Mercurial > repos > cstrittmatter > ss2v110
changeset 3:8e36dd436ac4 draft
planemo upload commit c50df40caef2fb97c178d6890961e0e527992324-dirty
| author | cstrittmatter |
|---|---|
| date | Mon, 27 Apr 2020 01:20:42 -0400 |
| parents | d0350fe29fdf |
| children | 3e981acf8565 |
| files | bin/Initial_Conditions.py bin/SeqSero2_package.py bin/SeqSero2_update_kmer_database.py bin/__pycache__/Initial_Conditions.cpython-36.pyc bin/deinterleave_fastq.sh build/lib/LICENSE build/lib/MANIFEST.in build/lib/README.md build/lib/SeqSero2.egg-info/PKG-INFO build/lib/SeqSero2.egg-info/SOURCES.txt build/lib/SeqSero2.egg-info/dependency_links.txt build/lib/SeqSero2.egg-info/not-zip-safe build/lib/SeqSero2.egg-info/requires.txt build/lib/SeqSero2.egg-info/top_level.txt build/lib/bin/Initial_Conditions.py build/lib/bin/SeqSero2_package.py build/lib/bin/SeqSero2_update_kmer_database.py build/lib/bin/deinterleave_fastq.sh build/lib/seqsero2_db/H_and_O_and_specific_genes.fasta build/lib/seqsero2_db/antigens.pickle build/lib/seqsero2_db/invA_mers_dict build/lib/seqsero2_db/special.pickle build/lib/version.py build/scripts-3.6/Initial_Conditions.py build/scripts-3.6/SeqSero2_package.py build/scripts-3.6/SeqSero2_update_kmer_database.py build/scripts-3.6/deinterleave_fastq.sh salmid/__init__.py salmid/core.py salmid/invA_mers_dict salmid/rpoB_mers_dict salmid/version.py |
| diffstat | 31 files changed, 0 insertions(+), 13584 deletions(-) [+] |
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--- a/bin/Initial_Conditions.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -#!/usr/bin/env python - -subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 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- -remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] - -rename_dict={'Nitra': 'Enteritidis', - 'Kiel': 'Dublin', - 'Koessen': 'Panama', - 'Phaliron': 'Kalumburu', - 'Istanbul': 'Hadar', - 'Haardt': 'Blockley', - 'Ferruch': 'Kottbus', - 'Sanga': 'Eboko', - 'Pakistan': 'Litchfield', - 'Bellevue': 'Lezennes', - 'Sunnycove': 'Daarle', - 'Noya': 'Akanji', - 'Virginia': 'Muenchen', - 'Djelfa': 'Skansen', - 'Konstanz': 'Gatuni', - 'Bardo': 'Newport', - 'Houston': 'Panama', - 'Martonos': 'Finkenwerder', - 'Midway': 'Florida', - 'Lindern': 'Charity', - 'Bahrenfeld': 'Onderstepoort', - 'Schalkwijk': 'Moussoro', - 'Amberg': 'Boecker', - 'Madelia': 'Carrau', - 'Soahanina': 'Sundsvall', - 'Stafford': 'Poano', - 'Chichiri': 'Uzaramo', - 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', - 'Hindmarsh':'Bovismorbificans', - 'Yovokome': 'Manhattan'} - - #potential merge for O22 and O23 - #'Ibadan': 'Mississippi', - #'Bracknell': 'Oudwijk', - #'Vaertan': 'Ullevi', - #'Bahati': 'Durham', - #'Wichita': 'Friedenau', - #'Diguel': 'Telelkebir', - #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', - #'Washington': 'Kintambo', - #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', - #'Serenli': 'Winslow', - #'Farmsen': 'Poona', - #'Durance': 'Ivrysurseine', - #'Agoueve': 'Cubana', - #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', - #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', - #'Picpus': 'Mampong', - #'Anna': 'Nimes', - #'Fanti': 'Leiden', - #'Ried': 'Ajiobo', - - #potential O68 list - #'Djelfa': 'Skansen', - #'Korbol': 'Nagoya', - #'Sanga': 'Eboko', - #'Konstanz': 'Gatuni', - #'Presov': 'Shipley', - #'Heistopdenberg': 'Bukuru', - #'Tounouma': 'Banalia', - #'Gaillac': 'Utah', - #'Santiago': 'Belem', - #'Virginia': 'Muenchen', - #'Yovokome': 'Manhattan', - #'Portanigra': 'Dunkwa', - #'Bardo': 'Newport', - #'Ferruch': 'Kottbus', - #'Alminko': 'Nanergou', - #'Bargny': 'Takoradi', - #'Magherafelt': 'Cyprus', - #'Haardt': 'Blockley', - #'Pakistan': 'Litchfield', - #'Yokoe': 'Bassa', - #'Noya': 'Akanji', - #'Lamphun': 'Giza', - #'Tananarive': 'Brunei', - #'Inchpark': 'Alagbon', - #'Sunnycove': 'Daarle', - #'Sindelfingen': 'Benue', - #'Phaliron': 'Kalumburu', - #'Bazenheid': 'Zerifin', - #'Paris': 'Mapo', - #'Istanbul': 'Hadar', - #'Chomedey': 'Glostrup', - #'Wippra': 'Molade', - #'Uno': 'Tamale', - #'Kolda': 'Yarm', - #'Bellevue': 'Lezennes', - #'Albany':'Duesseldorf'
--- a/bin/SeqSero2_package.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1575 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import time -import random -import os -import subprocess -import gzip -import io -import pickle -import argparse -import itertools -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()
--- a/bin/SeqSero2_update_kmer_database.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os,subprocess -import pickle - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') - return parser.parse_args() - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - -def multifasta_to_kmers_dict(multifasta): - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) - return lib_dict - -def get_salmid_invA_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/invA_mers_dict', 'rb') - invA_dict = pickle.load(a) - try: - del invA_dict['version'] - except: - pass - return invA_dict - -def get_salmid_rpoB_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/rpoB_mers_dict', 'rb') - rpoB_dict = pickle.load(a) - try: - del rpoB_dict['version'] - except: - pass - return rpoB_dict - -def main(): - args = parse_args() - ex_dir = os.path.dirname(os.path.realpath(__file__)) - lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') - invA_dict=get_salmid_invA_database(ex_dir) - #rpoB_dict=get_salmid_rpoB_database(ex_dir) - lib_dict_new = lib_dict.copy() - #print(len(lib_dict_new)) - lib_dict_new.update(invA_dict) - #print(len(lib_dict_new)) - #lib_dict_new.update(rpoB_dict) - #print(len(lib_dict_new)) - f = open(ex_dir + '/antigens.pickle', "wb") - pickle.dump(lib_dict_new, f) - f.close() - -if __name__ == '__main__': - main()
--- a/bin/deinterleave_fastq.sh Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi
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--- a/build/lib/MANIFEST.in Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -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
--- a/build/lib/README.md Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,117 +0,0 @@ -# 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)
--- a/build/lib/SeqSero2.egg-info/PKG-INFO Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,132 +0,0 @@ -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
--- a/build/lib/SeqSero2.egg-info/SOURCES.txt Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -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
--- a/build/lib/SeqSero2.egg-info/dependency_links.txt Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -
--- a/build/lib/SeqSero2.egg-info/not-zip-safe Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -
--- a/build/lib/SeqSero2.egg-info/requires.txt Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -biopython==1.73
--- a/build/lib/SeqSero2.egg-info/top_level.txt Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -
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16:b:e,n,x', u'Hvittingfoss', u'II 41:b:1,5', u'Pharr', u'Eboko', u'Tonev', u'Sanga', u'Kuntair', u'Tucson', u'IIIb (6),14:b:e,n,x', u'Schleissheim (Schleissheim is extremely rare)', u'II 3,10:b:e,n,x', u'Atento', u'Leeuwarden', u'Wohlen', u'Korbol', u'VI 11:b:e,n,x', u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II [1],4,12,[27]:g,[m],[s],t:e,n,x', u'II 6,7:g,[m],s,t:[z42]', u'II 11:g,[m],s,t:z39', u'II 50:g,[m],s,t:[1,5]', u'II 57:g,[m],s,t:z42', u'II [1],4,12,[27]:g,[m],t:[1,5]', u'Senftenberg', u'II [1],13,23:g,[s],t:z42', u'Okatie', u'Enteritidis', u'Luke', u'Abadina', u'Yardley', u'Warragul', u'Bijlmer', u'Abuja', u'Bron', u'Essen', u'Hillingdon', u'Nitra', u'Suberu', u'Pontypridd', u'Montevideo', u'Korovi', u'Chincol', u'Gamaba', u'Tornow', u'Agbeni', u'II 6,7:g,m,[s],t:e,n,x', u'II [1],9,12:g,m,[s],t:[1,5,7]', u'II [1],13,23:g,m,[s],t:[e,n,x]', u'II 43:g,m,[s],t:[z42]', u'Godesberg', u'Othmarschen', u'Adeoyo', u'Kouka', u'Blegdam', u'Hato', u'Gueuletapee', u'Amsterdam', u'Nikolaifleet', u'Macclesfield', u'IIIb 13,22:g,m,s:z', u'Giessen', u'Ealing', u'Caracas', u'II 30:g,m,s:e,n,x', u'Croft', u'Athens', u'Emek', u'II [1],13,23:g,m,s,t:1,5', u'II 3,{10}{15}:g,m,s,t:[1,5]', u'II [1],9,12:g,m,s,t:e,n,x', u'II 45:g,m,s,t:1,5', u'II 17:g,m,s,t:-', u'II 6,7:g,m,s,t:z39', u'II 45:g,m,s,t:e,n,x', u'II [1],13,23:g,m,s,t:z42', u'II 41:g,m,s,t:z6', u'II 35:g,m,s,t:-', u'II 28:g,m,t:z39', u'II 28:g,m,t:e,n,x', u'II 60:g,m,t:z6', u'Reubeuss', u'II 6,8:g,m,t:1,7', u'II 45:g,m,t:e,n,x,z15', u'California', u'II 4,12:g,m,t:z39', u'Ebrie', u'II [1],13,22:g,m,t:[1,5]', u'II 48:g,m,t:-', u'Sylvania', u'Kiel', u'Dublin', u'Naestved', u'Rostock', u'Moscow', u'Menston', u'Plumaugat', u'Gateshead', u'Missouri', u'Catanzaro', u'Newyork', u'Sternschanze', u'Binningen', u'Anecho', u'II 9,12:g,s,t:e,n,x', u'Alminko', u'Nanergou', u'Cardoner', u'Ona', u'II 51:g,s,t:e,n,x', u'Lowestoft', u'Dessau', u'II 28:g,s,t:e,n,x', u'Splott', u'Kingston', u'Eaubonne', u'Uccle', u'Westhampton', u'II [1],13,22:g,t:[1,5]', u'IIIb [1],44:g,t:1,5', u'II 44:g,t:z42', u'IIIb 43:g,t:-', u'II 30:g,t:-', u'II 38:g,t:-', u'II 41:g,t:-', u'II 43:g,t:[1,5]', u'II 13,22:g,t:z6', u'II [1],13,23:g,t:1,5', u'Saintemarie', u'IV [1],40:g,t:-', u'II 17:g,t:[e,n,x,z15]', u'II 42:g,t:-', u'II 17:g,t:z39', u'II 65:g,t:-', u'Budapest', u'II 3,10:g,t:-', u'II 9,12,46,27:g,t:e,n,x', u'II [1],40:g,t:e,n,x,z15', u'II 57:g,t:-', u'Bloomsbury', u'II 13,23:g,t:e,n,x', u'II 52:g,t:-', u'II 35:g,t:1,5', u'II 35:g,t:z42', u'Agodi', u'II 40:g,t:z39', u'II 6,7:g,t:[e,n,x]', u'IIIa 50:g,z51:-', u'IIIa 51:g,z51:-', u'IV 48:g,z51:-', u'Larose', u'IV 21:g,z51:-', u'IIIa 21:g,z51:-', u'IIIa 63:g,z51:-', u'IIIa 62:g,z51:-', u'IV [1],53:g,z51:-', u'IV 43:g,z51:-', u'IV 11:g,z51:-', u'IV 6,7:g,z51:-', u'IIIa 35:g,z51:-', u'Wayne', u'IIIa 43:g,z51:-', u'Carswell', u'IV 44:g,z51:-', u'IIIa [1],13,23:g,z51:-', u'IIIa 53:g,z51:-', u'IIIa 47:g,z51:-', u'Newmexico', u'IIIa 18:g,z51:-', u'IV 18:g,z51:-', u'IV 45:g,z51:-', u'IV [1],40:g,z51:-', u'IV 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- -remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] - -rename_dict={'Nitra': 'Enteritidis', - 'Kiel': 'Dublin', - 'Koessen': 'Panama', - 'Phaliron': 'Kalumburu', - 'Istanbul': 'Hadar', - 'Haardt': 'Blockley', - 'Ferruch': 'Kottbus', - 'Sanga': 'Eboko', - 'Pakistan': 'Litchfield', - 'Bellevue': 'Lezennes', - 'Sunnycove': 'Daarle', - 'Noya': 'Akanji', - 'Virginia': 'Muenchen', - 'Djelfa': 'Skansen', - 'Konstanz': 'Gatuni', - 'Bardo': 'Newport', - 'Houston': 'Panama', - 'Martonos': 'Finkenwerder', - 'Midway': 'Florida', - 'Lindern': 'Charity', - 'Bahrenfeld': 'Onderstepoort', - 'Schalkwijk': 'Moussoro', - 'Amberg': 'Boecker', - 'Madelia': 'Carrau', - 'Soahanina': 'Sundsvall', - 'Stafford': 'Poano', - 'Chichiri': 'Uzaramo', - 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', - 'Hindmarsh':'Bovismorbificans', - 'Yovokome': 'Manhattan'} - - #potential merge for O22 and O23 - #'Ibadan': 'Mississippi', - #'Bracknell': 'Oudwijk', - #'Vaertan': 'Ullevi', - #'Bahati': 'Durham', - #'Wichita': 'Friedenau', - #'Diguel': 'Telelkebir', - #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', - #'Washington': 'Kintambo', - #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', - #'Serenli': 'Winslow', - #'Farmsen': 'Poona', - #'Durance': 'Ivrysurseine', - #'Agoueve': 'Cubana', - #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', - #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', - #'Picpus': 'Mampong', - #'Anna': 'Nimes', - #'Fanti': 'Leiden', - #'Ried': 'Ajiobo', - - #potential O68 list - #'Djelfa': 'Skansen', - #'Korbol': 'Nagoya', - #'Sanga': 'Eboko', - #'Konstanz': 'Gatuni', - #'Presov': 'Shipley', - #'Heistopdenberg': 'Bukuru', - #'Tounouma': 'Banalia', - #'Gaillac': 'Utah', - #'Santiago': 'Belem', - #'Virginia': 'Muenchen', - #'Yovokome': 'Manhattan', - #'Portanigra': 'Dunkwa', - #'Bardo': 'Newport', - #'Ferruch': 'Kottbus', - #'Alminko': 'Nanergou', - #'Bargny': 'Takoradi', - #'Magherafelt': 'Cyprus', - #'Haardt': 'Blockley', - #'Pakistan': 'Litchfield', - #'Yokoe': 'Bassa', - #'Noya': 'Akanji', - #'Lamphun': 'Giza', - #'Tananarive': 'Brunei', - #'Inchpark': 'Alagbon', - #'Sunnycove': 'Daarle', - #'Sindelfingen': 'Benue', - #'Phaliron': 'Kalumburu', - #'Bazenheid': 'Zerifin', - #'Paris': 'Mapo', - #'Istanbul': 'Hadar', - #'Chomedey': 'Glostrup', - #'Wippra': 'Molade', - #'Uno': 'Tamale', - #'Kolda': 'Yarm', - #'Bellevue': 'Lezennes', - #'Albany':'Duesseldorf'
--- a/build/lib/bin/SeqSero2_package.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1575 +0,0 @@ -#!/usr/bin/env python3 - -import sys -import time -import random -import os -import subprocess -import gzip -import io -import pickle -import argparse -import itertools -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()
--- a/build/lib/bin/SeqSero2_update_kmer_database.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/usr/bin/env python3 - -import argparse -import os,subprocess -import pickle - -### SeqSero Kmer -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = argparse.ArgumentParser(usage='Just type "SeqSero2_update_kmer_database.py", it will update kmer database automatically') - return parser.parse_args() - -def reverse_complement(sequence): - complement = { - 'A': 'T', - 'C': 'G', - 'G': 'C', - 'T': 'A', - 'N': 'N', - 'M': 'K', - 'R': 'Y', - 'W': 'W', - 'S': 'S', - 'Y': 'R', - 'K': 'M', - 'V': 'B', - 'H': 'D', - 'D': 'H', - 'B': 'V' - } - return "".join(complement[base] for base in reversed(sequence)) - -def multifasta_dict(multifasta): - multifasta_list = [ - line.strip() for line in open(multifasta, 'r') if len(line.strip()) > 0 - ] - headers = [i for i in multifasta_list if i[0] == '>'] - multifasta_dict = {} - for h in headers: - start = multifasta_list.index(h) - for element in multifasta_list[start + 1:]: - if element[0] == '>': - break - else: - if h[1:] in multifasta_dict: - multifasta_dict[h[1:]] += element - else: - multifasta_dict[h[1:]] = element - return multifasta_dict - -def createKmerDict_reads(list_of_strings, kmer): - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer].upper() - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - -def multifasta_to_kmers_dict(multifasta): - multi_seq_dict = multifasta_dict(multifasta) - lib_dict = {} - for h in multi_seq_dict: - lib_dict[h] = set( - [k for k in createKmerDict_reads([multi_seq_dict[h]], 27)]) - return lib_dict - -def get_salmid_invA_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/invA_mers_dict', 'rb') - invA_dict = pickle.load(a) - try: - del invA_dict['version'] - except: - pass - return invA_dict - -def get_salmid_rpoB_database(ex_dir): - # read invA kmer and return it - a = open(ex_dir + '/rpoB_mers_dict', 'rb') - rpoB_dict = pickle.load(a) - try: - del rpoB_dict['version'] - except: - pass - return rpoB_dict - -def main(): - args = parse_args() - ex_dir = os.path.dirname(os.path.realpath(__file__)) - lib_dict = multifasta_to_kmers_dict(ex_dir + '/H_and_O_and_specific_genes.fasta') - invA_dict=get_salmid_invA_database(ex_dir) - #rpoB_dict=get_salmid_rpoB_database(ex_dir) - lib_dict_new = lib_dict.copy() - #print(len(lib_dict_new)) - lib_dict_new.update(invA_dict) - #print(len(lib_dict_new)) - #lib_dict_new.update(rpoB_dict) - #print(len(lib_dict_new)) - f = open(ex_dir + '/antigens.pickle', "wb") - pickle.dump(lib_dict_new, f) - f.close() - -if __name__ == '__main__': - main()
--- a/build/lib/bin/deinterleave_fastq.sh Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi
--- a/build/lib/seqsero2_db/H_and_O_and_specific_genes.fasta Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7094 +0,0 @@ ->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 -
--- a/build/lib/version.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -SeqSero2_version = '1.1.0'
--- a/build/scripts-3.6/Initial_Conditions.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,109 +0,0 @@ -#!/gal2001/Seqserotest/env/bin/python - -subs=['II', 'I', 'I', 'II', 'I', 'II', 'II', 'I', 'II', 'II', 'II', 'II', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'IIIb', 'I', 'II', 'II', 'II', 'II', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'II', 'II', 'II', 'II', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'VI', 'II', 'I', 'VI', 'I', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'I', 'I', 'II', 'I', 'IV', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 'IV', 'I', 'I', 'I', 'I', 'II', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'I', 'II', 'II', 'I', 'I', 'II', 'I', 'I', 'II', 'I', 'I', 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u'II [1],13,23:a:1,5', u'Chagoua', u'Oran', u'IV 50:a:-', u'Burundi', u'Doba', u'Baildon', u'Detmold', u'II 6,7:a:z42', u'Wyldegreen', u'Miami', u'Lomalinda', u'Kinondoni', u'Saarbruecken', u'Jangwani', u'Graz', u'Berkeley', u'II 43:a:1,5', u'II 43:a:z6', u'Be', u'Os', u'II [1],4,[5],12,[27]:a:e,n,x', u'Bonames', u'Valdosta', u'II [1],9,12:a:e,n,x', u'Curacao', u'Niumi', u'Juba', u'Gwoza', u'Alkmaar', u'Sendai', u'Doncaster', u'Paratyphi A', u'Huettwilen', u'II 6,8:a:z39', u'II 6,8:a:z52', u'II [1],4,12,[27]:a:z39', u'Banjul', u'Nakuru', u'Tinda', u'Nordufer', u'Fulica', u'II 9,12:a:z39', u'Garba', u'VI [1],6,14:a:1,5', u'Niakhar', u'Tiergarten', u'Niarembe', u'Kisangani', u'II 9,12:a:1,5', u'Hessarek', u'Durban', u'Marseille', u'Gallen', u'Leith', u'II 6,8:a:e,n,x', u'Narashino', u'Arechavaleta', u'Brazos', u'Bispebjerg', u'VI [1],6,14,[25]:a:e,n,x', u'II 11:a:e,n,z15', u'Tchad', u'Abony', u'Uppsala', u'II 42:b:e,n,x,z15', u'Bamboye', u'Tomegbe', u'II 9,46:b:e,n,x', u'Linguere', u'Frederiksberg', u'Accra', u'Worb', u'Zadar', u'Cheltenham', u'Montaigu', u'Georgia', u'Lockleaze', u'Ibadan', u'Wagenia', u'Niederoderwitz', u'Ede', u'II 43:b:z42', u'Tambacounda', u'Kande', u'II 4,12:b:1,5', u'Broughton', u'Kolar', u'II 42:b:1,5', u'Canada', u'Kotte', u'Leopoldville', u'Ohio', u'II 6,7:b:[e,n,x]', u'Koumra', u'II [1],4,[5],12,[27]:b:[e,n,x]', u'Orbe', u'II 6,7:b:z39', u'Elbeuf', u'Vaugirard', u'Sedgwick', u'Wa', u'Melaka', u'Hull', u'Kirkee', u'Dahra', u'Mattenhof', u'II 17:b:e,n,x,z15', u'Wandsworth', u'II 17:b:z6', u'Glasgow', u'48:b:-', u'II 48:b:e,n,x,z15', u'II 48:b:z6', u'Shahalam', u'Riogrande', u'Saugus', u'Johannesburg', u'Duval', u'Benguella', u'II 40:b:-', u'Bignona', u'Paratyphi B', u'II 38:b:1,2', u'IV 50:b:-', u'II 50:b:z6', u'Rochdale', u'Rittersbach', u'Sica', u'Vietnam', u'Gnesta', u'VI 41:b:1,7', u'Abidjan', u'Limete', u'Adime', u'II 16:b:z42', u'II 16:b:z39', u'Malstatt', u'Visby', u'Edinburg', u'Brazzaville', u'Vegesack', u'Sangera', u'II 16:b:e,n,x', u'Hvittingfoss', u'II 41:b:1,5', u'Pharr', u'Eboko', u'Tonev', u'Sanga', u'Kuntair', u'Tucson', u'IIIb (6),14:b:e,n,x', u'Schleissheim (Schleissheim is extremely rare)', u'II 3,10:b:e,n,x', u'Atento', u'Leeuwarden', u'Wohlen', u'Korbol', u'VI 11:b:e,n,x', u'Fomeco', u'Erfurt', u'Yaba', u'Neudorf', u'Epicrates', u'Egusitoo', u'Sanktjohann', u'Stourbridge', u'Tripoli', u'Durham', u'II 6,8:b:1,5', u'Nagoya', u'VI 11:b:1,7', u'Maryland', u'Onarimon', u'Shipley', u'Presov', u'Frintrop', u'Kalina', u'Butantan', u'Bata', u'Allerton', u'Huvudsta', u'II 21:b:1,5', u'II [1],9,12:b:e,n,x', u'Konstanz', u'Batonrouge', u'Gatuni', u'Bukuru', u'Heistopdenberg', u'II [1],9,12:b:z6', u'Ghana', u'Tounouma', u'Benfica', u'Minnesota', u'II [1],9,12:b:z39', u'II 56:b:[1,5]', u'Banalia', u'Riverside', u'Chittagong', u'Mana', u'Westminster', u'Wien', u'II 60:b:-', u'Mississippi', u'Ndjamena', u'Wenatchee', u'II 47:b:1,5', u'II 47:b:e,n,x,z15', u'Sya', u'II 47:b:z6', u'Cochise', u'Djelfa', u'Wilmington', u'Oudwijk', u'II 3,10:b:z39', u'Louga', u'Aschersleben', u'Tempe', u'IV 51:b:-', u'Karaya', u'II 58:b:1,5', u'Urbana', u'II [1],13,22:b:z42', u'II 30:b:z6', u'II 42:b:z6', u'Fluntern', u'II [1],13,23:b:[1,5]', u'II 28:b:z6', u'Vaertan', u'Rottnest', u'II 28:b:e,n,x', u'Soumbedioune', u'Langford', u'Bracknell', u'Freefalls', u'Bokanjac', u'Bahati', u'Skansen', u'Flottbek', u'Molesey', u'Ullevi', u'Moero', u'Ashanti', u'II [1],40:c:z39', u'Antwerpen', u'Montreal', u'IIIb 41:c:e,n,x,z15', u'Bida', u'Kampala', u'IIIb 47:c:z35', u'IIIb 47:c:z', u'IIIb 47:c:e,n,x,z15', u'Eastglam', u'Madigan', u'Kassberg', u'Blijdorp', u'Minna', u'Haouaria', u'Luedinghausen', u'Ridge', u'Alabama', u'IIIb 47:c:1,5,7', u'Keurmassar', u'Madiago', u'Elokate', u'Ipeko', u'Deversoir', u'II 41:c:z6', u'Runby', u'Goeteborg', u'Quebec', u'Kodjovi', u'Lonestar', u'Chiredzi', u'Schwabach', u'II 21:c:e,n,x', u'Utah', u'IIIb 21:c:e,n,x,z15', u'Bronx', u'Belfast', u'Alexanderpolder', u'Santiago', u'Belem', u'Yolo', u'Tado', u'II 40:c:z6', u'Wingrove', u'II 53:c:1,5', u'Rhone', u'Brindisi', u'Hermannswerder', u'Eberswalde', u'Halle', u'II 52:c:k', u'Dresden', u'Wedding', u'Techimani', u'II 11:c:e,n,z15', u'Woodinville', u'Namibia', u'Cotonou', u'Kaduna', u'Rawash', u'Victoriaborg', u'II 17:c:z39', u'IIIb 65:c:z53', u'IIIb 65:c:z', u'IIIb 65:c:1,5,7', u'Okefoko', u'Anderlecht', u'Agege', u'Pramiso', u'IIIb 61:c:z35', u'IIIb 61:c:1,5,(7)', u'Ikayi', u'Gaillac', u'Asylanta', u'II 1,9,12,46,27:c:z39', u'IIIb 59:c:e,n,x,z15', u'Legon', u'Abortusovis', u'Altendorf', u'II 58:c:z6', u'Bissau', u'Jericho', u'Hallfold', u'IIIb 57:c:z', u'IIIb 57:c:e,n,x,z15', u'Bury', u'Hydra', u'Gbadago', u'Morningside', u'Gouloumbo', u'Itutaba', u'II 39:c:e,n,x', u'Vancouver', u'Gafsa', u'Paratyphi C', u'Choleraesuis', u'Typhisuis', u'II 30:c:z39', u'Hissar', u'Kidderminster', u'IIIb 48:c:z', u'Sheffield', u'Quiniela', u'Argenteuil', u'Hithergreen', u'Zaire', u'II 51:c:-', u'Birkenhead', u'Yoruba', u'II [1],40:c:e,n,x,z15', u'Shamba', u'Groenekan', u'Sculcoates', u'II 16:d:1,5', u'Usumbura', u'Sherbrooke', u'II 38:d:z39', u'II 38:d:[1,5]', u'Willamette', u'Oldenburg', u'Nieukerk', u'Orleans', u'Wil', u'Gaminara', u'Livingstone', u'II 6,7:d:z42', u'II 3,10:d:e,n,x', u'Driffield', u'Berlin', u'Karlshamn', u'Niamey', u'II 40:d:-', u'Logone', u'Maron', u'Weybridge', u'Stormont', u'Madjorio', u'Gombe', u'Souza', u'Onireke', u'Lekke', u'II 43:d:z42', u'II 43:d:z39', u'II 43:d:e,n,x,z15', u'Shangani', u'Barranquilla', u'Birmingham', u'Plymouth', u'Dembe', u'Midway', u'Florida', u'Lindern', u'Charity', u'Quentin', u'Typhi', u'II 9,12:d:z39', u'Jaffna', u'Finkenwerder', u'Olten', u'Martonos', u'Sontheim', u'Messina', u'Amoutive', u'Hatfield', u'Mundonobo', u'Mocamedes', u'Patience', u'Cullingworth', u'II 42:d:z6', u'Encino', u'Strasbourg', u'Eschberg', u'Nottingham', u'Caen', u'Barmbek', u'II 35:d:1,5', u'Teko', u'Tarshyne', u'Spartel', u'Magwa', u'Madison', u'Woodhull', u'Ndolo', u'II 16:d:e,n,x', u'II 41:d:z6', u'Bangui', u'Zega', u'Ontario', u'Amersfoort', u'Kambole', u'Kivu', u'Isangi', u'Kisii', u'Albuquerque', u'Egusi', u'Niloese', u'II 47:d:z39', u'II 47:d:e,n,x,z15', u'Stellingen', u'II 47:d:1,5', u'Liverpool', u'Tilburg', u'Wanatah', u'II 13,22:d:1,5', u'Ayinde', u'Friedenau', u'Wichita', u'Grumpensis', u'II [1],9,12:d:e,n,x', u'Diguel', u'II 48:d:1,2', u'Telelkebir', u'Putten', u'Ati', u'Gustavia', u'Warmsen', u'Karachi', u'Dugbe', u'Isuge', u'Chandans', u'Findorff', u'Hemingford', u'IV 50:d:-', u'II 13,23:d:e,n,x', u'Stanley', u'Brezany', u'Schwarzengrund', u'Ahmadi', u'II 4,12:d:e,n,x', u'Sarajane', u'Duisburg', u'Mons', u'II 53:d:z42', u'II [1],53:d:z39', u'II 53:d:1,5', u'Eppendorf', u'II 56:d:-', u'Buckeye', u'Umbadah', u'II 48:d:z6', u'II 57:d:1,5', u'Virginia', u'Muenchen', u'II 58:d:z6', u'II 52:d:z39', u'II 52:d:e,n,x,z15', u'Utrecht', u'Yovokome', u'Manhattan', u'Portanigra', u'Dunkwa', u'Sterrenbos', u'Mishmarhaemek', u'Chennai', u'Palamaner', u'Handen', u'II 6,8:d:z6', u'Fischerstrasse', u'Kermel', u'Gokul', u'Bobo', u'Labadi', u'Herston', u'Newlands', u'Kaapstad', u'Korkeasaari', u'Kpeme', u'Gozo', u'Israel', u'Westafrica', u'Eastbourne', u'Chester', u'Eko', u'Redhill', u'Bahrenfeld', u'Nyborg', u'Anatum', u'Muenster', u'Vejle', u'Hayindogo', u'Kottbus', u'Cremieu', u'Fitzroy', u'Meleagridis', u'Vilvoorde', u'Winnipeg', u'Jubilee', u'Sekondi', u'Saintpaul', u'Weston', u'Beaudesert', u'Guerin', u'Waedenswil', u'Derkle', u'Butare', u'Bergedorf', u'Newport', u'Reading', u'Magumeri', u'Larochelle', u'Lomita', u'Norwich', u'Nola', u'Tilene', u'Onderstepoort', u'Lamberhurst', u'Ferruch', u'Atakpame', u'Bardo', u'Tschangu', u'Braenderup', u'Saboya', u'Rechovot', u'Chingola', u'Chartres', u'Vridi', u'Torhout', u'Livulu', u'Astridplein', u'Sao', u'Bournemouth', u'Calabar', u'Gassi', u'Fillmore', u'Tshiongwe', u'Willemstad', u'Meskin', u'Rhydyfelin', u'Moabit', u'Sanktmarx', u'Adamstua', u'Bruebach', u'Mara', u'Kasenyi', u'Thiaroye', u'Sandiego', u'Malakal', u'Rossleben', u'II 50:e,n,x:1,7', u'II 6,7:e,n,x:1,6', u'II 16:e,n,x:1,6', u'II 3,10:e,n,x:1,7', u'II [1],4,12,[27]:e,n,x:1,[5],7', u'II [1],40:e,n,x:1,[5],7', u'II 56:e,n,x:1,7', u'II 16:e,n,x:1,(5),7', u'II [1],13,23:e,n,x:1,[5],7', u'II 4,12:e,n,x:1,2,7', u'II 9,46:e,n,x:1,5,7', u'II [1],44:e,n,x:1,6', u'II 9,12:e,n,x:1,[5],7', u'II 39:e,n,x:1,7', u'II 28:e,n,x:1,7', u'II 9,12:e,n,x:1,6', u'II 42:e,n,x:1,6', u'II 48:e,n,x,z15:z6', u'II [1],40:e,n,x,z15:1,6', u'II 47:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,6', u'II 43:e,n,x,z15:1,(5),7', u'II 43:e,n,x,z15:1,6', u'II 17:e,n,x,z15:1,[5],7', u'II 28:e,n,z15:z87', u'6,14:e,n,z15:-', u'Kastrup', u'Wernigerode', u'Derby', u'Raus', u'Vleuten', u'Sljeme', u'Good', u'Friedrichsfelde', u'Rissen', u'Alfort', u'Suelldorf', u'Sandow', u'Rideau', u'Tees', u'Adelaide', u'Havana', u'Regent', u'Milwaukee', u'II 6,8:f,g,m,t:[e,n,x]', u'Borreze', u'Agona', u'II [1],4,[5],12:f,g,t:z6', u'Eingedi', u'Afula', u'Bilu', u'Petahtikve', u'Maiduguri', u'II 28:g,(m),[s],t:1,5', u'Riggil', u'II [1],40:g,[m],[s],[t]:e,n,x', u'II 21:g,[m],[s],t:-', u'II [1],40:g,[m],[s],t:[1,5]', u'II 9,46:g,[m],[s],t:[e,n,x]', u'II 16:g,[m],[s],t:[e,n,x]', u'II [1],40:g,[m],[s],t:z42', u'II 16:g,[m],[s],t:[1,5]', u'II [1],4,12,[27]:g,[m],[s],t:e,n,x', u'II 6,7:g,[m],s,t:[z42]', u'II 11:g,[m],s,t:z39', u'II 50:g,[m],s,t:[1,5]', u'II 57:g,[m],s,t:z42', u'II [1],4,12,[27]:g,[m],t:[1,5]', u'Senftenberg', u'II [1],13,23:g,[s],t:z42', u'Okatie', u'Enteritidis', u'Luke', u'Abadina', u'Yardley', u'Warragul', u'Bijlmer', u'Abuja', u'Bron', u'Essen', u'Hillingdon', u'Nitra', u'Suberu', u'Pontypridd', u'Montevideo', u'Korovi', u'Chincol', u'Gamaba', u'Tornow', u'Agbeni', u'II 6,7:g,m,[s],t:e,n,x', u'II [1],9,12:g,m,[s],t:[1,5,7]', u'II [1],13,23:g,m,[s],t:[e,n,x]', u'II 43:g,m,[s],t:[z42]', u'Godesberg', u'Othmarschen', u'Adeoyo', u'Kouka', u'Blegdam', u'Hato', u'Gueuletapee', u'Amsterdam', u'Nikolaifleet', u'Macclesfield', u'IIIb 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- -remove_list=['Schleissheim', 'Sendai', 'Blegdam', 'Naestved', 'Rostock', 'Moscow', 'Antarctica', 'Rosenberg', 'Chittagong', 'Bilu', 'Dessau', 'Cannonhill', 'Ilugun'] - -rename_dict={'Nitra': 'Enteritidis', - 'Kiel': 'Dublin', - 'Koessen': 'Panama', - 'Phaliron': 'Kalumburu', - 'Istanbul': 'Hadar', - 'Haardt': 'Blockley', - 'Ferruch': 'Kottbus', - 'Sanga': 'Eboko', - 'Pakistan': 'Litchfield', - 'Bellevue': 'Lezennes', - 'Sunnycove': 'Daarle', - 'Noya': 'Akanji', - 'Virginia': 'Muenchen', - 'Djelfa': 'Skansen', - 'Konstanz': 'Gatuni', - 'Bardo': 'Newport', - 'Houston': 'Panama', - 'Martonos': 'Finkenwerder', - 'Midway': 'Florida', - 'Lindern': 'Charity', - 'Bahrenfeld': 'Onderstepoort', - 'Schalkwijk': 'Moussoro', - 'Amberg': 'Boecker', - 'Madelia': 'Carrau', - 'Soahanina': 'Sundsvall', - 'Stafford': 'Poano', - 'Chichiri': 'Uzaramo', - 'II 16:g,[m],[s],t:[e,n,x]': 'II 16:g,[m],[s],t:[1,5]', - 'Hindmarsh':'Bovismorbificans', - 'Yovokome': 'Manhattan'} - - #potential merge for O22 and O23 - #'Ibadan': 'Mississippi', - #'Bracknell': 'Oudwijk', - #'Vaertan': 'Ullevi', - #'Bahati': 'Durham', - #'Wichita': 'Friedenau', - #'Diguel': 'Telelkebir', - #'II 13,22:l,z28:1,5': 'II 13,23:l,z28:1,5', - #'Washington': 'Kintambo', - #'II 13,23:m,t:z42': 'II 13,22:m,t:z42:z39', - #'Serenli': 'Winslow', - #'Farmsen': 'Poona', - #'Durance': 'Ivrysurseine', - #'Agoueve': 'Cubana', - #'II 13,23:z29:1,5': 'II 13,22:z29:1,5', - #'II 13,23:z29:e,n,x': 'II 13,22:z29:e,n,x', - #'Picpus': 'Mampong', - #'Anna': 'Nimes', - #'Fanti': 'Leiden', - #'Ried': 'Ajiobo', - - #potential O68 list - #'Djelfa': 'Skansen', - #'Korbol': 'Nagoya', - #'Sanga': 'Eboko', - #'Konstanz': 'Gatuni', - #'Presov': 'Shipley', - #'Heistopdenberg': 'Bukuru', - #'Tounouma': 'Banalia', - #'Gaillac': 'Utah', - #'Santiago': 'Belem', - #'Virginia': 'Muenchen', - #'Yovokome': 'Manhattan', - #'Portanigra': 'Dunkwa', - #'Bardo': 'Newport', - #'Ferruch': 'Kottbus', - #'Alminko': 'Nanergou', - #'Bargny': 'Takoradi', - #'Magherafelt': 'Cyprus', - #'Haardt': 'Blockley', - #'Pakistan': 'Litchfield', - #'Yokoe': 'Bassa', - #'Noya': 'Akanji', - #'Lamphun': 'Giza', - #'Tananarive': 'Brunei', - #'Inchpark': 'Alagbon', - #'Sunnycove': 'Daarle', - #'Sindelfingen': 'Benue', - #'Phaliron': 'Kalumburu', - #'Bazenheid': 'Zerifin', - #'Paris': 'Mapo', - #'Istanbul': 'Hadar', - #'Chomedey': 'Glostrup', - #'Wippra': 'Molade', - #'Uno': 'Tamale', - #'Kolda': 'Yarm', - #'Bellevue': 'Lezennes', - #'Albany':'Duesseldorf'
--- a/build/scripts-3.6/SeqSero2_package.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1575 +0,0 @@ -#!/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()
--- a/build/scripts-3.6/SeqSero2_update_kmer_database.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -#!/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()
--- a/build/scripts-3.6/deinterleave_fastq.sh Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -#!/bin/bash -# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress] -# -# Deinterleaves a FASTQ file of paired reads into two FASTQ -# files specified on the command line. Optionally GZip compresses the output -# FASTQ files using pigz if the 3rd command line argument is the word "compress" -# -# Can deinterleave 100 million paired reads (200 million total -# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s) -# -# Latest code: https://gist.github.com/3521724 -# Also see my interleaving script: https://gist.github.com/4544979 -# -# Inspired by Torsten Seemann's blog post: -# http://thegenomefactory.blogspot.com.au/2012/05/cool-use-of-unix-paste-with-ngs.html - -# Set up some defaults -GZIP_OUTPUT=0 -PIGZ_COMPRESSION_THREADS=10 - -# If the third argument is the word "compress" then we'll compress the output using pigz -if [[ $3 == "compress" ]]; then - GZIP_OUTPUT=1 -fi - -if [[ ${GZIP_OUTPUT} == 0 ]]; then - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > $1) | cut -f 5-8 | tr "\t" "\n" > $2 -else - paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $1) | cut -f 5-8 | tr "\t" "\n" | pigz --best --processes ${PIGZ_COMPRESSION_THREADS} > $2 -fi
--- a/salmid/core.py Mon Apr 27 01:11:53 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,386 +0,0 @@ -#!/usr/bin/env python3 - - -import gzip -import io -import pickle -import os -import sys - -from argparse import ArgumentParser -try: - from .version import SalmID_version -except ImportError: - SalmID_version = "version unknown" - - -def reverse_complement(sequence): - """return the reverse complement of a nucleotide (including IUPAC ambiguous nuceotide codes)""" - complement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'N': 'N', 'M': 'K', 'R': 'Y', 'W': 'W', - 'S': 'S', 'Y': 'R', 'K': 'M', 'V': 'B', 'H': 'D', 'D': 'H', 'B': 'V'} - return "".join(complement[base] for base in reversed(sequence)) - - -def parse_args(): - "Parse the input arguments, use '-h' for help." - parser = ArgumentParser(description='SalmID - rapid Kmer based Salmonella identifier from sequence data') - # inputs - parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + SalmID_version) - parser.add_argument( - '-i', '--input_file', type=str, required=False, default='None', metavar='your_fastqgz', - help='Single fastq.gz file input, include path to file if file is not in same directory ') - parser.add_argument( - '-e', '--extension', type=str, required=False, default='.fastq.gz', metavar='file_extension', - help='File extension, if specified without "--input_dir", SalmID will attempt to ID all files\n' + - ' with this extension in current directory, otherwise files in input directory') - - parser.add_argument( - '-d', '--input_dir', type=str, required=False, default='.', metavar='directory', - help='Directory which contains data for identification, when not specified files in current directory will be analyzed.') - parser.add_argument( - '-r', '--report', type=str, required=False, default='percentage', metavar='percentage, coverage or taxonomy', - help='Report either percentage ("percentage") of clade specific kmers recovered, average kmer-coverage ("cov"), or ' - 'taxonomy (taxonomic species ID, plus observed mean k-mer coverages and expected coverage).') - parser.add_argument( - '-m', '--mode', type=str, required=False, default='quick', metavar='quick or thorough', - help='Quick [quick] or thorough [thorough] mode') - if len(sys.argv) == 1: - parser.print_help(sys.stderr) - sys.exit(1) - return parser.parse_args() - - -def get_av_read_length(file): - """Samples the first 100 reads from a fastq file and return the average read length.""" - i = 1 - n_reads = 0 - total_length = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - if i % 4 == 2: - total_length += len(line.strip()) - n_reads += 1 - i += 1 - if n_reads == 100: - break - return total_length / 100 - - -def createKmerDict_reads(list_of_strings, kmer): - """Count occurence of K-mers in a list of strings - - Args: - list_of_strings(list of str): nucleotide sequences as a list of strings - kmer(int): length of the K-mer to count - - Returns: - dict: dictionary with kmers as keys, counts for each kmer as values""" - kmer_table = {} - for string in list_of_strings: - sequence = string.strip('\n') - if len(sequence) >= kmer: - for i in range(len(sequence) - kmer + 1): - new_mer = sequence[i:i + kmer] - new_mer_rc = reverse_complement(new_mer) - if new_mer in kmer_table: - kmer_table[new_mer.upper()] += 1 - else: - kmer_table[new_mer.upper()] = 1 - if new_mer_rc in kmer_table: - kmer_table[new_mer_rc.upper()] += 1 - else: - kmer_table[new_mer_rc.upper()] = 1 - return kmer_table - - -def target_read_kmerizer_multi(file, k, kmerDict_1, kmerDict_2, mode): - mean_1 = None - mean_2 = None - i = 1 - n_reads_1 = 0 - n_reads_2 = 0 - total_coverage_1 = 0 - total_coverage_2 = 0 - reads_1 = [] - reads_2 = [] - total_reads = 0 - if file.endswith(".gz"): - file_content = io.BufferedReader(gzip.open(file)) - else: - file_content = open(file, "r").readlines() - for line in file_content: - start = int((len(line) - k) // 2) - if i % 4 == 2: - total_reads += 1 - if file.endswith(".gz"): - s1 = line[start:k + start].decode() - line = line.decode() - else: - s1 = line[start:k + start] - if s1 in kmerDict_1: - n_reads_1 += 1 - total_coverage_1 += len(line) - reads_1.append(line) - if s1 in kmerDict_2: - n_reads_2 += 1 - total_coverage_2 += len(line) - reads_2.append(line) - i += 1 - if mode == 'quick': - if total_coverage_2 >= 800000: - break - - if len(reads_1) == 0: - kmer_Dict1 = {} - else: - kmer_Dict1 = createKmerDict_reads(reads_1, k) - mers_1 = set([key for key in kmer_Dict1]) - mean_1 = sum([kmer_Dict1[key] for key in kmer_Dict1]) / len(mers_1) - if len(reads_2) == 0: - kmer_Dict2 = {} - else: - kmer_Dict2 = createKmerDict_reads(reads_2, k) - mers_2 = set([key for key in kmer_Dict2]) - mean_2 = sum([kmer_Dict2[key] for key in kmer_Dict2]) / len(mers_2) - return kmer_Dict1, kmer_Dict2, mean_1, mean_2, total_reads - - -def mean_cov_selected_kmers(iterable, kmer_dict, clade_specific_kmers): - ''' - Given an iterable (list, set, dictrionary) returns mean coverage for the kmers in iterable - :param iterable: set, list or dictionary containing kmers - :param kmer_dict: dictionary with kmers as keys, kmer-frequency as value - :param clade_specific_kmers: list, dict or set of clade specific kmers - :return: mean frequency as float - ''' - if len(iterable) == 0: - return 0 - return sum([kmer_dict[value] for value in iterable]) / len(clade_specific_kmers) - - -def kmer_lists(query_fastq_gz, k, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode): - dict_invA, dict_rpoB, mean_invA, mean_rpoB, total_reads = target_read_kmerizer_multi(query_fastq_gz, k, allmers, - allmers_rpoB, mode) - target_mers_invA = set([key for key in dict_invA]) - target_mers_rpoB = set([key for key in dict_rpoB]) - if target_mers_invA == 0: - print('No reads found matching invA, no Salmonella in sample?') - else: - p_bongori = (len(uniqmers_bongori & target_mers_invA) / len(uniqmers_bongori)) * 100 - p_I = (len(uniqmers_I & target_mers_invA) / len(uniqmers_I)) * 100 - p_IIa = (len(uniqmers_IIa & target_mers_invA) / len(uniqmers_IIa)) * 100 - p_IIb = (len(uniqmers_IIb & target_mers_invA) / len(uniqmers_IIb)) * 100 - p_IIIa = (len(uniqmers_IIIa & target_mers_invA) / len(uniqmers_IIIa)) * 100 - p_IIIb = (len(uniqmers_IIIb & target_mers_invA) / len(uniqmers_IIIb)) * 100 - p_VI = (len(uniqmers_VI & target_mers_invA) / len(uniqmers_VI)) * 100 - p_IV = (len(uniqmers_IV & target_mers_invA) / len(uniqmers_IV)) * 100 - p_VII = (len(uniqmers_VII & target_mers_invA) / len(uniqmers_VII)) * 100 - p_VIII = (len(uniqmers_VIII & target_mers_invA) / len(uniqmers_VIII)) * 100 - p_bongori_rpoB = (len(uniqmers_bongori_rpoB & target_mers_rpoB) / len(uniqmers_bongori_rpoB)) * 100 - p_Senterica = (len(uniqmers_S_enterica_rpoB & target_mers_rpoB) / len(uniqmers_S_enterica_rpoB)) * 100 - p_Escherichia = (len(uniqmers_Escherichia_rpoB & target_mers_rpoB) / len(uniqmers_Escherichia_rpoB)) * 100 - p_Listeria_ss = (len(uniqmers_Listeria_ss_rpoB & target_mers_rpoB) / len(uniqmers_Listeria_ss_rpoB)) * 100 - p_Lmono = (len(uniqmers_Lmono_rpoB & target_mers_rpoB) / len(uniqmers_Lmono_rpoB)) * 100 - bongori_invA_cov = mean_cov_selected_kmers(uniqmers_bongori & target_mers_invA, dict_invA, uniqmers_bongori) - I_invA_cov = mean_cov_selected_kmers(uniqmers_I & target_mers_invA, dict_invA, uniqmers_I) - IIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIa & target_mers_invA, dict_invA, uniqmers_IIa) - IIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIb & target_mers_invA, dict_invA, uniqmers_IIb) - IIIa_invA_cov = mean_cov_selected_kmers(uniqmers_IIIa & target_mers_invA, dict_invA, uniqmers_IIIa) - IIIb_invA_cov = mean_cov_selected_kmers(uniqmers_IIIb & target_mers_invA, dict_invA, uniqmers_IIIb) - IV_invA_cov = mean_cov_selected_kmers(uniqmers_IV & target_mers_invA, dict_invA, uniqmers_IV) - VI_invA_cov = mean_cov_selected_kmers(uniqmers_VI & target_mers_invA, dict_invA, uniqmers_VI) - VII_invA_cov = mean_cov_selected_kmers(uniqmers_VII & target_mers_invA, dict_invA, uniqmers_VII) - VIII_invA_cov = mean_cov_selected_kmers(uniqmers_VIII & target_mers_invA, dict_invA, uniqmers_VIII) - S_enterica_rpoB_cov = mean_cov_selected_kmers((uniqmers_S_enterica_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_S_enterica_rpoB) - S_bongori_rpoB_cov = mean_cov_selected_kmers((uniqmers_bongori_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_bongori_rpoB) - Escherichia_rpoB_cov = mean_cov_selected_kmers((uniqmers_Escherichia_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Escherichia_rpoB) - Listeria_ss_rpoB_cov = mean_cov_selected_kmers((uniqmers_Listeria_ss_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Listeria_ss_rpoB) - Lmono_rpoB_cov = mean_cov_selected_kmers((uniqmers_Lmono_rpoB & target_mers_rpoB), dict_rpoB, - uniqmers_Lmono_rpoB) - coverages = [Listeria_ss_rpoB_cov, Lmono_rpoB_cov, Escherichia_rpoB_cov, S_bongori_rpoB_cov, - S_enterica_rpoB_cov, bongori_invA_cov, I_invA_cov, IIa_invA_cov, IIb_invA_cov, - IIIa_invA_cov, IIIb_invA_cov, IV_invA_cov, VI_invA_cov, VII_invA_cov, VIII_invA_cov] - locus_scores = [p_Listeria_ss, p_Lmono, p_Escherichia, p_bongori_rpoB, p_Senterica, p_bongori, - p_I, p_IIa, p_IIb, p_IIIa, p_IIIb, p_IV, p_VI, p_VII, p_VIII] - return locus_scores, coverages, total_reads - - -def report_taxon(locus_covs, average_read_length, number_of_reads): - list_taxa = [ 'Listeria ss', 'Listeria monocytogenes', 'Escherichia sp.', # noqa: E201 - 'Salmonella bongori (rpoB)', 'Salmonella enterica (rpoB)', - 'Salmonella bongori (invA)', 'S. enterica subsp. enterica (invA)', - 'S. enterica subsp. salamae (invA: clade a)', 'S. enterica subsp. salamae (invA: clade b)', - 'S. enterica subsp. arizonae (invA)', 'S. enterica subsp. diarizonae (invA)', - 'S. enterica subsp. houtenae (invA)', 'S. enterica subsp. indica (invA)', - 'S. enterica subsp. VII (invA)', 'S. enterica subsp. salamae (invA: clade VIII)' ] # noqa: E202 - if sum(locus_covs) < 1: - rpoB = ('No rpoB matches!', 0) - invA = ('No invA matches!', 0) - return rpoB, invA, 0.0 - else: - # given list of scores get taxon - if sum(locus_covs[0:5]) > 0: - best_rpoB = max(range(len(locus_covs[1:5])), key=lambda x: locus_covs[1:5][x]) + 1 - all_rpoB = max(range(len(locus_covs[0:5])), key=lambda x: locus_covs[0:5][x]) - if (locus_covs[best_rpoB] != 0) & (all_rpoB == 0): - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - elif (all_rpoB == 0) & (round(sum(locus_covs[1:5]), 1) < 1): - rpoB = (list_taxa[0], locus_covs[0]) - else: - rpoB = (list_taxa[best_rpoB], locus_covs[best_rpoB]) - else: - rpoB = ('No rpoB matches!', 0) - if sum(locus_covs[5:]) > 0: - best_invA = max(range(len(locus_covs[5:])), key=lambda x: locus_covs[5:][x]) + 5 - invA = (list_taxa[best_invA], locus_covs[best_invA]) - else: - invA = ('No invA matches!', 0) - if 'Listeria' in rpoB[0]: - return rpoB, invA, (average_read_length * number_of_reads) / 3000000 - else: - return rpoB, invA, (average_read_length * number_of_reads) / 5000000 - - -def main(): - ex_dir = os.path.dirname(os.path.realpath(__file__)) - args = parse_args() - input_file = args.input_file - if input_file != 'None': - files = [input_file] - else: - extension = args.extension - inputdir = args.input_dir - files = [inputdir + '/' + f for f in os.listdir(inputdir) if f.endswith(extension)] - report = args.report - mode = args.mode - f_invA = open(ex_dir + "/invA_mers_dict", "rb") - sets_dict_invA = pickle.load(f_invA) - f_invA.close() - allmers = sets_dict_invA['allmers'] - uniqmers_I = sets_dict_invA['uniqmers_I'] - uniqmers_IIa = sets_dict_invA['uniqmers_IIa'] - uniqmers_IIb = sets_dict_invA['uniqmers_IIb'] - uniqmers_IIIa = sets_dict_invA['uniqmers_IIIa'] - uniqmers_IIIb = sets_dict_invA['uniqmers_IIIb'] - uniqmers_IV = sets_dict_invA['uniqmers_IV'] - uniqmers_VI = sets_dict_invA['uniqmers_VI'] - uniqmers_VII = sets_dict_invA['uniqmers_VII'] - uniqmers_VIII = sets_dict_invA['uniqmers_VIII'] - uniqmers_bongori = sets_dict_invA['uniqmers_bongori'] - - f = open(ex_dir + "/rpoB_mers_dict", "rb") - sets_dict = pickle.load(f) - f.close() - - allmers_rpoB = sets_dict['allmers'] - uniqmers_bongori_rpoB = sets_dict['uniqmers_bongori'] - uniqmers_S_enterica_rpoB = sets_dict['uniqmers_S_enterica'] - uniqmers_Escherichia_rpoB = sets_dict['uniqmers_Escherichia'] - uniqmers_Listeria_ss_rpoB = sets_dict['uniqmers_Listeria_ss'] - uniqmers_Lmono_rpoB = sets_dict['uniqmers_L_mono'] - # todo: run kmer_lists() once, create list of tuples containing data to be used fro different reports - if report == 'taxonomy': - print('file\trpoB\tinvA\texpected coverage') - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [round(cov, 1) for cov in coverages] - report = report_taxon(pretty_covs, get_av_read_length(f), reads) - print(f.split('/')[-1] + '\t' + report[0][0] + '[' + str(report[0][1]) + ']' + '\t' + report[1][0] + - '[' + str(report[1][1]) + ']' + - '\t' + str(round(report[2], 1))) - else: - print( - 'file\tListeria sensu stricto (rpoB)\tL. monocytogenes (rpoB)\tEscherichia spp. (rpoB)\tS. bongori (rpoB)\tS. enterica' + # noqa: E122 - '(rpoB)\tS. bongori (invA)\tsubsp. I (invA)\tsubsp. II (clade a: invA)\tsubsp. II' + # noqa: E122 - ' (clade b: invA)\tsubsp. IIIa (invA)\tsubsp. IIIb (invA)\tsubsp.IV (invA)\tsubsp. VI (invA)\tsubsp. VII (invA)' + # noqa: E122 - '\tsubsp. II (clade VIII : invA)') - if report == 'percentage': - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_scores = [str(round(score)) for score in locus_scores] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_scores)) - else: - for f in files: - locus_scores, coverages, reads = kmer_lists(f, 27, - allmers, allmers_rpoB, - uniqmers_bongori, - uniqmers_I, - uniqmers_IIa, - uniqmers_IIb, - uniqmers_IIIa, - uniqmers_IIIb, - uniqmers_IV, - uniqmers_VI, - uniqmers_VII, - uniqmers_VIII, - uniqmers_bongori_rpoB, - uniqmers_S_enterica_rpoB, - uniqmers_Escherichia_rpoB, - uniqmers_Listeria_ss_rpoB, - uniqmers_Lmono_rpoB, - mode) - pretty_covs = [str(round(cov, 1)) for cov in coverages] - print(f.split('/')[-1] + '\t' + '\t'.join(pretty_covs)) - - -if __name__ == '__main__': - main() -