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Table view (130 sequence regions)

Original order	Download FASTA	Accession	Bit score	Type	Start	End	Description	Species	View context
0		BX950851.1	N/A	seed	4,733,293	4,732,994	Erwinia carotovora subsp. atroseptica SCRI1043, complete genome	Pectobacterium atrosepticum SCRI1043
1		CP001790.1	N/A	seed	4,659,105	4,658,806	Pectobacterium wasabiae WPP163, complete genome.	Pectobacterium wasabiae WPP163
2		CP001657.1	N/A	seed	4,554,960	4,554,661	Pectobacterium carotovorum subsp. carotovorum PC1, complete genome.	Pectobacterium carotovorum subsp. carotovorum PC1
3		AFWW01000001.1	N/A	seed	265,103	265,404	Brenneria sp. EniD312 BrE3212scaffold_1_Cont1, whole genome shotgun sequence.	Brenneria sp. EniD312
0		CGIG01000001.1	285.90	full	1,982,494	1,982,792	Brenneria goodwinii strain OBR1 genome assembly, contig: Contig	Brenneria goodwinii
1		CP034035.1	278.00	full	3,647,424	3,647,121	CP034035.1 Brenneria rubrifaciens strain 6D370 chromosome, complete genome	Brenneria rubrifaciens
2		CP002038.1	267.60	full	4,598,225	4,597,927	Dickeya dadantii 3937, complete genome.	Dickeya dadantii 3937
3		CP025084.1	245.50	full	803,888	804,186	CP025084.1 Prodigiosinella confusarubida strain ATCC 39006 chromosome, complete genome	Serratia sp. ATCC 39006
4		FNQS01000015.1	212.80	full	3,880	4,180	Lonsdalea quercina strain ATCC 29281 genome assembly, contig: Ga0052894_scaffold00015.15	Lonsdalea quercina
5		UHJG01000001.1	201.80	full	2,395,352	2,395,653	UHJG01000001.1 Yersinia ruckeri strain NCTC10476 genome assembly, contig: ERS1545397SCcontig000001, whole genome shotgun sequence	Yersinia ruckeri
6		GG753567.1	200.90	full	1,170,951	1,170,649	Serratia odorifera DSM 4582 genomic scaffold SCAFFOLD1, whole genome shotgun sequence.	Serratia odorifera DSM 4582
7		VYKJ01000014.1	198.50	full	178,637	178,339	VYKJ01000014.1 Affinibrenneria salicis strain L3-3HA Scaffold14, whole genome shotgun sequence	Affinibrenneria salicis
8		LT906479.1	194.90	full	5,020,452	5,020,150	LT906479.1 Serratia ficaria strain NCTC12148 genome assembly, chromosome: 1	Serratia ficaria
9		CP006569.1	193.50	full	310,871	311,166	Sodalis praecaptivus strain HS1, complete genome.	Sodalis praecaptivus
10		SJOI01000001.1	190.10	full	3,515,650	3,515,367	SJOI01000001.1 Sodalis ligni strain 159R Ga0299867_11, whole genome shotgun sequence	Sodalis ligni
11		AP008232.1	189.40	full	4,107,774	4,107,478	Sodalis glossinidius str. 'morsitans' DNA, complete genome.	Sodalis glossinidius str. 'morsitans'
12		JMPJ01000069.1	189.40	full	5,089	5,387	JMPJ01000069.1 Ewingella americana ATCC 33852 GEAM.assembly.076, whole genome shotgun sequence	Ewingella americana ATCC 33852
13		MNBX01000279.1	189.20	full	6,860	6,564	Sodalis sp. TME1 V4_final_sodalis.fa.Contig279, whole genome shotgun sequence.	Sodalis sp. TME1
14		WUBS01000012.1	188.50	full	10,272	10,569	WUBS01000012.1 Acerihabitans arboris strain SAP-6 contig12, whole genome shotgun sequence	Acerihabitans arboris
15		SMCR01000008.1	185.50	full	150,629	150,300	SMCR01000008.1 Biostraticola tofi strain DSM 19580 Ga0244679_108, whole genome shotgun sequence	Biostraticola tofi
16		AL590842.1	182.50	full	4,375,391	4,375,091	Yersinia pestis CO92 complete genome	Yersinia pestis CO92
17		CP006568.1	181.10	full	381,657	381,363	Candidatus Sodalis pierantonius str. SOPE, complete genome.	primary endosymbiont of Sitophilus oryzae
18		LR134493.1	180.10	full	1,798,509	1,798,811	LR134493.1 Serratia rubidaea strain NCTC10036 genome assembly, chromosome: 1	Serratia rubidaea
19		CP011254.1	176.00	full	1,542,676	1,542,375	Serratia fonticola strain DSM 4576, complete genome.	Serratia fonticola
20		CP003244.1	174.50	full	4,673,560	4,673,252	Rahnella aquatilis CIP 78.65 = ATCC 33071, complete genome.	Rahnella aquatilis CIP 78.65 = ATCC 33071
21		CAADJD010000020.1	173.00	full	254,813	255,094	CAADJD010000020.1 Kluyvera cryocrescens strain NCTC12993 genome assembly, contig: ERS473437SCcontig000020, whole genome shotgun sequence	Kluyvera cryocrescens
22		LS483466.1	172.60	full	4,530,465	4,530,171	LS483466.1 Salmonella enterica subsp. arizonae strain NCTC7307 genome assembly, chromosome: 1	Salmonella enterica subsp. arizonae
23		CP040428.1	172.20	full	1,412,530	1,412,830	CP040428.1 Jejubacter calystegiae strain KSNA2 chromosome, complete genome	Jejubacter calystegiae
24		JABXSS010000001.1	172.10	full	4,181,698	4,181,408	JABXSS010000001.1 Citrobacter freundii strain RHB34-C11 RHB34-C11_1, whole genome shotgun sequence	Citrobacter freundii
25		CP000880.1	171.60	full	3,686,515	3,686,225	Salmonella enterica subsp. arizonae serovar 62:z4,z23:--, complete genome.	Salmonella enterica subsp. arizonae serovar 62:z4,z23:--
26		AE006468.2	171.30	full	4,108,676	4,108,966	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genome.	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
27		CH400091.1	170.60	full	3,525	3,223	Oryza sativa Indica Group scaffold004564 genomic scaffold, whole genome shotgun sequence.	Oryza sativa Indica Group
28		WEIW01002365.1	170.60	full	81,622	81,320	WEIW01002365.1 Chloropsis hardwickii isolate B10K-IZ-033-78 scaffold_2234_1, whole genome shotgun sequence	Chloropsis hardwickii
29		WEIY01000806.1	170.60	full	4,695	4,997	WEIY01000806.1 Pteruthius melanotis isolate B10K-IZ-033-77 scaffold_699_1_1, whole genome shotgun sequence	Pteruthius melanotis
30		CP000822.1	170.40	full	102,235	102,526	Citrobacter koseri ATCC BAA-895, complete genome.	Citrobacter koseri ATCC BAA-895
31		PYKI01002313.1	169.30	full	2,187	1,898	PYKI01002313.1 Salmonella enterica subsp. enterica serovar Poona strain 22sa NODE_413_length_2671_cov_2.73824, whole genome shotgun sequence	Salmonella enterica subsp. enterica serovar Poona
32		JMPI01000001.1	169.20	full	78,091	77,795	Buttiauxella agrestis ATCC 33320 GBAG.assembly.001, whole genome shotgun sequence.	Buttiauxella agrestis ATCC 33320
33		CAACVG010003419.1	167.70	full	5,808	5,514	CAACVG010003419.1 Callosobruchus maculatus genome assembly, contig: 13104|quiver, whole genome shotgun sequence	Callosobruchus maculatus (cowpea weevil)
34		GL636121.1	167.70	full	86,310	86,612	Serratia symbiotica str. Tucson genomic scaffold scaffold00333, whole genome shotgun sequence.	Serratia symbiotica str. Tucson
35		CP000783.1	167.60	full	3,735,461	3,735,165	Cronobacter sakazakii ATCC BAA-894, complete genome.	Cronobacter sakazakii ATCC BAA-894
36		CP011427.1	167.00	full	4,281,388	4,281,695	CP011427.1 Pantoea vagans strain ND02 chromosome, complete genome	Pantoea vagans
37		FN543502.1	166.50	full	4,208,381	4,208,088	Citrobacter rodentium ICC168, complete genome	Citrobacter rodentium ICC168
38		WAAG01102940.1	164.90	full	3,341	3,635	WAAG01102940.1 Tichodroma muraria voucher UWBM:61504 isolate B10K-DU-012-47 scaffold102704, whole genome shotgun sequence	Tichodroma muraria
39		PJZK01000024.1	164.70	full	9,660	9,961	PJZK01000024.1 Chimaeribacter arupi strain 2016-Iso1 NODE_24_length_73278_cov_38.6424_ID_5689, whole genome shotgun sequence	Chimaeribacter arupi
40		CP000653.1	163.90	full	4,357,023	4,356,726	Enterobacter sp. 638, complete genome.	Enterobacter sp. 638
41		CP003938.1	162.80	full	4,590,685	4,590,391	CP003938.1 Enterobacteriaceae bacterium strain FGI 57, complete genome	Enterobacteriaceae bacterium strain FGI 57
42		CP014136.1	162.60	full	2,720,789	2,721,095	CP014136.1 Gibbsiella quercinecans strain FRB97 chromosome, complete genome	Gibbsiella quercinecans
43		CP002272.1	161.40	full	4,617,537	4,617,240	Enterobacter cloacae SCF1, complete genome.	Enterobacter cloacae SCF1
44		CP007044.2	160.50	full	1,150,104	1,150,406	Chania multitudinisentens RB-25, complete genome.	Chania multitudinisentens RB-25
45		CP000800.1	160.30	full	4,272,149	4,272,438	Escherichia coli E24377A, complete genome.	Escherichia coli E24377A
46		JRXE01000022.1	160.00	full	3,680	3,989	Erwinia iniecta strain B120 contig000022, whole genome shotgun sequence.	Erwinia iniecta
47		LGIT01000005.1	159.60	full	3,533	3,830	Klebsiella sp. RIT-PI-d NODE_9_length_82592_cov_38.342_ID_17, whole genome shotgun sequence.	Klebsiella sp. RIT-PI-d
48		CP000038.1	159.60	full	4,159,604	4,159,893	Shigella sonnei Ss046, complete genome.	Shigella sonnei Ss046
49		AE014075.1	158.80	full	4,451,289	4,451,578	Escherichia coli CFT073, complete genome.	Escherichia coli CFT073
50		CP000468.1	158.80	full	4,243,916	4,244,205	Escherichia coli APEC O1, complete genome.	Escherichia coli APEC O1
51		CP001855.1	158.80	full	3,971,339	3,971,628	CP001855.1 Escherichia coli O83:H1 str. NRG 857C, complete genome	Escherichia coli O83:H1 str. NRG 857C
52		CU928161.2	158.80	full	4,158,624	4,158,913	Escherichia coli S88 chromosome, complete genome.	Escherichia coli S88
53		FM180568.1	158.80	full	4,246,873	4,247,162	Escherichia coli 0127:H6 E2348/69 complete genome, strain E2348/69	Escherichia coli O127:H6 str. E2348/69
54		CP001665.1	157.40	full	4,503,322	4,503,030	CP001665.1 Escherichia coli 'BL21-Gold(DE3)pLysS AG', complete genome	Escherichia coli BL21(DE3)
55		MTSM01000167.1	157.40	full	120	412	Oceanospirillum multiglobuliferum strain ATCC 33336 NODE_171_length_461_cov_0.721557, whole genome shotgun sequence.	Oceanospirillum multiglobuliferum
56		U00096.3	157.40	full	3,950,248	3,950,540	Escherichia coli str. K-12 substr. MG1655, complete genome.	Escherichia coli K-12
57		BAFF01000017.1	156.90	full	77,632	77,335	Escherichia hermannii NBRC 105704 DNA, contig: EH10570417.	Atlantibacter hermannii NBRC 105704
58		BBMZ01000029.1	156.80	full	31,417	31,119	Escherichia vulneris NBRC 102420 DNA, contig: EV10242029.	Escherichia vulneris NBRC 102420
59		CP009706.1	156.70	full	331,793	332,089	Hafnia alvei FB1, complete genome.	Hafnia alvei FB1
60		AE005674.2	156.70	full	3,959,692	3,959,980	Shigella flexneri 2a str. 301, complete genome.	Shigella flexneri 2a str. 301
61		CP000802.1	156.60	full	3,978,659	3,978,951	Escherichia coli HS, complete genome.	Escherichia coli HS
62		BA000007.3	156.50	full	4,743,821	4,744,110	BA000007.3 Escherichia coli O157:H7 str. Sakai DNA, complete genome	Escherichia coli O157:H7
63		WBMX01016312.1	156.50	full	7,023	6,726	WBMX01016312.1 Corythaeola cristata voucher FMNH:AVES:357942 isolate B10K-CU-031-40 scaffold_16383, whole genome shotgun sequence	Corythaeola cristata (great blue turaco)
64		WJYB01000015.1	156.10	full	82,595	82,303	WJYB01000015.1 Enterobacteriaceae bacterium RIT714 15, whole genome shotgun sequence	Enterobacteriaceae bacterium RIT714
65		VCHQ01000044.1	155.00	full	12,469	12,178	VCHQ01000044.1 Klebsiella indica strain TOUT106 salmonela_mira_c44, whole genome shotgun sequence	Klebsiella indica
66		LDZF01000025.1	154.70	full	3,685	3,973	Pluralibacter gergoviae strain JS81F13 contig_25, whole genome shotgun sequence.	Enterobacter gergoviae
67		CU928145.2	154.60	full	4,330,544	4,330,833	Escherichia coli 55989 chromosome, complete genome.	Escherichia coli 55989
68		CP019706.1	154.30	full	1,790,258	1,790,565	CP019706.1 Pantoea alhagi strain LTYR-11Z chromosome, complete sequence	Pantoea alhagi
69		CP000034.1	153.80	full	3,714,140	3,713,851	Shigella dysenteriae Sd197, complete genome.	Shigella dysenteriae Sd197
70		VZSZ01007109.1	153.60	full	384	649	VZSZ01007109.1 Ibidorhyncha struthersii voucher IZCAS:2150 isolate B10K-DU-030-25 scaffold13111, whole genome shotgun sequence	Ibidorhyncha struthersii
71		CP001875.2	152.70	full	4,239,747	4,239,440	Pantoea ananatis LMG 20103, complete genome.	Pantoea ananatis LMG 20103
72		KZ478071.1	152.60	full	84,169	83,870	KZ478071.1 Enterobacterales bacterium CwR94 genomic scaffold scf_19201_13, whole genome shotgun sequence	Enterobacterales bacterium CwR94
73		CP001063.1	151.50	full	3,878,672	3,878,381	Shigella boydii CDC 3083-94, complete genome.	Shigella boydii CDC 3083-94
74		MRWE01000014.1	151.50	full	9,865	10,174	MRWE01000014.1 Rouxiella badensis strain DSM 100043 NODE_14_covk_35.2581_covr_70.58_cutoff_49, whole genome shotgun sequence	Rouxiella badensis
75		KK036986.1	151.00	full	442,701	443,016	KK036986.1 Klebsiella michiganensis strain MGH 27 adjbQ-supercont1.1, whole genome shotgun sequence	Klebsiella michiganensis
76		CP019447.1	150.90	full	89,731	89,434	CP019447.1 Kosakonia cowanii JCM 10956 = DSM 18146 strain 888-76 plasmid p888-76-2, complete sequence	Kosakonia cowanii JCM 10956 = DSM 18146
77		CP003200.1	149.90	full	129,193	129,478	CP003200.1 Klebsiella pneumoniae subsp. pneumoniae HS11286, complete genome	Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)
78		LN907827.1	148.90	full	150,288	150,595	Erwinia sp. EM595 isolate E_g_EM595 genome assembly, chromosome: 1	Erwinia gerundensis
79		CABFKN010051460.1	147.60	full	561	272	CABFKN010051460.1 Panagrolaimus superbus genome assembly, contig: PSU_contig_99510, whole genome shotgun sequence	Panagrolaimus superbus
80		CP054212.1	147.60	full	4,535,559	4,535,251	CP054212.1 Erwiniaceae bacterium PD-1 chromosome, complete genome	Erwiniaceae bacterium PD-1
81		CP009451.1	146.30	full	2,493,484	2,493,185	CP009451.1 Cedecea neteri strain SSMD04, complete genome	Cedecea neteri
82		JNGI01000186.1	144.10	full	3,296	3,591	JNGI01000186.1 Trabulsiella odontotermitis strain 12 SAMPLE12_CONTIG_186, whole genome shotgun sequence	Trabulsiella odontotermitis
83		JMEE01000008.1	143.90	full	84,768	84,460	JMEE01000008.1 [Pantoea] beijingensis strain LMG 27579 contig16, whole genome shotgun sequence	[Pantoea] beijingensis
84		ANFO01000029.1	143.50	full	8,717	8,421	Beauveria bassiana D1-5 contig00032, whole genome shotgun sequence.	Beauveria bassiana D1-5
85		UGLZ01000005.1	143.20	full	537,134	536,848	UGLZ01000005.1 Klebsiella pneumoniae subsp. ozaenae strain NCTC5050 genome assembly, contig: ERS513128SCcontig000005, whole genome shotgun sequence	Klebsiella pneumoniae subsp. ozaenae
86		JPKR02000005.1	142.80	full	515,087	514,779	Tatumella morbirosei strain LMG 23360 Contig5, whole genome shotgun sequence.	Tatumella morbirosei
87		QRAP01000012.1	142.40	full	4,688	4,987	QRAP01000012.1 Enterobacillus tribolii strain DSM 103736 Ga0215724_112, whole genome shotgun sequence	Enterobacillus tribolii
88		UGSO01000001.1	142.00	full	209,360	209,666	UGSO01000001.1 Pantoea agglomerans strain NCTC9381 genome assembly, contig: ERS513136SCcontig000001, whole genome shotgun sequence	Pantoea agglomerans
89		CP022114.1	141.60	full	4,823,022	4,822,739	CP022114.1 Kluyvera genomosp. 3 strain YDC799 chromosome, complete genome	Kluyvera genomosp. 3
90		JJMI01000051.1	141.00	full	3,881	4,180	Mangrovibacter sp. MFB070 Contig-051, whole genome shotgun sequence.	Mangrovibacter sp. MFB070
91		AYKS02000076.1	140.60	full	3,547	3,845	Serratia sp. DD3 SRDD_contig000076, whole genome shotgun sequence.	Serratia sp. DD3
92		LMLK01000008.1	140.40	full	3,703	3,993	Erwinia sp. Leaf53 contig_16, whole genome shotgun sequence.	Erwinia sp. Leaf53
93		VWUI01000234.1	140.10	full	3,297	2,996	VWUI01000234.1 Pantoea sp. M_5 Scaffold_232, whole genome shotgun sequence	Pantoea sp. M_5
94		AP012551.1	139.60	full	3,187,932	3,187,621	Plautia stali symbiont DNA, complete genome.	Plautia stali symbiont
95		VWUI01000147.1	139.40	full	3,725	4,031	VWUI01000147.1 Pantoea sp. M_5 Scaffold_144, whole genome shotgun sequence	Pantoea sp. M_5
96		CP001560.1	138.30	full	3,951,239	3,950,941	Shimwellia blattae DSM 4481 = NBRC 105725, complete genome.	Escherichia blattae DSM 4481
97		JMPR01000012.1	137.20	full	3,361	3,669	Tatumella ptyseos ATCC 33301 GTPT.assembly.012, whole genome shotgun sequence.	Tatumella ptyseos ATCC 33301
98		CP046509.1	134.20	full	4,469,578	4,469,280	CP046509.1 Erwinia sorbitola strain J780 chromosome, complete genome	Erwinia sorbitola
99		SZZY01000009.1	133.40	full	210,543	210,234	SZZY01000009.1 Pantoea sp. Eser Euschistus_servus_symbiont_contig9, whole genome shotgun sequence	Pantoea sp. Eser
100		JAERJD010000013.1	133.30	full	77,594	77,303	JAERJD010000013.1 Citrobacter sp. JGM124 scaffold13_size81070, whole genome shotgun sequence	Citrobacter sp. JGM124
101		JAEPBH010000013.1	131.90	full	87,291	86,990	JAEPBH010000013.1 Tenebrionibacter intestinalis strain BIT-L3 Scaffold13, whole genome shotgun sequence	Tenebrionibacter intestinalis
102		CP021659.1	128.40	full	2,273,198	2,272,900	CP021659.1 Candidatus Fukatsuia symbiotica strain 5D chromosome, complete genome	Candidatus Fukatsuia symbiotica
103		RBZS01000378.1	126.40	full	176	470	RBZS01000378.1 Sodalis-like symbiont of Bactericera trigonica isolate IL scaffold_332097, whole genome shotgun sequence	Sodalis-like symbiont of Bactericera trigonica
104		JXNU01000003.1	125.40	full	2,959,679	2,959,977	Erwinia tracheiphila strain BuffGH Etrach_2, whole genome shotgun sequence.	Erwinia tracheiphila
105		FP236843.1	121.10	full	206,131	206,430	Erwinia billingiae strain Eb661 complete chromosome.	Erwinia billingiae
106		RHUM01000016.1	121.10	full	86,003	85,695	RHUM01000016.1 Erwinia sp. 198 NODE_16_length_89756_cov_52.9515, whole genome shotgun sequence	Erwinia sp. 198
107		JFHN01000055.1	120.10	full	42,880	42,581	Erwinia mallotivora strain BT-MARDI contig_55, whole genome shotgun sequence.	Erwinia mallotivora
108		LJAM02000043.1	119.70	full	9,423	9,125	LJAM02000043.1 Candidatus Erwinia dacicola strain Oroville edac.contig.38_1, whole genome shotgun sequence	Candidatus Erwinia dacicola
109		UFXZ01000001.1	118.40	full	3,625,244	3,624,950	UFXZ01000001.1 Edwardsiella hoshinae strain NCTC12121 genome assembly, contig: ERS1295689SCcontig000001, whole genome shotgun sequence	Edwardsiella hoshinae
110		PDDX01000001.1	117.40	full	723,209	722,909	PDDX01000001.1 Budvicia aquatica strain FDAARGOS_387 pRIID_90.contig.0, whole genome shotgun sequence	Budvicia aquatica
111		LGAA01000003.1	115.80	full	274,565	274,288	Moellerella wisconsensis ATCC 35017 Sequence00003, whole genome shotgun sequence.	Moellerella wisconsensis ATCC 35017
112		CP029185.2	112.50	full	3,715,747	3,715,458	CP029185.2 Limnobaculum parvum strain HYN0051 chromosome, complete genome	Limnobaculum parvum
113		LS483470.1	111.00	full	3,850,957	3,850,675	LS483470.1 Leminorella richardii strain NCTC12151 genome assembly, chromosome: 1	Leminorella richardii
114		CBXF010000146.1	105.30	full	913	627	Xenorhabdus szentirmaii DSM 16338, WGS project CBXF01000000 data, contig: XENSZ_2115_Contig_82	Xenorhabdus szentirmaii DSM 16338
115		MNCH01000072.1	104.70	full	864	566	MNCH01000072.1 Erwinia sp. OLSSP12 NODE_72_length_4437_cov_31.2675_ID_143, whole genome shotgun sequence	Erwinia sp. OLSSP12
116		BX470251.1	104.20	full	5,465,224	5,464,934	Photorhabdus luminescens subsp. laumondii TTO1 complete genome	Photorhabdus luminescens subsp. laumondii TTO1
117		JMSP01000314.1	100.70	full	7,575	7,289	Bacteria symbiont BFo2 of Frankliniella occidentalis strain BFo2 contig161, whole genome shotgun sequence.	bacteria symbiont BFo2 of Frankliniella occidentalis
118		CU468135.1	100.40	full	220,105	220,404	Erwinia tasmaniensis strain ET1/99 complete chromosome.	Erwinia tasmaniensis
119		FPBJ01000009.1	99.60	full	3,858	4,132	FPBJ01000009.1 Xenorhabdus koppenhoeferi strain DSM 18168 genome assembly, contig: Ga0111672_109, whole genome shotgun sequence	Xenorhabdus koppenhoeferi
120		FOVC01000007.1	97.90	full	3,757	4,054	FOVC01000007.1 Izhakiella capsodis strain N6PO6 genome assembly, contig: Ga0105830_107, whole genome shotgun sequence	Izhakiella capsodis
121		LXEN01000093.1	96.90	full	3,612	3,835	LXEN01000093.1 Proteus myxofaciens ATCC 19692 Sequence00093, whole genome shotgun sequence	Proteus myxofaciens ATCC 19692
122		FOVO01000001.1	93.90	full	3,949	4,236	FOVO01000001.1 Xenorhabdus japonica strain DSM 16522 genome assembly, contig: Ga0111655_101, whole genome shotgun sequence	Xenorhabdus japonica
123		HG427707.1	91.40	full	3,685	3,976	HG427707.1 Xenorhabdus bovienii str. kraussei Quebec genomic scaffold, XBKQ_3535_scaffold219, whole genome shotgun sequence	Xenorhabdus bovienii str. kraussei Quebec
124		LVIE01000170.1	90.10	full	4,076	4,359	LVIE01000170.1 Providencia stuartii strain Crippen contig_31, whole genome shotgun sequence	Providencia stuartii
125		RYVQ01000278.1	88.80	full	1,319	1,037	RYVQ01000278.1 MAG: Candidatus Symbiopectobacterium sp. Dall1.0 n278, whole genome shotgun sequence	Candidatus Symbiopectobacterium sp. Dall1.0

There are various ways to view or download the seed alignments that we store. You can use a sequence viewer to look at them, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

You can view Rfam seed alignments in your browser in various ways. Choose the viewer that you want to use and click the "View" button to show the alignment in a pop-up window.

Formatting options

You can view or download Rfam seed alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Download

Download a gzip-compressed, Stockholm-format file containing the seed alignment for this family. You may find RALEE useful when viewing sequence alignments.

Submit a new alignment

We're happy receive updated seed alignments for new or existing families. Submit your new alignment and we'll take a look.

In this page you can view static images showing the secondary structure of this family using a variety of colouring schemes:

Conservation (cons): this plot colours each character by how well conserved it is. A site with 100% sequence conservation is coloured red, 0% is violet.

Covariation (cov): this plot colours each base-pair according to how much the corresponding nucleotides are co-varying. A base-pair position at which every pair of nucleotides is co-variant with respect to every other pair in the alignment gets a score of 2 and is coloured red. Conversely, a base-pair position at every pair is anti-co-variant with respect to every other pair (e.g. lots of mutations to non-canonical pairs) gets a score of -2 and is coloured violet. Further information on this metric can be found in this document.

Sequence entropy (ent): this plot colours each character by how under- or over-represented the residues at the site are. Sites where one or more nucleotides are over-represented while the other nucleotides are either non-existent or near the background frequencies, receive positive scores; sites where all the nucleotides are under-represented receive negative scores. Further information on this metric can be found in this document.

Fraction of canonical basepairs (fcbp): this plot colours each base-pair by the percentage of canonical basepairs (A:U, C:G, G:U) which are found in the corresponding position in the alignment. A pair of sites with 100% canonical pairs is coloured red, a site with 0% is violet.

Maximum parse of the covariance model (maxcm): this plot takes the covariance model for the family and generates the sequence with the maximum possible score for that model. Each character is coloured by how many bits it contributes to the total score.

Sequence: for most of the above cases, the representative sequence used for the backbone is the most informative sequence (MIS). Any residue that has a higher frequency than than the background frequency is projected into the IUPAC redundancy codes.

Normal: this plot simply colours each stem loop

R-chie (rchie): arc diagrams showing secondary structure, calculated using the R-chie package. The consensus secondary structure is visualized as arc diagrams on top of each diagram, where a basepair in an arc, connect two columns of the block of sequences below. The block of sequences below represent the multiple sequence alignment of the Rfam seed, where each sequence is a horizontal strip. Sequences in the alignments are ordered so sequences that best fit the structure are on top, and those that do not fit as well are towards the bottom. For seed alignments for over 500 sequences, 500 random sequences were chosen. Rfam entries without sturcture have a blank plot. Colour information can be found on the R-chie FAQ.

You can also view the secondary structure in the VARNA applet. The applet is shown in a separate pop-up window.

Acknowledgements

The bulk of the code for generating these graphics was kindly supplied by Andreas Gruber and Ivo Hofacker. The statistics were implemented by Rfam.

The VARNA applet is developed by Yann Ponty et al:

The R-chie arc diagrams were calculated using R-chie:

These trees were generated using either a maximum likelihood approach or neighbour-joining. If the number of sequences in the alignment was less than or equal to 64 then the maximum likelihood approach of Rivas and Eddy was used [1]. For families with more than 64 sequences in the alignment the neighbour-joining approach with F84 distances as implemented in phylip was used [2].

Note: You can also download the data file for the seed tree.

We do not have tree information for this family. This is most likely due to the size of the family and the number of species covered. For very large families it is too computationally expensive to calculate trees and the resulting tree images would be too large to display in a browser.

There are 3 motifs which match this family.

This section shows the Rfam motifs that match sequences within the seed alignment of this family. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order	Motif Accession	Motif Description	Number of Hits	Fraction of Hits	Sum of Bits	Image
7	RM00008	GNRA tetraloop	4	1.000	68.4
7	RM00022	Rho independent terminator 1	4	1.000	97.8
7	RM00023	Rho independent terminator 2	4	1.000	75.3