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Results for RAREFAN run mlw6l19k

Parameters

reference_strain: Smalt_AB550.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

mlw6l19k is a rerun of yy72i755.

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 27 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	0	112	0
	REPINs	87	0	111	0
Smalt_AB550	REP/REPINs	344	50	137	255
	REPINs	142	44	72	75
Smalt_CF13	REP/REPINs	388	45	0	123
	REPINs	171	33	0	26
Smalt_CPBW01	REP/REPINs	98	33	201	111
	REPINs	18	26	121	24
Smalt_CSM2	REP/REPINs	288	53	58	230
	REPINs	128	43	55	201
Smalt_Col1	REP/REPINs	133	50	362	207
	REPINs	95	43	359	193
Smalt_D457	REP/REPINs	300	56	285	210
	REPINs	116	46	273	61
Smalt_DHHJ	REP/REPINs	355	54	37	269
	REPINs	175	40	5	94
Smalt_FDAARGOS_1044	REP/REPINs	729	45	0	212
	REPINs	631	34	0	186
Smalt_FDAARGOS_325	REP/REPINs	421	46	0	125
	REPINs	184	34	0	35
Smalt_FDAARGOS_507	REP/REPINs	411	43	44	0
	REPINs	181	30	12	0
Smalt_FDAARGOS_649	REP/REPINs	539	46	0	176
	REPINs	212	34	0	28
Smalt_FDAARGOS_92	REP/REPINs	407	46	0	261
	REPINs	191	32	0	223
Smalt_ICU331	REP/REPINs	424	46	36	162
	REPINs	190	36	9	27
Smalt_ISMMS2	REP/REPINs	123	32	203	0
	REPINs	92	25	120	0
Smalt_ISMMS2R	REP/REPINs	123	32	203	0
	REPINs	92	25	120	0
Smalt_ISMMS3	REP/REPINs	265	44	0	264
	REPINs	141	38	0	229
Smalt_JV3	REP/REPINs	447	53	45	136
	REPINs	413	46	6	21
Smalt_K279a	REP/REPINs	677	46	42	171
	REPINs	635	34	9	38
Smalt_KMM349	REP/REPINs	250	52	120	0
	REPINs	127	40	115	0
Smalt_MER1	REP/REPINs	203	0	52	249
	REPINs	74	0	20	55
Smalt_NCTC10257	REP/REPINs	729	45	0	212
	REPINs	631	34	0	186
Smalt_NCTC10258	REP/REPINs	637	44	0	211
	REPINs	599	31	0	188
Smalt_NCTC10259	REP/REPINs	293	55	296	158
	REPINs	101	47	289	38
Smalt_NCTC10498	REP/REPINs	548	46	34	156
	REPINs	226	33	10	18
Smalt_NCTC13014	REP/REPINs	218	50	298	238
	REPINs	184	43	291	211
Smalt_NEB515	REP/REPINs	436	49	0	0
	REPINs	208	38	0	0
Smalt_O1	REP/REPINs	460	43	34	166
	REPINs	220	26	10	25
Smalt_OUC_Est10	REP/REPINs	222	39	93	0
	REPINs	104	26	32	0
Smalt_PEG-141	REP/REPINs	366	53	0	352
	REPINs	173	40	0	336
Smalt_PEG-173	REP/REPINs	257	47	0	358
	REPINs	117	33	0	332
Smalt_PEG-305	REP/REPINs	511	52	0	0
	REPINs	242	40	0	0
Smalt_PEG-390	REP/REPINs	191	31	207	62
	REPINs	75	20	115	31
Smalt_PEG-42	REP/REPINs	263	48	282	96
	REPINs	187	37	279	90
Smalt_PEG-68	REP/REPINs	293	54	290	216
	REPINs	112	45	282	61
Smalt_R551-3	REP/REPINs	244	54	130	0
	REPINs	122	42	126	0
Smalt_SJTH1	REP/REPINs	220	44	246	315
	REPINs	187	34	241	271
Smalt_SJTL3	REP/REPINs	512	49	91	298
	REPINs	469	39	31	275
Smalt_SKK55	REP/REPINs	162	37	381	55
	REPINs	50	21	376	7
Smalt_SM866	REP/REPINs	399	54	41	322
	REPINs	191	40	8	123
Smalt_Sm53	REP/REPINs	429	48	0	212
	REPINs	204	36	0	177
Smalt_SoD9b	REP/REPINs	470	50	148	0
	REPINs	200	36	70	0
Smalt_T50-20	REP/REPINs	369	59	44	347
	REPINs	157	41	11	312
Smalt_U5	REP/REPINs	260	0	0	0
	REPINs	100	0	0	0
Smalt_W18	REP/REPINs	265	47	271	101
	REPINs	196	37	266	94
Smalt_WP1-W18-CRE-01	REP/REPINs	450	45	0	0
	REPINs	205	34	0	0
Smalt_X28	REP/REPINs	264	60	71	0
	REPINs	116	49	30	0
Smalt_sm-RA9	REP/REPINs	250	51	124	0
	REPINs	129	41	119	0
Smalt_sm454	REP/REPINs	415	44	0	161
	REPINs	202	31	0	134

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