AutoCloner

Multiple sequence alignment - TraesCS7D01G285200

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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	TraesCS7D01G285200	chr7D	100.000	2319	0	0	1	2319	306772708	306775026	0.000000e+00	4283
1	TraesCS7D01G285200	chr7D	95.476	2343	82	10	1	2319	626698513	626696171	0.000000e+00	3718
2	TraesCS7D01G285200	chr7D	95.474	2342	83	11	1	2319	203556368	203554027	0.000000e+00	3716
3	TraesCS7D01G285200	chr5A	95.647	2343	78	12	1	2319	300072956	300075298	0.000000e+00	3740
4	TraesCS7D01G285200	chr5A	95.301	2341	86	11	1	2319	16602942	16600604	0.000000e+00	3692
5	TraesCS7D01G285200	chrUn	95.604	2343	79	11	1	2319	189392516	189394858	0.000000e+00	3735
6	TraesCS7D01G285200	chr2A	95.559	2342	80	11	2	2319	618279978	618277637	0.000000e+00	3727
7	TraesCS7D01G285200	chr7B	95.519	2343	81	12	1	2319	743086176	743088518	0.000000e+00	3723
8	TraesCS7D01G285200	chr6A	95.346	2342	85	12	1	2319	289128609	289130949	0.000000e+00	3699
9	TraesCS7D01G285200	chr6A	95.735	211	9	0	1	211	608893980	608893770	7.940000e-90	340
10	TraesCS7D01G285200	chr7A	95.271	2347	83	12	1	2319	4959815	4962161	0.000000e+00	3694
11	TraesCS7D01G285200	chr4A	95.013	2346	88	6	1	2319	67587554	67585211	0.000000e+00	3657
12	TraesCS7D01G285200	chr5B	94.159	1147	44	4	1	1125	713025951	713024806	0.000000e+00	1725
13	TraesCS7D01G285200	chr1D	93.673	980	38	4	1	956	141321623	141320644	0.000000e+00	1445
14	TraesCS7D01G285200	chr1B	95.261	211	10	0	1	211	285997884	285997674	3.690000e-88	335

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	TraesCS7D01G285200	chr7D	306772708	306775026	2318	False	4283	4283	100.000	1	2319	1	chr7D.!!$F1	2318
1	TraesCS7D01G285200	chr7D	626696171	626698513	2342	True	3718	3718	95.476	1	2319	1	chr7D.!!$R2	2318
2	TraesCS7D01G285200	chr7D	203554027	203556368	2341	True	3716	3716	95.474	1	2319	1	chr7D.!!$R1	2318
3	TraesCS7D01G285200	chr5A	300072956	300075298	2342	False	3740	3740	95.647	1	2319	1	chr5A.!!$F1	2318
4	TraesCS7D01G285200	chr5A	16600604	16602942	2338	True	3692	3692	95.301	1	2319	1	chr5A.!!$R1	2318
5	TraesCS7D01G285200	chrUn	189392516	189394858	2342	False	3735	3735	95.604	1	2319	1	chrUn.!!$F1	2318
6	TraesCS7D01G285200	chr2A	618277637	618279978	2341	True	3727	3727	95.559	2	2319	1	chr2A.!!$R1	2317
7	TraesCS7D01G285200	chr7B	743086176	743088518	2342	False	3723	3723	95.519	1	2319	1	chr7B.!!$F1	2318
8	TraesCS7D01G285200	chr6A	289128609	289130949	2340	False	3699	3699	95.346	1	2319	1	chr6A.!!$F1	2318
9	TraesCS7D01G285200	chr7A	4959815	4962161	2346	False	3694	3694	95.271	1	2319	1	chr7A.!!$F1	2318
10	TraesCS7D01G285200	chr4A	67585211	67587554	2343	True	3657	3657	95.013	1	2319	1	chr4A.!!$R1	2318
11	TraesCS7D01G285200	chr5B	713024806	713025951	1145	True	1725	1725	94.159	1	1125	1	chr5B.!!$R1	1124
12	TraesCS7D01G285200	chr1D	141320644	141321623	979	True	1445	1445	93.673	1	956	1	chr1D.!!$R1	955

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
603	631	1.071699	CAAACCCAAACTCTCCTCCGA	59.928	52.381	0.0	0.0	0.0	4.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1509	1541	0.03582	TTTTATTGAGAGCGGGCGGT	60.036	50.0	0.0	0.0	0.0	5.68	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
39	40	8.328758	CAGGGTTATATATCATAAAGGGCTTCA	58.671	37.037	0.00	0.00	0.00	3.02
95	96	5.661759	AGATAAGGTCGGAATACCAGAGTTT	59.338	40.000	0.00	0.00	42.40	2.66
96	97	6.837568	AGATAAGGTCGGAATACCAGAGTTTA	59.162	38.462	0.00	0.00	42.40	2.01
108	109	8.635765	AATACCAGAGTTTATTCTTTGCTTCA	57.364	30.769	0.00	0.00	0.00	3.02
179	180	4.912586	TCTAACTCGCATATCTAGAGCCT	58.087	43.478	0.00	0.00	35.56	4.58
192	193	4.172020	TCTAGAGCCTAGCATCTCTCCTA	58.828	47.826	9.68	0.00	40.00	2.94
207	208	5.087323	TCTCTCCTAAATGACACCTTCTGT	58.913	41.667	0.00	0.00	34.96	3.41
254	277	2.933495	TATCGGTCAGGAAACGACAG	57.067	50.000	0.00	0.00	39.64	3.51
257	280	1.557443	CGGTCAGGAAACGACAGTGC	61.557	60.000	0.00	0.00	36.18	4.40
354	377	5.676837	GCATTCATTGTCACCGATCATTGAA	60.677	40.000	0.00	0.00	37.88	2.69
407	430	7.110155	ACTTAAGGAATCTTTAGATTTGGCGA	58.890	34.615	7.53	0.00	44.14	5.54
477	505	6.485648	GCTAACTAAAGTCCAACTTCCTTTGA	59.514	38.462	0.00	0.00	37.47	2.69
489	517	4.570930	ACTTCCTTTGACGAAAGAGGATC	58.429	43.478	0.00	0.00	41.12	3.36
573	601	5.357742	TCTCAATCCAAAATCTCCGATCA	57.642	39.130	0.00	0.00	0.00	2.92
603	631	1.071699	CAAACCCAAACTCTCCTCCGA	59.928	52.381	0.00	0.00	0.00	4.55
619	647	9.142014	CTCTCCTCCGATTTTGGATATATAGAT	57.858	37.037	0.00	0.00	37.41	1.98
630	658	8.838649	TTTGGATATATAGATAGTGCCTGCTA	57.161	34.615	0.00	0.00	0.00	3.49
679	707	3.754850	TCCTATCGAGAACAAGACGACAA	59.245	43.478	0.00	0.00	38.79	3.18
760	789	6.430007	AGCTCAGTGAAATGGAATAAGGAAT	58.570	36.000	0.00	0.00	0.00	3.01
786	815	4.473477	AGTGTAGTGTGATAAGGGAAGC	57.527	45.455	0.00	0.00	0.00	3.86
838	867	6.274157	AGGGCTCAGATAGATATACAAACG	57.726	41.667	0.00	0.00	0.00	3.60
915	945	6.639563	TCGAATCACATTTTGATCTCCTACA	58.360	36.000	0.00	0.00	44.86	2.74
937	967	4.047883	ACTTGCTTTCATAGTCCCCCTAT	58.952	43.478	0.00	0.00	36.79	2.57
1013	1043	8.765219	GCGTAGATTCAATATGTTGATTGTACT	58.235	33.333	21.20	13.00	43.49	2.73
1055	1085	2.679355	CGAAAGCCACATTCGTTTCA	57.321	45.000	0.82	0.00	43.41	2.69
1158	1190	2.208872	AGCCCCTATCACAAGACCAAT	58.791	47.619	0.00	0.00	0.00	3.16
1237	1269	3.982475	TGGATGTGATCTATTCTCGTGC	58.018	45.455	0.00	0.00	0.00	5.34
1313	1345	6.366877	ACACATAAATCAAAGAAGCATTGTGC	59.633	34.615	0.00	0.00	45.46	4.57
1328	1360	4.496360	CATTGTGCAATAGTGGCATTTCA	58.504	39.130	0.00	0.00	44.11	2.69
1386	1418	0.465460	AAACCGGCAAACTCAGAGCA	60.465	50.000	0.00	0.00	0.00	4.26
1442	1474	1.308998	CAAGCCAAACACGTCTCCTT	58.691	50.000	0.00	0.00	0.00	3.36
1466	1498	1.228657	AAGGGTCTTCTCGCGCAAAC	61.229	55.000	8.75	0.00	0.00	2.93
1509	1541	8.927721	CAACTGATTTTGATTAATGCATGTCAA	58.072	29.630	14.77	14.77	0.00	3.18
1526	1558	0.742990	CAACCGCCCGCTCTCAATAA	60.743	55.000	0.00	0.00	0.00	1.40
1528	1560	0.035820	ACCGCCCGCTCTCAATAAAA	60.036	50.000	0.00	0.00	0.00	1.52
1576	1608	6.423302	CAGAGAAAGATTACCGATTCATCCAG	59.577	42.308	0.00	0.00	0.00	3.86
1616	1653	8.677148	AAGTGAGTTCATTGTTGTTGTATAGT	57.323	30.769	0.00	0.00	0.00	2.12
1772	1809	1.591863	GGGCTCGAAGGCGATGTAC	60.592	63.158	0.00	0.00	46.80	2.90
1848	1885	2.608268	CAAATCATTTGCCGACATGCA	58.392	42.857	0.00	0.00	40.07	3.96
1874	1911	7.127032	AGACTCACTTCTCTTTTATGGGATGAT	59.873	37.037	0.00	0.00	0.00	2.45
1914	1951	5.640357	TGTCTATTTACGTGGGTGAATCAAC	59.360	40.000	0.00	0.00	34.56	3.18
1929	1966	4.515191	TGAATCAACTACAACAAGTCAGGC	59.485	41.667	0.00	0.00	0.00	4.85
1997	2034	6.927416	TCAACTAGGAAAGAAGTACGCATTA	58.073	36.000	0.00	0.00	0.00	1.90
2056	2093	5.900123	AGCTAATCAAGTCATAGTAGGGTGT	59.100	40.000	0.00	0.00	0.00	4.16
2091	2128	1.535204	CCGGTGCCCTCAAAAGCAAT	61.535	55.000	0.00	0.00	41.48	3.56
2106	2143	4.808414	AAGCAATGCACAGACTCTACTA	57.192	40.909	8.35	0.00	0.00	1.82
2144	2181	2.965831	CCTACGGAGGGAGAAATCATCA	59.034	50.000	5.47	0.00	39.48	3.07
2289	2326	8.727910	GCAGCATAATTATTAGTTAGGGGTAAC	58.272	37.037	0.00	0.00	0.00	2.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
39	40	3.562182	AGAACGAATCAAACCCCTTGTT	58.438	40.909	0.00	0.00	39.43	2.83
108	109	7.394641	GGGTTGAAGAAGGAATCTATGTTCTTT	59.605	37.037	0.00	0.00	38.94	2.52
160	161	3.442273	GCTAGGCTCTAGATATGCGAGTT	59.558	47.826	11.96	0.00	0.00	3.01
179	180	5.211973	AGGTGTCATTTAGGAGAGATGCTA	58.788	41.667	0.00	0.00	0.00	3.49
192	193	3.617531	CGCCTCTACAGAAGGTGTCATTT	60.618	47.826	0.00	0.00	40.94	2.32
207	208	3.006537	GCACATATTTACCCTCGCCTCTA	59.993	47.826	0.00	0.00	0.00	2.43
254	277	1.443802	CCGGAAAGAAGAAGAGGCAC	58.556	55.000	0.00	0.00	0.00	5.01
257	280	2.937433	GCTTCCCGGAAAGAAGAAGAGG	60.937	54.545	19.49	0.48	42.80	3.69
354	377	7.901889	GTCGTACGACTTCTTTTTCTTCTTTTT	59.098	33.333	34.97	0.00	41.57	1.94
407	430	4.160626	GTCTGTGCCCTTTGAGTCTATAGT	59.839	45.833	0.00	0.00	0.00	2.12
477	505	3.522553	GATCCGTTTGATCCTCTTTCGT	58.477	45.455	0.00	0.00	43.53	3.85
573	601	4.082125	GAGTTTGGGTTTGGATCACAGAT	58.918	43.478	0.00	0.00	0.00	2.90
603	631	8.776119	AGCAGGCACTATCTATATATCCAAAAT	58.224	33.333	0.00	0.00	36.02	1.82
619	647	3.343617	GTTGGTTTGATAGCAGGCACTA	58.656	45.455	0.00	0.00	36.02	2.74
630	658	2.624838	CTGCTGTCTTGGTTGGTTTGAT	59.375	45.455	0.00	0.00	0.00	2.57
701	729	7.548196	TTTTCACGTATTCACCCAAGATATC	57.452	36.000	0.00	0.00	0.00	1.63
708	736	4.200874	ACACTTTTTCACGTATTCACCCA	58.799	39.130	0.00	0.00	0.00	4.51
760	789	7.578955	GCTTCCCTTATCACACTACACTTTCTA	60.579	40.741	0.00	0.00	0.00	2.10
786	815	5.811613	TGAAAACCTCAAAATTGACTTGCAG	59.188	36.000	0.00	0.00	32.90	4.41
838	867	5.495640	AGGGTTCTGATGTGAATTCTTCTC	58.504	41.667	7.05	1.37	0.00	2.87
915	945	2.279173	AGGGGGACTATGAAAGCAAGT	58.721	47.619	0.00	0.00	0.00	3.16
937	967	0.749091	CATTGATTCCGGGCAGCTCA	60.749	55.000	0.00	0.00	0.00	4.26
942	972	0.623194	TCCTTCATTGATTCCGGGCA	59.377	50.000	0.00	0.00	0.00	5.36
1055	1085	2.368875	AGGACGTGTGACTTCCTCAAAT	59.631	45.455	0.00	0.00	42.47	2.32
1119	1151	1.209261	CTTGAGGAGGAAGAAGAGGGC	59.791	57.143	0.00	0.00	0.00	5.19
1214	1246	4.500545	GCACGAGAATAGATCACATCCAGT	60.501	45.833	0.00	0.00	0.00	4.00
1216	1248	3.243873	GGCACGAGAATAGATCACATCCA	60.244	47.826	0.00	0.00	0.00	3.41
1237	1269	4.457257	GGGAGAAGAAAGAAAGTGATGTGG	59.543	45.833	0.00	0.00	0.00	4.17
1313	1345	6.518493	AGCCATTAATGAAATGCCACTATTG	58.482	36.000	17.23	0.00	43.18	1.90
1386	1418	4.774726	TGCTCCTATTCACTTTCAGAGACT	59.225	41.667	0.00	0.00	0.00	3.24
1442	1474	0.809385	CGCGAGAAGACCCTTGACTA	59.191	55.000	0.00	0.00	0.00	2.59
1493	1525	2.098934	GGCGGTTGACATGCATTAATCA	59.901	45.455	0.00	0.00	0.00	2.57
1495	1527	1.408702	GGGCGGTTGACATGCATTAAT	59.591	47.619	0.00	0.00	0.00	1.40
1509	1541	0.035820	TTTTATTGAGAGCGGGCGGT	60.036	50.000	0.00	0.00	0.00	5.68
1526	1558	5.127845	TCTTGTGAGAGAGAGTCACTTGTTT	59.872	40.000	4.96	0.00	44.02	2.83
1528	1560	4.037446	GTCTTGTGAGAGAGAGTCACTTGT	59.963	45.833	4.96	0.00	44.02	3.16
1576	1608	6.205464	TGAACTCACTTCTGATCAAATTGGAC	59.795	38.462	0.00	0.00	0.00	4.02
1616	1653	4.528596	TGGTTTTGTCAAGGAAAGGTTTCA	59.471	37.500	4.89	0.00	38.92	2.69
1716	1753	5.163622	ACTGGTTTCTAATCGCAATGGATTG	60.164	40.000	7.06	0.00	37.24	2.67
1762	1799	6.100004	CCATTATTTCTATCGTACATCGCCT	58.900	40.000	0.00	0.00	39.67	5.52
1772	1809	6.407202	CCCTAACTCCCCATTATTTCTATCG	58.593	44.000	0.00	0.00	0.00	2.92
1848	1885	6.441924	TCATCCCATAAAAGAGAAGTGAGTCT	59.558	38.462	0.00	0.00	0.00	3.24
1914	1951	2.693069	CTCTGGCCTGACTTGTTGTAG	58.307	52.381	8.48	0.00	0.00	2.74
1929	1966	3.902881	ATCTTCTACCACAAGCTCTGG	57.097	47.619	8.55	8.55	34.62	3.86
1997	2034	3.520290	TCGTTCAAACAGTCAGTCAGT	57.480	42.857	0.00	0.00	0.00	3.41
2046	2083	1.284198	AGCTTCTCGGACACCCTACTA	59.716	52.381	0.00	0.00	0.00	1.82
2056	2093	1.079819	CGGCAAGAAGCTTCTCGGA	60.080	57.895	28.58	0.00	44.79	4.55
2081	2118	3.216800	AGAGTCTGTGCATTGCTTTTGA	58.783	40.909	10.49	0.66	0.00	2.69
2091	2128	2.561419	GTGGGTTAGTAGAGTCTGTGCA	59.439	50.000	1.86	0.00	0.00	4.57
2106	2143	2.483197	GGTGGAAAACGCGTGGGTT	61.483	57.895	14.98	7.79	0.00	4.11
2144	2181	5.709594	CCTTTCAGGGGATGAGGATATTTT	58.290	41.667	0.00	0.00	39.68	1.82
2274	2311	4.042884	GTCCCCTGTTACCCCTAACTAAT	58.957	47.826	0.00	0.00	34.38	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.