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Results for RAREFAN run t8v7cf77

Parameters

reference_strain: Smalt_Sm53.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

t8v7cf77 is a rerun of _1a8l7wu.

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 31 21bp long sequences in the reference genome that occur more frequently than 55 times.

REP/REPIN counts

	Group	0	1	2	3
Strain
Smalt_AA1	REP/REPINs	228	274	291	0
	REPINs	87	37	44	0
Smalt_AB550	REP/REPINs	344	136	0	50
	REPINs	142	9	0	44
Smalt_CF13	REP/REPINs	388	187	697	45
	REPINs	171	26	670	33
Smalt_CPBW01	REP/REPINs	98	184	170	34
	REPINs	18	17	116	25
Smalt_CSM2	REP/REPINs	288	239	467	53
	REPINs	128	43	408	43
Smalt_Col1	REP/REPINs	133	186	204	51
	REPINs	95	18	123	44
Smalt_D457	REP/REPINs	300	0	471	56
	REPINs	116	0	410	46
Smalt_DHHJ	REP/REPINs	355	254	602	54
	REPINs	175	39	525	40
Smalt_FDAARGOS_1044	REP/REPINs	729	200	104	45
	REPINs	631	29	10	35
Smalt_FDAARGOS_325	REP/REPINs	421	203	126	46
	REPINs	184	21	14	34
Smalt_FDAARGOS_507	REP/REPINs	411	207	516	43
	REPINs	181	28	200	30
Smalt_FDAARGOS_649	REP/REPINs	539	204	736	46
	REPINs	212	23	634	34
Smalt_FDAARGOS_92	REP/REPINs	407	188	679	46
	REPINs	191	20	637	32
Smalt_ICU331	REP/REPINs	424	201	739	46
	REPINs	190	26	616	36
Smalt_ISMMS2	REP/REPINs	123	197	175	33
	REPINs	92	20	119	25
Smalt_ISMMS2R	REP/REPINs	123	197	175	33
	REPINs	92	20	119	25
Smalt_ISMMS3	REP/REPINs	265	141	58	44
	REPINs	141	15	3	39
Smalt_JV3	REP/REPINs	447	240	568	53
	REPINs	413	36	549	46
Smalt_K279a	REP/REPINs	677	201	122	46
	REPINs	635	25	86	34
Smalt_KMM349	REP/REPINs	250	146	443	52
	REPINs	127	10	383	40
Smalt_MER1	REP/REPINs	203	320	0	0
	REPINs	74	64	0	0
Smalt_NCTC10257	REP/REPINs	729	200	104	45
	REPINs	631	29	10	35
Smalt_NCTC10258	REP/REPINs	637	202	745	44
	REPINs	599	27	636	31
Smalt_NCTC10259	REP/REPINs	293	134	52	55
	REPINs	101	9	5	47
Smalt_NCTC10498	REP/REPINs	548	194	774	46
	REPINs	226	30	655	34
Smalt_NCTC13014	REP/REPINs	218	167	299	50
	REPINs	184	15	284	43
Smalt_NEB515	REP/REPINs	436	201	782	49
	REPINs	208	27	759	38
Smalt_O1	REP/REPINs	460	195	120	43
	REPINs	220	22	13	26
Smalt_OUC_Est10	REP/REPINs	222	201	0	39
	REPINs	104	30	0	26
Smalt_PEG-141	REP/REPINs	366	243	429	53
	REPINs	173	39	181	40
Smalt_PEG-173	REP/REPINs	257	203	427	47
	REPINs	117	30	368	33
Smalt_PEG-305	REP/REPINs	511	167	0	52
	REPINs	242	25	0	40
Smalt_PEG-390	REP/REPINs	191	199	90	32
	REPINs	75	26	7	21
Smalt_PEG-42	REP/REPINs	263	157	99	48
	REPINs	187	16	96	39
Smalt_PEG-68	REP/REPINs	293	131	465	54
	REPINs	112	9	400	45
Smalt_R551-3	REP/REPINs	244	136	60	54
	REPINs	122	12	6	42
Smalt_SJTH1	REP/REPINs	220	301	280	44
	REPINs	187	56	263	34
Smalt_SJTL3	REP/REPINs	512	159	535	49
	REPINs	469	15	495	39
Smalt_SKK55	REP/REPINs	162	149	94	37
	REPINs	50	13	91	21
Smalt_SM866	REP/REPINs	399	238	647	54
	REPINs	191	37	580	41
Smalt_Sm53	REP/REPINs	429	196	756	48
	REPINs	204	25	739	36
Smalt_SoD9b	REP/REPINs	470	133	424	50
	REPINs	200	9	184	36
Smalt_T50-20	REP/REPINs	369	246	581	59
	REPINs	157	37	519	42
Smalt_U5	REP/REPINs	260	368	68	0
	REPINs	100	56	5	0
Smalt_W18	REP/REPINs	265	150	320	47
	REPINs	196	15	301	38
Smalt_WP1-W18-CRE-01	REP/REPINs	450	188	136	45
	REPINs	205	22	109	34
Smalt_X28	REP/REPINs	264	235	321	60
	REPINs	116	42	127	49
Smalt_sm-RA9	REP/REPINs	250	129	325	51
	REPINs	129	10	142	41
Smalt_sm454	REP/REPINs	415	197	114	44
	REPINs	202	27	11	32

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