---

Results for RAREFAN run lvoiii5i

Parameters

reference_strain: Smalt_FDAARGOS_649.fas
nmer_length: 21
min_nmer_occurrence: 55
query_rayt: yafM_SBW25
distance_group_seeds: 15
distance_repin_rayt: 130
analyse_repins: y
e_value_cutoff: 1e-30

lvoiii5i is a rerun of pgfmaxx5.

Status: complete

Stage	Status	Return code
rarefan	complete
tree	complete
rayt alignment	complete
rayt phylogeny	complete
zip	complete

RAYTs

RAREFAN discovered 138 RAYTs across all submitted genomes using tblastn with yafM_SBW25 at an e-value threshold of 1e-30.

Seed sequences

RAREFAN identified 37 21bp long sequences in the reference genome that occur more frequently than 55 times.

REP/REPIN counts

	Group	0	1	2	3	4
Strain
Smalt_AA1	REP/REPINs	228	273	291	0	44
	REPINs	87	38	44	0	18
Smalt_AB550	REP/REPINs	344	130	0	50	0
	REPINs	142	9	0	44	0
Smalt_CF13	REP/REPINs	388	187	697	45	135
	REPINs	171	26	670	33	131
Smalt_CPBW01	REP/REPINs	98	201	170	33	15
	REPINs	18	185	116	26	13
Smalt_CSM2	REP/REPINs	288	240	467	53	0
	REPINs	128	43	408	43	0
Smalt_Col1	REP/REPINs	133	208	204	50	0
	REPINs	95	189	123	43	0
Smalt_D457	REP/REPINs	300	132	471	56	0
	REPINs	116	7	410	46	0
Smalt_DHHJ	REP/REPINs	355	259	602	54	0
	REPINs	175	39	525	40	0
Smalt_FDAARGOS_1044	REP/REPINs	729	201	104	45	130
	REPINs	631	29	10	34	124
Smalt_FDAARGOS_325	REP/REPINs	421	200	126	46	135
	REPINs	184	21	14	34	128
Smalt_FDAARGOS_507	REP/REPINs	411	205	516	43	140
	REPINs	181	28	200	30	134
Smalt_FDAARGOS_649	REP/REPINs	539	202	736	46	143
	REPINs	212	26	634	34	137
Smalt_FDAARGOS_92	REP/REPINs	407	187	679	46	92
	REPINs	191	19	637	32	84
Smalt_ICU331	REP/REPINs	424	198	739	46	110
	REPINs	190	24	616	36	101
Smalt_ISMMS2	REP/REPINs	123	221	175	32	0
	REPINs	92	201	119	25	0
Smalt_ISMMS2R	REP/REPINs	123	221	175	32	0
	REPINs	92	201	119	25	0
Smalt_ISMMS3	REP/REPINs	265	142	58	44	0
	REPINs	141	15	3	38	0
Smalt_JV3	REP/REPINs	447	238	568	53	0
	REPINs	413	37	549	46	0
Smalt_K279a	REP/REPINs	677	201	122	46	131
	REPINs	635	25	86	34	122
Smalt_KMM349	REP/REPINs	250	147	443	52	22
	REPINs	127	10	383	40	14
Smalt_MER1	REP/REPINs	203	387	0	0	0
	REPINs	74	372	0	0	0
Smalt_NCTC10257	REP/REPINs	729	201	104	45	130
	REPINs	631	29	10	34	124
Smalt_NCTC10258	REP/REPINs	637	203	745	44	125
	REPINs	599	26	636	31	118
Smalt_NCTC10259	REP/REPINs	293	130	52	55	0
	REPINs	101	8	5	47	0
Smalt_NCTC10498	REP/REPINs	548	192	774	46	133
	REPINs	226	29	655	33	121
Smalt_NCTC13014	REP/REPINs	218	168	299	50	55
	REPINs	184	16	284	43	35
Smalt_NEB515	REP/REPINs	436	201	782	49	0
	REPINs	208	27	759	38	0
Smalt_O1	REP/REPINs	460	194	120	43	135
	REPINs	220	22	13	26	130
Smalt_OUC_Est10	REP/REPINs	222	200	0	39	13
	REPINs	104	31	0	26	9
Smalt_PEG-141	REP/REPINs	366	239	429	53	0
	REPINs	173	38	181	40	0
Smalt_PEG-173	REP/REPINs	257	235	427	47	103
	REPINs	117	221	368	33	96
Smalt_PEG-305	REP/REPINs	511	179	0	52	559
	REPINs	242	165	0	40	269
Smalt_PEG-390	REP/REPINs	191	196	90	31	34
	REPINs	75	26	7	20	26
Smalt_PEG-42	REP/REPINs	263	162	99	48	52
	REPINs	187	16	96	37	37
Smalt_PEG-68	REP/REPINs	293	131	465	54	0
	REPINs	112	9	400	45	0
Smalt_R551-3	REP/REPINs	244	135	60	54	0
	REPINs	122	11	6	42	0
Smalt_SJTH1	REP/REPINs	220	297	280	44	0
	REPINs	187	57	263	34	0
Smalt_SJTL3	REP/REPINs	512	158	535	49	0
	REPINs	469	15	495	39	0
Smalt_SKK55	REP/REPINs	162	158	94	37	0
	REPINs	50	14	91	21	0
Smalt_SM866	REP/REPINs	399	241	647	54	0
	REPINs	191	38	580	40	0
Smalt_Sm53	REP/REPINs	429	200	756	48	136
	REPINs	204	25	739	36	120
Smalt_SoD9b	REP/REPINs	470	129	424	50	0
	REPINs	200	9	184	36	0
Smalt_T50-20	REP/REPINs	369	247	581	59	0
	REPINs	157	36	519	41	0
Smalt_U5	REP/REPINs	260	368	68	0	0
	REPINs	100	56	5	0	0
Smalt_W18	REP/REPINs	265	149	320	47	47
	REPINs	196	16	301	37	32
Smalt_WP1-W18-CRE-01	REP/REPINs	450	186	136	45	128
	REPINs	205	22	109	34	125
Smalt_X28	REP/REPINs	264	235	321	60	0
	REPINs	116	41	127	49	0
Smalt_sm-RA9	REP/REPINs	250	130	325	51	0
	REPINs	129	10	142	41	0
Smalt_sm454	REP/REPINs	415	197	114	44	145
	REPINs	202	25	11	31	142

Plot data

Browse data

Download results

Rerun this job