Mercurial > repos > cstrittmatter > ss2v110

--- a/LICENSE	Tue Apr 21 12:49:07 2020 -0400
+++ b/LICENSE	Mon Apr 27 01:11:53 2020 -0400
@@ -1,339 +1,21 @@
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--- a/README.md	Tue Apr 21 12:49:07 2020 -0400
+++ b/README.md	Mon Apr 27 01:11:53 2020 -0400
@@ -1,117 +1,51 @@
-# SeqSero2 v1.1.0
-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).
+[![DOI](https://zenodo.org/badge/97020646.svg)](https://zenodo.org/badge/latestdoi/97020646)

-Allele micro-assembly workflow depends on:
-
-1. Python 3;
-
-2. Biopython 1.73;
+# SalmID
+Rapid tool to check taxonomic ID of single isolate samples. Currently only IDs Salmonella species and subspecies, and some common contaminants (Listeria, Escherichia).

-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);
+## Requirements:
+Python 3

-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);
-
+## 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!

-(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
+Alternatively download from GitHub:

-# Installation
-### Conda
-To install the latest SeqSero2 Conda package (recommended):
-```
-conda install -c bioconda seqsero2=1.1.0
-```
-### Git
-To install the SeqSero2 git repository locally:
-```
-git clone https://github.com/denglab/SeqSero2.git
-cd SeqSero2
-python3 -m pip install --user .
+```bash
+git clone https://github.com/hcdenbakker/SalmID.git
 ```
-### 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.
+build a wheel using [poetry](https://poetry.eustace.io/):

-    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)
+```bash
+cd SalmID
+poetry build
+```

-    -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)
+and install using `pip`

-    -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)
+```bash
+pip install dist/salmid*.whl
+```

-    -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:
+To execute:
+```
+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'

-    # 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)
+## 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero2.egg-info/PKG-INFO	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,132 @@
+Metadata-Version: 1.1
+Name: SeqSero2
+Version: 1.1.0
+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 v1.1.0
+        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=1.1.0
+        ```
+        ### 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	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero2.egg-info/not-zip-safe	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SeqSero2.egg-info/requires.txt	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+
Binary file __pycache__/version.cpython-36.pyc has changed
Binary file bin/__pycache__/Initial_Conditions.cpython-36.pyc has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/lib/LICENSE	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,339 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/lib/MANIFEST.in	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,117 @@
+# SeqSero2 v1.1.0
+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=1.1.0
+```
+### 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,132 @@
+Metadata-Version: 1.1
+Name: SeqSero2
+Version: 1.1.0
+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 v1.1.0
+        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=1.1.0
+        ```
+        ### 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	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/lib/SeqSero2.egg-info/requires.txt	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/lib/bin/Initial_Conditions.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,109 @@
+#!/usr/bin/env python
+
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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', 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 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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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1575 @@
+#!/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: v1.1.0')#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
+    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 "+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	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 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	Mon Apr 27 01:11:53 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
+TGCGGTACAGAACCGTTTCAACTCCGCTATCACCAACCTGGGCAATACCGTAAATAACCTGTCTTCTGCCCGTAGCCGTA
+TCGAAGATTCCGACTACGCGACCGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTG
+GCGCAGGCGAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA
+>fliC_z36,z38_Salmonella.enterica_IV.1,53:z36,z38:-_AY353485_z36,z38__1266
+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCCGCTCTGGGCAC
+CGCTATTGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGGTCAGGCGATTGCTAACCGTT
+TCACGTCTAACATTAAAGGTCTGTCTCAGGCTTCCCGTAATGCAAACGACGGTATTTCCATTGCGCAGACGACTGAAGGC
+GCGTTGAACGAAATCAACAACAACCTGCAGCGTGTGCGCGAACTGTCTGTCCAGGCAGCAAACGGCTCAAACTCTGACTC
+TGATCTTAAATCCATCCAGGATGAAATCGATCAGCGCCTGAACGAAATTAACCGTGTCGCGGAACAAACCGATTTTAACG
+GGAAAAAAGTATTAAGCCAGGATGGACAGCTGACCATTCAGGTTGGGGCGAATGACGGTGAAACTATTACAATCGATCTT
+CAGAAAATCGATAAAACCGAGCTGGGCTTAGATAAATTAGATGTGACTAAAGGAATTGCTACAACAGTTAAAGAAGGTAC
+GAAGCTCACTGCCGATTTTGCAGTTAAGGTCGCAGATTTTGATGATAAAGCAACAACTGGTAAATTAACTGCAAACTTAG
+AATTGAAGCAGGATAAATCCGGAAATTATTTTGCCTACGATAAAACAGCCAGTAAATACTATGATGCGACTGTAGATACT
+GCTACAGGTAAAATAGAATTTACTTCTGGGGCAGGTAAAGAGACAACGAAAGATACATCTAAACTTACGGATGTTACTTC
+TTTGTCCAAAGAAGTAACGATAGATAGTGGACTTACGGATGATAAATCATTAGTAAAATACAAAGGGGATGATGGTAAAG
+AACAGTATGCCGTTCAAACTCTTGATAATAAAGGTAATGCGACCTATAAGACTGCCGTTATAGCGCGTGACGGCAAAGTG
+ACAGAGGGCACTGCCGTAGCCTTGGCTGCAAACGTTGATCCGCTGGCAAAAATTGATGATGCGCTTAAAACCGTTGACGC
+TTTCCGTAGCCAGTTGGGTGCGGTGCAGAACCGTTTTGAATCTGCCATCACTAACCTGGGCAACACCGTCAACAACCTGT
+CTTCTGCACGTAGCCGTATCGAAGATTCCGACTATGCGACCGAAGTCTCCAACATGTCTCGCGCGCAGATTCTGCAGCAG
+GCAGGGACTTCTGTTCTGGCACAGGCTAACCAGGTTCCGCAAAACGTCCTCTCTTTACTGCGTTAA
+>O-9,46_wzy_partial__216
+TCAACCATTATTTTTAAGTGGGAGTAAATTATAGATGAAATAAAAAATCATCATAAATATGAACAAAAGA
+GAAATATATTTAACACCATAGGTGAGGTCTTTTCTCATTGCAACAAATATTAGGGAAATAATTGGAAAAT
+GATAAATTATGAGTCTGCTTTTCTTGGCTACAAGATAAAATACTATTAGCATTACGCCCAAGATTAAACC
+ATCAGG
+>fliC_z_6,14:z:l,z13,z28_inhouse_k,z__1500
+ATGGCACAAGTCATTAATACAAACAGCCTGTCGCTGTTGACCCAGAATAACCTGAACAAATCCCAGTCTG
+CTCTGGGTACCGCTATCGAGCGTCTGTCTTCCGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGG
+TCAGGCAATTGCTAACCGTTTCACCGCGAACATCAAAGGCCTGACTCAGGCTTCCCGTAACGCTAACGAC
+GGTATCTCCATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTG
+AACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTTGACTCCATCCAGGCTGAAATCAC
+CCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAG
+GACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCA
+ACTCTCAGACCCTGGGTCTGGATACGCTGAATGTGCAGAAAGCGTATGATGTAGATAGCAAAGCTGTGAC
+TGGTGTTTCTACTTTGGATACTACAGGTCTTACTGGCGCGAATATTAAAACTGGCGTTGATGGAGCTACC
+ACTACGAGTGGCTCCATTAAAGATGGCAAAGTATACTATGATGGTGCTACTAAAAATTATTATGTTGAAG
+TAGACTTTTCTGATGCCGCTGATACTGCTAAAAATGGCTACTATAAAGTCAATGTTGCTGATGATGGCAC
+TGTTACAATGGGGGCCTCGACTACTAAAGAAACTGCGAAACCTGCAGGTGTTGTTGAAGTAACGAAAACC
+CAAGAAGAGAAAGCAATTAAGGCGTCTGCTGAGGTGAAAGCTGCTTTGACTGCTGGTGGCGTCGATGCTG
+CTGATGCAGCTACGGCAGAAATGGTCAAAATGTCTTATACCGATAAAAACGGTAAGACGATTGATGGTGG
+TTATGCTGTAAAAGTAGGCGATAGCTACTATGCCGCTACCCAGAAAAAAGATGGTAGTTTCAGTGTTAAT
+ACTACTTCTTACACTGATAAAGACGGCAACACTAAATCTGCACTAAACCAACTGGGTGGCGTAGACGGTA
+AAACCGAAGTTGTTACTATCGACGGTAAAACCTACAATGCCAGCAAAGCTGCTGGTCATGATTTCAAAGC
+ACAGCCAGAGCTGGCTGAAGCAGCCGCTAAAACCACCGAAAATCCGCTGCAGAAAATTGATGCCGCGCTG
+GCGCAGGTTGATGCGCTGCGTTCTGACCTGGGTGCGGTTCAGAACCGTTTCAACTCCGCTATCACCAACC
+TGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGACCGAAGT
+CTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACCTCCGTTCTGGCGCAGGCGAACCAAGTT
+CCGCAAAACGTCCTCTCTTTACTGCGTTAA
+>fljB_e,n,z15_47:l,z13,z28:e,n,z15_inhouse_e__1506
+ATGGCACAAGTAATCAACACTAACAGTCTGTCGCTGCTGACCCAGAATAACCTGAACAAATCCCAGTCCG
+CACTGGGCACCGCTATCGAGCGTCTGTCTTCTGGTCTGCGTATCAACAGCGCGAAAGACGATGCGGCAGG
+TCAGGCGATTGCTAACCGTTTTACCGCGAACATCAAAGGTCTGACTCAGGCTTCCCGTAACGCTAACGAC
+GGTATTTCTATTGCGCAGACCACTGAAGGCGCGCTGAACGAAATCAACAACAACCTGCAGCGTGTGCGTG
+AACTGGCGGTTCAGTCTGCTAACAGCACCAACTCCCAGTCTGACCTTGACTCCATCCAGGCTGAAATCAC
+CCAGCGCCTGAACGAAATCGACCGTGTATCCGGCCAGACTCAGTTCAACGGCGTGAAAGTCCTGGCGCAG
+GACAACACCCTGACCATCCAGGTTGGTGCCAACGACGGTGAAACTATCGATATCGATCTGAAGCAGATCA
+ACTCTCAGACCCTGGGTCTGGATTCACTGAACGTGCAGAAAGCGTATGATGTTTCTGCGACAGACGTTAT
+CAGCTCTACCTATAGTGATGGTACTCAGGCGCTTACGGCACCAACTGCAACTGAGATTAAAGCTGCATTA
+GGCAACCCGACAGTAACTGGCGATACATTGACTGCCACCGTATCCTTTAAGGATGGTAAATATTATGCCA
+CTGTAGGTGGTTATACCGATGCAGGGGATACTGCCAAAAATGGTAAATATGAAGTTACCGTTGATAGTGC
+TACAGGGGCTGTATCATTCGGTGCTACTCCAACTAAATCTACTGTTACAGGTGATACCACTGTTACTAAG
+GTACAGGTTAATGCTCCTGTAGCAGCAGATGCTGCTACGAAAAAAGCCTTACAAGATGGGGGCGTTTCAT
+CTGCGGATGCAAGTGCCGCGACATTGGTCAAAATGTCTTATACCGATAAAAATGGTAAGACAATTGAAGG
+TGGTTATGCGCTTAAAGCTGGCGATAAGTATTACGCCGCAGATTACGATGAAGCGACAGGAGCAATTAAA
+GCTAAAACCACAAGTTATACTGCTGCTGACGGCACTACCAAAACAGCGGCTAACCAACTGGGTGGCGTAG
+ACGGTAAAACCGAAGTCGTTACTATCGACGGTAAAACTTACAATGCCAGCAAAGCCGCTGGTCATGATTT
+CAAAGCACAACCAGAGCTGGCGGAAGCAGCCGCTAAAACCACCGAAAACCCGCTGCAGAAAATTGATGCC
+GCGCTGGCGCAGGTGGATGCGCTGCGCTCTGATCTGGGTGCGGTACAAAACCGTTTCAACTCCGCTATCA
+CCAACCTGGGCAATACCGTAAACAACCTGTCTGAAGCGCGTAGCCGTATCGAAGATTCCGACTACGCGAC
+CGAAGTTTCCAACATGTCTCGCGCGCAGATTCTGCAGCAGGCCGGTACTTCCGTTCTGGCGCAGGCTAAC
+CAGGTCCCGCAGAACGTGCTGTCTCTGTTACGTTAA
+>fliC_b_Wien_CDC_b,d,j__1488
+TTAACGCAGTAAAGAGAGGACGTTTTGCGGAACCTGGTTAGCCTGCGCCAGAACGGAAGTACCGGCCTGC
+TGCAGAATCTGCGCGCGAGACATGTTGGAGACTTCGGTCGCGTAGTCGGAATCTTCGATACGGCTACGCG
+CTTCAGACAAGTTGTTTACGGTATTGCCCAGATTGGTGATAGCGGAGTTGAAACGGTTCTGAACCGCACC
+CAGGTCAGAACGCAGCGCATCAACCTGCGCCAGCGCGGCATCAATTTTAGCCAGCGGGTTTTCAGTTTTA
+GTAGTCACAGCCTCACTTAAAGCGCCACCACTCTGGAAATTATGCCCTTTCACATCACTAGCCTGATAAG
+TATTACCATCAACTGTAGTCACAACTTCAGTTTTACCATTCGCGCCGCCAAATTTCACAGCACCAGTTTT
+TGTTGCACCAGTAGCGTCAGTATAATTTACAGTCTTAGCTTTTATCTCACCAGTCTTTTCATCGTAATCA
+GCGGCATAATAATCATTTCCAACTTTAAGCGCGTAACCCGCATCAGTAACTTTGCCATTTTTATCTTCAA
+ATGACATTTTAACCAAGCTGGTATTACCTGTCGCACCTGTCACACCTGCATTGGTCAATGCAGTAGCTGC
+TGCGACTGTATCAACTGGTGCCGGAGTAACAGCGTCTACAATTTGGTTTTTGGTAACTGTGCCGGCCCCA
+GTTACTGTTGATTTATTTGCGGTCATTGTCACCGCGCCAGCTGCATCAACTGTCGCTTCATACAGACCAT
+TTTTAGCAGTTGTACCGGTCACCTCAACGAAGTAGTTACCGTCTTTAAATTTCACAGCCGCAGTACCCGT
+CGCACCAGTCAAACCTAAGGCGGTATCAATTTCTGCTGCGGTAGGTGCTGTAAGAGTAGTACCACCATCT
+TTATAGGTGGTAACATCCCTGGTAACAGCGGTACCTTTTGGCGTATAGGCGTCCTGTACACTTAAAGTAT
+CCAGACCCAGGGTCTGAGAGTTGATCTGCTTCAGATCGATATCAATAGTTTCACCATCGTTGGCGCCAAC
+CTGGATGGTCAGGGTGTTGTCCTGCGCCAGGACTTTCACGCCGTTGAACTGAGTCTGGCCGGATACACGG
+TCGATTTCGTTCAGACGCTGGGTGATTTCAGCCTGGATGGAGTCGAGGTCAGACTGGGAGTTGGTGCTGT
+TAGCAGACTGAACCGCCAGTTCACGCACACGCTGCAGGTTGTTGTTGATTTCGTTCAGCGCGCCTTCAGT
+GGTCTGCGCAATGGAGATACCGTCGTTAGCGTTACGGGAAGCCTGCGTCAGGCCTTTGATGTTCGCGGTG
+AAACGGTTAGCAATCGCCTGACCTGCCGCATCGTCTTTCGCGCTGTTGATACGCAGACCAGAAGACAGAC
+GCTCGATAGCGGTGCCCAGTGCGGACTGGGATTTGTTCAGGTTATTCTGGGTCAACAGCGACAGGCTGTT
+TGTATTAATGACTTGTGCCAT
+
Binary file build/lib/seqsero2_db/antigens.pickle has changed
Binary file build/lib/seqsero2_db/invA_mers_dict has changed
Binary file build/lib/seqsero2_db/special.pickle has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/lib/version.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+SeqSero2_version = '1.1.0'
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build/scripts-3.6/Initial_Conditions.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,109 @@
+#!/gal2001/Seqserotest/env/bin/python
+
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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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1575 @@
+#!/gal2001/Seqserotest/env/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: v1.1.0')#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
+    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 "+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	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,113 @@
+#!/gal2001/Seqserotest/env/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	Mon Apr 27 01:11:53 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/core.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,386 @@
+#!/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()
+
Binary file dist/SeqSero2-1.1.0-py3.6.egg has changed
Binary file dist/salmid-0.1.23-py3-none-any.whl has changed
Binary file dist/salmid-0.1.23.tar.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyproject.toml	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,19 @@
+[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"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salmid/core.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,386 @@
+#!/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()
+
Binary file salmid/invA_mers_dict has changed
Binary file salmid/rpoB_mers_dict has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/salmid/version.py	Mon Apr 27 01:11:53 2020 -0400
@@ -0,0 +1,1 @@
+SalmID_version = '0.1.23'