AutoCloner

Multiple sequence alignment - TraesCS7A01G282000

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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	TraesCS7A01G282000	chr7A	100.000	2273	0	0	1	2273	307379211	307376939	0.000000e+00	4198.0
1	TraesCS7A01G282000	chr7A	83.374	409	48	8	295	686	493654061	493654466	5.970000e-96	361.0
2	TraesCS7A01G282000	chr7B	94.462	1264	43	9	853	2095	264005184	264006441	0.000000e+00	1921.0
3	TraesCS7A01G282000	chr7B	95.283	106	5	0	2168	2273	264006441	264006546	3.880000e-38	169.0
4	TraesCS7A01G282000	chr2D	90.810	1469	48	32	843	2273	483066989	483068408	0.000000e+00	1884.0
5	TraesCS7A01G282000	chr2A	90.591	1456	64	26	841	2273	625564821	625566226	0.000000e+00	1862.0
6	TraesCS7A01G282000	chr2A	87.613	775	78	6	26	786	734771927	734772697	0.000000e+00	883.0
7	TraesCS7A01G282000	chr2B	89.288	1475	62	32	842	2273	567577894	567579315	0.000000e+00	1760.0
8	TraesCS7A01G282000	chr2B	93.223	723	18	6	842	1556	567576440	567577139	0.000000e+00	1035.0
9	TraesCS7A01G282000	chr7D	94.145	871	25	10	805	1658	273855586	273854725	0.000000e+00	1303.0
10	TraesCS7A01G282000	chr7D	95.667	577	23	2	1699	2273	273854717	273854141	0.000000e+00	926.0
11	TraesCS7A01G282000	chr5A	84.464	811	83	16	15	786	546387699	546386893	0.000000e+00	760.0
12	TraesCS7A01G282000	chr1A	87.055	618	62	7	185	786	7524506	7525121	0.000000e+00	682.0
13	TraesCS7A01G282000	chr1A	78.717	639	90	21	26	645	32188990	32189601	3.540000e-103	385.0
14	TraesCS7A01G282000	chr1D	84.790	618	63	14	185	786	23325846	23325244	1.940000e-165	592.0
15	TraesCS7A01G282000	chr1D	82.810	605	73	18	185	784	419998133	419998711	1.560000e-141	512.0
16	TraesCS7A01G282000	chr5D	78.657	670	89	23	29	659	434353090	434352436	1.640000e-106	396.0
17	TraesCS7A01G282000	chr5D	75.415	301	60	12	42	328	245773899	245774199	1.420000e-27	134.0
18	TraesCS7A01G282000	chr4B	85.479	365	37	6	300	652	107963905	107963545	1.280000e-97	366.0
19	TraesCS7A01G282000	chr4B	83.041	342	40	6	15	354	107964220	107963895	6.140000e-76	294.0
20	TraesCS7A01G282000	chr3A	82.935	293	41	4	49	332	620617252	620616960	2.900000e-64	255.0
21	TraesCS7A01G282000	chr4A	79.180	317	44	10	28	327	494034218	494033907	1.380000e-47	200.0
22	TraesCS7A01G282000	chr4A	87.255	102	13	0	1103	1204	615164039	615163938	1.430000e-22	117.0
23	TraesCS7A01G282000	chr1B	78.758	306	48	6	38	327	661998571	661998267	2.980000e-44	189.0
24	TraesCS7A01G282000	chr5B	87.255	102	13	0	1103	1204	697499818	697499717	1.430000e-22	117.0
25	TraesCS7A01G282000	chr3D	85.841	113	10	3	33	145	477021115	477021009	5.130000e-22	115.0
26	TraesCS7A01G282000	chr3D	89.831	59	4	2	1985	2043	241398086	241398030	8.710000e-10	75.0
27	TraesCS7A01G282000	chr6B	80.435	92	11	4	1862	1946	80968315	80968406	1.880000e-06	63.9

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	TraesCS7A01G282000	chr7A	307376939	307379211	2272	True	4198.0	4198	100.0000	1	2273	1	chr7A.!!$R1	2272
1	TraesCS7A01G282000	chr7B	264005184	264006546	1362	False	1045.0	1921	94.8725	853	2273	2	chr7B.!!$F1	1420
2	TraesCS7A01G282000	chr2D	483066989	483068408	1419	False	1884.0	1884	90.8100	843	2273	1	chr2D.!!$F1	1430
3	TraesCS7A01G282000	chr2A	625564821	625566226	1405	False	1862.0	1862	90.5910	841	2273	1	chr2A.!!$F1	1432
4	TraesCS7A01G282000	chr2A	734771927	734772697	770	False	883.0	883	87.6130	26	786	1	chr2A.!!$F2	760
5	TraesCS7A01G282000	chr2B	567576440	567579315	2875	False	1397.5	1760	91.2555	842	2273	2	chr2B.!!$F1	1431
6	TraesCS7A01G282000	chr7D	273854141	273855586	1445	True	1114.5	1303	94.9060	805	2273	2	chr7D.!!$R1	1468
7	TraesCS7A01G282000	chr5A	546386893	546387699	806	True	760.0	760	84.4640	15	786	1	chr5A.!!$R1	771
8	TraesCS7A01G282000	chr1A	7524506	7525121	615	False	682.0	682	87.0550	185	786	1	chr1A.!!$F1	601
9	TraesCS7A01G282000	chr1A	32188990	32189601	611	False	385.0	385	78.7170	26	645	1	chr1A.!!$F2	619
10	TraesCS7A01G282000	chr1D	23325244	23325846	602	True	592.0	592	84.7900	185	786	1	chr1D.!!$R1	601
11	TraesCS7A01G282000	chr1D	419998133	419998711	578	False	512.0	512	82.8100	185	784	1	chr1D.!!$F1	599
12	TraesCS7A01G282000	chr5D	434352436	434353090	654	True	396.0	396	78.6570	29	659	1	chr5D.!!$R1	630
13	TraesCS7A01G282000	chr4B	107963545	107964220	675	True	330.0	366	84.2600	15	652	2	chr4B.!!$R1	637

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
743	888	0.036732	TGGCAAGAAAGTCAGCGGAT	59.963	50.0	0.0	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2124	3804	1.306997	CCCCTCTCCCCTGTTAGCA	60.307	63.158	0.0	0.0	0.0	3.49	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
96	97	1.174712	ATGCAGCAACTTTCGCCAGT	61.175	50.000	0.00	0.00	0.00	4.00
147	184	2.652530	GGTAGCGTTGGTCACCGA	59.347	61.111	0.00	0.00	0.00	4.69
294	351	2.609916	TGTCGTCGTTGAAGCAAAATCA	59.390	40.909	0.00	0.00	0.00	2.57
308	411	4.279671	AGCAAAATCAATCACCGGTTGTAA	59.720	37.500	2.97	0.00	0.00	2.41
317	420	2.683867	TCACCGGTTGTAACTTTTGTGG	59.316	45.455	2.97	0.00	0.00	4.17
348	473	4.393834	TGTAGCTTTTGTGATTGCCAGTA	58.606	39.130	0.00	0.00	0.00	2.74
368	495	4.640201	AGTAGCAGCAAAAACAACTTCTGA	59.360	37.500	0.00	0.00	0.00	3.27
434	574	3.181533	GCATCGTCTTTTCTACACGGTTC	60.182	47.826	0.00	0.00	34.24	3.62
438	578	4.083110	TCGTCTTTTCTACACGGTTCTAGG	60.083	45.833	0.00	0.00	34.24	3.02
485	625	0.240945	CACTTCGCAAAAATCCGCCT	59.759	50.000	0.00	0.00	0.00	5.52
553	694	0.736053	TCGGTTGCAGCGTTTTTCTT	59.264	45.000	7.43	0.00	40.41	2.52
577	718	1.464023	CGGATGCAACACTTTGTAGCG	60.464	52.381	0.00	0.00	34.83	4.26
613	755	2.708861	TGTGGCTGGAGGTAGAAGAAAA	59.291	45.455	0.00	0.00	0.00	2.29
621	763	5.861727	TGGAGGTAGAAGAAAAGGTAACAC	58.138	41.667	0.00	0.00	41.41	3.32
627	769	8.877195	AGGTAGAAGAAAAGGTAACACATAAGA	58.123	33.333	0.00	0.00	41.41	2.10
631	773	9.574516	AGAAGAAAAGGTAACACATAAGACAAT	57.425	29.630	0.00	0.00	41.41	2.71
646	789	9.884814	ACATAAGACAATAGATAACTAGGGAGT	57.115	33.333	0.00	0.00	37.59	3.85
661	805	1.743394	GGGAGTAAAAATGGGCAGTCG	59.257	52.381	0.00	0.00	0.00	4.18
668	812	2.063015	AAATGGGCAGTCGTGTGGGA	62.063	55.000	0.00	0.00	0.00	4.37
671	815	3.626924	GGCAGTCGTGTGGGACCT	61.627	66.667	0.00	0.00	37.66	3.85
677	821	2.494471	CAGTCGTGTGGGACCTATAACA	59.506	50.000	0.00	0.00	37.66	2.41
690	834	2.459934	CTATAACATGCGCGTGAGACA	58.540	47.619	34.95	16.51	0.00	3.41
693	837	0.670239	AACATGCGCGTGAGACATGA	60.670	50.000	34.95	0.00	44.84	3.07
700	844	1.226802	CGTGAGACATGAGGGAGCG	60.227	63.158	0.00	0.00	0.00	5.03
741	886	1.576421	GTGGCAAGAAAGTCAGCGG	59.424	57.895	0.00	0.00	0.00	5.52
742	887	0.884704	GTGGCAAGAAAGTCAGCGGA	60.885	55.000	0.00	0.00	0.00	5.54
743	888	0.036732	TGGCAAGAAAGTCAGCGGAT	59.963	50.000	0.00	0.00	0.00	4.18
744	889	1.277842	TGGCAAGAAAGTCAGCGGATA	59.722	47.619	0.00	0.00	0.00	2.59
745	890	1.666189	GGCAAGAAAGTCAGCGGATAC	59.334	52.381	0.00	0.00	0.00	2.24
790	935	4.440127	GCCGGCCGAAAGTCCGTA	62.440	66.667	30.73	0.00	43.87	4.02
791	936	2.497770	CCGGCCGAAAGTCCGTAT	59.502	61.111	30.73	0.00	43.87	3.06
792	937	1.735360	CCGGCCGAAAGTCCGTATA	59.265	57.895	30.73	0.00	43.87	1.47
793	938	0.316204	CCGGCCGAAAGTCCGTATAT	59.684	55.000	30.73	0.00	43.87	0.86
794	939	1.541147	CCGGCCGAAAGTCCGTATATA	59.459	52.381	30.73	0.00	43.87	0.86
795	940	2.030007	CCGGCCGAAAGTCCGTATATAA	60.030	50.000	30.73	0.00	43.87	0.98
796	941	2.982470	CGGCCGAAAGTCCGTATATAAC	59.018	50.000	24.07	0.00	40.72	1.89
797	942	3.320626	GGCCGAAAGTCCGTATATAACC	58.679	50.000	0.00	0.00	0.00	2.85
798	943	2.982470	GCCGAAAGTCCGTATATAACCG	59.018	50.000	0.00	0.00	0.00	4.44
799	944	3.550842	GCCGAAAGTCCGTATATAACCGT	60.551	47.826	0.00	0.00	0.00	4.83
800	945	4.610945	CCGAAAGTCCGTATATAACCGTT	58.389	43.478	0.00	0.00	0.00	4.44
801	946	5.043248	CCGAAAGTCCGTATATAACCGTTT	58.957	41.667	0.00	0.00	0.00	3.60
802	947	5.173854	CCGAAAGTCCGTATATAACCGTTTC	59.826	44.000	0.00	0.00	0.00	2.78
803	948	5.173854	CGAAAGTCCGTATATAACCGTTTCC	59.826	44.000	0.00	0.00	0.00	3.13
833	979	1.271656	GAAATTGCTGCCTGCTGACTT	59.728	47.619	0.00	0.00	43.37	3.01
834	980	1.335145	AATTGCTGCCTGCTGACTTT	58.665	45.000	0.00	0.00	43.37	2.66
835	981	1.335145	ATTGCTGCCTGCTGACTTTT	58.665	45.000	0.00	0.00	43.37	2.27
836	982	1.113788	TTGCTGCCTGCTGACTTTTT	58.886	45.000	0.00	0.00	43.37	1.94
1281	1455	2.422803	CCTCGCCAAATAAATCCCTCCA	60.423	50.000	0.00	0.00	0.00	3.86
1356	2981	7.815549	TCGTTTTGCTAGTATCATAAGTTGTCA	59.184	33.333	0.00	0.00	0.00	3.58
1507	3156	6.586082	GTGTTTGTTTGTGATGCCTATTTAGG	59.414	38.462	0.00	0.00	46.42	2.69
1599	3252	1.683011	CCACCACCAGAATTAGCAGGG	60.683	57.143	0.00	0.00	0.00	4.45
1617	3275	4.103311	GCAGGGTAGGGAACTAGAAATCAT	59.897	45.833	0.00	0.00	45.49	2.45
1648	3306	3.490078	GCTCCTTGTACTGATCCTCGAAG	60.490	52.174	0.00	0.00	0.00	3.79
1721	3382	2.829023	AGGGGTTTGATTCTACCGAGA	58.171	47.619	0.00	0.00	35.19	4.04
1827	3501	7.651027	CTTGATTCCAAGGAATTCCATAAGT	57.349	36.000	26.22	7.56	43.98	2.24
1939	3613	8.689061	TGGAATTCATTTGTTTCTCCTATGATG	58.311	33.333	7.93	0.00	0.00	3.07
1949	3623	6.998074	TGTTTCTCCTATGATGTCAAACACTT	59.002	34.615	0.00	0.00	29.58	3.16
1950	3624	8.154203	TGTTTCTCCTATGATGTCAAACACTTA	58.846	33.333	0.00	0.00	29.58	2.24
1956	3631	8.708378	TCCTATGATGTCAAACACTTATCATCT	58.292	33.333	0.00	0.00	38.83	2.90
2124	3804	3.079478	TCTCCTGCCGCATGCTCT	61.079	61.111	17.13	0.00	42.00	4.09
2186	3883	4.199432	AGTTACTCAGTCTTGCTCCATG	57.801	45.455	0.00	0.00	0.00	3.66
2251	3949	2.129363	TCTCCCATGATCATCAAGGCA	58.871	47.619	4.86	0.00	34.12	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
96	97	4.704833	GCGAGGGAGCTGCAACCA	62.705	66.667	7.79	0.00	0.00	3.67
167	204	0.442699	CCAGTACTTTTTCGCGAGCC	59.557	55.000	9.59	0.00	0.00	4.70
280	337	3.674753	CCGGTGATTGATTTTGCTTCAAC	59.325	43.478	0.00	0.00	36.02	3.18
294	351	4.202070	CCACAAAAGTTACAACCGGTGATT	60.202	41.667	8.52	0.00	0.00	2.57
308	411	0.174617	CAACCGGCAACCACAAAAGT	59.825	50.000	0.00	0.00	0.00	2.66
317	420	1.066454	ACAAAAGCTACAACCGGCAAC	59.934	47.619	0.00	0.00	0.00	4.17
348	473	4.660789	ATCAGAAGTTGTTTTTGCTGCT	57.339	36.364	0.00	0.00	0.00	4.24
368	495	0.172803	GTACCGACGTGAGCTGGAAT	59.827	55.000	0.00	0.00	0.00	3.01
417	557	5.048154	AGTCCTAGAACCGTGTAGAAAAGAC	60.048	44.000	0.00	0.00	0.00	3.01
434	574	4.956700	TGGAACCAATAGAGTCAGTCCTAG	59.043	45.833	0.00	0.00	0.00	3.02
438	578	3.055819	TGCTGGAACCAATAGAGTCAGTC	60.056	47.826	0.00	0.00	0.00	3.51
553	694	1.164411	CAAAGTGTTGCATCCGGCTA	58.836	50.000	0.00	0.00	45.15	3.93
577	718	5.010617	TCCAGCCACATTAAGTTCTTTTTCC	59.989	40.000	0.00	0.00	0.00	3.13
631	773	7.348801	TGCCCATTTTTACTCCCTAGTTATCTA	59.651	37.037	0.00	0.00	37.15	1.98
646	789	1.883275	CCACACGACTGCCCATTTTTA	59.117	47.619	0.00	0.00	0.00	1.52
652	796	3.936203	GTCCCACACGACTGCCCA	61.936	66.667	0.00	0.00	0.00	5.36
661	805	2.210116	CGCATGTTATAGGTCCCACAC	58.790	52.381	0.00	0.00	0.00	3.82
668	812	1.407618	TCTCACGCGCATGTTATAGGT	59.592	47.619	5.73	0.00	0.00	3.08
671	815	2.570442	TGTCTCACGCGCATGTTATA	57.430	45.000	5.73	0.00	0.00	0.98
677	821	1.520120	CCTCATGTCTCACGCGCAT	60.520	57.895	5.73	0.00	0.00	4.73
690	834	1.271840	TAGGCAAACCGCTCCCTCAT	61.272	55.000	0.00	0.00	42.76	2.90
693	837	2.670148	CCTAGGCAAACCGCTCCCT	61.670	63.158	0.00	0.00	42.76	4.20
700	844	2.399356	GCGCAGTCCTAGGCAAACC	61.399	63.158	2.96	0.00	0.00	3.27
836	982	3.063725	CGAATGGCGACGGGTATTAAAAA	59.936	43.478	0.00	0.00	44.57	1.94
837	983	2.608546	CGAATGGCGACGGGTATTAAAA	59.391	45.455	0.00	0.00	44.57	1.52
838	984	2.203401	CGAATGGCGACGGGTATTAAA	58.797	47.619	0.00	0.00	44.57	1.52
839	985	1.538634	CCGAATGGCGACGGGTATTAA	60.539	52.381	8.52	0.00	44.59	1.40
892	1040	1.648116	ACGGAGTAGTGGGCCTTTTA	58.352	50.000	4.53	0.00	41.94	1.52
1507	3156	7.430992	TCATGTATGTACTCCGAGTATGTAC	57.569	40.000	11.43	15.48	37.60	2.90
1599	3252	8.738645	ACAATGAATGATTTCTAGTTCCCTAC	57.261	34.615	0.00	0.00	32.78	3.18
1617	3275	4.713553	TCAGTACAAGGAGCAACAATGAA	58.286	39.130	0.00	0.00	0.00	2.57
1648	3306	4.023739	AGCAACGTCTTGTTTTGGTTAC	57.976	40.909	0.00	0.00	39.29	2.50
1721	3382	7.563188	AGAATGTGTCTCCTTAGTGATCAGTAT	59.437	37.037	11.06	0.00	0.00	2.12
1956	3631	8.714906	CCCAAGGATTAGAAGACTAGGAATTTA	58.285	37.037	0.00	0.00	0.00	1.40
2043	3723	2.255316	CAAGACGCCGTTTTTGTGTTT	58.745	42.857	0.00	0.00	0.00	2.83
2082	3762	3.377573	ACGGCTGGGATAACCTTACTTA	58.622	45.455	0.00	0.00	41.11	2.24
2124	3804	1.306997	CCCCTCTCCCCTGTTAGCA	60.307	63.158	0.00	0.00	0.00	3.49
2186	3883	1.704582	CAGAAGCTACGCGCAAGAC	59.295	57.895	5.73	0.67	42.61	3.01
2251	3949	1.627297	GGAGGGAGCGAGGAAATGGT	61.627	60.000	0.00	0.00	0.00	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.