forked from widdowquinn/find_differential_primers
-
Notifications
You must be signed in to change notification settings - Fork 0
/
O104_primers_5.conf
103 lines (100 loc) · 14.8 KB
/
O104_primers_5.conf
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
# Configuration file for a script to find differential primers in the O104
# genomes.
#
# This file defines the following data, in tab-separated format:
# Column 1: Organism abbreviation
# Column 2: Family/group for the organism, comma-separated for multiple groups
# Column 3: Location of sequence data in FASTA format
# Column 4: Location of GenBank file describing features ('-' if none)
# Column 5: Location of ePrimer3 primer definitions ('-' if none)
# Column 6: Location of PrimerSearch input format primer definitions ('-' if none)
#
# BLANK COLUMNS ARE IGNORED! USE '-' IF THERE IS NO DATA.
#
# Copyright Leighton Pritchard 2011
#
# E. coli O104 primer prediction 20110627
GOS1 O104 O104_sequences/GOS1_contigs_stitched.fasta O104_sequences/GOS1_contigs_stitched.prodigalout O104_sequences/GOS1_contigs_stitched.eprimer3 -
GOS2 O104 O104_sequences/GOS2_contigs_stitched.fasta O104_sequences/GOS2_contigs_stitched.prodigalout O104_sequences/GOS2_contigs_stitched.eprimer3 -
H112180280 O104 O104_sequences/Sample280_contigs_stitched.fasta O104_sequences/Sample280_contigs_stitched.prodigalout O104_sequences/Sample280_contigs_stitched.eprimer3 -
H112240282 O104 O104_sequences/Sample282_contigs_stitched.fasta O104_sequences/Sample282_contigs_stitched.prodigalout O104_sequences/Sample282_contigs_stitched.eprimer3 -
H112240283 O104 O104_sequences/Sample283_contigs_stitched.fasta O104_sequences/Sample283_contigs_stitched.prodigalout O104_sequences/Sample283_contigs_stitched.eprimer3 -
H112240540 O104 O104_sequences/Sample540_contigs_stitched.fasta O104_sequences/Sample540_contigs_stitched.prodigalout O104_sequences/Sample540_contigs_stitched.eprimer3 -
H112240541 O104 O104_sequences/Sample541_contigs_stitched.fasta O104_sequences/Sample541_contigs_stitched.prodigalout O104_sequences/Sample541_contigs_stitched.eprimer3 -
LB226692-NCBI O104 O104_sequences/LB226692_contigs_stitched.fasta O104_sequences/LB226692_contigs_stitched.prodigalout O104_sequences/LB226692_contigs_stitched.eprimer3 -
LB226692-Muenster O104 O104_sequences/wgs.AFOB.1_stitched.fasta O104_sequences/wgs.AFOB.1_stitched.prodigalout O104_sequences/wgs.AFOB.1_stitched.eprimer3 -
TY2482-BGI1 O104 O104_sequences/TY-2482-BGI_stitched.fasta O104_sequences/TY-2482-BGI_stitched.prodigalout O104_sequences/TY-2482-BGI_stitched.eprimer3 -
TY2482-LOMAN O104 O104_sequences/TY2482.fasta_stitched.fasta O104_sequences/TY2482.fasta_stitched.prodigalout O104_sequences/TY2482.fasta_stitched.eprimer3 -
Escherichia_coli_str._K-12_substr._W3110_chromosome,_complete_genome not_O104 sequences/AC_000091_fixed.fasta sequences/AC_000091_fixed.prodigalout sequences/AC_000091_fixed.eprimer3 -
Escherichia_coli_str._K-12_substr._MG1655_chromosome,_complete_genome not_O104 sequences/NC_000913_fixed.fasta sequences/NC_000913_fixed.prodigalout sequences/NC_000913_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._Sakai_plasmid_pOSAK1,_complete_sequence not_O104 sequences/NC_002127_fixed.fasta sequences/NC_002127_fixed.prodigalout sequences/NC_002127_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._Sakai_plasmid_pO157,_complete_sequence not_O104 sequences/NC_002128_fixed.fasta sequences/NC_002128_fixed.prodigalout sequences/NC_002128_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._EDL933_chromosome,_complete_genome not_O104 sequences/NC_002655_fixed.fasta sequences/NC_002655_fixed.prodigalout sequences/NC_002655_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._Sakai,_complete_genome not_O104 sequences/NC_002695_fixed.fasta sequences/NC_002695_fixed.prodigalout sequences/NC_002695_fixed.eprimer3 -
Escherichia_coli_CFT073,_complete_genome not_O104 sequences/NC_004431_fixed.fasta sequences/NC_004431_fixed.prodigalout sequences/NC_004431_fixed.eprimer3 -
Escherichia_coli_O157:H7_EDL933_plasmid_pO157,_complete_sequence not_O104 sequences/NC_007414_fixed.fasta sequences/NC_007414_fixed.prodigalout sequences/NC_007414_fixed.eprimer3 -
Escherichia_coli_UTI89_plasmid_pUTI89,_complete_sequence not_O104 sequences/NC_007941_fixed.fasta sequences/NC_007941_fixed.prodigalout sequences/NC_007941_fixed.eprimer3 -
Escherichia_coli_UTI89,_complete_genome not_O104 sequences/NC_007946_fixed.fasta sequences/NC_007946_fixed.prodigalout sequences/NC_007946_fixed.eprimer3 -
Escherichia_coli_536,_complete_genome not_O104 sequences/NC_008253_fixed.fasta sequences/NC_008253_fixed.prodigalout sequences/NC_008253_fixed.eprimer3 -
Escherichia_coli_APEC_O1,_complete_genome not_O104 sequences/NC_008563_fixed.fasta sequences/NC_008563_fixed.prodigalout sequences/NC_008563_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_80,_complete_sequence not_O104 sequences/NC_009786_fixed.fasta sequences/NC_009786_fixed.prodigalout sequences/NC_009786_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_35,_complete_sequence not_O104 sequences/NC_009787_fixed.fasta sequences/NC_009787_fixed.prodigalout sequences/NC_009787_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_73,_complete_sequence not_O104 sequences/NC_009788_fixed.fasta sequences/NC_009788_fixed.prodigalout sequences/NC_009788_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_6,_complete_sequence not_O104 sequences/NC_009789_fixed.fasta sequences/NC_009789_fixed.prodigalout sequences/NC_009789_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_74,_complete_sequence not_O104 sequences/NC_009790_fixed.fasta sequences/NC_009790_fixed.prodigalout sequences/NC_009790_fixed.eprimer3 -
Escherichia_coli_E24377A_plasmid_pETEC_5,_complete_sequence not_O104 sequences/NC_009791_fixed.fasta sequences/NC_009791_fixed.prodigalout sequences/NC_009791_fixed.eprimer3 -
Escherichia_coli_HS,_complete_genome not_O104 sequences/NC_009800_fixed.fasta sequences/NC_009800_fixed.prodigalout sequences/NC_009800_fixed.eprimer3 -
Escherichia_coli_E24377A,_complete_genome not_O104 sequences/NC_009801_fixed.fasta sequences/NC_009801_fixed.prodigalout sequences/NC_009801_fixed.eprimer3 -
Escherichia_coli_APEC_O1_plasmid_pAPEC-O1-ColBM,_complete_sequence not_O104 sequences/NC_009837_fixed.fasta sequences/NC_009837_fixed.prodigalout sequences/NC_009837_fixed.eprimer3 -
Escherichia_coli_APEC_O1_plasmid_pAPEC-O1-R,_complete_sequence not_O104 sequences/NC_009838_fixed.fasta sequences/NC_009838_fixed.prodigalout sequences/NC_009838_fixed.eprimer3 -
Escherichia_coli_ATCC_8739,_complete_genome not_O104 sequences/NC_010468_fixed.fasta sequences/NC_010468_fixed.prodigalout sequences/NC_010468_fixed.eprimer3 -
Escherichia_coli_str._K-12_substr._DH10B,_complete_genome not_O104 sequences/NC_010473_fixed.fasta sequences/NC_010473_fixed.prodigalout sequences/NC_010473_fixed.eprimer3 -
Escherichia_coli_SMS-3-5_plasmid_pSMS35_8,_complete_sequence not_O104 sequences/NC_010485_fixed.fasta sequences/NC_010485_fixed.prodigalout sequences/NC_010485_fixed.eprimer3 -
Escherichia_coli_SMS-3-5_plasmid_pSMS35_4,_complete_sequence not_O104 sequences/NC_010486_fixed.fasta sequences/NC_010486_fixed.prodigalout sequences/NC_010486_fixed.eprimer3 -
Escherichia_coli_SMS-3-5_plasmid_pSMS35_3,_complete_sequence not_O104 sequences/NC_010487_fixed.fasta sequences/NC_010487_fixed.prodigalout sequences/NC_010487_fixed.eprimer3 -
Escherichia_coli_SMS-3-5_plasmid_pSMS35_130,_complete_sequence not_O104 sequences/NC_010488_fixed.fasta sequences/NC_010488_fixed.prodigalout sequences/NC_010488_fixed.eprimer3 -
Escherichia_coli_SMS-3-5,_complete_genome not_O104 sequences/NC_010498_fixed.fasta sequences/NC_010498_fixed.prodigalout sequences/NC_010498_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._EC4115_plasmid_pO157,_complete_sequence not_O104 sequences/NC_011350_fixed.fasta sequences/NC_011350_fixed.prodigalout sequences/NC_011350_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._EC4115_plasmid_pEC4115,_complete_sequence not_O104 sequences/NC_011351_fixed.fasta sequences/NC_011351_fixed.prodigalout sequences/NC_011351_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._EC4115,_complete_genome not_O104 sequences/NC_011353_fixed.fasta sequences/NC_011353_fixed.prodigalout sequences/NC_011353_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-4,_complete_sequence not_O104 sequences/NC_011407_fixed.fasta sequences/NC_011407_fixed.prodigalout sequences/NC_011407_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-5,_complete_sequence not_O104 sequences/NC_011408_fixed.fasta sequences/NC_011408_fixed.prodigalout sequences/NC_011408_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-6,_complete_sequence not_O104 sequences/NC_011411_fixed.fasta sequences/NC_011411_fixed.prodigalout sequences/NC_011411_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-2,_complete_sequence not_O104 sequences/NC_011413_fixed.fasta sequences/NC_011413_fixed.prodigalout sequences/NC_011413_fixed.eprimer3 -
Escherichia_coli_SE11,_complete_genome not_O104 sequences/NC_011415_fixed.fasta sequences/NC_011415_fixed.prodigalout sequences/NC_011415_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-3,_complete_sequence not_O104 sequences/NC_011416_fixed.fasta sequences/NC_011416_fixed.prodigalout sequences/NC_011416_fixed.eprimer3 -
Escherichia_coli_SE11_plasmid_pSE11-1,_complete_sequence not_O104 sequences/NC_011419_fixed.fasta sequences/NC_011419_fixed.prodigalout sequences/NC_011419_fixed.eprimer3 -
#Escherichia_coli_O127:H6_str._E2348/69,_complete_genome not_O104 sequences/NC_011601_fixed.fasta sequences/NC_011601_fixed.prodigalout sequences/NC_011601_fixed.eprimer3 -
#Escherichia_coli_O127:H6_str._E2348/69_plasmid_pE2348-2,_complete_sequence not_O104 sequences/NC_011602_fixed.fasta sequences/NC_011602_fixed.prodigalout sequences/NC_011602_fixed.eprimer3 -
#Escherichia_coli_O127:H6_str._E2348/69_plasmid_pMAR2,_complete_sequence not_O104 sequences/NC_011603_fixed.fasta sequences/NC_011603_fixed.prodigalout sequences/NC_011603_fixed.eprimer3 -
Escherichia_coli_UMN026_plasmid_p2ESCUM,_complete_sequence not_O104 sequences/NC_011739_fixed.fasta sequences/NC_011739_fixed.prodigalout sequences/NC_011739_fixed.eprimer3 -
Escherichia_fergusonii_ATCC_35469,_complete_genome not_O104 sequences/NC_011740_fixed.fasta sequences/NC_011740_fixed.prodigalout sequences/NC_011740_fixed.eprimer3 -
Escherichia_coli_IAI1,_complete_genome not_O104 sequences/NC_011741_fixed.fasta sequences/NC_011741_fixed.prodigalout sequences/NC_011741_fixed.eprimer3 -
Escherichia_coli_S88,_complete_genome not_O104 sequences/NC_011742_fixed.fasta sequences/NC_011742_fixed.prodigalout sequences/NC_011742_fixed.eprimer3 -
Escherichia_fergusonii_ATCC_35469_plasmid_pEFER,_complete_sequence not_O104 sequences/NC_011743_fixed.fasta sequences/NC_011743_fixed.prodigalout sequences/NC_011743_fixed.eprimer3 -
Escherichia_coli_ED1a,_complete_genome not_O104 sequences/NC_011745_fixed.fasta sequences/NC_011745_fixed.prodigalout sequences/NC_011745_fixed.eprimer3 -
Escherichia_coli_S88_plasmid_pECOS88,_complete_sequence not_O104 sequences/NC_011747_fixed.fasta sequences/NC_011747_fixed.prodigalout sequences/NC_011747_fixed.eprimer3 -
Escherichia_coli_55989,_complete_genome not_O104 sequences/NC_011748_fixed.fasta sequences/NC_011748_fixed.prodigalout sequences/NC_011748_fixed.eprimer3 -
Escherichia_coli_UMN026_plasmid_p1ESCUM,_complete_sequence not_O104 sequences/NC_011749_fixed.fasta sequences/NC_011749_fixed.prodigalout sequences/NC_011749_fixed.eprimer3 -
Escherichia_coli_IAI39,_complete_genome not_O104 sequences/NC_011750_fixed.fasta sequences/NC_011750_fixed.prodigalout sequences/NC_011750_fixed.eprimer3 -
Escherichia_coli_UMN026,_complete_genome not_O104 sequences/NC_011751_fixed.fasta sequences/NC_011751_fixed.prodigalout sequences/NC_011751_fixed.eprimer3 -
Escherichia_coli_BW2952,_complete_genome not_O104 sequences/NC_012759_fixed.fasta sequences/NC_012759_fixed.prodigalout sequences/NC_012759_fixed.eprimer3 -
#Escherichia_coli_BL21-Gold(DE3)pLysS_AG_chromosome,_complete_genome not_O104 sequences/NC_012947_fixed.fasta sequences/NC_012947_fixed.prodigalout sequences/NC_012947_fixed.eprimer3 -
Escherichia_coli_B_str._REL606_chromosome,_complete_genome not_O104 sequences/NC_012967_fixed.fasta sequences/NC_012967_fixed.prodigalout sequences/NC_012967_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._TW14359,_complete_genome not_O104 sequences/NC_013008_fixed.fasta sequences/NC_013008_fixed.prodigalout sequences/NC_013008_fixed.eprimer3 -
Escherichia_coli_O157:H7_str._TW14359_plasmid_pO157,_complete_sequence not_O104 sequences/NC_013010_fixed.fasta sequences/NC_013010_fixed.prodigalout sequences/NC_013010_fixed.eprimer3 -
Escherichia_coli_O103:H2_str._12009,_complete_genome not_O104 sequences/NC_013353_fixed.fasta sequences/NC_013353_fixed.prodigalout sequences/NC_013353_fixed.eprimer3 -
Escherichia_coli_O103:H2_str._12009_plasmid_pO103,_complete_sequence not_O104 sequences/NC_013354_fixed.fasta sequences/NC_013354_fixed.prodigalout sequences/NC_013354_fixed.eprimer3 -
Escherichia_coli_O26:H11_str._11368,_complete_genome not_O104 sequences/NC_013361_fixed.fasta sequences/NC_013361_fixed.prodigalout sequences/NC_013361_fixed.eprimer3 -
Escherichia_coli_O26:H11_str._11368_plasmid_pO26_2,_complete_sequence not_O104 sequences/NC_013362_fixed.fasta sequences/NC_013362_fixed.prodigalout sequences/NC_013362_fixed.eprimer3 -
Escherichia_coli_O26:H11_str._11368_plasmid_pO26_3,_complete_sequence not_O104 sequences/NC_013363_fixed.fasta sequences/NC_013363_fixed.prodigalout sequences/NC_013363_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128,_complete_genome not_O104 sequences/NC_013364_fixed.fasta sequences/NC_013364_fixed.prodigalout sequences/NC_013364_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128_plasmid_pO111_1,_complete_sequence not_O104 sequences/NC_013365_fixed.fasta sequences/NC_013365_fixed.prodigalout sequences/NC_013365_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128_plasmid_pO111_3,_complete_sequence not_O104 sequences/NC_013366_fixed.fasta sequences/NC_013366_fixed.prodigalout sequences/NC_013366_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128_plasmid_pO111_4,_complete_sequence not_O104 sequences/NC_013367_fixed.fasta sequences/NC_013367_fixed.prodigalout sequences/NC_013367_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128_plasmid_pO111_5,_complete_sequence not_O104 sequences/NC_013368_fixed.fasta sequences/NC_013368_fixed.prodigalout sequences/NC_013368_fixed.eprimer3 -
Escherichia_coli_O26:H11_str._11368_plasmid_pO26_1,_complete_sequence not_O104 sequences/NC_013369_fixed.fasta sequences/NC_013369_fixed.prodigalout sequences/NC_013369_fixed.eprimer3 -
Escherichia_coli_O111:H-_str._11128_plasmid_pO111_2,_complete_sequence not_O104 sequences/NC_013370_fixed.fasta sequences/NC_013370_fixed.prodigalout sequences/NC_013370_fixed.eprimer3 -
Escherichia_coli_O55:H7_str._CB9615_chromosome,_complete_genome not_O104 sequences/NC_013941_fixed.fasta sequences/NC_013941_fixed.prodigalout sequences/NC_013941_fixed.eprimer3 -
Escherichia_coli_O55:H7_str._CB9615_plasmid_pO55,_complete_sequence not_O104 sequences/NC_013942_fixed.fasta sequences/NC_013942_fixed.prodigalout sequences/NC_013942_fixed.eprimer3 -
Escherichia_coli_O26:H11_str._11368_plasmid_pO26_4,_complete_sequence not_O104 sequences/NC_014543_fixed.fasta sequences/NC_014543_fixed.prodigalout sequences/NC_014543_fixed.eprimer3 -