---

Results for RAREFAN run mko71vtk

Parameters

reference_strain: chlTAMOak81.fas
nmer_length: 21
min_nmer_occurrence: 55
query_rayt: yafM_SBW25.faa
distance_group_seeds: 15
distance_repin_rayt: 130
analyse_repins: y
e_value_cutoff: 1e-30

mko71vtk is a rerun of t5dvaibm.

Status: complete

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

RAYTs

RAREFAN discovered 33 RAYTs across all submitted genomes using tblastn with yafM_SBW25.faa at an e-value threshold of 1e-30.

Seed sequences

RAREFAN identified 59 21bp long sequences in the reference genome that occur more frequently than 55 times.

REP/REPIN counts

	Group	0	1	2	3	4	5
Strain
chl17411	REP/REPINs	80	401	170	401	167	27
	REPINs	21	179	83	179	84	2
chl17415	REP/REPINs	254	141	529	141	467	174
	REPINs	163	33	414	33	261	32
chl17809	REP/REPINs	80	401	170	401	167	27
	REPINs	21	179	83	179	84	2
chl189	REP/REPINs	222	129	393	129	392	145
	REPINs	153	35	223	35	223	25
chl19603	REP/REPINs	53	243	326	243	326	95
	REPINs	19	82	183	82	182	15
chl21509	REP/REPINs	54	439	180	439	179	46
	REPINs	9	262	94	262	92	7
chl2210	REP/REPINs	62	254	332	254	332	95
	REPINs	21	91	187	91	186	11
chl449	REP/REPINs	55	240	331	240	329	88
	REPINs	18	78	190	78	190	11
chl464	REP/REPINs	55	240	331	240	329	88
	REPINs	18	78	190	78	190	11
chl50083	REP/REPINs	73	271	324	271	324	106
	REPINs	29	116	189	116	188	24
chl66	REP/REPINs	182	345	323	345	322	105
	REPINs	129	177	153	177	150	6
chl6698	REP/REPINs	191	342	303	342	302	0
	REPINs	128	177	142	177	141	0
chlB25	REP/REPINs	138	150	269	150	270	84
	REPINs	83	39	146	39	147	21
chlC50	REP/REPINs	185	351	294	351	294	97
	REPINs	128	175	142	175	141	6
chlCW2	REP/REPINs	49	240	316	240	315	80
	REPINs	19	88	190	88	190	14
chlChPhzS135	REP/REPINs	77	398	169	398	167	29
	REPINs	21	177	86	177	84	3
chlChPhzS140	REP/REPINs	77	389	175	389	175	0
	REPINs	24	177	90	177	89	0
chlChPhzS23	REP/REPINs	180	342	309	342	308	103
	REPINs	127	158	143	158	143	8
chlChPhzS24	REP/REPINs	190	338	321	338	320	118
	REPINs	130	155	140	155	140	8
chlChPhzTR18	REP/REPINs	192	338	321	338	319	117
	REPINs	135	154	142	154	142	8
chlChPhzTR36	REP/REPINs	186	328	308	328	308	113
	REPINs	131	157	146	157	144	10
chlChPhzTR38	REP/REPINs	194	339	321	339	318	118
	REPINs	134	153	139	153	139	8
chlChPhzTR39	REP/REPINs	189	337	323	337	320	118
	REPINs	132	151	139	151	139	8
chlChPhzTR44	REP/REPINs	77	397	164	397	165	0
	REPINs	22	181	83	181	82	0
chlDTR133	REP/REPINs	76	398	165	398	165	0
	REPINs	23	175	86	175	85	0
chlJD37	REP/REPINs	86	210	326	210	325	102
	REPINs	36	69	180	69	180	11
chlK27	REP/REPINs	88	247	410	247	410	132
	REPINs	49	88	211	88	212	18
chlLzh-T5	REP/REPINs	185	346	332	346	332	110
	REPINs	130	174	147	174	146	6
chlM12	REP/REPINs	50	233	357	233	357	114
	REPINs	17	76	195	76	196	15
chlM71	REP/REPINs	66	262	396	262	396	126
	REPINs	30	85	204	85	205	12
chlO6	REP/REPINs	188	325	322	325	321	122
	REPINs	126	159	144	159	142	9
chlP2	REP/REPINs	168	345	306	345	307	0
	REPINs	119	173	141	173	140	0
chlPA23	REP/REPINs	190	344	320	344	318	104
	REPINs	129	168	142	168	140	6
chlPCL1391	REP/REPINs	79	386	175	386	173	0
	REPINs	25	174	91	174	90	0
chlPCL1606	REP/REPINs	68	460	0	460	0	0
	REPINs	28	243	0	243	0	0
chlPCL1607	REP/REPINs	75	384	171	384	172	0
	REPINs	22	175	90	175	88	0
chlPb-St2	REP/REPINs	222	159	256	159	256	74
	REPINs	131	39	125	39	127	11
chlQ16	REP/REPINs	59	245	338	245	338	99
	REPINs	22	81	187	81	187	12
chlSLPH10	REP/REPINs	76	395	168	395	166	28
	REPINs	21	179	87	179	85	3
chlStFRB508	REP/REPINs	89	250	358	250	358	111
	REPINs	36	99	199	99	200	14
chlTAMOak81	REP/REPINs	392	293	241	293	242	98
	REPINs	255	179	109	179	108	15
chlToZa7	REP/REPINs	77	393	173	393	174	0
	REPINs	22	173	88	173	87	0
chlZJU60	REP/REPINs	70	401	172	401	168	29
	REPINs	19	192	85	192	86	4
spMRSN12121	REP/REPINs	66	467	0	467	0	0
	REPINs	23	249	0	249	0	0

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