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Results for RAREFAN run z07h748j

Parameters

reference_strain: Smalt_ISMMS3.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

z07h748j is a rerun of mlw6l19k.

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 24 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	230	81	275	42	0
	REPINs	87	29	38	9	0
Smalt_AB550	REP/REPINs	347	0	127	90	255
	REPINs	139	0	10	22	75
Smalt_CF13	REP/REPINs	576	0	184	0	0
	REPINs	546	0	25	0	0
Smalt_CPBW01	REP/REPINs	122	0	176	348	0
	REPINs	112	0	18	224	0
Smalt_CSM2	REP/REPINs	289	0	236	101	230
	REPINs	130	0	43	24	201
Smalt_Col1	REP/REPINs	134	0	172	149	207
	REPINs	107	0	19	40	193
Smalt_D457	REP/REPINs	429	0	0	47	210
	REPINs	402	0	0	7	61
Smalt_DHHJ	REP/REPINs	355	62	256	210	269
	REPINs	178	32	39	41	94
Smalt_FDAARGOS_1044	REP/REPINs	776	0	197	0	212
	REPINs	646	0	27	0	186
Smalt_FDAARGOS_325	REP/REPINs	622	0	192	0	52
	REPINs	605	0	16	0	5
Smalt_FDAARGOS_507	REP/REPINs	415	0	207	0	0
	REPINs	181	0	28	0	0
Smalt_FDAARGOS_649	REP/REPINs	774	0	199	0	176
	REPINs	655	0	26	0	28
Smalt_FDAARGOS_92	REP/REPINs	410	0	184	0	261
	REPINs	193	0	20	0	223
Smalt_ICU331	REP/REPINs	428	0	195	0	162
	REPINs	192	0	24	0	27
Smalt_ISMMS2	REP/REPINs	176	0	189	349	0
	REPINs	114	0	21	229	0
Smalt_ISMMS2R	REP/REPINs	176	0	189	349	0
	REPINs	114	0	21	229	0
Smalt_ISMMS3	REP/REPINs	411	95	140	132	264
	REPINs	396	47	14	43	229
Smalt_JV3	REP/REPINs	557	0	243	157	136
	REPINs	438	0	38	56	21
Smalt_K279a	REP/REPINs	679	0	202	0	171
	REPINs	647	0	23	0	38
Smalt_KMM349	REP/REPINs	250	0	136	117	0
	REPINs	128	0	10	38	0
Smalt_MER1	REP/REPINs	204	0	390	0	249
	REPINs	75	0	344	0	55
Smalt_NCTC10257	REP/REPINs	776	0	197	0	212
	REPINs	646	0	27	0	186
Smalt_NCTC10258	REP/REPINs	640	0	199	0	211
	REPINs	617	0	26	0	188
Smalt_NCTC10259	REP/REPINs	406	0	126	102	65
	REPINs	374	0	8	23	65
Smalt_NCTC10498	REP/REPINs	774	0	190	0	156
	REPINs	647	0	29	0	18
Smalt_NCTC13014	REP/REPINs	220	34	162	204	238
	REPINs	200	16	20	54	211
Smalt_NEB515	REP/REPINs	660	0	195	0	0
	REPINs	631	0	26	0	0
Smalt_O1	REP/REPINs	463	0	186	0	166
	REPINs	221	0	22	0	25
Smalt_OUC_Est10	REP/REPINs	229	33	197	0	0
	REPINs	104	18	28	0	0
Smalt_PEG-141	REP/REPINs	364	67	237	133	352
	REPINs	174	34	39	31	336
Smalt_PEG-173	REP/REPINs	262	73	197	94	358
	REPINs	119	41	32	18	332
Smalt_PEG-305	REP/REPINs	559	0	156	0	57
	REPINs	269	0	18	0	51
Smalt_PEG-390	REP/REPINs	193	0	190	261	49
	REPINs	78	0	26	169	3
Smalt_PEG-42	REP/REPINs	262	38	159	178	141
	REPINs	200	21	19	56	11
Smalt_PEG-68	REP/REPINs	418	0	127	98	216
	REPINs	388	0	9	23	61
Smalt_R551-3	REP/REPINs	243	28	127	134	0
	REPINs	123	7	12	120	0
Smalt_SJTH1	REP/REPINs	230	69	299	0	315
	REPINs	207	36	58	0	271
Smalt_SJTL3	REP/REPINs	512	0	152	192	298
	REPINs	486	0	15	179	275
Smalt_SKK55	REP/REPINs	164	0	153	255	39
	REPINs	50	0	14	163	2
Smalt_SM866	REP/REPINs	446	72	235	88	322
	REPINs	199	30	38	16	123
Smalt_Sm53	REP/REPINs	651	0	192	0	212
	REPINs	632	0	25	0	177
Smalt_SoD9b	REP/REPINs	472	0	125	0	0
	REPINs	198	0	9	0	0
Smalt_T50-20	REP/REPINs	370	80	243	137	94
	REPINs	159	32	36	34	6
Smalt_U5	REP/REPINs	365	0	371	0	0
	REPINs	348	0	57	0	0
Smalt_W18	REP/REPINs	263	39	152	177	138
	REPINs	209	20	15	56	15
Smalt_WP1-W18-CRE-01	REP/REPINs	670	0	187	0	0
	REPINs	648	0	22	0	0
Smalt_X28	REP/REPINs	310	0	235	0	116
	REPINs	122	0	41	0	14
Smalt_sm-RA9	REP/REPINs	252	23	124	122	0
	REPINs	130	7	10	41	0
Smalt_sm454	REP/REPINs	625	0	199	0	52
	REPINs	607	0	25	0	3

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