---

Results for RAREFAN run uq4d_ut9

Parameters

reference_strain: Nmen_2594.fas
nmer_length: 21
min_nmer_occurrence: 55
query_rayt: NMAA_0235.faa
distance_group_seeds: 15
distance_repin_rayt: 130
analyse_repins: y
e_value_cutoff: 1e-30

uq4d_ut9 is a rerun of f5ztr_t0.

Status: complete

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

RAYTs

RAREFAN discovered 311 RAYTs across all submitted genomes using tblastn with NMAA_0235.faa at an e-value threshold of 1e-30.

Seed sequences

RAREFAN identified 184 21bp long sequences in the reference genome that occur more frequently than 55 times.

REP/REPIN counts

	Group	0	7	8	9
Strain
Ngon_1090	REP/REPINs	148	151	154	0
	REPINs	87	88	12	0
Ngon_32867	REP/REPINs	144	148	160	0
	REPINs	83	84	14	0
Ngon_34530	REP/REPINs	151	153	156	60
	REPINs	75	76	13	27
Ngon_34769	REP/REPINs	152	154	155	0
	REPINs	80	83	13	0
Ngon_FA19	REP/REPINs	169	172	156	0
	REPINs	92	93	13	0
Ngon_FA6140	REP/REPINs	150	154	151	0
	REPINs	83	84	12	0
Ngon_FC428	REP/REPINs	144	147	156	61
	REPINs	77	77	13	26
Ngon_FC460	REP/REPINs	144	147	156	61
	REPINs	77	77	13	26
Ngon_FC498	REP/REPINs	144	147	158	61
	REPINs	77	77	13	26
Ngon_FDAARGOS_204	REP/REPINs	143	145	152	0
	REPINs	77	78	15	0
Ngon_FDAARGOS_205	REP/REPINs	162	165	155	0
	REPINs	94	95	12	0
Ngon_FDAARGOS_207	REP/REPINs	155	158	152	0
	REPINs	83	84	14	0
Ngon_FQ01	REP/REPINs	149	151	164	0
	REPINs	82	83	12	0
Ngon_FQ02	REP/REPINs	142	145	156	0
	REPINs	82	83	13	0
Ngon_FQ04	REP/REPINs	152	155	155	0
	REPINs	89	90	13	0
Ngon_FQ20	REP/REPINs	156	158	146	0
	REPINs	85	86	12	0
Ngon_FQ35	REP/REPINs	156	158	146	0
	REPINs	85	86	12	0
Ngon_FQ36	REP/REPINs	146	150	160	0
	REPINs	86	87	13	0
Ngon_FQ48	REP/REPINs	151	153	160	60
	REPINs	76	77	13	27
Ngon_FQ82	REP/REPINs	150	153	156	0
	REPINs	88	89	13	0
Ngon_FQ84	REP/REPINs	153	156	156	0
	REPINs	90	91	13	0
Ngon_MS11	REP/REPINs	153	156	154	0
	REPINs	88	89	13	0
Ngon_NCCP11945	REP/REPINs	153	156	162	61
	REPINs	82	83	13	26
Ngon_NG-k51_05	REP/REPINs	144	147	165	61
	REPINs	77	78	13	26
Ngon_NJ1711654	REP/REPINs	144	147	158	61
	REPINs	77	77	13	26
Ngon_NJ189125	REP/REPINs	144	147	156	58
	REPINs	77	77	13	25
Ngon_RIVM0610	REP/REPINs	152	154	158	60
	REPINs	76	77	13	27
Ngon_RIVM0640	REP/REPINs	154	156	158	60
	REPINs	77	78	13	27
Ngon_SS3160	REP/REPINs	142	146	158	61
	REPINs	77	76	13	26
Ngon_TFG-A2	REP/REPINs	146	150	160	0
	REPINs	84	85	13	0
Ngon_TFG-B2	REP/REPINs	144	147	161	0
	REPINs	82	83	13	0
Nmen_053442	REP/REPINs	475	477	356	95
	REPINs	280	281	20	26
Nmen_06-178	REP/REPINs	452	453	374	94
	REPINs	280	283	23	26
Nmen_09-292	REP/REPINs	445	447	0	94
	REPINs	262	268	0	26
Nmen_11-14	REP/REPINs	453	454	372	94
	REPINs	278	282	23	26
Nmen_11-7	REP/REPINs	454	455	375	96
	REPINs	278	281	23	26
Nmen_12-176	REP/REPINs	451	452	374	94
	REPINs	278	282	23	25
Nmen_12-221	REP/REPINs	454	455	374	94
	REPINs	281	285	23	26
Nmen_12-330	REP/REPINs	445	446	374	94
	REPINs	272	276	23	25
Nmen_13-600	REP/REPINs	448	449	374	94
	REPINs	275	279	23	25
Nmen_14-563	REP/REPINs	449	450	372	94
	REPINs	277	281	23	25
Nmen_2594	REP/REPINs	375	378	370	0
	REPINs	224	227	27	0
Nmen_331401	REP/REPINs	396	396	364	0
	REPINs	235	239	26	0
Nmen_38277	REP/REPINs	441	444	358	94
	REPINs	266	271	28	35
Nmen_510612	REP/REPINs	389	390	0	0
	REPINs	236	239	0	0
Nmen_8013	REP/REPINs	485	490	368	88
	REPINs	301	303	24	30
Nmen_95-134	REP/REPINs	454	454	373	96
	REPINs	275	279	23	26
Nmen_98-182	REP/REPINs	466	467	375	96
	REPINs	290	293	23	26
Nmen_COL-201504-11	REP/REPINs	428	430	373	94
	REPINs	264	268	29	30
Nmen_DE10444	REP/REPINs	372	375	366	92
	REPINs	226	230	25	25
Nmen_DE8555	REP/REPINs	416	412	375	95
	REPINs	252	256	32	30
Nmen_DE8669	REP/REPINs	400	403	346	0
	REPINs	248	251	28	0
Nmen_FAM18	REP/REPINs	433	430	371	92
	REPINs	269	273	33	29
Nmen_FDAARGOS_209	REP/REPINs	431	431	377	0
	REPINs	268	273	30	0
Nmen_FDAARGOS_210	REP/REPINs	456	457	372	95
	REPINs	268	273	27	30
Nmen_FDAARGOS_211	REP/REPINs	556	555	382	93
	REPINs	343	349	22	29
Nmen_FDAARGOS_212	REP/REPINs	487	485	377	95
	REPINs	293	297	30	28
Nmen_FDAARGOS_214	REP/REPINs	565	565	360	101
	REPINs	347	351	29	41
Nmen_FDAARGOS_215	REP/REPINs	556	555	382	93
	REPINs	343	349	22	29
Nmen_G2136	REP/REPINs	444	444	370	92
	REPINs	270	273	30	29
Nmen_L91543	REP/REPINs	426	418	375	94
	REPINs	261	262	30	29
Nmen_LNP21362	REP/REPINs	405	407	361	90
	REPINs	231	237	28	30
Nmen_M01-240149	REP/REPINs	404	405	344	0
	REPINs	243	248	28	0
Nmen_M01-240355	REP/REPINs	476	477	381	99
	REPINs	290	295	29	32
Nmen_M04-240196	REP/REPINs	409	410	371	93
	REPINs	259	262	23	28
Nmen_M0579	REP/REPINs	450	454	377	99
	REPINs	277	279	29	37
Nmen_M07149	REP/REPINs	450	446	377	91
	REPINs	273	277	29	28
Nmen_M07161	REP/REPINs	452	448	376	93
	REPINs	272	277	29	30
Nmen_M07162	REP/REPINs	448	445	371	92
	REPINs	273	277	30	29
Nmen_M08000	REP/REPINs	447	443	376	89
	REPINs	270	275	30	28
Nmen_M08001	REP/REPINs	447	443	376	89
	REPINs	270	275	30	28
Nmen_M09261	REP/REPINs	446	442	376	89
	REPINs	269	274	30	28
Nmen_M09293	REP/REPINs	446	442	376	89
	REPINs	269	274	30	28
Nmen_M10208	REP/REPINs	425	421	373	92
	REPINs	260	265	30	27
Nmen_M12752	REP/REPINs	450	446	377	91
	REPINs	273	277	29	28
Nmen_M18727	REP/REPINs	414	417	368	90
	REPINs	258	261	23	27
Nmen_M18755	REP/REPINs	462	462	371	91
	REPINs	284	287	23	30
Nmen_M21273	REP/REPINs	443	442	375	99
	REPINs	274	278	29	30
Nmen_M21374	REP/REPINs	427	425	369	95
	REPINs	262	266	30	30
Nmen_M21717	REP/REPINs	410	408	373	95
	REPINs	252	255	31	29
Nmen_M21955	REP/REPINs	449	450	376	93
	REPINs	262	268	27	29
Nmen_M22160	REP/REPINs	450	446	377	91
	REPINs	270	274	29	28
Nmen_M22189	REP/REPINs	450	446	377	91
	REPINs	270	274	29	28
Nmen_M22191	REP/REPINs	445	441	376	89
	REPINs	270	275	30	28
Nmen_M22293	REP/REPINs	500	506	360	94
	REPINs	314	318	30	38
Nmen_M22425	REP/REPINs	432	432	385	96
	REPINs	267	269	28	33
Nmen_M22718	REP/REPINs	449	445	377	91
	REPINs	272	276	29	28
Nmen_M22722	REP/REPINs	450	446	377	91
	REPINs	273	277	29	28
Nmen_M22740	REP/REPINs	450	446	377	91
	REPINs	273	277	29	28
Nmen_M22745	REP/REPINs	447	443	376	89
	REPINs	270	275	30	28
Nmen_M22748	REP/REPINs	443	439	376	91
	REPINs	267	272	30	28
Nmen_M22759	REP/REPINs	448	444	376	90
	REPINs	269	274	30	27
Nmen_M22769	REP/REPINs	448	444	376	89
	REPINs	269	274	30	27
Nmen_M22772	REP/REPINs	449	445	376	90
	REPINs	272	276	29	28
Nmen_M22783	REP/REPINs	498	497	0	98
	REPINs	311	315	0	33
Nmen_M22801	REP/REPINs	447	443	377	91
	REPINs	270	275	29	28
Nmen_M22804	REP/REPINs	477	476	0	99
	REPINs	293	297	0	32
Nmen_M22809	REP/REPINs	490	489	0	99
	REPINs	304	308	0	32
Nmen_M22811	REP/REPINs	498	497	0	99
	REPINs	311	315	0	33
Nmen_M22814	REP/REPINs	403	405	366	111
	REPINs	244	249	29	37
Nmen_M22819	REP/REPINs	447	446	0	97
	REPINs	281	285	0	31
Nmen_M22822	REP/REPINs	456	455	0	99
	REPINs	285	288	0	32
Nmen_M22828	REP/REPINs	456	455	0	99
	REPINs	285	289	0	32
Nmen_M23347	REP/REPINs	540	542	380	96
	REPINs	349	351	20	32
Nmen_M23413	REP/REPINs	430	427	376	91
	REPINs	260	264	29	28
Nmen_M24705	REP/REPINs	485	485	0	100
	REPINs	301	304	0	33
Nmen_M24730	REP/REPINs	436	433	376	91
	REPINs	263	267	29	28
Nmen_M25070	REP/REPINs	433	430	374	90
	REPINs	261	265	29	28
Nmen_M25087	REP/REPINs	430	427	374	90
	REPINs	260	264	29	28
Nmen_M25419	REP/REPINs	426	422	374	93
	REPINs	259	264	30	27
Nmen_M25438	REP/REPINs	430	427	375	90
	REPINs	260	264	29	28
Nmen_M25456	REP/REPINs	430	427	376	91
	REPINs	260	264	29	28
Nmen_M25459	REP/REPINs	430	427	376	91
	REPINs	260	264	29	28
Nmen_M25462	REP/REPINs	430	427	376	91
	REPINs	260	264	29	28
Nmen_M25472	REP/REPINs	430	427	374	90
	REPINs	260	264	29	28
Nmen_M25474	REP/REPINs	430	427	376	91
	REPINs	259	263	29	28
Nmen_M25476	REP/REPINs	433	430	374	90
	REPINs	261	265	29	28
Nmen_M25964	REP/REPINs	436	432	373	93
	REPINs	261	265	32	30
Nmen_M26263	REP/REPINs	437	437	369	98
	REPINs	266	270	30	31
Nmen_M26417	REP/REPINs	437	437	368	97
	REPINs	266	270	30	31
Nmen_M27559	REP/REPINs	430	427	376	91
	REPINs	260	264	29	28
Nmen_M7124	REP/REPINs	450	446	377	91
	REPINs	273	277	29	28
Nmen_MC58	REP/REPINs	456	456	372	93
	REPINs	267	272	27	31
Nmen_NM3682	REP/REPINs	455	451	375	93
	REPINs	274	278	31	29
Nmen_NM3683	REP/REPINs	455	451	375	93
	REPINs	274	278	31	29
Nmen_NM3686	REP/REPINs	444	440	375	91
	REPINs	260	264	30	27
Nmen_WUE2121	REP/REPINs	412	408	372	94
	REPINs	250	254	31	30
Nmen_Z2491	REP/REPINs	445	447	381	107
	REPINs	272	276	27	35
Nmen_alpha14	REP/REPINs	428	430	382	101
	REPINs	265	267	30	35
Nmen_alpha710	REP/REPINs	420	421	346	96
	REPINs	251	256	28	37

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