AutoCloner

Multiple sequence alignment - TraesCS1B01G204400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS1B01G204400	chr1B	100.000	3066	0	0	1	3066	368539349	368542414	0.000000e+00	5662.0
1	TraesCS1B01G204400	chr1B	100.000	2290	0	0	3584	5873	368542932	368545221	0.000000e+00	4229.0
2	TraesCS1B01G204400	chr1B	99.213	127	0	1	4934	5060	269261813	269261688	1.650000e-55	228.0
3	TraesCS1B01G204400	chr1B	96.296	54	1	1	5556	5609	368544872	368544924	2.920000e-13	87.9
4	TraesCS1B01G204400	chr1B	96.296	54	1	1	5524	5576	368544904	368544957	2.920000e-13	87.9
5	TraesCS1B01G204400	chr1B	93.333	60	3	1	5063	5121	626498579	626498520	2.920000e-13	87.9
6	TraesCS1B01G204400	chr1A	95.053	2345	75	14	654	2985	313752000	313749684	0.000000e+00	3650.0
7	TraesCS1B01G204400	chr1A	89.646	734	40	15	5146	5873	313748704	313748001	0.000000e+00	902.0
8	TraesCS1B01G204400	chr1A	97.802	364	5	3	3598	3960	313749360	313748999	5.000000e-175	625.0
9	TraesCS1B01G204400	chr1A	86.000	500	52	10	1	487	313752660	313752166	2.430000e-143	520.0
10	TraesCS1B01G204400	chr1A	93.846	260	16	0	4517	4776	313749005	313748746	5.520000e-105	392.0
11	TraesCS1B01G204400	chr1A	91.935	62	3	2	5063	5123	498452794	498452734	1.050000e-12	86.1
12	TraesCS1B01G204400	chr1D	90.303	2475	153	38	1	2436	233893110	233895536	0.000000e+00	3160.0
13	TraesCS1B01G204400	chr1D	90.275	874	59	13	4082	4932	233896478	233897348	0.000000e+00	1120.0
14	TraesCS1B01G204400	chr1D	88.813	733	49	19	5146	5873	233897357	233898061	0.000000e+00	869.0
15	TraesCS1B01G204400	chr1D	93.151	584	36	4	2476	3057	233895536	233896117	0.000000e+00	854.0
16	TraesCS1B01G204400	chr1D	91.633	251	17	4	3584	3831	233896161	233896410	1.570000e-90	344.0
17	TraesCS1B01G204400	chr1D	86.441	118	12	3	3963	4076	35756868	35756985	6.180000e-25	126.0
18	TraesCS1B01G204400	chr1D	93.939	66	3	1	3873	3938	233896413	233896477	1.350000e-16	99.0
19	TraesCS1B01G204400	chr1D	96.491	57	2	0	5071	5127	476229522	476229466	1.740000e-15	95.3
20	TraesCS1B01G204400	chr1D	96.226	53	2	0	5071	5123	449490166	449490218	2.920000e-13	87.9
21	TraesCS1B01G204400	chr1D	82.192	73	7	6	619	689	18859886	18859818	2.290000e-04	58.4
22	TraesCS1B01G204400	chr7D	89.082	403	39	4	4145	4545	33677505	33677904	4.090000e-136	496.0
23	TraesCS1B01G204400	chr7D	81.416	226	34	7	142	366	167547334	167547116	1.680000e-40	178.0
24	TraesCS1B01G204400	chr7D	80.603	232	41	4	137	364	633525201	633524970	6.050000e-40	176.0
25	TraesCS1B01G204400	chr7D	80.702	228	28	7	139	364	312574059	312573846	4.710000e-36	163.0
26	TraesCS1B01G204400	chr7B	85.217	230	29	4	137	364	151431080	151430854	1.270000e-56	231.0
27	TraesCS1B01G204400	chr7B	98.438	128	1	1	4933	5060	483806807	483806681	2.130000e-54	224.0
28	TraesCS1B01G204400	chr7B	79.389	262	45	7	112	371	111367328	111367074	6.050000e-40	176.0
29	TraesCS1B01G204400	chr7B	88.710	124	12	2	3963	4085	475307981	475308103	3.670000e-32	150.0
30	TraesCS1B01G204400	chr7B	77.419	217	44	5	149	364	79054863	79055075	2.220000e-24	124.0
31	TraesCS1B01G204400	chr7B	92.683	41	3	0	648	688	59954005	59954045	6.360000e-05	60.2
32	TraesCS1B01G204400	chr3B	98.438	128	1	1	4933	5060	760560999	760560873	2.130000e-54	224.0
33	TraesCS1B01G204400	chr3B	95.105	143	1	5	4919	5060	360009704	360009841	2.760000e-53	220.0
34	TraesCS1B01G204400	chrUn	98.413	126	1	1	4935	5060	401125181	401125057	2.760000e-53	220.0
35	TraesCS1B01G204400	chrUn	91.057	123	10	1	3963	4084	65138953	65138831	1.310000e-36	165.0
36	TraesCS1B01G204400	chrUn	86.087	115	14	2	3963	4076	22763200	22763087	7.990000e-24	122.0
37	TraesCS1B01G204400	chr2B	97.656	128	3	0	4933	5060	133004718	133004591	2.760000e-53	220.0
38	TraesCS1B01G204400	chr2B	97.638	127	3	0	4934	5060	959832	959958	9.910000e-53	219.0
39	TraesCS1B01G204400	chr2B	89.552	67	5	1	5072	5138	551551625	551551561	3.770000e-12	84.2
40	TraesCS1B01G204400	chr2D	97.656	128	2	1	4934	5060	383551070	383550943	9.910000e-53	219.0
41	TraesCS1B01G204400	chr2D	79.111	225	36	9	149	371	78433631	78433846	1.710000e-30	145.0
42	TraesCS1B01G204400	chr2D	86.555	119	12	2	3963	4080	31733412	31733297	1.720000e-25	128.0
43	TraesCS1B01G204400	chr2D	86.207	116	7	2	3962	4076	79387430	79387323	3.720000e-22	117.0
44	TraesCS1B01G204400	chr2D	98.113	53	1	0	5071	5123	215846505	215846453	6.270000e-15	93.5
45	TraesCS1B01G204400	chr2D	92.063	63	4	1	5062	5123	109700338	109700400	2.920000e-13	87.9
46	TraesCS1B01G204400	chr4B	97.638	127	2	1	4934	5060	47022047	47022172	3.560000e-52	217.0
47	TraesCS1B01G204400	chr4B	94.828	58	2	1	5071	5128	616316216	616316272	8.110000e-14	89.8
48	TraesCS1B01G204400	chr7A	83.478	230	30	6	137	364	341444519	341444296	2.140000e-49	207.0
49	TraesCS1B01G204400	chr6B	78.481	237	43	7	137	371	658243056	658242826	1.320000e-31	148.0
50	TraesCS1B01G204400	chr6B	87.603	121	11	2	3961	4077	365700753	365700873	2.850000e-28	137.0
51	TraesCS1B01G204400	chr6B	100.000	30	0	0	332	361	6175239	6175210	8.220000e-04	56.5
52	TraesCS1B01G204400	chr5D	78.541	233	30	9	139	368	482115123	482114908	1.030000e-27	135.0
53	TraesCS1B01G204400	chr5D	88.372	86	9	1	137	221	393749933	393750018	1.040000e-17	102.0
54	TraesCS1B01G204400	chr6D	86.777	121	12	2	3961	4077	221219670	221219550	1.330000e-26	132.0
55	TraesCS1B01G204400	chr6D	80.800	125	17	5	128	249	439511928	439512048	2.250000e-14	91.6
56	TraesCS1B01G204400	chr5B	85.950	121	10	2	3963	4076	312761818	312761938	7.990000e-24	122.0
57	TraesCS1B01G204400	chr5B	82.051	117	15	6	137	248	476925103	476924988	1.740000e-15	95.3
58	TraesCS1B01G204400	chr2A	77.273	242	33	10	139	358	360764299	360764058	7.990000e-24	122.0
59	TraesCS1B01G204400	chr4A	81.507	146	23	4	144	285	37019320	37019465	3.720000e-22	117.0
60	TraesCS1B01G204400	chr5A	85.185	108	12	4	137	243	495832396	495832500	2.240000e-19	108.0
61	TraesCS1B01G204400	chr6A	93.333	60	4	0	5064	5123	277889676	277889735	8.110000e-14	89.8

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS1B01G204400	chr1B	368539349	368545221	5872	False	2516.700000	5662	98.148000	1	5873	4	chr1B.!!$F1	5872
1	TraesCS1B01G204400	chr1A	313748001	313752660	4659	True	1217.800000	3650	92.469400	1	5873	5	chr1A.!!$R2	5872
2	TraesCS1B01G204400	chr1D	233893110	233898061	4951	False	1074.333333	3160	91.352333	1	5873	6	chr1D.!!$F3	5872

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
482	496	1.308047	TGGCAATACATCATCCGCAC	58.692	50.0	0.0	0.0	0.00	5.34	F
1149	1243	0.323451	CCAAACTCCCCTTGCTACCC	60.323	60.0	0.0	0.0	0.00	3.69	F
1198	1292	0.323451	AAATTTCCCGCTGACCCCTC	60.323	55.0	0.0	0.0	0.00	4.30	F
2297	2411	1.053835	TGCACAGTCCCTTGAGGTGA	61.054	55.0	0.0	0.0	36.75	4.02	F
2608	2723	2.161410	CACACATGGGTATTGTTGTCCG	59.839	50.0	0.0	0.0	0.00	4.79	F
4077	4197	0.178970	TATGGGACGGAGGGAGTAGC	60.179	60.0	0.0	0.0	0.00	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1425	1520	0.673644	CACGCAGTACTTCTTGGGGG	60.674	60.000	0.00	0.00	41.61	5.40	R
2985	3101	1.205417	CTGCTTTTAGGGTGCCAATGG	59.795	52.381	0.00	0.00	0.00	3.16	R
3019	3135	2.834549	TCATGAGGACAGAACTCTTCCC	59.165	50.000	0.00	0.00	35.98	3.97	R
4062	4182	0.175989	CAAAGCTACTCCCTCCGTCC	59.824	60.000	0.00	0.00	0.00	4.79	R
4227	4354	0.867753	CAGCAGTCCGATCGTGCTAC	60.868	60.000	25.47	13.05	45.82	3.58	R
5065	5208	1.134491	CGGATGGAGGAAGTACCAACC	60.134	57.143	0.00	0.00	42.93	3.77	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	3.561143	TGACAAAAGTAGGTGGTGCATT	58.439	40.909	0.00	0.00	0.00	3.56
66	67	5.105146	ACAAAAGTAGGTGGTGCATTTTTCA	60.105	36.000	0.00	0.00	0.00	2.69
175	186	1.473080	GGCACAAACACATGGCAACTT	60.473	47.619	0.00	0.00	40.91	2.66
180	191	4.571580	CACAAACACATGGCAACTTTGAAT	59.428	37.500	13.29	0.00	32.71	2.57
235	247	5.105797	TGGCAACTTTAGTTATCAAGCATGG	60.106	40.000	0.00	0.00	36.32	3.66
302	314	3.483808	TTTCCTTTTTGGATGGCAACC	57.516	42.857	6.88	6.88	45.68	3.77
323	335	3.435671	CCTTAGTTGTAGAAAACGCCAGG	59.564	47.826	0.00	0.00	35.13	4.45
328	340	2.585341	TAGAAAACGCCAGGGCCGA	61.585	57.895	4.42	0.00	37.98	5.54
336	348	2.282462	CCAGGGCCGAAGTGCTTT	60.282	61.111	0.00	0.00	0.00	3.51
343	355	1.959085	CCGAAGTGCTTTGTGCCAT	59.041	52.632	0.00	0.00	42.00	4.40
479	493	1.881324	TGCATGGCAATACATCATCCG	59.119	47.619	0.00	0.00	34.76	4.18
480	494	1.401931	GCATGGCAATACATCATCCGC	60.402	52.381	0.00	0.00	0.00	5.54
481	495	1.881324	CATGGCAATACATCATCCGCA	59.119	47.619	0.00	0.00	0.00	5.69
482	496	1.308047	TGGCAATACATCATCCGCAC	58.692	50.000	0.00	0.00	0.00	5.34
487	501	3.547468	GCAATACATCATCCGCACAAAAC	59.453	43.478	0.00	0.00	0.00	2.43
488	502	3.673746	ATACATCATCCGCACAAAACG	57.326	42.857	0.00	0.00	0.00	3.60
500	585	3.564511	GCACAAAACGTATCAGCAATGT	58.435	40.909	0.00	0.00	0.00	2.71
531	616	4.887071	ACAATTAGTGCAAGTGAAAGACCA	59.113	37.500	0.00	0.00	35.76	4.02
537	622	2.167487	TGCAAGTGAAAGACCAAAACCC	59.833	45.455	0.00	0.00	0.00	4.11
576	661	9.974750	GCTAATAAGTTCCGAATTATAAGATGC	57.025	33.333	0.00	0.00	0.00	3.91
583	668	7.233757	AGTTCCGAATTATAAGATGCTCTACCT	59.766	37.037	0.00	0.00	0.00	3.08
644	729	5.771469	TGCATTCGTTCATTCATTTCAGTT	58.229	33.333	0.00	0.00	0.00	3.16
645	730	5.858049	TGCATTCGTTCATTCATTTCAGTTC	59.142	36.000	0.00	0.00	0.00	3.01
696	781	5.741388	ACATCTCATAATTTGAAGCGGAC	57.259	39.130	0.00	0.00	32.78	4.79
710	795	1.414919	AGCGGACGGAATAATAAGGCA	59.585	47.619	0.00	0.00	0.00	4.75

Showing 1 to 25 of 294 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	7.118680	CACCACCTACTTTTGTCAAATACGTAT	59.881	37.037	1.14	1.14	0.00	3.06
42	43	5.105146	TGAAAAATGCACCACCTACTTTTGT	60.105	36.000	0.00	0.00	0.00	2.83
66	67	3.265995	TGCATGGCTCTATCATGGATCAT	59.734	43.478	0.00	0.00	41.49	2.45
132	141	2.548057	CACGTGTGGCACTTATCAAGTT	59.452	45.455	19.83	0.00	40.46	2.66
133	142	2.143122	CACGTGTGGCACTTATCAAGT	58.857	47.619	19.83	3.45	44.06	3.16
134	143	2.096268	CACACGTGTGGCACTTATCAAG	60.096	50.000	35.65	9.89	42.10	3.02
135	144	1.870402	CACACGTGTGGCACTTATCAA	59.130	47.619	35.65	0.00	42.10	2.57
193	205	3.124466	TGCCATCATTTCGTCACTAAACG	59.876	43.478	0.00	0.00	43.92	3.60
302	314	3.435671	CCCTGGCGTTTTCTACAACTAAG	59.564	47.826	0.00	0.00	0.00	2.18
323	335	2.050077	GCACAAAGCACTTCGGCC	60.050	61.111	0.00	0.00	44.79	6.13
343	355	5.726397	ACTAAATGATAAGTGCCACACGTA	58.274	37.500	0.00	0.00	39.64	3.57
414	428	7.651027	AGCTGGAATAATATGCTCAACTTTT	57.349	32.000	0.00	0.00	0.00	2.27
479	493	3.564511	ACATTGCTGATACGTTTTGTGC	58.435	40.909	0.00	0.00	0.00	4.57
480	494	8.946935	CAATATACATTGCTGATACGTTTTGTG	58.053	33.333	0.00	0.00	35.44	3.33
523	608	6.434340	AGTGATATCAAGGGTTTTGGTCTTTC	59.566	38.462	7.07	0.00	0.00	2.62
531	616	7.961326	ATTAGCAAGTGATATCAAGGGTTTT	57.039	32.000	7.07	0.00	0.00	2.43
537	622	8.491152	CGGAACTTATTAGCAAGTGATATCAAG	58.509	37.037	7.07	1.91	38.74	3.02
610	695	6.844696	ATGAACGAATGCATAAACGTATCT	57.155	33.333	20.61	10.17	38.00	1.98
613	698	6.410243	TGAATGAACGAATGCATAAACGTA	57.590	33.333	20.61	10.99	38.00	3.57
620	705	5.957798	ACTGAAATGAATGAACGAATGCAT	58.042	33.333	0.00	0.00	0.00	3.96
687	772	3.724374	CCTTATTATTCCGTCCGCTTCA	58.276	45.455	0.00	0.00	0.00	3.02
689	774	2.158871	TGCCTTATTATTCCGTCCGCTT	60.159	45.455	0.00	0.00	0.00	4.68
696	781	3.548014	CCAAGCGTTGCCTTATTATTCCG	60.548	47.826	0.00	0.00	0.00	4.30
710	795	5.659440	AAATTACATCCATTCCAAGCGTT	57.341	34.783	0.00	0.00	0.00	4.84
739	824	6.160576	AGTTACCCGTAAGTAAAAGACACA	57.839	37.500	0.00	0.00	34.13	3.72

Showing 1 to 25 of 332 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.