7', u'IIIb 40:r:z53', u'Southampton', u'Brefet', u'Jamaica', u'IIIb 43:r:e,n,x,z15', u'13,22:r:-', u'Adjame', u'Linton', u'Grampian', u'Papuana', u'IIIb 43:r:z53', u'IIIb 43:r:z', u'Weltevreden', u'Simi', u'Elisabethville', u'Ughelli', u'Bochum', u'Emmastad', u'Infantis', u'Campinense', u'Lome', u'Virchow', u'IIIb 42:r:-', u'II 42:r:-', u'Nigeria', u'IIIb 38:r:e,n,x,z15', u'IIIb 38:r:z', u'IIIb 38:r:1,5,7', u'Lindi', u'Dapango', u'IIIb 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u'Saphra', u'Akuafo', u'Harvestehude', u'Selby', u'Avignon', u'Freetown', u'Colombo', u'Trachau', u'Pomona', u'Oskarshamn', u'Nima', u'Ball', u'Steinwerder', u'Kingabwa', u'Farcha', u'Jos', u'Steinplatz', u'Carrau', u'Spalentor', u'Kitenge', u'Telaviv', u'Madelia', u'Fischerkietz', u'Mornington', u'Shomolu', u'II 17:y:-', u'Kamoru', u'Moualine', u'Solt', u'Delan', u'Gatineau', u'Kikoma', u'Herzliya', u'Woumbou', u'Windermere', u'Odienne', u'Cannonhill', u'Blitta', u'Jalisco', u'Lokomo', u'Slade', u'Thies', u'II 18:y:e,n,x,z15', u'Troy', u'Tunis', u'Ordonez', u'Hadejia', u'Yarrabah', u'Tanger', u'Anfo', u'Kinson', u'Krefeld', u'Tendeba', u'Warengo', u'Gori', u'II 17:z:l,w', u'II 47:z:e,n,x,z15', u'Daula', u'II 17:z:1,7', u'Mountpleasant', u'Potengi', u'Arusha', u'Uhlenhorst', u'Brackenridge', u'II 45:z:1,5', u'Yopougon', u'II 6,8:z:1,5', u'II 6,7:z:z42', u'Kuru', u'Kaolack', u'Bolama', u'Mowanjum', u'Marmande', u'Phaliron', u'Kalumburu', u'II 45:z:z39', u'Lawndale', u'Vanier', 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf'
--- a/bin/SeqSero2_package.py Thu Apr 30 21:47:42 2020 -0400 +++ b/bin/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -1236,12 +1236,14 @@ def judge_subspecies(fnameA,dirpath): #seqsero2 -a; judge subspecies on just forward raw reads fastq samid_strcmd = "python " + dirpath + "/../SalmID.py -i "+fnameA - #subprocess.check_call(samid_strcmd + " > Salmidoutput.txt",shell=True) print(samid_strcmd) + #seqsero2 -a; judge subspecies on just forward raw reads fastq + #salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) salmID_output=subprocess.Popen(samid_strcmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) out, err = salmID_output.communicate() - print("judge_subspecies -> err = salmID_output.communicate() " + err) out=out.decode("utf-8") + print(out) + print(err) file=open("data_log.txt","a") file.write(out) file.close()
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/MANIFEST.in Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,10 @@ +include LICENSE +include README.md +include MANIFEST.in +include version.py +include setup.py +include seqsero2_db/antigens.pickle +include seqsero2_db/H_and_O_and_specific_genes.fasta +include seqsero2_db/invA_mers_dict +include seqsero2_db/special.pickle +include bin/deinterleave_fastq.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/README.md Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,117 @@ +# SeqSero2 v1.1.1 +Salmonella serotype prediction from genome sequencing data. + +Online version: http://www.denglab.info/SeqSero2 + +# Introduction +SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + +# Dependencies +SeqSero2 has three workflows: + +(A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + +Allele micro-assembly workflow depends on: + +1. Python 3; + +2. Biopython 1.73; + +3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + +4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + +5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + +6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + +7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + +8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + +9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + +(B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + +Raw reads k-mer workflow (originally SeqSeroK) depends on: + +1. Python 3; +2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + +(C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + +# Installation +### Conda +To install the latest SeqSero2 Conda package (recommended): +``` +conda install -c bioconda seqsero2=1.1.1 +``` +### Git +To install the SeqSero2 git repository locally: +``` +git clone https://github.com/denglab/SeqSero2.git +cd SeqSero2 +python3 -m pip install --user . +``` +### Other options +Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ +https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ +https://github.com/denglab/SeqSero2/issues/13 + + +# Executing the code +Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i <file> (/path/to/input/file) + + -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n <string> (optional, to specify a sample name in the report output) + + -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check <flag> (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + +# Examples +Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + +K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + +# Output +Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + +# Citation +Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. +SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. +**Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + +Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. +Salmonella serotype determination utilizing high-throughput genome sequencing data. +**J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/PKG-INFO Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,132 @@ +Metadata-Version: 1.1 +Name: SeqSero2 +Version: 1.1.1 +Summary: Salmonella serotyping +Home-page: https://github.com/denglab/SeqSero2/ +Author: Shaokang Zhang, Hendrik C Den-Bakker and Xiangyu Deng +Author-email: zskzsk@uga.edu, Hendrik.DenBakker@uga.edu, xdeng@uga.edu +License: GPLv2 +Description: # SeqSero2 v1.1.1 + Salmonella serotype prediction from genome sequencing data. + + Online version: http://www.denglab.info/SeqSero2 + + # Introduction + SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies + + # Dependencies + SeqSero2 has three workflows: + + (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing). + + Allele micro-assembly workflow depends on: + + 1. Python 3; + + 2. Biopython 1.73; + + 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/); + + 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/); + + 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download); + + 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software); + + 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades); + + 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/); + + 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID). + + + (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants. + + Raw reads k-mer workflow (originally SeqSeroK) depends on: + + 1. Python 3; + 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files); + + + (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow + + # Installation + ### Conda + To install the latest SeqSero2 Conda package (recommended): + ``` + conda install -c bioconda seqsero2=1.1.1 + ``` + ### Git + To install the SeqSero2 git repository locally: + ``` + git clone https://github.com/denglab/SeqSero2.git + cd SeqSero2 + python3 -m pip install --user . + ``` + ### Other options + Third party SeqSero2 installations (may not be the latest version of SeqSero2): \ + https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \ + https://github.com/denglab/SeqSero2/issues/13 + + + # Executing the code + Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions. + + Usage: SeqSero2_package.py + + -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a) + + -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq) + + -i <file> (/path/to/input/file) + + -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1) + + -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode) + + -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number) + + -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files) + + -n <string> (optional, to specify a sample name in the report output) + + -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv) + + --check <flag> (use '--check' flag to check the required dependencies) + + -v, --version (show program's version number and exit) + + + # Examples + Allele mode: + + # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10") + SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz + + K-mer mode: + + # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2") + SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz + + # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k") + SeqSero2_package.py -m k -t 4 -i assembly.fasta + + # Output + Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode). + + + # Citation + Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. + SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data. + **Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19.** [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long) + + Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. + Salmonella serotype determination utilizing high-throughput genome sequencing data. + **J Clin Microbiol. 2015 May;53(5):1685-92.** [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15) + +Keywords: Salmonella serotyping bioinformatics WGS +Platform: UNKNOWN +Classifier: Development Status :: 3 - Alpha +Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2) +Classifier: Programming Language :: Python :: 3 +Classifier: Topic :: Text Processing :: Linguistic
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/SOURCES.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,19 @@ +LICENSE +MANIFEST.in +README.md +setup.py +version.py +SeqSero2.egg-info/PKG-INFO +SeqSero2.egg-info/SOURCES.txt +SeqSero2.egg-info/dependency_links.txt +SeqSero2.egg-info/not-zip-safe +SeqSero2.egg-info/requires.txt +SeqSero2.egg-info/top_level.txt +bin/Initial_Conditions.py +bin/SeqSero2_package.py +bin/SeqSero2_update_kmer_database.py +bin/deinterleave_fastq.sh +seqsero2_db/H_and_O_and_specific_genes.fasta +seqsero2_db/antigens.pickle +seqsero2_db/invA_mers_dict +seqsero2_db/special.pickle \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/dependency_links.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/not-zip-safe Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/requires.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +biopython==1.73
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/SeqSero2.egg-info/top_level.txt Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/usr/bin/env python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 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16:b:e,n,x', u'Hvittingfoss', u'II 41:b:1,5', u'Pharr', u'Eboko', u'Tonev', u'Sanga', u'Kuntair', u'Tucson', u'IIIb (6),14:b:e,n,x', u'Schleissheim (Schleissheim is extremely rare)', u'II 3,10:b:e,n,x', u'Atento', u'Leeuwarden', u'Wohlen', u'Korbol', u'VI 11:b:e,n,x', u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II [1],4,12,[27]:g,[m],[s],t:e,n,x', u'II 6,7:g,[m],s,t:[z42]', u'II 11:g,[m],s,t:z39', u'II 50:g,[m],s,t:[1,5]', u'II 57:g,[m],s,t:z42', u'II [1],4,12,[27]:g,[m],t:[1,5]', u'Senftenberg', u'II [1],13,23:g,[s],t:z42', u'Okatie', u'Enteritidis', u'Luke', u'Abadina', u'Yardley', u'Warragul', u'Bijlmer', u'Abuja', u'Bron', u'Essen', u'Hillingdon', u'Nitra', u'Suberu', u'Pontypridd', u'Montevideo', u'Korovi', u'Chincol', u'Gamaba', u'Tornow', u'Agbeni', u'II 6,7:g,m,[s],t:e,n,x', u'II [1],9,12:g,m,[s],t:[1,5,7]', u'II [1],13,23:g,m,[s],t:[e,n,x]', u'II 43:g,m,[s],t:[z42]', u'Godesberg', u'Othmarschen', u'Adeoyo', u'Kouka', u'Blegdam', u'Hato', u'Gueuletapee', u'Amsterdam', u'Nikolaifleet', u'Macclesfield', u'IIIb 13,22:g,m,s:z', u'Giessen', u'Ealing', u'Caracas', u'II 30:g,m,s:e,n,x', u'Croft', u'Athens', u'Emek', u'II [1],13,23:g,m,s,t:1,5', u'II 3,{10}{15}:g,m,s,t:[1,5]', u'II [1],9,12:g,m,s,t:e,n,x', u'II 45:g,m,s,t:1,5', u'II 17:g,m,s,t:-', u'II 6,7:g,m,s,t:z39', u'II 45:g,m,s,t:e,n,x', u'II [1],13,23:g,m,s,t:z42', u'II 41:g,m,s,t:z6', u'II 35:g,m,s,t:-', u'II 28:g,m,t:z39', u'II 28:g,m,t:e,n,x', u'II 60:g,m,t:z6', u'Reubeuss', u'II 6,8:g,m,t:1,7', u'II 45:g,m,t:e,n,x,z15', u'California', u'II 4,12:g,m,t:z39', u'Ebrie', u'II [1],13,22:g,m,t:[1,5]', u'II 48:g,m,t:-', u'Sylvania', u'Kiel', u'Dublin', u'Naestved', u'Rostock', u'Moscow', u'Menston', u'Plumaugat', u'Gateshead', u'Missouri', u'Catanzaro', u'Newyork', u'Sternschanze', u'Binningen', u'Anecho', u'II 9,12:g,s,t:e,n,x', u'Alminko', u'Nanergou', u'Cardoner', u'Ona', u'II 51:g,s,t:e,n,x', u'Lowestoft', u'Dessau', u'II 28:g,s,t:e,n,x', u'Splott', u'Kingston', u'Eaubonne', u'Uccle', u'Westhampton', u'II [1],13,22:g,t:[1,5]', u'IIIb [1],44:g,t:1,5', u'II 44:g,t:z42', u'IIIb 43:g,t:-', u'II 30:g,t:-', u'II 38:g,t:-', u'II 41:g,t:-', u'II 43:g,t:[1,5]', u'II 13,22:g,t:z6', u'II [1],13,23:g,t:1,5', u'Saintemarie', u'IV [1],40:g,t:-', u'II 17:g,t:[e,n,x,z15]', u'II 42:g,t:-', u'II 17:g,t:z39', u'II 65:g,t:-', u'Budapest', u'II 3,10:g,t:-', u'II 9,12,46,27:g,t:e,n,x', u'II [1],40:g,t:e,n,x,z15', u'II 57:g,t:-', u'Bloomsbury', u'II 13,23:g,t:e,n,x', u'II 52:g,t:-', u'II 35:g,t:1,5', u'II 35:g,t:z42', u'Agodi', u'II 40:g,t:z39', u'II 6,7:g,t:[e,n,x]', u'IIIa 50:g,z51:-', u'IIIa 51:g,z51:-', u'IV 48:g,z51:-', u'Larose', u'IV 21:g,z51:-', u'IIIa 21:g,z51:-', u'IIIa 63:g,z51:-', u'IIIa 62:g,z51:-', u'IV [1],53:g,z51:-', u'IV 43:g,z51:-', u'IV 11:g,z51:-', u'IV 6,7:g,z51:-', u'IIIa 35:g,z51:-', u'Wayne', u'IIIa 43:g,z51:-', u'Carswell', u'IV 44:g,z51:-', u'IIIa [1],13,23:g,z51:-', u'IIIa 53:g,z51:-', u'IIIa 47:g,z51:-', u'Newmexico', u'IIIa 18:g,z51:-', u'IV 18:g,z51:-', u'IV 45:g,z51:-', u'IV [1],40:g,z51:-', u'IV 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1576 @@ +#!/usr/bin/env python3 + +import sys +import time +import random +import os +import subprocess +import gzip +import io +import pickle +import argparse +import itertools +from distutils.version import LooseVersion +from distutils.spawn import find_executable +sys.path.insert(1,sys.path[0]+'/..') + +try: + from .version import SeqSero2_version +except Exception: #ImportError + from version import SeqSero2_version + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.1')#add "-m <data_type>" in future + parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data. + parser.add_argument("-t",choices=['1','2','3','4','5','6'],help="<int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") + parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") + parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") + parser.add_argument("-m",choices=['k','a'],default="a",help="<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") + parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output") + parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") + parser.add_argument("-c",action="store_true",help="<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") + parser.add_argument("-s",action="store_true",help="<flag>: if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv") + parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies") + parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) + return parser.parse_args() + +### check paths of dependencies +check_dependencies = parse_args().check +dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] +if check_dependencies: + for item in dependencies: + ext_path = find_executable(item) + if ext_path is not None: + print ("Using "+item+" - "+ext_path) + else: + print ("ERROR: can not find "+item+" in PATH") + sys.exit() +### end of --check + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + + +def multifasta_single_string(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') + if (len(line.strip()) > 0) and (line.strip()[0] != '>') + ] + return ''.join(multifasta_list) + + +def chunk_a_long_sequence(long_sequence, chunk_size=60): + chunk_list = [] + steps = len(long_sequence) // 60 #how many chunks + for i in range(steps): + chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) + chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) + return chunk_list + + +def target_multifasta_kmerizer(multifasta, k, kmerDict): + forward_length = 300 #if find the target, put forward 300 bases + reverse_length = 2200 #if find the target, put backward 2200 bases + chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences + target_mers = [] + long_single_string = multifasta_single_string(multifasta) + multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) + unit_length = len(multifasta_list[0]) + forward_lines = int(forward_length / unit_length) + 1 + reverse_lines = int(forward_length / unit_length) + 1 + start_num = 0 + end_num = 0 + for i in range(len(multifasta_list)): + if i not in range(start_num, end_num): #avoid computational repetition + line = multifasta_list[i] + start = int((len(line) - k) // 2) + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + if i - forward_lines >= 0: + start_num = i - forward_lines + else: + start_num = 0 + if i + reverse_lines <= len(multifasta_list) - 1: + end_num = i + reverse_lines + else: + end_num = len(multifasta_list) - 1 + target_list = [ + x.strip() for x in multifasta_list[start_num:end_num] + ] + target_line = "".join(target_list) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(target_line)], k) + ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + else: + pass + return set(target_mers) + + +def target_read_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = [] + if file.endswith(".gz"): + file_content = io.BufferedReader(gzip.open(file)) + else: + file_content = open(file, "r").readlines() + for line in file_content: + start = int((len(line) - k) // 2) + if i % 4 == 2: + if file.endswith(".gz"): + s1 = line[start:k + start].decode() + line = line.decode() + else: + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + n_reads += 1 + total_coverage += len(line) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(line)], k) + ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + i += 1 + if total_coverage >= 4000000: + break + return set(target_mers) + + +def minion_fasta_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 2 == 0: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def minion_fastq_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 4 == 2: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def multifasta_single_string2(multifasta): + single_string = '' + with open(multifasta, 'r') as f: + for line in f: + if line.strip()[0] == '>': + pass + else: + single_string += line.strip() + return single_string + + +def kmers(seq, k): + rev_comp = reverse_complement(seq) + for start in range(1, len(seq) - k + 1): + yield seq[start:start + k], rev_comp[-(start + k):-start] + + +def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) + return lib_dict + + +def Combine(b, c): + fliC_combinations = [] + fliC_combinations.append(",".join(c)) + temp_combinations = [] + for i in range(len(b)): + for x in itertools.combinations(b, i + 1): + temp_combinations.append(",".join(x)) + for x in temp_combinations: + temp = [] + for y in c: + temp.append(y) + temp.append(x) + temp = ",".join(temp) + temp = temp.split(",") + temp.sort() + temp = ",".join(temp) + fliC_combinations.append(temp) + return fliC_combinations + + +def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): + #like test_output_06012017.txt + #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) + from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict + rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] + rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to + seronames = [] + seronames_none_subspecies=[] + for i in range(len(phase1)): + fliC_combine = [] + fljB_combine = [] + if phaseO[i] == Otype: # no VII in KW, but it's there + ### for fliC, detect every possible combinations to avoid the effect of "[" + if phase1[i].count("[") == 0: + fliC_combine.append(phase1[i]) + elif phase1[i].count("[") >= 1: + c = [] + b = [] + if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( + "[") == 1: + content = phase1[i].replace("[", "").replace("]", "") + fliC_combine.append(content) + fliC_combine.append("-") + else: + for x in phase1[i].split(","): + if "[" in x: + b.append(x.replace("[", "").replace("]", "")) + else: + c.append(x) + fliC_combine = Combine( + b, c + ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t + ### end of fliC "[" detect + ### for fljB, detect every possible combinations to avoid the effect of "[" + if phase2[i].count("[") == 0: + fljB_combine.append(phase2[i]) + elif phase2[i].count("[") >= 1: + d = [] + e = [] + if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( + "[") == 1: + content = phase2[i].replace("[", "").replace("]", "") + fljB_combine.append(content) + fljB_combine.append("-") + else: + for x in phase2[i].split(","): + if "[" in x: + d.append(x.replace("[", "").replace("]", "")) + else: + e.append(x) + fljB_combine = Combine(d, e) + ### end of fljB "[" detect + new_fliC = fliC.split( + "," + ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings + new_fliC.sort() + new_fliC = ",".join(new_fliC) + new_fljB = fljB.split(",") + new_fljB.sort() + new_fljB = ",".join(new_fljB) + if (new_fliC in fliC_combine + or fliC in fliC_combine) and (new_fljB in fljB_combine + or fljB in fljB_combine): + ######start, remove_list,rename_dict, added on 11/11/2018 + if sero[i] not in remove_list: + temp_sero=sero[i] + if temp_sero in rename_dict: + temp_sero=rename_dict[temp_sero] #rename if in the rename list + if temp_sero not in seronames:#the new sero may already included, if yes, then not consider + if subs[i] == subspecies: + seronames.append(temp_sero) + seronames_none_subspecies.append(temp_sero) + else: + pass + else: + pass + ######end, added on 11/11/2018 + #analyze seronames + subspecies_pointer="" + if len(seronames) == 0 and len(seronames_none_subspecies)!=0: + # ed_SL_12182019: modified to fix the subspecies output problem + #seronames=seronames_none_subspecies + seronames=["N/A"] + #subspecies_pointer="1" + subspecies_pointer="0" + if len(seronames) == 0: + seronames = [ + "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" + ] + star = "" + star_line = "" + if len(seronames) > 1: #there are two possible predictions for serotypes + star = "*" + #changed 04072019 + #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" + if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: + star="*" + star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line + #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line + if Otype=="": + Otype="-" + predict_form = Otype + ":" + fliC + ":" + fljB + predict_sero = (" or ").join(seronames) + ###special test for Enteritidis + if predict_form == "9:g,m:-": + sdf = "-" + for x in special_gene_list: + if x.startswith("sdf"): + sdf = "+" + #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene detected. " + #predict_form = predict_form + " Sdf prediction:" + sdf + predict_form = predict_form #changed 04072019 + if sdf == "-": + star = "*" + #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene not detected. " + #changed in 04072019, for new output + #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" + #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement + predict_sero = "Gallinarum or Enteritidis" + ###end of special test for Enteritidis + elif predict_form == "4:i:-": + predict_sero = "I 4,[5],12:i:-" # change serotype name + elif predict_form == "4:r:-": + predict_sero = "N/A (4:r:-)" + elif predict_form == "4:b:-": + predict_sero = "N/A (4:b:-)" + #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo + #predict_sero = "Newport" + #star = "*" + #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." + claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" + if "N/A" in predict_sero: + claim = "" + #special test for Typhimurium + if "Typhimurium" in predict_sero or predict_form == "4:i:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "oafA-O-4_full" in x: + normal = float(special_gene_list[x]) + elif "oafA-O-4_5-" in x: + mutation = float(special_gene_list[x]) + if normal > mutation: + pass + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(O5-)" + predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 + star = "*" + #star_line = "Detected the deletion of O5-." + star_line = "Detected a deletion that causes O5- variant of Typhimurium. " + else: + pass + #special test for Paratyphi B + if "Paratyphi B" in predict_sero or predict_form == "4:b:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "gntR-family-regulatory-protein_dt-positive" in x: + normal = float(special_gene_list[x]) + elif "gntR-family-regulatory-protein_dt-negative" in x: + mutation = float(special_gene_list[x]) + #print(normal,mutation) + if normal > mutation: + #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() + star = "*" + #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." + star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip() + star = "*" + #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." + star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. " + else: + star = "*" + #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." + star_line = " " ## ed_SL_05152019: do not report this situation. + #special test for O13,22 and O13,23 + if Otype=="13": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 + f = open(ex_dir + '/special.pickle', 'rb') + special = pickle.load(f) + O22_O23=special['O22_O23'] + if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze + O22_score=0 + O23_score=0 + for x in special_gene_list: + if "O:22" in x: + O22_score = O22_score+float(special_gene_list[x]) + elif "O:23" in x: + O23_score = O23_score+float(special_gene_list[x]) + #print(O22_score,O23_score) + for z in O22_O23[0]: + if predict_sero.split(" or ")[0] in z: + if O22_score > O23_score: + star = "*" + #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[0] + elif O22_score < O23_score: + star = "*" + #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[1] + else: + star = "*" + #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 + if " or " in predict_sero: + star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "." + #special test for O6,8 + #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list + #for x in merge_O68_list: + # if x in predict_sero: + # predict_sero=x + # star="" + # star_line="" + #special test for Montevideo; most of them are monophasic + #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list + #star="*" + #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." + return predict_form, predict_sero, star, star_line, claim +### End of SeqSero Kmer part + +### Begin of SeqSero2 allele prediction and output +def xml_parse_score_comparision_seqsero(xmlfile): + #used to do seqsero xml analysis + from Bio.Blast import NCBIXML + handle=open(xmlfile) + handle=NCBIXML.parse(handle) + handle=list(handle) + List=[] + List_score=[] + List_ids=[] + List_query_region=[] + for i in range(len(handle)): + if len(handle[i].alignments)>0: + for j in range(len(handle[i].alignments)): + score=0 + ids=0 + cover_region=set() #fixed problem that repeated calculation leading percentage > 1 + List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) + for z in range(len(handle[i].alignments[j].hsps)): + hsp=handle[i].alignments[j].hsps[z] + temp=set(range(hsp.query_start,hsp.query_end)) + if len(cover_region)==0: + cover_region=cover_region|temp + fraction=1 + else: + fraction=1-len(cover_region&temp)/float(len(temp)) + cover_region=cover_region|temp + if "last" in handle[i].query or "first" in handle[i].query: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + else: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + List_score.append(score) + List_ids.append(ids) + List_query_region.append(cover_region) + temp=zip(List,List_score,List_ids,List_query_region) + Final_list=sorted(temp, key=lambda d:d[1], reverse = True) + return Final_list + + +def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number + Old=L + L.sort() + L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] + count=[] + for j in range(len(L)): + y=0 + for x in Old: + if L[j]==x: + y+=1 + count.append(y) + if sort_on_fre!="none": + d=zip(*sorted(zip(count, L))) + L=d[1] + count=d[0] + return (L,count) + +def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): + #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test + #this is mainly used for + a=nodes_vs_score_list + fliC_score=0 + fljB_score=0 + for z in a: + if "fliC" in z[0]: + fliC_score+=z[1] + elif "fljB" in z[0]: + fljB_score+=z[1] + if fliC_score>=fljB_score: + role="fliC" + else: + role="fljB" + return (role,abs(fliC_score-fljB_score)) + +def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): + #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) + #also used when no head or tail got blasted score for the contig + role="" + for z in Final_list_passed: + if node_name in z[0]: + role=z[0].split("_")[0] + break + return role + +def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): + #nodes_list is the c created by c,d=Uniq(nodes) in below function + first_target="" + role_list=[] + for x in nodes_list: + a=[] + role="" + for y in tail_head_list: + if x in y[0]: + a.append(y) + if len(a)==4: + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + elif len(a)==3: + ###however, if the one with highest score is the fewer one, compare their accumulation score + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###end of above score comparison + elif len(a)==2: + #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) + temp=[] + for z in a: + temp.append(z[0].split("_")[0]) + m,n=Uniq(temp)#should only have one choice, but weird situation might occur too + if len(m)==1: + pass + else: + pass + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation + elif len(a)==1: + #that one + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" + else:#a==0 + #use Final_list_passed best match + for z in Final_list_passed: + if x in z[0]: + role=z[0].split("_")[0] + break + #print x,role,len(a) + role_list.append((role,x)) + if len(role_list)==2: + if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase + #just use score to do a final test + role_list=[] + for x in nodes_list: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + role_list.append((role,x)) + return role_list + +def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): + #used to decide which contig is FliC and which one is fljB + contigs=[] + nodes=[] + for x in Final_list_passed: + if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: + nodes.append(x[0].split("___")[1].strip()) + c,d=Uniq(nodes)#c is node_list + #print c + tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] + roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) + return roles + +def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): + #decide O based on Final_list + O_choice="?" + O_list=[] + special_genes={} + nodes=[] + for x in Final_list_passed: + if x[0].startswith("O-"): + nodes.append(x[0].split("___")[1].strip()) + elif not x[0].startswith("fl"): + special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] + #print "special_genes:",special_genes + c,d=Uniq(nodes) + #print "potential O antigen contig",c + final_O=[] + O_nodes_list=[] + for x in c:#c is the list for contigs + temp=0 + for y in Final_list_passed: + if x in y[0] and y[0].startswith("O-"): + final_O.append(y) + break + ### O contig has the problem of two genes on same contig, so do additional test + potenial_new_gene="" + for x in final_O: + pointer=0 #for genes merged or not + #not consider O-1,3,19_not_in_3,10, too short compared with others + if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region + pointer=x[0].split("___")[1].strip()#store the contig name + print(pointer) + if pointer!=0:#it has potential merge event + for y in Final_list: + if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O + potenial_new_gene=y + #print(potenial_new_gene) + break + if potenial_new_gene!="": + print("two differnt genes in same contig, fix it for O antigen") + print(potenial_new_gene[:3]) + pointer=0 + for y in final_O: + if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: + pointer=1 + if pointer!=0: #changed to consider two genes in same contig + final_O.append(potenial_new_gene) + ### end of the two genes on same contig test + final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted + if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): + #print "$$$No Otype, due to no hit"#may need to be changed + O_choice="-" + else: + highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) + O_list=[] + O_list_less_contamination=[] + for x in final_O: + if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off + O_list.append(x[0].split("__")[0]) + O_nodes_list.append(x[0].split("___")[1]) + if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: + O_list_less_contamination.append(x[0].split("__")[0]) + ### special test for O9,46 and O3,10 family + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list or "O-9,46_wzy_partial" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + else: + O_choice="O-9"#next, detect O9 vs O2? + O2=0 + O9=0 + for z in special_genes: + if "tyr-O-9" in z: + O9=special_genes[z] + elif "tyr-O-2" in z: + O2=special_genes[z] + if O2>O9: + O_choice="O-2" + elif O2<O9: + pass + else: + pass + #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility." + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score=0 + for x in final_O: + if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold + max_score=x[2]#change from x[-1] to x[2],08172018 + O_choice=x[0].split("_")[0] + if O_choice=="O-1,3,19": + O_choice=final_O[1][0].split("_")[0] + #print "$$$Most possilble Otype: ",O_choice + except: + pass + #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" + if O_choice=="O-9,46,27" and len(O_list)==2 and "O-4_wzx" in O_list: #special for very low chance sitatuion between O4 and O9,27,46, this is for serotypes like Bredeney and Schwarzengrund (normallly O-4 will have higher score, but sometimes sequencing quality may affect the prediction) + O_choice="O-4" + #print "O:",O_choice,O_nodes_list + Otypes=[] + for x in O_list: + if x!="O-1,3,19_not_in_3,10": + if "O-9,46_" not in x: + Otypes.append(x.split("_")[0]) + else: + Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 + #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] + Otypes_uniq,Otypes_fre=Uniq(Otypes) + contamination_O="" + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + else: + contamination_O="potential contamination from O antigen signals" + return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq +### End of SeqSero2 allele prediction and output + +def get_input_files(make_dir,input_file,data_type,dirpath): + #tell input files from datatype + #"<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" + for_fq="" + rev_fq="" + os.chdir(make_dir) + if data_type=="1": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + rev_fq=input_file.replace(".sra","_2.fastq") + else: + core_id=input_file.split(".fastq")[0].split(".fq")[0] + for_fq=core_id+"_1.fastq" + rev_fq=core_id+"_2.fastq" + if input_file.endswith(".gz"): + subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + else: + subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + elif data_type=="2": + for_fq=input_file[0].split("/")[-1] + rev_fq=input_file[1].split("/")[-1] + elif data_type=="3": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + else: + for_fq=input_file + elif data_type in ["4","5","6"]: + for_fq=input_file[0].split("/")[-1] + os.chdir("..") + return for_fq,rev_fq + +def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): + #get O and H types from Final_list from blast parsing; allele mode + from Bio import SeqIO + fliC_choice="-" + fljB_choice="-" + fliC_contig="NA" + fljB_contig="NA" + fliC_region=set([0]) + fljB_region=set([0,]) + fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + O_choice="-"#no need to decide O contig for now, should be only one + O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification + O_choice=O_choice.split("-")[-1].strip() + if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": + O_choice="-" + H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB + #add alignment locations, used for further selection, 03312019 + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) + break + log_file=open("SeqSero_log.txt","a") + extract_file=open("Extracted_antigen_alleles.fasta","a") + handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) + + #print("O_contigs:") + log_file.write("O_contigs:\n") + extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") + extract_file.write("#O_contigs:\n") + for x in O_nodes_roles: + if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker + #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) + log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") + title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[0].split("___")[-1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if len(H_contig_roles)!=0: + highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output + else: + highest_H_coverage=0 + for x in H_contig_roles: + #if multiple choices, temporately select the one with longest length for now, will revise in further change + if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list + fliC_contig=x[1] + fliC_length=len(x[-1]) + elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: + fljB_contig=x[1] + fljB_length=len(x[-1]) + for x in Final_list_passed: + if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: + fliC_choice=x[0].split("_")[1] + elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: + fljB_choice=x[0].split("_")[1] + elif fliC_choice!="-" and fljB_choice!="-": + break + #now remove contigs not in middle core part + first_allele="NA" + first_allele_percentage=0 + for x in Final_list: + if x[0].startswith("fliC") or x[0].startswith("fljB"): + first_allele=x[0].split("__")[0] #used to filter those un-middle contigs + first_allele_percentage=x[2] + break + additional_contigs=[] + for x in Final_list: + if first_allele in x[0]: + if (fliC_contig == x[0].split("___")[-1]): + fliC_region=x[3] + elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): + fljB_region=x[3] + else: + if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 + additional_contigs.append(x) + #else: + #print x[:3] + #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off + if first_allele_percentage>0.9: + if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: + target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000: + target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + else: + target_region=set()#doesn't do anything + else: + target_region=set()#doesn't do anything + #print(target_region) + #print(additional_contigs) + target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best + target_region=target_region2|target_region + for x in additional_contigs: + removal=0 + contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) + if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5<len(x[3])<contig_length*1.5: #consider length and alignment length for now, but very loose,0.5 and 1.5 as cut-off + removal=1 + else: + if first_allele_percentage > 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) + removal=1 + else: + pass + if removal==1: + for y in H_contig_roles: + if y[1] in x[0]: + H_contig_roles.remove(y) + else: + pass + #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) + #end of removing none-middle contigs + #print("H_contigs:") + log_file.write("H_contigs:\n") + extract_file.write("#H_contigs:\n") + H_contig_stat=[] + H1_cont_stat={} + H2_cont_stat={} + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + a=0 + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide + for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it + if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB + #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + H_contig_roles[i]="can't decide fliC or fljB, may be third phase" + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + break + else: + #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if x[0]=="fliC": + if y[0].split("_")[1] not in H1_cont_stat: + H1_cont_stat[y[0].split("_")[1]]=y[2] + else: + H1_cont_stat[y[0].split("_")[1]]+=y[2] + if x[0]=="fljB": + if y[0].split("_")[1] not in H2_cont_stat: + H2_cont_stat[y[0].split("_")[1]]=y[2] + else: + H2_cont_stat[y[0].split("_")[1]]+=y[2] + break + #detect contaminations + #print(H1_cont_stat) + #print(H2_cont_stat) + H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] + H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] + contamination_H="" + if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: + contamination_H="potential contamination from H antigen signals" + elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": + contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" + #get additional antigens + """ + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + """ + additonal_antigents=[] + #print(contamination_O) + #print(contamination_H) + log_file.write(contamination_O+"\n") + log_file.write(contamination_H+"\n") + log_file.close() + return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list + +def get_input_K(input_file,lib_dict,data_type,k_size): + #kmer mode; get input_Ks from dict and data_type + kmers = [] + for h in lib_dict: + kmers += lib_dict[h] + if data_type == '4': + input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later + input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '5':#minion_2d_fasta + input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) + if data_type == '6':#minion_2d_fastq + input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) + return input_Ks + +def get_kmer_dict(lib_dict,input_Ks): + #kmer mode; get predicted types + O_dict = {} + H_dict = {} + Special_dict = {} + for h in lib_dict: + score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 + if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases + if h.startswith('O-') and score > 25: + O_dict[h] = score + if h.startswith('fl') and score > 40: + H_dict[h] = score + if (h[:2] != 'fl') and (h[:2] != 'O-'): + Special_dict[h] = score + return O_dict,H_dict,Special_dict + +def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): + log_file=open("SeqSero_log.txt","a") + log_file.write("O_scores:\n") + #call O: + highest_O = '-' + if len(O_dict) == 0: + pass + else: + for x in O_dict: + log_file.write(x+"\t"+str(O_dict[x])+"\n") + if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + #if 'O-9,46_wzy__1191' in O_dict or "O-9,46_wzy_partial__216" in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 + #modified to fix miscall of O-9,46 + if ('O-9,46_wzy__1191' in O_dict and O_dict['O-9,46_wzy__1191']>40) or ("O-9,46_wzy_partial__216" in O_dict and O_dict["O-9,46_wzy_partial__216"]>40): # and float(O946_wzy)/float(num_1) > 0.1 + highest_O = "O-9,46" + elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 + highest_O = "O-9,46,27" + else: + highest_O = "O-9" # next, detect O9 vs O2? + O2 = 0 + O9 = 0 + for z in Special_dict: + if "tyr-O-9" in z: + O9 = float(Special_dict[z]) + if "tyr-O-2" in z: + O2 = float(Special_dict[z]) + if O2 > O9: + highest_O = "O-2" + elif ("O-3,10_wzx__1539" in O_dict) and ( + "O-9,46_wzy__1191" in O_dict + ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 + highest_O = "O-3,10" + else: + highest_O = "O-1,3,19" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score = 0 + for x in O_dict: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + if highest_O == "O-1,3,19": + highest_O = '-' + max_score = 0 + for x in O_dict: + if x == 'O-1,3,19_not_in_3,10__130': + pass + else: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + except: + pass + #call_fliC: + if len(H_dict)!=0: + highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not + else: + highest_H_score_both_BC=0 + highest_fliC = '-' + highest_fliC_raw = '-' + highest_Score = 0 + log_file.write("\nH_scores:\n") + for s in H_dict: + log_file.write(s+"\t"+str(H_dict[s])+"\n") + if s.startswith('fliC'): + if float(H_dict[s]) > highest_Score: + highest_fliC = s.split('_')[1] + highest_fliC_raw = s + highest_Score = float(H_dict[s]) + #call_fljB + highest_fljB = '-' + highest_fljB_raw = '-' + highest_Score = 0 + for s in H_dict: + if s.startswith('fljB'): + if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other + #highest_fljB = s.split('_')[1] + #highest_fljB_raw = s + #highest_Score = float(H_dict[s]) + if s.split('_')[1]!=highest_fliC: + highest_fljB = s.split('_')[1] + highest_fljB_raw = s + highest_Score = float(H_dict[s]) + log_file.write("\nSpecial_scores:\n") + for s in Special_dict: + log_file.write(s+"\t"+str(Special_dict[s])+"\n") + log_file.close() + return highest_O,highest_fliC,highest_fljB + +def get_temp_file_names(for_fq,rev_fq): + #seqsero2 -a; get temp file names + sam=for_fq+".sam" + bam=for_fq+".bam" + sorted_bam=for_fq+"_sorted.bam" + mapped_fq1=for_fq+"_mapped.fq" + mapped_fq2=rev_fq+"_mapped.fq" + combined_fq=for_fq+"_combined.fq" + for_sai=for_fq+".sai" + rev_sai=rev_fq+".sai" + return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai + +def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): + #seqsero2 -a; do mapping and sort + print("building database...") + subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) + print("mapping...") + if mapping_mode=="mem": + subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + elif mapping_mode=="sam": + if fnameB!="": + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + else: + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) + subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) + ### check the version of samtools then use differnt commands + samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = samtools_version.communicate() + version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() + print("check samtools version:",version) + ### end of samtools version check and its analysis + if LooseVersion(version)<=LooseVersion("1.2"): + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) + else: + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) + +def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): + #seqsero2 -a; extract, assembly and blast + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) + #print("fnameA:",fnameA) + #print("fnameB:",fnameB) + if fnameB!="": + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output + else: + pass + outdir=current_time+"_temp" + print("assembling...") + if int(threads)>4: + t="4" + else: + t=threads + if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" + if fnameB!="": + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + else: + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" + #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging + subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) + #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta + subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) + print("blasting...","\n") + xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" + subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 + subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" + else: + xmlfile="NA" + return xmlfile,new_fasta + +def judge_subspecies(fnameA): + #seqsero2 -a; judge subspecies on just forward raw reads fastq + salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = salmID_output.communicate() + out=out.decode("utf-8") + file=open("data_log.txt","a") + file.write(out) + file.close() + salm_species_scores=out.split("\n")[1].split("\t")[6:] + salm_species_results=out.split("\n")[0].split("\t")[6:] + max_score=0 + max_score_index=1 #default is 1, means "I" + for i in range(len(salm_species_scores)): + if max_score<float(salm_species_scores[i]): + max_score=float(salm_species_scores[i]) + max_score_index=i + prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0] + #if float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare + if float(out.split("\n")[1].split("\t")[4]) > 10 and float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): ## ed_SL_0318: change SalmID_ssp_threshold + prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part + #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold + if max_score<60: + prediction="-" + return prediction + +def judge_subspecies_Kmer(Special_dict): + #seqsero2 -k; + max_score=0 + prediction="-" #default should be I + for x in Special_dict: + #if "mer" in x: ## ed_SL_0318: change ssp_threshold + if "mer" in x and float(Special_dict[x]) > 60: + if max_score<float(Special_dict[x]): + max_score=float(Special_dict[x]) + prediction=x.split("_")[-1].strip() + if x.split("_")[-1].strip()=="bongori" and float(Special_dict[x])>95:#if bongori already, then no need to test enterica + prediction="bongori" + break + return prediction + +## ed_SL_11232019: add notes for missing antigen +def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note): + antigen_note = '' + if ssp != '-': + if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:- + antigen_note = 'H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2 + antigen_note = 'fliC was not detected. This is an atypical result that should be further investigated. Most Salmonella strains have fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen != '-': # -:H1:X + antigen_note = 'O antigen was not detected. This result may be due to a rough strain that has deleted the rfb region. For raw reads input, the k-mer workflow is sometimes more sensitive than the microassembly workflow in detecting O antigen. Caution should be used with this approach because the k-mer result may be due to low levels of contamination. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:- + antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. ' + NA_note = '' + else: + antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. ' + NA_note = '' +# if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2: +# antigen_note = 'No subspecies marker was detected and less than 2 serotype antigens were detected; further, this genome was not identified as Salmonella. This is an atypical result that should be further investigated. ' +# else: +# antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. ' + return (antigen_note,NA_note) + +def main(): + #combine SeqSeroK and SeqSero2, also with SalmID + args = parse_args() + input_file = args.i + data_type = args.t + analysis_mode = args.m + mapping_mode=args.b + threads=args.p + make_dir=args.d + clean_mode=args.c + sample_name=args.n + ingore_header=args.s + k_size=27 #will change for bug fixing + dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging + seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging + database="H_and_O_and_specific_genes.fasta" + note="Note: " + NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format + if len(sys.argv)==1: + subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file + else: + request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) + request_id += str(random.randint(1, 10000000)) + if make_dir is None: + make_dir="SeqSero_result_"+request_id + make_dir=os.path.abspath(make_dir) + if os.path.isdir(make_dir): + pass + else: + subprocess.check_call("mkdir -p "+make_dir,shell=True) + #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging + #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). + ############################begin the real analysis + if analysis_mode=="a": + if data_type in ["1","2","3"]:#use allele mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + os.chdir(make_dir) + ###add a function to tell input files + fnameA=for_fq.split("/")[-1] + fnameB=rev_fq.split("/")[-1] + current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) + sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id + map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort + ### avoid error out when micro assembly fails. ed_SL_03172020 + try: + xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast + except (UnboundLocalError, subprocess.CalledProcessError): + xmlfile="NA" + H1_cont_stat_list=[] + H2_cont_stat_list=[] + ### + if xmlfile=="NA": + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") + else: + Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results + file=open("data_log.txt","a") + for x in Final_list: + file.write("\t".join(str(y) for y in x)+"\n") + file.close() + Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB + subspecies=judge_subspecies(fnameA) #predict subspecies + ###output + predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) + claim="" #04132019, disable claim for new report requirement + contamination_report="" + H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] + if contamination_O!="" and contamination_H=="": + contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." + elif contamination_O=="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." + elif contamination_O!="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." + if contamination_report!="": + #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 + contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. " + #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version + #if contamination_report+star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if O_choice=="": + O_choice="-" + antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + else: + new_file=open("SeqSero_result.txt","w") + ### ed_SL_01152020: add new output + conta_note="yes" if "inter-serotype contamination" in contamination_report else "no" + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tPotential inter-serotype contamination\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file[0].split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+conta_note+"\t"+contamination_report+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line="" #04132019, for new output requirement, diable star_line if "NA" in output + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+conta_note+"\t"+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + #subprocess.check_call("cat Seqsero_result.txt",shell=True) + #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) + subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + else: + print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") + elif analysis_mode=="k": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging + #output_mode = args.mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + input_file = for_fq #-k will just use forward because not all reads were used + os.chdir(make_dir) + f = open(ex_dir + '/antigens.pickle', 'rb') + lib_dict = pickle.load(f) + f.close + input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) + O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) + highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) + subspecies=judge_subspecies_Kmer(Special_dict) + if subspecies=="IIb" or subspecies=="IIa": + subspecies="II" + predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( + highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) + claim="" #no claim any more based on new output requirement + #if star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if highest_O.split('-')[-1]=="": + O_choice="-" + else: + O_choice=highest_O.split('-')[-1] + antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + # ### + else: + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) + new_file=open("SeqSero_result.txt","w") + #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## + ### ed_SL_01152020: add new output + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file.split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line = "" #changed for new output requirement, 04132019 + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+NA_note+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/SeqSero2_update_kmer_database.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,113 @@ +#!/usr/bin/env python3 + +import argparse +import os,subprocess +import pickle + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') + return parser.parse_args() + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + +def multifasta_to_kmers_dict(multifasta): + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) + return lib_dict + +def get_salmid_invA_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/invA_mers_dict', 'rb') + invA_dict = pickle.load(a) + try: + del invA_dict['version'] + except: + pass + return invA_dict + +def get_salmid_rpoB_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/rpoB_mers_dict', 'rb') + rpoB_dict = pickle.load(a) + try: + del rpoB_dict['version'] + except: + pass + return rpoB_dict + +def main(): + args = parse_args() + ex_dir = os.path.dirname(os.path.realpath(__file__)) + lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') + invA_dict=get_salmid_invA_database(ex_dir) + #rpoB_dict=get_salmid_rpoB_database(ex_dir) + lib_dict_new = lib_dict.copy() + #print(len(lib_dict_new)) + lib_dict_new.update(invA_dict) + #print(len(lib_dict_new)) + #lib_dict_new.update(rpoB_dict) + #print(len(lib_dict_new)) + f = open(ex_dir + '/antigens.pickle', "wb") + pickle.dump(lib_dict_new, f) + f.close() + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/bin/deinterleave_fastq.sh Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,30 @@ +#!/bin/bash +# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] +# +# Deinterleaves a FASTQ file of paired reads into two FASTQ +# files specified on the command line. Optionally GZip compresses the output +# FASTQ files using pigz if the 3rd command line argument is the word "compress" +# +# Can deinterleave 100 million paired reads (200 million total +# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) +# +# Latest code: https://gist.github.com/3521724 +# Also see my interleaving script: https://gist.github.com/4544979 +# +# Inspired by Torsten Seemann's blog post: +# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html + +# Set up some defaults +GZIP_OUTPUT=0 +PIGZ_COMPRESSION_THREADS=10 + +# If the third argument is the word "compress" then we'll compress the output using pigz +if [[ $3 == "compress" ]]; then + GZIP_OUTPUT=1 +fi + +if [[ ${GZIP_OUTPUT} == 0 ]]; then + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 +else + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/seqsero2_db/H_and_O_and_specific_genes.fasta Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,7094 @@ +>fliC_g,m_Enteritidisstr_AKFY01000033_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m,s_Montevideostr_AESV01000018_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Salmonella.enterica_Stanley_AY353267_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,2_Saintpaulstr_AYDS01000021_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_z4,z23_Cerrostr_AYVH01000420_z4,z23__1257 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATACAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_4,[5],12_i_-str_ABAO01000026_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Typhistr_AJGK01000049_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAATGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATTGATTTA +AAAGAAATCAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATCCTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTGGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCAGCAGGGGTTACTGGCGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTGCAATTACTGCTAAAACCACTACTTATACAGATGGTACTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAGACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCAACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Salmonella.enterica_Kentucky_AY353427_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r_Heidelbergstr_AJGW01000023_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Heidelbergstr_AMMX01000009_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z6_Kentuckystr_AYDR01000034_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCTGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_g,s,t_Senftenbergstr_AOYU01000052_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTGATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Manhattanstr_CBKW010000019_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_e,h_Salmonella.enterica_Saintpaul_AY353377_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCGCGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5,7_Salmonella.enterica_IIIb.6,7:l,v:1,5,7_AY353273_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,p_Dublinstr_ATFR01000073_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,2_Salmonella.enterica_Muenchen_AY353269_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAATAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,m_Salmonella.enterica_Enteritidis_AY353386_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Typhimuriumstr_AUQT01000018_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTAAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Hadarstr_ALPP01000007_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z29_Salmonella.enterica_Tennessee_AY353474_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGACAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGCCTTGGAATGGATGGTTTTAACGTTAATGGCGCGCACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAAAGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTGCAGTGTTTTCCTTTGTAATTACTGGTGGTACAACACCTTCCTCTGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATGATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGCAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAAGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Infantisstr_ASRF01000034_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTGACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCAGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_i_Salmonella.enterica_Typhimurium_AY353420_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,p,s_Montevideostr_AETD01000005_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AAAAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,6_Anatumstr_AOZZ01000116_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_k_Salmonella.enterica_IIIb.38:k:z35_AY353439_k,z__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAACCAACAAG +TATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTA +AAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGC +GGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAA +ACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAG +GCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGAT +GGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACACTAC +GTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTT +CTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCT +ACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCG +AAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCG +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z6_Sloterdijkstr_AOXT01000012_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGATCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_1,7_Salmonella.enterica_Bredeney_AY353296_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCCGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_e,n,x_Minnesotastr_AOYO01000082_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCCTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_z4,z32_Salmonella.enterica_Tallahassee_AY353507_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGGCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGGGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2_Typhimuriumstr_AHVA01000007_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACTACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,5_Salmonella.enterica_Thompson_AY353285_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTGC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCTTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,2_Salmonella.enterica_Typhimurium_AY353264_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,7_Pomonastr_AHIA01000072_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCGCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATATTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_k_Salmonella.enterica_IIIb.65:k:z_AY353438_k,z__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCTTGGGTCTGGATGCGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAACCAACAAG +TATGAAGTTGGATACTAGCGGTATAACAGCGGAGGCAATTAAAAACGGTGTAACTGGCGCAACGACAGATGGTGCACTTA +AAGACGGCAAGATTTATTCCGATGGTACTAACTACTACGTAGAAGTTAGCTTTGCTGCTACCGCAGACACAAGTAAAGGC +GGTTTTCTTAAAGTGGATGTTGATTCCTCTAATGGTAAAGTGTCTATTCCTACCACTGCTGCATCTGCTGTCGCGGCAAA +ACCAGCTGGAGTAAAAGAAGTTTCTGAAGTTCAAGGGAAAATTGCTGCATCAACAGATGTTAAAAATCAATTGACAGCAG +GCGGTATTGATGCTGGTGTTGCCGCCAATGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGAT +GGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACACTAC +GTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTT +CTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCT +ACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCG +AAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCG +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_j_Salmonella.enterica_Typhi.var.j+_AY353433_b,d,j__1260 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAATGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATTGATTTA +AAAGAAATCAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATCCTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGCGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAG +GTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTGCAATTAC +TGCTAAAACCACTACTTATACAGATGGTACTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAAT +CTGAAGTTGTTACTGCTACCGATGGTAAGACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAG +CTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCAACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Anatumstr_AOZZ01000009_e__1497 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,6_Salmonella.enterica_Poona_AY353295_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCGCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACCATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_f,g,t_Salmonella.enterica_Berta_AY353532_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATCCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTAACAACTGAC +GATGCGGAAAATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGC +TGGTGCCATTAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCA +ATGACGGTAATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCG +GCGAATGTTGATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTTAGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCT +AAAGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_d_Schwarzengrundstr_ABEJ01000027_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGA +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTGTTACAGCCCAGAGCAATACTGATATCGAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTT +GGCACAGGTTGATACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_k_Thompsonstr_AMSN01000007_k,z__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAAACTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z23_Salmonella.enterica_IIIa.43:z4,z23:-_AY353495_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCCGCTGATTTCGATAACGCAAAAGCAACGGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z39_Salmonella.enterica_Grancanaria_AY353489_other.z39__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCCTCCGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAGCGTATGATGTGAATAGTGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCACTAAATATTAGCGGTCTTGATGATGCTGCGATTAAAACCGCGGTTGGGGGGACACCAA +CTGGTACTGGTGAAATTAAAGATAACAAAGTTTATCACAACAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAACGGTTTCTATGAAGTAGAGGCAAACCCTACTGATGGTACAGTTACATTTGCTACCGGTGCTACTAA +AATAACGGCTAAACCAGCTGGTGTTGAAGAAGTTACAACTGTCCAATCAAAACCCGTAGCTCTCAGTGCTGATGTTAAAA +CTCAATTAACTAATAGTGGAGTTAGTACTGCAGACGCTGATAAAGGTCAGTTAGTCACTATGTCTTATACGGATAAAAAC +GGTAAGACGATTGATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTT +TAGTATCAACACCACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCACAGCCAGAA +CTGGCGGAAGCGGCTACTACAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTGGATGCACTGCG +TTCTGACCTGGGCGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACCTCCGTTCTGGCACAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Chesterstr_AOZI01000020_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_r_Infantisstr_ASRF01000003_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCTTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>sdf-I_AF370707__333 +GATCTATCCTAATGAAAATAAATGTGTTTTATCTGATGCAAGAGGGGGAGGGAGGAGCTTTAGCCAAAAGAAAACCGCCG +GGAGAGGCGGTTTGATGTGGTTGGTTCGTCACTGATTTTTTAGGCGCTTTTGTGCAGCGAGCATGTTCTGGAAAGCCTCT +TTATATAGCTCATTCTGACCTCTAAGCCGGTCAATGAGTTTTTCTTTCTCAGATTCAGGGAGTATATCAAAAAGGTTTAG +TAAATCAGCCTGTTGTCTGCTCACCATTCGCCAGCCACCACCTTCGAAGTTGTCATCGTAAGTACCAGAAGAACGAACGT +AGTTCATTAGATC +>fljB_z35_Salmonella.enterica_III.b.65:z52:z35_AY353342_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_r_Infantisstr_AFYI01000002_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAGGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_k_Salmonella.enterica_II.52:c:k_AY353328_k,z__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGGCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACTCTGACCATTCAGGTTGGCGCCAACGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTGATAGCAAAGCTGCGCA +AAGCGTTAAACTGGATACCAGTGCTCTTACTGCCGCTGCAATCAAAGGCGGTGTAACAGGTGCAACAACAGATGGTGCCC +TCAAAGACGGTAAAGTTTACTCTAATGGCACAGACTATTATGTAGAAGTAAGCTTTGCTGATGCAACGGACTCTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCACTACTGGTAAAGTTACCGTACCGGGTACGGCAGCAGCAGCTTCTTCAAC +TAAACCTGTTGGTGTGAACGAGGTTACAGAAGTACAAGGTAAAATCCCTGCATCTACTGCTATCCAGGACCAATTGAAAG +CTGGTGGTGTGAGTAACGCAGATGCTGCTACTGCTGAGGTTGTCAAAATGTCTTATACCGATAAAAATGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTAGGTGATGACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +CACGTCTTACACCGATAAAGACGGCAACACTAAATCCGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAACCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCCGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_k_Salmonella.enterica_Inverness_AY353441_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAGACTGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Hadarstr_ARYR01000012_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fliC_g,m,q_Salmonella.enterica_Blegdam_AY353393_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGGCGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2,7_Salmonella.enterica_Kambole_AY353275_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGGGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAACAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTGGACGCTACCAATGCTAATGGCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_m,t_Salmonella.enterica_Oranienburg_AY353411_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGCTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGCGAGTGCA +ACAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_g,p_Salmonella.enterica_Dublin_AY353399_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Augustenborg_AY353418_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCTCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,s_Salmonella.enterica_Agona_AY353383_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Muensterstr_AOYX01000059_1__1511 +ATGGCACAAGTAATCAACACTAAcagtctgtcgctgctgacccagaataacctgaacaaatcccagtccgcactgggcac +cgctatcgagcgtctgtcttctggtctgcgtatcaacagcgcgaaagacgatgcggcaggtcaggcgattgctaaccgtt +ttaccgcgaacatcaaaggtctgactcaggcttcccgtaacgctaacgacggtatctccattgcgcagaccactgaaggc +gcgctgaacgaaatcaacaacaacctgcagcgtgtgcgtgaactggcggttcagtctgctaacagcaccaactcccagtc +tgacctcgactccatccaggctgaaatcacccagcgcctgaacgaaatcgaccgtgtatccggtcagactcagttcaacg +gcgtgaaagtcctggcgcaggacaacaccctgaccatccaggttggtgccaacgacggtgaaactatcgatatcgatctg +aagcagatcaactctcagaccctgggcctggattcactgaacgtgcagaaagcgtatgatgtgaaagatacagcagtaac +cacgaaaacttatgccaataatggtactacactggatgtatcgggtcttgatgatgcagccatcaaagcggccataggtg +gtacgactggtacgcctgctgtaacgggcggtacagttaaatttgacgcagataataataagtattttgtttctattggt +ggctatactggtgctgatgcatccaaaaatggcgattatgaagttaacgttgctgctgacggtaaagttacacttgctac +aggtgcaactaaaaccacaataccggcaggtgcgacaactaaaacagaagtacaggagttaaaagatacaccaacagttg +tttcagcagatgcgaaaaatgccttaatcgctggcggcgtggatgctaccgatgctaatggcgctgagttggtcaaaatg +tcttataccgataaaaatggtaagacaattgaaggcggttatgcgcttaaagctggcgataagtattacgccgcagatta +cgatgaagcgacaggagcaattaaagctaaaaccacaagttataccgctgctgacggcgctaccaaaacagcggctaacc +aactgggtggcgtagacggtaaaaccgaagtcgttactatcgacggtaaaacctacaatgccagcaaagccgctggtcat +gatttcaaagcacaaccagagctggctgaagcagccgctaaaaccaccgaaaacccgctgcagaaaattgatgccgcgct +ggcgcaggtggatgcgctgcgttctgacctgggtgcggtacagaaccgttttaactccgctatcaccaacctgggcaata +ccgtaaacaacctgtctgaagcgcgtagccgtatcgaagattctgactatgcgaccgaagtttccaacatgtctcgcgcg +cagatcctgcagcaggccggtacttccgttctggcacaggctaaccaggtcccgcagaaCGTGCTGTCTcT +>fliC_z_Indianastr_AOZC01000051_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCGCGAATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGA +ACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAG +CTGCTTTGACTGCTGGTGGCGTCGATGCTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTT +CAGTGTTAATACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_b_Salmonella.enterica_Paratyphi.B_AY353358_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Salmonella.enterica_Sandiego.var.d+_AY353378_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGATGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAGGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGCTGCGTTCTGACCTGGGTGCGGTCCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACC +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_Braenderupstr_AOZM01000055_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGTGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAGTTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_l,v_Litchfieldstr_APAN01000015_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTATTGCGTTAA +>O-9,46,27_partial_wzy__1019 +ATGTTACCGCATACATTTATGTTCCTGATTTTTAATATAGTATATATGTTACCAGTAGCCTATGTACATTTTTTTGGGTT +CTCCCTTGGAGGGGTTGAAGAGATTCTCAACGGTGATCCCAGTATGCTTGCAGATATGATGGTCTTTTACGTCGCTGTCT +GGTTCTTTTATCTTGCCGGTTCGGCATTATTAGGATTTGGTATAAAAAATAAAAATATACAATGGATTATAGCATTCGAA +CTTCCAATTATTGTAAAGATTTTATTCAGTTTAGTTTTATTTTTTATAGTACTATCAAAAGTATTGCTTTATCCTGAAGG +GGTTTACTCATCTTATGCCTTTGATTCTGGCGCTATGGCAAGTCGTGTCTGGAATATCTCGATGGGATTATCAGAACTAG +GTATAATAATTTTTACATTTTGTTTAGTTACAAAGAATATAAAGTTTGCAGTTGTTACCTTTCTTATAGTCTCATTAAAT +CTACTACATGGGACTAGAATATTTACATTGATATTACTTTTAATGATCATATTTTATATAATTTTTATTAATAAAAAAAT +ATCAAAGCTGAAATTATTTATTATTTTGAGCCTTTTTTTTGGCGCAATAGTGATATCATTTTTGATAATATTCATTATCC +GTTCTAATGTTTCAATTGAAAATATAAATATAGACCTAATTCTAAGTCCAATAGTATATGAGTCTTTATTTAATCAAATA +TCTTTTATGCGGATGCTGGATTGGCTACATCAAGGGGCAGTTCCGTTTGCACCACAAATGCTTTTTTCTGATTCAGCTAT +ATTTACGTTACCGACTTTTCTTTTTGATGAAAAATCATCTTTAATGTATATAAATAAATTTGGAGAACTTAGCCCTTTAG +GTGGGCTTTCCGGTTATGCTAGTGCAGTAATATATTTTTCGTATTATTATTTCCTGTGGTATTTTATTCTCGGTATTACA +TCAAGCTTATTATTAAGGTTTACATCGAGTGTAAACTTTGTAATATTGTCGAGAGTTAT +>fliC_z69_Salmonella.enterica_Pietersburg_AY353520_k,z__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACCGCAAACATCAAAGGTCTGAGCCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACGCAGCGTCTGAACGAAATCGACCGCGTATCCGGTCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACTCTGACCATCCAGGTTGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAATTCGCAGACCCTGGGTCTGGATACGCTGAATGTACAGAAAGCGTATGATGTTGATAGTAAAGCTGTAAC +AGTAGCTGCTGATTTAGATATTACCGCTCTTAATACCGATGCAGCTCTTAAAGCAGGAACGGGAGCTACAACAGGTACTC +CATCAATAAAAGATGACAAAGTTTATTATGATAGTGCCAGCAAAAACTACTACGTTGAAGTTACCGGATTAACCGCCCCT +GATGATGCTAAGAATGGCTTCTATAAAGTAAATGTTGCTGATGACGGTACAGTATCCATGGCCGCTAATACAGCTATAGA +GGCGGGTAAACCAGCCGGTGCAGTAGAAGTAACAAAAACTCAAGAAGAAAAAAACCCATTACCATTATCAGCAGATCTCA +AAACTTCTCTTAAATCTGGCGAGATTACAGATCCAGACATTGCTACCGCCCAAGTTGTCAAAATGTCTTATACCGATAAA +AACGGTAAGACGATTGATGGCGGTTATGCTGTAAAAGTAGGGAATGATTACTATGCTGCCACTCAGAAAAAAGACGGTAG +CTTTAGCGTTAATACCACTTCTTATACCGATAAAGATGGCAATACTAAATCTGCACTGAATCAACTTGGCGGCGTAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAACGCCAGCAAAGCCGCTGGTCACGATTTCAAAGCGCAGCCA +GAGCTGGCTGAAGCCGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTCCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.62:z4,z23:-_AY353545_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-9,46_wzy__1191 +ATGAGATGTGCTATGGTATTTTTAGCGTGGTTTATTGCTATTGGGATATATATAATATGTGGTATTTTTTATCTTCAATT +TCCTCAATTATCACCACTAGGGGCTCTTGCATATACTGATACAGTGGGCGATGTAATCATTGTCGTATCCACGGGGATAG +TGGGAGTTTTTCTCGGCTATTTTGCATTTTCTAAAATCAAGTTAGTAGGAATAAAAGATTTTAATAATTCGTGTTTTATA +AATTTTTGTTCAGTATGCTTTATTATTTCAGCGTTTCTAATTTTCGCCTTAGGCGTCGCTGCATATGGTGGTTACATAGC +ATTTCTACATACGCCTTATATAGCAATCTATGAAGGTAGTGCAGAAAATCAAACCAGAGATATCCTCATATCTTCATCGG +GATTGCTTGCTAACTATGCACTATTAACTAGCATTCGTGTCAACTTTAAAGAAATATCAATAACTAATAAAGTTGTCATA +GCAGTATCGCTATTAATACTTGTTTCTATATTTATTCAGGGACGAAGAGAAAATTTAATTTTGCTAATATTATGTTTCGT +GTCATTCTATATGCTAAATTATAAAATTAATTTTAAACGTATTATCAAAGTAAGCATTATTTGTATAATAATGTTTTTCA +TTGCTGGATTAGGTTTATATTTGCGTGAAAGCACTTCAACTTCAGGAGGAAGTATTTTTACAGCTATACCTTTTGCCGTG +ATGTATGAAACACATTTTTCTTTAGCGACTTTGGCTAATGAAGTGAGAACGCATTTATATAATAATTTACCTTATGGGGG +AGTATTAGATTTATTTTCTCCCATATTATTTATTATCCCTGCTTTTATATATGGGATTTTTGGTTTAGATAAACAATCTT +TGTTCGAGAATAATGAGATGCGTTTTTATGAGGATAAAGGCGGCCAGTTTATATTCACAGAGGCTTTTCATTCACTTGGT +TATGTCGGAGTATTCCTGCATGGTTTAATCTTGGGTGTAATGCTAATAGTATTTTATCGTGTAGCCAAGAAAAGCAGGCT +CATAATTTATCATTTTCCAATTATTTCCCTCATATTTGTTGCAATGAGAAAAGACCTTACCTATGGTGTTAAATATATTT +CTCTTTTGTTCATATTTATGATGATTTTTTATTTCATCTATAAGTTACTCCCACTTAAAAATAATGGTTGA +>fliC_f,g_Havanastr_APAH01000011_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTTTACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>O-45_wzy__1164 +ATGTCGTACAAAAGTAATAATTTCTATAGAAATATACTTTTATTGAGTTTTTTCTTTTCTGGCTTTAGCTTGTATACTGT +TTTTATACCGTTACTATTTTTGACTATTCTTCTTTCTTTGCACAAAAATAAGGCACTGTATTTTGGAAGGCTAGCAGCAA +GCGCTAATATATTATTTATTATTTTATTTATTTTATTTGTTTTTTTTATAGGGGAAGATAGGCTATTATTAGAAAAACCA +TTTAAATATGCAGCATATATTATATTTATGATTTTTTGTTTGACATTATTACTATTGAATAATATAGAATATGCACAGAA +AGCAATACTATTTTTTATTTTTGGAATATTTTTACGAGCAGAGATTATTGTTATATATAGTTTCCTTGACCCATCAGGAG +TCTATGGATATGGTAAATTATTAGATCCTTTTAACCATGAAGAAATTAACTCACCAGGTATCAGTAATTCACTGGCTATG +GTTTTTGTATTTTTATTAGTTGTTTTCGAACCGAAGACATTAGCCAGAAAAATTTTTCTTATACTAGTTTACCCGTTACT +TTTATTATCCTCTATATTTTTAGGAGGGCGAGCATTTTTTATAATTGCAATTCTTGGGTTGGTTTATCAATACAAAAATA +ATACAAATATAAAGGCGATTATTTTTTTATTATTTTCTGCTCTTGGATGCTTAGTGCTATTTTTTATTATGTTTAAGGAC +GCTCCAGTTTTCGAAAAATATTTTAATTTAATTTTTGAGCGTTTTGGAAGTGAAGGATTAAAATCAGCACGCTTTGAACT +AATACAGGACGGGATTAGTAAATTCTTTATGTATCCGTTTGGAGGGTTTACTCCATATGCAAGTGAATACTCAGGTAGTT +GGTATCATAATATATACTTGGATAGTGCCAGAGTTGCAGGTTTTTTACCTTTGATAATGTTTCTTATATCAAATATTATT +TTATTTTCATGCTATTTCAAGTGTAAAAAGCGTAATCACAAAAATAAATATTTTTTCTTGTCAGTTATTACCTTAATTAT +AATGTGCCAGGACGTTATTCTCGAAGGAAATATGATGTTGCTGATTTGTTATGCATTATTCACAACAATGCAACTTCAAA +CGGGAGGGAGAAGTAAAAATGAAATTATATTACAGAGTAAATGA +>fljB_1,7_Indianastr_AOZC01000015_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTTGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGTGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTACGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCG +CAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z6_Kentuckystr_AOYY01000105_k,z__1493 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCTGCTAAAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,5_Bareillystr_AOZP01000315_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACATACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_z39_Salmonella.enterica_II.6,7:z39:1,5,7_AY353349_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAATCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTACGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATACAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGTTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z39_Salmonella.enterica_II.51:l,z28:z39_AY353348_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGCCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGTCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Manhattanstr_CBKW010000016_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACATACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCT +>fljB_1,5_Idikan_SRR1272896__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACGACACTGGATGTATCGGGTCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O-44_wzy__1134 +ATGATAATAAATAATATATTATTAATGGCATTATTAGCTGTATGTACTATAGACCTACCTTCCTTTATAGTAGTTTATGG +CTTGCAATTGTATATTCTGCCGTGTATTGTACTAATGTGTCTAATAAGAGGGGGAGTGTTTCCATTAAAATTTTTTTTCG +TAGCATCTTTTCTATCATTAATAATAATTATTATTACCGTAATCCAGGAGACTTATACTCCCTATCCTGATTTACTATGG +AGTTATACTGCTAGATTAATTTATTGGATTATGGTTTTTACACTGCTTATTCCATTTATACAAAAAATACCACTGATAGA +TTTAATAAAAATAATAAGAAGATGGATATTGTTATATTCTACATTCTTATTTATACAGTTTATAGCATTTTATCTATTTC +ATATTATAGTTGATTACTCATTAATTATTGGTGGTCAGGAATCAAGAATACTAAACGAAGTAGGTTTAAGAGCTTCCGGC +TTGACTGCTGAACCCTCAATTTATTCCGGGATAATGATTTCACTATTGATACTATTGTATCTCATGACTGGGAAAAATAA +TATAATAACATACATAGGGTTAATAAGTATATTATGTACTTTATCTACTTTAGGAATTTTTTTGGTTATTATTTATTTAG +CTATAACAAATTTATATCGAATTAAAATTTCTAGAATAGTCTTTTTTATATCCCTTTCAATTGCAATTATTTTTATTTTA +TGGGATTTTATTTTAAAAAGAATAGAACTTTTTCTGCAGGGCGGGGATGTTAGTAATAATATAAAAATCATGGTCATTGA +TAATCTGTTTAATAATGAGTCTTTATTTTTGCTTGGATATGGGTTGGTTGGTTATAGTGATAAAGCTCCCCCATATTATC +AGGCTCTTTATGACCTAACTTTATTTGGGAATTTATGTGTTATCTTTGGTATTCCTATTGGTCTTATGTTATCTATAACT +GTTTTTTTATTTACGTTGAATATGAGGATTTGTTTCGAGAAGAAAATACTGATAATTCTTTCTTTTATAAAAATCACTAT +CCCAAACTATATATTTTTTTATTTTTTCTTGGTTTTACTATATGTCATAACTAATAAAATATCGGTAAGATATCACAATA +GAAGAGAAGTATGA +>fljB_1,2_Saintpaulstr_AOXF01000050_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_1,2_Newportstr_AJMO01000050_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_e,h_Meleagridisstr_AOYN01000134_e__1497 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGATGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCACGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGCCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Salmonella.enterica_Istanbul_AY353471_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGGCGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z35_Salmonella.enterica_Tema_AY353480_other.z35__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCACAGACCACGGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAATC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGTGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +GGCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTACACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTCG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACGATTTCAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,v_Salmonella.enterica_Brandenburg_AY353444_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGCCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r,i_Salmonella.enterica_Bovismorbificans_AY353463_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTA +GCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACAC +TGCAGAAGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTG +GTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCTACAACC +ACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAA +CCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCG +ACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAAC +CAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z6_Salmonella.enterica_II.48:e,n,x,z15:z6_AY353519_k,z__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +AGTAGCTGCTAATTTAGATATTACTGATCTTAATAAAGATGCGGCCCTTAAAGCAGGGACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGACAAAGTTTATTATGATAGTGCTAGCAAAAACTACTACGTTGAAGTTACCGGTCTGACTACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTATCTATGGCCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAGAAAAATCCATTACCGTTATCAGCAGATCTCA +AGACTTCTCTTAAATCTGGCGGGGTTACAGATCCAGAAATTGCTGCTGCCCAAGTTGTCAAAATGTCTTATACCGATAAA +AACGGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAG +CTTTAGTATTAACACCACGTCTTACACCGCAGCTGACGGTACATCCAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTCAAAGCACAGCCT +GATCTGGCGGAAGCGGCTGCTACAACCACCGAAAATCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTT +ACGTTCTGACTTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Bareillystr_ALPN01000010_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Kentuckystr_AYDR01000065_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCTATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGGTGGCTATTATGAAGTTTCCGTTAATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z23_Salmonella.enterica_IIIa.18:z4,z23:-_AY353546_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGAAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Albanystr_AOZW01000055_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATTAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAATTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACCTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Salmonella.enterica_Agama_AY353430_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-44_wzy2__1247 +AATACGCTCTGTACCACCTGAATTACTTAGATCGTTTATAAAAAAACAAATAGTTTTCATAGTTCTCTTCTATTATGATA +ATTTTACCGATATTTTATTAGTTATAGCGTATAGCAAAACCAAGAAGAAATAAAAAAATATATAGTTTGGAATAGTAATC +TTTAGAAAAGAAAGAATTATCAGCATTTTCTTTTCAAAACAAATTTTCATATTTAGCACAAATGCAAAAACGATTATAGT +TAATATAAGACCAATAGGGACACCAAAGATAACACATAAATTCCCAAATAGCGTTAGATCATAAAGGGCCTGATAATATG +GGGGAGCTTTATCACTATAACCAACCAGCCCATAACCAAGCAGAAATAAAGATTCATTATTAAATAGGTTATCAATAACC +ATAATTTTAATATTATTACTAACATCTCCCCCCTGCAGAAAAAGCTCTACTCTTTTTAAAATAAAATCCCATAATACAAA +AACAATTATAATTGAAAGAGATATAAAAAAAATTATTTTAGAGGGTTTGAGTCTATATAAATTTGTTATAGCCAAATATA +GAATAACCAGAAAAATCCCTAATGTAGATAAGGTACATAATATACTTGTCAGACCTATGTATGTTATTATATTATTTTCC +CCGGTCATAAGGTATAACAATATTAACAAAGAAATCATTATGCCAGAATAAATTGAAGGTTCAGCAGTCAAACCTGAGGC +TCTTAAGCCTACTTCATTTAATATTCTTGATTCTTGGCCACCAATAATTAATGAGTAATCAACGGTAATATGAAATAGAT +AAAATGCTATAAACTGTATAAATAAAAATGCAGAATATATTACTATCCATTTTTTTATTACTTTTATTAAAATTTTCGGT +GGTATTTTTTTTATAAATGGAACAAGCATTGTAAAAAGCATAATCCAATAAATTAACCTAGCAGTATAACTCCATAGTAA +ATCAGGATAAGGTGTATAGGTCTTTTGGATTAAAGTAATAATTATTATTATGAATGATAAAGAGAAGGTGACGAAAAATA +GTTTTACTGGGAAAACCTTTCCTCTAATTAAACACATTAGTACTATGCATGGTAAAATATACAATTGCAAACCATAAACT +ACTATAGAAGCTGGCAAATCTATAGTACATATAGCTAATAATGCCATTAATAATGTATTATTTATTAACATATTAATATC +TTATTTATTTCTTATAAAAATATAATATAAACATTGAAAATATCGTA +>O-51_wzy__1026 +ATGCTTATCTATAATACAGTGTTCTTATTTTTGGTATTATGTGCATTGCTGGATTTAGCTGACAAGAAAAATTTTTTTTT +GTTTACATTGTCATTTATAGTATTACTTATATTAATGGGATTTCGTGGAAATGGTGGTGATGATTTTTTGGTTTATCAAC +AATACTTTAATTCACTACCAATAATATTGTATGATTATGGTGTTGGCTATTTTTATCTGAATTCTTTTGCTAAATATTTT +GGCAATTATGAATTTTTTATTTTTGTGTCTTCTTTATTATGTCTCTCGCTGCAATCATTTTTTATTTATAGCGAAACAGA +AAAACCATGTCTTGTCTTGCTGCTATTTTATTCAACTAGTTTTTTATGGCTTGACTTTATTCTTATAAGGCAGTCTATTG +CCGTAGGATTTTTTGTAGTTGCAATAAGTTTATATAAGAATAGCAGGAATAAATTGAGTTTTTTATTTTTTGTTTTTTCT +GCATTGTTCCACGAAACAGCATTTTTTGCTGCAGCTTTATTTTACATTTTTAGTAAACTAGAGAAAAAGGGGATTCTCAT +TGCCATTTTGATATTACTCATTTTATCTCCTTTTCTTTCAGATATTTTAGTTATCATCAATAATATTACTATAAAAAACA +AAAATGTAGAGTTATATCTCGGAGAGCATGCTTTACCAAGTATAGCTAATATAGCTGAGTTTTTGATGGCAGTATTAGCT +TTTATTATAATTAAAAAAGATGATATATTTAGAAATAGTAAAGAATATAGATTGTATAAAGTTATAATTATAGCATCCTT +TTGTATATTAGTGTTATCCTATACTGTTCCTACCTTGGCTCGCTTTCTTGAATACTATCGATTATTTTATTTCTTATTGC +TAACTCGTATGTTCATGTATTTTAATTTAAGAAGCCGATATATGATATTTATTGCTCTTACAGTATATGGTTTTGTCCGT +ATGAATAGTTTTATATATCAGTTCGATTCTGGATTTGATTATATATTTAATGGGAGTTCTATATGA +>O-3,10_wzx__1539 +ATGTTTAGAAATAAAGTTGCTCTTGGGTCTCAGATAGGATTGTTTACTTCAGTTCTTATATTAATAACAAACTTTTTTTT +AAGAAGTTACTTTGTTAAAGTATATGGTGCTGATTTAACCGGGTATTATTTATTAGTAGTACAGTTGATGGGAGTATTAA +ATCTTGCTGAGCTAGGTATAAGTACAGCCTTAACATATATCCTATTTAAACCACTGCATAGAAAAGAAAATAGTGAGTTA +AGACAATTATATTTTATAATAAAGAAAATATACCATTTTATAGCATTGGGCATATTAGTTATTGGACTACTTTTCTTTTT +GTTATTAAATTCTATAGTAAATGCAAGTATATCCCCTGAAAATCTATATATAACATGGGGGGTGTTTGTTATAAGTACAT +CATTATCATATTTATACTCTGCTCAATCTGTCATTTTAACAGCAGACCAGAATGTCTATTTGGTTAAATTAATTACTGGG +TTAACTAGAAGTTTAGCGTATATATTGCAAATATTTCTAATGATTTGCGGCGTCTCCTTTTGGATTGTGTGCGCTATTGA +ATTACTTTCTAATGTAATACAACTTATTCTTTTTAACAAACTAACATTAAAAAAATATCCGCAATTAGTAAAGTTGGATA +TTACTGATACTATCAATAAAGAAAATATAATAAGTGTAAAATCTAAAATAAAAAGAGAGATAAAATATACGTTTGTACAT +AAAATTGCCGGTGTTGTTGTATTTAATACAGATTATTTAATTATATCTGTCTTTCTAGGTATAACGGTTATCACATCTTT +TTCTTCCTATATGATGTTAATTCAAGCATTGGCTTTTCTGATATCAGCAATAGCTTCCCCACTGGGTGCCTATATAGGAG +CAAAACTATATTCTGATAGTAAGGAAAAAGTTATCAGGATTATATCACTTTATAATTCACTTTTTTTTATGCTAGGTATT +TTTTGCGCGTATATGTTTTATATATCTTCAAGTACATTTGTATCCTTATGGATGGGAAAAGAAATTGTACTTAGCCAACA +ATTAGTTTTGTTACTTTCTGTTAATTGCTTCGTATTGATTGCAAGGATCTCTTTTGATGTTGCAAAAGTAGGCCTTGGTT +ATATGTCAGATATTGAATTACCCCTACTGGAAGCCATAATTAATATTATCGTTTCATTAGTTTTAGTACATTATTTAGGT +TTAAATGGGATAGTTATTGGAACTATCGTTAGTAATATCATCGTTGTCATGATCTTGAAACCAGTATTTTTATACAAAAA +TGCCCTTAAATCGGATAATGCATTTATTATTCATGAGCTTATAAGGTCATGGTTCTTTATAAGCATATTCTTGCTTTCCA +TCTTTTTTATTACAAGGGCAAAAGTTATAGTCAGCAACGAATGGCTAGATTTCTTTATACAAGTGTGTATGAGTAGCATT +ACTCCTTTATTGTTATTGATAATGATATACAGCGTCTTTGATAGCAACGTTCGGAAATTCATGTTTGTTATGTTTAAAAA +AAAGTATAGGGAAAATTGA +>O-13_wzx__1236 +ATGGAAAAGCGTATTTATATAAATACCATTGCTAATTTATGTGGGGTTTTTTGGCAGGGAGCTATAATTCTTTTAATGGC +TCCTTTTTACCTGAAGTTATTAGGGAAAGAACAATGGGGTATGGTGGCTGCATGTTTATCCTTACAAGGGATATTATTAC +TGCTTGATGCAGGAATGTCACAAGTTATGCCAAGGGACTTTGCACAAAAAAAACAGAATATTAAAGAGATATATTCAAAC +TATATAGCTTTATATTTTTTGATTGCGCTTTGTGCTGTGTTTTTCTTGTATTTTTCTGCAGAGGCTATTGCTGAAAAATG +GTTTAGATTGGATGCTTTTTCTGCAAAGCAACTTGAACTCGCTATAAAAATTTTTGCAGGGCAGTTTTTTTTCCAGTTTT +GCAATAACGTTAATTTGGCATATTGGAATGGGAATGAAGAGCAAGTAAAAGCAAACTTATCGCAATGTATATTCATTTCT +TTGAAAAATATTACAGCAGTAATTTTAATTCTAAACGTTAGCCGACAAACATATATTTATGTATTATCTTTCTTCCTAAT +TGCTATGATTGAGTTTATCTGTAATTTTTCTTTTATCGTATCAAGGATAGGAGCGTGTAAACCGTCATGGGGAAAAATCA +AAAGAATTATTATTACTAACTATAAAATATCCTTAGGGATTCTGTTAGGCGTTTTTTCTTCACAATTAGATAGAATATTT +ATGTCAAGGTTTTTAAGCATTCAAAACTTTGGCTTGTATGTTATGACTATGCAATTTGGACTTGCGTTATTGCAGTTACA +GTATCCAATGGTTAAAGCAATATTACCTCATATCGCAAAAATTGGCGATACAACTAAGTTGGGATTATATAAAACAATAG +CTTTTTTTTGTGTCTTAATGCCATCTTGCATATTATTTTTTTGGGCAAAAGACATACTTTGGTTATGGAGTCATAATATT +GAAGTTGTAGAGTATGGAGTTATTATTGTCAAAATTTTGAGCGTTGCTGTGCTGATAAACTTTTTTTATAACTTTATTCA +CGTTAAGTTAATTGTTGAAAATAGAGGTGGGGTGATATTTATTTCGCAACTTTTGATTATTATTATTAACTCTATTTTCC +TAATATTCTTTTCCCCAAGAATTCATGAGGTGGCTGGAGCATTATCATGGATGATTAATTTTAGCATAGTCTTATTATGT +GGTTTGTTTTTTCTCCATAAAGGAAAAAAAAGATAA +>fliC_z81_Salmonella.bongori_40:z81:-_AY353261_other.z81__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCTGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATTGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCAC +GCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTT +CTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACA +GCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAAC +GACAACCCCAACAGGTATTACTGCAGTGGCTCAGGTTCAGAAGCCTGTAGCAGCGCCATCAGCTATCCAGGATCAGTTGA +CAGCGGCAAGTGTTGCTAATGCTGACAAAGCAGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACTATTGAT +GGCGGTTACGCTGTAAAAGTGGGGGACGATTACTACGCTGCTACTCAGAAAAAAGACGGTAGCTTTACCATTAACACCAC +TTCTTACACGGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTGTTT +CGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCGGAAGCGGCT +ACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTTGATGCGCTGCGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCG +AAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCAGGGACCTCCGTTCTGGCA +CAGGCGAACCAGGTACCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,t_Salmonella.enterica_Agodi_AY353407_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATTAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.48:i:z_AY353419_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_d_Salmonella.enterica_Isangi_AY353376_b,d,j__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCACTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_g,p,u_Salmonella.enterica_Rostock_AY353402_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,2_Salmonella.enterica_Heidelberg_AY353265_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACACCACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAACCTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,z62_Salmonella.enterica_II.9,46:g,z62:-_AY353415_g,m__1515 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAATAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCACAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGTTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGCAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCGCGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.61:i:z_AY353417_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCCTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.57:c:z:z60_AY353366_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,s,t_Salmonella.enterica_Missouri_AY353405_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAGGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAAGCTGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Gloucester_AY353429_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.44:z4,z23,z32:-_AY353502_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGTTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z52_Salmonella.enterica_IIIb.50:z52:z35_AY353516_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCATTTGATCTCACCGCGCTTAATGATACTAACCTTAAGGCTGCAGTTGGTGGGACTCCTG +CTCCGACAGGAACCGCTGTAGTAAAAGATGATAAAGTATATTATAACAGCGCTGACGATAAATATTTCGTCGAGATTGAT +GGGCTAAGTAGTGGTAATGGCTTCTATGAAGTTAGCGCAAATGCAACAACTGGTGCTCTTACAATTGGTGCAGGGTTAAC +AACGGCTGGCGCAACGGTACCGGCGGGTGCTGAAGAAGTTACATCTGTGCAGTCAAAACCCGTAGCTCTCAGTGCTGATG +TTAAAAAACAATTGACTGATAGTGGCGTTAGCGTAGCGGACGCTGGTAAAGGCCGATTAGTCACAATGTCTTATACTGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCAGATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCAACTGGGTGGCGCAG +ACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCCGATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z53_IIIb.60:(k):z53_HM142067_other.z53__1497 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGCTAAGACTATTGATCTCTCCGCCTTAAACGAAGCCGCGCTCAAAGCTGGTACTACTGGTACAACAGGTGCTCCGG +TCGTTAAAGATGATAAAATTTATTATGACGAAGCCAGTAAAAACTACTATGTTGAGGTTGATGGTTTCACTACTGGTGAT +GTAGGTAAAAACGGTTTTTATAAAGTTACTGTTGATGCTGATGGTAAAGCGACTATGGCTGCCTCTACTACGATGGAGGC +TGCGAAACCAGCTGGCGCTGTCGAAGTGACTAAGACTCAAACAGAAACACCAGTTAAACTAAGCGCAGCACTTAAAAAAT +CGTTGACTGATGGTGGTGTTGACACTGCTGCTGCAGGTACTGCCCAAATTGTCAAAATGTCTTATACCGATAAAAACGGT +AAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAG +TGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAA +CCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTG +GCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTC +TGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCAC +GTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACT +TCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_l,v_Salmonella.enterica_IIIb.38:l,v:z54_AY353445_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGTGAGGCTGTTAA +AAGCGGCGGTGGGGCAACACTAAGTACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACTGCTGCCATTAAAGATAATAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTGCTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGTGGTATGCCAGCAACGGCGGCGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACTGAAGTTA +AAGCTCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTCACAATGTCTTATACTGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATC +GATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCAACTGGGTGGCGCAGACG +GCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCT +GATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCACTGGCACAGGTTGACACGTT +ACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCA +GGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Choleraesuis_AY353365_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTAGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Salmonella.enterica_Adelaide_SRR1068324__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATCCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGCAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_z39_Salmonella.enterica_IIIb.40:z39:1,6_AY353350_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGCCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_l,w_Salmonella.enterica_Gloucester_AY353332_l,v__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACCCTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGCTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_l,z13,z28_Salmonella.enterica_Poano_AY353333_l,v__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Bareilly_CFSAN000189__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCTATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACTTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O:22-gene2__1023 +TTCCTTATGACAAATGTTGCATTCATTATCACAAAATCTGAAATCGGCGGTGCTCAAACTTGGGTAAATGAGATAGCTAA +ACTTATAGAACAGGATTGCAAAGTATTTCTCATAACATCCGAGTATGGATGGTTAACTCAATGTAGTGTTTTTTCTGAGG +TTTATATAATTCCAGGGATAAAAAAATATTTTGATGTTATTGCATATATAAAATTAATTAAGTTTATAAAAAAAAATAAC +ATTAAATCTATAGTGGCTAGTTCTGCAAATGCGGGGGTTTATTCTAGACTTGCCAGATTAACGTGCTCTTTTAAATGTAT +TTACGTTTCACATGGGTGGTCATGCTTATATAATGGTGGTCGGCTAAAAAGTATATTTTGCAAAATAGAAAAATACCTTT +CCAAATTAACGGATGTCATCTGGTGTATTTCTGAAAGTGATAGAGAAAAAGCTATAAAAAAAATAGGAATTGATGAGGGT +AAGATTATTACAGCTACGAATGCTGTTCCACCCATGCCTGCTCGTTTAAAAGAGTGTTTGGAATATAAAATTTTGTTTGT +TGGTAGATTGACACATCCTAAGCGCCCATGTTTATTGGCCCAAGTGATATCAAAAAAACCGCAATATAAGCTGGATATTG +TTGGAGGGGGAGAACAGTTAGAATCTCTCAAAGCCCAGTTCAAGGATTTTAAAAATATTCGTTTTTTAGGTGAAATAAAA +GGTTTTTCTGCTTATAAAGATTATGATATTTTTGCTCTTATATCCGATAGTGAGGGTTTGCCCATGTCGGGAATTGAGGC +TCATACTGCAGGTGTTCCCCTCCTTCTCAGTGATGTTGGAGGATGCCATGAGTTAATCGAGAAGAATGGAGTTTTGGTAG +AAAATATTGAAAGAGACATTGAGCTTAGTATAGATAGAATTTTTGAAAGATATGATTTTTTCCATACGCAAGCTGTCCTT +TCTGCTGATAGGTTTGTTATTGATAATTATATTCAATTATATAAAGAAATTATTTTGAATTAA +>fliC_b_Salmonella.enterica_Urbana_No-upload-yet_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACTACCTATAAAGATGGTGGTACTACTCTTGCAGCACCTGACGCAGCAGCAATTGATGCCGCCTTAGGTA +CGACTGGTGCGTCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAAAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACCATGACCGCAAATAAAGCAACAGTAACTGGTGCCGGCAC +AGTTACCAAAAACCAAGTTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGGCAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGACATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z81_Salmonella.bongori_66:z81:-_AY353260_other.z81__1485 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCTAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAAAATATGATGTGAAGAGCGAGGTTGCCAC +GCCAACAGCAAAACTGGATATTTCAGGCTTGGATGGCGCTGCGCTAAAAACGGGGACGGGTTCTACTGGTGATACTGGTT +CTATCAAAGATGGCAAAGTTTATTATGATGGAACAGATTATTACGCAGAAATTACTTTCACCGATACTGCTGATCAAACA +GCGAAAGGTGGTTATTACAAAGTCAACGTTGATGATGCAACCGGTGCTGTTACTATGACAGCATCAACAACTAAAGAAAC +GACAACCCCAACAGGTATTACTGCAGTGGCTCAGGTTCAGAAGCCTGTAGCAGCGCCATCAGCTATCCAGGATCAGTTGA +CAGCGGCAAGTGTTGCTAATGCTGACAAAGCAGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACTATTGAT +GGCGGTTACGCTGTAAAAGTGGGGGACGATTACTACGCTGCTACTCAGAAAAAAGACGGTAGCTTTACCATTAACACCAC +TTCTTACACGGATAAAGATGGTAATACGCAAACTGCACTCAATAAATTAGGCGGCGTTGACGGAAAAACTGAAGTTGTTT +CGATTGAAGGTAAAACCTACACCGCAGCTAAAGCAAAAGATCATAATTTCAAAGCTGATCCTGATCTGGCGGAAGCGGCT +ACTACAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTGGATGCGCTGCGTTCTGACCTGGGTGC +GGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCG +AAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCAGGGACCTCCGTTCTGGCA +CAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_Salmonella.enterica_IIIb.6,14:b:e,n,x,z15_AY353362_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCAGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAGCTAAAGAT +GGTCTGTATGAAGCGACAGTTGATACAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGCAC +AGTTACCGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +TAATTATACTGACGCTACTGGTGCAGCAAAAACTGGTGCTGTGAAATTTGGTGGTGCGAATGGTAAGACTGAAGTTGTGA +CCACAGTTGATGGTAATACTTATCAAGCTAGTGATGTTAAAGGACATAATTTCCAGAGTGGCGGCGCTTTAAGCGAGGCT +GTAACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCTGATTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_l,z13,z28_Salmonella.enterica_Lutetia_AY353334_l,v__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z35_Salmonella.enterica_Kolar_AY353341_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGACAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAATACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCATATGATGTGAAGAGTGAAGCTGTCAC +GCCTCCGGCAAAACTTGATATTTCAGGATTAACTGGAACTGCAATTAAAACTGGTGTTGATGGTGCTACGGTTGATACAG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGGACTATTACGTAGAAGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAACGTTGCTGATGATGGTACAGTCTCAATGGCAGCTTCTACCACTAAAGA +GGGTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCTCATGTGACTGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGGGATGACTACTACGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTAAATAC +TACTTCTTACACTGATAAAGACGGCAATACTAAAACCGCACTGAACCAACTTGGCGGCGTAGACGGAAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCA +GCCGCTAAAACCACCGAAAACCCACTGCAAAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGATCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCTAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.56:e,n,x:1,7_AY353314_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AAAAAGCTTTACAAGATGGAGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Choleraesuis_CP007639_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGACTGGTACGGCTGCTGTAACCGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCAGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_e,n,x,z15_Salmonella.enterica_Verity_AY353311_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAATCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTACGTATCAATAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATACAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTAAAGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AGAAAGCCTTACAAGATGGAGGCGTCTCATCTACAGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAACGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGGACTTCCGTTCTGGCGCAGGCAAACCAGGTCCCGCAGAACGTGCTGTCTTTGTTACGTTAA +>O-48_wzy__1194 +GTGATTATAAAGAAGAATAAATTTGTTTATTCGGTACTTAAAGTCTGGTTAATAGTCTCTTCATTGTATTATTTAAATGC +TATTTTTTCCGGTGTTGATGCGTTAAAATATAATGAAGATTTGACGCAAAAGTTCATCAAATATGCAATATGTTTTATAA +TAAGTTTTTTTATTCTGTTCAATAGTAAACGAGTCAAATTTTTGGGGGCTTCGTTATTTTTCATAATCCTTTCGGTAGCT +TCAGTAGTTATTGGTAATGTAGTAACGGTATATGCTACCGCGATGCTGATAATTGCTACCATGGTTGGTTTCAGCCAAAT +TATTCTTTATTTTTCTAATGATATGTCGAAGATTAATATGGTTTTATTATGGACTGGAATTATAATAGGCGCCATTTCTG +TATTAGAATTAACAGTATTCTACGATTATATGGTCTCATATTGGGTTTCGACTGGTGGAGTCCGATCAATATCTTCTCTT +CTTAATCCTACAAATAGCGGGGCTTATTCAGCGATTATAATTTTAATTGCTTTAGGGACTAATATAAGGAGTAAATTTAA +GAGAACTTTATTTGCTTTAATGCCAATGATTACTTTAATCAGCAGCGGATCACGTACAGCATGGTTATCATTAGCATTAA +CATTATTATTGACGGTATTATTAAATGATAAGGCTAGTATACGATTACGGAAAAAAATATTAGCTATTGCAGGTATTGGA +GCTATTTGTGGTGTGTTATATGTAGCATTTTATATGAGTAGTATCTCTGGTATTCAATCCCAACATCGAGGGCTTGATAC +ATATACCGCATCAATTCGAGTTGAAAACTTTATAACATATATGAATTCAATTGATTTTGATATGTTATTACCTGATTTCC +TTGATAAAAATATTAACCTTATATCAGATAATTTTTATCTAGTGTTATTAAATTATTTTGGAATTATTGGGGGTTATATT +GTTTTTTTTATTTCAGTATTATTATTCTATTATAATATGCAAACAAAGGATTTTGATAAAAATATAGATGAAAGTATTTC +TGTTTGGAGAGTGATATTCATCTATTTTCTGATATCTGGACTTTCAAACTCATTCATAAATTCTTTTCCTGTAAACCAAC +TATTTTTTATCTCATGCGGGTATTATGTGTATAAATATAACTTAATAAAGAAAAATGCTGGAAAGCAAATATGA +>O-48_wzy-from-2013K-0909__1194 +TCATATTTACTTTCCAGCATTTTTCTTTATTAGTTTATATTTATATACATAATACCCACATGATATAAAAAATAGTTGGT +TTACAGGAAAAGAACTTATGAATGAGTTTGAAAGACCAGATATCAAAAAATAGATAAATATCACTCTCCAAATAGCAATA +TCTTCATCTATAACTTCACTAAAATATTTTATTTGTGCATTATAATAGAACAGTAACATTGAGATTAAAAAGAAAATATA +AAACCCAATAATCCCAAAATAATTCACTAATACCAGATAAAAATTATCTGATATAAGGTTAATATTTTTATCAAGAAAAT +CAGGAAATAACATACCAAGGTCAATTGAGTTTATATATGTCATAAAGTTCTCAACTCGAATTGACGCGGTATATGTATCA +AGCCCTCGATATTGTGATTGTATATTAGAGATACTACTCATATAAAATACTGCATATAGCACACCACAAATAGCTCCAAC +ACCTGCAATAGCTAATATTTTTTTCCGTAATCGCATGCTAGCCTTATCATTTAAGAGAACCGTCAGTAATAATGTTAGCG +CCAATGATAACCATGCTGTGCGTGATCCACTACTGATTAAAGTAATCATTGGCATTAAAACAAACAAAGTTTTCTTAAAT +TTATTCCTTATATTAGTTGCTAAAGCAATTAATATTATGATTGCTGAATAAGCCCCGCTATTTGTAGGATTAAGAAGAGA +AGATATTGATCGTATTCCACCAGTCGAAGTCCAATATGAGACCATATAATCGTAGAACACCGTCAATTCTAACACGGAAA +TTGTGCCTACAATAACTCCCGTCCATAATAAAACCATATTAATCTTCGACATATCATTGGAAAGATAAACAATAATTTGG +CTAAAACCAAGCATGGTAGCAATTATCAGCATCGTGGTTGCATATACCGTCACTACATTACTAATAATTACTGAAGATAC +TGAAAGGAGTATGAAAAATAACGAAGCCCACAGATATTTGACTCTTCTATTATTGAACAGAACAAGAAAACTTATTATAA +AACAAATTGCATACTTGATGAACTTTTGCGTTAAATCTTCATTATATTTTAATGCATCCACACCGGAAAAAATAGCATTA +AGATAATATAATGAAGAGACTATTAACCAGACTTTAAGTAACGAATAAACAAATTTATTCTTCTTTATAATCAC +>O-1,3,19_not_in_3,10__130 +acgagaagtactgaataataattgtatcaaatagcctgcgtaaaatctgaacgcatcaatcgctaccttaatatcatacc +tttgagttaacatactattcacctttaacctgccatgaccgtttgtggca +>fliC_d_from-II-48:d:z6_SRR1168371__1521 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGAACGGAGGTACCGGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCGGAACGTAATGTGTCAACCTGCGC +CAGCGCAGCATCAATTTTCTGCAGCGGGTTTTCGGTCTTATCTGTATTCACCTCTTTAAGATCGCCGCCTGTCCTGAAAT +TATGTTTATCAAGATCACTTGCCAGGTAAGTTTTACCATCGGTAGCAGTAACCACTTCAGATTTACCATTTGCGCCACCA +AATTTCACAGCTCCAGTTTGAGCAGCGCCAGTACTATCTGTATAAGAAGCAGTTTTAGCAGTAATTGTACCTGTTTTCTC +ATCATAGGTAGCGGCATAGAAATCGTCGCCCATTTTCACTGCATAGCCACCATCAATAACCTTACCGTTTTTATCCTCAA +ACGATAGTTTTACAAGGCTGGTATTGTCCTTATCGGCACCAGTTACACCCGCAGCAGCAAGTTGAGCCGCAACTGCGGTT +GTATCAGCATCACCTTTTGTTATTTCAGCAACCTGGTTATTAGTTATGGTAGCTGTTGCCTGAATATCTGTAGCAGCCGC +ACCTGTTAACGGAGTTGTATCAGTTGTATCTATACTAACTTTCTTGGTAGCTTCATCATAAGTCGCTTTATAAACGCCAG +CAGAAGCACCACCTTTAACATCTAAATAGTATTGACCATCTTTAAATTTGATATCAGCCCCAGTGACACCCGTCGCACCA +CCACCAATCGCAGTTTGGATATCCGTATTGCTCTGGGCTGTGATAGTATCTGTACCATTTTTATAGGTAGTCCTATCAAC +TGTTACAGCAGTTTCTTTAGGTGTGTAAGCATCCTGTACATTAAGTTTATCAAGTCCCAGCGTTTTAGAGCTAATTTCTT +TTAGATCAATATCAATAGTTTCACCATCGTTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGAACTTTCACG +CCGTTGAACTGAGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTC +AGACTGGGAGTTGGTACCGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGCGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCA +T +>O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002 +ATGAAGGTGTCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGAGCTTCTTGAAAGTATTAATAATCAGTC +CTCTCACTCCTTAACGGTAGAAGTATGCATTTCAGATAATGCATCAACTGATGGAACTGAAGAATCAATAAATATCTGGA +GAGGTAGATTTAATTTTCCAATATTGTATCAAAGGCATAACGAGAATATTGGGCCGGATAGGAATTATTTATCTGCAGTT +AATATGGGGACTGGGGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAACTCCCTCGTATTGATGGAAGA +TAAATTGGCTAACGAAAGTGACATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAGGATATGTAATCCAC +ATCGGCGATGGTTAAGCGGTGGTAGTAGATTATTTTCTTTTAGCAATGAAGCCGATTTGATAGAGTACTTTAGTAAATGT +AACTCAGTTGGCGGACTTTTTAGCTATTTAAGCTCTATTATAGTGAAAAGGGATAAATGGTCTGACGTCATATTTGACGA +ATCCTACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTACAATACA +TATCACTGCCGCTGGTTGATTGCAGAGGCGATAACGATACATTCGAAACTAATGGGAAGGCTCGTCGAATAAAAATAGAT +TTCATCGGCTATTTAAAACTAAGGGAGGATTTTTATGATAAAAATACAAAAATATATAGCTCATTTGGGCGGGTTCTTAC +AAAAGAGCGCCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACAGACAGAGCTGAACTTGCATCCT +TTTATAAGAGGTTGGGCTATCCGGAAATAGCCACTAATTTTATATTTCGTCTTAAAGGACTGGCTAGCTACGCTAAAAGA +ATTAAATTAGCTAAAATGGTAATAAAAAAAATATTTTCATAG +>fliC_z_Salmonella.enterica_Poona_AY353467_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGA +ACCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAG +CTGCTTTGACTGCTGGTGGTGTCGATGCTGCTGATGTAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTT +CAGTGTTAATACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGT +ACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_Potosi_AY353482_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATTATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAGTCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_r_Salmonella.enterica_Rubislaw_AY353458_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAGGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Salmonella.enterica_Derby_AY353381_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCTACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s,t_Salmonella.enterica_II.43:g,m,s,t:z42_AY353397_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGATGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCTGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_from-cdc_Stk2184_1__1521 +TTAACGTAACAGCGACAGCACGTTTTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCAGAACGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGTGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCCGCGGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTTCCGTCTACGCCGCCAAGT +TGGTTAGCCGCAGTTTTGGTAGTACCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATGGCTCCTGTCGCTTCATC +GTAATCTGCGGCGTAATACTTATCACCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAACTCAGCGCCATTAGCATCGGTAGCGTCAACGCCGCCAGCGATTAAGGCATTTTTAGCATCGGCTGAT +ACAACTGCCGGTGTATCTTTTAATTCCTGCACTTCTGTTTTGGTTGCAGCACCAGCAGGCATTGTGGTTTTAGTTGCGCC +AGCCGCAAGGGTTACTGTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCACCAGTAAAGC +CACCAATAGTAACAAAGTACTTGTTATTATCTGCGTCAAATTTAACCGCACCACCGGTTACAGCAGCCGTACCAGTCGTA +CCACCCGTAGCCGTTTTAATAGCTGCATCAGTAAGACCCGATACATCCAGTGTAGTACCATTATCGGCATAAGCTTTCGT +TGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACGTTCAGTGAATCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATATCGATAGTTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGGGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACTGCCAGTTCACGCACGCGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGAGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,2,7_Salmonella.enterica_Eingedi_AY353276_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGATGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACTGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGTGCGGCAACTAAAACAGAAGTACAGGAGTTAAAATATACACCAGCAGTTG +TTTCAACAGATGCTAAGAATGCCTTAATCGCTGGCGGCGTGGACGCTACCAATGCTAATGGCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_k_Salmonella.enterica_IIIb.50:k:z_AY353538_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATTCTGCTAAA +AGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTGAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z39_Salmonella.enterica_IIIb.6,7:z39:1,2_AY353491_other.z39__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAGGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTGGATAATGAGGTTGTTAC +TGATGGTAGTGGTGGTAAGGCACTAAATATTAGTGGTCTTGATGATGCTACGATTAAAACCGCCGTCGGGGGGACACCAA +CTGGTACTGGTGTAATTAAAGATAACAAGGTTTATCACAATAGCACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGTTTCTATGAGGTAGATGCAAATCCTACTGATGGTACAGTTACATTTGCTGCCGGTGCTACGAA +AATAACGGCTAAACCAGCTGGTGTTGAAGAAGTTACAACCGTACAATCAAAACCTGTAGCTCTCAGCGCTGATGTTAAAA +CACAATTAACTAATAATGGTGTTAGCACAGCGGACGCTGATAAAGGCCAATTAGTCACAATGTCTTACACTGATAAAAAC +GGTAAGACTATTGATGGCGGTTTAGGTGTTAAAGTTGGAGCCGATATTTATGCTGCAACAAAAAATAAAGATGGCTCTAT +CAGTATTAACACCACAAAATATACAGATAAAGACGGTAATACTCAAACTGCACTGAATAAACTTGGTGGGGTTGATGGTA +AAACTGAAGTGGTTACTATTGATAGTAAAACCTATGCAGCTGCTAAAGCTAAAGATCATAACTTCAAAGCTGATCCTGAC +CTAGCGTTGGTAGCTACTGATACCACTGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCCGACTTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTGAACAACCTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,t_Salmonella.enterica_II.6,8:g,m,t:1,7_AY353537_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTGACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAGCTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGGCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGGTAA +ATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-54_wbbF__1380 +ATGAATGATTATATAATTGACATAGTGGAATATGTTTTATATGTGCTTGTAACTGCCATGACATGGTATTTGTTTGCCCT +GTCTTCCTATTCCATTTTTTTGAGTGTATTTGGGTTTGCTAAAAATAAAAAAGACTATCCTGACTGTCCTCCTGAAGCCC +GCTTTCTAATTCTTGTGGCTGCGCATAATGAAGAGGCTGTGATTGGCTCAACACTTATTAATCTTAAGAATATTCAATAT +GATAAAAAACTCTTTGATATAGTAGTGGTTAATGATAATTCCACTGATCGGACAGGACTTATCTGTGATAGTCATGAAGT +AAAGCATGTGGATACTATAGAAGGCGAGTTTGAACGTGAAGGTGTGGGCAAACCAGCTGGTATTCAGTACGCTCTGCGCA +AGCTTGGATTTGAAACTGTTAAAGAAAATTATGATTTGGTCATGGTGTTGGATGCCGACAATTTTGTTGATGCGAATATC +CTTACTGAGCTTAATTCTCAATGGATATCAAAGGACAAGCCGGAAGCTATACAGGCGTATCTGGATTGTAAAAACTCAAC +ATCTCTTCTCTCTTTTGGCTACTGTACATCATACTGGATGATGAATCGATTTTTCCAATTATCAAAATATCGCTTAGGTC +TACCTAATGCAATTGGCGGAACAGGATTTGTAGTGTCCAGTAACTTTCTGATAAATACTGGAGGATTTTGTTTTAAATCT +CTGACCGAGGACATTGAACTGGAAATTGAAATTGTGCGCAAGCGTGGTCGTGTACTATGGAATCACAATGTACGAGTCTA +TGATGAAAAGCCAGACAATCTAAGAATAAGCCTCAAACAACGCTATCGCTGGTCAAAGGGACACTGGTATGTGGCTTTTA +CTAACTTTTTTAACTTGTTCAAGTTGACCTTTGTTGAGCGTAAGTGGAAATATGTAGATCAATTGTTATATCTGTTCTCT +ATGGGCCGTGCTTTCGAGGTTTGTATTATTTTCATCAATATCTTTCTATTAAGTCTTCTTAAAGAAAATTACCATCCAGA +GATTGGAAATATTTCTACGGCGATAAAAGATCTTACTGTGACCAATATGAGTTTTGCCGACAGCGTGAGTGCGCAGTTTA +GCTCAATAAATTGGATTAGAGTTATTACTAATATTAATATCGTCACATTAATATCCATCTGTTATGGTATGCTGATTTTA +CCTATTTATGGTGCATGGATGGATAAAGGTATTTTCCTTAATCCATTCAGGGTATTTTTTTCCGGTCTTTATTTTGGATT +GTCGTTTGTGTTTGTTCAGTTTTTGGCTCTTTTTCGTTGGAAAAAACAGCATAAATGGGTAGTTACGCCGCATAATAAAA +TAAAGGAAGAGCACAAATGA +>fljB_1,2_Salmonella.enterica_1,4,5,12:i:1,2,7_AY353272_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTTCGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATA +CCGTAAACAATCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_Salmonella.enterica_Bovismorbificans_AY353283_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_z35_Salmonella.enterica_IIIb.38:k:z35_AY353262_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCACGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fliC_g,m,t_Salmonella.enterica_II.28:g,m,t:e,n,x_AY353536_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCTGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAAATGGTAATGATGGTA +ATGGTACTGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGGTAA +ATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_d_Muenchenstr_AOYT01000015_b,d,j__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACACTGGGACTTGATAAGCTTAATGTCCAAGATGCCTACACCCCGAAAGAAACTGCTGTAAC +CGTTGATAAAACTACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCG +GTGGTGCAACGGGGGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCT +GCTGGTGTTTATAAAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAAC +TGCGGAAGCTACAGCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATA +CGACCACAGTTGCGGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCACTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>oafA-O-4_full__332 +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATT +AGTCATTATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACAC +TTATGCGAGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTT +GTATACATAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGT +TGCTGTTGTTAT +>fljB_z6_from-II-48:d:z6_SRR1168371__1503 +TTAACGTAACAGAGACAGCACGTTCTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGCTGCAGGATCT +GCGCACGAGACATGTTGGAAACTTCGGTCGCATAGTCAGAATCTTCGATACGGCTACGCGCTTCAGACAAGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCGGAACGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCAGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCGTCTACGCCACCCAGT +TGGTTCAGGGCAGTTTTGGTAGAACCATCAGCTGCAGTGTAAGACGTGGTGTTAACACTAAAGCTACCATCTTTGTTCTG +GGTAGCGGCATAATAGTTATCGCCCACTTTTACAGCGTAACCGCCATCAATCGTCTTACCGTTTTTATCGGTATAAGACA +TTTTAACAACTTGGGCAGCAGCAATTTCTGGATCTGTAACCCCGCCAGATTTGAGAGAAGTTTTGAGATCTGCTGATAAC +GGTAATGGATTTTTTTCTTCCTGAGTTTTTGTTACTTCTACCGCACCAGCTGGTTTACCCGTCTCCATAGCCGTACCAGC +GGTCATAGATACCTTACCATCATCGGCGACATTTACTTTATAGAAACCATTTTTACCATCATCAGGGGTAGTCAGGCCAG +TAACTTCAACGTAGTAGTTTTTGCTAGCACTATCATAATAAACTTTGCCATCTTTTATTGCTGCAGTACCTGTTGTAGCA +CCAGTCCCTGTTTTAAGGGCCGCGTCTTTATTAAGATCAGTAATATCTAAATTAGCAGCTACTGTCATAGCTTTGCTATC +TACATCATACGCTTTCTGCACGTTCAGTGAATCCAGGCCCAGGGTCTGAGAGTTAATCTGCTTCAGATCGATATCGATAG +TTTCACCGTCGTTCGCGCCAACCTGAATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGG +CCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTCAGACTGGGAGTTGGTGCT +GTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTATTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCG +CAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGGCCTTTGATGTTCGCGGTGAAACGGTTAGCAATCGCC +TGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTGCCCAGTGCGGACTG +GGATTTGTTCAGGTTATTCTGGGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCAT +>fljB_z39_Salmonella.enterica_II.52:z39:1,5,7_AY353347_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGCCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCATTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.9,46:e,n,x:1,5,7_AY353316_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATTCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGATGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTACCACGA +AAAAAGCTTTACAAGATGGAGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_II.9,12:lw:enx_AY353320_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +TGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGATGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACAGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACGGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCGGCAGATGCTACCACGA +AAAAAGCCTTACAAGATGGAGGTGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACGGTGGCTAACCAACTGGGGGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACTTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAG +GCCGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_g,m,s,t_Salmonella.enterica_II.50:.g,m,s,t:1,5_AY353396_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTACGATACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGATCTATTCAAGACCACTAAATCTGCTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCTGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m_Salmonella.enterica_Enteritidis_AY353398_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCGCTAGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Montevideo_AY353392_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-58_wzy__1263 +GTGTATTTAACAAATAATTATTGTAATTTCCTTTTTCGCACTCGTATTGTTAGGCGCATATTTTTACTAGTTTACTTGGT +TTCTAATGTTTATGCTTATATGGTGCTTACTGATACAGGGTTATTGATTGGCGATTATCAAGGAATACTCATTAAGTATA +AAGAACAAGTTGCATATTTGTTAACGCTAACTATATTATCATATTATATTGTCTGTGGACCAGTGTTTTCCTGTATAGCA +AAGATAAAAGTTAAGTTGTCTACAATTAAAGGCTTAAATTCTTTTGCTTATTTATTGCTTTTTTTTCAGGTGTTATTTTT +TGCTTTTAATATTTCAACAGGTTCCAACACTGCGGGTACTGATTTCCAAACTGGTGGGTTTATAAGACTATTATGGCTTT +TTTTACCTGTCGATTATTTATTCTATATATATTATTTTGTTGGAAGAGAGACTAAAGTAAATAAAATATATCTGGTCAAT +GTAATCGTTTTTATTCTGTCGATGTTAAGTCGGGGGTGGCTCGGCTGGACTTTAGTTTTGCTTTATGCAGAGCTTTGTTT +CTTTTTTTGTTCGCAAAAATCCATCAAAAATAAAAAAATTAACTATTTGATCTTATTGTGTTTCTTTCTTATTGTTGCGC +CATTGGTATTTAGTCTGAAAGTGCAACTCCGTGCTGATTTGTATTTCAGTGGTATTGGTGGGGTGGTATCAACTTTAAGT +AATATTGATTACATTCAATCTTATAATAATTTTATCGCTAGTTTTTTATCCCGAATACAGCAGCTATCAAATGTTGTTTT +CTTTTATGACCATAAACAAGAATTGTATAAATTTGTTTCTTCGGAAATTGTATCAACCTATGCTTGGGAAGGCTTACCTC +AACAAACAGTAGCAAAATTGTTAGGATTAGCTCCAGGTGTTGACATGCATGTTTTTCTTTACAGTCATTACATTTCTTCA +TCTGCTGAAGCTGTAACTACATTGCAAGTTGGCTTCATTTCATGGTTCTTTTTAGATACACTATCATCTGTATTTTATCC +GTTGTACGTTCTGATTATCATTGGATTATCTTTATTTTTATCCAAAAAAATCGGTGGAGAAAAACTATGTGCGCTTACAT +GGATTATGATTTTTCTTTCTGTCATGTGCGGGTGGTACAATGCTTATCTGGTTTATCTGCAGGCATTAATTACGTTTTAC +TTTATCATGGGGTTATTGACTTTAATTACTCAAGAAAAAGCAAAGGGTAATCATAATGGGTAA +>O-61_wzy__1326 +GTGACTATTTATTATATTAAATGCTATTTAGGGGGATGTGTGATTTATCGGTTTGCTATTTTAATAGTCATTGTTATATT +AGGTATTATTTCTATTGCAACAGCTTATGCCATTGGCGCACCAACTTCTATATTTTTTTATATTTTTTATATTGTATTGT +TTATTTTTTATCCCCCTAAATATGTAATATCACCACTCACGATCCTTTATGTTTACTATGGCTTATGGTTCTTATTAGCT +CCACTTTTTGCTCAGCGTTATGTGGGTATTAACAACGAGTTATCTTATTCATATTCTTTTATTTTGCTTTCGGTTACTTT +TGGTATTGGCGTAATATTTCTTTATGATAAAAAAGATTTTAGACATTTTTCAGATTCTACAATTAGCAGTAAAAATGTTC +GGATACCATCCAAAAAAACACTGTTACTCTTATTTTTAATATCAACCTTATTTGTTATATTGATTGTGGCAAATTCTGGC +GGAATTGATAAATGGATTCATTCGCCCGGTGATGCTTTTCTGAATCGCAGCGGTTCAGGGGTATATGTTGTTGGTAGTCA +TTTTTCATCATTAGCATTAGCTGCACTCTGTGGCTACCATGCTTTCGTTACCCGTCAAAAAAAGATCTTGTGCTTATTTT +TATTATGGTTGTTGCTGACATCCCCTGTGCATGGAAGTAAGTTTCAAATTTCGCTTTTATTAATTATGTCGTTACTTCCA +TGGTTAAAGGAATTACGTTTCTATAGTAGGGGAACTTTGATCTTAGGGATAGCTCTTCTCGGGATCCTGTTTCTTGGGCT +TTATTTTCGCAATATATCTTGGATGACATGGCATGATCTAGTTCCCTACACTCTAAATTACTTTGACACGCTTGATAACT +TAGCGCTGTCTTTGAAGGAATTATCTCCTGCATTAAATAAAACATTTTTTATGCCTTTTAATAAATTGCTTACTCCTTTC +GGAAATGATGGCGGTATCATATTTTACGATATGAGTCAGTGGCTAACTTCGATCTACGATCCTGACGCATGGAAAATAAG +AGCAACAATACAGTTTCCTGTTGAAACTGACATGTATCTTAATTTTTATTTTTATCTTGGAATTCCTATATTAATGTCTT +TTTTCTTTTTTATTGCAAGGATATATTCAGCAGCTCATAGTAAACAACATTTGGGTGCATGGTTTGCGGCAATGCTAATG +ACATTATTTATGATTTCACATTTGCGGGGTAGCATTTATAACCATACTGATTTTTATATGTATCCCTATATTGCAGTGAT +GTTCTTCCTTTTCAGGAAGTATAAATTTCCATCGAAACGGATGTGA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.13,23:z4,z23,z32:-_AY353500_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z52_Salmonella.enterica_IIIb.65:z52:z35_AY353517_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGTTGTTAC +TGATGGTAGTGGTGGTAAGGCATTTGATCTCACCGCGCTTAATGATACTAACCTTAAGGCTGCAGTTGGTGGGACTCCTG +CTCCGACAGGAACCGCTGTAGTAAAAGATGATAAAGTATATTATAACAGCGCTGACGATAAATATTTCGTCGAGATTGAT +GGGCTAAGTAGTGGTAATGGCTTCTATGAAGTTAGCGCAAATGCAACAACTGGTGCTCTTACAATTGGTGCAGGGTTAAC +AACGGCTGGCGCAACGGTACCGGCGGGTGCTGAAGAAGTTACATCTGTGCAGTCAAAACCCGTAGCTCTCAGTGCTGATG +TTAAAAAACAATTGACTGATAGTGGCGTTAGCGTAGCGGACGCTGGTAAAGGCCGATTAGTCACAATGTCTTATACTGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGATCAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCTGCACTAAACAAACTGGGTGGCGCAG +ACGGCAAAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCCGATCTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z28_Salmonella.enterica_Javiana_AY353454_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTTTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACTGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_IIIb.21:i:e,n,x,z15_AY353431_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCTAACATGTCTCGTGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13_Salmonella.enterica_Kenya_AY353449_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTCATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACTACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACGAAAAATAAAGATGGTTC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCTCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCACAACTTTAAAGCACAGCCT +GATCTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACTGTAAACAACCTGACTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_I.8,20:z4,z23:-_AY353544_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTGAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.41:z4,z23:-_AY353547_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTCAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGGGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z41_Salmonella.enterica_Ottawa_AY353510_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACCATCGATATTGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTCGATAGCAAAGCTGTTAC +TGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGGATCAGTGCAGGTAATCCTG +CTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACG +AAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTAC +TCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGA +TTGCTGGAGATATTGATACTGCTGATGCAGATGCTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAACTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAATACTAAATCCGCACTGAACCAACTGGGTGGTGCAGACGGTAAAACCGAAG +TCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCTGATCTGGCGGAA +GCGGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTT +CTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_Romanby_AY353503_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAATTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACCTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_z4,z32_Salmonella.enterica_IV.44:z4z32:-_AY353506_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GTAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGTCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_from-Chailey_SRR1049702_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGTTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Tiergarten_AY353315_e__1506 +ATGGCACAAGTAATCAACACTAACAGTTTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACGGATATTAAAGCTGCATTAGGCAACCCGA +CGGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAGAATGGTAAATATGAAGTTACCGTTGATAGTACTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCAGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAGGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_d_Muenchenstr_ARYX01000110_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTAAAGTCCTGGCGCAGG +ACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTAAAAGAAATTAGCTCTAAAACA +CTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACTACCTATAA +AAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGGGGTTACTG +GGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATAAAGCCACT +TATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACAGCTATTCG +GGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGCGGCTCAAC +TTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAAACGGTAAG +GTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAACAGGTACAATTAC +TGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAATGGTAAAT +CTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAGGCGGTGAG +CTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGATACACTTCG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_i_Kentuckystr_AOYZ01000062_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCTATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGAAACT +GGTAAAAATGGCTATTATGAAGTTTCCGTTAATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z10_Mbandakastr_AOYR01000081_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGGGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_l,z13,z28_Salmonella.enterica_Fallowfield_AY353453_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCTGAAGCTGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z29_Salmonella.enterica_IIIa.41:z29:-_AY353478_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGATAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGTCTTGGAATGGATGGCTTTAACGTCAATGGCGCACACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAATGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTACAGTAATTTCCTTTGAAATTACTGGTGGTACAACACCTTCCTCCGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATAATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.50:k:z53_AY353440_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGMTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,p,s_Salmonella.enterica_Naestved_AY353401_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCATTGGCGCGGCGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,z51_Salmonella.enterica_IIIa.45:g,z51:-_AY353414_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCTCACTGAGTTC +CGCTATCGAGCGTTTGTCCTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATCAAAGGACTGACTCAGGCTTCCCGTAATGCGAACGACGGTATCTCCATTGCGCAGACCACCGAAGGG +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATTCAGGATGAAATTCAGCAGCGCTTATCGGAAATTGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAGACTATTACCATTGATCTA +CAAAAAATTGATGTGAAAAGTCTTGGTCTGGATGGGTTCAACGTGAATGGGCCTAAACAAGCAACCGCTGGGGATTTGAA +ATCTAATTTCAAAAACGTTACTGGTTATGATACGTATGCTGTTGGTGCTGATAGTTATCGTGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAAT +AACACCGCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATG +GTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAAT +GCGGCAACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACCTTTGATGATAAAACGAAAAA +CGAAGGTGCGAAATTATCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGTGCTGAAT +ATACAGCTAACGCTGAGGGTGATAAAATTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACAGCCTCTGGCGTTAGC +ACATTAATTAATGAAGATGCTGCTGCAGCTAAGAAGAGTACCGCTAATCCACTCGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCATTGGGGGCTATTCAGAACCGTTTTGATTCTGCCATTACCAACTTGGGTAATACGGTAA +ATAATCTGACTTCCGCACGTAGCCGTATCGAAGATGCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Gera_AY353498_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACTTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23,z32_Salmonella.enterica_IIIa.56:z4,z23,z32:-_AY353501_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACACCGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z36,z38_Salmonella.enterica_IV.43:z36,z38:-_AY353486_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAG +AATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z29_Salmonella.enterica_IIIa.62:z29:-_AY353479_other.z29__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAGGGT +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGACTGTTCAGGCAACTAATGGGACAAACTCTGATAG +CGACCTGACCTCTATTCAAAATGAAATCACACAACGTTTGAGTGAAATTGATCGTGTCTCTGGTCAAACTCAATTTAACG +GCGTGAAAGTGCTGGCCCAAGACAATACGCTGAAAATTCAAGTAGGAGCCAACGACGGCGAAACCATTTCTATTGATCTT +AAGAAAATTGACTCAAAAAGTCTTGGAATGGATGGCTTTAACGTCAATGGCGCACACAAAGCAACAGGAAGTGATTTAAT +TTCTCAATTTGGTGCTACAGGTACTGATAATTATAACGTTACCAAAGGGGCTACTACCACTACTTATTCGGTAGACATTA +AATCTGGCGCTGTTACTACTGGTACACCAGCTGAAGCTGTCTTTGTTAACGCGGCTGATGGTAGCTTGACAACTGATGCT +ACTACCAAAAACACTGAAATTAATGGTAACGATGACTTTACAAAGGGACTTGCAGACGCAGCAAAAGGCGCTGTTAAAGA +TTCTACATTTACCTACAGTGGCATCGAATTTACTGCTAAGACTGCTGGTACAGCAGATGGTAATGGTACTTTTGAAGCGA +AAATTGATGGTACAGTAATTTCCTTTGAAATTACTGGTGGTACAACACCTTCCTCCGCAGTAACTGGAGCTGGTGGTGCA +AAAGCTTATGTTTCTAAAATTGATGGTAGTATTACGACAACAGCTGAAGTCGATAACCGTGCTGCGAAAATGTCCGATTT +GGATTTAAACAACGCGGTTAAAATAGGTAGTACATTAAATGTTAACGGTGCTACCTATAATGTTAATGCTAAAGGTGATG +AAGTTACTGGTAAGTTTGATAATGGTGCAGGCGGACTGGTTGATAAACAAGTATTCTTGGGAAAAACCGCTGGCGGAGCT +GCAACATTAATTAATGAGGATGCTGCTAAATCCCAACAATCTACCGTAGATCCGTTGAAAACTATTGATGATGCACTTGC +TCAGGTTGATGCGCTTCGCTCCGATTTGGGCGCAGTACAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTATAAAGCGCAG +ATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_IIIa.43:z36:-_AY353484_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAACTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACAAAAGGAATTGCTACAACGGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATACAGCAAACAGTAAATATTACGACGCAACTGTAGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,z15_Salmonella.enterica_Brandenburg_AY353323_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTAACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGTTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>O-7_wzy__1080 +ATGATATATTATATTTTTATTGTAATTTTTCCGTTCTTTTCATTTGTTAAGAATAAAAATATAAAAATTTACGCCTTGAT +GCTAAGTTTTTTATTTCTTGTCTCGTTTTGTTCTTTACGTTGGCAGACTGGTACTGATTGGCTCCCCTATTACGATGATT +TCATGAGTCCAGGGAATCGACATGACTTTGAAATCGGGTATGTATTATACGTCAAATTAATAAGATATTTGACAGATAAT +TATACATTGTTTCTATTCACTACATCAATTATTCCTATCGCGTTAATATTCTGGGGATGCCTGAAAACACAAAAAAATAT +ATCATTAACTATTCTGTCTGTTTGTGTTTTTTATAGTTATTATTATCTGGGGTCTTTTTTTGGGGCCGAAAGAAGAATTA +TTGCAATTGGGTTATCTTTTTTCGCTTTAATCCAATATAAAAGTAATAAAAAGGTGCAATCGCTTATTCTTATTCTATGT +GCGTCGACATTTCATATCTCGTCTTTAGTTACCTTATCTGTTTTTTTAATCAATAAGTTATCTTTAAACTTATATAAAAT +ATTACTTGTGCTTGGTGCCATTCTATCATTGCCTTTGTCACATTATTTATCAGATATAATTTCTTCCGTTATTAGTCTAA +TTCCTGTCGAAATTGTTCGCTATAAACTCACTGTTTATACTCAAAATGCACAAGAATATGGGTCCATAAGTATATCTGGA +ATTTTAAAAAGGGTGGTAATTTCTGCTATTTTTATTTACACATTATCTTTTGATATAAAAAATAATAAGGCAAATTTATT +TTTGGTAAAAACATATTTATTTGGAACTATCATATATTTATTTTTATCTCCGATCTCAGCCATGTTCTCAGTAATTAGTA +TATATTTTACTATAGTCGAAATATTGTTGATTCCTGCAGTATTAGTGCGTGTAGGAATTTTTACACGGATTCCTGCTCTG +ATTTTTATAGTGATTTTTTATTTTGGCTATCAAGTTTACTCTATACTAGGGTCTTATCCTGAACTTTTCTATCCTTACAT +ATCGGTATTTTCAGAAATTCAGCGTCAAGGTATTTACTAA +>fliC_z65_Salmonella.bongori_V.66:z65:-_AY353259_other.z65__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAACGTCTGTCTTCCGGTCTGCGTATCAACAGCGCAAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TTACCGCCAACATCAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCACTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCGAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAGGATGAAGCTGTTAC +TGCTGGTACTTTCAGTGTAGATAGTGGTGTGGCAATTAAATCTGCAACGGTTGACGTTAAAACAGCTTTAAGCACGACTG +GTAATGACGGTACTGTAAGTAAAATTGAACTTGATAAGGCAACAGGTAAATATTACGCAACTGTATCAGGGCTTACAGAT +TCTGCAGATACAAGTAAAAATGGCACTTATGAAGTTAATGTTAGTTCTACTGGCGATATTACTTTTGTTGATACAACCAA +AGACACTGTCACTGCTGGCTCGGTAGAAGTACAAAATGTTCATACGAAAGCTGCTGGTGCACTTCCTGATTTAGCCGACG +CAAAAGCAGCTTTAACCAAAGCCAATGTTGCTAATGCAGACACTGCTTCTTTAGTGAAAATGTCTTATACGGATAAGAAC +GGTAAGGTCATTGACGGCGGTTATGCATTAAAAACAGATGATACCAAATATTATGTTGCATCATATAACGAAACTACTGG +AAAAGTCGAAGCTGCGGTTACAAAATATACCGATTCAAATGGATTTTCTAAAACAGCTGCTAATCAATTAGGTGGTGTAG +ATCGCAAAACAGAAGTTGTGGAAATTGGTGGTAAAACTTACACAGCAGCCAAAGCTAAAGACCATAACTTTAAAGCTGAT +CCAGATCTGGCAGTTGTTGCAGCTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCACAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCAGGGACCTCCGTTCTGGCACAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-67_wzt__741 +ATGGAACCAGTAATAAACTTTAGTCACGTTACGAAAGAGTATCCTCTTTACCACCATATTGGCTCAGGAATTAAGGATCT +CGTATTTCACCCTAAAAGAGCTTTTCAGCTGTTAAAAGGGCGTAAATATCTTGCGATCGAAGACATTACCTTCACCGTGG +GTAAAGGCGAGGCCGTAGCGCTGATTGGTCGTAACGGCGCAGGGAAAAGTACCTCCCTCGGGCTGGTGGCCGGCGTCATT +AAGCCTACAAAAGGCACTGTTACAACCCAGGGGCGCGTTGCCTCAATGCTTGAGCTAGGCGGCGGTTTTCACCCTGAATT +AACCGGGCGAGAAAATATTTATCTCAATGCGACCCTGCTTGGGCTACGCCGCAAAGAGGTTCAGCAACGGATGGATCGGA +TAATTGAGTTCTCCGAGCTGGGTGATTTCATTGACGAACCTATTCGCGTGTACTCAAGTGGTATGCTTGCGAAGCTTGGA +TTCTCTGTCATCAGCCAGGTAGAACCCGATATACTTATTATCGATGAGGTACTTGCTGTCGGTGACATTTCGTTCCAGGC +CAAATGTATACAAACAATACGAGACTTCAAAAATAAGGGTGTAACGATATTATTCGTTAGCCACAATATGAGTGATGTTG +AAAAAATCTGTGACAGAGTTGTTTGGATCGAAAACCATAAACTCCGCGAAATTGGCTCAGCAGAGAGAATCATTGAACTT +TACAAGCAAGCAATGGCTTAA +>O-40_wzy__1368 +ATGTTTCAGATTAAAACCAGAAAAAAACCATTGTTAATATTATATTTAACTTTGTTATTAAGTATTTTGATGTCGTTAAT +TATCGATGATGGTATAAATCGATCCTTATACATACTTTGTATATCCACACTAAGTGTTTTTTTTATATGCTATTGTTGTA +ATAAAATAACCTCCCCTGCAAGTTTATTAATTATTTCTTCCTTTGTTTTCCTTGGTTGTAGGCCATTTCTCTCATTATTC +ACAAGTTTCGATTATAGAAATGCCGATTGGTTTATAACTGGTTATTTAGATGAGAATGTTATCTATACTAATTATGCTGT +TTCTTTTATGTATTTTGGATATAGTGTTGCATTGATATTAAGTAATAATAATTCAGCACATAGAGAATGTTACAATCTAA +ATAAAATAAAACCTAATATTATATTTTTGTCTATGCTTTTTCTTTTTGGCTCATTAGGACAAATCCTTAAAGGTTTTTAT +TTTTATTCCTTCATTGAGTCGAATAGTTATGTTGGAATTTATCAAGATAAAGTAAATTTACCCATGGGATATAATTTTTT +ATCATATCTGTTTTATTGTTCATTTTTCCTCATCTGTGCATTTTATGACAAATTCCGAGTTAATAAATCATTTTTATTAA +TATCAATATTGATTGCTGCTTTTAGTGCCATGAAAGGTAGTCGAGGGGAGTTTGTTACATTCTTGCTTACAGTTTTTTGT +ATTTATTATAATGAGAAGAAAGTAAGCAATATTAGCTTATTATTGAAAATGTTTTTAATATTTATTGCTGTTTTTATTAT +AAGTGAATTTGTTTCAATGTGGCGGTCAGGCGGTAGCTTTATTGCTCTTATTGAAGGCGATAATCCACTCATGCAATTTA +TATATGGAATGGGAGTATCATATATTACACTTTACCAATCGGTTAAAATAAGTTTGATCTCGGGAGTGTTTGAGTTTCAT +TATTTAATCAGTCAACTATTAATTACTATATTTTCAGTGTTAGGAGTTCAGGTATATTTACCTGGAATTAGTTACAGCCA +TTTGGCATCTAAAACTGCGAACCCACAATTATATGAACAAGGGTTTGGATTAGGAGGAAGCTATCTTGGTGAATCATATA +TAGCTATGGGACTAATAGGATGCTTTATTATTCCATTTATAGTTTTATTTCTTATTAATAAGCTAGAAGTATTTACCAGA +TATAATAAAACTTTTTATTTTGTATATTATAGCTCTCTACCATCTGTTTTATTTATACCCAGAGAAACCTTGTTCTATTT +TTTCCCTTATGCAGTTAAAGGCATTATTGTGGTATTTATATTTACATTTTACGCGAATATTAAAATGAGAAGATTTAATA +ATGGTTGA +>O-56_wzy__1179 +ATGGAATTGAAAAAAAACAATACCAGGATTCTTGTCTTTTTTTTATACCTTACCGTTAATATTATAGCATTTATATTATC +TTGTGTTCAGGGGTACATATTAGTCGAAAATTATAGTTTTAGCTTTAACGTTGATAACGGAGCGCTGGGTTTTGCATATG +TGATATTTTCGTTACTATTCATAACTCTATTGTATATTTTTTTTACTTTCCTGTTGAGGCCATATAATGAGCATATAAAT +ATTACAAGATTTTATGAAAATAAAAAAATCAGTATTTCTATTTTTAGTATACAAACTTTATTTATAGTCTTTAATTTATA +TTATGGACTAAATGTCGCCGGTGCTGGTGAAGACGTTAATATTGCACCATCATTGCTACGTTATTTTTTTGTGATATTTA +ATCCAGATATTTTGTTTTTAATATATGCATGCACGAACATTAACAATCAGCTTTATAAAGTTAATTGTTGTGCTTATTTT +GTATCGACTCTAATAAGAGGCTGGAGTGGTGGTGTTCTGTTCTTGTTATTTATTTTTTTATGCCGCAGTGATAAAATTAA +TTTAAAATTAATTTTACTTTTTATCATATGTCTCTTATTCGCACCATTTATTATGGAAATAAAATGGCTAATTAGAAGTA +ATACATTTGATTATAATAATATAATATCTGAGTTTGATTATGGTAAAAGTTTAGGGCAGTTCTTAGAGTATTTAGTGTAT +CGATTACAGCAGGTCACTAATGTTATCTATCTTATCGACCGGGTAGAGCACATTTCTATTTTATATCAAGATAATACTTT +AGTTCCATATTGGGGGGAATTTATCGGATTAAAAAACTTATATCAGCTTTATTATCCACAGGCAATTCCTTTGGGGCAGT +GGCTCGGAAGCAGTATTGAAAACTCACTAGTTTCATGGAATTCTAATCCTGGGCTTGCAGGATGGTTTATAATACTTACA +AATTACTCACTATTTTATGGTGGGCTTTTTATATTAATTACAGTAACTGCAATTTTTTTTAATGTGTATTTTTCTATTAT +AATTGGAAGAGGGTGTATAACTGGTTTTTCTTATATTTTATGTATTCTTTATCTTTTTCCGGGATGGATGGGAATGTATT +TTAATTTGATATTTTATCTAATTATTTGGTGTGTTGTAATTAAAATCTTAAAGGTATAA +>fliC_b_Salmonella.enterica_Niederoderwitz_AY353360_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTGACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTACCACTAAAACTGGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_Salmonella.enterica_IIIa.47:b:-_AY353363_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCCATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACTATCCAGGTTGGCGCCAACGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGACGCCTATACGCCAAAAGGTACCGCTGTTAC +CAAGGATGTTACCACTTATAAAGATGGTGGTACTACTCTTACAGCACCTACCGCAGCAGCAATTGATACCGCCTTAGGTA +CGACTGGTGCGTCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTATTTCGTTGAGGTGACCGGTACAACTAAAAAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAATCAACAGTAACTGGGGCCGGCAC +AGTTACCAAAAACCAAATTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGGCAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAGACTGGTGAGATAAAAGCTAAGACTGT +AAATTATACTGACGCTACTGGTGCAACAAAAACTGGTGCTGTGAAATTTGGCGGCGCGAATGGTAAAACTGAAGTTGTGA +CTACAGTTGATGGTAATACTTATCAGGCTAGTGATGTGAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAATCTGGGCAATACTGTAAACAACTTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_a_Salmonella.enterica_from-cdc-Stk2184_other.a__1488 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGATCAGAACGCAGCGCATCAACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCAGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCAGCAGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCATCTACGCCGCCAAGT +TGGTTCAGTGCGGTTTTAGTATTGCCGTCTTTATCGGTATATTTAGTGGTGTTAATGCTGAACGATCCATCTTTATTTTT +TGTTGCCGCATAAATATCAGCCCCAACTTTAACACCAAAACCGCCATCAATCGTCTTACCGTTTTTATCGGTATAGGACA +TTTTGACCATTTCAGCAGTATCAGCTCCGGCCACATGGGCAGCTGTCAACTGAGCCTGAATAGCTGCTGGAGCAGCTACA +GGTTTTTGAACCTGAGTAACTTCAGTAATACCAGTAGGAGTTGTACCCTCTTTAGTGGTAGCCGCAGTCATTGTGACTGC +ACCATCATCAGCAACATTAACTTTATAGAATCCGCCTTTGTTAGTTTGATCGGTCGCATCGGTAAATTCTACTTCAACAT +AATAATCTTTAGAGGTGCTATTATAGTAAACCTTACCATCCTTAATTGAACCAGTGTCAGTTGTAGAACCGGTTCCGGTT +TTGAGGCCAGCACCATCAAGTGCAGTTGTGCTTAACGTAGCCGGAGGCGTGACAGCTTCACTCTTCACATCATACGCTTT +CTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCGATAGTTTCACCGTCATTGG +CGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGGGTCTGGCCGGATACACGGTCG +ATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTCAGACTGGGAGTTGGTGCTGTTAGCAGACTGAAC +TGCCAGTTCACGCACGCGCTGCAAGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCGCAATAGAAATACCGT +CGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTGAAACGGTTAGCAATCGCCTGACCTGCCGCATCG +TCTTTCGCGCTGTTGATACGCAGACCGGAAGACAAACGCTCGATAGCGGTGCCCAGTGCGGACTGGGATTTGTTCAGGTT +ATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>fliC_a_Salmonella.enterica_Paratyphi.A_AY353356_other.a__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCGGTCAC +GCCTTCGGCTACATTAAGCACTACTGCACTTGATGGTGCTGGCCTCAAAACCGGAACCGGTTCTACAACTGATACTGGTT +CAATTAAGGATGGTAAGGTTTACTATAACAGCACCTCTAAAAATTATTATGTTGAAGTAGAATTTACCGATGCGACCGAT +CAAACCAACAAAGGCGGATTCTATAAAGTTAATGTTGCTGATGATGGTGCAGTCACAATGACTGCGGCTACCACCAAAGA +GGCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTCCAAAAACCTGTGGCTGCTCCAGCTGCTATCCAGGCTCAGT +TGACTGCTGCCCATGTGACCGGCGCTGATACTGCTGAAATGGTTAAGATGTCTTATACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAGCCAGAGCTGGCTGAAGCG +GCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_a_Salmonella.enterica_Paratyphi.A_AY353357_other.a__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATTGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCGGTCAC +GCCTTCGGCTACATTAAGCACTACTGCACTTGATGGTGCTGGCCTCAAAACCGGAACCGGTTCTACAACTGATACTGGTT +CAATTAAGGATGGTAAGGTTTACTATAACAGCACCTCTAAAAATTATTATGTTGAAGTAGAATTTACCGATGCGACCGAT +CAAACCAACAAAGGCGGATTCTATAAAGTTAATGTTGCTGATGATGGTGCAGTCACAATGACTGCGGCTACCACCAAAGA +GCCTACAACTCCTACAGGTATTACTGAAGTTACTCAAGTCCAAAAACCTGTGGCTGCTCCAGCTGCTATCCAGGCTCAGT +TGACTGCTGCCCATGTGACCGGCGCTGATACTGCTGAAATGGTTAAGATGTCTTATACGGATAAAAACGGTAAGACTATT +GATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGTTCAGCATTAACAC +CACTGAATATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTAAAACTGAAGTTG +TTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAGCCAGAGCTGGCTGAAGCG +GCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACTTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_1,5_Panamastr_AOYJ01000008_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAATACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGGCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACGCTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>oafA-O-4_5-__325 +TCATCATCAGAGTTCAACTTTTTGCTTCACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATCCTTTATTAGTCATT +ATAGTTAAAAAATTACGGTTTCCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCG +AGTGACTGGAACCAAAGAAGATATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACA +TAGCATCTGTACGTTACAAAATGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTGCTGTT +GTTAT +>fljB_e,n,z15_Mbandakastr_AMRS01000032_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATAGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_e,n,z15_Salmonella.enterica_Uno_AY353325_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCTAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCTACGA +AAAAAGCCTTACAAGATGGGGGCGTATCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCAGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.48:i:z_AY353336_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCTTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O-28_wzy-another-lineage__1296 +ATGGAATATTTAATTATTTTGATTTTCTTTACTCTCTTATTTTTTACGACTAAAAGTACATGGCCTTTTGGTGGAGTGAA +TGCTCATCCTATATATTTTGTATTTCTTACTCAAATTTTTATATTAACGCTCCCCGGTGTTCTTATTTTAACATTTTTCA +GGAACTGTGTTGGATCTATTACATGTGAAATTGTCACTAATGCCACTAAAATAAATGTGATGCTTGATTATTTTACAATT +CTTAGTTCTATCGTTTTGGCAATATTATTTTCCTACTTATTAATGCGAGGGCGTAAAGATTTTACTCCTTCTGCGTTGTC +TCAAAAACGTTTTCTTAATTTTTGTTTTTTTATAACAATTCTAATTATTATAATTAAAATTATCTTTGTGAAGCATGTTC +CTCTCTTTATGGTTTTATTTGGCAACAAAGAGGCTGCAGAAATTCAAAAGGCAGCTATTTTACGTGGTGAGGATGGGTTT +TCTTTTCCTGTTCTCAATTTTCTTATTAAGTATTTTCCTCTCTATTTTTATTACTCAGTATTAATAACTTTTTTTAAGCG +CAAAATTAGCTTTTTTTATTTAATAATAGCTTTTGCTACAACATGTTTAGCAATGCTTTATGATTTACAAAAAGCACCGG +TAGTCATTATGATTATAGGTTCATTTTGGCTATACTGGGCTTTTTTTGGTAAATCTAAAATGATTATCATTGGGGCATTA +CTAAGCTTAGGATTGGTTAGTTTATTATTTTATATCTCGTATGATTTTGGTGGAAATACAAATTATTTTATTGACGCTAT +TCTCAATAGGACTTTTGTTGCGCAAGATGATGGTATGTACTGGGTATATCAATATTATGATTCATTGCCTAATAAAGAAC +TATACGCCTATTGGGGTATACCTTTTGCTCAACAGTTTGGTTTACCACAGATAGATCCTTTAAGTGATATTATCGGTGTG +GTATTTCCAAATGCTAGTGATAATTGGGTTAATACAACAACATTTCTTCTGGGGGAGGCTAAAGCAATATTCGGAAGTTA +TAGTTTGATTCTTGCTACTTTTGTAGTATTCATTAATGTGATTATTATAATGATAGTTTCATCAGTATTGGTTAGAATAT +CAAAAGACCTTTTTTATCCAGCTATATTTGTTATGTTGCAAACAATTCCATTTGCTAATAATATCACGGATTTGATTTAT +GGCCGATTTATATTTGGTTTTCTGACGTTTATGCTATTTCCGACACTTTTTTGTTTGCTATGTAACGGCAAGATGAGTAA +ATACGATGCGAAGTGA +>O-35_wzy__1065 +ATGTCTATTGATTTTCTTTTTTCAATTACTGAGATTGCAGTTGTTTTTTCTTGTGCTATTTATATATTTGTTCAATGCTT +GTTAATGCACAAGATTTATTTAGATAAAGTTGTTTTAATTCTATTGTGTTTACTCCTTTGCTTGGTCATTATTCAACTTC +CCGAACTTAATGAGCAAGGTTTGATAGATGCTGTAAAGCTATTATTACCTTTACTAATAGTATTTATCGCTTTTCAAAAA +CCGAAATTATGCTTGTGGATCATTATTGCATTATTGTTCTTCAATTCCACGCTAAATTTCTGGCACTTCAAAGTTTTTGA +TAAATTTAGCTCATTTCCTTTTACATTTTTTATATTATTATATTTTTTGTACAAATTGGTCAATGATCAACCTCCAAGGC +AGAGGAATAAAAAATTTTACGTTGTAATTTTCATATTTATATTAATTGATGTAACACAATCATTATTAATAAGTTACAGA +GGACAGATTCTATACTCTTTAATATGTGTTATAATGCTTGTATTGAGGATTAATTTAAGGAAAACAATCCCATATATTTT +TCTAACTTTACCGTTTATATATGTTTTTATAATGACTTTTATTGGTTTTAATTACTTTAATAAAGACGTGGTTTTTTTTG +AACCTACGGCAAGTAATATTGAACGTACGGGGATGATATATTATTTGGTTATCCATGCAAATGATTATATATTTCACGGT +ATGGGGACGTTACATTTCTTAAATGAGGGGGGGCAATATAAAATGTTATATGGATTTCCTTCTCTAATACCAAATGATCC +TCATGATTTTTTATTAAGATTCTTTATAAGTATTGGTATGATGGGGGCGTTGATCTATCATTGTATATTTTTTGTTTTTT +TTAAAAATATATCTTCGTTATTGCGTCAAAAAAACAGTTATTTTGTCATAGTAAGTTGTTTATTATTATTACAAGTTGTG +TTGTTTTATACACTAAACCCTTTTAATGCATTTAATCGATTAATTTGCGGGCTTACAATCGGAGTCATTTATGGATTTTC +AAAGAGTAGACAGATATATATGTAG +>O-11_wzy-new-from-CP019192__1080 +ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGCTATTATTTTCCCTCGCATATACTAATAAAAATAAAAATATAAA +TGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGACTTAGAGTTAATGATAGTGATTATCTTGAGT +ATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCTGCGATAAAAGATATTCATGGAGAGATTGGC +TATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATCTACCGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTT +GATGCTTACTTATTTTTCTTTTAAAAAAGCAAGTATTATACCAATATTGTCTCTAGTTTTTTATTTAAGTCATGCTTTTA +TTGTTAGGGATATGATACAAATAAGAGCTGGATTAGCTGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAGAAT +CGAAATGTGATCGCAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTAT +AAGAAAAAGATATTTATCGTTAAGAAAAATATTTTCTCTTTTTCTGGTTGCCTTAATATTTTCTTATTTACATGGGCTCG +ACTTTATATTAAATACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATATTGGGTGGGAAGAATATGAT +TATAGAATTAATATTTTCACTAATCCAGTGTTTATTAAAGGGGTGATGATAGTTTTTTTAATGAAAAAATATATTAAAAT +AAATATAAATAATGAAAAGGATAAGGTGGTTATATTATATAATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGATTAA +GTGAGATGGCTATTCTTTCAGGACGTCTCTCATCATTTTTAACACTAGGTGAAAGCATATTAATAGTATATGGTCTTTTT +TATAAAAGAAATATCTCGGTAGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTC +AAACGTACATCCGAAGCTCTCTCTTTTTATATTTGGATAA +>gntR-family-regulatory-protein_dt-negative__291 +AATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATT +CTTCAATTCTATTAATCACGTCCAGTAACGATCTAACCACGATCTTGATGTAGATCCCACTCCTGCATCTTTCCTGAGAA +ACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCCTGTCAACATTGGATACAATATCATATATCATTGATTGGATA +ATTATAAATATAGAACCCATTACCCTTACCTTATGTTTATTGGTGTTCGCT +>O:22-gene1__1071 +GCCAGGGGCGGTAGCGTATATAAAAATAATTTTTGTTTATTAATAGGAGATATGAGTATGTTAGTTTTAATCACTGGCGG +TGCAGGCTATATAGGTTCACATACTATTATACCCCTATTAGAAAATAATCATGATGTAATTGTACTTGATAATTTGTGTA +ATTCATCAATTGAATCTATAAAACGAGTCGAATATCTTACTAAGAAACAAGTAACTTTATATATAGGTGATGTTCGTGAT +CGGGATTTATTGAATAAAATATTTATGTCTCATCAAATTGATGCAGTTATGCACTTTGCTGCTTTAAAGTCAGTGGGAGA +GTCAAATAATATTCCGCTAACTTATTATTCTAATAATATTACAGGCACGCTTAACTTACTTGAAAGCATGCAGCGATATA +ACGTAAAAAAATTAATATTTAGTTCTTCTGCAACCGTCTATACTGCCGGGAATAAGATGCCAAATACAGAAAGTGATAAA +ACTGGAATAGCTAAAAATCCTTATGGCACATCGAAGTTTATTATGGAAACTATACTGAAAGATATTAGTAAAAGTGATCC +GAGTTTCTCCATTATTTCTTTAAGATATTTTAACCCTACAGGAGCTCACCCTTCAGGTATGATTGGAGAGAACCCTAACG +GCATACCTAATAATCTTATCCCTTACGTTGCAAAAGTTGCACAGAATACACTCCCCGTTTTACATATTTATGGCAACGAT +TACCCAACGAAGGATGGCACCGGTGTAAGAGACTATATACATGTAATGGATTTAGCTTTGGGACATGTAAAAGCTTTGGA +TTATATCTTTCTAAATAAGATTAATTATGAGGTTTTTAATTTAGGAACTGGACGCGGGTATTCAGTGCTCGATGTTGTTT +ATCTGTTCGAAAAAGTTTCACAAAAAAAAATATCATATGTCTTCTGTGATAAAAGAGAAGGGGACGTTGCAGTTTCATGG +GCATGCCCTCAACTAGCTAATGAAAAATTAAAATGGCAGGCAACTAAAGATTTAGAGGAAATGTTGAAAGACGTCTGGCA +TTGGCAAACAAAAAATCCGAATGGTTATTAA +>fljB_z39_Salmonella.enterica_II.43:d:z39_AY353345_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAATAACCTGCAGCGTGTACGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGACGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGAGGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGCTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAATTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z39_Salmonella.enterica_II.4,12:g,m,t:z39_AY353346_other.z39__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTACAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGATGGTAGTGGTGGTAAGACATTAAATATTAGTGGTCTTGATGCTGCTGCAATTAAAACCGCTGTTGGAGGGACACCAA +CTGGTACTGGCGAAATTAAGGATAATAAGGTTTATCACAATAGTACTGATGGTAAATATTATGTTGAAGTTGCTGGTTAT +ACCTCAGGGGAGAATGGCTTCTATGAGGTAGATGCAAATCCTGCTGATGGTACAGTTACATTTGCTACCGGTGCTACGAA +AATAACGGCTAAACCTGCTGATGTTGAAGAGGTTACAACTGTCCAATCAAAACCTATAGCTCTCAGTGCTGATGTTAAAA +CACAATTAACTGCTAATGGAGTTAGCACAGCGGCCGCTGATAAAGGCCAATTGGTCACAATGTCTTATACAGATAAAAAT +GGTAAGACTATTGATGGTGGCTTCGGTGTTAAAGTTGGCGCTGATATTTATGCTGCAACTAAGAATAAAGATGGCTCTTT +TAGTATCAATACCACGAAATATACTGATAAAGACGGTAATACCCAAACTACACTGAATAAACTTGGTGGCGTTGATGGTA +AAACTGAAGTTGTTTCGATTGAAGGTAAAACCTACACCGCAGCGAAAGCAAAAGATCATAATTTCAAAGCCGATCCTGAT +CTAGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCTGCG +TTCCGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACTTGTCTGAAG +CACGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATCCTGCAGCAGGCCGGT +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.53:z:1,5,7_AY353338_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,2_from-Brazzaville_SRR2058145_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGACAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCAGGCCTTGATGATGCAGCTATTAAAGCGGCTACAGGTG +GTACGGCTGGTACGGCTTCTGTAACAGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATCGGT +GGTTTTACTGGCGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACCCTTGCGAC +TGGCGCAACTAAAACTACAATGCCTGCAGGTGCTGCAACCAAAACAGAAGTGCAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCCGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAACGACAGGAGCCATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACTGCGGCTAATC +AACTTGGCGGCGTAGACGGAAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCAT +GATTTCAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAAAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACTTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_z_Salmonella.enterica_IIIb.50:k:z_AY353337_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O:22-gene3__411 +GCAGAAAAACCTTTTATTTCACCTAAAAAACGAATATTTTTAAAATCCTTGAACTGGGCTTTGAGAGATTCTAACTGTTC +TCCCCCTCCAACAATATCCAGCTTATATTGCGGTTTTTTTGATATCACTTGGGCCAATAAACATGGGCGCTTAGGATGTG +TCAATCTACCAACAAACAAAATTTTATATTCCAAACACTCTTTTAAACGAGCAGGCATGGGTGGAACAGCATTCGTAGCT +GTAATAATCTTACCCTCATCAATTCCTATTTTTTTTATAGCTTTTTCTCTATCACTTTCAGAAATACACCAGATGACATC +CGTTAATTTGGAAAGGTATTTTTCTATTTTGCAAAATATACTTTTTAGCCGACCACCATTATATAAGCATGACCACCCAT +GTGAAACGTAA +>fliC_d_Salmonella.enterica_Livingstone_SRR1299429__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATTGATATTGATTTA +AAAGAAATTAGCTCTAAAACGCTGGGACTTGATAAACTTAATGTACAGGATGCTTACACACCTAAAGAAACTGCTGTAAT +AGTTGATAGGACTACCTATAAAGATGGTACAGATACTATCTCAGCCCAGAGCAATGCGGATATCCAAACTGCAATTGGCG +GTGGTGCGACGGGTGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGTGGTGCTGCT +GCTGGCATTTATAAAGCAACTTATGATGAAACTACCAAGAAAGTTAGTATAGATACAACTGATAAAACTCCGTTAACAGG +TACGGCTGCTGCAGATATTCAGGCAACAACTGCCATAACTAAGAACCAAGTTGCTGAAGTAACAAAAGGTAATGCTGATA +CAACCACAGTTGCGGCTCAACTTGCTGCAGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCG +TTTGAGGATAAAAACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGA +TGAGAAAACAGGTACAATTACTGCTAAAACAACTACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAAT +TTGGTGGCGCAAATGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACAT +AACTTCAGAACAGGCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>O:23-gene3__454 +CCAATGAGAAACATCATTCACATATCCTACATAGTTAATTATTTCTTCTTTAATAATTGTATCAAGTTCATTTTGTTTTA +GACTACCAGGGTTTGCTGGATCAATATTACCCAGCACATTAAACGTCACCCCTTCAAATCTTTCTTTTATATTTTTAGCA +GCAGCGATAAATTCATAAATCCCCTTTTCTCTGAGCAATCGGCCAATGAAAATAAAAGAAATTGGTTCAAGTGGTGCTGG +TGAATACTTGTAATGCTCTAAATTTATTCCAATACCCCCCAATACATATACTTTTCTATCTTCTATACAACCAGCGTTAA +GTAAATCATTCCTATCATCTTCATTAAGTACAATAAGTGTATTAATTTTCTTAAAAGCTATTCTATAGAGCAGAATCTGT +ATTCTTTTTAGGATTTTTGTCTTTTGGGGAATCCCAGATGGTTGTTCGGTAAAT +>fljB_e,n,x_Hadarstr_AOZE01000017_e__1496 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>gntR-family-regulatory-protein_dt-positive__291 +AATATGCTGACCCGCTATGTTGGTGACCCTTCTGCCTGATCTTTTCGCCTGCGTGAGCATCGCAGGCGCTTCAACCAATT +CTTCAATTCTATTAATCACGTCCAGTAACGATCTAACCACGATCTTGATGTAGATCCCACTCCTGCATCTTTCCTGAGAA +ACGATTTGACTTAGTTTTTGTATGGGAATAATTTCTCCCTGTCAACATTGGATACAATATCATATATCATTGATTGGATA +ATTATAAATATGGAACCCATTACCCTTACCTTATGTTTATTGGTGTTCGCT +>fliC_z4,z23_Namurstr_AWGG01000011_z4,z23__1257 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATTAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGCGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCACCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,s,t_Salmonella.enterica_Senftenberg_AY353406_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATTCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTGACAACTGACGATGCGGAG +AACAACACTGCGGTTAACCTATTCAAGACGACTAAATCTACTGCTGGTACCGATGAAGCCAAAGCGATAGCTAGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCAGCGAATGTT +AATGATGCCACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13,z28_Salmonella.enterica_Connecticut_AY353452_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAATC +TGACCTCGACTCCATCCAGGCGGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAGGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,q_Salmonella.enterica_Moscow_AY353403_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGGCGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGAATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,m,t_Salmonella.enterica_II.6,8:f,g,m,t:.e,n,x_AY353382_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGATGGTATCTCCATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTACGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATTCAGGTTGGTGCTAACGATGGTGAATCTATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTGACGGGGTACGATACCTATGCAGCTGGTGCCGATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCTGCAAACGGTCAGTTGACAACTGATGATGCGCAA +AATAACACTGCAGTTGCTCTATTCAATACCACTAAATCTACTGCTGGTACCGATGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +AATGATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCAGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGCTTTGATTCTGCCATTACCAACCTTGGTAATACGG +TAAATAACTTATCTTCTGCCCGTAGTCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Amsterdam.var.O15+_AY353394_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z44_Salmonella.enterica_Quinhon_AY353513_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCACGGATATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +ACTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTGCTAAAAATTATTATGTTGAAGTAGACTTTTCTGATACTGCT +AAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTACTAAAGAACCTGCGAA +ACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGACGTCTGCTGAGGTGAAAGCTGCTTTGA +CTGCTGGTGGTGTCGATACTGCTGATGTAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAG +TTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAA +GCAGCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTT +CTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Mbandakastr_AMRS01000012_other.z10__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAGCTGGTATTACTGGTACAACGACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGATTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TAGTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACTACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGT +ACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z4,z32_Salmonella.enterica_IIIa.41:z4,z32:-_AY353509_z4,z23__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTATCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGAT +ACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCT +ATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAG +ATCTCTATGCTATCCAAACGTTAGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACT +ACGGAGGGCGCTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGC +ATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCACAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Salmonella.enterica_IIIb.28:z10:z57_AY353473_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATAACCCAGCGTCTGAACGAAATCGATCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACACCACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAAAATATGATGTTGATAGTACCGGTGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACTGGTGCTACATTAAAAACAAGCATTACTGGTACTACGACAGAAACTG +GTAGTGTTAAAGATGGTAAAGTTTACTACGATAAAGATAGTAAAAATTACTATGTAGAAGTTGATTTTACTGATACTACG +GATAAAACAGCGCATGCTGGCTTCTATAAAGCTGACGTTGATGCTGACGGCAATGTTGTTTTGGCGGCTGGTGCTACTAA +AGAAACAAAACCAACGAATGCAGTTGAAGTTAAGAAAACTATTGATGAAAAACCACTGAAAGCATCAAGTGATGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCAGTTGCAGAAGCGGCGACAGTAGTGAAGATGTCGTACACTGATAAAAAT +GGTAAAACCATTGATGGTGGATATGGTATTAAAGTAGGTAATGATTACTATGCTGCAACCAAAGAAAAAGACGGCAGCTA +TAGTATTAATACTACTTCTTACACTGATAAAGACGGCAATACTAAATCCGCACTGAACCAACTGGGTGGTGCAGACGGTA +AAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_IIIa.53:z4,z24:-_AY353505_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTAGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTTTGGTAAAAGATGATAAAGGAAACTATCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTCACTTTAGCTGGTGGTGCTTCAACCCCAAG +TGCGGTTGATACTTTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCC +TCTGACGGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACA +CGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCTAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_z38_Salmonella.enterica_Fresno_AY353487_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACG +GGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTAC +GAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAG +AATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGACTTACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTA +ACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACTTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Ajiobo_AY353493_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGCGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAG +CAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z_Salmonella.enterica_II.40:z:z42_AY353470_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGATGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACTATCCAGGTTGGCGCCAACGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +CGGTGTTTCTACTTTGGATACTGCAGGACTTACTGGCGCAGCTATTAAAACTGGCGTTGATGGAGCTACCACTACGAGTG +GTTCCATTAAAGATGGCAAAGTATACTTTGATGATGCTACTAAAAATTATTATGTTGAAGTAGAGTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGTACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCCGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGTTGATGTGAAAG +CTGCTCTGACTGCTGGTGGCGTTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAT +GGTAAGACGATTGACGGAGGTTATGCTGTAAAAGTGGGTGATAACTACTATGCTGCGACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAATACCACGTCTTACATCGCAACTGACGGTACTACCAAAACAGCACTGAACCAACTGGGTGGCGCAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCGCAGGTTGACACATTACG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z28_Salmonella.enterica_Javiana_AY353455_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACAAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAATTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCGCCGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACTGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTAAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCAGAGCTGGCTGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_r,i_Salmonella.enterica_Hidalgo_AY353464_r,i__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCTGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCTAAAGCCGCATTGACAG +CAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGTGGTTTA +GCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAAATACAC +TGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTATTGGTG +GTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCTACAACC +ACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAA +CCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAGATTCCG +ACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAAC +CAGGTTCCACAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.61:k:1,5_AY353539_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACCGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACAACCGAAAACCCGCTGCAGAAAATTGATGCTGCGTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAACACCGTAAWCAACYTGACTTCTGCCCGTAGCYGTA +TCGAAGATTCCGACTATGCGWCCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAAGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_I.47:z4,z23:-_AY353549_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTAAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCTGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATATGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGACTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,t_Salmonella.enterica_II.1,40:f,g,t:z42_AY353535_g,m__1518 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCACACTGAGTTC +CGCCATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATTGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCCCCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.40:z4,z23:-_AY353496_z4,z23__1242 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATTGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCTGCTGCGGATAAAT +TATCTCTGACAAAAGATGATACTGCTGCAGCTAAATACTATGCAGCTACCGTAGATACGACAACGGGTAAAATCAGTTTT +GATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAACCCTATCACGCGAAGTGAAATTTGATGG +AGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTAAAGATCTCTATGCTATCCAAACGTTAG +ATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAAACTACGGAGGGCGCTGCCGTAGCCTTA +GCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACTGTTGACGCATTCCGTAGCCAGTTGGGTGCGGT +GCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACCTGTCTTCTGCACGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGCACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z24_Salmonella.enterica_II.1,9,12,46,27:z4,z24:1,5_AY353504_z4,z23__1281 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGTTGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAAGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGTCCCGCAGCAGATAAAT +TATCTTTGATAAAAGATGATAAAGGAAATTACCTTGTTAAAGATGTTACTGTCACTGCTACTCCTAAATATTATGCCGCT +ACCGTAGATAATAGTACTGGGGAAATTAGCTTTGATTCGGCTAAAGAAGTTACTTTAGCTGGTGGTGCACCAGCTCCGAG +TACGGTTGATACTTTGTCGCGTGAAGTGAAATTTGATGGAGCAAATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAG +ATGATAAGGGTAAAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCC +GCGGACGGTAAAACAACAGAGGGTACTACCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCT +TAAAACCGTTGACGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCTATCACTAACTTGGGCAACA +CCGTCAACAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_l,v_Salmonella.enterica_Give_AY353443_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGACAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGCCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-48_unknown-from-serveral-cdc-new-genomes__4477 +CTGCAGCAAGCTCCTGAAGCTTATCCCCACCTTGAGCACCAAATTTCCAATTTTGTAAAATGTTACTCTTAAAGTTGCTA +CAATAATCACACTCTCCACTATTATCAAAAACTATGTTAGGATCAGATGTATCCATAATACAATGGCTACAAACTTTATA +ACTTTGATTTTCCATGTTCCCCCCTATTTAAAATGACTTTCATAACAATTTCATTAATTTCTTCTGTTTGTACTACATGT +AATCCATGAAATAACACTAGTGTTCCCATTTCTTCATATTTATATGCAAGAGTTGATGGATATGAGATAACTACATCAAC +CTTAGGAAAAAAGTTATCGTCTATAATAAAATTGAATTTAAATTGCCTGACTTTTGAGGAAGCTCTTGCCTTAGGATGCT +CTTTATAATAAATAGAACAATTTTCAATTTGTTGATTAATTAGAGAGCAAATTTTTAGCTGACCTTTCTCACACAATGAA +TGCCCAATAACTAACAATGTTAGCTGGTTCGATGATACTTGAGTAAGGGACAACATAGGTTTACTATATTCCACCTTTAT +AATTTCGGCCAAATTATAATCCAGTATGTTGTTTATAAACAATTGAAATTCAACTTCATCGAAAACAATTATTTTATCCA +AATGCTTTAATTTATATGGTATCTTAAAAAGTAAATAGGCACTTGAATCAAGGGCTCTCAAAGATCCATGCTGGATAAGA +GTATATTGAATTCCTTTTTCTCCTAACATTGAATCAATCAGGACCGCCCAACGATCATAATGTTCACTACTTATAACCTT +TCCTTGTATTCTATTCATCACTAATGCGACAAGGAACCAAGATGGAGCTGTGTATATTTGCAGGCACCATTTGATAGTAT +GCTTCGATTTAAAAAAATAGAAAAACGCAAATATGCTTAGCAACATGCTTTTGAAAATATCTAAATACGAAGCCATCTCA +TAAATTGAAATAACTGTAGCATCACTTCTATCATTACACGATGATAATTTAATAACATTTAACTTTTTTCCATCCGAAAT +TTTACTATTATAATAATTAATTGCTTGCTCCGTACCTATTTCAGCGAATGAAAAATAGTAAAAGTCGCTTCTATCAATCA +ATTTATTTTTATCTGTAATTATTTTTTTGTATAATGCAACTATACATTTTAATATAGGATAAAATATAAACCCCCCTAAT +ATGAAGAAAATCATAAGAGAGATATATCCCCCCCACAATTTATGCCTCCCATATGCCCATTTGCTGATCCGAGGTAATGG +TGGTATTCTACCTTTCATGCCAGCGATCAACAATTTATCAATAGAGATTTCATTTTCCGTAGCTAACATATAGTAGCGTA +AATATGTTTTATAAGAAATTCTCATCCGACATGCCCGTCATTAATAATATGTAGACGCTCTAATTAATAATCAATTATTG +ACTTTTTTAGAGATATTTGTAACTAGTTAACATGAAAAATTCATATAAAAATGCTAAGTCATCTTCTTATTTATATTTTT +CTTGTTGACTAAATAAATTATCGATATAAAAATCATAACTGCTGACGGTGTAAAATACCCAGAACCTCTTAGCAAAAAAT +ATATTATGCTCATTATTAAAACTATACTAAAAAACTTTATTTTTTTGTCATTGCATTTAAACCGCATGACACCTAAAAAT +AATGTATAAAGAAAAAAAATGCCCCCTAAGATACCAAATTCAACAATCAATTTAGAAATAAATAGTCCACCATCATATAA +GTTAGAATCTGTATTCCCTCCCCTTAACCGCCCAATGATTGATACAAACTCTCCTCTTTCATTTGCATATCCCATATTTT +GTAAACCATAACCAAGGCCATAGCTATCTCGCAACGCTAGATATGCTTGTTCATATCCAGATAATAAAGTTAATGTTGAT +GTATTTTTCGATTCTTGGCTTATATCTAATCGTTGCGAATAATAACTTAGTTTATCAATAGGTAAGATTCCAGCAATCAG +CATACACGATGAAGATACGCAAATCATAATAATGAACATTGATTTAACTCTCATATAGTTTATAGCTATCGCTACAACAA +TACCTATAATCAATGTTAAATTCTGGACAATAAGAGCCGTAAATAAAAGAGGAATTCCATAGAGCAAATTTAATTTTTTC +TGAGATATCTTATAGCAATAAAAGATTGTAACTATTAGTGCATAATGAGAGGGCTCAGTAAAAAACAACATTTCCTTTGA +AGTGCTACTGCTTGATAATATAAAAAGAGATGACAATACCCCCAAAGCTATTAGTAATTTAAATAATTTTGATACTATTC +TATCAAACTCCTGGTGAGTAATATTATCAATTGCCACCGATGAAAAATAACATGCGAGTAAAATATAAAATAAGAATAAC +AATGATGTAATATTCTTAGTGAAAGTAGTATTACCATTCTGAAATAGTAGACTACTTAACCCAAAATGAAACAATATTAG +AAAAAAACTAATAACACTAAAAATTAAAAATGAATAACTTATAGTTAATTTATTAAAGCCAGAAATAACCACTAAAAATA +ATATTATAGTTGATATAAAGAAAATACCAATGAAATTCGAACCAACTTTATCATTTAACACCATTAACAGGCCTGGAACC +AGCACCATTCCATAAAAAAATATTGAGGTCAGAACTTTATTAGTATTAAATTGCATTATAGTTAAACCTTATTATTCCTT +TTAATTACAATAAAAAATTATATAGCATAAGTATTTTAATTTAAAACAATTAAACTTTTCGTACTTTTCGTAGTTCATGC +TTTTAATAATAAACTATGTATCTCACCGAGAAATTCGCTATAACAAACGTAACACTATGCATTTTATATCTATATAAAAT +ACAATAGGTAAGATATCATCTATTAGAATAAAATAAACTCTCGCCGGCAGATCGTCTAATTATAACCAAGAGTTTTATAA +ACATAGCCAGCTTTAAAAATAATAAAACTGAAAAAGAAATAATCATACCATAAGCAATGTAATTAATATTCGCGACCTTA +AGTGCAATATAAAGAAAAGATGAAAACAGTAAAAAAGTTAAACACTGGCTCCAGACTATCATTTTATCTTTTCTTAGTGC +ATACAGACCCAGATGTGGTATAAGGCTTAAACAATATATAAACGTCGCCACAATTAGCAACTGAAATAGTGGAAGTAATT +CCCAATATTCGATCTTTCCAATCCACTGAATGAGGATATAACCGGTAAAAAAACAACAAATACATAACAGAAGCGACACT +GCTATTAATTTGAATGCGAATGACTTCATTCCAGCGATGAATCCAATGTAGTCCTTTCGATAACACAATTTTGCCAATTT +TGGGAATGAAAAAGATATTAGGATCGTATCGAGGAAAGATTGTATAGCCGCCGTCATACTAATAAACAAAGTATATACAC +CAAGGATCTTTAGTCCAGCAATATGTTCAACGGCAAACCTATCAAATGTAAAAAAACCTCTGAGCGCCAAAGCGGCAATT +AGCATTGGTGCGGAAAGGATAATTCCTCTCATTATCCAGCGCCAGCTAAATGGCGATGTAAACTTCCGTTTATTATTTTT +TAGAATATAAAAAAAGCCCATTGCACTAGCACAGAATGTACCAAATAGCCATAATGTAAATACAATAAATAGATTTCTTG +ACGTAGGAAATAATAGCATAATGGCTATCACGAGCCAGCACCAAAGTCCTTGTCGTATAAACAACACAAGACTTGCGAAA +GCTTGATTCTCGAGAGTTATTAATATTCTATTAATTTCTTGAGCTATATGTTCAAAAAAGAGAATAGCAAGAAACCAGTA +CTCACTTCCGTGGGGAAGAAAGGAATAATGTTGGATAACAATAAAAATGGGGATATAAAATATATATGATAATACATAAA +AAAATGACTGATTTTTTAAAATAAAAAAAAGATCGTCACTTTTTGAGTTTATTATCTCTCTAGTACTATAAGTATAAAAT +TCAAATCCAATAGCAAAAATTGCGTAGCCCACAGCGGCGCTTATAAGACCATAGACTCCCAAATCTGATGATTGCAACAA +TTTTGCTAATAAAATTATAAACACAAACTTGCTTATCAAAGTAAAGCCACGTATACCTATACTTAAATAATATATAAAAA +GAGATTTTTTCATTTGAATAAGCCAATAATGCTTAAAAATATCGTTAACATAATATTAAAAATAGGCCATATACTAATAG +ATAGCTTTTTAGAAGTTTACAGATCATAGAATGCTTTGAAGCCTAGATTAGCAGGATCATTTGATAAAAATGCTTTAATT +ATATCCACAATTCTATCTTTTACATTTTCCATAAAATATGGGTTTTTAGAGCTTTCTAGCTTAGAAATAAAAACTTTATC +AGTCACACTCGAAATAGCTTCACGTATAGCATTTTTTTCACAAATAGTATCGACAACGCTTTCACCACGAATGCGCC +>O-4_wzx__1293 +GTGAAAGTTCAATTGTTAAAAATTCCGAGTCATTTAATTGTTGCAGGTTCATCATGGTTATCCAAAATAATAATTGCCGG +GGTGCAGTTAGCAAGTATTTCATATCTTATTTCTATGCTAGGTGAAGAGAAATATGCAATCTTTAGTTTGTTAACTGGTT +TATTAGTATGGTGTAGCGCTGTTGATTTTGGCATAGGTACAGGACTGCAAAATTATATATCAGAATGCAGAGCCAAAAAC +AAAAGTTATGATGCATATATTAAATCAGCATTACATCTAAGCTTTATAGCTATTATTTTTTTTATTGCTTTATTTTATAT +TTTTTCTGGGGTAATTTCCGCTAAATATCTTTCTTCTTTTCATGAGGTATTACAGGACAAAACCAGAATGCTCTTTTTTA +CCTCATGTCTGGTTTTCAGTTCTATTGGAATCGGAGCTATTGCTTATAAAATACTTTTTGCCGAATTGGTCGGGTGGAAA +GCTAATCTATTAAACGCATTATCTTATATGATAGGTATGCTCGGCTTGCTATATATATACTATAGGGGGATCTCAGTTGA +CATAAAATTATCACTAATAGTCCTGTATCTTCCAGTGGGTATGATTTCATTGTGCTATATTGTATATAGATACATAAAGC +TTTATCATGTTAAAACAACAAAATCTCATTATATAGCAATTTTACGTAGATCTTCAGGGTTTTTTCTTTTTACTTTATTA +TCGATAGTGGTGCTTCAAACAGATTATATGGTCATTTCTCAAAGGCTAACTCCTGCTGATATTGTTCAATATACAGTAAC +GATGAAAATTTTTGGTTTAGTCTTTTTTATTTATACTGCTATTTTGCAAGCATTATGGCCTATATGTGCTGAATTGAGAG +TCAAACAGCAATGGAAAAAACTTAACAAAATGATAGGTGTCAATATTTTGCTTGGCTCACTATATGTTGTTGGATGTACA +ATATTTATTTATTTATTTAAAGAACAGATATTTTCAGTAATAGCCAAAGATATTAATTATCAAGTTTCTATTTTATCTTT +TATGTTAATTGGCATATATTTCTGTATTCGCGTTTGGTGTGACACTTATGCAATGTTATTGCAAAGTATGAATTATTTAA +AAATACTTTGGATATTAGTACCACTACAAGCAATAATTGGTGGAATAGCACAATGGTATTTTTCTAGTACGCTTGGAATC +AGTGGAGTGCTGCTTGGCTTGATTATATCTTTTGCTTTAACTGTTTTTTGGGGGCTTCCACTAACTTACTTAATTAAGGC +AAATAAGGGATAA +>O-41_wzy__1221 +GTGTCGAAAAGTAATAGAATTTTAATCATTGCATTTTTGTTGTTATATATTATATCTGCGTTAATATCAATGTTTCAGAC +TTTAACGCAAAATAACTATCCAGGCGAATTAGAAGAGTTCACAAGGTCTATCTCTACTGTTGAAGTTATCCTGTTGAGCA +TGTTAAACATTATCTCATTCATACTTTGCTATTTTGTGTTTCTCGTGCTTTCTAGTTTTAGGCTTAAGCTTAATAAAAAT +ATCAACGTGATTTTTAATAAGACAAAAATTAATAAATTATTCTTTTTCTTATTAATTGCACAAATATTTTTTTTAGTAAC +AACGGGAGTAGGAAAAGTAACTACTAGTGCTAATGAAATTGCAACTTCCATTTACAGTCCTTTATTTTCTTTTCTGAAAC +CTGAGCCGTTTATATATTTATTTTTTCTGTATTTTAGAATGGATAAGAATTTCTCTTATAAAGGTAATATTCTGTTTACA +ATAAACATTGTATTATTTATTTTCTTTAAAATACTTCAAGGATGGACAAGTTTTCTTCTTATACTGTTTTTTTTAGAGAT +GTACGCGCGATACCGCCTAAAAAATAAAAAAATTATTTTATTGCTACCCCTGTTTATTATTTTTTTTGGTGGCTGGGTAT +ATCAGTATGCCTTTGTATTAAAAAATGAAATTCGTGGGAATGATGTGGCTCCTTTGAGTTATTACCAAGGGGTTGAACAG +TTAACATCTAGGCTATCAATGAATCCTGTTTCATTAGGTGCTTATGAAAATTACGATACTGTAGTACATCTATATCAAAA +AGAAAATAGAGTTTTTAAAGAATCTGGATCTTTATTGAGGCCAATACTACCTGCAGGTTTTATAAATAAAGATTTTAGAA +TACTCAATAATAATGTTATGACATCATTTTATCCAGACTTAAATCCATATACGAGCTCTGATTTTGGTGTTGTAATGTAT +TACAGCATATTGTTTAATTCTAGCCTACCTGGTTTTATACTGTTAACTATACTTACTATCCTGTTGTTTATTATAGCAAA +AATATATTTTGATTCTATGTCGTCTTATAATGGGCAATATGATATCTTACTTTTTTTTATTATTTTTTATTCATTTTATA +CAGTAAGTATAGAAAACGTATTTGGACAAGGGTTCTTTCCATACATATTTAGTACTTTATTTTTTTTCTTAACTGGTTGT +ATCAAATTTAGCCGAAGGTAA +>O-41_wzy-from-Waycross-SRR1233896__1221 +CTATCTTCGGTTAAATTTGATCCCACCAGTTGCGTAAAAAAATATAGTACTAAATATGTATGGAAAGAATCCTTGTCCAA +ATACGTTTTCTATACTTACTGTATAAAATGAATAAAAAACAATAAAAAAAAGTAAGATATCATATTGTCCATCATAAGAG +GACATAGAATCAAAATATACTTTATCTATCAAAAACAACATTATAGTAAGTATTGTTAACAGTATAAAGTCAGGCAAACT +GGAATTAAACAATATACTGTAATACATAACAATACCAAAATCAGAACTCGTATATGGGTTTAAATCCGGATAAAATGATG +CCATGACATTATTATTAAGTATTCTAAAATCTTTATTTATAAAACCTCCAGGTAGTATTGGTCTCAATAAAGATTCCGAT +TCTTTAAAAACTCTATTTTCTTTTTGATATAGATGCACAACCACATCGTAATTTTCATATGCACCTAAAGAAACAGGATT +CATTGATAGCCTGGATGTTAGCTGCTCAACTCCCTGGTAATAACTCAAAGGAGCAACATCATTCCCACGAATTTCGTTTT +TTAATACAAAGGCATACTGATATACCCAGCCACCAAAAAAAATAATAAACAGGGGTAATAATAAAATGATTTTTTTATTT +TTTAGCCGATATCGAGCGTACATTTCTAAAAAAAATAGTATAAGAAGGAAGCTTGTCCACCCCTGAAGTATTTTAAAAAA +AACAAACAATAGTATATTTGTTGTAAATAGAATATCGCCTTTGTAAGAGAAATTTTTATTCATTCGGAAATATAGAAAAA +ATAAATATATAAAAGGCTCTGGTTTTAGAAAAGAAAATAAAGGACTGTAAATCGAAGTTGTAATTTCGTTAGCATTAGTA +GTTACTTTTCCTACTCCCGTTGTTACTAAAAAAAATATTTGCGCTATTAATAAAAACAAAAATATCTTATTGATTCTTCT +CTTATTAAAAATCACACTGATATTTTTATTAAATTTAAGTCTAAAGCTTGAAAGCACGAGAAACACGAAGTAGCAAACTA +TGAACGAGATAATGTTTAACATGCTCAATAGAATAACTTCAACAGTAGATATAGATCGTGTGAATTCTTCTAATTCTCCC +GGATAGTTATTTTGCGTTAAGGTCTGAAACATTGATATTAACGCAGATATGATATACAACAGCAAAAAGGAAATGATTAA +AGTTCTATTACTTTTCGACAC +>O-16_wzy__1233 +ATGAATAACCAAGATTTAAAAATTGGTACTGCATTTATTTCAATGATTTATTTTCCCTTGGGATTTTTGGTATCACTTAT +TGAAGTAATTAATGGATATAGGTGGGGAAACTTTCTATTCGCATTTATCTTGGGTCTATTAGCATTCTCACTAATACCGT +ATAGTGATTGGGATCTAACAAGACATTATGAAACCTATTTAAGTTATAATAATACCTCTTTTAGTGAAGTATGGGAACAA +AGTGATAATCGATATTTAGTAATAAATACTATAATTTATCTATTTAATACTTTCGCTATCAAAAAGGAGTTTTTACCGTT +CTTTGCTGTTTTTATATCTTATTTGTTTTACTTAAATGTATTTTCGAAATTTATTAGAGAAAAAAAGCCTAATATTTTAA +TCCGAAGCATCTATTTATATATTTTATTAACGGTAATACCTTTTTTTGCTATAGCTAGTTCACTACGACAATATTTAGCC +TTCAGTATTATATTATATATAATAATTACCTACTGTAGTAAGCAAGATAGACGTACTTTCCTTATATCTTTCCCACTAGT +TGTTATGGCAATAGGAATACATCCAAGCGTAATTCTGTTAATAGCACTGTTTCTATTTAGCAGATTTATACGCCTAAATC +GAATAGTTGTGCTTCTTATTTTTTTCATATTAGTTCTAAATTTTAATGGTTATATTTCAATACAATTATTCAAGCTATTT +AAACCATTATTAATGAATACAGGTTTTTATTATCCGGAATATATGGATGCAGAGGTTATTCATATGAATAACCAACTATT +AAGCACGAATGAATTTATACTTAATAAATTGATTTTACCCAGTATATTTTATTTGTTAATCCCAGTCTTTTTGATTTTCT +ATAAAAAATCAAACAGTAAACAGGAAAAGCAACTAAAAAACTATTGCGCACTACTCCTTTTGACTATATGCCTGTTATCT +TTATCACCTGATCTTTTTTATCGATTTTCAATATTTTGGACATTATTCTATAGCTATATATATTTCACTTATGATAGTGA +GAGAATGAGTTTGCCTGCCAAACAGTGCTATCTTGTAATTATAATTGTTGCATCATGTGTCATAAACTTAGCTCAAGCTA +ATATGGGCAAGAAAATCATATATAATTCATGGGGATCATTTTTTTACCAACCTTCACTATTCGTGTTTGTTAAAGAAATC +AAAACGACTGACTATATAAATGTGAGCCAATAA +>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353409_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTAGCGTGGGTGCA +GCAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_k_Salmonella.enterica_IIIb.17:k:z_AY353437_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACTATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAGATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACTGCAGATGACGGTACATCCAAAACTGCACTAAACCAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_e,h_Salmonella.enterica_Newport_AY353379_e__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTATCAGCAACTGCTGCAAT +GGATCCGAAATCATTTACTGACGGTACTAAAAATCTTACAGCGCCTGATGCTACTGCTATCAAAGCCGCGTTGGGAAATC +CCGCGGCAACAGGCGATTCCTTGTCTGCTACGCTTTCGTTTAAAGATGGTAAGTATTACGCCACTGTTGCAGGGTATACG +AATGCTGCCGATACCAGTAAGAATGGTAAATATGAAGTGAATGTTGATAGTGCGACAGGTGCGGTAACTTTCAATGCAGC +ACCAACTAAAGCCACAGTAACTGGGGATACAACAGTAACCAAAGTACAGGTTAATGCTCCTGTTGCAGTCAGTACTGATG +TTAAAAAAGCGCTAGAAGATGGTGGCGTTTCAAATGCGGACGCTACCGCAGCTAAATTAGTAAAAATGTCTTATACCGAT +AAAAATGGAAAATCTATTGACGGTGGTTATGCGCTTGAAGCCGGTGGCAAGTACTATGCTGCAACCTATGACGAAGGTAC +AGGTAAAATCACAGCTAATGTAACCACTTATACTGATTCCACGGGAGTCACAAAAACTGCGGCTAACCAACTTGGTGGCG +TAGACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCTAGTAAAGCCGCTGGTCACGATTTCAAAGCG +CAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGA +TGCGTTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACT +TGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATCCTGCAG +CAGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-63_wzy__945 +ATGATAAACAAAAATCGATATAAAGGCTATTATTTAATTCTTTCGTTTTTTCTGACATTAATTTTTGCACTTCGGTTTTT +TTATTTTTCCCATTATGAGATATTATTGGTCAGTGATACCTTAGAGTATTATAATAATTTTTCTGATATCGAAAATGATT +TATTCCCATATGGCTTAGAAATATTGATGCCAATTTTAATGTTTTTTATAAAAGCGATAGGGGGAAATTTTTATGACTTT +TTATTCTTTGTTTTAACACTATGGCTCCCGTTGATTTTTATTATTATTTATAGAAGTTGCTATAACCCATTATTTTTCAT +AATAGTTTTTATTTCTTCGTTCTTTTATATGAACGCTGTATTAATTATTAGGCAATATATTTCTGGGGTTTTTTTTATTT +ATTGTATGCTTTTTGCGTATCAACATAAAAAGATATCCTTATTTTTAGCATTTTTATCAATCTTATCTCATTCCTATGCA +ATAGTATGGTTAATAGTTGTCGGACGTTGGTTTAGAAATTTTATCACCAATAAAATTATTTTAAGTGTTATTATACCAAT +ATCATTATTTGCTGTAAGCTTCTCATTTTCTTCTTATCAATTGCAGTCAGTTTCTTCCTTTCTCCTCCAATACAATATGC +CAGGTTTGTTACAAAGGAAAATACAATATTATAATAATAATAATGATCCTGTAGAGTCAGTTTCAAATATAAGTTTGATT +CTTGTTGATATTATATTTATATTAAGTATAATAAACCTTTTGAAACAAAAAAATGAATTTGTTTTAAAGTTATCATCTCT +CCTAATTTTTAATTCCTTTTGTTTCATTATGCTTGGTTCAAATATTGTTTCAGCGAGTCGTTTTGGCTTTTGGTCATACT +ATTTTTCAATACCTTCATTAGTAATACTATTGTATTATTGTCTTAATCTTGTTAAAGATAAATAA +>O-9,46_wbaV__1002 +ATGAAGGTATCATTTTGTATCCCAACGTATAATCGAGTAAAATTCATTGAAGACCTTCTTGAAAGTATTAATAATCAATC +TTCTCACTCCTTAATTGTAGAAGTATGTATTTCAGATAATGCATCAACTGATGGAACTGAAGAGTCAATAAATATCTGGA +GAGATAGATTTAATTTTCCAATTTTGTATCAAAGGCATAACGAAAATATTGGGCCAGATAGGAATTATTTATCTGCAGTT +AATATGGGGACTGGAGATTATTGTTGGATTTTCGGAAGTGATGATATTCTTACAAAAAATTCCCTTGCATTGATGGAAGA +TAAATTGGCTGCCGGAAGTGGCATTTATTTATGTGACAGACGAGAATTAGATATTTCAATGACGAAAATATCTAATCCAC +ATCGGCGATGGTTAAATGGTGGCAGTAGATTATTTTCTTTTAGCAATGAAGCTGATTTGATAGAGTACTTTAGTAAATGT +AACTCAGTCGGCGGACTTTTTAGCTACTTAAGCTCTATTATAGTGAAAAGGAATAAATGGTCTGACGTCATATTTGACGA +GTCATACATTGGTACAGCTTATGCGCATGTATATATTTTATTAAGAATAATTAACAATATGAATTCGACCCTGCAGTACA +TATCACTGCCACTGGTTGATTGCAGAGGAAATAACGATACATTCGAAAGTAATGGGAAGGCTCGTCGAATAAAAATTGAT +TTCATCGGTTATTTAAAACTGAGGGAGGATTTTTATAATAACAATACAAAAATATATATCTCATTTGGACGGGTTCTTAC +AAAAGAGCGTCCTTGGTTTTATACTTCTTTAGCTATGGCATGTTATGGTGATTCCACCGATAGGGCTGAACTTGCATCAT +TTTATAAGAAGTTGGGATATCCGAAAATAGCCACCAATTTAATATTTCGTCTTAAAGGGCTGGCTAGCTACACTAAAAAA +ATAAAATTAGCAAAAATGGTAATAAAAAAAATATTTTCATAG +>O-65_wzy__1125 +ATGGTAATCTATCTGGTTCTTCTTATTTTTATTTTTTCTTTCTCTATAGTGATGATGTTAAATCCTTCGAAAAGGACTGC +TAACAAATTTTTAGGCATATATGTATTGTTGCTATCACTATTTGCAGGTTTAAGATTTCATACTGGTTGGGATTGGGAAG +CGTATGATTATTTTTTTAATCTATTAAATCAAGCTAACATTTATGATTTTTTTAGTTACAATATATTTAACTATGAACCC +GGTTTTGTATTACTTTCATATATATCAATATTATTAAATATTCCACCTTTTCTGCTTTTTGCTATAATAACTGTATCTCT +CATCGTATCCTCTGCTCATAAATACTTAGGTAAATTTGTCCCCTATATATTTTGTTTGATTTATCTGTATTATGGTTATT +TTCATAACTTTTCAATAGTACGACAAGGAATAGCAGCTGCTTTATTTGCTTACTCTATTCGTTTTCTTATTGTTAGGAGT +TACAAATTTTATTTTGTCATAATTTTTGCTTCGTTATTCCATATATCAGCAGCCATGTTACTAGCTATACCGTTACTCCT +TGTGATAGCTAATCGGGTTCCGTTTTTTTTACTACTGCTATTATCTATATGTATGGTTCTTTTGCCTTTAAGTGATATGC +TGGGCTTAAAATCATTAATGTCTAAAATACCGGCATTAAATATTTACCTAAATAATAGCACGTTAAGTTACAAAGTCGGA +TTTTCATTAAAATACCTAGAGTTGCTAATTGTATTTTATTGTTATTATGAAAGAAAGTTTTTTTTGCCACTTATAAATAA +TTTTGGAATAAGACAGTTTTGGATCTTTAAAGGGCTCATTATAATTGAGCTGATGATTTATTCTATTTTTAATGATTATA +GTATCATTTATGAAAGATTGAGTGTATATTTTGAATTTTCACACGCTATCGCAATAGCAATGATCGTTTCAACTTTTAAA +TATAAAAGAATACAATTTTTTCTAATGCTTATATTGCTTTTTTTTGTATTTGCAAGATACTATCAATTAGTTTATTCCCC +TGTCCGAGTGCCAGGCGAAATGTCACATCTTGAACGATTCGAAAATTATTGTTCTATTTTTAACGAAAGAGAATGCCAAA +GGTAA +>fliC_i_Salmonella.enterica_IIIb.57:i:e,n,x,z15_AY353432_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,w_Salmonella.enterica_Ayton_AY353446_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTCGGCGCGAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACTAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTGCAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_m,p,t,u_Salmonella.enterica_Haelsingborg_AY353410_g,m__1527 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGGTATGATACCTATGCTGTTGGTGCCAATAAATATCGCGTGGATGTCAACTCAGGGG +CGGTAGTAACTGACACCACTGCTCCAACTGTTCCTGATAAAGTATACGTAAACGCTGCAAACGGTCAGTTGACAACTGCC +GATGCGCAAAATAACACCGCGGTTGATTTGTTTAAATCTACTAAATCTGTTGCAGGTACTGACGATGCCAAGGCTATCGC +AACTTCTATCAAAGGCGGAAAAGTTGGTGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATATAAAAGCTGGTG +ATGACGGTAATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACATTAACAATTAGTGATATTGGCGTGGGTGCA +GCAGACGTAAATAGCGCGAAGATTCAATCAAGTAAAGATGTTTATACTTCCGTTGTAAGCGGTCAGTTTACTTTTGCTGA +TAAAACCAAAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAA +ATGGGGCTGAATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCT +TCTGGCGTAAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTC +TGCATTGTCAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTG +GCAATACGGTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCC +AAAGCGCAGATCCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACT +GCGTTAA +>fliC_b_Salmonella.enterica_I.6,7:b:z33_AY353361_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCAGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGCTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACTTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Choleraesuis_AY353364_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTAGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTAGACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z36_Salmonella.enterica_Weslaco_AY353483_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCAAACTCTGACTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC +GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATCAAGCAACAACTGGTAAATTAACTGCAGACTTAG +AATTGAAGCAGGATAAATCCGGAAACTACTTTGCCTTCGATAAAGCAAACAGTAAATATTACGACGCAACTGTGGATGCT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGGCTCACGGATGATAAATTATTAGTAAAATACAAAGGGGATGATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG +ACAGAGGGTACTGCCGTAGCCTTAGCTGCAAACGTCGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAGTCTGCCATAACTAACCTGGGCAACACGGTAAATAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGCACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IIIa.44:z4,z23:-_AY353497_z4,z23__1275 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCGGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTACTACTGGGGCGGCTAAATACTATGCAGCT +ACCGTAGATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGACTCCGCCAGCAGT +AACTACCTTATCACGCGAAGTGAAATTTGATGGAGCAGATTTAAAAGCCGATCAATCTTTAGTGAAATATAAAGATGATA +AGGGTAAAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGAC +GGTAAAACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAAC +CGTTGACGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAA +ATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z_Salmonella.enterica_II.16:z:z42_AY353469_k,z__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +CGGTGTTTCTAATTTGGATACTACAGGTCTTACTGGCGCAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACGAGTG +GTTCCATTAAAAATGACAAAGTATACTATGATGATGCTACTAAAAATTATTATGTTGAAGTAGACTTTTCTGATGCCGCT +GATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCCTCGACTGCTAAAGA +AGCCGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCGTCTGCTGATGTGAAAG +CTGCTCTGACTGCTGGTGGCGTTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAT +GGTAAGACGATTGACGGAGGTTATGCTGTAAAAGTGGGTGATAACTACTATGCTGCGACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAATACCACGTCTTACATCGCAACTGACGGTACTACCAAAACAGCACTGAACCAACTGGGTGGCGCAGACGGTA +AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGTAGCTACTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCGCAGGTTGACACATTACG +TTCTGACCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,w_Salmonella.enterica_Glidji_AY353447_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATATCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACCGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGACAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCACAACTTCAAAGCACAGCCA +GAGCTGGCTGAAGCGGCTGCTACAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACTTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Salmonella.enterica_Freetown_AY353466_other.y__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGCTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGAACTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_b_Salmonella.enterica_from-cdc_Stk1415_b,d,j__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTGCAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAATGATGTTACCACCTATAAAAATGGTGGTACTACTCTCACAGCTCCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTTCTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACTGGTACAGCTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCAGTGACAATGACCGCAAATAAATCGACAGTAACTGGGGCTAGCAC +AGTTACCGAAAACCAAATTGTAGACGCTGTTACTCCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGGGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCA +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAGACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACTGGCGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACAGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGTGCTTTAAGCGAGGCT +GTGACTACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-42_wzy__1017 +ATGCCAGTAAAAACTAACAACTTTCTTTATTTCATAATGGTCATAAGTGCTACCATTTTTGCTGTTAAAATAGTGCCTTA +TTCGAATGACTATCAGGCATATATTGATTTATTCAAATATACAATTCAAGATCCTTCTTACGAGAGAATGGAAATTGGCT +TTAAAAACCTTATTGGTTTTTCAAAATTTCTTGATTTGAATTTTGATGTATTATGGTTTTTAGTTGCTTTTATTTCTTTG +TCGCTAAAATGTTATGTATTAAAATCCTATGATTCAGATATCCTTGTATTATTTTTGTTGTACTTTTTGTACGCTATATC +ATTATTAGCTTTACACGAAACCACACAGATACGAGCGGCTATTGCAATTGCTTTAGGTATAGCAGGCTTTCGATGTACGA +ATAAATTTGTTGGTATCTGTTTAATCCTTTCTTCTGTATTATTTCACTATTCAGCAATTTTATTTATTATTTTGTATACT +TTGAGCTTTATAGTTAAACCGTATAAGTTCACATGGTTAATAGTTGTTGTTACTATGGCGATACTAATACCCTTGCTTCT +GGAACAATACTCAGATCCATTAATTAGTATTAATCCATTATTTTCATTATATTTAGAAAACTCTGATAATGCCAAGGTAA +ATAAATTTTCTTTTACTTTAATTCTTGCTACAATATTTTTTGTAATAAATTTTTTTATTGGAAGAAAAATTAACTATTAT +AGCAATAATAATTTCATATTTAAGCAATATAATCTTTTTTCTTTTCTTTATCTTTCTAGCGTAGTACTTTTATCTGCGTT +GTCTTTTTCGCCAGTCATTTCAATAAGATTATATGAGTTATTTTCGTTAAGCCCTTTTATTATTATCGCATGCCTTTATT +CTAAAAGTATGAAATACGTTTTTTATTCTAATATAAATTTGCGCTTGCTAAGAAGAGTTTTGCTTTTAACATTATGGCTA +ATCTCAGTGCATCGCTTTATTGCTTATTACTTTGTTAATCCAATCATTAAATTTTAA +>O-47_wzy__1095 +ATGATTGAAGGATATGTAGTATATAATAGTATTTTTCTTCTTGCCTTACTATTTGGCTTTATGAAGAATTACTGTCTTCG +GAAATATTTTTTATTATGCTTATTCCTTGTCTTATGGGTTCCACTTGCCACTCGTTATGGCATTGGTCGTGACTATTTTA +GCTATGTTGATATTTATAAAAATGTGTTAGTTACCAGAGATGGTATTGAAGTAGGTTTTTATTATCTAAATTATCTGTTG +GCATATTTTGGTTTCCATTATCAATCTATATTTATATTGACATCTTTTATTACTGTCTATTTAAGTGTTAAAAGTTTTGA +TAGAGAATATACAATAGTATCAATTATATTATTTGGGGTTTTGGTTTACTTACAGGCGTTTAGTATTGTTAGGCAAATGC +TTGCTGTAGCCTTATGTCTTTATAGCTGTTCGTTATGGAATAAAGGTGTTAAGGTTAAAGCAATTATTTTTCTTATGCTG +GCACCTTTGTTTCATTATTCTGCTGTAATAATATTTATATTGGCAATAATTAGCAGATGTGTTAAAATCGATACGTTTAA +ATGTCTTGCTATGTTAGGGCTTAGCCTTATTTTTGTTTTTGTATTTAATGGGATCGATTTTATATTTTCAAATCCTATAC +TATTAAATAGTAAGTATGGATATTATGTAACATCAGCCTTTAACAGACCGACTGAAATAGGTTCAGGCATTGGAGTGGCA +ATAGCATTATTTCTTCCATTCTTGATTTTTATGAAAGCATCAAAAATATATAAACATAATAAAAATTATAATCTGATGCT +ATTAATAAACCTTGTATATGTTGTTTCATTTGTTTTATCTTTGAAAATATATATATTCGCCAGATTCACTGATGCGCTAT +CCTTTGTCCTGATATTACTTATCCCTGCTGCTCTTAAAATATCAAATACTAGAGGCCTATATTATAACTGTATGTTATCT +GTTGTTATTCTTCACATTATGCTATTTGAAGTAAATCTTAAAGCAAATACAATTGCAGCTGGAGATATGTCTAATAGCGG +GCTTGGAATCATGCCGTATAGCAACATAATAAACGCACATATGCTAAAATACTAG +>O-39_wzy__1341 +ATGCCTATAGCTGTACATTTGATTGAGCTAGCATATGTATTAATAATAATATCATTTATTATCTTGTTTTACATGAAAAA +TGTCCCATTATTAGAGGGAGGGTTTTTATTACTTATTATTTGTTCACCTTACTCTATTTCAATTATACCATTTAGACAAG +ATACAATAGAACTCTATGGATTGTATAGTAATAGCGGGCTTCTTAATTTATTTAATTTTTACAAAGTAGCCGGCTTATCT +ATTTTAGATCTAATAGCATTACTAGTTATAGTGAAAAACTTTAAATTAGCATTGAAGATGCCAATCTTTTTTAAGTTTTT +TTATATACTAATAAGTTTTTTTTCAATAATAGCTTATGCAATATCAGCTTATTTAATATGGTCTCCTGAACTAGATAATG +TAATTCGCGCTTTATCTGTCTTCAAATCAATTATATATATAATAAGTATTTATTGTGTTATTGAGAAAATTTGTTCACGT +ATTGGTTTTAAATTATTTCTCAAAATACTTATGAATATAATACTAACATATTGTATTATTAATTGTGTACTACTAAGTTT +TCTCCCCAGCTGGTATACGTGGGTGAAATATTCATTCAATTATTTATTTCTTGACCAAACAGATCAATTCCTTGTTTTTT +TATTTTGTCTGTTAACTTTTTGGGGGCCATTAAGTAAGCTATATCGTTATAAGCTGTATGCTTTTTTATTATGTATTATG +CTTTTTCTTAGTGGAGGAAAGGCTGGAGTCTATTCAATAATGATATTAGCAATGGGATGGCTATATCAAAAAAGTAATAT +TAAAGGCTCTAATCTTGGAGTAATTTTCCTCTGTGCTATGATATTTTCATGGCTATTATCATATTTTATTGGAGTATATG +AACTAGATATATCAATATACAGTCGTTATTTTCAAGTACAGCAATTATTTCTTAATTACTCTAATAATATTCTTTTGGTA +TTTTTTGGTATTGGACCCTCAAAAGCTTATATTTTTTATGATTTTCCAACTATATTCGATCCCGGAGCCTATACATCAGA +AGAGTTAAGCTCCAGTTTTAGATTGGGTTTTCAAATGCCGTATTTATCATGGATTAAAAACTTTGGTCTGTCTGGAGTTA +TATTGCTATTATTGGCACTTAATTATATTATTAAAGTCGCATGGTCATTTAAGAAAGACGATATATTTTTTTCTGGGGCA +GTATATTCTTTAGGCTTATATTTTATTCTAATTGGATTCATGGATTTTCCTGCTTTTGGTTTAAAGACAATTATCCCAAT +AAGTTTATATATATATATAATAAATAATAAGCTAACATATAAAAAACAGGAGATTATATGA +>O-17_wzx__1221 +ATGAAATTTTCCCATAATACTGTATTTTTTTATTTGTTAACTATCGTAAATGGTTTGGTTCCGTTAATAACAATTTCATT +TATATCAAGGATAGTAACAAGTGAGCAGCTAGGTATCTATTTATTATCATTTACGATAATGAATGTTTTAGGCTTAGTTA +TAGATTGGGGCTTTACAATATCTGGCATTAGATTTTTAAAAAATAGTAATAAAAAAATGCCTGAAACAATATTCGTTTCA +ACTACTTTTTTTATTAAAATTACTATATCTTGTGTGGTTTTTATTTCATACTTCTTTTTTTATATATTTTACTCGCATGA +TGAAGTGTCTTTTTTTTTAATAACTATAATAGGAGCCTTTGTTACGGGGTTAGATAGCATTTGGATTTTACAGGCAAATA +ACCGATTAATGAAAGTTATAAAAAGGAGTTTATACTCAAATTTAATATATGTTATAAGCGTTTTACCTGTAATTATCTTT +TATAAAAATATCTACTACATATTATGGTTGTTTATTATATATAAATCTTACATGTTTCTGATATCTTTCCATGAGGTGAG +GGCTATATATGCTATTACTTGGCGAAATATCCACAAGGAAGAAGTTATTACTGTTTTTAAAAGTACATGCGGCGTAGCTA +TATTTAGAATATTTGCGCTGTCCTATACATCCGCAAATGGTATTTTTCTTAATTATTTGACTAATAAATATCAAGTGGCC +TTGTTTTTAGCTTTTGAAAAAATAAATAAAGCCATATTGTTTATTGCAACGCCAATTAGTCAGGCTTTGCTACCTTATTT +TTCGGAAAAGTCTAATAAGAAAAAACTTACGCAATATATTCTTATTATATTTTGTTTTTGCAGTCTAGGACTAATTATTG +GTAATATGTTTTCTCGGGATATAGTCGGAATTTTTATGGGGTATCCTTATCTAAGTGACAATACTGGCGAGTTATTTTTC +TTTATGACAATTATAACGCCATTTATTTTAGTCAGTAATGCAATTGGCATGCTCTATATTATTCCTCAAAAACTTGATAA +AGTATTAAATATAATTATTATTAGCGCTGCAGTGATAAATACATTACTTGTTTTTAATTTTGTTCATTCATCTACCGATG +GTGCATTGCAAATGGCGAAAGTAATAGCATTTAGTGAGTTCTTTGTTATGTCTTTAATGATAATAGTAATGTTTATTCAT +GGGAGGAAAAGTGGCGAATAG +>O-38_wzy__1083 +ATGATATATATTATAATAAATACTCTCACGACTATATTTTTATACTTATATAGTAGTTATAAGTATACCCCCTTAAGTCG +ACTGTTTATTGGTGGCATGTGTATTTTTTTAATAGCACTGTTGCCCGCATTCCAGTATGGTGTCGGTACTGATTATTTTA +GCTATCAAAATATATATAATAATGCCAATGTGCTAGATACTTTTTATCAAAATAAAGAATACTTATTCTATGCATATGTG +AAATTTTTTCAATTTTTAGGGGGGGGATTTAAAACTTTTGTTATCTATACGTCTTTATTGCAATCATTATTAATATTTAT +TATTATTACTCAGATGTGTAAAAATTATGGTCAATCGATTATCATAATATTTTTCCTTTTCTGGACTGTGACAAATTTAT +TACACACTCAGATGAATATAATAAGGGCTTCGTTTGCTATATATATATTTATAATATCCATGCTTTTTAAGTTTAGAGGT +AAAATAATTATTTGTTTTGCCTTAATGATTATTGCAATTGGATTTCATCGTTCAGCATTATTAGGGTTGTGTTTTGCATT +AATTCCCTTAAAAACATATTACTTTGCATATAATCATGTTGTTAAATTTTATTTTTTATCTTTTTTGTTATTTGTTACCC +CATTTTTACATCAGGTGGTGTTTTATATTGTTCAGGAGTTGTTTCCATATTATACACATTATCTATTTTCATTTGATGAA +AATGCAGTGAGCTTTTGGAATGTGGCTACAAAAATATACTGGCTTCCGTTTGGGTTATTTTTTATATATTTAATTAAATG +TAATGCTATTTTTATTAAGGGTTGTGAGCGTGGTTTGATTGGTTTGTGGATATTAACTGGGAATGTTTATTTATTAATTC +TTAATTTTGATTTTGTTTCCAGAGTTAATTTTTATTTTGTGTTTTTCTATGTAATTCCTATTGCATATGTTTTTCGTTAC +TTTATTAGAAATAAGAATGTTATTTTATTATATATTAGTGTGCTATATTGTTTTATACCGTATTTATTAAAAGTTACTTT +GTTTCCTATAGCTGAATTTTATTATAAAACTTATCTTTTTTAA +>O-60_wzy__1050 +ATGGAATTCTATTTCATTATATTATTCTTTCTAAGCACTTTGGGACTGTTATCCTTAGCAAATAAAGAAAAAAATAATTT +TTCGTTTTTTGCATGTTTTATAATATGCTTTTTTTTCATAGTGTTGTCTTCAATCAGATGGGATAGAGGTACTGACTGGT +CCGCATATTATGAGATCTATCAGGCGACGAACATTATCGGCGTATGCTTGAAGATATATTGCATAGGTGTCGAACCCGGA +TTTTATTTTATTAATTGGCTATTCTCCTCTTTTTATTCTTATAGCTTTTTTTTGTTTTTTTTAGCCTGCGTTATAATTCC +ATTAAAAACGTTGTTTTTCTTTAAGAAAAGTGAATATCCATTTATTGCTTTATTATTATATTTTAGCATTTTAGTGTTTG +ACATTTTTCCTGTTAGGCAAAGTTTATCTAGCTCTTTATGTCTTTTATTTTACTTGATCTATAAGAACCATAAAAAAAGT +TCATTTTTAGTTGCTCTATTGGCATTAATGGTACATTATTCGGCAATAATATTTTTTATTGGTTTATTAGTCTGCTCAAC +GAAAAAAATTCATAAGGGAAAAGTAGTAATTTTTTCAATTTTTATATTAGTTTTATTTTTTATAGTTGTTAAATACCCAC +CTGAAATCCTTTCTAGTAGGATAAATGATTATATTATTAACCAAAAGGTTTACTCAGACGACATCACACCGTTGAGGAAT +TTATTAAAATGCCTAGATCAAATATTTATTATGTTTCTATGTTGGCGCTTAATGTTAGTTGGTTGTGTCGATAAGATTAT +TTTAAGATTATCAATATTTGGCTCATTTTTATTTATATCAGCTACGCTTCTTGCTCCTCAACTTGCTCGACTTGGGTTAT +TCTTTGTTCCCTTTCAAATAATTACTTTATCTTCACTTATATTACTCTTCTCTAAAAATTCAAGACTTCTTGCTTATTTG +ATTTTAGTAGTTTATGCGGCTATTAAATTGAATTTAATAATACGGCCTTTTTATGATTTATTTGTGCCATTCAAAACGTT +TTTTATGTGA +>O-8_wzy__1200 +ATGCTGCCATTTCCACCAGGAGCAATCCTAAGGGATGTACTCAATGTATTTTTTGTGGCGTTAGTGCTAGTTCGATTTGT +CATTGATAGGAAAAAAACTTATTTCCCGTTGGTTTTTACTATTTTTTCATGGTCGGCGGTAATACTATGGGTAATAGCGT +TAACTATATTCTCACCGGATAAAATTCAAGCAATTATGGGGGGGCGGAGTTATATTTTATTCCCGGCAGTTTTCATAGCA +TTAGTGATTTTAAAAGTATCATACCCGCAATCCTTAAATATTGAAAAAATAGTTTGCTACATAATTTTTCTAATGTTTAT +GGTTGCGACAATATCTATTATTGATGTACTAATGAATGGAGAGTTCATTAAATTGCTCGGATATGATGAGCATTATGCAG +GAGAACAATTAAACTTAATTAATAGCTATGATGGGATGGTCCGGGCTACAGGCGGTTTTAGTGATGCTCTCAATTTTGGA +TATATGCTCACATTAGGTGTTTTGTTATGTATGGAGTGTTTTTCCCAAGGATATAAAAGATTATTGATGCTTATTATTAG +TTTTGTGCTATTTATAGCGATCTGCATGAGTCTTACTAGAGGAGCAATACTTGTTGCTGCGCTTATTTACGCACTTTATA +TAATTTCAAATCGGAAGATGCTTTTTTGTGGAATAACTTTATTTGTAATAATTATACCCGTTTTAGCAATTTCTACTAAT +ATTTTTGACAACTATACAGAAATTTTGATCGGCAGGTTTACAGATTCGTCTCAGGCATCGCGTGGATCTACACAGGGGCG +GATAGATATGGCAATTAATTCATTAAACTTCCTGTCAGAACATCCATCAGGTATAGGTCTGGGTACTCAAGGTTCAGGAA +ACATGCTTTCGGTAAAAGATAATAGGTTAAATACGGATAATTATTTTTTCTGGATCGCCCTTGAGACTGGTATTATTGGC +TTAATCATAAATATTATTTATCTGGCAAGTCAATTTTATTCTTCAACTTTACTAAATAGAATATATGGCAGTCATTGTAG +CAATATGCACTATAGATTATATTTTCTCTTTGGAAGTATATATTTTATAAGTGCAGCGTTAAGTTCAGCACCTTCGTCAT +CAACTTTTTCTATATATTATTGGACAGTTTTAGCTTTGATTCCATTTTTAAAATTAACAAATAGACGGTGCACGCGATAA +>O-59_wzy__1236 +ATGCTGTTATTTTATTGGTTCTTATATGTTTTTTCGTTATCAATTCCTATTTTTTATCATTCAGCGTTTCTGGTTGGATT +CGTATCAGCCATCCATTACCTATTGATTTACAAAAGGAATTTATTAGTTTTAAGCAGATATCAAATATTTTATTTTTCTT +CGTTTTTGCTTGGGTATATCATTGTCGGGTTAATAATTATTTTAAATGAGACATATGATATTAGCTTCTTTAAAACATAT +ACTAACTCTTTTTTATCAGCAATAAGTGGCGTACCACTTGTTTTAATATTTTTAGAACGATTTGGGAAAAACGCCCCAGC +TTATGTAATGAAATATACGTTTTATATTTTTATTATACAAAGCATAATTATAATATTGGTTCTGTTTGTACCTGCATTAA +AACCTTTCGTTATGTATTTTCAGAGAAATGCTGAGTTAGCTAGCGAATTAGACCTTTTTTCTAATGGCTTAAGAACAAAT +GCTCTGTCAGGAGGGTTATTTTATGGATTGAGCTTAAGCTTTAGTATGGCTATAATATTATATCTATATTATATTCTTGT +TTATAAATTTCAACTTAAACTGAGATATGTTTTTCTTTTTACTTTGGTCAATATTGGCCTTATATGTACAGGTAGGTTTG +GTTTTATATATGTTATATGTATAATCCCTATAATATGTACAATAAAAATCACAAGGAAGATTAAGCTTATACTCTTTTCG +CTTTGCATGATAGTTTTGCTTTGTATATTGTTCTTCACACTATATGAGTTATTCCCACAAGTAAAAAAAATATATAATGA +AACTATTTACCCCTATGCTTTTGAGTTTTTATCAAATTATCAAAAAAGTGGTGATTTCGATACAAGTTCAACAAACGAAT +TGGCCTCAATGTATAATGTAACAATAACGGATAATACATGGTTTTTTGGGGATGGACTATACACAGGAAATGATGGCCTT +TATTATCAACATACAGATGTAGGATATTTGAGGTTATTGTTGCTTGGTGGCGTTGGACTAAATATATACTTCATTTCCTT +TACGGTTTTAATGCTAATACCAATATTAAAATCTACCTTGCCTAATAATAAATCATTATATTTTTCATTGCTCTTACTTT +TTTTACTGTCACAGTTTAAAGGTGAGGCTATGATAACATTAGTGCAGTTAAATAATATGTGCTTTATATTATGCAGTACA +ATCAGTTTTCTTTACAGAAAGGACGTGAATGAGTAA +>O-50_wzy__978 +ATGTTCAAAAAGAAAAGTATATTTGTTTTTTTAGGGCTTCTTAGCTCTATACTTCTTGCGTTACCTTTAGCTATGCAAGG +CGGTTTTGATGATTCCTTAGTTTACTATTCACAAGCTGATTATATATGGAGTTACGGTTTATATGATGGACTAAGAGCTA +TTTATATCCAAACAAATAAATTTGAGCCCGCTATGGGGCTACTATTTTTTATAGAAGGGTTTATTGTTACCGAAAAATTC +TATTTTTTATTACTTAATTTAACACTAGTGAATTTTATTACAGTTTTGATATATATAAAAATTAATGAACAATCAAATAC +AAGTATAAGTTTTATATATGCAATACTATTGCTCTCTACATATTATATTTTTTCTAATAATATTTACGTGTGGAGGACTA +TCATTTCTTTATACTTTTTTATTTTGTTTGTTTTTTCTAAATCAAAGAGTTGCAAGGTTATTTTTTTCTCATTGGGGTTT +TTGTTTCATTACTCATTTTTACTATTTTATTTTTGTTATATAATATGTAAATTTAATAAGTCAAGTTTGAAATTTTTTTT +GATATATGCATTTTTATTTTCTTTATTTATTTCTAATGTATTAAATTTTTTAAGTTATTTTTCTTTTTTTGTTTCAGGGG +GGGAACTAACGATCTTCTTGGATAAAAGTAGTGATAGTATTAAGAGGATTATTATTGGAGTATCATTCCTTATTATATTG +ATTATGGTTAAGGTTGATAAGAAAAGTTATAGTTGGAGTCTTTATAAATTATCCTTGTTTTTCTGTATATTATCGATTGC +GCTTTATCAAAACTGGCAGTTATCCTGGAGGGTATTTGTTCCCGCAGCTACTTTAGGGAGTGCTATAGTTTTAGCGAATA +TAAGAAAGGATAATATAATCCCTTTTTTGGGGGTGGTTTTATCAACTATCCCCACAATGAGAATAATTTATAATTTATTA +TATCTAGGACATCCATAA +>O-52_wzy__1065 +ATGAAAGGCGGTCTTATTGTTATTCTGTGGTATTCAGGCTTTTTATTTATTGCAGCAACAGGTTTAACCGGGCTTCAGGA +GTTAAGTTCAAAATCTATACTAATGTATATTGCTTTTTTGTTTTGCTTCCTTTTAGGGATGGTACTATCTGGTGTATCCC +TTTATGAACCGAAAAAGGAAATGCATCAGCAGATTCTCAAAAGAAAACATAACTTAGTGATAGTGAGTATATTCTATCTA +TTTATAATATATTGTTTTTTAGTTGCATTAAATATTTATTTTTTCAATAAAGTTGATCTTTCGTCTTATAGGCAGGCATT +CTTTGATGGCTCAAGAGATAATGTAAAGTTCTTTTTTGGTTCATTTGGATTTTATTTTTATTATTTCTTAAGTTTAATCA +TTTATGCGTTAGTTCCATTTGTTGTTATAATGAATAATAAAAAAGTGTTATTCCTATGCTTTCTGTCATTATTGCTATAT +GATATAATTTTTCTTTCGAGAACCGGAGTTTATTACTATATATTGTCATATATAGTGGCATGTATCATCCAGAAAAAGCA +ATTAAAAAAAATAATTATTTTTATCGTGATTGCATTGCTGTTTTCTTTTGTAATAAGCTATACTCGCGATATGCAAAGTA +ACATAATTAATTCAATTTTTAGCTCAATTATTAATTATCACGTAGCCCCTTTTATTCTATTAGATAACAACATAATTTCA +AAAAATGTAATAACATACCATGGTGTTGGTTTAGCATCACTTGGTATATATAATATTATTTTCTTTCCTATAGATGTAAC +AATAATGCAAACTATAAACGACTTTAGAACTCAGTTAAATATGTTCTATGATCTAGGATTAAAAGAATATTTACCATATA +ATGCTTACTACACATCACTAGGGGGAGTATACATAGATAGTGGTTTTTTGGGATGCATGATAGTTACCTTTTTTTTCGGT +TTTATTATCGTAGCAATAGAAAAAAAAGCTTATAAATCAAGAAAATACTTAGCGTCAACTGTGTTTTTTACAACATTATG +CTTAGAGTCAATTTTGCTCCAATAA +>O:23-gene1__1029 +AAGGTGCGGATGATGATATTAGTCACTGGTGGAGCTGGTTATATAGGATCGCATACTTGTTTAGCGCTTATTGCCAAAGG +GCACGACATTATTGTTATTGATAATTTAAGTAATTCCTCTTATGAGTCGATTAGGCGTGTTGAGAATTTAACCAATAAAA +AAATAAAATTTATAAAAAGTGATATAAAAGAACGACATTGCCTGGATGAAGTGTTTAATAATTATTCGATAGAAGCAGTA +ATACATTTTGCAGCATTAAAATCAGTAAGTGAGTCTGTTGAAAAACCATTGGTTTATTATGATAATAATATCACAGGTAC +CTTGACTCTACTGGCTGCAATGCAAAGTGCAAATGTAAATAATTTGATTTTTAGTTCGTCTGCTACCGTATATGGTTGTT +CTTCGATTGTTCCAAATAAAGAGAACGATACAATTGGGGGGACTACAAATCCCTATGGAACATCAAAATATTTTAGTGAG +ATTATTCTGCAGGATTTTTGTAAGTCTAATGAGTTATTTTCCGCAGTAAGTCTTCGTTATTTTAATCCTACTGGTGCTCA +TAAATCAGGTATGATTGGGGAAGATCCTAATGGAATACCAAATAACCTCATTCCATATATATCACAAGTTGCCACTGGAA +AACTTAAATATTTAAATGTATATGGTGGTGATTATGACACAATTGATGGCACTGGCATGCGAGATTATATACATGTAGAT +GATTTAGCTGAAGGACATGTCAAGACATTAGAATACATGTTATCAACAAAAGTAGGTTATGATGTTTTTAATTTGGGGTC +AGGTCGAGCATATAGTGTTTTGCAAATCATTAAAGCTTTTGAGCTCGTCACTAAAAAAGAGATTCCCTATAATATTGTCG +CACGAAGAAATGGTGATTTAGACAAATCTTGGGCTGATACTGAAAAAGCCAGAAACCTCCTGGGGTGGGAGGCAAAATAT +GGAATAGAGGATATGTTGCAAGATGTTTGGAACTGGCAATCACACAATCCAAATGGTTATAGAGTTTAA +>O-11_wzy__1080 +ATGAATATATTATTTTTTTTGCTTCTAAGTGTTGGGTTATTATTTTCCCTCGCATATAAAAATAAAAATAAAAATATAAA +TGATAGTATCATGTTTATGCTTGTCGTCCTGATGATATTAATGTCAGGCCTTAGAGTTAATGATAGTGATTATCTTGAGT +ATAATAAAATGTATAATGAAGTTCCTTCATTATACAATTTTACGTTATCTGCGATAAAAGATATTCATGGAGAGATTGGC +TATCTTTTCCTTTCATCTTTTTTTAAAACATTTGATTTACCGTTTCAGTTTTTTTTATTCTTTATAGCATCGTTATCTTT +GATGCTTACTTATTTTTCTTTTAAAAAAGCAAGTATTATACCAATATTATCTCTAGTTTTTTATTTAAGTCATGCTTTTA +TTGTTAGGGATATGATACAAATAAGAGCTGGATTAGCGGTGAGTATGTCTCTATACACAATTGTGACATATAAGAAAAAT +CGAAATGTGATCACAGGGATACTGCTTGCATCGCTGATTCATTCTGGAGCAATTATAATTGCTATTTGCTACCCATTTAT +AAGAAAAAGATATTTATCGTTAAAAAAAATATTTTCTCTTTTCTTGGTTGCCTTAATATTTTCTTATTTACATGGGCTCG +ACTTTATATTAAACACCCTTATTCATTATAATCTTCTGCCAGATGCTGTTGCAAATTATATTGGGTGGGAAGAATATGAT +TATAGAATTAATATTTTCACTAATCCAGTATTTATTAAAGGGATAATGATAGTTTTTTTAATGAGAAAATATATTAAAAC +AAATATAAATAATGAAAATGATAAGGTGGTTATATTATATAATTTATATGTTTTAGGTGTTTTAGCAATGGTTGGGTTAA +GTGAGATGGCTATACTTTCAGGACGTCTTTCATCGTTTTTAACACTAGGTGAAAGCATATTAATAGTATATAGTGTTTTT +TATAAAAGAAATATCTCGGTAGGTTTTGTTTTCTTTTTGTTATTAACTTTCATACAGATGGGATATGATCTGTTAATTTC +AAACGTACATCCGAAGCTCTCTCTTTTTATATTTGGATAA +>fljB_1,2_Newportstr_AYDZ01000021_1__1510 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAACCTACAATGCCAGCAAAGCCGCTGGTCATG +ATTTCAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTG +GCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATAC +CGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGC +AGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z35_Salmonella.enterica_IIIb.35:z52:z35_AY353343_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +ACCTCCGGCAAAACTTGATATTGCAGGATTAACTGGAACTGCAATTAAAACGGGCGTTGATAGCGCTACGGTTGATACTG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGAACTATTACGTAGAGGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAATGTTGCTGATGATGGTACAGTCTCAATGACAGCTTCTACCACTAAAGA +GGCTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCCGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCCCATGTGACCGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGTGATGACTACTACGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTATTAACAC +CACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_Infantisstr_AFYI01000002_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGACAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTACTGATGCAGCTATTAAAACGGCTACGGGTG +GTACGACTGGTACGGCTTCTGTAACCGGTGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGCGTAACAACTAAAACAGAAGTACAGGAGTTAACAACTACACCGGTAGTTG +CTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGCCGCTACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>O-6,14_wzy__1344 +ATGAATAAAGAATATTATTTACTGCCTTCGAATAAATTAAGATTTAAACACTTGATTATATATCTTGTGGTATGCCTGTG +CCTTTTTTCTGGCTTTCTTATCAATGATGCAAAGACTCAGATAGCTCAAGAAATTACTGATATATTAGCAATAATATCCA +GCGCGTTGCTAATTGTGCTAATTCTGTATTATTATATATATCGGGTGCGCTTTTTTTCTCTGACGCTACTATTTTCTTTT +GTTTTTTCACTAATAATTGGTTTGCCTTCGATATATCTCTTTTATTTTAAAAACACAGATAATGACTTTGGGATTATTTG +TATATGGGCAATGCTAATTAATGTTGCTCTCTATCTACTTTCAACAAAAACTTTTTATAAAAAAGAAGAAAGGCGTTTAT +CCAACCTCTTTTATGCGATATTTTTTATTGCAGCATTTTGCCAGATCTATAAGGTTATGATTTATTTTCTTTTTATTCTT +AATTCTGGTGCCGGGCATCTCGCAATATATACAGAAAGCGAAGAGTTATTATCCCAAGTGCCCTTTGTTATACGTGCTAT +AAGTGGTTTTACAGTAACTATGGCATTGGCTGTTTTTTATTTTAAAAGTCCAAGTATAATAAAATTTATTGCATTTATCC +TGCTAGCTTCAGATTTAATTATAGGGATACGTAATAAATTCTTTTTTTCAATGATATGCATATTTATACTATATTTATAT +TCAAATGAGATTAGAGTAAAGCATATTTTCAAAAAAATCTCAAAACCTACTGTTCTTCTGGTTGGTTTTATATTATTTTC +TTTGGTTTCATATTTTAGAGAAGGCTACCAGATTAATTTTGTAAATTATATTGGTATTGTATTAGATTCTTTGTCGTCTA +CTCTTGGTGGTATGCAGAATTTATTTAGTGGACAAATAGGGAGTTGGGATAAGTTAAGTCCTGAAGTCGTATTCACACAG +ATATTGCCGTTAAGTGGTTTAGGTTTTATTAACAACCATCAAATTGCAAAGGATTTTTCTATCATTGTACTAGGCGATGT +TTCATCAGGTATTGCATTGTCATCCTCCGGATTATTAGAGTCGACAATATTAAGCCTACACTTTGGATCTGTATTTTATT +TAATCTATCTAATAGGCTTTATTTCATTAATAACACGCGCATTGAATAGTCAAAAAGTATTAATAAACTTCATTGCTATT +TCAATGATTTCCGGTTTCTTCTATGCAGTGCGGGGAGAGTTGATATTACCTTTAGCTTTCTTATTAAAGTCTCTGCCTAT +CGTTATAATATCCCCCTTGCTTGTAAAAGGGCATTTTAGGGCTTTGTCAGTAGAATCAAAATGA +>O-6,14_wzy-from-Stk2184__1344 +ATGAATAAAGAATATTATTTGCTGCCTTCGAATAAATTAAGATTTAAACACTTGATTATATATCTTGTAGTATGCCTGTG +TCTTTTTTCTGGTTTTCTTATCGATAATGCAAAGACTCAGATAGCTCAAAAGATTACTGATATATTAGCAATAATATCCA +GCGCGTTATTAATTGTGCTCATTCTGTATTATTATATATATCGAGTGCGCTTTTTTTCTCTAACGCTACTATTTTCTTTT +GTTTTTTCACTAATAATCGGTTTGCCTTCGGTATATCTATTTTATTTTAAAAACACAGATAATGACTTTGGGATTATTTG +TATATGGGCAATGCTAATTAATATTGTTCTCTATCTGCTTTCAACAAAAACTTTTTATAAAAAAGAAGAAAGATGTTTAT +CTAGCCTTTTTTATGCGATATTTTTTATTGCGGCATTTTGCCAGATCTATAAGATTATAATTTATTTTATTTTTATTCTG +AATTCTGGCGCTGGGCATCTCGCAATATATACAGAAAGCGAAGAGTTATTATCCCAAGTTCCCTTTGTTATACGTGCTAT +AAGTGGTTTTACAGTAACTATGGCATTGGCTGTTTTTTATTTTAAAAGCCCAAGTATAATAAAATTTATTGCATTTATCT +TGCTGGCTTCAGATTTAGTTATAGGAATACGTAATAAATTCTTTTTTTCAATGATATGCATATTTGTACTATATTTATAT +TCAAATGAGATTAGAGTAAAGCATATTTTCAAAAAAATCTCAAAACCTACTGTACTTCTAGTTGGTTTTATATTGTTTTC +TTTGGTCTCATATTTTAGAGAAGGCTATCAGATTAATTTTATAAATTATATTGGTATTGTATTAGACTCTTTGTCGTCTA +CTCTTGGTGGTATGCAGAATCTATTTAGTGGACAAATAGGGTATTGGGATAAGTTAAGCCCTGAAGTCGTATTCACACAG +ATATTACCGTTAAGTGGTTTAAGTTTTATTAACGACCACCAAATTGCAAAGGATTTTTCTATCATTGTACTAGGCGATGT +TTCATCAGGTATTGCATTGTCATCCTCCGGGTTATTAGAGTCGACGATATTAAGCTTACATTTTGGATCTGTATTTTATT +TAATCTATCTAGTGGGCTTTATTTCATTAATAACACGTGCATTGAATAGTCAAAAAGTATTAATAAACTTCATTGCTATC +TCAATGATTTCCGGTTTCTTCTATGCAGTGCGTGGAGAGTTGATATTACCTTTAGCTTTCTTATTAAAGTCTCTGCCAAT +CGTTATAATATCCCCCTTGCTTGTAAAAGGGCGTTTTGGGGCTTTATCAGTAGAATCAAAATGA +>O-55_wzy__1128 +ATGTTTGTTTTAATAAATGTATTTATCTTGTTGTTTTTTTCTTGTTTTTGGGGACGTTTTGATTTTAAGAGTAAAGTCAT +TCTTAGGTTTCTAATATGGTCAGGGTTAGTATTCTCTTTTTCTTCATTTTATATCAATGGTGTTGATTGGACTGTTTATT +TCAGCAAATTTAGTTATGAGGATAATTATTATTTATTTTTGTCATTTGAACCTGGTTTTGTCATCTTTTTAAAAGCATTG +CTGTTCTTGACTTATGGTAATTTTGGGGGGGCTATTTTTTGTTTTTTCATGATTACATTTGGTTTTCTAATGTACTCATT +AGAAAAATATAAAATTAATGAACCGCTGTTTCTTGCTGGATTAATATTGGCATGTGGATATACACTGATACTTGAGCAGC +TTAGGCAATTTATAGCATGTCTTATTGTTTTTGTTTTTCTTATTAATTATAATAAAAATAAATCTTTAGTTAGATTAATT +TTTGGTGTGACAATTGCTTCATTTTTTCATATTTCTGCACTTGTGGTAATTCCTGCCGTTATTCTATGTAATATTAAAAA +TCGATTTGTATTTATTGTTACAACAATTATTTTTGGTATTCTGTTTGTTTTATTTTTATTTTTCGGTTTATATATACTGG +AGCAAATTCCACAATTTGCTTTTGTAGTCCGGAAAATTAATTTTTATCTGGAACAAAACCCAACGATCTTACAACTGGGA +TGGTTGAATTTATTCGTGCTTATTTATACGGTAGCTTATGTTTTTTTTAGCTATTCTATAGAAAGAAACTCGAATGCTAA +TTTATTGAATCGTTTTATTTTTGTTGGTTCTATAATTTTTATTTTTAGTGGAACATTCCCTTTTTTGGGGCGGATGACGC +TTTATTTCATATTTATCGCTCTTTATATAATCTCAGATCCTAAAAAGAATTGGCGAATTGGTAATGCGATAGTAGTAAAC +GGATATTTTTCTATTTTCTTGGTGTTGAATTTTTCTTCATATTTTCGTAATGATTTAGCACCCGTAGACTTTGATAATTT +AAATTATTGTTTTTTAAATTTGTTTGATAATAACTATATGCAGAAAATAGCGACTGAAAATTTACCTGAAATGTTAGTTG +GAGAATAA +>O-3,10_not_in_1,3,19__1519 +TTTTATATTATATTTGGCAGAGTGTTAGTATAATTGTCATGTTCAGTTTGAGGTAATTTATGTACTAATTATCTTATATT +GTAAATCATGTGCAATTATTTTCATATTTTTATATGAAAAACGTCCAGTATATATATTGAGAAACATTATTGTTATGGAG +ACATCATCGGAGTTATGATGGAAAAAAACTCTTTTCCCATAAGCCACGAACATTCCTTAACTATGGATTATGTTAAAGCT +TTTGGTATGATTTTCGTATTGGTTGGGCATATAAATAATGACATATTTAATGTTTATTATGCCTATCTTTTCCATATGCC +ATTATTTTTCTTTATTGGTGGGGTTTTATATAAAGATACACGGTGTATAACAAATTTTACAGCGCATGTTATAAAAAAAC +AGTTACCTTATCTTATAGTAACTTATTTGATTATTGGTTCTATTGCATTATTAATTAATGTACGTTATGGAATACACACA +GGTGATGCTTTTTCGACAGGACTATATGAAACGGTTAAACTTGCTATAAAATCAAATTTTCATAACAATAAAATGTTTCT +AACAGGTTGGTTTCTGTTTGCTTATATATTTGTGAGCATTTTGTCGGTGATTATAATAAAAAGCATAAAACGGGTCGTTG +TTAGCAATGCTTTATTATTATCGGTATTGGTGGCGATTAGTGTATTATTAATAACTGTCTCAATAACATATTTATCCCCT +CAATATATTCTGGTAAAAGACTATAAGCTGAATTTTATATGCCAAGTGTTAACCGGTATGTCGTTTTATATTTTTGGATA +CGTGATCAGAAATCAGATATATAACTTATTAAATTTTTATGTTTTTATTTTATTAACTGTAATATTATATGTTTCGAAAA +GTTATGGTTTCTCTACGCAGACAATTATGTCATGGAGTTATTATCCGGATGGGTTAATAATGTCTGTTATTAACGCGCTG +ATAGGTATTTATGCTGTGTTTTTTATCTCTCTATTAATTACAAGGGGAATGAAAGAAATTAAGCTGCTAAAAATGATAGG +TCAGAATTCAAGAGCTATCATGGCATATCATTTACTTGTATATGTAATTTTAGATATAATTGCTTCAATTTTAGGTGATT +ATAGCCTATCGGGAACAGATGTATATGATAATCACTTTATCACTAAATGGTCCGTTCCTGTCTACATTGCATTAGGTTTG +CTACTGCCTCTAATTTTTAGTATTCTGAAACAGAAAGTAATAGGGAAGATAAAATTTAAGCGGGATTTTAGAATCAATTA +AAAGCTAATTTTAGCTTTAATGCAGCCTAATGTTTAAGTATTAATTTTTGGATAAATATCACATAATAGGTTACTCAGGA +GATTTTTATTTAGTCTACCGACGCGTTCCCAGATAAGGATTCCGGTGTGTCGTAGGTAGAAATAGGTAATTAATGATTGT +TTCTTCGGGCTTTAAGTCTGGGTTATCATATTATTCACTTTATCTCATTGGATATAGTTCCTATGAGTAACCACACCTG +>O-48_wzy-from-blake-2014K-0232__1194 +GTGATAATAAAAAAGTACAAAATTTTTTATTCAGCACTTAAAGTCTGGTTAATAGCCTCTTCATTGTATTATTTAAATGC +TATTTTTTTAGGTGTTGATGCTTTAAAATATAATGAAGATTTGACGCAAAAGTTCATCAAATATGCAGTTTGTTTCATCA +TAAGCATCTATATTCTGATCAATAATAAACGAGTCAAATATCTGTGGGCTTCATTTTTTTTCATAATTCTTTCTGTAGCT +TCAGTAGTTATTGATAGTGTTGTAACGGTATATGCAACCACGATGTTGATAATTGCTACCATGCTTGGTTTTAGCCAAAT +CATTGTTTATTTATCCAATGATATGTCGAGAATTAATATTGTTTTATTATGGACAGGTGTTATTGTAGGCACAATTTCTG +TGTTAGAGCTGACTGTGTTCTACGATTATATGGTTTCATATTGGATTTCGACTGGCGGAATTCGATCAATATCTTCCCTT +CTGAATCCTACAAATAGTGGAGCTTACTCAGCGATCATAATTTTAATTGCTTTAGCGACTAATATAAAGAATAAGTTTAG +GAAAAGTTTATTTGTTTTAATGCCAATGATTACTTTAATCAGTAGTGGATCACGCACCGCATGGTTATCATTAGCATTAA +CATTGTTATTGACAGTATTGTTAAATGATAAGGCTAGCATACGATTACGGAAAAAAATATTAGCTGTTGCAGGTATTGGA +GCTATTTGTGGTCTATTATATGTAGTATTTTATATGAATGCTACCTCTAGCATTCAATCTCAATATCGAGGACTTGATAC +ATATACCGCATCAATTCGGATTGAAAACTTTATATCGTATATAAATTCAATTGATCTTTGCATGTTATTTCCTGATTTTT +TTGACAAAAATATTATTCTTATATCAGATAATTTTTACCTTGTTTTATTAAATTATTTTGGGATTATTGGTTTTTATATT +ATTCTCTTAATGTCAATGTTGCTATTCTATTGTAATGTACAGATAAAGGATTTTAATGATATTATAAATGAAGATATTGC +TATTTGGAGAGTAATCTTTATCTATTTTTTGATATCTGGTTTTTCAAACTCATTTATAAGTTCTTTTCCTGTAAACCAGC +TATTCTTTATCTCATGCGGGTATTATGTGTATAAATATAAGTTAATAAAAGAAAATGTTGGAAAGTAAATATGA +>fliC_l,z13,z28_Salmonella.enterica_Hiduddify_DTU-unknown_l,v__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAGGCAGTTAA +AAGCGGCGGTGGGACAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAAGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAATGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCGCTGC +GAAAGTGACAGGTGGCATACCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAG +TTAAAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGAT +AAAAACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGG +ATCGTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAG +ACGGTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_b_ParatyphiBstr_AOXH01000168_b,d,j__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACTTTAAGTGTACAGGATGCCTATACGCCAAAAGGTACCGCTGTTAC +CAGAGATGTTACCACCTATAAAAATGGTGGTACTACTCTTACAGCACCTAACGCAGCAGCAATTGATACCGCTTTAGGTA +CGACTGGTGCGGCGGGTACTGCGGCTGTGAAATTTAAAGACGGTAACTACTTCGTTGAGGTGACCGGTACAACTAAAGAT +GGTCTGTATGAAGCGACAGTTGATGCAGCTGGCGCGGTGACAATGACCGCAAATAAAGCAACAGTAACTGGGGCTAGTAC +AGTTACTGAAAACCAAATTGTAGACGCTGTTACACCGACGCCAGTTGATACAGTCGCAGCAGCTACTGCATTGACCAATG +CAGGTGTGACAGGTGCGACAGGTAATACCAGCTTGGTTAAAATGTCATTTGAAGATAAAAATGGCAAAGTTACTGATGCG +GGTTACGCGCTTAAAGTTGGAAATGATTATTATGCCGCTGATTACGATGAAAAAACTGGTGAGATAAAAGCTAAAACTGT +AAATTATACTGACGCTACTGGTGCGACAAAAACCGGTGCTGTGAAATTTGGCGGTGCGAATGGTAAAACTGAAGTTGTGA +CCACCGTTGATGGTAATACTTATCAGGCTAGTGATGTAAAAGGGCATAATTTCCAGAGTGGTGGCGCTTTAAGCGAGGCT +GTAACCACTAAAACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAAGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCCCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_f,g_Rissenstr_AHUI01000019_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAACGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTTTACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALHY01000185_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTAGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z41_Salmonella.enterica_Maska_AY353511_k,z__1491 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAGCGTATGATGTCGATAGCAAAGCTGTTAC +TGCAACTCTTGATCTGGATGTGACAGATCTTGATACTAATGCTTTGAAAACCGCAACTGGTATCAGTGCAGGTAATCCTG +CTGTTAAAGACGATAAAGTTTATTATGACAGCGCAAATAATAATTATTATGTAGAGGTTGAGGGCTTTACTGATAATACG +AAAGATGGTTTCTACAAAGTTCAGGTTGGTGATGATGGCAAAGTGTCAATGGCCACAACTACCAATAAAGAAACAGCTAC +TCCTCCCGGAATTGTTGAAGTAAGTAAAACTCATGATGAGAAAGCTCTTAAAGCTTCTGCAGAGGTTAAAGCAGCTCTGA +TGGCTGGAAATATTGATACTGCTGATGCAGATGCTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACG +ATTGATGGTGGTTATGCTGTAAAAGTAGGCGATAACTACTATGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTTAA +TACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTGAACCAACTTGGCGGCGTAGACGGCAAAACCGAAG +TTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGAAGGTCACAACTTTAAAGCACAGCCAGAACTGGCGGAA +GCGGCTACTGCAACCACCGAAAACCCGCTGCAGAAAATCGATGCTGCGCTGGCACAGGTTGATGCGCTGCGTTCTGACCT +GGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGTCTGAAGCGCGTAGCC +GTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTT +CTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IV.48:z4,z32:-_AY353548_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GTAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGTTCTGGAGC +CTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACAACGGGTGGCCCCGCAGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAACTGCGGGGTCTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGATTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Salmonella.enterica_Kokomlemle_AY353319_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCTATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCGGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGTGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCTACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAGAATGTGCTGTCTCTGTTACGTTAA +>fljB_k_Salmonella.enterica_II.13,23:k:z41_AY353329_k,z__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGGCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTGATAGCAAGGCTGCGCA +AAGCGTTAAACTGGATACCAGTGCTCTTACTGCCGCTGCAATCAAAGGCGGCGTAACAGGTGCAACAACAGATGGTGCCC +TCAAAGACGGTAAAGTTTACTCTAATGGCACAGACTATTATGTAGAAGTAAGCTTTGCTGATGCAACGGACTCTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCACTACTGGTAAAGTTACCGTACCGGGTACGGCAGCAGCAGCTTCTTCAAC +TAAACCTGTTGGTGTGAACGAGGTTACAGAAGTACAAGGTAAAATCCCTGCATCTACTGCTATCCAGGACCAATTGAAAG +CTGGTGGTGTGAGTAACGCAGATGCTGCTACTGCTGAGGTTGTCAAAATGTCTTATACCGATAAAAATGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTAGGTGATGACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +CACGTCTTACACCGATAAAGACGGCAACACTAAATCCGCACTGAACCAACTGGGTGGCGCAGACGGTAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCTGAAGCA +GCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATCGATGCCGCGCTGGCACAGGTTGACACGTTACGTTCCGACCTGGG +TGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAATAACCTGACTTCTGCACGTAGTCGTA +TCGAAGATTCTGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,z15_Salmonella.enterica_Sandiego.var.d+_AY353303_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATTAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATTGATATTGATTTA +AAACAAATTAGCTCTAAAACACTGGGACTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGTTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_z35_Sloterdijkstr_AOXT01000110_other.z35__1476 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAAAATATGATGTGAAGAGTGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGCGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +AGCTACAACTCCTACTGATATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTATACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTTTAGTATCAACAC +CACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTG +TTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCAGAAGCG +GCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTAGCACAGGTTGATGCGCTGCGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_1,5_Salmonella.enterica_I.43:e,h:1,5_AY353284_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATTTCTATTGCGCAAACTACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACTCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAACTTATGCCGATAATGGTATTACACTGGATGCCTCAGGCCTTGATGATGCAGCCATCAAAGCGGCCATTGGTG +GTACGACTGGTACGGCTGCTGTTACGGGTGGTACAGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGG +GGCTTTAGTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGTGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAAGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_f,g_Salmonella.enterica_Derby_AY353380_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,m,s_Salmonella.enterica_Amsterdam_AY353395_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTGCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTATGACACCTATGCAGCGGGTGCCAATAAATATCGTGTAGATATTAATTCAGGTG +CTGTAGTAACTGATGATGCAGCACCGGATAAAGTATATGTAAATGCAGCAAATGGTCAGTTGACAACTGACGATGCGGAA +AATAACACTGCGGTTAACCTATTCAAGACGACTAAATCTGCTGCTGGTACCGATGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCGCGGGTGATAAGGTCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.57:c:e,n,x,z15_AY353370_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCACACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-62_wzy__1023 +ATGAATGGAGTAGCCAAACCCATTATAATTTTTTTGTTCGCCTGTTGTACTCTTGTGACTTTTCTTTCATGTAATTTAAA +TTTATTTCCTGATTATTATTCATATCTAAATTGGTATGAGTTATCAGCATCCACAAATATGAATAATGATTGGGTCTTTT +TTAAAGATCCTGGATTTTATCTGTTGTCAGTTATATCAAATAATTTTGGCTTTGGTGTCATTGGAGTGATTTTTTCGCTT +TTTATAATATCACTTTCGTCTAAGATTTTTTTTTGTATTAAGTTACTTAATAGAGAAACTCTATTCTGGGTGCTACTTTT +ATATCTGTCTAGGCTCTTTATTGTTCATGATCTTGTTCAATATCGAGCCGGTGCGTCAATTGGTTTGTCAGCATTATTTT +TGTATTTTTATTTAGAGAAAAAAAAGTTTAAGTCTTTTTTTTTCTTATGCCTCGCACTTTCTATCCATCTTTCTAGTTTG +CTGATTGTGTCAGTTATCCCTATAGTGTGGTATCTTAATAGGAATATAGGTAACAATATATTCAACCAGATAATAATAAT +AAGTTTACTATTGTCTGTGATTTTACTTTTTGACCCTTACATTAATTTGCTAAGGTTGGTCGCAGAGTTTCCTATGATGC +ATGAAAGAATTGCTCCATATTTGGATGGTTCATATGCTGTTAATAATGCACCAATGTTTAATAGCTTTGTAGTAATTAAA +ATTATATCATATGTAATTTTTTTTATATGGATCTATAAAAATAAAAAAGTTGGTTTAACCATAGAAAACTACTTAATTTA +TCTATGTTTCTTTCTGTCTATTGTAGGATTGTTTCTTTTTTGGTGTTTCAGAAGTAATGACTCGCTATCCATTAGATTTT +CTGACTTTTTCGCCATATACGATATTATTTTTTTTGCTCTATTATTAAATGTTTTTGATGTGTTTGGGAAATTTATCTAT +AGATACTATCTTTTAGTTATGATGATTGCTTTTTTTATATCTTCATTTAAGTTGATAAATTAG +>O-66_wzx__1257 +ATGCATAGTAAATTAAAAATGAAAAAATTATTAGACAATGCTATTGTTAAGAATATCTTGTGGCTTATAAGTGAGAAGCT +ATATTTCGTTATTCTTATTTTTTTTGGCGAGGGGCTTATAAGTCGTACACTTGGAGTGAATGATTATGGTAAGTGGATTT +ATTCCTTGAACATAATAATTATTATATCCTCAGTTGCACTAATTGCTGGAAGTGAGGTCATGGTGCCGGCTTTGAGCAAG +AATAAAAAATTAGCAGGGGAATTAATAACTTCAGCTTTCATAATTAGATTCTCAGGCGCATTACTATCATTTTTGGTTTT +GAATATATACTCTCTTGTGTTAGTAAATGATTTAGTGATACAACATATGCTTCTTTCTCTTTCGTTAGTGCTTTTATTCA +ATGAGCCTTTCGGTGCGATAACTAACTATTTTCAAGCAAAAATAGACATGAAAAAAGTAGTTCTGGCTCGCTGCTTATCA +CTAGCATTGCGTACAATATTTGTTTTGGTCGCATTTAAAATTTTCGAAAGTAATCTCATTTATTTTTCAAGAGCCAGTGA +ATCTATTCTTTTGGCTCTAATACTATCATTGCTTTTATATAAAAGTAAAATAAGGCTGAATTTTTCAAAAAAAGTATTTT +TAATAGTATTAAAAAGAGGGTGTTTATTATGGGTCCCTCTAATTAGTATGATGATTTATCTTAGAATTGACAGGTTTTTT +GTTGAAAAGTACTTCTCTTATGAGACGTTAGCTATGTATGGCGTTGCTGTTCAGTTTATTGAACAGGCATTTTTATTATT +AGTTATAGTGATTCAGACAATTTCCCCAAAATATATTTTTCAATCAATGCCAAAAAAAACAATGTTGAAAAATATAAAGC +TTATATCTTTATTGCTCATTATGCTTGTTTTTATGATGCAGGTCTTTTGCTTGTTTTTTTTGAAAAGTATTATTACCATA +GTATATGGGGATTCATATATTCAAGCAGCTACGTTGGCTATCTCGTTATTACCTTCATTATTATTTTATGCAGTAGATAC +CATTCTTATGCAGGTGTTTTACAAGTATAGGAATAATAAAGCGATACTAACTAAATGGATTTCAATGATGTTTTTCTCCT +GTGCGATGTATTACATTTGGTTCGACTTGCTTTCAAAATCTAATGTAACTATGGTTTTTAATATTAATTATTTGACTATG +TCAGTAATTACATTTGTTTTATTTAGACGTGGATTAAAAGATTGCAAAAATGATTAA +>fliC_i_Salmonella.enterica_Lindenburg_AY353428_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTTTCTGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACTTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_k_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353436_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATGCGCTGAATGTGCAGAAAGCTTATGATGTAGATAGCAAACCAGCGCA +GAGCATTAAACTGGATACCAGTGCTCTTACTGCTACTGCAATTAAAAATGGTGTAACTGGTGCATCGACAGATGGTGCCC +TAAAAGACGGTAAAGTTTACTCTAATGGCACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGATACTGCTAAA +GGTGGTTTCCTTAAAGTAGATGTTGATTCCGCTACTGGTGCAGTTACCGTTCCGGGTACGGCAGCAACAGCAGCTGCAAC +TAAACCTGCCGGTGTGAAAGAGGTTACAGAAGTACAAGGTAAAATCCCAGCATCTACTGCTATTCAAGACCAATTGAAAG +CAGGCGGTGTGACTACTGCAGATGCAGCTACTGCTGAAGTTGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTATGCTGTAAAAGTAGGCAATGACTACTACGCCGCTACTCAGAAAAAAGATGGTAGCTTTAGTGTTAACAC +TACGTCTTACACCGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_II.4,12,27:i:z35_AY353425_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAATGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCAATACTGCGATTGCTTTAAACAATGGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACAG +ACCAGCAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TGCAGGTGGATTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCCAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCGAGCAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCAGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACTGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,t_Salmonella.enterica_II.16:g,t:1,5_AY353408_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATTGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACCTCTGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_g,z62_Salmonella.enterica_II.50:g,z62:e,n,x_AY353416_g,m__1515 +ATGGCACAAGTCATTAACACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAATAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCACAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGTTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTGCTGCTGGTACCGCTGACGCCAAAGCGATAGCTAATGTCAT +TAAGGGTGGTAAAGAGGGAGATACCTTTGATTATAAAGGCGTATCTTTTACTATTGATACAAAAACTGGTAATGATGGTA +ATGGTACGGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGGTGGTGGTAGTGTTAAT +GATGCTACCTTACAATCAAGCAGAAATGTTTATACATCTGCAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAAAAA +TGAGAGTGCGAAACTTTCTGATTTGGAAGCAAATAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTGAAT +ATACTGCTAACGCCGCGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTTAGT +ACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTCAAA +AGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGGTAA +CCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>O-57_wzy__1038 +ATGATACCATATATAATTGTATTTCTTATTTTTGCAACTATTGCTTTACTTAATTATGATAGGTGTAAACTATTTTACTC +CTCCATGATTTTTTTGGGTTTTGCCTGTGTAATGAGAGGAAGTGACGTAGATAGGGATTACGAGACATATGTAAATATTT +ATAATTATATAATTCATGGTTATAGTTATACAATTGAACCAACTTTTTTTATAATCTCAAAAATTTCTTATTTAGTGGCT +GGGACCCCTTTTTTTATTTTTATTCTCTATGGCTTGCTGGCGATTTACTTTAAGGCTAAGTTTATAATCGATTGGTCTCC +CTATCCTCTACTTTCTGTTATAGTTTACTTTTCAAATGTTTATCTCTTACATGAGATGACTCAAATAAGAATAGGTTTAG +CCAGTGCGATTGGATTCTATAGCCTAAAATATCTTATTACTAATGAAAAAAGAAAATATTTTATATGTATCTTTGTTGCA +ACCCTTTTTCATTATTCAATGGTTATTTTTTTGTTTCTTCCATTATTCAATGTAAGAAAAATATCGTCACAGTATAAATT +ATTTTATTTTATTCTTATTGTATTATTATATTTTTTGTATCTGTTTAATATAGATTTATCACTTTTAATAAAATATATTG +ATATAGGATTAATACAATCGAAATACAATATATATAAGGAACAGGTTATAGATAATGGTACTAATGTAAATGTCTTTTCA +GTAATGCAAATATTAAATTTACTTATTATTTTTTTTGCTATGTCATATTCTTCGCATTTTAAAGAAAATAGAAAATTAAT +TTTAATAGTAAAGGTTTTTTCATTAGGCCCTATCTCATTAATATTTTTCTCTGCAATTCCTGGATTTGCGTTAAGATTAA +GTGAATTATTTACTGTAGGACAAATAGTATTACTTCCTATGCTTGTGAAGCAGATACGACAAGTAAAACTGGCTTATTTA +GGTGTTATACTTTTATCGTTTATCATACTATTGAATAATTTATATTATCTGTCACTTGTTAAGGCATATTCTATTTAA +>fljB_l,w_Salmonella.enterica_Ohio_AY353331_l,v__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGTGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCACAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAATACTGCTGGTCTTAATGATACAGCTCTTAAAGCGGGTGTTGGTGGTGCAACAAACG +GTACTGCTGCAATTAAGGATGGTAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTAGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAATTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACAAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCACTGAACCAACTGGGTGGCGCAGACG +GTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAGCCA +GAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGTGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_z_Salmonella.enterica_IIIb.61:i:z_AY353335_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTAAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCCGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTACACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCTTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCAGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Chester_AY353321_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCAGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.42:k:e,n,x,z15_AY353309_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTTAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +GCGGGGGATGTTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.57:i:e,n,x,z15_AY353312_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>O-43_wzy__1344 +ATGCAAATATTAAAAGCTAAAGAAAGTAATAAACAATCTGTTCTATTTATTTGCATGCTTGTTTTTTTTTACTTACTTAC +TTTTGTTTTGTTTCTTTTAGATGAAGGTTTATTTAGTTTTCTTTTTTTTATTGAAGCTTTGCTGGTATTATTATGTTGCT +TGTTTGTTGTGTTTTCAGAAAAGAAAAATGGTTTTTTAAATCCTTTATCTTTTTTTATTATATCAACATTTTTTTTTATA +ATAGTTAGACCTATTTTCTATTCACTGAGTATAGCTGAAAATGTGAATGAGGTTATCACTGCTGGTTATTCTATAGATAA +GAATTATTTATTTTATTCTTTATTTGTAGTGAATATTTGTTCAGCTTTGACGATACTTAGCTGTTTATTGCTAAGGCCAT +TATGTAAATCTATTACTGTCAATATATATGACTTATATTTTTATAATGGAAATGTATCTCGTCTTTTTATGTTATCAGGA +GTAATTTTTACAGGTGTTTTTTTAATAAAATCATATTCTAAATTTATCCTGTTAGGTGATGTTTCGGTTTTTGAGGTAGA +TAAATATGGTTTACATGACGACCTTTACTGGTTCACATTTGCGAAATATTCATATATTGTGTCTTTGTTGTTTGCTAAAC +GTAAAGATTTTATTTTTTACTCCCTTCTAATCTTTCTTGCATCTATAGGCTATATTATGGTAGGTCTAAGAGGGTATACT +ATATCTTATGCTTTTCTATTGTTATTCTTTTTAGATCTTAGATATAAATTAAAGTTTAGGTATTTACTAGTTTTTGCTAT +TCTGGTAGCTATAGTTTCATCTCTTATTCTTAATTACAGGATAGGTATCGAGGTAAATCGTGGCTTTTGGGAAATGATAT +TTAATCCCTTATTACAGCAAGGGGCCTCTTTTGAAACCGTATATGGAGTTTTAAAATATCATAGTAGCGTACTTAATTGT +ATTTCTTATTATGACTATTTTTTTTCAATTAAGGATATTGGCAGTTGTATTGATAGCGCGCGTGGTATATATTTTGCTGA +AGGTGGAAGTTTTGCAACAAGCTTTTATAGTGAGTTGATATACTTTGGTTGGTTTATTGGAGGCATAGCCTTGCTTCTGT +TTTCTTTCTCATTATCCTTTATTCAGTCCTGTTATGATTGTATTGTAAAAAACAAAAGAATATCAGAAAATTACACATAT +AAATTAATTTTATTCCTATTATTACCAAACCTTATATACTTTGCTCGTTCTTCTCTATTTGATTTTAGTATTAAGCTGGT +TTTTGTATTGTTTTTTATTATTCTTTTGTGGTTTATGAAAAAAACATTAGTGAATGTTAAATAA +>O-53_wzy__1119 +ATGTCTTATTTATATCTATTGTTTTCCGGTATCTCCTTAACCAGTAAATTGGGGGTCATAGTATTTTGGTTATCAATTCC +TGTGATTTTTTTTTACTGTTTTGGAGTATCATTGCTTTATAATAGAAAAGTGCATAAAAAATACTTCATTATAGTTATTT +GGAGTGTTTTTTTTATTCTTATGGCTGGTTTAAGCGGGTATTTTCTTGATGATTTTAATTCAAGGGTTATCAGTAATGTC +TATTTATCTCTAGTTGGTCTATTTATGGCATTAGTGTTTTATAATAGGGGAAATAGCTCTAATGATAAATCCTTTCTTAC +AGCGATAAAGATCACTATTTCTATAAATTTATGTGCTTTCTATATACAATTCGTTTCGTTCTATCTCTTTCATTACATCA +TTGATTATAATTTATTAAGTGGAGGGCTGGGGGGACGTTTTTACTGGGGCGATCTTTTTCGGGCAGCAGGATTTTTTGAC +GAGCCTGCTGTATATTCATTACATATGGTTGCTTTGACAGTAATGCTATATATGCAGGAGAGAAAATTTTCAATTCTAAT +TATTGTTACATTGCTCAGTCTATTGCTATCTTTTTCGTTTATTGCTATTTTTCAAGCAATGATTTTGAGCTTGCTTTTTA +TTAAAAATAAACGAGGCCTGCTTGTGCCTCTCGTAGTGTGTTTGGTTGTTGCATTACTATTTAAAGATAATATTTATGAG +CGTTATTTACAATTCGTTAGTGGAGGTGATGGTAGCAACAATACTAAGTTAGATACTATTTATAACTTATTTCAGGGAGT +AAAGTGGCTTTATGGCTATGGTCTTGTAGGATATTCACAATCATTCCCACTATACTATCAAGGTTTGTATGATTTAACAT +TTTGGGGAGCAAATATAAGTTTATATGGGATAGTTTTAGGCTTAATTATAAATGTAACTGTATTATTCTTTCTGCTTAAA +TTTACTATGAGGGACTTTTTATTAATAAACGTTGTCCTGTTGAAATTATCAACTCCCACATATGGAATATATTTTTGTTT +TCTTTTTTTTCTACTATGGTATAAACAGAATATGGTAATTCGAGATGCCAAAAATATCAGTTTTAATGGCGATAAATAA +>O-30_wzx__1392 +ATGATTAAAGAAAAAATCAAAATATTATTTAAATATTGCACGTTAAGAAAATATAACACTACAACTGACTATGGTAGACA +GCAAGAAAGATATAGGATTATTTCATTATCTATCATATCGAATTTTATTAGTAAACTATTAGCGCTACTTTCGCTTATTT +TAACTGTTAGTCTGACTTTACCATATTTGGGGCAAGATCGTTTTGGAATATGGATGACAATCGCAAGCTTTAGTGCAGCT +TTAACTTTTTTAGACTTAGGTATTGGAAATGCATTAACAAACAGGATTGCACATTCATTTGCGCGTGGCAAAAAAATTAG +AATGATTAGACAGATTAGTGGAGGGTTGACTCTCCTCGCTATATTAGCATTCATCATTATTGCTATTTTCTTAACCATTG +CTAATTTTGTCAACTGGGGAAGCTTGCTTAAAGGAATTAACGATAACACACATGATGAAGTACAGTTTGCTATAAAACTG +TTCGCCATTATATTTGGTATTGGTATATTCTCGAATGGTGTTCAAAGAATTTATATGGGAATGCAAAAAGCATATATTAG +TTATATATCTAATGCCTTCTTTATTTTAATATCTATAATATCTCTTTTTATTTCATCTAGGCTTCATGCAGGAATACCGA +TGCTAATCCTTTCGACAATTGGTGTTCAATATCTTTCAGGCCTAAGCTTAACTATACTTCTAATTTATAAAAAACTTATA +ACTCTTAATAAAATAAGAATAAATGTAAAAAAGGAAACGCCCTATTTAATCTCTAATGGTTTCTTCTTTTTCATTTTGCA +GATGGGGACATTAGCAACTTGGAGTGGGGATAACTTTATAATATCTACAACATTAGGGGTGACATATGTATCAATATTGA +GTATAACTCAGAGGCTTTTTCAAATTTCTACAGTACCTTTAACTATCTACAATGCACCGTTATGGGCAGCCTATGCTGAT +GCGCATGCTCGCCATGATGTTGATTTTATAAGAAAAACTCTTTTAGGCTCACTTAAAATTGTTGGGATCTCTTCTACTAC +TTTGGCATTAATATTAGTAATATTTGGTCAATCCATCATAGCAATATGGACTGGGGAAGAATTAAGAGTTCCGCAATCGC +TTATTGTTGCTTACGCAGTCTGGTCTATTATTGATGCTTATTCAAATACATTATCAAGTTTTTTAAATGGCTTAAATATT +ATTAAACAACAAGTTTTTGCAGTAGTTACTTTGATATTGATTTCAATTCCATCAAAATACTTTATCGTTAGTCACTTTGG +ATTAACGGCTATGCTAAGTTGTTTTATTATTTTGTATGTAACTAATTATCTAATATGGTATAAATGTTCTTTTAAAAAGA +GTATTCATTTACAGTTAAATATAAGAGGGTGA +>O-21_wzy__1089 +ATGAGAATAGCTATAGAGAATAGCGCTGTCTTTTTATTAACTGCGTTTTCTGGTATTTATTTACGTAGTACAATGATTAA +GCCGGGGTATATAGCAGTTATTATATCAATGTTATTAATGGTAATTTTTATTGTTTATAGAAAAACTGTAATATCGGCCT +TATTATGTTTTTTTATTCTTTTTTTTGTTGGTTATATATGGGGAACCCAGCCTTTTTTACAGGGGGAGTATGCAACGCTA +ATTTTTACAAGCTCGATTATAATGTTGATTTTTCTGCCACAGATGATTAGAAAGAGTACATTTAATATAAATATAGCTTT +TATAGTGATAATTATATTTTATTCTCTTGAGAGTTACATAAGGATAAAAAACCCCGATTATGATTTTGAGCCAAAAGAGA +TTTCTAATAGCATTTTAGATACTTTTTATATTTATAAAGTAAATAGCATTGCGTTTGAAGATTCAAATTTTGTAGCTATG +ATTTTAACATGCTATTATATTCTATGTAGGGTGTTGGGGAAAGAAAATGTATATGGCAAGACCAATGTTATTTATTCATT +ATTATTTCTTGCTCTCATAGTATTGACATTTTCAAGATCTGCCTACATAGGGGTGATAGTTTTTGAGTCGCTAATGTTTT +ATCAGTACTCCAAACGATATAGAGTCTTGTCTATCTTTTCTATAGTGATAGCAGTGATAGTGTTTTTATATTTTCTGCTT +GATAAAATTCAATCAGACGGCAGTTTTCAAAGTAAGTTTTATATATTTGATTTGTTTTTAAACTATATCAAAGTTGCACC +ACTATTTGATGTGTTAACGGGAGTTGGTTTCGGTAATACATTTTCATACATTGGTATTGGACCTCATAATATATATATAG +CCTTATTTATTGAGACAGGATTAATCGGACTGATCTTATACTTATTAATTTTTATCTATATCTATATTAAATACAAGTTT +TCTAGGCTAATTATTTTACCAATTATGATCATGGGATTATCGTTTTCGCCAATTGCGTTACCATATTTTTATGTTGCTCT +ATCTTGGTTAATGTATTTAGAGAGAAAAAATGGATATTTTGAAAGGTAA +>O-28_wzy__1317 +ATGGAGTTTACTATAAATTTACTCATAATTTTATTGAGTTTTATTCCCGGTTACTACTTGGGGGTCTTTTATTTTAAACG +ACTTAATTATTATTGCGTCCTTTTTTGGACTATGTTCTTATTTTGTGTTGTGGGATCGTTTATAATATATTCTGGCATAA +TGGACAATTCATTTTTTGTCGAACCGATTGCGAATAATACAAAAGCAAAGAACCTTGGCCTTTTTATTACCACTATTTCT +TTTTTTATATTTTTTCTTGCTGCTTTTATTGTTGAGATTTTTTATTCATTCTACACAAAAAATACCACTAGCAAAGTGAA +TTGGGATAGGTACTACTCACGTTTGATACTTAATAGTAATAGCCTACTCATGTTAGTCTTATTTTTACTGTCGTGTATGC +TGATTTTATATTATATAGTATCAATATACCCTGCCCCACTATTTATGGTACTCAAAGGAGCTTCTGCGGAAGAAATTGCC +ATTCGAAGATTAGAAGTGACAAAAGATTATTCAGGAATCGGTTATTTCAAAACATTGGCTGGAATATTACCAACAATTTT +TTCATATTATTGTTTTATTTCATATTTAAAATTCAAGAAACACTTTTTTATTTTTATCATTACTTTATTTCTCTCTATGT +TAACATTAATTATAAATGGAGAGAAAGCACCGCTAGTTTTTTATTTTTTGGGGCTTTTAGTGTCATATTCATCTGTAAAA +GACATTAGTAAAAAGATTTACTTTTTTGCGCTGTTATTAATATTTTCTTTGATTTTTTTGATGTATATTATTCTTTTTCA +GTTTGATAGCTCAGATTATCTTCTGTATATACTTATTGAGAGATTATTTATTGCTCAGGAAGCCGCTGTATTCTATGCGG +CAGATTACTTTTCAAGCCATAATGTTTTGGGTCTATCCAGTATGGATACGATTTTTAATAAATTATTGAATATTACTCCA +GCACCTAGAGCATCAGAGATTTTCATGTACCAATATCTGCCAACAATGGTTGAAAATGGTGGTTGGAATGTGAATGGATT +TTTTGCTCACGAAACTTTCTCCAATTTTGGTTACATAGGGGTTGTTTTTGGAAGTTTTTATGGTGGCATAGTAAATAGTT +TGTTGTGTATATTTTTCCGGACAAGAAAAAAGACATTATTAACAATGAGTTTTTATAGCTTTTTCATCGTTTCCGTAACT +ACGGTTATCAGTAATTTTAATGCGATGTTATTTAATACACAATTAATATTAATATTTATTATTTATATTTTATTGTCTTT +TCTCGATAGGGGAGGTAAATATCATGTATCAAAGTGA +>fljB_e,n,x_Salmonella.enterica_Singapore_AY353305_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAAACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Bessi_AY353317_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAATGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,6_Salmonella.enterica_Agama_AY353294_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATACAGCTATCAAAGCGGCTATAGGTG +GTACGCTTGGCACGGCTTCTGTAACCGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTATACTGGTGCTGATGCCACCAAAAATGGCGATTATGAAGTTAACGTCGCTACTGACGGTAAAGTAACCCTTGCGCC +TGGCGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCGACAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_Salmonella.enterica_Rough:r:1,5_AY353281_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATACAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5,7_Salmonella.enterica_Hisingen_AY353289_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGCCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCCAACATAAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGATGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCTGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGACTCACTGAATGTGCAGAAAGCGTATGATGTGAAAGACACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATTAAAGCAGCTACGGGGG +GGACGGCTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGTTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGATGGTAAAGTAACACTTGCGAC +TGGCGCAACTAAAACCACAATGCCTGCAGGTGCGACAACCAAAACAGAAGTACAGGAGTTGAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGGCGGTGTTGATACTACAGATGCAAATGCTGCGACACTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACTACAAGTTATACTGCTGCTGACGGCACTACCAAGACGGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGGCAT +GATTTTAAAGCACAGCCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAATCCGTTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGTTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTGAAGCACGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAAAACGTGCTGTCTCTGCTACGTTA +A +>fljB_z6_Salmonella.enterica_Bere_AY353352_k,z__1503 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGT +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTAGATAGTAAGGCTGTGAC +AGTAGCTGCCAATTTAGATATTACTGATCTTAATAAAGACGCAGCCCTTAAAGCAGGCACTGGTGCTACAACAGGTACTG +CAGCAATAAAAGATGGCAAAGTTTATTATGATAGTGCTAGCAAAAACTACTATGTTGAAGTTACCGGTCTGACCACCCCT +GATGACGGTAAAAATGGCTTCTATAAAGTAAATGTCGCCGATGATGGTAAGGTGTCTATGACCGCTGGTACGGCTATGGA +GGCGGGTAAACCAGCTGGTGCGGTAGAAGTAACAAAAACTCAGGAAGAAAAAAATCCATTACCATTATCAACAGATCTCA +AAACCTCCCTTAAATCTGGCGGGATTACAGACCCAGAAATTGCTGCTGCCCAGGTTGTCAAAATGTCTTACACCGATAAA +AATGGTAAGACGATTGATGGCGGTTACGCTGTAAAGGTGGGCGATAATTACTATGCCGCTACCCAGAAAAAAGATGGTAG +CTTCAGTGTTAACACCACGTCTTACACCGCAGCTGACGGTACTACCAAAACTGCCCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATTGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAGCCA +GAGCTGGCGGAAGCAGCCGCTAAAACCACTGAAAATCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTG +AAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,7_Gaminarastr_AOZF01000073_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fljB_z35_Salmonella.enterica_Tamilnadu_AY353340_other.z35__1488 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTTTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCATATGATGTGAAGAGTGAAGCTGTCAC +GCCTCCGGCAAAACTTGATATTTCAGGATTAACTGGAACTGCAATTAAAACTGGTGTTGATGGTGCTACGGTTGATACAG +GCTCCATTAAAGATGGCAAAGTTTATTATAATAGTACCTCTAAGGACTATTACGTAGAAGTTGATTTTGGTACATCAGCC +GATGCTGCTAAGAGTGGTTACTATAAAGTCAACGTTGCTGATGATGGTACAGTCTCAATGGCAGCTTCTACCACTAAAGA +GGGTACAACTCCTACTGGTATTACTGAAGTTACTCAGGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATTCAGGCTCAGT +TGACAGCTGCTCATGTGACTGGAGCTGATACTGCTGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATT +GATGGCGGTTACGCTGTAAAAGTGGGGGATGACTACTACGCCGCTACCCAGAAAAAAGACGGTAGTTTCAGTGTAAATAC +TACTTCTTACACTGATAAAGACGGCAATACTAAAACCGCACTGAACCAACTTGGCGGCGTAGACGGAAAAACCGAAGTCG +TTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCA +GCCGCTAAAACCACCGAAAACCCACTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCGTTCTGATCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTA +TCGAAGATTCCGACTATGCGACTGAAGTTTCTAACATGTCTCGCGCGCAGATTCTGCAACAGGCCGGTACTTCCGTTCTG +GCGCAGGCTAACCAGGTCCCACAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Gatuni_AY353322_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCCGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,z15_Salmonella.enterica_Sanktgeorg_AY353326_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCAGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACAGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCTACCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAGGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ATGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCATGATTTTAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATCCTGCAGCAG +GCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fliC_y_Bareillystr_AOZP01000027_other.y__1508 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTGT +TGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATGT +CTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTAC +GATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCA +ACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCACA +ACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTTG +GCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATAC +CGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGC +AGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Salmonella.enterica_IIIb.35:r:z61_AY353460_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z10_Salmonella.enterica_Harrisonburg_AY353472_other.z10__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAGCACTGGCGTTAC +TCAATCTCTTGATTTAAAAACTGCTGGAATTACCGGTGCTACATTAAAAACCAGTATTACTGGTACAACAACAGAAACCG +GTAGCGTTAAAGATGGTAAAGTCTACTATGATGCAGATAGCAAAAATTACTATGTAGAGGTTGACTTTACTGATACTACG +GATAAAGCAGCGCATGCTGGTTTCTACAAAGCTGACGTCGATGCTGACGGTAATGTTTCTTTAGCAACTGGTGCGACTAA +AGAAGCAAAACCAACGAATGCAGTTGAAGTTGAAAAAACTATTGATGAAAAACCGCTGAAAGCATCAAGTAGTGTTCAGG +ATGCCTTAAAAGCGAGTGGTATTGCTGATGCGGTTGCAGAAGCTGCGACGGTAGTGAAAATGTCGTACACTGATAAGAAT +GGTAAAACTATTGATGGTGGATACGGTATTAAAGTAGGTGATGACTACTATGCTGCAACTAAAGAAAAAGACGGCAGCTA +TACTATTAATAGTACTTCTTATACCGATAAAGACGGCAACACTAAAACTGCACTAAACCAATTGGGTGGCGCAGACGGTA +AAACTGAAGTTGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCACAACTTCAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCTGCG +TTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGT +ACCTCCGTTCTGGCGCAAGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13,z28_Salmonella.enterica_from-CDC_2011K-0215_l,v__1506 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGGACGGAAGTCCCTGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGTCAGGTTGTTTACG +GTGTTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGGTCAGAACGTAACGTGTCAACCTGTGC +CAAAGCAGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTGCGGTAGCCGCTTCCGCCAGATCAGGCTGTGCTTTAAAGT +TGTGACCTTCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGAAACGACTTCAGTTTTACCGTCTGCGCCACCCAGT +TGGTTCAGTGCGGATTTAGTGTTGCCATCTTTATCGGTGTATTTCGTGGTGTTAATGCTGAACGAGCCATCTTTATTTTT +TGTTGCAGCATAAATATCAGCCCCAACTTTAACACCGAAACCGCCATCAATAGTCTTACCGTTTTTATCCGTATAAGACA +TCGTAACTAATTGACCTTTTGCAGCATCAGCAGTACTAATACCGCTGTCAGTCAACTGAGCTTTAACTTCAGTACTGAGA +GCTACAGGTTTTGGCTGCGTTTCGGTTACTGCCGTCGCCGTTGCTGGCATACCACCTGTCACTTTCGTGGTGGTTGCCGG +CATTGTAACAGTACCATCATCTGCAACATTAACTTCATAAACACCATTTTTACCAGCGTCGCCAACGGTTAAACCTTCTA +CTTCAATAAAATATTTATTATCAGTTGCATCGAAGAAGACTTTACCATCCTTAATTGCAGCGGTACCGCTTGTTGCACCA +CCAATACCTGCTTTAAGAGCTGCATCATCAAGACCTGTGGTATTGAGTGTTGCCCCACCGCCGCTTTTAACTGCCTCACT +CTTCACATCATATTTTTTCTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCAA +TAGTTTCACCGTCGTTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTC +TGGCCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATAGAGTCGAGGTCAGACTGGGAGTTGGT +GCTGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCT +GCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGGCCTTTGATGTTCGCGGTGAAACGGTTAGCAATC +GCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTGCCCAGTGCGGA +CTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>fliC_k_Salmonella.enterica_Blockley_AY353442_k,z__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCACAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTTCAAGCTACAGTTGAAAA +CAGTGTCAAACTGGATACTAGTGCTCTTACTGCCGATGCAATTAAAGGTGGCGTAACAGGTGCGACAACAGCTGGTGCCC +TCAAGGACGGTAAAGTTTACTCTAATGGTACAGATTACTATGTAGAAGTAAGCTTTGCTGATGCGACTGACTCAGGTAAA +AATGGTTTCCTTAAAGTTGACGTTAATACAACTACTGGAGCGGTTACAGTTCCTGCAGCAGCAGCAAATACTGTAGCAGC +AAAACCAGCAGGTGTGTCTGAAGTTACTGAAGTTCAGGGACTAAATACACCGAGTTCGGCTGTACAAGATCAGTTAACAG +CTGCAGGTGTAAGTGCCGCTGATGCTGCTAAATCTGAAGTTGTGAAAATGTCTTACACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAAAATAAAGATGGATCGATCAGCATTAACGC +CACTGAATATACCGATAAAGACGGCAACACAAAAACTGCACTGAACCAACTGGGTGGCGTAGACGGTAAAACCGAAGTTG +TTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAGCTGGCGGAAGCG +GCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCGCAGGTGGATGCGCTGCGTTCTGACCTGGG +TGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCTGGTACTTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_l,z13_Salmonella.enterica_Westerstede_AY353450_l,v__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAAGAGCGAAGCAGTTAA +AAGCGGCGGTGGGGCAACACTCAGTACCACTGGTCTTGATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCG +GTACCGCTGCAATTAAGGATGGTAAAGTCTTCTTTGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACC +GCTGGCGACGCTACTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGCACTGTTACAATGCCGGCAACCACGAA +AGTGGCAGGAGGCATGCCAGCCACGGCGACGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACAGCAGTTA +AAGATCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTTACGATGTCTTATACGGATAAA +AACGGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTAATATTTATGCTGCAACGAAAAATAAAGATGGATC +GTTCAGCATTAACACCACTGAATATACCGATAAAGGCGGCAACACTAAAACTGCTCTGAACCAACTGGGTGGCGCAGACG +GTAAAACTGAAGTCGTTTCTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCACAACTTTAAAGCACAGCCA +GAGCTGGCGGAAGCGGCTGCTGCAACCACTGAAAACCCGCTGGCTAAAATTGATGCCGCGCTGGCGCAGGTTGATGCGCT +GCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTT +CTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCC +GGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z47_Salmonella.enterica_IIIb.38:z47:z53_AY353514_l,v__1500 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACCATTGATATCGATCTG +AAAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGGCAGAAAAAATATGATGTGAAGAGTGAGGCTGTTAAAAG +CGGCGGTGGGGCAACACTAAGTACCACTGGTCTTAATGATGCAGCTCTTAAAACGGGTGTTGGTGGTGCAACAAGCGGTA +CTGCTGCCATTAAAGATAATAAAGTCTTCTTCGATGCAACTGATAATAAATATTTTATTGAAGTTGAAGGTTTAACCGCT +GGCGACGCTGCTAAAAATGGTGTTTATGAAGTTAGTGTTGCAGATGATGGTACTGTTACAATGCCGGCAACCACGAAAGT +GGCAGGTGGTATGCCAGCAACGGCGGCGGCAGTAACCGAAACGCAGCCAAAACCTGTAGCTCTCAGTACTGAAGTTAAAG +CTCAGTTGACCGACAGTGGTATTAGTGCTGCTGATGCTGCAAAAGGTCAATTAGTCACAATGTCTTATACTGATAAAAAC +GGTAAGACTATTGATGGCGGTTTCGGTGTTAAAGTTGGGGCTGATATTTATGCTGCAACAAAAAATAAAGATGGATCGAT +CAGCATTAACACCACTAAATATACCGATAAAGACGGCAATACTAAATCCGCACTAAACCACTGGGTGGCGCAAGACGGCA +AAACCGAAGTTGTTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGAT +CTGGCGGAAGCGGCTACCACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CCCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g,t_Salmonella.enterica_II.17:f,g,t:e,n,x,z15_AY353534_g,m__1518 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCTCAGTCCTCACTGAGTTC +CGCTATCGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAGTTCAACG +GCGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTGGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGTGTGTCTTTTACTATTGATACAAAAGCTGGTAATGACGGTA +ATGGTACGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCGCTGGTGCGGCAGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAATGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGTGAAAGTAAGATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAATCCACTGGCTGCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCGCTGGGGGCAATTCAGAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IIIa.63:z4,z32:-_AY353508_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TAACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_IV.1,40:z4,z23:-_AY353492_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCGAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACTGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCCGCTGATTTCGATAACGCAAAAGCAACTGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGATACTGGGGCGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCAGATAAAGATGCAACTGCAACTGCGGGGACTCCGCCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z23_Salmonella.enterica_Ekotedo_AY353494_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCGAACGGCTCAAACTCTGGTTC +CGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACTGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +CTCGGTAGTTGGTGATGTAAAAATTGCGGCAGCTGATTTCGATAACGCAAAAACAACTGGTGGTCCGGCTGCAGATAAAT +TATCTCTGACAAAAGATGATAAAGGTAATTACTTTGTCAAAGATGTTACTGCGACGGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATTAGTTTTGATTCGGATAAAGATGTAACTGCAGCTGCGGGGACTCCGTCAGCAGTAACTAC +CTTATCACGTGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGATCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACCTTAGATAAAGACGGAAATGCAACTTTCAAATCTGTCACGTTTGCCGCGGACGGTAAA +ACAACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCTTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAG +CAGGCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fljB_e,n,x_Salmonella.enterica_from-CDC_Stk0811_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACTCAGAATAACCTGAACAAATCCCAGTCTGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGCGTGCGTGAACTGGCAGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACCCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAACCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCACTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAACGACAGG +AGCCATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACCAAAACTGCGGCTAACCAACTTGGCGGCGTAG +ACGGAAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCGGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCACTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGTTCTGATCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACTGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACTGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAACAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAAAACGTGCTGTCGCTGTTACGTTAA +>O-18_wzy__1323 +ATGACTCTATTATCTGAACGGCAAACATCAGTTAAAAACTTTTCAAGATATATTCCACTGTACTTTTGTTTATGCTTAGC +TATCGCATTGTTATTGTGTGAGAGTATATTCACTCAAGCATTATACGAGGTGATACTTAAGGTGGTTTCATCATCATTGT +CAGCTTTATTAATTGTTATTATTGCTTACTTTTATATTAAGAGAGCTTATTTTTTTTCATTGCAGTTAATGTATGCATAC +GCCTTTTCTTTAATAATAGGAATACCTTCCGTATACTTACTCAATTTTGGCGAAGCAAAGGGAGGTTTTGAATTAGTATG +CTTATGGTGTATATTATTAAATATTATATTATATTTTTCTGCATGCTCTAGTAAAGTAATAGAACAAAAAAAAACGGTTA +ATAAAATATTTGTTGTGATATTTTTCGTTGTCGGTTTTTGTCAGTTAGTTAAAACGTTGCTCTATTTTAGATTTATTATT +GACTCAGGCTTAGGTCATTTGGCTATTTATACTGAAGGCGAAATTTTAACCGCCCAAGTGCCCTTTGTTATTAGAGCCAT +TAGCGGCCTTTCATTAATCATGTCACTAGCGACGTTTTATTTTAAGGCACCAAGATATTTAAGGTGGATAGGGTTTATAT +TATTAGCATCTGAACTTTTGATTGGGATAAGAAGTAAATTCTTTTTCTCATTGATTTGTATTATTGCTTTATCCTTATAT +AGTAATAGACACTTAATTCAATCAAAATTCGTAAAACTTTCCAAGATACAATATTTATTAATTGGATTCATATTATTCTC +CTTAATTTCTTATTTTAGGGAGGGTTACGAAATTAATTTCATTAACTATTTAGTCATAGTATTAGACTCACTCTCTTCGA +CGCTAGCAGGTTTACAAGATGTATTTCTTTTACCGACAGCGCAGGGTTGGGATAAAATAGATGCACATGTTATATTAACG +CAAATATTACCAATAAGCGGTTTTGGATTTATAAGCGATTCTCAAATTTATAAGCAATTTTCTATCATAGTGCTCGGAGA +TATTTCAAGTGGTATTGCACTATCATCTTCTGGAATTCTAGAAGCAACAGTTTTAAATATAAAGTTTGGTTTTTTTATTT +ATTTATTTTATCTTTTAATTATGCTTGCATTGATCCAGAAATGTCTAAATAGCTCGCTTAATTTGTTGAATTTTATTGCT +ATCGCGATGTTGCCCGGATTATTATATTCAATTCGGGGAGAGTTGGTTTTACCTTTTGCATATATAATAAAATCACTACC +CATTATATTTCTATCTCCTTTTTTAACTTCAACAAATAAATAA +>O-40_wzy-from-blake-2014K-0489__1368 +ATGTTTCAGATTAAAACCAGAAAAAAACCATTGTTGATATTATATTTAACTTTGCTATTAAGTGTTTTAGTGTCATTGAT +TATCGATGATGGTACAAATCGATCCTTATACATACTTTTTATATCCACACTAAGTGTTTTTTTTATCTGCTATTCTTGTA +ATAAAATAACTTCTCCTGCAAGTTTGTTAATTATATCTTCATTTGTTTTTCTTGGTTGTAGACCATTTCTCTCATTATTT +ACAAGTTTCGATTATAGAAATGGCGATTGGTTTATAACTGGTTATTTAGATAAGGATGTTATCTATGCTAATTATGCTAT +TTCTTTTATGTATTTTGGGTATAGTGTTGCATTAATACTAAGTAATAATAATTCAACACGTAGAGAATGTTACAGTTTAA +ATCAAATAAATCCTAATATTAGATTTTTGTTTGTACTCTTTCTTTTTGGCTCTTTAGGCCAAATCCTTAAAGGTTTGTAT +TTTTATTCTTTCATTGAGTCGAATAGTTATGTTGGAATTTATCAAGATAAAGTAAATTTACCAATGGGATATGATTTTTT +ATCATATCTATTTTATTGCTCCTTTTTCCTCATATGCGCATTTTATGATAAACTTCGTGTTAATAAATTATTTTTATTGA +TATCTATATTGATTGCCGCTTTTAGTGCCATGAAAGGCAGTCGAGGGGAGTTTATTACATTTCTGCTTACGGTTTTTTGT +ATTTATTATAATGAGAGAAAAGTAAGTAACATTAGATTGCTATTAAAAATGTTTTTAATATTTATTGCTATTTTCACTGT +TAGTGAATTTGTTTCGATGTGGCGGTCAGGCGGCAGCTTTATTGCTCTTATTGAAGGCGATAATCCACTTTTGCAATTTA +TATATGGAATGGGAGTGTCATATATTGCAATTTACCAATCGGTTAAAATAACTTTAATTTCTGGAGTGTTTGATTTTCAT +TATTTAATCAGTCAACTATTAATTACTATATCTTCTGTGTTAGGGGTTCAGGTGTATTTACCTGACATTAGTTATAGCCA +TTTGGTGTCTAAGACTGCTAACCCACAATTATACCAACAAGGGTTTGGATTAGGAGGAAGCTATCTTGGTGAATCATTTT +TAGCTATGGGGCTAATAGGGTGTTTTATCATTCCATTTATAGTTTTGTTTCTTATTAATAATTTAGAGCGATTTACTAAA +TATAATAAAACTTTTTATTTTTTATATTATAGCTCTCTGCCATCTGTTTTATTTATACCCAGAGAAACTTTGCTCTATTT +TTTCCCTTATGTAATTAAAGGTATTGTTGTGGCATTTTTGTTTATATGCTATTCAAATATTAAAATGAGAAGATTTAATA +ATGGTTGA +>fliC_l,v_from-Nchanga_SRR1153349__1503 +TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTCGCCTGCGCCAGAACGGAAGTACCAGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGGGCAGAAGACAGGTTATTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGAACCGCACCCAGGTCAGAACGCAGCGCATCCACCTGCGC +CAAAGCAGCATCAATTTTCTGCAGCGGGTTTTCAGTGGTTGTAGCAGCCGCTTCCGCCAGCTCTGGCTGTGCTTTGAAGT +TGTGCCCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGAAACGACTTCAGTTTTACCGTCTGCGCCACCCAGT +TGGTTCAGTGCAGTTTTAGTGTTGCCGCCTTTATCGGTATATTCAGTGGTGTTAATGCTGAACGATCCATCTTTATTTTT +TGTTGCAGCATAAATATTAGCCCCAACTTTAACACCGAAACCGCCATCAATAGTCTTACCGTTTTTATCCGTATAAGACA +TCGTAACTAATTGACCTTTTGCAGCATCAGCAGCACTAATACCACTGTCGGTCAACTGATCTTTAACTGCTGTACTGAGA +GCTACAGGTTTTGGCTGCGTTTCGGTTACTGCCGTCGCCGTGGCTGGCATGCCTCCTGTCACTTTCGTGGTTGCCGGCAT +TGTAACAGTGCCATCATCTGCAACACTAACTTCATAAACACCATTTTTAGTAGCGTCGCCAGCGGTTAAACCTTCTACTT +CAATAAAATATTTATTATCAGTTGCATCGAAGAAGACTTTACCATCCTTAATTGCAGCAGTACCGTTTGTTGCACCACCA +ACACCCGTTTTAAGAGCTGCATCATTAAGACCAGTGGTATTGAGTGTTGCCCCACCGCCGCTTTTAACTGCTTCGCTCTT +CACATCATATTTTTTCTGCACATTCAGCGTATCCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCGATGG +TTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGG +CCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATGGAGTCAAGGTCAGACTGGGAGTTGGTGCT +GTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGTGGTCTGCG +CAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTGATGTTCGCGGTGAAACGGTTAGCAATTGCC +TGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCGGAAGACAGACGCTCGATAGCGGTACCCAGAGCAGACTG +GGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTTTGTATTAATGACTTGTGCCAT +>tyr-O-9__609 +ATGAAGCTTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT +>O:23-gene2__1146 +CCGGAATTTTATAAAAAGAATATGAAAATATTAATGATTGGTACTACGGTGCAATCTTTATTAGGATTCAGATATGAATT +ACTTAAAGATTTAGTTAGCGCAGGACATGAAGTATATGCGTTATCTGTTGATTATGATTACAAATCGAAGCAGACATTGA +TTGATATCGGTGTCGTACCGATAGATTATACAATAAGTCGCTCAGGAATTAATCCCTTCAAGGATTTTGTTAATTTTATT +TTTTTATATAAGCTAATAAAAAAAATAACACCAGACATCGTTTTTTCTTATTTTACTAAGCCTTGTATTTGGGGATCGCT +TGCCGCATATTATGCTGGTGTTCATAAGATTATCGCGATGCTTGAAGGGTTAGGTTTTTTATTTACCGAACAACCATCTG +GGATTCCCCAAAAGACAAAAATCCTAAAAAGAATACAGATTCTGCTCTATAGAATAGCTTTTAAGAAAATTAATACACTT +ATTGTACTTAATGAAGATGATAGGAATGATTTACTTAACGCTGGTTGTATAGAAGATAGAAAAGTATATGTATTGGGGGG +TATTGGAATAAATTTAGAGCATTACAAGTATTCACCAGCACCACTTGAACCAATTTCTTTTATTTTCATTGGCCGATTGC +TCAGAGAAAAGGGGATTTATGAATTTATCGCTGCTGCTAAAAATATAAAAGAAAGATTTGAAGGGGTGACGTTTAATGTG +CTGGGTAATATTGATCCAGCAAACCCTGGTAGTCTAAAACAAAATGAACTTGATACAATTATTAAAGAAGAAATAATTAA +CTATGTAGGATATGTGAATGATGTTTCTCATTGGTTAAGTAAGAGCAGTGTTTTCGTTTTACCTTCTTATAGAGAAGGAT +TTCCTCGAAGTACACAGGAGGCTATGGCTATAGGAAGAGCTGTAATAACTACCGATGTTCCTGGATGTAGAGATACTGTT +GTTAATAATTCTAATGGTTTTTTAATACAACGGTGGTCTAGCGATGCTCTTGCAGAGGCGATGGAAAAATTTATTTTATC +TAAAGAATTGATTCGCGACTGTGGTAAAGAAAGTGCCAGGATAGCTAAAGAAAAATTTGACACCCGAATTACCAATAAGA +AAATAATTACTATATTATTGTCTTAA +>fliC_f,g,s_Salmonella.enterica_DTU-genomes_unknown_g,m__1518 +atggcacaagtcattaatacaaacagcctgtcgctgttgacccagaataacctgaacaaatctcagtcctcactgagttc +cgctattgagcgtctgtcctctggtctgcgtatcaacagcgcgaaagacgatgcggcaggccaggcgattgctaaccgct +tcacttctaatatcaaaggtctgactcaggcttcccgtaacgctaacgacggcatttctattgcgcagaccactgaaggt +gcgctgaatgaaattaacaacaacctgcagcgtgtgcgtgagttgtctgtgcaggccactaacgggactaactctgattc +cgatctgaaatctatccaggatgaaattcagcaacgtctggaagaaatcgatcgcgtttctaatcagactcaatttaacg +gtgttaaagtcctgtctcaggacaaccagatgaaaatccaggttggtgctaacgatggtgaaaccattaccatcgatctg +caaaaaattgatgtgaaaagccttggccttgatgggttcaatgttaatgggccaaaagaagcgacagtgggtgatctgaa +atccagcttcaagaatgttacgggttatgacacctatgcagcgggtgccaataaatatcgtgtagatattaattcaggtg +ctgtagtaactgatgatgcagcaccggataaagtatatgtaaatgcagcaaatggtcagttgacaactgacgatgcggaa +aataacactgcggttaacctattcaagacgactaaatctgctgctggtaccgatgaagccaaagcgatagctggtgccat +taagggtggtaaggaaggagatacctttgattataaaggcgtgacttttactattgatacaaaaactggtaatgacggta +atggtaaggtttctactaccatcaatggtgaaaaagttacgttaactgtcgctgatattaccggtggtgcggcgaatgtt +gatgctgctaccttacaatcaagcaaaaatgtttttacatctgtagtgaacggtcagtttacttttgatgataaaaccaa +aaacgagagtgcgaaactttctgatttggaagcaaacaatgctgttaaaggcgaaagtaaaattacagtaaatggggctg +aatatactgctaacgccacgggtgataaggtcaccttagcaggcaaaaccatgtttattgacaaaacagcttctggcgtt +agtacattaatcaatgaagacgctgccgctgctaagaaaagtaccgctaacccactggcttcaattgattctgcattgtc +aaaagtggacgcagttcgttcttctctgggggcaattcaaaaccgttttgattcagccattaccaaccttggcaatacgg +taaccaatctgaactccgcgcgtagccgtatcgaagatgctgactatgcaacggaagtttctaatatgtctaaagcgcag +attctgcagcaggctggtacttccgttctggcgcaggctaaccaggttccgcaaaacgtcctctctttactgcgttaa +>fliC_g,z51_Salmonella.enterica_Travis_AY353413_g,m__1515 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGACGCAGGCTTCCCGTAACGCTAACGACGGTATCTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAATGGTACTAACTCTGATTC +CGATTTGAAATCCATTCAGGATGAAATCCAGCAGCGCTTATCGGAAATCGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGTCTGGATGGATTCAATGTTAACGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGATACGTATACTGCTGGTGCTAATACTTATCGCGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAATGCAGCAAACGGTCAGCTCACAACTGATGATGCACAGAAT +AACACTGCAGTTGATCTATTTAAGACAGCAAAATCATCAGCAGGTACAGCTGAATCTAAAGCAATAGCTGGCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTCACCATTGATACAAAGAATGGCGCTGACGGTAATG +GTACTGTTTCCACTATGATCAATGGTGAAAAAGTTACGTTGACTGTTGCTGATATTACCACTGGTGCGGCGGACGTTAAT +GCGGCTACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTAAACGGCCAGTTTACTTTTGATGATAAAACCAAAAA +CGAGAGTGCGAAACTTTCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGCGCTGAGT +ATACAGCTAACGCTGAAGGTGATAAAGTTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACCGCTTCTGGCGTTAGC +ACATTAATCAATGAAGATGCTGCTGCTGCTAAGAAGAGTACAGCTAATCCACTGGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCACTGGGGGCGATCCAGAATCGCTTTGATTCTGCCATCACTAACCTGGGCAACACGGTAA +ATAACCTGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAGCGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_IIIb.41:c:e,n,x,z15_AY353369_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGTACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGAAGGTCACAACTTTAAAGCACAG +CCTGATCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Jericho_AY353367_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACCATCGATATCGATCTG +AAACAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAACAGCTATTACTGCAAAAATTGGTGCAGCAACCA +CTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACGGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAGGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AACGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACTGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAAGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGT +CTTCTGCTCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTTTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_c_Salmonella.enterica_Goeteborg_AY353368_other.c__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGGATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTGAGCGATACTGCTGTAGC +TGCTTCCTATTCCGACTCGAAACAGAATATTGCTGTTCCTGATAAAGCAGCTATTACTGCAAAAATTGGTGCAGCAACCA +GTGGTGGTGCTGGTATAAAAGCAGATATTAGCTTTAAAGATGGCAAGTATTACGCGACTGTCAGTGGATACGATGATGCC +GCAGATACAGATAAAAATGGAACCTATGAAGTCACTGTTGCCGCAGATACAGGAGCAGTTACTTTTGCGACTACACCAAC +AGTGGTTGACTTACCAACTGATGCAAAAGCAGTTTCAAAAGTTCAACAGAATGATACTGAAATAGCAGCAACAAATGCGA +AAGCTGCATTAAAAGCTGCAGGAGTTGCAGATGCAGAAGCTGATACAGCTACTTTAGTGAAAATGTCTTATACAGATAAT +AATGGCAAAGTTATTGATGGTGGGTTCGCATTTAAGACCTCCGGTGGTTATTATGCAGCATCTGTTGATAAATCTGGCGC +AGCTAGCTTGAAAGTTACTAGCTACGTTGACGCTACCACTGGTACCGAAAAAACTGCTGCGAATAAATTAGGTGGCGCAG +ACGGTAAAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGGCACAACTTCAAAGCACAG +CCAGAGCTGGCGGAAGCGGCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGATGC +GCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGT +CTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>tyr-O-2__608 +ATGAAGCTTTAATTACCGGTGGATGTGGCTTCCTTGGGAGTAATCTTGCCTCCTTTGCTTTAAGTCAAGGGATTGATTTAATTGTATTCGATAATCTATCACGTAAAGGTGCAACAGATAATTTACATTGGTTATCCTCCTTAGGAAACTTTGAGTTTGTACATGGTGATATTCGCAACAAAAATGATGTTACAAGATTAATAACTAAGTATATGCCTGATAGCTGTTTTCATCTTGCAGGTCAAGTGGCAATGACTACATCTATTGACAATCCTTGTATGGATTTTGAAATTAATGTAGGTGGAACTTTAAATTTACTTGAGGCAGTACGGCAGTATAATTCAAATTGTAATATAATTTATTCATCAACAAATAAAGTATACGGCGATCTTGAGCAATATAAATACAATGAAACAGAAACTAGATACACTTGTGTAGATAAGCCTAATGGATATGATGAGAGCACACAATTAGATTTCCACTCACCATATGGTTGTTCAAAAGGTGCTGCAGACCAATACATGCTTGATTATGCAAGGATTTTTGGTTTGAATACAGTGGTGTTCAGGCATTCATCAATGTATGGTGGGAGACAGTTTGCTACTTAT +>fliC_y_Pomonastr_AHIA01000046_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGACAGGCAATTGCTAACCGTT +TTACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGCTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGAACTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Weltevredenstr_ABFF01000030_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCGAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +TCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_y_Hartfordstr_ALPO01000014_other.y__1509 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGTGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,z51_50_g,z51_-str_AOXJ01000042_g,m__1503 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCTCACTGAGTTC +CGCTATCGAGCGTTTGTCCTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATCAAAGGCCTGACTCAGGCTTCCCGTAATGCGAACGACGGTATCTCCATTGCGCAGACCACCGAAGGG +GCGTTGAATGAAATTAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATTCAGGATGAAATTCAGCAGCGCTTATCGGAAATTGACCGTGTTTCTAACCAGACTCAGTTTAACG +GTGTTAAAGTCCTGTCTCAGGATAATCAGATGAAAATTCAGGTGGGCGCTAACGATGGCGAGACTATTACCATTGATCTA +CAAAAAATTGATGTGAAAAGTCTTGGTCTGGATGGGTTCAACGTGAATGGGCCTAAACAAGCAACCGCTGGGGATTTGAA +ATCTAATTTCAAAAACGTTACTGGTTATGATACGTATGCTGTTGGTGCTGATAGTTATCGTGTAGATATTAATTCTGGAG +CAGTAACTGATGATGCTGGTACCGATAAGATTTACGTAAACGCAGCAAACGGTAAACTCACAACTGATGATGCACAGAAT +AACACCCCAGTTGATCTATTTAAGACAACAAAATCATCAGCCGGTACAGCTGAATCTAAAGCAATTGCTACCGCTATTAA +AGGTGGTAAAGAAGGAGATACTTTTGATTATAAAGGTGTTTCTTTTACCATTGATACAAAGAATGGCACTGACGGTAATG +GTACAGTTTCTACTACTATCAATGGTGAAAAAGTTACGTTGACTGTCGCTGACATTACCACGGGTGCGGCAGACGTTAAT +GCGGCAACCTTACAATCAAGTAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACCTTTGATGATAAAACGAAAAA +CGAAGGTGCGAAATTATCTGATTTAGAAGCAAATAATGCTGTTAAAGGTGAAAGTAAAATCACGGTAAACGGTGCTGAAT +ATACAGCTAACGCTGAGGGTGATAAAATTACCTTAGCAGGTAAAACCATGTTTATTGATAAGACAGCCTCTGGCGTTAGC +ACATTAATTAATGAAGATGCTGCTGCAGCTAAGAAGAGTACCGCTAATCCACTCGCTTCAATTGATTCTGCATTGTCAAA +AGTGGATGCTGTACGTTCTTCATTGGGGGCTATTCAGAACCGTTTTGATTCTGCCATTACCAACTTGGGTAATACGGTAA +ATAATCTGACTTCCGCACGTAGCCGTATCGAAGATGCTGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATT +CTGCAGCAGGCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALGW01000034_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGACGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_z_Salmonella.enterica_IIIb.48:z:1,5,7_AY353339_k,z__1500 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGTTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTAGATAGCAAAGCTGTGAC +TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGTACAGCTATTAAAACTGGCGTTGCTGGAGCTACCACTACAACTG +GTTCCATTAAAGATGACAAAGTATATTATGATAGTGCTACTAAAAATTATTATGCTGAAGTGAACTTTACAGATGCCGCT +GATACCGCTAAAAATGGTTTCTATAAAGTCAATGTTGCTGATGATGGCACTGTTACAATGGGGGCTTCGACTACTAAAGA +AGCTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACCCAAGAAGAGAAAGCAATTAAGGCATCTGCAGATGTGAAAG +CTGCTCTGACTGCTGGAGGTATTGATACTGCTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAAC +GGTAAGACGATTGATGGCGGTTACGCTGTAAAAGTGGGCGATAACTACTATGCCGCTACCCAGAAAAAAGATGGTAGCTT +TAGTGTTAACACCACGTCTTACACCGCAGCGGACGGTACATCCAAAACTGCCCTGAACCAACTTGGTGGCGCAGACGGTA +AAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAGCCAGAG +CTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACG +TTCTGACTTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTG +CACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCGGGG +ACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGCTACGTTAA +>oafA__1830 +ATGATCTACAAGAAATTCAGACTCGATATAAATGGGCTAAGAGCTTTTGCATTGATAAGTGTTGTGCTGTATCACTTCGG +TGTACCTTATGTGTCAGGTGGCTTTATAGGTGTAGATGTTTTCTTTGTAATTTCTGGTTTTCTTATGACTGGAATTGTCC +TTGAACGCGTAGACCACAAAGGAGTACTTGATTTTTATATTGCAAGATTCCTAAGAATTGTACCAGCTCTGGTATTTGCA +ATTCTCTTGTTGATGATTTTCGGTTTATTTACACTAAGTACAAATGAATACGAAGCACTTAGCAAGAACGCAATATCGTC +TTTACTTTTTTATTCAAATAATTATTACGCAATTCACTCTAGTTATTTCGACTCATCATCAGAGTTCAACTTTTTGCTTC +ACACCTGGTCACTATCAGTTGAGTGGCAATTTTATATTTTATATCCTTTATTAGTCATTATAGTTAAAAAATTACGGTTT +CCTGTTGGACTCTCATTATCTGTAATTTTAGCCATGTCACTTGCAATTACACTTATGCGAGTGACTGGAACCAAAGAAGA +TATTTTCTATCTTATCCCTACCAGGGCATGGGAAATGCTGGCTGGCGGCCTTGTATACATAGCATCTGTACGTTACAAAA +TGCCAGAATGGATAAAGCATTGTGAGGTTTATGGGATAGTCCTCATTGTTGTTCGTGTTGTTATACTCGACAGTAATGGT +TACTGGCCAAGCTATTCAGCACTCGCTCCCGTGCTGGGTGCTTCGATGGTTATTCTGGCTAACAAACAGAACTCTTTATT +CACATCAAACAGAATTGCACAGTGGGTGGGTAAGATTTCTTACTCAGTTTATTTATGGCACTGGCCTGTAATTGTAGCGA +TGAAACATTATGATATTGAGTTCAGCGCTATAAATATTTTCTTTGGTGTAATTGTGTCTTTTGCGCTTGGGGATATTTCA +GACAGAACAATTGAAAACACGCTCAGGAAACGAGTTAAGCTACAATTTAATATTGTATTATTTTCCTCTACTCTGGCTCT +ATGCTTGTTTGTCATGTTCACAAAAGGTGTTAGTTTTAGATTTTCAGACACCCTAAAGCAAGTCGTTGAGTATCGTATGG +ACAACTCTCCCTGGAGGCCTGATATTTGCTTCCTCAATCCAGATCAAGATTATTCAGCATTCTCAAAATGTCAGGATAAA +ATGACTGAAAAGTCTTTTGTTGTATGGGGTGACTCGCATGCCGCACATCTTATGCCAGGGCTGAAATCGGTATTTGGAAA +TTCACTTAACATTACGCAGAGAACTGCAAGCTTGTGCCCACCAATCATTGGGCTTCAAAAAGATGACAGGCCGTATTGCA +AAGACATCAATGATATGGTAGCCAAGGAAATTTCAGACAACAAGCCTACTACGGTATTAATGTCCGCGTTGTGGCCTGTC +TATCCTATGCGTGATTATCTGCCTGAGACTATTAAATTCCTGAAGGATAACAAAGTAAAAAACATCATCATTGTTGGCCC +GTTCCCGGTTTGGAAGAAAACGATGATTGATACTATTGAGGATATGGGGATTAATTCCGGAAGGACCGTTCCATGGAGCA +TGACGGATGAAACCCGTAATCTGAGAGATAATGACAAATATCTTAGAGAGCTGGCGAAAGAGCATTCCCTTACTTATATT +TCACCACTTGAGACTATGTGTACAGAAAGTTATTGCAAAGCAATAATAGGGAATAGAATTGCTTACCCTATACAATATGA +CAATGCGCACCTAACACCAGAAGGCTCAGGGTGGTTTATTGAGGAAGTGAGAAAGCAGATTTCAAAATAA +>fljB_e,n,x,z15_Salmonella.enterica_IIIb.47:i:e,n,x,z15_AY353313_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAATGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCAACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGCCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,5_from-Ibadan-micro-assembly_SRR1753831_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCACAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTG +GTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGT +GGCTATACTGGTGCTGATGCATCCAAAAATGGCGATTATGAAGTTAACGTTGCTGCTGACGGTAAAGTTACACTTGCTAC +AGGTGCAACTAAAACCACAATACCGGCAGGTGCTACAACCAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCTGATGCAAATGCCGCCGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACCATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGTT +GGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5,7_Salmonella.enterica_IIIb.47:r:1,5,7_AY353291_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTTTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATACGTTGAATGTGCAAAAAGCGTATGATGTGAAAGATACAGCAGCAAC +AACGAAAGCTTATGCTGATAATGGTACTACACTGGATGTATCAGGTCTTGATGATGCAGCGATTAAAGCGGCTACGGGTG +GTACGACTGGTGCGCCTACTGTAACGGGCGGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGGTGATGCTGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTAACACTTGCGAC +TGGTGCAACTAAAACCACAATGCCTGCAGGTGCTACAACCAAAACAGAAGTACAGGAATTAAAAGATACACCGGCAGTTG +TATCAGCTGATGCTAAAAATGCTTTAATTGCTGCTGGCGTTGATACTACAGATGCAAATGCCGCGACATTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTA +CAATGAAACTACAGGAGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACC +AACTTGGTGGCGCAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCAT +GATTTCAAAGCACAGCCAGATCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCT +GGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACA +CCGTAAACAACCTGACTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTA +A +>fljB_1,5_from-Infantis-micro-assembly_SRR1106258_1__1521 +TTAACGTAACAGAGACAGCACGTTCTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGCTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACG +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTTTGTACCGCACCCAGATCAGAGCGCAGCGCATCCACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGCGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGTTGTGCTTTGAAAT +CATGACCAGCGGCTTTGCTGGCATTGTAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTACCGTCTACGCCACCCAGT +TGGTTAGCTGCTGTTTTGGTAGTGCCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATTGCTCCTGTCGCTTCATC +GTAATCTGCGGCGTAATACTTATCGCCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAACTCAGCGCCATTAGCATCGGTAGCGTCAACGCCGCCAGCAATTAAGGCATTTTTAGCATCTGCTGAA +ACAACTGCCGGTGTATCTTTTAACTCCTGTACTTCTGTTTTAGTTGTCGCACCAGCAGGCATTGTGGTTTTAGTTGCGCC +AGCCGCAAGGGTTACTGTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCACCAGTAAAGC +CACCAATAGTAACAAAGTACTTGTTATTATCTGCGTCAAATTTAACCGCACCACCGGTTACAGCAGCCGTACCAGTCGTA +CCACCCGTAGCCGTTTTAATAGCTGCATCAGTAAGACCCGATACATCCAGTGTAGTACCATTATCGGCATAAGCTTTCGT +TGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACGTTCAGTGAGTCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATATCGATAGTTTCACCGTCGTTGGCACCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGAGTCTGGCCGGATACACGGTCGATTTCGTTCAGGCGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTGATGTTCGCGGTA +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,5_Javiana_SAMN02902435_1__1511 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCGATAATGGTACTACACTGGATGCCTCAGGCCTTGATGATGCGGCCATCAAAGCAGCCATTGGTG +GTACGACTGGTACGGCTGCTGTAACGGGTGGTACAGTTAAATTTGACGCAGATAATAATAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATGCCGCCAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTAAAGTTACACTTGCTAC +GGGTGCAACTAAAACCACAATGCCTGCTGGCGCGGCAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATCGCTGGCGGCGTTGACACTGCCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATATTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACTACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCTGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATCCTGCAGCAGGCCGGTACTTCCGTTCTGGCACAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCT +>fliC_r_Virchowstr_ABFH02000002_r,i__1470 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACTAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATTACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTACCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGCTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACTCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCTGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTGCT +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAG +GCGAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_g,m_Enteritidisstr_ALGQ01000046_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGTTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACGATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGTA +AGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_d_Muenchenstr_ARYW01000085_b,d,j__1496 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACGGTACTAACTCCCAGTC +TGACCTTGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGTGATATTGATTTAAAAGAAATTAGCT +CTAAAACACTGGGACTTGATAAGCTTAATGTCCAGGATGCCTACACCCCGAAAGAAACTGCTGTAACCGTTGATAAAACT +ACCTATAAAAATGGTACAGATACTATTACAGCCCAGAGCAATACTGATATCCAAACTGCAATTGGCGGTGGTGCAACGGG +GGTTACTGGGGCTGATATCAAATTTAAAGATGGTCAATACTATTTAGATGTTAAAGGCGGTGCTTCTGCTGGTGTTTATA +AAGCCACTTATGATGAAACTACAAAGAAAGTTAATATTGATACGACTGATAAAACTCCGTTAGCAACTGCGGAAGCTACA +GCTATTCGGGGAACGGCCACTATAACCCACAACCAAATTGCTGAAGTAACAAAAGAGGGTGTTGATACGACCACAGTTGC +GGCTCAACTTGCTGCTGCAGGGGTTACTGGTGCCGATAAGGACAATACTAGCCTTGTAAAACTATCGTTTGAGGATAAAA +ACGGTAAGGTTATTGATGGTGGCTATGCAGTGAAAATGGGCGACGATTTCTATGCCGCTACATATGATGAGAAAATAGGT +ACAATTACTGCTAAAACAACCACTTATACAGATGGTGCTGGCGTTGCTCAAACTGGAGCTGTGAAATTTGGTGGCGCAAA +TGGTAAATCTGAAGTTGTTACTGCTACCGATGGTAAAACTTACTTAGCAAGCGACCTTGACAAACATAACTTCAGAACAG +GCGGTGAGCTTAAAGAGGTTAATACAGATAAGACTGAAAACCCACTGCAGAAAATTGATGCTGCCTTGGCACAGGTTGAT +ACACTTCGTTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCT +GTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGC +AGGCCGGTACCTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fljB_e,n,x,z15_Salmonella.enterica_16:z10:e,n,x,z15_AY353306_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGATAACACCCTGACCATCCAGGTTGGTGCCAATGACGGTGAAACCATCGATATCGATCTG +AAGCAGATCAACTCTCAGACTCTGGGTCTGGATTCACTGAATGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +TAGCTCTACCTATAGTGATGGTACTAAGGCTCTTACGGCACCAACTGCAACTGATATTAAAACTGCATTAGGCAACCCGA +CGGTAACTGGTGATACATTAACTGCCACCGTATCCTTCAAGGATGGTAAATATTACGCCACCGTAGGTGGTTATACCGAT +ACGGGGGATGCTGCCAAAAATGGCAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACTCC +GACTAAAGCTACAGTAACTGGGGATACAACCGTAACTAAAGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGAGGCGTCTCATCTGCGGACGCAAATGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAATATTACGCTGCTGATTACAATGAAACTACAGG +AGCTATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGTACTACTAAAACGGCGGCTAACCAACTTGGTGGCGCAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGCACAG +CCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACAC +GTTACGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAATTCCGCCATCACCAACCTGGGCAACACCGTAAACAACCTGA +CTTCTGCACGTAGCCGTATCGAAGATTCTGACTACGCGACTGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCGGGGACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCACAAAACGTGCTGTCTCTGTTACGTTAA +>fljB_e,n,x_Salmonella.enterica_Bonn_AY353308_e__1506 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT +CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGATATTAAAGCTGCATTAGGCAACCCGA +CAGTAACTGGCGATACATTGACTGCCGCCGTATCCTTTAAGGATGGTAAATATTATGCCACTGTAAGTGGTTATACCGAT +GCGGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGCTACAGGGGCTGTATCATTCGGTGCTACCCC +AACTAAATCTACTGTTACAGGTGATACCGCTGTTACTAAGGTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCCACGA +AAAAAGCCTTACAAGATGGGGGCGTTTCATCTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAA +AATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCTGCAGATTACGATGAAGCGACAGG +AGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG +ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCATGATTTCAAAGCACAA +CCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCTGGCGCAGGTGGATGC +GCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCTGCTATCACCAACCTGGGCAATACCGTAAACAACCTGT +CTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG +GCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA +>fljB_1,7_Salmonella.enterica_from-cdc_Stk1415_1__1521 +TTAACGTAACAGCGACAGCACGTTTTGCGGGACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGTTGCAGAATCT +GCGCGCGAGACATGTTGGAAACTTCAGTCGCATAGTCGGAATCTTCGATACGGCTACGCGCTTCAGACAGGTTGTTTACA +GTATTGCCCAGGTTGGTGATAGCGGAGTTGAAACGGTTCTGTACCGCACCCAGATCAGAACGCAGCGCATCAACCTGCGC +CAGCGCGGCATCAATTTTCTGCAGTGGGTTTTCGGTGGTTTTAGCGGCTGCTTCCGCCAGCTCTGGCTGTGCTTTGAAAT +CATGACCCGCGGCTTTGCTGGCATTATAGGTTTTACCGTCGATAGTAACGACTTCGGTTTTTCCGTCTACGCCGCCAAGT +TGGTTAGCCGCAGTTTTGGTAGTACCGTCAGCAGCAGTATAACTTGTGGTTTTAGCTTTAATGGCTCCTGTCGTTTCATC +GTAATCTGCGGCGTAATACTTATCGCCAGCTTTAAGCGCATAACCGCCTTCAATTGTCTTACCATTTTTATCGGTATAAG +ACATTTTGACCAATGTCGCAGCATTTGCATCTGTAGTATCAACGCCAGCAGAAATTAAAGCATTTTTAGCATCGGCTGAT +ACAACTGCCGGTGTATCTTTTAATTCCTGCACTTCTGTTTTGGTTGCAGCACCTGCAGGCATTGTGGTTTTAGTTGCACC +CGTAGCAAGTGTAACTTTACCGTCAGTAGCAACGTTAACTTCATAATCGCCATTTTTGGCGGCATCAGCGCCAGTAAAAC +CACCGATAGTAACAAAATACTTGTTATTATCTGCGTCAAATTTAACCGCACTACCTGTTACACTAGGTGCACCATTCGTA +CCACCCGTAGCCGCTTTAATAGCTGCATCATCAAGGCCTGATACATCCAGTGTAGTACCATTATTGGCATAAGCTTTCGT +GGTTACTGCTGTATCTTTCACATCATACGCTTTCTGCACATTCAGTGAATCCAGACCCAGGGTCTGAGAGTTGATCTGCT +TCAGATCGATGTCGATAGTTTCACCGTCATTGGCGCCAACCTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACG +CCGTTGAACTGGGTCTGGCCGGATACACGGTCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTC +AGACTGGGAGTTGGTGCTGTTAGCAGACTGAACTGCCAGTTCACGCACGCGCTGCAGGTTGTTGTTGATTTCGTTCAGCG +CGCCTTCAGTGGTCTGCGCAATAGAAATACCGTCGTTAGCGTTACGGGAAGCCTGAGTCAGACCTTTAATGTTCGCGGTG +AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGACGCTCGATAGC +GGTGCCCAGAGCAGACTGGGATTTGTTCAGGTTATTCTGAGTCAGCAGCGACAGACTGTTAGTGTTGATTACTTGTGCCA +T +>fljB_1,5_Muenster_DTU-unknown(tail&head may be fliC due to extract by mapping)_1__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGCCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +CACGAAAACTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCCATCAAAGCGGCCATAGGTG +GTACGACTGGTACGCCTGCTGTAACGGGCGGTACAGTTAAATTTGACGCAGATAATAATAAGTATTTTGTTTCTATTGGT +GGCTATACTGGTGCTGATGCATCCAAAAATGGCGATTATGAAGTTAACGTTGCTGCTGACGGTAAAGTTACACTTGCTAC +AGGTGCAACTAAAACCACAATACCGGCAGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCAACAGTTG +TTTCAGCAGATGCGAAAAATGCCTTAATCGCTGGCGGCGTGGATGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCGCTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCCGCTGGTCAT +GATTTCAAAGCACAACCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTACAGAACCGTTTTAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fljB_1,7_Salmonella.enterica_Nola_AY353298_1__1521 +ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATTAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAAACTACTGAAGGT +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTGAAAGATACAGCAGTAAC +AACGAAAGCTTATGCCAATAATGGTACTACACTGGATGTATCGGGTCTTGATGATGCAGCTATTAAAGCGGCTACGGGTG +GTACGAATGGTGCACCTAGTGTAACAGGTAGTGCGGTTAAATTTGACGCAGATAATAACAAGTACTTTGTTACTATTGGT +GGCTTTACTGGTGCTGATCTCGACAAAAATGGCGATTATGAAGTTAACGTTGCTACTGACGGTACAGTAACCCTTGCGGC +TGGCGCAACTAAAACCACAATGCCTGCTGGTGCGACAACTAAAACAGAAGTACAGGAGTTAAAAGATACACCGGCAGTTG +TTTCAGCAGATGCTAAAAATGCCTTAATTGCTGGCGGCGTTGACGCTACCGATGCTAATGGCGCTGAGTTGGTCAAAATG +TCTTATACCGATAAAAATGGTAAGACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACCGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACCTATAATGCCAGCAAAGCCGCTGGTCAT +GATTTTAAAGCACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCCGCGCT +GGCGCAGGTTGATGCGCTGCGCTCTGACCTGGGTGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTCTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTA +A +>fliC_g,m_Enteritidisstr_ALHD01000038_g,m__1507 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGCT +TCACTTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAAGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +ATCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGCAGCACCGGATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGATCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAAGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTGATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTGCCACTGGCGCGACGGATGTT +AATGCTGCTACCTTACAATCAAGACAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCA +AAAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAGGGCGAAAGTAAAATTACAGTAAATGGGGCT +GAATATACTGCTAACGCCACGGGTGATAAGATCACCTTAGCTGGCAAAACCATGTTTATTGATAAAACAGCTTCTGGCGT +AAGTACATTAATCAATGAAGACGCTGCCGCAGCCAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGT +CAAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACG +GTAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCA +GATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_r_Salmonella.enterica_IIIb.38:r:e,n,x,z15_AY353462_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATCGACATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCCGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAAACCGTTTAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_y_Salmonella.enterica_Giza_AY353465_other.y__1521 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAAAATATGATGTTGATAACACGGTTGTCAC +GAACCCTAATTATGTTGATGGTGCAGCGTTAAGCACTACGATGCCTACTGCGGCTGAGATTAAAACGGCTATTGGCACTG +GTGCGGGAACTCCGGCAGTTAAAGGTAATGAAGTTCAATTTGATAAGAGCACTGGGAAGTATTACGTTGAAATTGAAGGA +TATTCAGCTCCTGATGCAGCTAAAAACGGCATTTATGAAGCCAAAGTTGCTGATGATGGCACAATATCTTTGGAGACTGG +GACCAAAAAAATTGGCACCGCAATGCCTGCTGGTGCTGAAGTTATTACTCACGTGCAGAAAAAAGATCAACCAGTTGTTG +TTGATGCCAGCGTTAAAGATGCTCTAAAAGCTGGTGGGGTAGATGATGCAGTTGCAGATACCGCGCAATTAGTCAAAATG +TCTTACACTGATAAGAATGGTAAAACAATTGAAGGCGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTA +CGATGAAGCGACAGGAGCAATTAAAGCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACC +AACTGGGTGGCGTAGACGGCAAAACCGAAGTTGTTACTATCGATGGTAAAACCTATAATGCCAGCAAAGCTGAAGGTCAC +AACTTTAAAGCACAGCCTGATCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGGCTAAAATTGATGCTGCTTT +GGCGCAGGTGGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATA +CCGTAAATAACCTGTCTTCTGCCCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCG +CAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTA +A +>fliC_r_Salmonella.enterica_IIIb.58:r:z53:z47_AY353461_r,i__1482 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCACTGGGCAC +CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACTGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATTTCTATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCTATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGTCAGACTCAGTTCAACG +GCGTGAAAGTTCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGCGCCAATGACGGTGAAACTATTGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTCACTGGCTATACAGATTCTGCTACTGCTATTGACAAATCTACGTTTGCTGCATCAGCAACTGCCTTAGGTGGTACTC +CTGCTATTACTGGTGATCTGAAGTTTGATGATACTACTGGAAAATATTACGCTGATGTTTCAGGTACTACGGCTAAAGAT +GGTGTTTATGAAGTAACAGTTGCAGCCGATGGAAAAGTCACTTTAACTGGCACACCAACAGGACCAATTACTGGTGGCTT +CCCTTCAACTGCAACAAAAGATGTTAAACAAACCCAGCAAGAAAACGCTGATTTGACAGAGGCCAAAGCCGCATTGACAG +CAGCGGGTGTTGCAGCGGCCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATTGATGGT +GGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGCTCCATAAGTATTAATACTACGAA +ATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTGTTTCTA +TTGGTGGTAAAACTTACGCTGCGAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCGGCTACC +ACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCGCTGGCACAGGTTGACACGTTACGTTCTGACCTGGGTGCGGT +ACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTATCGAAG +ATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCAGGGACTTCCGTTCTGGCGCAG +GCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Bandia_AY353421_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTCGACTCCATCCAGGCTGAAATCACCCAGCGTCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCGCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGATGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGATACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_i_Salmonella.enterica_Idikan_AY353422_r,i__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCAATTGCTAACCGTT +TCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAGGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTCCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAACAAAAATATAAGGTCAGCGATACGGCTGCAAC +TGTTACAGGATATGCCGATACTACGATTGCTTTAGACAATAGTACTTTTAAAGCCTCGGCTACTGGTCTTGGTGGTACTG +ACCAGAAAATTGATGGCGATTTAAAATTTGATGATACGACTGGAAAATATTACGCCAAAGTTACCGTTACGGGGGGAACT +GGTAAAGATGGCTATTATGAAGTTTCCGTTGATAAGACGAACGGTGAGGTGACTCTTGCTGGCGGTGCGACTTCCCCGCT +TACAGGTGGACTACCTGCGACAGCAACTGAGGATGTGAAAAATGTACAAGTTGCAAATGCTGATTTGACAGAGGCTAAAG +CCGCATTGACAGCAGCAGGTGTTACCGGCACAGCATCTGTTGTTAAGATGTCTTATACTGATAATAACGGTAAAACTATT +GATGGTGGTTTAGCAGTTAAGGTAGGCGATGATTACTATTCTGCAACTCAAAATAAAGATGGTTCCATAAGTATTAATAC +TACGAAATACACTGCAGATGACGGTACATCCAAAACTGCACTAAACAAACTGGGTGGCGCAGACGGCAAAACCGAAGTTG +TTTCTATTGGTGGTAAAACTTACGCTGCAAGTAAAGCCGAAGGTCACAACTTTAAAGCACAGCCTGATCTGGCGGAAGCG +GCTGCTACAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTGGCACAGGTTGACACGTTACGTTCTGACCTGGG +TGCGGTACAGAACCGTTTCAACTCCGCTATTACCAACCTGGGCAACACCGTAAACAACCTGACTTCTGCCCGTAGCCGTA +TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG +GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z4,z32_Salmonella.enterica_IIIa.18:z4,z32:-_AY353543_z4,z23__1269 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAATAAATCCCAGTCCGCTCTGGGCAC +CGCTATCGAGCGTCTCTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATCGCGCAGACTACCGAAGGC +GCATTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCAGCAAACGGCTCGAACTCTGGTTC +AGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG +GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTAACTAAAGGAATCGCAACCACTGTAAGCTCTGGAGC +TTCGGTAGTTGGTGATGTTAAGATCAAAGAAGCTGATTTCAAAGATGCAAAAACCGGCGGTCCGGCTGCGGATAAATTAT +CTCTGACACAAGATGATAAAGGCAATTACTTTGTCAAAGATGATACTGCTGCTGCAGCTAAATACTATGCAGCTACCGTA +GATACGACAACGGGTAAAATCAGTTTTGATTCGGATAAAGATGTAACAGCTAGCGCAGGGACACCAACAGCAGTGTCAAC +CCTATCACGCGAAGTGAAATTTGATGGAGCAGATCTAAAAGCCGACCAGTCTTTAGTGAAATATAAAGATGATAAGGGTA +AAGATCTCTATGCTATCCAAACTTTGGATAAAGACGGAAATGCAAGTTTTAAATCTGTAACATTTTCCTCTGACGGTAAA +ACTACGGAGGGTACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGA +CGCATTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACGGTAAATAACC +TGTCTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAG +CAGGCCGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_f,g_Derbystr_AOZH01000145_g,m__1506 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCTCAGTCCTCACTGAGTTC +CGCTATTGAGCGTCTGTCCTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGCCAGGCGATTGCTAACCGTT +TCACGTCTAATATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGCATTTCTATTGCGCAGACCACTGAAGGT +GCGCTGAATGAAATCAACAACAACCTGCAGCGTGTGCGTGAGTTGTCTGTTCAGGCCACTAACGGGACTAACTCTGATTC +CGATCTGAAATCTATCCAGGATGAAATTCAGCAACGTCTGGAGGAAATCGATCGCGTTTCTAATCAGACTCAATTTAACG +GTGTTAAAGTCCTGTCTCAGGACAACCAGATGAAAATCCAGGTTGGTGCTAACGATGGTGAAACCATTACCATCGATCTG +CAAAAAATTGATGTGAAAAGCCTTGGCCTTGATGGGTTCAATGTTAATGGGCCAAAAGAAGCGACAGTGGGTGATCTGAA +GTCCAGCTTCAAGAATGTTACGGGTTACGACACCTATGCAGCGGGTGCCGATAAATATCGTGTAGATATTAATTCCGGTG +CTGTAGTGACTGATGCAGTAGCACCGAATAAAGTATATGTAAATGCAGCAAACGGTCAGTTAACAACTGACGATGCGGAA +AATAACACTGCGGTTGACCTCTTTAAGACCACTAAATCTACTGCTGGTACCGCTGAAGCCAAAGCGATAGCTGGTGCCAT +TAAGGGTGGTAAGGAAGGAGATACCTTTGATTATAAAGGCGTGACTTTTACTATTGATACAAAAACTGGTAATGACGGTA +ATGGTAAGGTTTCTACTACCATCAATGGTGAAAAAGTTACGTTAACTGTCGCTGATATTACCAGTGGTGCGGCGAATGTT +GATGCTGCTACCTTACAATCAAGCAAAAATGTTTATACATCTGTAGTGAACGGTCAGTTTACTTTTGATGATAAAACCAA +AAACGAGAGTGCGAAACTTTCTGATTTGGAAGCAAACAATGCTGTTAAAGGCGAAAGTAAAATTACAGTAAACGGGGCTG +AATATACTGCTAACGCCACGGGTGATAAGGTCACCTTAGCAGGCAAAACCATGTTTATTGACAAAACAGCTTCTGGCGTT +AGTACATTAATCAATGAAGACGCTGCCGCTGCTAAGAAAAGTACCGCTAACCCACTGGCTTCAATTGATTCTGCATTGTC +AAAAGTGGACGCAGTTCGTTCTTCTCTGGGGGCAATTCAAAACCGTTTTGATTCAGCCATTACCAACCTTGGCAATACGG +TAACCAATCTGAACTCCGCGCGTAGCCGTATCGAAGATGCTGACTATGCAACGGAAGTTTCTAATATGTCTAAAGCGCAG +ATTCTGCAGCAGGCTGGTACTTCCGTTCTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCT +>fliC_z38_Salmonella.enterica_Lille_AY353488_z36,z38__1266 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC +TGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCGAACGACGGTATTTCCATTGCGCAGACCACTGAAGGC +GCGTTGAATGAAATCAACAACAACCTGCAGCGCGTGCGCGAACTGTCCGTCCAGGCAGCAAACGGCTCGAACTCTGATTC +TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAGCAAACCGATTTTAACG +GGAAAAAAGTCTTAAGCCAGGATGGACAGTTGACCATTCAGGTTGGGGCGAATGACGGCGAAACTATCACAATCGATCTT +CAGAAAATCGATAAAACCGAGCTGGGTTTAGATAAATTAGATGTGACTAAAGGGATTGCCACAACCGTTAAAGAAGGTAC +GAAGCTTACAGCCGATTTTGCAGTTAAGGATGCCGATTTTGATGATAAATCAACTGGTACAAAAGTAACTGCAAACTTAG +AATTAAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT +GCTACAGGTAAAATAGAATTTACTTCTGGGACAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC +TTTGTCCAAAGAAGTAACGATAGATAGTGGACTTACGGATGATAAATCATTAGTAAAATACAAAGGGGATAATGGTAAAG +AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTA +ACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATCGATGATGCGCTTAAAACCGTTGACGC +TTTCCGTAGCCAGTTGGGGGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGT +CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTTTCCAACATGTCTCGTGCGCAGATTCTGCAGCAG +GCAGGGACGTCCGTACTGGCGCAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA +>fliC_z35_Salmonella.enterica_Tienba_AY353481_other.z35__1488 +ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTGCTCTGGGTAC +CGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT +TTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGACGGTATCTCCATTGCGCAGACCACTGAAGGC +GCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTGAACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTC +TGACCTTGACTCCATCCAAGCTGAAATCACCCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACG +GCGTGAAAGTGCTGGCGCAGGACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTG +AAGCAGATCAACTCTCAGACCCTGGGTCTGGATACGCTGAATGTTCAGAAAAAATATGATGTGAAGAGTGAAGCCGTCAC +GCCTCCGGCAAAACTTGATATTACAGGATTAACTGGAGCTGATATTAAAACTGGCGTTGATGGCGCTACGGTTGATACTG +GCTCAATTAAAGATGGCAAAGTTTATTATAATAGTACTTCTAAGGACTATTACGTACAGGTTGATTTTGGTACATCAGCT +GATGCTGCTAAGAGCGGTTACTATAAGGTCAATGTTAATGATGATGGTACAGTCTCAATGACGGCTGATACCACCAAAGA +AGCTACAACTCCTACTGATATTACTGAAGTTACTCAAGTTCAAAAACCTGTAGCTGCTCCAGCCGCTATCCAGGACCAGT +TGACTGCCGCTCATGTCACCGGGGCTGATACAGCTGAAATGGTCAAGATGTCTTATACGGATAAAAACGGTAAGACGATT +GATGGCGGCTTCGGTGTTAAAGTTGGAGACGATATTTATGCTGCAACTAAGAATAAAGATGGTTCTTTTAGTATCAACAC +CACGAAATATACCGATAAAGACGGTAATACCCAAACTGCATTGAACAAACTTGGTGGTGTAGACGGTAAAACTGAAGTTG +TTTCGATTGAAGGTAAAACCTACACTGCAGCGAAAGCAAAAGATCACGATTTCAAAGCGCAGCCAGAGCTGGCAGAAGCG +GCTACTGCAACCACCGAAAACCCGCTGCAGAAAATTGATGCTGCTTTAGCACAGGTTGATGCGCTGCGTTCTGACCTGGG 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/lib/version.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1 @@ +SeqSero2_version = '1.1.1'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/Initial_Conditions.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,109 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 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9,46:b:e,n,x', u'Linguere', u'Frederiksberg', u'Accra', u'Worb', u'Zadar', u'Cheltenham', u'Montaigu', u'Georgia', u'Lockleaze', u'Ibadan', u'Wagenia', u'Niederoderwitz', u'Ede', u'II 43:b:z42', u'Tambacounda', u'Kande', u'II 4,12:b:1,5', u'Broughton', u'Kolar', u'II 42:b:1,5', u'Canada', u'Kotte', u'Leopoldville', u'Ohio', u'II 6,7:b:[e,n,x]', u'Koumra', u'II [1],4,[5],12,[27]:b:[e,n,x]', u'Orbe', u'II 6,7:b:z39', u'Elbeuf', u'Vaugirard', u'Sedgwick', u'Wa', u'Melaka', u'Hull', u'Kirkee', u'Dahra', u'Mattenhof', u'II 17:b:e,n,x,z15', u'Wandsworth', u'II 17:b:z6', u'Glasgow', u'48:b:-', u'II 48:b:e,n,x,z15', u'II 48:b:z6', u'Shahalam', u'Riogrande', u'Saugus', u'Johannesburg', u'Duval', u'Benguella', u'II 40:b:-', u'Bignona', u'Paratyphi B', u'II 38:b:1,2', u'IV 50:b:-', u'II 50:b:z6', u'Rochdale', u'Rittersbach', u'Sica', u'Vietnam', u'Gnesta', u'VI 41:b:1,7', u'Abidjan', u'Limete', u'Adime', u'II 16:b:z42', u'II 16:b:z39', u'Malstatt', u'Visby', u'Edinburg', u'Brazzaville', u'Vegesack', u'Sangera', u'II 16:b:e,n,x', u'Hvittingfoss', u'II 41:b:1,5', u'Pharr', u'Eboko', u'Tonev', u'Sanga', u'Kuntair', u'Tucson', u'IIIb (6),14:b:e,n,x', u'Schleissheim (Schleissheim is extremely rare)', u'II 3,10:b:e,n,x', u'Atento', u'Leeuwarden', u'Wohlen', u'Korbol', u'VI 11:b:e,n,x', u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II [1],4,12,[27]:g,[m],[s],t:e,n,x', u'II 6,7:g,[m],s,t:[z42]', u'II 11:g,[m],s,t:z39', u'II 50:g,[m],s,t:[1,5]', u'II 57:g,[m],s,t:z42', u'II [1],4,12,[27]:g,[m],t:[1,5]', u'Senftenberg', u'II [1],13,23:g,[s],t:z42', u'Okatie', u'Enteritidis', u'Luke', u'Abadina', u'Yardley', u'Warragul', u'Bijlmer', u'Abuja', u'Bron', u'Essen', u'Hillingdon', u'Nitra', u'Suberu', u'Pontypridd', u'Montevideo', u'Korovi', u'Chincol', u'Gamaba', u'Tornow', u'Agbeni', u'II 6,7:g,m,[s],t:e,n,x', u'II [1],9,12:g,m,[s],t:[1,5,7]', u'II [1],13,23:g,m,[s],t:[e,n,x]', u'II 43:g,m,[s],t:[z42]', u'Godesberg', u'Othmarschen', u'Adeoyo', u'Kouka', u'Blegdam', u'Hato', u'Gueuletapee', u'Amsterdam', u'Nikolaifleet', u'Macclesfield', 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+ +remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] + +rename_dict={'Nitra': 'Enteritidis', + 'Kiel': 'Dublin', + 'Koessen': 'Panama', + 'Phaliron': 'Kalumburu', + 'Istanbul': 'Hadar', + 'Haardt': 'Blockley', + 'Ferruch': 'Kottbus', + 'Sanga': 'Eboko', + 'Pakistan': 'Litchfield', + 'Bellevue': 'Lezennes', + 'Sunnycove': 'Daarle', + 'Noya': 'Akanji', + 'Virginia': 'Muenchen', + 'Djelfa': 'Skansen', + 'Konstanz': 'Gatuni', + 'Bardo': 'Newport', + 'Houston': 'Panama', + 'Martonos': 'Finkenwerder', + 'Midway': 'Florida', + 'Lindern': 'Charity', + 'Bahrenfeld': 'Onderstepoort', + 'Schalkwijk': 'Moussoro', + 'Amberg': 'Boecker', + 'Madelia': 'Carrau', + 'Soahanina': 'Sundsvall', + 'Stafford': 'Poano', + 'Chichiri': 'Uzaramo', + 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', + 'Hindmarsh':'Bovismorbificans', + 'Yovokome': 'Manhattan'} + + #potential merge for O22 and O23 + #'Ibadan': 'Mississippi', + #'Bracknell': 'Oudwijk', + #'Vaertan': 'Ullevi', + #'Bahati': 'Durham', + #'Wichita': 'Friedenau', + #'Diguel': 'Telelkebir', + #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', + #'Washington': 'Kintambo', + #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', + #'Serenli': 'Winslow', + #'Farmsen': 'Poona', + #'Durance': 'Ivrysurseine', + #'Agoueve': 'Cubana', + #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', + #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', + #'Picpus': 'Mampong', + #'Anna': 'Nimes', + #'Fanti': 'Leiden', + #'Ried': 'Ajiobo', + + #potential O68 list + #'Djelfa': 'Skansen', + #'Korbol': 'Nagoya', + #'Sanga': 'Eboko', + #'Konstanz': 'Gatuni', + #'Presov': 'Shipley', + #'Heistopdenberg': 'Bukuru', + #'Tounouma': 'Banalia', + #'Gaillac': 'Utah', + #'Santiago': 'Belem', + #'Virginia': 'Muenchen', + #'Yovokome': 'Manhattan', + #'Portanigra': 'Dunkwa', + #'Bardo': 'Newport', + #'Ferruch': 'Kottbus', + #'Alminko': 'Nanergou', + #'Bargny': 'Takoradi', + #'Magherafelt': 'Cyprus', + #'Haardt': 'Blockley', + #'Pakistan': 'Litchfield', + #'Yokoe': 'Bassa', + #'Noya': 'Akanji', + #'Lamphun': 'Giza', + #'Tananarive': 'Brunei', + #'Inchpark': 'Alagbon', + #'Sunnycove': 'Daarle', + #'Sindelfingen': 'Benue', + #'Phaliron': 'Kalumburu', + #'Bazenheid': 'Zerifin', + #'Paris': 'Mapo', + #'Istanbul': 'Hadar', + #'Chomedey': 'Glostrup', + #'Wippra': 'Molade', + #'Uno': 'Tamale', + #'Kolda': 'Yarm', + #'Bellevue': 'Lezennes', + #'Albany':'Duesseldorf'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/SeqSero2_package.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,1576 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +import sys +import time +import random +import os +import subprocess +import gzip +import io +import pickle +import argparse +import itertools +from distutils.version import LooseVersion +from distutils.spawn import find_executable +sys.path.insert(1,sys.path[0]+'/..') + +try: + from .version import SeqSero2_version +except Exception: #ImportError + from version import SeqSero2_version + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='SeqSero2_package.py -t <data_type> -m <mode> -i <input_data> [-d <output_directory>] [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com\n\nVersion: v1.1.1')#add "-m <data_type>" in future + parser.add_argument("-i",nargs="+",help="<string>: path/to/input_data",type=os.path.abspath) ### add 'type=os.path.abspath' to generate absolute path of input data. + parser.add_argument("-t",choices=['1','2','3','4','5','6'],help="<int>: '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6' for nanopore fastq") + parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default 'mem' mode") + parser.add_argument("-p",default="1",help="<int>: number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1") + parser.add_argument("-m",choices=['k','a'],default="a",help="<string>: which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a") + parser.add_argument("-n",help="<string>: optional, to specify a sample name in the report output") + parser.add_argument("-d",help="<string>: optional, to specify an output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number") + parser.add_argument("-c",action="store_true",help="<flag>: if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files") + parser.add_argument("-s",action="store_true",help="<flag>: if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv") + parser.add_argument("--check",action="store_true",help="<flag>: use '--check' flag to check the required dependencies") + parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SeqSero2_version) + return parser.parse_args() + +### check paths of dependencies +check_dependencies = parse_args().check +dependencies = ['bwa','samtools','blastn','fastq-dump','spades.py','bedtools','SalmID.py'] +if check_dependencies: + for item in dependencies: + ext_path = find_executable(item) + if ext_path is not None: + print ("Using "+item+" - "+ext_path) + else: + print ("ERROR: can not find "+item+" in PATH") + sys.exit() +### end of --check + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + + +def multifasta_single_string(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') + if (len(line.strip()) > 0) and (line.strip()[0] != '>') + ] + return ''.join(multifasta_list) + + +def chunk_a_long_sequence(long_sequence, chunk_size=60): + chunk_list = [] + steps = len(long_sequence) // 60 #how many chunks + for i in range(steps): + chunk_list.append(long_sequence[i * chunk_size:(i + 1) * chunk_size]) + chunk_list.append(long_sequence[steps * chunk_size:len(long_sequence)]) + return chunk_list + + +def target_multifasta_kmerizer(multifasta, k, kmerDict): + forward_length = 300 #if find the target, put forward 300 bases + reverse_length = 2200 #if find the target, put backward 2200 bases + chunk_size = 60 #it will firstly chunk the single long sequence to multiple smaller sequences, it controls the size of those smaller sequences + target_mers = [] + long_single_string = multifasta_single_string(multifasta) + multifasta_list = chunk_a_long_sequence(long_single_string, chunk_size) + unit_length = len(multifasta_list[0]) + forward_lines = int(forward_length / unit_length) + 1 + reverse_lines = int(forward_length / unit_length) + 1 + start_num = 0 + end_num = 0 + for i in range(len(multifasta_list)): + if i not in range(start_num, end_num): #avoid computational repetition + line = multifasta_list[i] + start = int((len(line) - k) // 2) + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + if i - forward_lines >= 0: + start_num = i - forward_lines + else: + start_num = 0 + if i + reverse_lines <= len(multifasta_list) - 1: + end_num = i + reverse_lines + else: + end_num = len(multifasta_list) - 1 + target_list = [ + x.strip() for x in multifasta_list[start_num:end_num] + ] + target_line = "".join(target_list) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(target_line)], k) + ] ##changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + else: + pass + return set(target_mers) + + +def target_read_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = [] + if file.endswith(".gz"): + file_content = io.BufferedReader(gzip.open(file)) + else: + file_content = open(file, "r").readlines() + for line in file_content: + start = int((len(line) - k) // 2) + if i % 4 == 2: + if file.endswith(".gz"): + s1 = line[start:k + start].decode() + line = line.decode() + else: + s1 = line[start:k + start] + if s1 in kmerDict: #detect it is a potential read or not (use the middle part) + n_reads += 1 + total_coverage += len(line) + target_mers += [ + k1 for k1 in createKmerDict_reads([str(line)], k) + ] #changed k to k1, just want to avoid the mixes of this "k" (kmer) to the "k" above (kmer length) + i += 1 + if total_coverage >= 4000000: + break + return set(target_mers) + + +def minion_fasta_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 2 == 0: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def minion_fastq_kmerizer(file, k, kmerDict): + i = 1 + n_reads = 0 + total_coverage = 0 + target_mers = {} + for line in open(file): + if i % 4 == 2: + for kmer, rc_kmer in kmers(line.strip().upper(), k): + if (kmer in kmerDict) or (rc_kmer in kmerDict): + if kmer in target_mers: + target_mers[kmer] += 1 + else: + target_mers[kmer] = 1 + if rc_kmer in target_mers: + target_mers[rc_kmer] += 1 + else: + target_mers[rc_kmer] = 1 + i += 1 + return set([h for h in target_mers]) + + +def multifasta_single_string2(multifasta): + single_string = '' + with open(multifasta, 'r') as f: + for line in f: + if line.strip()[0] == '>': + pass + else: + single_string += line.strip() + return single_string + + +def kmers(seq, k): + rev_comp = reverse_complement(seq) + for start in range(1, len(seq) - k + 1): + yield seq[start:start + k], rev_comp[-(start + k):-start] + + +def multifasta_to_kmers_dict(multifasta,k_size):#used to create database kmer set + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], k_size)]) + return lib_dict + + +def Combine(b, c): + fliC_combinations = [] + fliC_combinations.append(",".join(c)) + temp_combinations = [] + for i in range(len(b)): + for x in itertools.combinations(b, i + 1): + temp_combinations.append(",".join(x)) + for x in temp_combinations: + temp = [] + for y in c: + temp.append(y) + temp.append(x) + temp = ",".join(temp) + temp = temp.split(",") + temp.sort() + temp = ",".join(temp) + fliC_combinations.append(temp) + return fliC_combinations + + +def seqsero_from_formula_to_serotypes(Otype, fliC, fljB, special_gene_list,subspecies): + #like test_output_06012017.txt + #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list) + from Initial_Conditions import phase1,phase2,phaseO,sero,subs,remove_list,rename_dict + rename_dict_not_anymore=[rename_dict[x] for x in rename_dict] + rename_dict_all=rename_dict_not_anymore+list(rename_dict) #used for decide whether to + seronames = [] + seronames_none_subspecies=[] + for i in range(len(phase1)): + fliC_combine = [] + fljB_combine = [] + if phaseO[i] == Otype: # no VII in KW, but it's there + ### for fliC, detect every possible combinations to avoid the effect of "[" + if phase1[i].count("[") == 0: + fliC_combine.append(phase1[i]) + elif phase1[i].count("[") >= 1: + c = [] + b = [] + if phase1[i][0] == "[" and phase1[i][-1] == "]" and phase1[i].count( + "[") == 1: + content = phase1[i].replace("[", "").replace("]", "") + fliC_combine.append(content) + fliC_combine.append("-") + else: + for x in phase1[i].split(","): + if "[" in x: + b.append(x.replace("[", "").replace("]", "")) + else: + c.append(x) + fliC_combine = Combine( + b, c + ) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t + ### end of fliC "[" detect + ### for fljB, detect every possible combinations to avoid the effect of "[" + if phase2[i].count("[") == 0: + fljB_combine.append(phase2[i]) + elif phase2[i].count("[") >= 1: + d = [] + e = [] + if phase2[i][0] == "[" and phase2[i][-1] == "]" and phase2[i].count( + "[") == 1: + content = phase2[i].replace("[", "").replace("]", "") + fljB_combine.append(content) + fljB_combine.append("-") + else: + for x in phase2[i].split(","): + if "[" in x: + d.append(x.replace("[", "").replace("]", "")) + else: + e.append(x) + fljB_combine = Combine(d, e) + ### end of fljB "[" detect + new_fliC = fliC.split( + "," + ) #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings + new_fliC.sort() + new_fliC = ",".join(new_fliC) + new_fljB = fljB.split(",") + new_fljB.sort() + new_fljB = ",".join(new_fljB) + if (new_fliC in fliC_combine + or fliC in fliC_combine) and (new_fljB in fljB_combine + or fljB in fljB_combine): + ######start, remove_list,rename_dict, added on 11/11/2018 + if sero[i] not in remove_list: + temp_sero=sero[i] + if temp_sero in rename_dict: + temp_sero=rename_dict[temp_sero] #rename if in the rename list + if temp_sero not in seronames:#the new sero may already included, if yes, then not consider + if subs[i] == subspecies: + seronames.append(temp_sero) + seronames_none_subspecies.append(temp_sero) + else: + pass + else: + pass + ######end, added on 11/11/2018 + #analyze seronames + subspecies_pointer="" + if len(seronames) == 0 and len(seronames_none_subspecies)!=0: + # ed_SL_12182019: modified to fix the subspecies output problem + #seronames=seronames_none_subspecies + seronames=["N/A"] + #subspecies_pointer="1" + subspecies_pointer="0" + if len(seronames) == 0: + seronames = [ + "N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)" + ] + star = "" + star_line = "" + if len(seronames) > 1: #there are two possible predictions for serotypes + star = "*" + #changed 04072019 + #star_line = "The predicted serotypes share the same general formula:\t" + Otype + ":" + fliC + ":" + fljB + "\n" + if subspecies_pointer=="1" and len(seronames_none_subspecies)!=0: + star="*" + star_line="The predicted O and H antigens correspond to serotype '"+(" or ").join(seronames)+"' in the Kauffmann-White scheme. The predicted subspecies by SalmID (github.com/hcdenbakker/SalmID) may not be consistent with subspecies designation in the Kauffmann-White scheme. " + star_line + #star_line="The formula with this subspieces prediction can't get a serotype in KW manual, and the serotyping prediction was made without considering it."+star_line + if Otype=="": + Otype="-" + predict_form = Otype + ":" + fliC + ":" + fljB + predict_sero = (" or ").join(seronames) + ###special test for Enteritidis + if predict_form == "9:g,m:-": + sdf = "-" + for x in special_gene_list: + if x.startswith("sdf"): + sdf = "+" + #star_line="Detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene detected. " + #predict_form = predict_form + " Sdf prediction:" + sdf + predict_form = predict_form #changed 04072019 + if sdf == "-": + star = "*" + #star_line="Didn't detected sdf gene, a marker to differentiate Gallinarum and Enteritidis" + star_line="sdf gene not detected. " + #changed in 04072019, for new output + #star_line = "Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n" + #predict_sero = "Gallinarum/Enteritidis" #04132019, for new output requirement + predict_sero = "Gallinarum or Enteritidis" + ###end of special test for Enteritidis + elif predict_form == "4:i:-": + predict_sero = "I 4,[5],12:i:-" # change serotype name + elif predict_form == "4:r:-": + predict_sero = "N/A (4:r:-)" + elif predict_form == "4:b:-": + predict_sero = "N/A (4:b:-)" + #elif predict_form == "8:e,h:1,2": #removed after official merge of newport and bardo + #predict_sero = "Newport" + #star = "*" + #star_line = "Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare." + claim = "The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.\n" + if "N/A" in predict_sero: + claim = "" + #special test for Typhimurium + if "Typhimurium" in predict_sero or predict_form == "4:i:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "oafA-O-4_full" in x: + normal = float(special_gene_list[x]) + elif "oafA-O-4_5-" in x: + mutation = float(special_gene_list[x]) + if normal > mutation: + pass + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(O5-)" + predict_sero = predict_sero.strip() #diable special sero for new output requirement, 04132019 + star = "*" + #star_line = "Detected the deletion of O5-." + star_line = "Detected a deletion that causes O5- variant of Typhimurium. " + else: + pass + #special test for Paratyphi B + if "Paratyphi B" in predict_sero or predict_form == "4:b:-": + normal = 0 + mutation = 0 + for x in special_gene_list: + if "gntR-family-regulatory-protein_dt-positive" in x: + normal = float(special_gene_list[x]) + elif "gntR-family-regulatory-protein_dt-negative" in x: + mutation = float(special_gene_list[x]) + #print(normal,mutation) + if normal > mutation: + #predict_sero = predict_sero.strip() + "(dt+)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip()+' var. L(+) tartrate+' if "Paratyphi B" in predict_sero else predict_sero.strip() + star = "*" + #star_line = "Didn't detect the SNP for dt- which means this isolate is a Paratyphi B variant L(+) tartrate(+)." + star_line = "The SNP that causes d-Tartrate nonfermentating phenotype of Paratyphi B was not detected. " + elif normal < mutation: + #predict_sero = predict_sero.strip() + "(dt-)" #diable special sero for new output requirement, 04132019 + predict_sero = predict_sero.strip() + star = "*" + #star_line = "Detected the SNP for dt- which means this isolate is a systemic pathovar of Paratyphi B." + star_line = "Detected the SNP for d-Tartrate nonfermenting phenotype of Paratyphi B. " + else: + star = "*" + #star_line = " Failed to detect the SNP for dt-, can't decide it's a Paratyphi B variant L(+) tartrate(+) or not." + star_line = " " ## ed_SL_05152019: do not report this situation. + #special test for O13,22 and O13,23 + if Otype=="13": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019 + f = open(ex_dir + '/special.pickle', 'rb') + special = pickle.load(f) + O22_O23=special['O22_O23'] + if predict_sero.split(" or ")[0] in O22_O23[-1] and predict_sero.split(" or ")[0] not in rename_dict_all:#if in rename_dict_all, then it means already merged, no need to analyze + O22_score=0 + O23_score=0 + for x in special_gene_list: + if "O:22" in x: + O22_score = O22_score+float(special_gene_list[x]) + elif "O:23" in x: + O23_score = O23_score+float(special_gene_list[x]) + #print(O22_score,O23_score) + for z in O22_O23[0]: + if predict_sero.split(" or ")[0] in z: + if O22_score > O23_score: + star = "*" + #star_line = "Detected O22 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[0] + elif O22_score < O23_score: + star = "*" + #star_line = "Detected O23 specific genes to further differenciate '"+predict_sero+"'." #diabled for new output requirement, 04132019 + predict_sero = z[1] + else: + star = "*" + #star_line = "Fail to detect O22 and O23 differences." #diabled for new output requirement, 04132019 + if " or " in predict_sero: + star_line = star_line + "The predicted serotypes share the same general formula: " + Otype + ":" + fliC + ":" + fljB + "." + #special test for O6,8 + #merge_O68_list=["Blockley","Bovismorbificans","Hadar","Litchfield","Manhattan","Muenchen"] #remove 11/11/2018, because already in merge list + #for x in merge_O68_list: + # if x in predict_sero: + # predict_sero=x + # star="" + # star_line="" + #special test for Montevideo; most of them are monophasic + #if "Montevideo" in predict_sero and "1,2,7" in predict_form: #remove 11/11/2018, because already in merge list + #star="*" + #star_line="Montevideo is almost always monophasic, having an antigen called for the fljB position may be a result of Salmonella-Salmonella contamination." + return predict_form, predict_sero, star, star_line, claim +### End of SeqSero Kmer part + +### Begin of SeqSero2 allele prediction and output +def xml_parse_score_comparision_seqsero(xmlfile): + #used to do seqsero xml analysis + from Bio.Blast import NCBIXML + handle=open(xmlfile) + handle=NCBIXML.parse(handle) + handle=list(handle) + List=[] + List_score=[] + List_ids=[] + List_query_region=[] + for i in range(len(handle)): + if len(handle[i].alignments)>0: + for j in range(len(handle[i].alignments)): + score=0 + ids=0 + cover_region=set() #fixed problem that repeated calculation leading percentage > 1 + List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def) + for z in range(len(handle[i].alignments[j].hsps)): + hsp=handle[i].alignments[j].hsps[z] + temp=set(range(hsp.query_start,hsp.query_end)) + if len(cover_region)==0: + cover_region=cover_region|temp + fraction=1 + else: + fraction=1-len(cover_region&temp)/float(len(temp)) + cover_region=cover_region|temp + if "last" in handle[i].query or "first" in handle[i].query: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + else: + score+=hsp.bits*fraction + ids+=float(hsp.identities)/handle[i].query_length*fraction + List_score.append(score) + List_ids.append(ids) + List_query_region.append(cover_region) + temp=zip(List,List_score,List_ids,List_query_region) + Final_list=sorted(temp, key=lambda d:d[1], reverse = True) + return Final_list + + +def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number + Old=L + L.sort() + L = [L[i] for i in range(len(L)) if L[i] not in L[:i]] + count=[] + for j in range(len(L)): + y=0 + for x in Old: + if L[j]==x: + y+=1 + count.append(y) + if sort_on_fre!="none": + d=zip(*sorted(zip(count, L))) + L=d[1] + count=d[0] + return (L,count) + +def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list): + #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test + #this is mainly used for + a=nodes_vs_score_list + fliC_score=0 + fljB_score=0 + for z in a: + if "fliC" in z[0]: + fliC_score+=z[1] + elif "fljB" in z[0]: + fljB_score+=z[1] + if fliC_score>=fljB_score: + role="fliC" + else: + role="fljB" + return (role,abs(fliC_score-fljB_score)) + +def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list,Final_list_passed): + #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small) + #also used when no head or tail got blasted score for the contig + role="" + for z in Final_list_passed: + if node_name in z[0]: + role=z[0].split("_")[0] + break + return role + +def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list,Final_list_passed): + #nodes_list is the c created by c,d=Uniq(nodes) in below function + first_target="" + role_list=[] + for x in nodes_list: + a=[] + role="" + for y in tail_head_list: + if x in y[0]: + a.append(y) + if len(a)==4: + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + elif len(a)==3: + ###however, if the one with highest score is the fewer one, compare their accumulation score + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###end of above score comparison + elif len(a)==2: + #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37) + temp=[] + for z in a: + temp.append(z[0].split("_")[0]) + m,n=Uniq(temp)#should only have one choice, but weird situation might occur too + if len(m)==1: + pass + else: + pass + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation + elif len(a)==1: + #that one + role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a) + if diff<20: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0" + else:#a==0 + #use Final_list_passed best match + for z in Final_list_passed: + if x in z[0]: + role=z[0].split("_")[0] + break + #print x,role,len(a) + role_list.append((role,x)) + if len(role_list)==2: + if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase + #just use score to do a final test + role_list=[] + for x in nodes_list: + role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list,Final_list_passed) + role_list.append((role,x)) + return role_list + +def decide_contig_roles_for_H_antigen(Final_list,Final_list_passed): + #used to decide which contig is FliC and which one is fljB + contigs=[] + nodes=[] + for x in Final_list_passed: + if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]: + nodes.append(x[0].split("___")[1].strip()) + c,d=Uniq(nodes)#c is node_list + #print c + tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])] + roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list,Final_list_passed) + return roles + +def decide_O_type_and_get_special_genes(Final_list,Final_list_passed): + #decide O based on Final_list + O_choice="?" + O_list=[] + special_genes={} + nodes=[] + for x in Final_list_passed: + if x[0].startswith("O-"): + nodes.append(x[0].split("___")[1].strip()) + elif not x[0].startswith("fl"): + special_genes[x[0]]=x[2]#08172018, x[2] changed from x[-1] + #print "special_genes:",special_genes + c,d=Uniq(nodes) + #print "potential O antigen contig",c + final_O=[] + O_nodes_list=[] + for x in c:#c is the list for contigs + temp=0 + for y in Final_list_passed: + if x in y[0] and y[0].startswith("O-"): + final_O.append(y) + break + ### O contig has the problem of two genes on same contig, so do additional test + potenial_new_gene="" + for x in final_O: + pointer=0 #for genes merged or not + #not consider O-1,3,19_not_in_3,10, too short compared with others + if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])*x[2]+850 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 300*2 (for secureity can use 400*2) as flank region + pointer=x[0].split("___")[1].strip()#store the contig name + print(pointer) + if pointer!=0:#it has potential merge event + for y in Final_list: + if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])*1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])*y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O + potenial_new_gene=y + #print(potenial_new_gene) + break + if potenial_new_gene!="": + print("two differnt genes in same contig, fix it for O antigen") + print(potenial_new_gene[:3]) + pointer=0 + for y in final_O: + if y[0].split("___")[-1]==potenial_new_gene[0].split("___")[-1]: + pointer=1 + if pointer!=0: #changed to consider two genes in same contig + final_O.append(potenial_new_gene) + ### end of the two genes on same contig test + final_O=sorted(final_O,key=lambda x: x[2], reverse=True)#sorted + if len(final_O)==0 or (len(final_O)==1 and "O-1,3,19_not_in_3,10" in final_O[0][0]): + #print "$$$No Otype, due to no hit"#may need to be changed + O_choice="-" + else: + highest_O_coverage=max([float(x[0].split("_cov_")[-1].split("_")[0]) for x in final_O if "O-1,3,19_not_in_3,10" not in x[0]]) + O_list=[] + O_list_less_contamination=[] + for x in final_O: + if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis; to avoid contamination affect, use 0.15 of highest coverage as cut-off + O_list.append(x[0].split("__")[0]) + O_nodes_list.append(x[0].split("___")[1]) + if float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15: + O_list_less_contamination.append(x[0].split("__")[0]) + ### special test for O9,46 and O3,10 family + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list or "O-9,46_wzy_partial" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + else: + O_choice="O-9"#next, detect O9 vs O2? + O2=0 + O9=0 + for z in special_genes: + if "tyr-O-9" in z: + O9=special_genes[z] + elif "tyr-O-2" in z: + O2=special_genes[z] + if O2>O9: + O_choice="O-2" + elif O2<O9: + pass + else: + pass + #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility." + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score=0 + for x in final_O: + if x[2]>=max_score and float(x[0].split("_cov_")[-1].split("_")[0])>highest_O_coverage*0.15:#use x[2],08172018, the "coverage identity = cover_length * identity"; also meet coverage threshold + max_score=x[2]#change from x[-1] to x[2],08172018 + O_choice=x[0].split("_")[0] + if O_choice=="O-1,3,19": + O_choice=final_O[1][0].split("_")[0] + #print "$$$Most possilble Otype: ",O_choice + except: + pass + #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" + if O_choice=="O-9,46,27" and len(O_list)==2 and "O-4_wzx" in O_list: #special for very low chance sitatuion between O4 and O9,27,46, this is for serotypes like Bredeney and Schwarzengrund (normallly O-4 will have higher score, but sometimes sequencing quality may affect the prediction) + O_choice="O-4" + #print "O:",O_choice,O_nodes_list + Otypes=[] + for x in O_list: + if x!="O-1,3,19_not_in_3,10": + if "O-9,46_" not in x: + Otypes.append(x.split("_")[0]) + else: + Otypes.append(x.split("-from")[0])#O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254 + #Otypes=[x.split("_")[0] for x in O_list if x!="O-1,3,19_not_in_3,10"] + Otypes_uniq,Otypes_fre=Uniq(Otypes) + contamination_O="" + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + else: + contamination_O="potential contamination from O antigen signals" + return O_choice,O_nodes_list,special_genes,final_O,contamination_O,Otypes_uniq +### End of SeqSero2 allele prediction and output + +def get_input_files(make_dir,input_file,data_type,dirpath): + #tell input files from datatype + #"<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly),'5'(nanopore fasta),'6'(nanopore fastq)" + for_fq="" + rev_fq="" + os.chdir(make_dir) + if data_type=="1": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + rev_fq=input_file.replace(".sra","_2.fastq") + else: + core_id=input_file.split(".fastq")[0].split(".fq")[0] + for_fq=core_id+"_1.fastq" + rev_fq=core_id+"_2.fastq" + if input_file.endswith(".gz"): + subprocess.check_call("gzip -dc "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + else: + subprocess.check_call("cat "+input_file+" | "+dirpath+"/deinterleave_fastq.sh "+for_fq+" "+rev_fq,shell=True) + elif data_type=="2": + for_fq=input_file[0].split("/")[-1] + rev_fq=input_file[1].split("/")[-1] + elif data_type=="3": + input_file=input_file[0].split("/")[-1] + if input_file.endswith(".sra"): + subprocess.check_call("fastq-dump --split-files "+input_file,shell=True) + for_fq=input_file.replace(".sra","_1.fastq") + else: + for_fq=input_file + elif data_type in ["4","5","6"]: + for_fq=input_file[0].split("/")[-1] + os.chdir("..") + return for_fq,rev_fq + +def predict_O_and_H_types(Final_list,Final_list_passed,new_fasta): + #get O and H types from Final_list from blast parsing; allele mode + from Bio import SeqIO + fliC_choice="-" + fljB_choice="-" + fliC_contig="NA" + fljB_contig="NA" + fliC_region=set([0]) + fljB_region=set([0,]) + fliC_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + fljB_length=0 #can be changed to coverage in future; in 03292019, changed to ailgned length + O_choice="-"#no need to decide O contig for now, should be only one + O_choice,O_nodes,special_gene_list,O_nodes_roles,contamination_O,Otypes_uniq=decide_O_type_and_get_special_genes(Final_list,Final_list_passed)#decide the O antigen type and also return special-gene-list for further identification + O_choice=O_choice.split("-")[-1].strip() + if (O_choice=="1,3,19" and len(O_nodes_roles)==1 and "1,3,19" in O_nodes_roles[0][0]) or O_choice=="": + O_choice="-" + H_contig_roles=decide_contig_roles_for_H_antigen(Final_list,Final_list_passed)#decide the H antigen contig is fliC or fljB + #add alignment locations, used for further selection, 03312019 + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + H_contig_roles[i]+=H_contig_roles[i]+(y[-1],) + break + log_file=open("SeqSero_log.txt","a") + extract_file=open("Extracted_antigen_alleles.fasta","a") + handle_fasta=list(SeqIO.parse(new_fasta,"fasta")) + + #print("O_contigs:") + log_file.write("O_contigs:\n") + extract_file.write("#Sequences with antigen signals (if the micro-assembled contig only covers the flanking region, it will not be used for contamination analysis)\n") + extract_file.write("#O_contigs:\n") + for x in O_nodes_roles: + if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker + #print(x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%",str(min(x[-1]))+" to "+str(max(x[-1]))) + log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n") + title=">"+x[0].split("___")[-1]+" "+x[0].split("__")[0]+"; "+"blast score: "+str(x[1])+" identity%: "+str(round(x[2]*100,2))+"%; alignment from "+str(min(x[-1]))+" to "+str(max(x[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[0].split("___")[-1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if len(H_contig_roles)!=0: + highest_H_coverage=max([float(x[1].split("_cov_")[-1].split("_")[0]) for x in H_contig_roles]) #less than highest*0.1 would be regarded as contamination and noises, they will still be considered in contamination detection and logs, but not used as final serotype output + else: + highest_H_coverage=0 + for x in H_contig_roles: + #if multiple choices, temporately select the one with longest length for now, will revise in further change + if "fliC" == x[0] and len(x[-1])>=fliC_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13:#remember to avoid the effect of O-type contig, so should not in O_node list + fliC_contig=x[1] + fliC_length=len(x[-1]) + elif "fljB" == x[0] and len(x[-1])>=fljB_length and x[1] not in O_nodes and float(x[1].split("_cov_")[-1].split("_")[0])>highest_H_coverage*0.13: + fljB_contig=x[1] + fljB_length=len(x[-1]) + for x in Final_list_passed: + if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0]: + fliC_choice=x[0].split("_")[1] + elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]: + fljB_choice=x[0].split("_")[1] + elif fliC_choice!="-" and fljB_choice!="-": + break + #now remove contigs not in middle core part + first_allele="NA" + first_allele_percentage=0 + for x in Final_list: + if x[0].startswith("fliC") or x[0].startswith("fljB"): + first_allele=x[0].split("__")[0] #used to filter those un-middle contigs + first_allele_percentage=x[2] + break + additional_contigs=[] + for x in Final_list: + if first_allele in x[0]: + if (fliC_contig == x[0].split("___")[-1]): + fliC_region=x[3] + elif fljB_contig!="NA" and (fljB_contig == x[0].split("___")[-1]): + fljB_region=x[3] + else: + if x[1]*1.1>int(x[0].split("___")[1].split("_")[3]):#loose threshold by multiplying 1.1 + additional_contigs.append(x) + #else: + #print x[:3] + #we can just use the fljB region (or fliC depends on size), no matter set() or contain a large locations (without middle part); however, if none of them is fully assembled, use 500 and 1200 as conservative cut-off + if first_allele_percentage>0.9: + if len(fliC_region)>len(fljB_region) and (max(fljB_region)-min(fljB_region))>1000: + target_region=fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + elif len(fliC_region)<len(fljB_region) and (max(fliC_region)-min(fliC_region))>1000: + target_region=fliC_region|(fljB_region-set(range(min(fliC_region),max(fliC_region)))) #fljB_region|(fliC_region-set(range(min(fljB_region),max(fljB_region)))) + else: + target_region=set()#doesn't do anything + else: + target_region=set()#doesn't do anything + #print(target_region) + #print(additional_contigs) + target_region2=set(list(range(0,525))+list(range(1200,1700)))#I found to use 500 to 1200 as special region would be best + target_region=target_region2|target_region + for x in additional_contigs: + removal=0 + contig_length=int(x[0].split("___")[1].split("length_")[-1].split("_")[0]) + if fljB_contig not in x[0] and fliC_contig not in x[0] and len(target_region&x[3])/float(len(x[3]))>0.65 and contig_length*0.5<len(x[3])<contig_length*1.5: #consider length and alignment length for now, but very loose,0.5 and 1.5 as cut-off + removal=1 + else: + if first_allele_percentage > 0.9 and float(x[0].split("__")[1].split("___")[0])*x[2]/len(x[-1])>0.96:#if high similiarity with middle part of first allele (first allele >0.9, already cover middle part) + removal=1 + else: + pass + if removal==1: + for y in H_contig_roles: + if y[1] in x[0]: + H_contig_roles.remove(y) + else: + pass + #print(x[:3],contig_length,len(target_region&x[3])/float(len(x[3])),contig_length*0.5,len(x[3]),contig_length*1.5) + #end of removing none-middle contigs + #print("H_contigs:") + log_file.write("H_contigs:\n") + extract_file.write("#H_contigs:\n") + H_contig_stat=[] + H1_cont_stat={} + H2_cont_stat={} + for i in range(len(H_contig_roles)): + x=H_contig_roles[i] + a=0 + for y in Final_list_passed: + if x[1] in y[0] and y[0].startswith(x[0]): + if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide + for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it + if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB + #print(x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + H_contig_roles[i]="can't decide fliC or fljB, may be third phase" + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antiten\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + break + else: + #print(x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%",str(min(y[-1]))+" to "+str(max(y[-1]))) + log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n") + title=">"+x[1]+" "+x[0]+" "+y[0].split("_")[1]+"; "+"blast score: "+str(y[1])+" identity%: "+str(round(y[2]*100,2))+"%; alignment from "+str(min(y[-1]))+" to "+str(max(y[-1]))+" of antigen\n" + seqs="" + for z in handle_fasta: + if x[1]==z.description: + seqs=str(z.seq) + extract_file.write(title+seqs+"\n") + if x[0]=="fliC": + if y[0].split("_")[1] not in H1_cont_stat: + H1_cont_stat[y[0].split("_")[1]]=y[2] + else: + H1_cont_stat[y[0].split("_")[1]]+=y[2] + if x[0]=="fljB": + if y[0].split("_")[1] not in H2_cont_stat: + H2_cont_stat[y[0].split("_")[1]]=y[2] + else: + H2_cont_stat[y[0].split("_")[1]]+=y[2] + break + #detect contaminations + #print(H1_cont_stat) + #print(H2_cont_stat) + H1_cont_stat_list=[x for x in H1_cont_stat if H1_cont_stat[x]>0.2] + H2_cont_stat_list=[x for x in H2_cont_stat if H2_cont_stat[x]>0.2] + contamination_H="" + if len(H1_cont_stat_list)>1 or len(H2_cont_stat_list)>1: + contamination_H="potential contamination from H antigen signals" + elif len(H2_cont_stat_list)==1 and fljB_contig=="NA": + contamination_H="potential contamination from H antigen signals, uncommon weak fljB signals detected" + #get additional antigens + """ + if ("O-9,46_wbaV" in O_list or "O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254" in O_list) and O_list_less_contamination[0].startswith("O-9,"):#not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1 + O_choice="O-9,46" + #print "$$$Most possilble Otype: O-9,46" + elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1 + O_choice="O-9,46,27" + #print "$$$Most possilble Otype: O-9,46,27" + elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and (O_list[0].startswith("O-3,10") or O_list_less_contamination[0].startswith("O-9,46_wzy")):#and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1 + O_choice="O-3,10" + #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)" + else: + O_choice="O-1,3,19" + #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)" + ### end of special test for O9,46 and O3,10 family + + if O_choice=="O-9,46,27" or O_choice=="O-3,10" or O_choice=="O-1,3,19": + if len(Otypes_uniq)>2: + contamination_O="potential contamination from O antigen signals" + else: + if len(Otypes_uniq)>1: + if O_choice=="O-4" and len(Otypes_uniq)==2 and "O-9,46,27" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + elif O_choice=="O-9,46" and len(Otypes_uniq)==2 and "O-9,46_wbaV" in Otypes_uniq and "O-9,46_wzy" in Otypes_uniq: #for special 4,12,27 case such as Bredeney and Schwarzengrund + contamination_O="" + """ + additonal_antigents=[] + #print(contamination_O) + #print(contamination_H) + log_file.write(contamination_O+"\n") + log_file.write(contamination_H+"\n") + log_file.close() + return O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list + +def get_input_K(input_file,lib_dict,data_type,k_size): + #kmer mode; get input_Ks from dict and data_type + kmers = [] + for h in lib_dict: + kmers += lib_dict[h] + if data_type == '4': + input_Ks = target_multifasta_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '1' or data_type == '2' or data_type == '3':#set it for now, will change later + input_Ks = target_read_kmerizer(input_file, k_size, set(kmers)) + elif data_type == '5':#minion_2d_fasta + input_Ks = minion_fasta_kmerizer(input_file, k_size, set(kmers)) + if data_type == '6':#minion_2d_fastq + input_Ks = minion_fastq_kmerizer(input_file, k_size, set(kmers)) + return input_Ks + +def get_kmer_dict(lib_dict,input_Ks): + #kmer mode; get predicted types + O_dict = {} + H_dict = {} + Special_dict = {} + for h in lib_dict: + score = (len(lib_dict[h] & input_Ks) / len(lib_dict[h])) * 100 + if score > 1: # Arbitrary cut-off for similarity score very low but seems necessary to detect O-3,10 in some cases + if h.startswith('O-') and score > 25: + O_dict[h] = score + if h.startswith('fl') and score > 40: + H_dict[h] = score + if (h[:2] != 'fl') and (h[:2] != 'O-'): + Special_dict[h] = score + return O_dict,H_dict,Special_dict + +def call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir): + log_file=open("SeqSero_log.txt","a") + log_file.write("O_scores:\n") + #call O: + highest_O = '-' + if len(O_dict) == 0: + pass + else: + for x in O_dict: + log_file.write(x+"\t"+str(O_dict[x])+"\n") + if ('O-9,46_wbaV__1002' in O_dict and O_dict['O-9,46_wbaV__1002']>70) or ("O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002" in O_dict and O_dict['O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002']>70): # not sure should use and float(O9_wbaV)/float(num_1) > 0.1 + #if 'O-9,46_wzy__1191' in O_dict or "O-9,46_wzy_partial__216" in O_dict: # and float(O946_wzy)/float(num_1) > 0.1 + #modified to fix miscall of O-9,46 + if ('O-9,46_wzy__1191' in O_dict and O_dict['O-9,46_wzy__1191']>40) or ("O-9,46_wzy_partial__216" in O_dict and O_dict["O-9,46_wzy_partial__216"]>40): # and float(O946_wzy)/float(num_1) > 0.1 + highest_O = "O-9,46" + elif "O-9,46,27_partial_wzy__1019" in O_dict: # and float(O94627)/float(num_1) > 0.1 + highest_O = "O-9,46,27" + else: + highest_O = "O-9" # next, detect O9 vs O2? + O2 = 0 + O9 = 0 + for z in Special_dict: + if "tyr-O-9" in z: + O9 = float(Special_dict[z]) + if "tyr-O-2" in z: + O2 = float(Special_dict[z]) + if O2 > O9: + highest_O = "O-2" + elif ("O-3,10_wzx__1539" in O_dict) and ( + "O-9,46_wzy__1191" in O_dict + ): # and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1 + if "O-3,10_not_in_1,3,19__1519" in O_dict: # and float(O310_no_1319)/float(num_1) > 0.1 + highest_O = "O-3,10" + else: + highest_O = "O-1,3,19" + ### end of special test for O9,46 and O3,10 family + else: + try: + max_score = 0 + for x in O_dict: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + if highest_O == "O-1,3,19": + highest_O = '-' + max_score = 0 + for x in O_dict: + if x == 'O-1,3,19_not_in_3,10__130': + pass + else: + if float(O_dict[x]) >= max_score: + max_score = float(O_dict[x]) + #highest_O = x.split("_")[0] + # ed_SL_12182019: modified to fix the O-9,46 error example1 + if (x == 'O-9,46_wbaV__1002' or x == 'O-9,46_wbaV-from-II-9,12:z29:1,5-SRR1346254__1002') and ('O-9,46_wzy__1191' not in O_dict and 'O-9,46_wzy_partial__216' not in O_dict): + highest_O = "O-9" + else: + highest_O = x.split("_")[0] + except: + pass + #call_fliC: + if len(H_dict)!=0: + highest_H_score_both_BC=H_dict[max(H_dict.keys(), key=(lambda k: H_dict[k]))] #used to detect whether fljB existed or not + else: + highest_H_score_both_BC=0 + highest_fliC = '-' + highest_fliC_raw = '-' + highest_Score = 0 + log_file.write("\nH_scores:\n") + for s in H_dict: + log_file.write(s+"\t"+str(H_dict[s])+"\n") + if s.startswith('fliC'): + if float(H_dict[s]) > highest_Score: + highest_fliC = s.split('_')[1] + highest_fliC_raw = s + highest_Score = float(H_dict[s]) + #call_fljB + highest_fljB = '-' + highest_fljB_raw = '-' + highest_Score = 0 + for s in H_dict: + if s.startswith('fljB'): + if float(H_dict[s]) > highest_Score and float(H_dict[s]) > highest_H_score_both_BC * 0.65: #fljB is special, so use highest_H_score_both_BC to give a general estimate of coverage, currently 0.65 seems pretty good; the reason use a high (0.65) is some fliC and fljB shared with each other + #highest_fljB = s.split('_')[1] + #highest_fljB_raw = s + #highest_Score = float(H_dict[s]) + if s.split('_')[1]!=highest_fliC: + highest_fljB = s.split('_')[1] + highest_fljB_raw = s + highest_Score = float(H_dict[s]) + log_file.write("\nSpecial_scores:\n") + for s in Special_dict: + log_file.write(s+"\t"+str(Special_dict[s])+"\n") + log_file.close() + return highest_O,highest_fliC,highest_fljB + +def get_temp_file_names(for_fq,rev_fq): + #seqsero2 -a; get temp file names + sam=for_fq+".sam" + bam=for_fq+".bam" + sorted_bam=for_fq+"_sorted.bam" + mapped_fq1=for_fq+"_mapped.fq" + mapped_fq2=rev_fq+"_mapped.fq" + combined_fq=for_fq+"_combined.fq" + for_sai=for_fq+".sai" + rev_sai=rev_fq+".sai" + return sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai + +def map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode): + #seqsero2 -a; do mapping and sort + print("building database...") + subprocess.check_call("bwa index "+database+ " 2>> data_log.txt",shell=True) + print("mapping...") + if mapping_mode=="mem": + subprocess.check_call("bwa mem -k 17 -t "+threads+" "+database+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + elif mapping_mode=="sam": + if fnameB!="": + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameB+" > "+rev_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+fnameA+" "+fnameB+" > "+sam+ " 2>> data_log.txt",shell=True) + else: + subprocess.check_call("bwa aln -t "+threads+" "+database+" "+fnameA+" > "+for_sai+ " 2>> data_log.txt",shell=True) + subprocess.check_call("bwa samse "+database+" "+for_sai+" "+for_fq+" > "+sam) + subprocess.check_call("samtools view -@ "+threads+" -F 4 -Sh "+sam+" > "+bam,shell=True) + ### check the version of samtools then use differnt commands + samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = samtools_version.communicate() + version = str(err).split("ersion:")[1].strip().split(" ")[0].strip() + print("check samtools version:",version) + ### end of samtools version check and its analysis + if LooseVersion(version)<=LooseVersion("1.2"): + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" "+fnameA+"_sorted",shell=True) + else: + subprocess.check_call("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam,shell=True) + +def extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode): + #seqsero2 -a; extract, assembly and blast + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+combined_fq,shell=True) + #print("fnameA:",fnameA) + #print("fnameB:",fnameB) + if fnameB!="": + subprocess.check_call("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt",shell=True)#2> /dev/null if want no output + else: + pass + outdir=current_time+"_temp" + print("assembling...") + if int(threads)>4: + t="4" + else: + t=threads + if os.path.getsize(combined_fq)>100 and (fnameB=="" or os.path.getsize(mapped_fq1)>100):#if not, then it's "-:-:-" + if fnameB!="": + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + else: + subprocess.check_call("spades.py --careful --pe1-s "+combined_fq+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1",shell=True) + new_fasta=fnameA+"_"+database+"_"+mapping_mode+".fasta" + #new_fasta=fnameA+"_"+database.split('/')[-1]+"_"+mapping_mode+".fasta" # change path to databse for packaging + subprocess.check_call("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null",shell=True) + #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta + subprocess.check_call("rm -rf "+outdir+ " 2> /dev/null",shell=True) + print("blasting...","\n") + xmlfile="blasted_output.xml"#fnameA+"-extracted_vs_"+database+"_"+mapping_mode+".xml" + subprocess.check_call('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1',shell=True) #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015 + subprocess.check_call("blastn -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1",shell=True)###1/27/2015; 08272018, remove "-word_size 10" + else: + xmlfile="NA" + return xmlfile,new_fasta + +def judge_subspecies(fnameA): + #seqsero2 -a; judge subspecies on just forward raw reads fastq + salmID_output=subprocess.Popen("SalmID.py -i "+fnameA,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE) + out, err = salmID_output.communicate() + out=out.decode("utf-8") + file=open("data_log.txt","a") + file.write(out) + file.close() + salm_species_scores=out.split("\n")[1].split("\t")[6:] + salm_species_results=out.split("\n")[0].split("\t")[6:] + max_score=0 + max_score_index=1 #default is 1, means "I" + for i in range(len(salm_species_scores)): + if max_score<float(salm_species_scores[i]): + max_score=float(salm_species_scores[i]) + max_score_index=i + prediction=salm_species_results[max_score_index].split(".")[1].strip().split(" ")[0] + #if float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): #bongori and enterica compare + if float(out.split("\n")[1].split("\t")[4]) > 10 and float(out.split("\n")[1].split("\t")[4]) > float(out.split("\n")[1].split("\t")[5]): ## ed_SL_0318: change SalmID_ssp_threshold + prediction="bongori" #if not, the prediction would always be enterica, since they are located in the later part + #if max_score<10: ## ed_SL_0318: change SalmID_ssp_threshold + if max_score<60: + prediction="-" + return prediction + +def judge_subspecies_Kmer(Special_dict): + #seqsero2 -k; + max_score=0 + prediction="-" #default should be I + for x in Special_dict: + #if "mer" in x: ## ed_SL_0318: change ssp_threshold + if "mer" in x and float(Special_dict[x]) > 60: + if max_score<float(Special_dict[x]): + max_score=float(Special_dict[x]) + prediction=x.split("_")[-1].strip() + if x.split("_")[-1].strip()=="bongori" and float(Special_dict[x])>95:#if bongori already, then no need to test enterica + prediction="bongori" + break + return prediction + +## ed_SL_11232019: add notes for missing antigen +def check_antigens(ssp,O_antigen,H1_antigen,H2_antigen,NA_note): + antigen_note = '' + if ssp != '-': + if O_antigen != '-' and H1_antigen == '-' and H2_antigen == '-': # O:-:- + antigen_note = 'H antigens were not detected. This is an atypical result that should be further investigated. Most Salmonella strains have at least fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen != '-' and H1_antigen == '-' and H2_antigen != '-': # O:-:H2 + antigen_note = 'fliC was not detected. This is an atypical result that should be further investigated. Most Salmonella strains have fliC, encoding the Phase 1 H antigen, even if it is not expressed. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen != '-': # -:H1:X + antigen_note = 'O antigen was not detected. This result may be due to a rough strain that has deleted the rfb region. For raw reads input, the k-mer workflow is sometimes more sensitive than the microassembly workflow in detecting O antigen. Caution should be used with this approach because the k-mer result may be due to low levels of contamination. ' + NA_note = '' + elif O_antigen == '-' and H1_antigen == '-' and H2_antigen == '-': # -:-:- + antigen_note = 'No serotype antigens were detected. This is an atypical result that should be further investigated. ' + NA_note = '' + else: + antigen_note = 'The input genome cannot be identified as Salmonella. Check the input for taxonomic ID, contamination, or sequencing quality. ' + NA_note = '' +# if [O_antigen, H1_antigen, H2_antigen].count('-') >= 2: +# antigen_note = 'No subspecies marker was detected and less than 2 serotype antigens were detected; further, this genome was not identified as Salmonella. This is an atypical result that should be further investigated. ' +# else: +# antigen_note = 'No subspecies marker was detected. This genome may not be Salmonella. This is an atypical result that should be further investigated. ' + return (antigen_note,NA_note) + +def main(): + #combine SeqSeroK and SeqSero2, also with SalmID + args = parse_args() + input_file = args.i + data_type = args.t + analysis_mode = args.m + mapping_mode=args.b + threads=args.p + make_dir=args.d + clean_mode=args.c + sample_name=args.n + ingore_header=args.s + k_size=27 #will change for bug fixing + dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__))) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: add ex_dir for packaging + seqsero2_db=ex_dir+"/H_and_O_and_specific_genes.fasta" # ed_SL_11092019: change path to database for packaging + database="H_and_O_and_specific_genes.fasta" + note="Note: " + NA_note="This predicted serotype is not in the Kauffman-White scheme. " # ed_SL_09272019: add for new output format + if len(sys.argv)==1: + subprocess.check_call(dirpath+"/SeqSero2_package.py -h",shell=True)#change name of python file + else: + request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime()) + request_id += str(random.randint(1, 10000000)) + if make_dir is None: + make_dir="SeqSero_result_"+request_id + make_dir=os.path.abspath(make_dir) + if os.path.isdir(make_dir): + pass + else: + subprocess.check_call("mkdir -p "+make_dir,shell=True) + #subprocess.check_call("cp "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + #subprocess.check_call("ln -sr "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) + subprocess.check_call("ln -f -s "+seqsero2_db+" "+" ".join(input_file)+" "+make_dir,shell=True) # ed_SL_11092019: change path to database for packaging + #subprocess.check_call("ln -f -s "+dirpath+"/"+database+" "+" ".join(input_file)+" "+make_dir,shell=True) ### use -f option to force the replacement of links, remove -r and use absolute path instead to avoid link issue (use 'type=os.path.abspath' in -i argument). + ############################begin the real analysis + if analysis_mode=="a": + if data_type in ["1","2","3"]:#use allele mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + os.chdir(make_dir) + ###add a function to tell input files + fnameA=for_fq.split("/")[-1] + fnameB=rev_fq.split("/")[-1] + current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime()) + sam,bam,sorted_bam,mapped_fq1,mapped_fq2,combined_fq,for_sai,rev_sai=get_temp_file_names(fnameA,fnameB) #get temp files id + map_and_sort(threads,database,fnameA,fnameB,sam,bam,for_sai,rev_sai,sorted_bam,mapping_mode) #do mapping and sort + ### avoid error out when micro assembly fails. ed_SL_03172020 + try: + xmlfile,new_fasta=extract_mapped_reads_and_do_assembly_and_blast(current_time,sorted_bam,combined_fq,mapped_fq1,mapped_fq2,threads,fnameA,fnameB,database,mapping_mode) #extract the mapped reads and do micro assembly and blast + except (UnboundLocalError, subprocess.CalledProcessError): + xmlfile="NA" + H1_cont_stat_list=[] + H2_cont_stat_list=[] + ### + if xmlfile=="NA": + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H=("-","-","-",[],"","") + else: + Final_list=xml_parse_score_comparision_seqsero(xmlfile) #analyze xml and get parsed results + file=open("data_log.txt","a") + for x in Final_list: + file.write("\t".join(str(y) for y in x)+"\n") + file.close() + Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1].split("_")[0])>=0.9 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]) or x[1]>1000)] + O_choice,fliC_choice,fljB_choice,special_gene_list,contamination_O,contamination_H,Otypes_uniq,H1_cont_stat_list,H2_cont_stat_list=predict_O_and_H_types(Final_list,Final_list_passed,new_fasta) #predict O, fliC and fljB + subspecies=judge_subspecies(fnameA) #predict subspecies + ###output + predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list,subspecies) + claim="" #04132019, disable claim for new report requirement + contamination_report="" + H_list=["fliC_"+x for x in H1_cont_stat_list if len(x)>0]+["fljB_"+x for x in H2_cont_stat_list if len(x)>0] + if contamination_O!="" and contamination_H=="": + contamination_report="#Potential inter-serotype contamination detected from O antigen signals. All O-antigens detected:"+"\t".join(Otypes_uniq)+"." + elif contamination_O=="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected or potential thrid H phase from H antigen signals. All H-antigens detected:"+"\t".join(H_list)+"." + elif contamination_O!="" and contamination_H!="": + contamination_report="#Potential inter-serotype contamination detected from both O and H antigen signals.All O-antigens detected:"+"\t".join(Otypes_uniq)+". All H-antigens detected:"+"\t".join(H_list)+"." + if contamination_report!="": + #contamination_report="potential inter-serotype contamination detected (please refer below antigen signal report for details)." #above contamination_reports are for back-up and bug fixing #web-based mode need to be re-used, 04132019 + contamination_report="Co-existence of multiple serotypes detected, indicating potential inter-serotype contamination. See 'Extracted_antigen_alleles.fasta' for detected serotype determinant alleles. " + #claim="\n"+open("Extracted_antigen_alleles.fasta","r").read()#used to store H and O antigen sequeences #04132019, need to change if using web-version + #if contamination_report+star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if O_choice=="": + O_choice="-" + antigen_note,NA_note=check_antigens(subspecies,O_choice,fliC_choice,fljB_choice,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + else: + new_file=open("SeqSero_result.txt","w") + ### ed_SL_01152020: add new output + conta_note="yes" if "inter-serotype contamination" in contamination_report else "no" + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tPotential inter-serotype contamination\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file[0].split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+conta_note+"\t"+contamination_report+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line="" #04132019, for new output requirement, diable star_line if "NA" in output + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, add subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+" ".join(input_file)+"\t"+O_choice+"\t"+fliC_choice+"\t"+fljB_choice+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+conta_note+"\t"+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + #subprocess.check_call("cat Seqsero_result.txt",shell=True) + #subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null",shell=True) + subprocess.call("rm H_and_O_and_specific_genes.fasta* *.sra *.bam *.sam *.fastq *.gz *.fq temp.txt "+fnameA+"*_db* 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + #print("Output_directory:"+make_dir+"\nInput files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\nNote:"+contamination_report+star+star_line+claim+"\n")#+## + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+contamination_report+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+"\t".join(input_file)+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+ + "H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+contamination_report+star_line+claim+antigen_note+"\n") + else: + print("Allele modes only support raw reads datatype, i.e. '-t 1 or 2 or 3'; please use '-m k'") + elif analysis_mode=="k": + #ex_dir = os.path.dirname(os.path.realpath(__file__)) + ex_dir = os.path.abspath(os.path.join(os.path.dirname(os.path.dirname(__file__)),'seqsero2_db')) # ed_SL_09152019: change ex_dir for packaging + #output_mode = args.mode + for_fq,rev_fq=get_input_files(make_dir,input_file,data_type,dirpath) + input_file = for_fq #-k will just use forward because not all reads were used + os.chdir(make_dir) + f = open(ex_dir + '/antigens.pickle', 'rb') + lib_dict = pickle.load(f) + f.close + input_Ks=get_input_K(input_file,lib_dict,data_type,k_size) + O_dict,H_dict,Special_dict=get_kmer_dict(lib_dict,input_Ks) + highest_O,highest_fliC,highest_fljB=call_O_and_H_type(O_dict,H_dict,Special_dict,make_dir) + subspecies=judge_subspecies_Kmer(Special_dict) + if subspecies=="IIb" or subspecies=="IIa": + subspecies="II" + predict_form,predict_sero,star,star_line,claim = seqsero_from_formula_to_serotypes( + highest_O.split('-')[1], highest_fliC, highest_fljB, Special_dict,subspecies) + claim="" #no claim any more based on new output requirement + #if star_line+claim=="": #0413, new output style + # note="" + #else: + # note="Note:" + + ### ed_SL_11232019: add notes for missing antigen + if highest_O.split('-')[-1]=="": + O_choice="-" + else: + O_choice=highest_O.split('-')[-1] + antigen_note,NA_note=check_antigens(subspecies,O_choice,highest_fliC,highest_fljB,NA_note) + if sample_name: + print ("Sample name:\t"+sample_name) + ### + + if clean_mode: + subprocess.check_call("rm -rf ../"+make_dir,shell=True) + make_dir="none-output-directory due to '-c' flag" + # ### ed_SL_05282019, fix the assignment issue of variable 'O_choice' using "-m k -c" + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + # ### + else: + # if highest_O.split('-')[-1]=="": + # O_choice="-" + # else: + # O_choice=highest_O.split('-')[-1] + #print("Output_directory:"+make_dir+"\tInput_file:"+input_file+"\tPredicted subpecies:"+subspecies + '\tPredicted antigenic profile:' + predict_form + '\tPredicted serotype(s):' + predict_sero) + new_file=open("SeqSero_result.txt","w") + #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+## + ### ed_SL_01152020: add new output + tsv_file=open("SeqSero_result.tsv","w") + if ingore_header: + pass + else: + tsv_file.write("Sample name\tOutput directory\tInput files\tO antigen prediction\tH1 antigen prediction(fliC)\tH2 antigen prediction(fljB)\tPredicted subspecies\tPredicted antigenic profile\tPredicted serotype\tNote\n") + if sample_name: + new_file.write("Sample name:\t"+sample_name+"\n") + tsv_file.write(sample_name+'\t') + else: + tsv_file.write(input_file.split('/')[-1]+'\t') + ### + if "N/A" not in predict_sero: + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+predict_sero+"\t"+star_line+claim+antigen_note+"\n") + else: + #star_line=star_line.strip()+"\tNone such antigenic formula in KW.\n" + star_line = "" #changed for new output requirement, 04132019 + new_file.write("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + tsv_file.write(make_dir+"\t"+input_file+"\t"+O_choice+"\t"+highest_fliC+"\t"+highest_fljB+"\t"+subspecies+"\t"+predict_form+"\t"+subspecies+' '+predict_form+"\t"+NA_note+star_line+claim+antigen_note+"\n") + new_file.close() + tsv_file.close() + subprocess.call("rm *.fasta* *.fastq *.gz *.fq temp.txt *.sra 2> /dev/null",shell=True) + if "N/A" not in predict_sero: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+predict_sero+"\n"+ + note+star_line+claim+antigen_note+"\n")#+## + else: + print("Output directory:\t"+make_dir+"\n"+ + "Input files:\t"+input_file+"\n"+ + "O antigen prediction:\t"+O_choice+"\n"+ + "H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+ + "H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+ + "Predicted subspecies:\t"+subspecies+"\n"+ + "Predicted antigenic profile:\t"+predict_form+"\n"+ + "Predicted serotype:\t"+subspecies+' '+predict_form+"\n"+ # add serotype output for "N/A" prediction, subspecies + note+NA_note+star_line+claim+antigen_note+"\n")#+## + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/SeqSero2_update_kmer_database.py Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,113 @@ +#!/Users/charles.strittmatter/miniconda3/bin/python + +import argparse +import os,subprocess +import pickle + +### SeqSero Kmer +def parse_args(): + "Parse the input arguments, use '-h' for help." + parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') + return parser.parse_args() + +def reverse_complement(sequence): + complement = { + 'A': 'T', + 'C': 'G', + 'G': 'C', + 'T': 'A', + 'N': 'N', + 'M': 'K', + 'R': 'Y', + 'W': 'W', + 'S': 'S', + 'Y': 'R', + 'K': 'M', + 'V': 'B', + 'H': 'D', + 'D': 'H', + 'B': 'V' + } + return "".join(complement[base] for base in reversed(sequence)) + +def multifasta_dict(multifasta): + multifasta_list = [ + line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 + ] + headers = [i for i in multifasta_list if i[0] == '>'] + multifasta_dict = {} + for h in headers: + start = multifasta_list.index(h) + for element in multifasta_list[start + 1:]: + if element[0] == '>': + break + else: + if h[1:] in multifasta_dict: + multifasta_dict[h[1:]] += element + else: + multifasta_dict[h[1:]] = element + return multifasta_dict + +def createKmerDict_reads(list_of_strings, kmer): + kmer_table = {} + for string in list_of_strings: + sequence = string.strip('\n') + for i in range(len(sequence) - kmer + 1): + new_mer = sequence[i:i + kmer].upper() + new_mer_rc = reverse_complement(new_mer) + if new_mer in kmer_table: + kmer_table[new_mer.upper()] += 1 + else: + kmer_table[new_mer.upper()] = 1 + if new_mer_rc in kmer_table: + kmer_table[new_mer_rc.upper()] += 1 + else: + kmer_table[new_mer_rc.upper()] = 1 + return kmer_table + +def multifasta_to_kmers_dict(multifasta): + multi_seq_dict = multifasta_dict(multifasta) + lib_dict = {} + for h in multi_seq_dict: + lib_dict[h] = set( + [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) + return lib_dict + +def get_salmid_invA_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/invA_mers_dict', 'rb') + invA_dict = pickle.load(a) + try: + del invA_dict['version'] + except: + pass + return invA_dict + +def get_salmid_rpoB_database(ex_dir): + # read invA kmer and return it + a = open(ex_dir + '/rpoB_mers_dict', 'rb') + rpoB_dict = pickle.load(a) + try: + del rpoB_dict['version'] + except: + pass + return rpoB_dict + +def main(): + args = parse_args() + ex_dir = os.path.dirname(os.path.realpath(__file__)) + lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') + invA_dict=get_salmid_invA_database(ex_dir) + #rpoB_dict=get_salmid_rpoB_database(ex_dir) + lib_dict_new = lib_dict.copy() + #print(len(lib_dict_new)) + lib_dict_new.update(invA_dict) + #print(len(lib_dict_new)) + #lib_dict_new.update(rpoB_dict) + #print(len(lib_dict_new)) + f = open(ex_dir + '/antigens.pickle', "wb") + pickle.dump(lib_dict_new, f) + f.close() + +if __name__ == '__main__': + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/build/scripts-3.6/deinterleave_fastq.sh Fri May 01 13:30:43 2020 -0400 @@ -0,0 +1,30 @@ +#!/bin/bash +# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] +# +# Deinterleaves a FASTQ file of paired reads into two FASTQ +# files specified on the command line. Optionally GZip compresses the output +# FASTQ files using pigz if the 3rd command line argument is the word "compress" +# +# Can deinterleave 100 million paired reads (200 million total +# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) +# +# Latest code: https://gist.github.com/3521724 +# Also see my interleaving script: https://gist.github.com/4544979 +# +# Inspired by Torsten Seemann's blog post: +# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html + +# Set up some defaults +GZIP_OUTPUT=0 +PIGZ_COMPRESSION_THREADS=10 + +# If the third argument is the word "compress" then we'll compress the output using pigz +if [[ $3 == "compress" ]]; then + GZIP_OUTPUT=1 +fi + +if [[ ${GZIP_OUTPUT} == 0 ]]; then + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 +else + paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 +fi
--- a/core.py Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,386 +0,0 @@ -#!/usr/bin/env python3 - - -import gzip -import io -import pickle -import os -import sys - -from argparse import ArgumentParser -try: - from .version import SalmID_version -except ImportError: - SalmID_version = "version unknown" - - -def reverse_complement(sequence): - """return the reverse complement of a nucleotide (including IUPAC ambiguous nuceotide codes)""" - complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N', 'M': 'K', 'R': 'Y', 'W': 'W', - 'S': 'S', 'Y': 'R', 'K': 'M', 'V': 'B', 'H': 'D', 'D': 'H', 'B': 'V'} - return "".join(complement[base] for base in reversed(sequence)) - - -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = ArgumentParser(description='SalmID - rapid Kmer based Salmonella identifier from sequence data') - # inputs - parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SalmID_version) - parser.add_argument( - '-i', '--input_file', type=str, required=False, default='None', metavar='your_fastqgz', - help='Single fastq.gz file input, include path to file if file is not in same directory ') - parser.add_argument( - '-e', '--extension', type=str, required=False, default='.fastq.gz', metavar='file_extension', - help='File extension, if specified without "--input_dir", SalmID will attempt to ID all files\n' + - ' with this extension in current directory, otherwise files in input directory') - - parser.add_argument( - '-d', '--input_dir', type=str, required=False, default='.', metavar='directory', - help='Directory which contains data for identification, when not specified files in current directory will be analyzed.') - parser.add_argument( - '-r', '--report', type=str, required=False, default='percentage', metavar='percentage, coverage or taxonomy', - help='Report either percentage ("percentage") of clade specific kmers recovered, average kmer-coverage ("cov"), or ' - 'taxonomy (taxonomic species ID, plus observed mean k-mer coverages and expected coverage).') - parser.add_argument( - '-m', '--mode', type=str, required=False, default='quick', metavar='quick or thorough', - help='Quick [quick] or thorough [thorough] mode') - if len(sys.argv) == 1: - parser.print_help(sys.stderr) - sys.exit(1) - return parser.parse_args() - - -def get_av_read_length(file): - """Samples the first 100 reads from a fastq file and return the average read length.""" - i = 1 - n_reads = 0 - total_length = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - if i % 4 == 2: - total_length += len(line.strip()) - n_reads += 1 - i += 1 - if n_reads == 100: - break - return total_length / 100 - - -def createKmerDict_reads(list_of_strings, kmer): - """Count occurence of K-mers in a list of strings - - Args: - list_of_strings(list of str): nucleotide sequences as a list of strings - kmer(int): length of the K-mer to count - - Returns: - dict: dictionary with kmers as keys, counts for each kmer as values""" - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - if len(sequence) >= kmer: - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer] - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - - -def target_read_kmerizer_multi(file, k, kmerDict_1, kmerDict_2, mode): - mean_1 = None - mean_2 = None - i = 1 - n_reads_1 = 0 - n_reads_2 = 0 - total_coverage_1 = 0 - total_coverage_2 = 0 - reads_1 = [] - reads_2 = [] - total_reads = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - start = int((len(line) - k) // 2) - if i % 4 == 2: - total_reads += 1 - if file.endswith(".gz"): - s1 = line[start:k + start].decode() - line = line.decode() - else: - s1 = line[start:k + start] - if s1 in kmerDict_1: - n_reads_1 += 1 - total_coverage_1 += len(line) - reads_1.append(line) - if s1 in kmerDict_2: - n_reads_2 += 1 - total_coverage_2 += len(line) - reads_2.append(line) - i += 1 - if mode == 'quick': - if total_coverage_2 >= 800000: - break - - if len(reads_1) == 0: - kmer_Dict1 = {} - else: - kmer_Dict1 = createKmerDict_reads(reads_1, k) - mers_1 = set([key for key in kmer_Dict1]) - mean_1 = sum([kmer_Dict1[key] for key in kmer_Dict1]) / len(mers_1) - if len(reads_2) == 0: - kmer_Dict2 = {} - else: - kmer_Dict2 = createKmerDict_reads(reads_2, k) - mers_2 = set([key for key in kmer_Dict2]) - mean_2 = sum([kmer_Dict2[key] for key in kmer_Dict2]) / len(mers_2) - return kmer_Dict1, kmer_Dict2, mean_1, mean_2, total_reads - - -def mean_cov_selected_kmers(iterable, kmer_dict, clade_specific_kmers): - ''' - Given an iterable (list, set, dictrionary) returns mean coverage for the kmers in iterable - :param iterable: set, list or dictionary containing kmers - :param kmer_dict: dictionary with kmers as keys, kmer-frequency as value - :param clade_specific_kmers: list, dict or set of clade specific kmers - :return: mean frequency as float - ''' - if len(iterable) == 0: - return 0 - return sum([kmer_dict[value] for value in iterable]) / len(clade_specific_kmers) - - -def kmer_lists(query_fastq_gz, k, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode): - dict_invA, dict_rpoB, mean_invA, mean_rpoB, total_reads = target_read_kmerizer_multi(query_fastq_gz, k, allmers, - allmers_rpoB, mode) - target_mers_invA = set([key for key in dict_invA]) - target_mers_rpoB = set([key for key in dict_rpoB]) - if target_mers_invA == 0: - print('No reads found matching invA, no Salmonella in sample?') - else: - p_bongori = (len(uniqmers_bongori & target_mers_invA) / len(uniqmers_bongori)) * 100 - p_I = (len(uniqmers_I & target_mers_invA) / len(uniqmers_I)) * 100 - p_IIa = (len(uniqmers_IIa & target_mers_invA) / len(uniqmers_IIa)) * 100 - p_IIb = (len(uniqmers_IIb & target_mers_invA) / len(uniqmers_IIb)) * 100 - p_IIIa = (len(uniqmers_IIIa & target_mers_invA) / len(uniqmers_IIIa)) * 100 - p_IIIb = (len(uniqmers_IIIb & target_mers_invA) / len(uniqmers_IIIb)) * 100 - p_VI = (len(uniqmers_VI & target_mers_invA) / len(uniqmers_VI)) * 100 - p_IV = (len(uniqmers_IV & target_mers_invA) / len(uniqmers_IV)) * 100 - p_VII = (len(uniqmers_VII & target_mers_invA) / len(uniqmers_VII)) * 100 - p_VIII = (len(uniqmers_VIII & target_mers_invA) / len(uniqmers_VIII)) * 100 - p_bongori_rpoB = (len(uniqmers_bongori_rpoB & target_mers_rpoB) / len(uniqmers_bongori_rpoB)) * 100 - p_Senterica = (len(uniqmers_S_enterica_rpoB & target_mers_rpoB) / len(uniqmers_S_enterica_rpoB)) * 100 - p_Escherichia = (len(uniqmers_Escherichia_rpoB & target_mers_rpoB) / len(uniqmers_Escherichia_rpoB)) * 100 - p_Listeria_ss = (len(uniqmers_Listeria_ss_rpoB & target_mers_rpoB) / len(uniqmers_Listeria_ss_rpoB)) * 100 - p_Lmono = (len(uniqmers_Lmono_rpoB & target_mers_rpoB) / len(uniqmers_Lmono_rpoB)) * 100 - bongori_invA_cov = mean_cov_selected_kmers(uniqmers_bongori & target_mers_invA, dict_invA, uniqmers_bongori) - I_invA_cov = mean_cov_selected_kmers(uniqmers_I & target_mers_invA, dict_invA, uniqmers_I) - IIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIa & target_mers_invA, dict_invA, uniqmers_IIa) - IIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIb & target_mers_invA, dict_invA, uniqmers_IIb) - IIIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIIa & target_mers_invA, dict_invA, uniqmers_IIIa) - IIIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIIb & target_mers_invA, dict_invA, uniqmers_IIIb) - IV_invA_cov = mean_cov_selected_kmers(uniqmers_IV & target_mers_invA, dict_invA, uniqmers_IV) - VI_invA_cov = mean_cov_selected_kmers(uniqmers_VI & target_mers_invA, dict_invA, uniqmers_VI) - VII_invA_cov = mean_cov_selected_kmers(uniqmers_VII & target_mers_invA, dict_invA, uniqmers_VII) - VIII_invA_cov = mean_cov_selected_kmers(uniqmers_VIII & target_mers_invA, dict_invA, uniqmers_VIII) - S_enterica_rpoB_cov = mean_cov_selected_kmers((uniqmers_S_enterica_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_S_enterica_rpoB) - S_bongori_rpoB_cov = mean_cov_selected_kmers((uniqmers_bongori_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_bongori_rpoB) - Escherichia_rpoB_cov = mean_cov_selected_kmers((uniqmers_Escherichia_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Escherichia_rpoB) - Listeria_ss_rpoB_cov = mean_cov_selected_kmers((uniqmers_Listeria_ss_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Listeria_ss_rpoB) - Lmono_rpoB_cov = mean_cov_selected_kmers((uniqmers_Lmono_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Lmono_rpoB) - coverages = [Listeria_ss_rpoB_cov, Lmono_rpoB_cov, Escherichia_rpoB_cov, S_bongori_rpoB_cov, - S_enterica_rpoB_cov, bongori_invA_cov, I_invA_cov, IIa_invA_cov, IIb_invA_cov, - IIIa_invA_cov, IIIb_invA_cov, IV_invA_cov, VI_invA_cov, VII_invA_cov, VIII_invA_cov] - locus_scores = [p_Listeria_ss, p_Lmono, p_Escherichia, p_bongori_rpoB, p_Senterica, p_bongori, - p_I, p_IIa, p_IIb, p_IIIa, p_IIIb, p_IV, p_VI, p_VII, p_VIII] - return locus_scores, coverages, total_reads - - -def report_taxon(locus_covs, average_read_length, number_of_reads): - list_taxa = [ 'Listeria ss', 'Listeria monocytogenes', 'Escherichia sp.', # noqa: E201 - 'Salmonella bongori (rpoB)', 'Salmonella enterica (rpoB)', - 'Salmonella bongori (invA)', 'S. enterica subsp. enterica (invA)', - 'S. enterica subsp. salamae (invA: clade a)', 'S. enterica subsp. salamae (invA: clade b)', - 'S. enterica subsp. arizonae (invA)', 'S. enterica subsp. diarizonae (invA)', - 'S. enterica subsp. houtenae (invA)', 'S. enterica subsp. indica (invA)', - 'S. enterica subsp. VII (invA)', 'S. enterica subsp. salamae (invA: clade VIII)' ] # noqa: E202 - if sum(locus_covs) < 1: - rpoB = ('No rpoB matches!', 0) - invA = ('No invA matches!', 0) - return rpoB, invA, 0.0 - else: - # given list of scores get taxon - if sum(locus_covs[0:5]) > 0: - best_rpoB = max(range(len(locus_covs[1:5])), key=lambda x: locus_covs[1:5][x]) + 1 - all_rpoB = max(range(len(locus_covs[0:5])), key=lambda x: locus_covs[0:5][x]) - if (locus_covs[best_rpoB] != 0) & (all_rpoB == 0): - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - elif (all_rpoB == 0) & (round(sum(locus_covs[1:5]), 1) < 1): - rpoB = (list_taxa[0], locus_covs[0]) - else: - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - else: - rpoB = ('No rpoB matches!', 0) - if sum(locus_covs[5:]) > 0: - best_invA = max(range(len(locus_covs[5:])), key=lambda x: locus_covs[5:][x]) + 5 - invA = (list_taxa[best_invA], locus_covs[best_invA]) - else: - invA = ('No invA matches!', 0) - if 'Listeria' in rpoB[0]: - return rpoB, invA, (average_read_length * number_of_reads) / 3000000 - else: - return rpoB, invA, (average_read_length * number_of_reads) / 5000000 - - -def main(): - ex_dir = os.path.dirname(os.path.realpath(__file__)) - args = parse_args() - input_file = args.input_file - if input_file != 'None': - files = [input_file] - else: - extension = args.extension - inputdir = args.input_dir - files = [inputdir + '/' + f for f in os.listdir(inputdir) if f.endswith(extension)] - report = args.report - mode = args.mode - f_invA = open(ex_dir + "/invA_mers_dict", "rb") - sets_dict_invA = pickle.load(f_invA) - f_invA.close() - allmers = sets_dict_invA['allmers'] - uniqmers_I = sets_dict_invA['uniqmers_I'] - uniqmers_IIa = sets_dict_invA['uniqmers_IIa'] - uniqmers_IIb = sets_dict_invA['uniqmers_IIb'] - uniqmers_IIIa = sets_dict_invA['uniqmers_IIIa'] - uniqmers_IIIb = sets_dict_invA['uniqmers_IIIb'] - uniqmers_IV = sets_dict_invA['uniqmers_IV'] - uniqmers_VI = sets_dict_invA['uniqmers_VI'] - uniqmers_VII = sets_dict_invA['uniqmers_VII'] - uniqmers_VIII = sets_dict_invA['uniqmers_VIII'] - uniqmers_bongori = sets_dict_invA['uniqmers_bongori'] - - f = open(ex_dir + "/rpoB_mers_dict", "rb") - sets_dict = pickle.load(f) - f.close() - - allmers_rpoB = sets_dict['allmers'] - uniqmers_bongori_rpoB = sets_dict['uniqmers_bongori'] - uniqmers_S_enterica_rpoB = sets_dict['uniqmers_S_enterica'] - uniqmers_Escherichia_rpoB = sets_dict['uniqmers_Escherichia'] - uniqmers_Listeria_ss_rpoB = sets_dict['uniqmers_Listeria_ss'] - uniqmers_Lmono_rpoB = sets_dict['uniqmers_L_mono'] - # todo: run kmer_lists() once, create list of tuples containing data to be used fro different reports - if report == 'taxonomy': - print('file\trpoB\tinvA\texpected coverage') - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [round(cov, 1) for cov in coverages] - report = report_taxon(pretty_covs, get_av_read_length(f), reads) - print(f.split('/')[-1] + '\t' + report[0][0] + '[' + str(report[0][1]) + ']' + '\t' + report[1][0] + - '[' + str(report[1][1]) + ']' + - '\t' + str(round(report[2], 1))) - else: - print( - 'file\tListeria sensu stricto (rpoB)\tL. monocytogenes (rpoB)\tEscherichia spp. (rpoB)\tS. bongori (rpoB)\tS. enterica' + # noqa: E122 - '(rpoB)\tS. bongori (invA)\tsubsp. I (invA)\tsubsp. II (clade a: invA)\tsubsp. II' + # noqa: E122 - ' (clade b: invA)\tsubsp. IIIa (invA)\tsubsp. IIIb (invA)\tsubsp.IV (invA)\tsubsp. VI (invA)\tsubsp. VII (invA)' + # noqa: E122 - '\tsubsp. II (clade VIII : invA)') - if report == 'percentage': - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_scores = [str(round(score)) for score in locus_scores] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_scores)) - else: - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [str(round(cov, 1)) for cov in coverages] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_covs)) - - -if __name__ == '__main__': - main() -
--- a/deinterleave_fastq.sh Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi
--- a/pyproject.toml Thu Apr 30 21:47:42 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -[tool.poetry] -name = "salmid" -version = "0.1.23" -description = "Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia)." -authors = ["Henk den Bakker <hcd82599@uga.edu>"] -license = "MIT" -include = [ 'salmid/invA_mers_dict', 'salmid/rpoB_mers_dict' ] - -[tool.poetry.dependencies] -python = "^3.5" - -[tool.poetry.dev-dependencies] - -[tool.poetry.scripts] -'SalmID.py' = 'salmid.core:main' - -[build-system] -requires = ["poetry>=0.12"] -build-backend = "poetry.masonry.api"