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Results for RAREFAN run 2hh16ijv

Parameters

reference_strain: Smalt_AA1.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

2hh16ijv is a rerun of mknhxpv8.

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 52 21bp long sequences in the reference genome that occur more frequently than 55 times.

REP/REPIN counts

	Group	0	1	2	3	4	5	6
Strain
Smalt_AA1	REP/REPINs	228	291	273	347	81	112	44
	REPINs	87	44	38	324	29	111	38
Smalt_AB550	REP/REPINs	344	0	130	0	0	137	0
	REPINs	142	0	9	0	0	72	0
Smalt_CF13	REP/REPINs	388	697	187	0	0	0	0
	REPINs	171	670	26	0	0	0	0
Smalt_CPBW01	REP/REPINs	98	170	201	348	0	201	0
	REPINs	18	116	185	224	0	121	0
Smalt_CSM2	REP/REPINs	288	467	240	60	0	58	0
	REPINs	128	408	43	48	0	55	0
Smalt_Col1	REP/REPINs	133	204	208	103	0	362	0
	REPINs	95	123	189	88	0	359	0
Smalt_D457	REP/REPINs	300	471	132	0	0	285	0
	REPINs	116	410	7	0	0	273	0
Smalt_DHHJ	REP/REPINs	355	602	259	210	62	37	0
	REPINs	175	525	39	41	31	5	0
Smalt_FDAARGOS_1044	REP/REPINs	729	104	201	52	0	0	0
	REPINs	631	10	29	33	0	0	0
Smalt_FDAARGOS_325	REP/REPINs	421	126	200	58	0	0	0
	REPINs	184	14	21	43	0	0	0
Smalt_FDAARGOS_507	REP/REPINs	411	516	205	0	0	44	0
	REPINs	181	200	28	0	0	12	0
Smalt_FDAARGOS_649	REP/REPINs	539	736	202	48	0	0	0
	REPINs	212	634	26	38	0	0	0
Smalt_FDAARGOS_92	REP/REPINs	407	679	187	53	0	0	0
	REPINs	191	637	19	38	0	0	0
Smalt_ICU331	REP/REPINs	424	739	198	43	0	36	0
	REPINs	190	616	24	7	0	9	0
Smalt_ISMMS2	REP/REPINs	123	175	221	349	0	203	58
	REPINs	92	119	201	229	0	120	45
Smalt_ISMMS2R	REP/REPINs	123	175	221	349	0	203	58
	REPINs	92	119	201	229	0	120	45
Smalt_ISMMS3	REP/REPINs	265	58	142	0	95	0	0
	REPINs	141	3	15	0	45	0	0
Smalt_JV3	REP/REPINs	447	568	238	66	0	45	0
	REPINs	413	549	37	49	0	6	0
Smalt_K279a	REP/REPINs	677	122	201	52	0	42	0
	REPINs	635	86	25	37	0	9	0
Smalt_KMM349	REP/REPINs	250	443	147	357	24	120	0
	REPINs	127	383	10	342	7	115	0
Smalt_MER1	REP/REPINs	203	0	387	284	0	52	0
	REPINs	74	0	372	226	0	20	0
Smalt_NCTC10257	REP/REPINs	729	104	201	52	0	0	0
	REPINs	631	10	29	33	0	0	0
Smalt_NCTC10258	REP/REPINs	637	745	203	48	0	0	62
	REPINs	599	636	26	32	0	0	37
Smalt_NCTC10259	REP/REPINs	293	52	130	0	0	296	0
	REPINs	101	5	8	0	0	289	0
Smalt_NCTC10498	REP/REPINs	548	774	192	53	0	34	0
	REPINs	226	655	29	41	0	10	0
Smalt_NCTC13014	REP/REPINs	218	299	168	204	34	298	59
	REPINs	184	284	16	54	16	291	38
Smalt_NEB515	REP/REPINs	436	782	201	52	0	0	0
	REPINs	208	759	27	33	0	0	0
Smalt_O1	REP/REPINs	460	120	194	56	0	34	0
	REPINs	220	13	22	38	0	10	0
Smalt_OUC_Est10	REP/REPINs	222	0	200	130	33	93	58
	REPINs	104	0	31	118	16	32	39
Smalt_PEG-141	REP/REPINs	366	429	239	94	67	0	0
	REPINs	173	181	38	77	34	0	0
Smalt_PEG-173	REP/REPINs	257	427	235	101	73	0	56
	REPINs	117	368	221	87	41	0	36
Smalt_PEG-305	REP/REPINs	511	0	179	0	0	0	0
	REPINs	242	0	165	0	0	0	0
Smalt_PEG-390	REP/REPINs	191	90	196	261	0	207	0
	REPINs	75	7	26	169	0	115	0
Smalt_PEG-42	REP/REPINs	263	99	162	57	36	282	0
	REPINs	187	96	16	45	20	279	0
Smalt_PEG-68	REP/REPINs	293	465	131	0	0	290	0
	REPINs	112	400	9	0	0	282	0
Smalt_R551-3	REP/REPINs	244	60	135	374	28	130	0
	REPINs	122	6	11	361	8	126	0
Smalt_SJTH1	REP/REPINs	220	280	297	0	69	246	50
	REPINs	187	263	57	0	36	241	35
Smalt_SJTL3	REP/REPINs	512	535	158	59	0	91	0
	REPINs	469	495	15	50	0	31	0
Smalt_SKK55	REP/REPINs	162	94	158	255	0	381	0
	REPINs	50	91	14	163	0	376	0
Smalt_SM866	REP/REPINs	399	647	241	95	71	41	0
	REPINs	191	580	38	85	29	8	0
Smalt_Sm53	REP/REPINs	429	756	200	50	0	0	0
	REPINs	204	739	25	40	0	0	0
Smalt_SoD9b	REP/REPINs	470	424	129	0	0	148	0
	REPINs	200	184	9	0	0	70	0
Smalt_T50-20	REP/REPINs	369	581	247	76	80	44	0
	REPINs	157	519	36	4	32	11	0
Smalt_U5	REP/REPINs	260	68	368	486	0	0	0
	REPINs	100	5	56	456	0	0	0
Smalt_W18	REP/REPINs	265	320	149	0	37	271	62
	REPINs	196	301	16	0	19	266	45
Smalt_WP1-W18-CRE-01	REP/REPINs	450	136	186	56	0	0	0
	REPINs	205	109	22	33	0	0	0
Smalt_X28	REP/REPINs	264	321	235	146	0	71	62
	REPINs	116	127	41	129	0	30	45
Smalt_sm-RA9	REP/REPINs	250	325	130	357	0	124	0
	REPINs	129	142	10	340	0	119	0
Smalt_sm454	REP/REPINs	415	114	197	56	0	0	0
	REPINs	202	11	25	42	0	0	0

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