AutoCloner

Multiple sequence alignment - TraesCS5B01G199800

Loading Multiple Alignment...

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	TraesCS5B01G199800	chr5B	100.000	3101	0	0	1	3101	360862107	360859007	0.000000e+00	5727.0
1	TraesCS5B01G199800	chr5B	85.883	1523	164	20	1138	2624	360925005	360926512	0.000000e+00	1574.0
2	TraesCS5B01G199800	chr5B	92.537	134	8	1	1	134	360922457	360922588	1.140000e-44	191.0
3	TraesCS5B01G199800	chr5A	90.761	2208	139	26	1	2186	407126058	407123894	0.000000e+00	2887.0
4	TraesCS5B01G199800	chr5A	85.047	1284	135	21	847	2104	407156511	407157763	0.000000e+00	1254.0
5	TraesCS5B01G199800	chr5A	94.414	734	39	1	1	732	407153831	407154564	0.000000e+00	1127.0
6	TraesCS5B01G199800	chr5A	84.034	119	19	0	2113	2231	407157995	407158113	7.030000e-22	115.0
7	TraesCS5B01G199800	chr5A	91.935	62	1	1	2228	2289	407158193	407158250	1.980000e-12	84.2
8	TraesCS5B01G199800	chr5D	89.087	2016	144	27	1	1984	313332273	313334244	0.000000e+00	2435.0
9	TraesCS5B01G199800	chr5D	91.439	1133	91	5	974	2103	313151659	313150530	0.000000e+00	1550.0
10	TraesCS5B01G199800	chr5D	93.965	961	53	5	2146	3101	313150535	313149575	0.000000e+00	1448.0
11	TraesCS5B01G199800	chr5D	90.812	751	52	11	1	743	313152706	313151965	0.000000e+00	989.0
12	TraesCS5B01G199800	chr5D	88.705	664	65	6	1496	2150	313284296	313284958	0.000000e+00	802.0
13	TraesCS5B01G199800	chr5D	85.232	237	21	4	2202	2437	313344006	313344229	6.690000e-57	231.0
14	TraesCS5B01G199800	chr5D	91.429	140	8	3	2505	2644	313144502	313144367	4.080000e-44	189.0
15	TraesCS5B01G199800	chr5D	91.667	120	9	1	1987	2106	313343842	313343960	6.880000e-37	165.0
16	TraesCS5B01G199800	chr5D	86.897	145	12	3	2142	2283	313328078	313328218	4.140000e-34	156.0
17	TraesCS5B01G199800	chr5D	87.778	90	11	0	2644	2733	101481439	101481350	4.230000e-19	106.0
18	TraesCS5B01G199800	chr6D	83.654	208	26	7	2786	2991	86768176	86767975	4.080000e-44	189.0
19	TraesCS5B01G199800	chr1A	80.519	231	43	2	2644	2873	251937149	251937378	3.180000e-40	176.0
20	TraesCS5B01G199800	chr1A	78.488	172	36	1	2636	2806	483936567	483936738	9.090000e-21	111.0
21	TraesCS5B01G199800	chr2A	81.250	128	20	4	2643	2767	16373240	16373114	1.970000e-17	100.0

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	TraesCS5B01G199800	chr5B	360859007	360862107	3100	True	5727.00	5727	100.0000	1	3101	1	chr5B.!!$R1	3100
1	TraesCS5B01G199800	chr5B	360922457	360926512	4055	False	882.50	1574	89.2100	1	2624	2	chr5B.!!$F1	2623
2	TraesCS5B01G199800	chr5A	407123894	407126058	2164	True	2887.00	2887	90.7610	1	2186	1	chr5A.!!$R1	2185
3	TraesCS5B01G199800	chr5A	407153831	407158250	4419	False	645.05	1254	88.8575	1	2289	4	chr5A.!!$F1	2288
4	TraesCS5B01G199800	chr5D	313332273	313334244	1971	False	2435.00	2435	89.0870	1	1984	1	chr5D.!!$F3	1983
5	TraesCS5B01G199800	chr5D	313149575	313152706	3131	True	1329.00	1550	92.0720	1	3101	3	chr5D.!!$R3	3100
6	TraesCS5B01G199800	chr5D	313284296	313284958	662	False	802.00	802	88.7050	1496	2150	1	chr5D.!!$F1	654

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
813	2729	1.047002	TTTAGGTTTCGGGTCGGACA	58.953	50.0	10.76	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2708	7322	0.109153	GGGGTACAAGTTGTCGGGTT	59.891	55.0	12.82	0.0	0.0	4.11	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
80	81	2.884639	GCCGCAATGAAACCTGGTATAT	59.115	45.455	0.00	0.00	0.00	0.86
108	109	1.199624	GAAACGTTGTTGCAGCAAGG	58.800	50.000	27.44	27.44	39.35	3.61
410	413	3.011369	TCTCTTGGTCTGGAGGTAAGCTA	59.989	47.826	0.00	0.00	0.00	3.32
419	422	4.079154	TCTGGAGGTAAGCTAATCCTCTCA	60.079	45.833	22.36	18.39	44.85	3.27
431	434	5.163364	GCTAATCCTCTCAAGAGTTGATGGA	60.163	44.000	6.30	11.49	42.33	3.41
703	721	4.033894	GCAGCGCGTATCCATCTT	57.966	55.556	8.43	0.00	0.00	2.40
708	726	1.846648	CGCGTATCCATCTTGTCGC	59.153	57.895	0.00	0.00	40.19	5.19
813	2729	1.047002	TTTAGGTTTCGGGTCGGACA	58.953	50.000	10.76	0.00	0.00	4.02
835	2760	5.334319	CAAGGATTGTACGTACGTGACATA	58.666	41.667	30.25	17.96	42.34	2.29
836	2761	5.762825	AGGATTGTACGTACGTGACATAT	57.237	39.130	30.25	20.76	0.00	1.78
837	2762	6.866010	AGGATTGTACGTACGTGACATATA	57.134	37.500	30.25	14.78	0.00	0.86
851	2781	6.206829	ACGTGACATATATGCTGCTTCTACTA	59.793	38.462	12.79	0.00	0.00	1.82
886	2816	1.444933	TTGGGCTCCAAGAGAGGAAA	58.555	50.000	2.84	0.00	43.46	3.13
891	2821	4.230502	TGGGCTCCAAGAGAGGAAATTTAT	59.769	41.667	0.00	0.00	43.46	1.40
971	2981	2.835764	TCTCCGCTATTACCACCTGTTT	59.164	45.455	0.00	0.00	0.00	2.83
972	2982	4.025360	TCTCCGCTATTACCACCTGTTTA	58.975	43.478	0.00	0.00	0.00	2.01
973	2983	4.652421	TCTCCGCTATTACCACCTGTTTAT	59.348	41.667	0.00	0.00	0.00	1.40
974	2984	5.129815	TCTCCGCTATTACCACCTGTTTATT	59.870	40.000	0.00	0.00	0.00	1.40
1035	3053	2.025226	AGATTGGTCGTCTCTCCCAGTA	60.025	50.000	0.00	0.00	0.00	2.74
1135	4068	1.868251	GCCGTGTCGCTCTTCTACG	60.868	63.158	0.00	0.00	34.78	3.51
1207	5474	0.682209	TGTCCGCTACTACAGTCCCC	60.682	60.000	0.00	0.00	0.00	4.81
1449	5719	2.549754	CGCTCAAGAGATTGGTTGTTGT	59.450	45.455	0.32	0.00	0.00	3.32
1500	5770	1.530183	GGCGTACTCCTACCCCGAT	60.530	63.158	0.00	0.00	0.00	4.18
1587	5857	3.954904	TGCTAGAAGACGGAAGATTAGCT	59.045	43.478	0.00	0.00	0.00	3.32
1638	5908	5.098211	GGATTTGAAATTCTTGAGAAGCCG	58.902	41.667	0.00	0.00	37.48	5.52
1704	5974	1.136329	ACCAGGGTGAGCTGATGGTT	61.136	55.000	0.00	0.00	41.44	3.67
1829	6100	3.004106	ACAGGTACACTCACGACTGTAAC	59.996	47.826	0.00	0.00	37.41	2.50
1917	6189	5.283060	ACATCGTTTATGCTGACTTTGTC	57.717	39.130	0.00	0.00	39.39	3.18
2096	6374	8.402472	CAGTATTTGGGTCGATTTTAGCAATAA	58.598	33.333	0.00	0.00	0.00	1.40
2100	6378	9.965824	ATTTGGGTCGATTTTAGCAATAATTAG	57.034	29.630	0.00	0.00	0.00	1.73
2101	6379	8.740123	TTGGGTCGATTTTAGCAATAATTAGA	57.260	30.769	0.00	0.00	0.00	2.10
2102	6380	8.149973	TGGGTCGATTTTAGCAATAATTAGAC	57.850	34.615	0.00	0.00	0.00	2.59
2104	6382	8.837389	GGGTCGATTTTAGCAATAATTAGACTT	58.163	33.333	0.00	0.00	0.00	3.01
2105	6383	9.865484	GGTCGATTTTAGCAATAATTAGACTTC	57.135	33.333	0.00	0.00	0.00	3.01
2121	6621	5.630661	AGACTTCGATGGATAATACTCGG	57.369	43.478	3.12	0.00	0.00	4.63
2569	7182	2.481854	TGCAATGCAACATTTGTGGTC	58.518	42.857	5.01	0.00	34.76	4.02
2595	7208	7.509141	ACACCGAAAATCATTGCATATATCA	57.491	32.000	0.00	0.00	0.00	2.15
2625	7239	3.414549	TTTTCAAGAACAAGTGACCGC	57.585	42.857	0.00	0.00	0.00	5.68
2639	7253	3.880490	AGTGACCGCTGTTTGTCATTTTA	59.120	39.130	0.00	0.00	42.90	1.52
2644	7258	7.060633	GTGACCGCTGTTTGTCATTTTAATTAG	59.939	37.037	0.00	0.00	42.90	1.73
2698	7312	4.967707	GGCCAAGTCTAGATTTGGACCCT	61.968	52.174	37.71	9.88	46.90	4.34
2708	7322	7.176690	GTCTAGATTTGGACCCTCAATTTTGAA	59.823	37.037	0.00	0.00	36.64	2.69
2712	7326	2.969262	TGGACCCTCAATTTTGAAACCC	59.031	45.455	0.00	0.00	36.64	4.11
2722	7336	4.729227	ATTTTGAAACCCGACAACTTGT	57.271	36.364	0.00	0.00	0.00	3.16
2732	7346	1.202722	CGACAACTTGTACCCCCAACT	60.203	52.381	0.00	0.00	0.00	3.16
2748	7362	3.128589	CCCAACTATTGAAACCGGACATG	59.871	47.826	9.46	0.00	0.00	3.21
2771	7385	4.262592	GGTTTGTCCCTAGTCTCGGTTTTA	60.263	45.833	0.00	0.00	0.00	1.52
2796	7410	2.690653	TTTTGGTGCTGACTCCCCCG	62.691	60.000	0.00	0.00	0.00	5.73
2817	7431	2.508526	GTTTTGACCCATGCTGACTCT	58.491	47.619	0.00	0.00	0.00	3.24
2818	7432	2.887152	GTTTTGACCCATGCTGACTCTT	59.113	45.455	0.00	0.00	0.00	2.85
2819	7433	4.072131	GTTTTGACCCATGCTGACTCTTA	58.928	43.478	0.00	0.00	0.00	2.10
2825	7439	1.524355	CCATGCTGACTCTTATTCGCG	59.476	52.381	0.00	0.00	0.00	5.87
2841	7456	8.231161	TCTTATTCGCGTAACAAATTCAAATCA	58.769	29.630	5.77	0.00	0.00	2.57
2842	7457	6.853279	ATTCGCGTAACAAATTCAAATCAG	57.147	33.333	5.77	0.00	0.00	2.90
2902	7518	7.173907	TCCGTTTATTTTTCCCAAATACACGTA	59.826	33.333	17.87	6.35	41.18	3.57
2922	7538	7.761249	ACACGTACTTTATTTAGAACCGCTTAT	59.239	33.333	0.00	0.00	0.00	1.73
2995	7612	6.066054	TCGTGTAATTGTTTCAAATCTGCA	57.934	33.333	0.00	0.00	0.00	4.41
3022	7639	5.947663	TGTTTCAAATCCCAGAACTCCTTA	58.052	37.500	0.00	0.00	0.00	2.69
3025	7642	7.508977	TGTTTCAAATCCCAGAACTCCTTAAAT	59.491	33.333	0.00	0.00	0.00	1.40
3026	7643	8.367911	GTTTCAAATCCCAGAACTCCTTAAATT	58.632	33.333	0.00	0.00	0.00	1.82
3072	7689	5.733937	GCGTACTTTTCCAAGTTTGCCTAAA	60.734	40.000	0.00	0.00	40.66	1.85
3077	7695	8.208718	ACTTTTCCAAGTTTGCCTAAATTTTC	57.791	30.769	0.00	0.00	40.66	2.29
3090	7708	5.122239	GCCTAAATTTTCCAAATTCCTGCAC	59.878	40.000	0.00	0.00	0.00	4.57
3096	7714	5.860941	TTTCCAAATTCCTGCACTGTTTA	57.139	34.783	0.00	0.00	0.00	2.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
80	81	1.604755	CAACAACGTTTCCCAATCGGA	59.395	47.619	0.00	0.00	39.68	4.55
419	422	4.107072	TCCTCTGGAATCCATCAACTCTT	58.893	43.478	0.87	0.00	30.82	2.85
431	434	3.416156	GCACAACTCTTTCCTCTGGAAT	58.584	45.455	0.00	0.00	41.71	3.01
629	647	0.905357	CGTTTCCTCTGGATCCAGGT	59.095	55.000	35.95	0.00	43.75	4.00
766	2670	2.417097	GTGTGGGCAACAGCAACC	59.583	61.111	0.00	0.00	40.26	3.77
767	2671	2.026014	CGTGTGGGCAACAGCAAC	59.974	61.111	0.00	0.00	40.26	4.17
768	2672	3.215568	CCGTGTGGGCAACAGCAA	61.216	61.111	0.00	0.00	40.26	3.91
813	2729	3.921119	TGTCACGTACGTACAATCCTT	57.079	42.857	22.34	0.00	0.00	3.36
835	2760	4.469227	CCATCCCTAGTAGAAGCAGCATAT	59.531	45.833	0.00	0.00	0.00	1.78
836	2761	3.834813	CCATCCCTAGTAGAAGCAGCATA	59.165	47.826	0.00	0.00	0.00	3.14
837	2762	2.636893	CCATCCCTAGTAGAAGCAGCAT	59.363	50.000	0.00	0.00	0.00	3.79
906	2836	4.025015	TCGAGCTTTACCTTTACGCTAG	57.975	45.455	0.00	0.00	0.00	3.42
971	2981	1.899814	CTCCCCTATAGCCGCACAATA	59.100	52.381	0.00	0.00	0.00	1.90
972	2982	0.687354	CTCCCCTATAGCCGCACAAT	59.313	55.000	0.00	0.00	0.00	2.71
973	2983	0.397957	TCTCCCCTATAGCCGCACAA	60.398	55.000	0.00	0.00	0.00	3.33
974	2984	0.827925	CTCTCCCCTATAGCCGCACA	60.828	60.000	0.00	0.00	0.00	4.57
1035	3053	2.971330	CAGGATCAGGATAAGCAGGTCT	59.029	50.000	0.00	0.00	0.00	3.85
1127	4060	2.332362	GATCCACGCCGCGTAGAAGA	62.332	60.000	19.71	13.17	38.32	2.87
1207	5474	5.931441	ATCTCGAAGTTTTTCTGGAAGTG	57.069	39.130	0.00	0.00	33.76	3.16
1449	5719	1.226435	GCCGTCGTTGTTTTGCACA	60.226	52.632	0.00	0.00	0.00	4.57
1500	5770	2.431419	TGACGGTGTGAACTTTGTCCTA	59.569	45.455	0.00	0.00	0.00	2.94
1555	5825	5.299148	TCCGTCTTCTAGCAGTAGATAGAC	58.701	45.833	11.28	11.28	42.06	2.59
1587	5857	1.225855	GTTTGGACTCGTCACATGCA	58.774	50.000	0.00	0.00	0.00	3.96
1638	5908	0.743345	ATACAAGCCCGAAACTCCGC	60.743	55.000	0.00	0.00	0.00	5.54
1651	5921	5.744345	CCAAGTAGCTGTCTTCGTATACAAG	59.256	44.000	3.32	6.26	0.00	3.16
1829	6100	3.619038	GGACTTAATGGCAGTCTTCTTCG	59.381	47.826	0.00	0.00	40.60	3.79
1917	6189	2.677003	AAATTCACCGTCGCGCAGG	61.677	57.895	16.31	16.31	0.00	4.85
2096	6374	7.628794	GCCGAGTATTATCCATCGAAGTCTAAT	60.629	40.741	0.00	0.00	37.35	1.73
2099	6377	4.082679	GCCGAGTATTATCCATCGAAGTCT	60.083	45.833	0.00	0.00	37.35	3.24
2100	6378	4.082679	AGCCGAGTATTATCCATCGAAGTC	60.083	45.833	0.00	0.00	37.35	3.01
2101	6379	3.827302	AGCCGAGTATTATCCATCGAAGT	59.173	43.478	0.00	0.00	37.35	3.01
2102	6380	4.442375	AGCCGAGTATTATCCATCGAAG	57.558	45.455	0.00	0.00	37.35	3.79
2104	6382	6.152154	TCAATAAGCCGAGTATTATCCATCGA	59.848	38.462	0.00	0.00	37.35	3.59
2105	6383	6.330278	TCAATAAGCCGAGTATTATCCATCG	58.670	40.000	0.00	0.00	35.02	3.84
2366	6959	1.755395	AATGCTCGCATGGGCATGT	60.755	52.632	2.98	0.00	46.70	3.21
2569	7182	2.610219	TGCAATGATTTTCGGTGTCG	57.390	45.000	0.00	0.00	37.82	4.35
2651	7265	7.995488	CCAAGAGTTGAGGGATGAAAAGTATAT	59.005	37.037	0.00	0.00	0.00	0.86
2666	7280	2.557920	AGACTTGGCCAAGAGTTGAG	57.442	50.000	44.50	23.12	40.79	3.02
2698	7312	4.993029	AGTTGTCGGGTTTCAAAATTGA	57.007	36.364	0.00	0.00	34.92	2.57
2708	7322	0.109153	GGGGTACAAGTTGTCGGGTT	59.891	55.000	12.82	0.00	0.00	4.11
2712	7326	1.202722	AGTTGGGGGTACAAGTTGTCG	60.203	52.381	12.82	0.00	30.06	4.35
2722	7336	2.026075	CCGGTTTCAATAGTTGGGGGTA	60.026	50.000	0.00	0.00	0.00	3.69
2748	7362	1.264295	ACCGAGACTAGGGACAAACC	58.736	55.000	6.56	0.00	38.08	3.27
2771	7385	0.395173	AGTCAGCACCAAAACCGGTT	60.395	50.000	15.86	15.86	37.07	4.44
2796	7410	1.541588	GAGTCAGCATGGGTCAAAACC	59.458	52.381	0.00	0.00	45.65	3.27
2817	7431	8.018520	ACTGATTTGAATTTGTTACGCGAATAA	58.981	29.630	15.93	4.69	31.17	1.40
2818	7432	7.480229	CACTGATTTGAATTTGTTACGCGAATA	59.520	33.333	15.93	0.00	31.17	1.75
2819	7433	6.305399	CACTGATTTGAATTTGTTACGCGAAT	59.695	34.615	15.93	0.00	32.69	3.34
2825	7439	8.579682	AAAGCTCACTGATTTGAATTTGTTAC	57.420	30.769	0.00	0.00	32.52	2.50
2888	7504	9.941325	TTCTAAATAAAGTACGTGTATTTGGGA	57.059	29.630	15.77	9.06	30.74	4.37
2898	7514	8.707938	AATAAGCGGTTCTAAATAAAGTACGT	57.292	30.769	1.59	0.00	0.00	3.57
2930	7546	9.356929	GCGAATTTTAAAAAGTTCACAAATCTG	57.643	29.630	4.44	0.00	35.21	2.90
2931	7547	9.092876	TGCGAATTTTAAAAAGTTCACAAATCT	57.907	25.926	4.44	0.00	35.21	2.40
2935	7551	9.522804	AGTATGCGAATTTTAAAAAGTTCACAA	57.477	25.926	4.44	0.00	35.21	3.33
2948	7564	9.061610	CGAACTTGAAAATAGTATGCGAATTTT	57.938	29.630	8.76	8.76	35.95	1.82
2955	7572	9.769093	AATTACACGAACTTGAAAATAGTATGC	57.231	29.630	0.00	0.00	0.00	3.14
2973	7590	6.932901	ATGCAGATTTGAAACAATTACACG	57.067	33.333	0.00	0.00	0.00	4.49
2983	7600	9.195411	GATTTGAAACAGTATGCAGATTTGAAA	57.805	29.630	0.00	0.00	42.53	2.69
2995	7612	5.946377	GGAGTTCTGGGATTTGAAACAGTAT	59.054	40.000	0.00	0.00	32.92	2.12
3072	7689	4.961438	ACAGTGCAGGAATTTGGAAAAT	57.039	36.364	0.00	0.00	0.00	1.82
3077	7695	5.200368	AGTTAAACAGTGCAGGAATTTGG	57.800	39.130	0.00	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.