AutoCloner

Multiple sequence alignment - TraesCS3A01G157400

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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	TraesCS3A01G157400	chr3A	100.000	2300	0	0	1	2300	154385039	154382740	0.000000e+00	4248
1	TraesCS3A01G157400	chr3A	85.990	621	61	18	119	725	606746909	606746301	1.930000e-180	641
2	TraesCS3A01G157400	chr3D	90.360	1556	91	21	743	2286	136568631	136567123	0.000000e+00	1988
3	TraesCS3A01G157400	chr3B	90.683	1288	63	23	743	2001	199226744	199225485	0.000000e+00	1661
4	TraesCS3A01G157400	chr3B	80.995	221	20	8	1998	2197	199222967	199222748	3.060000e-34	156
5	TraesCS3A01G157400	chr7A	87.875	734	76	12	1	725	579009627	579010356	0.000000e+00	850
6	TraesCS3A01G157400	chr1B	87.118	753	85	9	1	744	31355661	31354912	0.000000e+00	843
7	TraesCS3A01G157400	chr4A	85.696	762	85	11	1	740	723592647	723593406	0.000000e+00	782
8	TraesCS3A01G157400	chr4D	90.750	573	45	6	1	571	85178331	85178897	0.000000e+00	758
9	TraesCS3A01G157400	chr7B	89.109	606	62	4	1	604	467620792	467620189	0.000000e+00	750
10	TraesCS3A01G157400	chr7B	88.779	606	63	5	1	604	467598720	467598118	0.000000e+00	737
11	TraesCS3A01G157400	chr7B	87.974	607	67	6	1	604	467712060	467711457	0.000000e+00	712
12	TraesCS3A01G157400	chr6D	89.510	572	56	4	1	571	421890670	421890102	0.000000e+00	721
13	TraesCS3A01G157400	chr6B	89.139	534	48	5	2	525	661840579	661840046	0.000000e+00	656

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	TraesCS3A01G157400	chr3A	154382740	154385039	2299	True	4248.0	4248	100.000	1	2300	1	chr3A.!!$R1	2299
1	TraesCS3A01G157400	chr3A	606746301	606746909	608	True	641.0	641	85.990	119	725	1	chr3A.!!$R2	606
2	TraesCS3A01G157400	chr3D	136567123	136568631	1508	True	1988.0	1988	90.360	743	2286	1	chr3D.!!$R1	1543
3	TraesCS3A01G157400	chr3B	199222748	199226744	3996	True	908.5	1661	85.839	743	2197	2	chr3B.!!$R1	1454
4	TraesCS3A01G157400	chr7A	579009627	579010356	729	False	850.0	850	87.875	1	725	1	chr7A.!!$F1	724
5	TraesCS3A01G157400	chr1B	31354912	31355661	749	True	843.0	843	87.118	1	744	1	chr1B.!!$R1	743
6	TraesCS3A01G157400	chr4A	723592647	723593406	759	False	782.0	782	85.696	1	740	1	chr4A.!!$F1	739
7	TraesCS3A01G157400	chr4D	85178331	85178897	566	False	758.0	758	90.750	1	571	1	chr4D.!!$F1	570
8	TraesCS3A01G157400	chr7B	467620189	467620792	603	True	750.0	750	89.109	1	604	1	chr7B.!!$R2	603
9	TraesCS3A01G157400	chr7B	467598118	467598720	602	True	737.0	737	88.779	1	604	1	chr7B.!!$R1	603
10	TraesCS3A01G157400	chr7B	467711457	467712060	603	True	712.0	712	87.974	1	604	1	chr7B.!!$R3	603
11	TraesCS3A01G157400	chr6D	421890102	421890670	568	True	721.0	721	89.510	1	571	1	chr6D.!!$R1	570
12	TraesCS3A01G157400	chr6B	661840046	661840579	533	True	656.0	656	89.139	2	525	1	chr6B.!!$R1	523

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
355	359	0.324552	CATCCAGATGGGCCCACAAA	60.325	55.0	31.51	11.93	35.24	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2078	4673	0.107752	GCTCTTGGCCTCTCCTGAAG	60.108	60.0	3.32	0.0	35.26	3.02	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
48	49	3.589654	CTCACCACGGCACCACGAT	62.590	63.158	0.00	0.00	37.61	3.73
139	140	1.678598	AACCTCCACCGTCAACGACA	61.679	55.000	3.71	0.00	43.02	4.35
284	285	1.220206	CACATCCGAGCTGCTCCTT	59.780	57.895	22.97	5.99	0.00	3.36
354	358	1.307309	CATCCAGATGGGCCCACAA	59.693	57.895	31.51	11.51	35.24	3.33
355	359	0.324552	CATCCAGATGGGCCCACAAA	60.325	55.000	31.51	11.93	35.24	2.83
796	840	7.307146	AGCATCGGAAGAAAAGTACTGCTCT	62.307	44.000	0.00	0.00	41.13	4.09
797	841	4.175787	TCGGAAGAAAAGTACTGCTCTC	57.824	45.455	0.00	0.00	37.03	3.20
891	935	1.206878	CCTCACCTCACATGATCCCA	58.793	55.000	0.00	0.00	0.00	4.37
917	961	4.043608	AGCACCAGAGTAGTAGTACCAA	57.956	45.455	4.02	0.00	0.00	3.67
1091	1136	4.077188	GCTCACAACTGCGACGGC	62.077	66.667	0.00	0.00	40.52	5.68
1201	1246	2.763215	CAGGGGCACAAGGGCTAA	59.237	61.111	0.00	0.00	42.84	3.09
1208	1253	2.359478	ACAAGGGCTAAACGGCGG	60.359	61.111	13.24	0.00	39.52	6.13
1306	1351	4.154918	GGAAGATCAACAACTAGCAACCTG	59.845	45.833	0.00	0.00	0.00	4.00
1312	1357	0.877071	CAACTAGCAACCTGGCAGTG	59.123	55.000	14.43	7.27	35.83	3.66
1411	1458	0.927994	ATGTTCGTTTGTTGCGCGTG	60.928	50.000	8.43	0.00	0.00	5.34
1512	1559	6.436532	AGGGATTGCCAGAATTTATCATCATC	59.563	38.462	0.00	0.00	35.15	2.92
1560	1607	8.704849	TCCTTTTCATTTCTCCTTGAATGTTA	57.295	30.769	0.00	0.00	34.24	2.41
1561	1608	9.312904	TCCTTTTCATTTCTCCTTGAATGTTAT	57.687	29.630	0.00	0.00	34.24	1.89
1618	1676	6.027749	CAGTTTATGGTTGTCGCTTATTTCC	58.972	40.000	0.00	0.00	0.00	3.13
1634	1692	6.969473	GCTTATTTCCTAAGTCATTGCAGTTC	59.031	38.462	0.00	0.00	39.30	3.01
1704	1762	4.747108	CGAAAGAAGTGCATATACCCTCTG	59.253	45.833	0.00	0.00	0.00	3.35
1706	1764	6.506538	AAAGAAGTGCATATACCCTCTGAT	57.493	37.500	0.00	0.00	0.00	2.90
1707	1765	5.480642	AGAAGTGCATATACCCTCTGATG	57.519	43.478	0.00	0.00	0.00	3.07
1719	1777	7.781324	ATACCCTCTGATGTTTCATGTTTTT	57.219	32.000	0.00	0.00	0.00	1.94
1724	1782	7.318141	CCTCTGATGTTTCATGTTTTTGCTAT	58.682	34.615	0.00	0.00	0.00	2.97
1749	1807	1.708551	CCCCTTAGAACTCCAAACCCA	59.291	52.381	0.00	0.00	0.00	4.51
1752	1810	3.307762	CCCTTAGAACTCCAAACCCAGAG	60.308	52.174	0.00	0.00	36.16	3.35
1852	1910	1.535204	AAAATGGCCACCTTGGAGCG	61.535	55.000	8.16	0.00	40.96	5.03
1900	1966	4.687215	GCTGCACACGGAGAGCCA	62.687	66.667	0.00	0.00	30.74	4.75
1931	2004	4.959399	GCAAGCTCTGCCTCATCT	57.041	55.556	9.03	0.00	46.13	2.90
1939	2012	1.744368	CTGCCTCATCTGCAACGCT	60.744	57.895	0.00	0.00	38.46	5.07
1988	2061	1.926561	CTGCGATGACTTCCGATTCA	58.073	50.000	0.00	0.00	0.00	2.57
2018	4612	3.611674	TGGTCTGGCTGCGACGAA	61.612	61.111	0.00	0.00	32.24	3.85
2022	4616	2.259818	CTGGCTGCGACGAACTCT	59.740	61.111	0.00	0.00	0.00	3.24
2028	4622	2.507324	GCGACGAACTCTGCCTCC	60.507	66.667	0.00	0.00	0.00	4.30
2057	4651	0.846693	AGAATAGCGGCCCCATTCTT	59.153	50.000	12.98	1.98	35.93	2.52
2063	4657	2.679996	GGCCCCATTCTTGCGGTT	60.680	61.111	0.00	0.00	0.00	4.44
2065	4659	3.005540	GCCCCATTCTTGCGGTTGG	62.006	63.158	0.00	0.00	0.00	3.77
2066	4660	1.606313	CCCCATTCTTGCGGTTGGT	60.606	57.895	0.00	0.00	0.00	3.67
2102	4697	1.002868	GAGAGGCCAAGAGCAGCAA	60.003	57.895	5.01	0.00	46.50	3.91
2104	4714	1.303155	GAGGCCAAGAGCAGCAAGT	60.303	57.895	5.01	0.00	46.50	3.16
2118	4728	2.423185	CAGCAAGTCCAACAACAGAACA	59.577	45.455	0.00	0.00	0.00	3.18
2223	4837	3.611025	TGTCAAAAAGGGGAATGACCT	57.389	42.857	0.00	0.00	41.08	3.85
2224	4838	3.230134	TGTCAAAAAGGGGAATGACCTG	58.770	45.455	0.00	0.00	41.08	4.00
2226	4840	2.448961	TCAAAAAGGGGAATGACCTGGA	59.551	45.455	0.00	0.00	38.63	3.86
2254	4868	6.042437	TCTGCATCATCATCATACAACCTAGT	59.958	38.462	0.00	0.00	0.00	2.57
2265	4879	9.561270	CATCATACAACCTAGTCATATAACTCG	57.439	37.037	0.00	0.00	0.00	4.18
2273	4887	8.046294	ACCTAGTCATATAACTCGACATCATC	57.954	38.462	0.00	0.00	31.92	2.92
2286	4900	0.867086	CATCATCACACACGCACACA	59.133	50.000	0.00	0.00	0.00	3.72
2287	4901	1.263752	CATCATCACACACGCACACAA	59.736	47.619	0.00	0.00	0.00	3.33
2288	4902	0.936600	TCATCACACACGCACACAAG	59.063	50.000	0.00	0.00	0.00	3.16
2289	4903	0.936600	CATCACACACGCACACAAGA	59.063	50.000	0.00	0.00	0.00	3.02
2290	4904	0.937304	ATCACACACGCACACAAGAC	59.063	50.000	0.00	0.00	0.00	3.01
2291	4905	0.390472	TCACACACGCACACAAGACA	60.390	50.000	0.00	0.00	0.00	3.41
2292	4906	0.445829	CACACACGCACACAAGACAA	59.554	50.000	0.00	0.00	0.00	3.18
2293	4907	0.726827	ACACACGCACACAAGACAAG	59.273	50.000	0.00	0.00	0.00	3.16
2294	4908	1.006086	CACACGCACACAAGACAAGA	58.994	50.000	0.00	0.00	0.00	3.02
2295	4909	1.599071	CACACGCACACAAGACAAGAT	59.401	47.619	0.00	0.00	0.00	2.40
2296	4910	2.799978	CACACGCACACAAGACAAGATA	59.200	45.455	0.00	0.00	0.00	1.98
2297	4911	2.800544	ACACGCACACAAGACAAGATAC	59.199	45.455	0.00	0.00	0.00	2.24
2298	4912	2.799978	CACGCACACAAGACAAGATACA	59.200	45.455	0.00	0.00	0.00	2.29
2299	4913	3.247411	CACGCACACAAGACAAGATACAA	59.753	43.478	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	49	2.591429	CGTTGTGCAGGCCTCACA	60.591	61.111	25.10	25.10	42.10	3.58
69	70	0.702902	CCCTAGTCCCGGCTCCTATA	59.297	60.000	0.00	0.00	0.00	1.31
139	140	1.255667	ATTGTGTCCGGTCGGCTACT	61.256	55.000	0.00	0.00	34.68	2.57
267	268	0.975040	AGAAGGAGCAGCTCGGATGT	60.975	55.000	16.47	0.61	0.00	3.06
284	285	1.344438	GTCATCTGTGTGGTGTGGAGA	59.656	52.381	0.00	0.00	0.00	3.71
336	339	0.324552	TTTGTGGGCCCATCTGGATG	60.325	55.000	31.45	3.79	37.39	3.51
338	341	1.383799	CTTTGTGGGCCCATCTGGA	59.616	57.895	31.45	11.81	37.39	3.86
354	358	2.270205	CGGCCCAGATCTGTGCTT	59.730	61.111	26.16	0.00	34.36	3.91
355	359	3.790437	CCGGCCCAGATCTGTGCT	61.790	66.667	26.16	0.00	34.36	4.40
394	400	4.758251	CGAGACGGCATGGTGGCA	62.758	66.667	0.00	0.00	43.94	4.92
675	711	3.701485	TTCCCCCTCCCGGATCCA	61.701	66.667	13.41	0.00	0.00	3.41
731	775	0.854218	TTTTCTAAGTGCCCCCACCA	59.146	50.000	0.00	0.00	43.09	4.17
796	840	0.171679	TTTAGCGGACGAGCAATCGA	59.828	50.000	4.44	0.00	40.15	3.59
797	841	0.297820	GTTTAGCGGACGAGCAATCG	59.702	55.000	0.00	0.00	40.15	3.34
891	935	5.185442	GGTACTACTACTCTGGTGCTTCTTT	59.815	44.000	0.00	0.00	0.00	2.52
917	961	2.042831	GGCTCAATGCTTCTGCCGT	61.043	57.895	0.00	0.00	42.39	5.68
1208	1253	4.492160	TCGCGGTCGACATGGCTC	62.492	66.667	18.91	0.00	40.21	4.70
1306	1351	6.099341	CCTTTGAACCAAAATATACACTGCC	58.901	40.000	0.00	0.00	32.75	4.85
1411	1458	2.046313	CACAACGAGCTGAAAACATGC	58.954	47.619	0.00	0.00	0.00	4.06
1512	1559	1.891150	ACCAGCTCAAAATGGAAGCAG	59.109	47.619	0.00	0.00	39.02	4.24
1618	1676	5.163913	CGAGGAAAGAACTGCAATGACTTAG	60.164	44.000	0.00	0.00	0.00	2.18
1704	1762	9.023967	GGTGATATAGCAAAAACATGAAACATC	57.976	33.333	0.00	0.00	0.00	3.06
1706	1764	7.319646	GGGTGATATAGCAAAAACATGAAACA	58.680	34.615	0.00	0.00	0.00	2.83
1707	1765	6.756542	GGGGTGATATAGCAAAAACATGAAAC	59.243	38.462	0.00	0.00	0.00	2.78
1719	1777	4.838986	GGAGTTCTAAGGGGTGATATAGCA	59.161	45.833	0.00	0.00	0.00	3.49
1724	1782	4.226620	GGTTTGGAGTTCTAAGGGGTGATA	59.773	45.833	0.00	0.00	0.00	2.15
1749	1807	7.979786	TGGTAGATCAGAGGATTAAAACTCT	57.020	36.000	6.49	6.49	44.50	3.24
1752	1810	9.841880	GTTTTTGGTAGATCAGAGGATTAAAAC	57.158	33.333	0.00	0.00	32.67	2.43
1767	1825	3.492337	GGGTGATGTGGTTTTTGGTAGA	58.508	45.455	0.00	0.00	0.00	2.59
1852	1910	1.648467	GAAGAGATTGCGTGCACCCC	61.648	60.000	12.15	3.00	0.00	4.95
1893	1959	1.220477	GCTCTTGGGAGTGGCTCTC	59.780	63.158	8.03	8.03	41.38	3.20
1939	2012	3.804411	GGACAATGTCGAAGGTGGTAACA	60.804	47.826	7.35	0.00	37.65	2.41
1988	2061	0.674581	CAGACCACATGATGTGCGGT	60.675	55.000	19.69	13.33	46.51	5.68
2018	4612	3.790437	CGCATGGGGAGGCAGAGT	61.790	66.667	0.89	0.00	0.00	3.24
2022	4616	4.113815	CTTCCGCATGGGGAGGCA	62.114	66.667	28.18	15.31	37.83	4.75
2028	4622	1.230635	CCGCTATTCTTCCGCATGGG	61.231	60.000	2.06	2.06	35.24	4.00
2063	4657	3.177884	AAGCCTCCTGGTGCACCA	61.178	61.111	35.49	35.49	45.30	4.17
2065	4659	1.673665	CTGAAGCCTCCTGGTGCAC	60.674	63.158	8.80	8.80	35.27	4.57
2066	4660	2.752358	CTGAAGCCTCCTGGTGCA	59.248	61.111	12.21	0.00	35.27	4.57
2078	4673	0.107752	GCTCTTGGCCTCTCCTGAAG	60.108	60.000	3.32	0.00	35.26	3.02
2102	4697	3.576078	TGGATGTTCTGTTGTTGGACT	57.424	42.857	0.00	0.00	0.00	3.85
2104	4714	3.625853	TGTTGGATGTTCTGTTGTTGGA	58.374	40.909	0.00	0.00	0.00	3.53
2204	4818	2.562738	CCAGGTCATTCCCCTTTTTGAC	59.437	50.000	0.00	0.00	38.17	3.18
2205	4819	2.448961	TCCAGGTCATTCCCCTTTTTGA	59.551	45.455	0.00	0.00	36.75	2.69
2207	4821	2.492753	GGTCCAGGTCATTCCCCTTTTT	60.493	50.000	0.00	0.00	36.75	1.94
2223	4837	2.121129	TGATGATGATGCAGAGGTCCA	58.879	47.619	0.00	0.00	0.00	4.02
2224	4838	2.924757	TGATGATGATGCAGAGGTCC	57.075	50.000	0.00	0.00	0.00	4.46
2226	4840	4.968971	TGTATGATGATGATGCAGAGGT	57.031	40.909	0.00	0.00	0.00	3.85
2254	4868	6.918022	GTGTGTGATGATGTCGAGTTATATGA	59.082	38.462	0.00	0.00	0.00	2.15
2259	4873	3.498082	CGTGTGTGATGATGTCGAGTTA	58.502	45.455	0.00	0.00	0.00	2.24
2265	4879	1.136252	GTGTGCGTGTGTGATGATGTC	60.136	52.381	0.00	0.00	0.00	3.06
2273	4887	0.445829	TTGTCTTGTGTGCGTGTGTG	59.554	50.000	0.00	0.00	0.00	3.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.