AutoCloner

Multiple sequence alignment - TraesCS5D01G086700

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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	TraesCS5D01G086700	chr5D	100.000	2582	0	0	1	2582	91874572	91871991	0.000000e+00	4769
1	TraesCS5D01G086700	chr5D	92.182	1164	35	20	854	1984	91656308	91655168	0.000000e+00	1594
2	TraesCS5D01G086700	chr5D	94.208	259	13	1	1726	1984	91872586	91872330	6.700000e-106	394
3	TraesCS5D01G086700	chr5D	94.208	259	13	1	1987	2243	91872847	91872589	6.700000e-106	394
4	TraesCS5D01G086700	chr5A	89.742	1784	92	43	855	2582	85358312	85356564	0.000000e+00	2196
5	TraesCS5D01G086700	chr5A	89.883	257	11	6	1993	2243	85357418	85357171	1.490000e-82	316
6	TraesCS5D01G086700	chr5A	84.892	278	22	7	1724	1984	85357171	85356897	1.970000e-66	263
7	TraesCS5D01G086700	chr5B	88.713	1772	97	45	856	2582	96911344	96909631	0.000000e+00	2069
8	TraesCS5D01G086700	chr5B	91.221	262	11	5	1724	1984	96910198	96909948	1.900000e-91	346
9	TraesCS5D01G086700	chr5B	88.583	254	18	6	1994	2243	96910444	96910198	5.400000e-77	298
10	TraesCS5D01G086700	chr7D	95.449	835	26	7	27	854	174792921	174792092	0.000000e+00	1321
11	TraesCS5D01G086700	chr1D	95.084	834	30	6	26	854	120221749	120222576	0.000000e+00	1303
12	TraesCS5D01G086700	chr4D	94.958	833	34	6	27	854	288214297	288213468	0.000000e+00	1299
13	TraesCS5D01G086700	chr2D	94.856	836	31	9	27	857	627520792	627519964	0.000000e+00	1295
14	TraesCS5D01G086700	chr3D	94.249	852	36	8	18	862	203344732	203343887	0.000000e+00	1290
15	TraesCS5D01G086700	chr6D	93.976	830	38	9	28	852	157674048	157673226	0.000000e+00	1245
16	TraesCS5D01G086700	chr7B	93.317	838	46	6	26	855	716137728	716136893	0.000000e+00	1229
17	TraesCS5D01G086700	chr2B	92.832	837	48	9	27	858	221735146	221735975	0.000000e+00	1203
18	TraesCS5D01G086700	chrUn	92.263	853	54	7	18	862	30343700	30344548	0.000000e+00	1199

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	TraesCS5D01G086700	chr5D	91871991	91874572	2581	True	1852.333333	4769	96.138667	1	2582	3	chr5D.!!$R2	2581
1	TraesCS5D01G086700	chr5D	91655168	91656308	1140	True	1594.000000	1594	92.182000	854	1984	1	chr5D.!!$R1	1130
2	TraesCS5D01G086700	chr5A	85356564	85358312	1748	True	925.000000	2196	88.172333	855	2582	3	chr5A.!!$R1	1727
3	TraesCS5D01G086700	chr5B	96909631	96911344	1713	True	904.333333	2069	89.505667	856	2582	3	chr5B.!!$R1	1726
4	TraesCS5D01G086700	chr7D	174792092	174792921	829	True	1321.000000	1321	95.449000	27	854	1	chr7D.!!$R1	827
5	TraesCS5D01G086700	chr1D	120221749	120222576	827	False	1303.000000	1303	95.084000	26	854	1	chr1D.!!$F1	828
6	TraesCS5D01G086700	chr4D	288213468	288214297	829	True	1299.000000	1299	94.958000	27	854	1	chr4D.!!$R1	827
7	TraesCS5D01G086700	chr2D	627519964	627520792	828	True	1295.000000	1295	94.856000	27	857	1	chr2D.!!$R1	830
8	TraesCS5D01G086700	chr3D	203343887	203344732	845	True	1290.000000	1290	94.249000	18	862	1	chr3D.!!$R1	844
9	TraesCS5D01G086700	chr6D	157673226	157674048	822	True	1245.000000	1245	93.976000	28	852	1	chr6D.!!$R1	824
10	TraesCS5D01G086700	chr7B	716136893	716137728	835	True	1229.000000	1229	93.317000	26	855	1	chr7B.!!$R1	829
11	TraesCS5D01G086700	chr2B	221735146	221735975	829	False	1203.000000	1203	92.832000	27	858	1	chr2B.!!$F1	831
12	TraesCS5D01G086700	chrUn	30343700	30344548	848	False	1199.000000	1199	92.263000	18	862	1	chrUn.!!$F1	844

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
822	844	0.541063	TCGTGTGGTGCCTCTCCTTA	60.541	55.0	0.0	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2534	2643	0.756294	TGAGCGTCCTCAAAGTCCAA	59.244	50.0	0.0	0.0	44.79	3.53	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	1.504359	CACCACGCTCGAGGTAAAAA	58.496	50.000	15.58	0.00	36.98	1.94
207	208	3.119779	TCCGTTTTCACCATTAAATCCGC	60.120	43.478	0.00	0.00	0.00	5.54
222	223	1.030488	TCCGCCTCGACGAGATCTTT	61.030	55.000	26.11	0.00	34.06	2.52
288	293	5.739935	GCCCAGAAGTTGTCATGATGTTTTT	60.740	40.000	0.00	0.00	0.00	1.94
327	332	4.385748	GTGCTTAAACTAAAGTTGCCATGC	59.614	41.667	0.00	1.05	38.44	4.06
366	375	8.309163	TGTAGATCATGGCAATTTTTGTTTTC	57.691	30.769	0.00	0.00	0.00	2.29
784	806	2.711311	GCATGCATGCGACGTGAT	59.289	55.556	33.99	0.00	44.67	3.06
822	844	0.541063	TCGTGTGGTGCCTCTCCTTA	60.541	55.000	0.00	0.00	0.00	2.69
828	850	1.592223	GTGCCTCTCCTTACGTGCT	59.408	57.895	0.00	0.00	0.00	4.40
1628	1686	1.660052	CGTGCGTGAAACATGTCTTGG	60.660	52.381	0.00	0.00	35.74	3.61
1815	1885	7.452880	TCCAAGATTTCCAAACAGTCTAATG	57.547	36.000	0.00	0.00	0.00	1.90
1906	1977	5.918426	TTAATGCTCATGGATTGCTTTGA	57.082	34.783	0.00	0.00	35.79	2.69
1941	2012	3.049206	GAGAGTTGCTATTAGCTGCTCG	58.951	50.000	22.17	0.00	42.69	5.03
1986	2057	2.039216	TGCAACTTCATCCCCGTTCTAA	59.961	45.455	0.00	0.00	0.00	2.10
2005	2076	7.254522	CGTTCTAAGTTTTGTACTGCTGGTTTA	60.255	37.037	0.00	0.00	37.12	2.01
2027	2098	5.983333	ATATGAATCCAAGACTCCCAAGT	57.017	39.130	0.00	0.00	38.88	3.16
2091	2163	8.190784	AGCAGTCTAATATAATGGTTTTGTTGC	58.809	33.333	0.00	0.00	0.00	4.17
2129	2203	6.889301	ATGTTGGAGTTAGCATTATCATGG	57.111	37.500	0.00	0.00	0.00	3.66
2162	2236	7.716799	TTTGGTTAATACTCATGGATTGCTT	57.283	32.000	0.00	0.00	0.00	3.91
2164	2238	7.099266	TGGTTAATACTCATGGATTGCTTTG	57.901	36.000	0.00	0.00	0.00	2.77
2243	2338	0.109532	TGCAACTTCATCCCCGTTCA	59.890	50.000	0.00	0.00	0.00	3.18
2244	2339	0.804989	GCAACTTCATCCCCGTTCAG	59.195	55.000	0.00	0.00	0.00	3.02
2245	2340	0.804989	CAACTTCATCCCCGTTCAGC	59.195	55.000	0.00	0.00	0.00	4.26
2246	2341	0.693049	AACTTCATCCCCGTTCAGCT	59.307	50.000	0.00	0.00	0.00	4.24
2247	2342	0.693049	ACTTCATCCCCGTTCAGCTT	59.307	50.000	0.00	0.00	0.00	3.74
2254	2349	0.527565	CCCCGTTCAGCTTGATTTGG	59.472	55.000	0.00	0.00	0.00	3.28
2256	2351	2.094675	CCCGTTCAGCTTGATTTGGAT	58.905	47.619	0.00	0.00	0.00	3.41
2257	2352	3.278574	CCCGTTCAGCTTGATTTGGATA	58.721	45.455	0.00	0.00	0.00	2.59
2258	2353	3.065371	CCCGTTCAGCTTGATTTGGATAC	59.935	47.826	0.00	0.00	0.00	2.24
2269	2364	4.155733	TGGATACACAGCCGGCCG	62.156	66.667	26.15	21.04	46.17	6.13
2363	2461	3.591196	TTGCCCAAAGTATGACAATGC	57.409	42.857	0.00	0.00	0.00	3.56
2387	2485	2.881513	TGTTGCCGCAGTTTGAATTCTA	59.118	40.909	7.05	0.00	0.00	2.10
2397	2495	7.173907	CCGCAGTTTGAATTCTATTCTCCATAT	59.826	37.037	7.05	0.00	0.00	1.78
2398	2496	8.562892	CGCAGTTTGAATTCTATTCTCCATATT	58.437	33.333	7.05	0.00	0.00	1.28
2425	2529	2.507407	TTTAGATGGCAGTGGGTTCC	57.493	50.000	0.00	0.00	0.00	3.62
2427	2531	1.668826	TAGATGGCAGTGGGTTCCTT	58.331	50.000	0.00	0.00	0.00	3.36
2432	2536	0.322008	GGCAGTGGGTTCCTTCAGAG	60.322	60.000	0.00	0.00	0.00	3.35
2472	2580	3.657537	CTTGCTTTAAGCCACGACG	57.342	52.632	14.80	0.00	41.51	5.12
2489	2598	6.658831	CCACGACGAAGATATATGCAATTTT	58.341	36.000	0.00	0.00	0.00	1.82
2490	2599	6.792250	CCACGACGAAGATATATGCAATTTTC	59.208	38.462	0.00	0.00	0.00	2.29
2501	2610	9.185192	GATATATGCAATTTTCTTTACCACTGC	57.815	33.333	0.00	0.00	0.00	4.40
2502	2611	4.662468	TGCAATTTTCTTTACCACTGCA	57.338	36.364	0.00	0.00	36.28	4.41
2534	2643	7.639113	TGATCACTTTTAGTTCCAACAAAGT	57.361	32.000	0.00	3.29	36.29	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.180456	TTTACCTCGAGCGTGGTGGA	61.180	55.000	22.43	11.01	41.43	4.02
1	2	0.320073	TTTTACCTCGAGCGTGGTGG	60.320	55.000	22.43	8.94	41.43	4.61
2	3	1.459592	CTTTTTACCTCGAGCGTGGTG	59.540	52.381	22.43	5.66	41.43	4.17
4	5	2.074547	TCTTTTTACCTCGAGCGTGG	57.925	50.000	6.99	9.21	35.14	4.94
5	6	3.660904	CGTTTCTTTTTACCTCGAGCGTG	60.661	47.826	6.99	0.00	0.00	5.34
7	8	2.159881	CCGTTTCTTTTTACCTCGAGCG	60.160	50.000	6.99	2.92	0.00	5.03
8	9	3.062042	TCCGTTTCTTTTTACCTCGAGC	58.938	45.455	6.99	0.00	0.00	5.03
9	10	5.662211	TTTCCGTTTCTTTTTACCTCGAG	57.338	39.130	5.13	5.13	0.00	4.04
10	11	6.093909	AGTTTTTCCGTTTCTTTTTACCTCGA	59.906	34.615	0.00	0.00	0.00	4.04
11	12	6.260377	AGTTTTTCCGTTTCTTTTTACCTCG	58.740	36.000	0.00	0.00	0.00	4.63
12	13	9.013490	GTTAGTTTTTCCGTTTCTTTTTACCTC	57.987	33.333	0.00	0.00	0.00	3.85
13	14	7.697710	CGTTAGTTTTTCCGTTTCTTTTTACCT	59.302	33.333	0.00	0.00	0.00	3.08
14	15	7.513505	GCGTTAGTTTTTCCGTTTCTTTTTACC	60.514	37.037	0.00	0.00	0.00	2.85
15	16	7.322260	GCGTTAGTTTTTCCGTTTCTTTTTAC	58.678	34.615	0.00	0.00	0.00	2.01
16	17	6.471841	GGCGTTAGTTTTTCCGTTTCTTTTTA	59.528	34.615	0.00	0.00	0.00	1.52
21	22	2.291465	GGGCGTTAGTTTTTCCGTTTCT	59.709	45.455	0.00	0.00	0.00	2.52
207	208	6.687958	GTCTAGTTTTAAAGATCTCGTCGAGG	59.312	42.308	21.63	0.00	0.00	4.63
222	223	7.867921	ACATATCAACATGGGGTCTAGTTTTA	58.132	34.615	0.00	0.00	0.00	1.52
288	293	8.701895	AGTTTAAGCACTATGGCAACTATAGTA	58.298	33.333	5.65	0.00	38.21	1.82
327	332	6.692681	CCATGATCTACAAACTAAAATTGCCG	59.307	38.462	0.00	0.00	0.00	5.69
408	422	8.658609	CACTTAAAATTGCCATGGTTCAATAAG	58.341	33.333	14.67	15.99	33.05	1.73
784	806	7.438160	CCACACGACTCTAATGCAAATAGATTA	59.562	37.037	11.67	0.00	0.00	1.75
828	850	1.540707	TCGATAACTGCCACACGTGTA	59.459	47.619	22.90	5.00	0.00	2.90
943	976	1.970640	GGCTTTGGGGTTCTGAATGTT	59.029	47.619	0.00	0.00	0.00	2.71
944	977	1.133199	TGGCTTTGGGGTTCTGAATGT	60.133	47.619	0.00	0.00	0.00	2.71
945	978	1.547372	CTGGCTTTGGGGTTCTGAATG	59.453	52.381	0.00	0.00	0.00	2.67
946	979	1.928868	CTGGCTTTGGGGTTCTGAAT	58.071	50.000	0.00	0.00	0.00	2.57
947	980	0.827507	GCTGGCTTTGGGGTTCTGAA	60.828	55.000	0.00	0.00	0.00	3.02
948	981	1.228552	GCTGGCTTTGGGGTTCTGA	60.229	57.895	0.00	0.00	0.00	3.27
949	982	2.629656	CGCTGGCTTTGGGGTTCTG	61.630	63.158	0.00	0.00	0.00	3.02
950	983	2.282462	CGCTGGCTTTGGGGTTCT	60.282	61.111	0.00	0.00	0.00	3.01
951	984	4.056125	GCGCTGGCTTTGGGGTTC	62.056	66.667	0.00	0.00	35.83	3.62
1815	1885	7.655328	TCATCAATCAACCAACAAAACCATTAC	59.345	33.333	0.00	0.00	0.00	1.89
1883	1953	6.474140	TCAAAGCAATCCATGAGCATTAAT	57.526	33.333	0.00	0.00	0.00	1.40
1906	1977	5.128919	AGCAACTCTCTGTTCTTGAAACAT	58.871	37.500	0.00	0.00	36.63	2.71
1941	2012	6.388435	AATCCAAATCAAGCTAGCAGAATC	57.612	37.500	18.83	0.00	0.00	2.52
1986	2057	8.630054	TTCATATAAACCAGCAGTACAAAACT	57.370	30.769	0.00	0.00	39.81	2.66
2005	2076	5.983333	ACTTGGGAGTCTTGGATTCATAT	57.017	39.130	0.00	0.00	0.00	1.78
2129	2203	9.180678	CCATGAGTATTAACCAAATTAATTCGC	57.819	33.333	0.10	0.00	40.00	4.70
2148	2222	5.244402	TGAAACATCAAAGCAATCCATGAGT	59.756	36.000	0.00	0.00	0.00	3.41
2162	2236	6.458751	GCAACTCTCTGTTCTTGAAACATCAA	60.459	38.462	0.00	0.00	36.63	2.57
2164	2238	5.238214	AGCAACTCTCTGTTCTTGAAACATC	59.762	40.000	0.00	0.00	36.63	3.06
2243	2338	3.019564	GGCTGTGTATCCAAATCAAGCT	58.980	45.455	0.00	0.00	0.00	3.74
2244	2339	2.223340	CGGCTGTGTATCCAAATCAAGC	60.223	50.000	0.00	0.00	0.00	4.01
2245	2340	2.355756	CCGGCTGTGTATCCAAATCAAG	59.644	50.000	0.00	0.00	0.00	3.02
2246	2341	2.364632	CCGGCTGTGTATCCAAATCAA	58.635	47.619	0.00	0.00	0.00	2.57
2247	2342	2.016604	GCCGGCTGTGTATCCAAATCA	61.017	52.381	22.15	0.00	0.00	2.57
2270	2365	1.233019	CAGCTCAAGCCCATATTCGG	58.767	55.000	0.00	0.00	43.38	4.30
2271	2366	1.233019	CCAGCTCAAGCCCATATTCG	58.767	55.000	0.00	0.00	43.38	3.34
2272	2367	2.355010	ACCAGCTCAAGCCCATATTC	57.645	50.000	0.00	0.00	43.38	1.75
2273	2368	4.459852	AATACCAGCTCAAGCCCATATT	57.540	40.909	0.00	0.00	43.38	1.28
2274	2369	4.459852	AAATACCAGCTCAAGCCCATAT	57.540	40.909	0.00	0.00	43.38	1.78
2275	2370	3.951563	AAATACCAGCTCAAGCCCATA	57.048	42.857	0.00	0.00	43.38	2.74
2276	2371	2.834638	AAATACCAGCTCAAGCCCAT	57.165	45.000	0.00	0.00	43.38	4.00
2277	2372	2.603075	AAAATACCAGCTCAAGCCCA	57.397	45.000	0.00	0.00	43.38	5.36
2278	2373	5.127031	TGAAATAAAATACCAGCTCAAGCCC	59.873	40.000	0.00	0.00	43.38	5.19
2279	2374	6.127619	ACTGAAATAAAATACCAGCTCAAGCC	60.128	38.462	0.00	0.00	43.38	4.35
2280	2375	6.856895	ACTGAAATAAAATACCAGCTCAAGC	58.143	36.000	0.00	0.00	42.49	4.01
2345	2443	3.874392	AAGCATTGTCATACTTTGGGC	57.126	42.857	0.00	0.00	0.00	5.36
2363	2461	1.919918	TTCAAACTGCGGCAACAAAG	58.080	45.000	3.44	0.00	0.00	2.77
2397	2495	4.701651	CCACTGCCATCTAAAAGTGATCAA	59.298	41.667	0.00	0.00	42.09	2.57
2398	2496	4.264253	CCACTGCCATCTAAAAGTGATCA	58.736	43.478	3.32	0.00	42.09	2.92
2400	2498	3.010584	ACCCACTGCCATCTAAAAGTGAT	59.989	43.478	3.32	0.00	42.09	3.06
2401	2499	2.375174	ACCCACTGCCATCTAAAAGTGA	59.625	45.455	3.32	0.00	42.09	3.41
2402	2500	2.795329	ACCCACTGCCATCTAAAAGTG	58.205	47.619	0.00	0.00	39.78	3.16
2403	2501	3.421844	GAACCCACTGCCATCTAAAAGT	58.578	45.455	0.00	0.00	0.00	2.66
2404	2502	2.755103	GGAACCCACTGCCATCTAAAAG	59.245	50.000	0.00	0.00	0.00	2.27
2405	2503	2.378547	AGGAACCCACTGCCATCTAAAA	59.621	45.455	0.00	0.00	0.00	1.52
2406	2504	1.992557	AGGAACCCACTGCCATCTAAA	59.007	47.619	0.00	0.00	0.00	1.85
2425	2529	6.535150	TGTGACACAGTTTCTAAACTCTGAAG	59.465	38.462	15.07	3.86	45.65	3.02
2427	2531	5.810587	GTGTGACACAGTTTCTAAACTCTGA	59.189	40.000	11.43	0.00	45.65	3.27
2466	2574	7.567571	AGAAAATTGCATATATCTTCGTCGTG	58.432	34.615	0.00	0.00	0.00	4.35
2467	2575	7.715265	AGAAAATTGCATATATCTTCGTCGT	57.285	32.000	0.00	0.00	0.00	4.34
2489	2598	5.252547	TCAATATGCTTGCAGTGGTAAAGA	58.747	37.500	0.87	0.00	0.00	2.52
2490	2599	5.565592	TCAATATGCTTGCAGTGGTAAAG	57.434	39.130	0.87	0.00	0.00	1.85
2501	2610	8.461222	TGGAACTAAAAGTGATCAATATGCTTG	58.539	33.333	0.00	0.00	0.00	4.01
2502	2611	8.579850	TGGAACTAAAAGTGATCAATATGCTT	57.420	30.769	0.00	0.00	0.00	3.91
2534	2643	0.756294	TGAGCGTCCTCAAAGTCCAA	59.244	50.000	0.00	0.00	44.79	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.