AutoCloner

Multiple sequence alignment - TraesCS3A01G529000

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	TraesCS3A01G529000	chr3A	100.000	3389	0	0	1	3389	742783750	742787138	0.000000e+00	6259.0
1	TraesCS3A01G529000	chr3A	85.787	591	68	13	1	579	503096724	503096138	2.240000e-171	612.0
2	TraesCS3A01G529000	chr3B	94.436	3397	151	16	1	3389	819947212	819950578	0.000000e+00	5192.0
3	TraesCS3A01G529000	chr3D	96.018	2687	97	5	706	3389	609231944	609234623	0.000000e+00	4361.0
4	TraesCS3A01G529000	chr3D	85.667	600	67	13	1	585	296163634	296163039	6.220000e-172	614.0
5	TraesCS3A01G529000	chr3D	84.932	73	11	0	1391	1463	604879439	604879511	1.300000e-09	75.0
6	TraesCS3A01G529000	chr6A	86.993	592	63	9	1	579	57890783	57891373	0.000000e+00	654.0
7	TraesCS3A01G529000	chr7D	84.500	600	64	17	1	584	635696495	635697081	1.770000e-157	566.0
8	TraesCS3A01G529000	chr7D	82.753	603	75	20	4	582	524860053	524859456	8.390000e-141	510.0
9	TraesCS3A01G529000	chr7D	84.348	115	14	4	585	699	269033089	269033199	3.580000e-20	110.0
10	TraesCS3A01G529000	chr5B	82.696	601	86	12	1	586	71285882	71285285	5.010000e-143	518.0
11	TraesCS3A01G529000	chr5B	74.696	411	87	16	1980	2377	708453260	708452854	2.090000e-37	167.0
12	TraesCS3A01G529000	chr5B	86.957	138	18	0	2240	2377	708657405	708657268	4.530000e-34	156.0
13	TraesCS3A01G529000	chr5B	87.023	131	17	0	2246	2376	708674202	708674072	7.580000e-32	148.0
14	TraesCS3A01G529000	chr7A	81.544	596	85	17	1	585	668568572	668567991	5.120000e-128	468.0
15	TraesCS3A01G529000	chr7A	77.727	440	84	11	1980	2413	91497554	91497985	1.210000e-64	257.0
16	TraesCS3A01G529000	chr1D	86.806	432	42	10	1	427	430421502	430421081	5.120000e-128	468.0
17	TraesCS3A01G529000	chr5A	76.637	672	109	39	1027	1677	605249005	605249649	9.070000e-86	327.0
18	TraesCS3A01G529000	chr5D	74.772	769	133	46	1027	1771	483810031	483810762	4.280000e-74	289.0
19	TraesCS3A01G529000	chr5D	74.704	506	99	21	1098	1600	564788511	564788990	7.420000e-47	198.0
20	TraesCS3A01G529000	chr5D	85.535	159	21	2	1121	1278	564752072	564751915	7.520000e-37	165.0
21	TraesCS3A01G529000	chr5D	87.770	139	15	2	1121	1258	564748973	564748836	9.730000e-36	161.0
22	TraesCS3A01G529000	chr5D	73.067	401	97	10	1980	2376	564758447	564758054	7.630000e-27	132.0
23	TraesCS3A01G529000	chr5D	90.000	80	8	0	2298	2377	564750483	564750404	1.660000e-18	104.0
24	TraesCS3A01G529000	chr2A	79.437	355	49	13	235	579	693892350	693892690	2.630000e-56	230.0
25	TraesCS3A01G529000	chr2A	80.000	120	16	8	583	699	47899915	47900029	7.790000e-12	82.4
26	TraesCS3A01G529000	chr2A	78.814	118	20	5	584	699	47901294	47901180	1.300000e-09	75.0
27	TraesCS3A01G529000	chr2A	85.000	60	6	1	528	584	276257608	276257549	1.310000e-04	58.4
28	TraesCS3A01G529000	chr4A	88.732	142	12	3	1120	1259	604667651	604667790	1.620000e-38	171.0
29	TraesCS3A01G529000	chr2D	88.793	116	10	3	585	699	560986248	560986361	4.560000e-29	139.0
30	TraesCS3A01G529000	chr2D	94.595	37	1	1	583	618	314041307	314041343	4.720000e-04	56.5

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	TraesCS3A01G529000	chr3A	742783750	742787138	3388	False	6259	6259	100.000	1	3389	1	chr3A.!!$F1	3388
1	TraesCS3A01G529000	chr3A	503096138	503096724	586	True	612	612	85.787	1	579	1	chr3A.!!$R1	578
2	TraesCS3A01G529000	chr3B	819947212	819950578	3366	False	5192	5192	94.436	1	3389	1	chr3B.!!$F1	3388
3	TraesCS3A01G529000	chr3D	609231944	609234623	2679	False	4361	4361	96.018	706	3389	1	chr3D.!!$F2	2683
4	TraesCS3A01G529000	chr3D	296163039	296163634	595	True	614	614	85.667	1	585	1	chr3D.!!$R1	584
5	TraesCS3A01G529000	chr6A	57890783	57891373	590	False	654	654	86.993	1	579	1	chr6A.!!$F1	578
6	TraesCS3A01G529000	chr7D	635696495	635697081	586	False	566	566	84.500	1	584	1	chr7D.!!$F2	583
7	TraesCS3A01G529000	chr7D	524859456	524860053	597	True	510	510	82.753	4	582	1	chr7D.!!$R1	578
8	TraesCS3A01G529000	chr5B	71285285	71285882	597	True	518	518	82.696	1	586	1	chr5B.!!$R1	585
9	TraesCS3A01G529000	chr7A	668567991	668568572	581	True	468	468	81.544	1	585	1	chr7A.!!$R1	584
10	TraesCS3A01G529000	chr5A	605249005	605249649	644	False	327	327	76.637	1027	1677	1	chr5A.!!$F1	650
11	TraesCS3A01G529000	chr5D	483810031	483810762	731	False	289	289	74.772	1027	1771	1	chr5D.!!$F1	744

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
795	833	1.202769	TAGTTTAGTTGGGCCCGGCT	61.203	55.0	19.37	19.7	0.0	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2748	2824	0.036875	GCACTCCACCCTTTAGCAGT	59.963	55.0	0.0	0.0	0.0	4.4	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
157	158	3.164011	CGACAACGACGACGAGGC	61.164	66.667	15.32	7.26	42.66	4.70
299	310	2.510906	GGCATGTAGATGGCGGGT	59.489	61.111	10.76	0.00	44.46	5.28
346	367	3.242870	CGTAGTTTGGCGTAGTAGTAGGG	60.243	52.174	0.00	0.00	0.00	3.53
347	368	2.812658	AGTTTGGCGTAGTAGTAGGGT	58.187	47.619	0.00	0.00	0.00	4.34
355	376	4.881850	GGCGTAGTAGTAGGGTGTAGTTTA	59.118	45.833	0.00	0.00	0.00	2.01
579	612	2.892425	CGAACGGCTGGAGATGCC	60.892	66.667	0.00	0.00	46.42	4.40
594	627	4.447290	GAGATGCCCTAAGAAAGAAGTCC	58.553	47.826	0.00	0.00	0.00	3.85
637	670	2.846827	CCAGAGAGACAAATAACCCCCT	59.153	50.000	0.00	0.00	0.00	4.79
683	716	3.827876	GACCCCAAAATCCTTAAAACCGA	59.172	43.478	0.00	0.00	0.00	4.69
685	718	4.083565	CCCCAAAATCCTTAAAACCGAGA	58.916	43.478	0.00	0.00	0.00	4.04
795	833	1.202769	TAGTTTAGTTGGGCCCGGCT	61.203	55.000	19.37	19.70	0.00	5.52
874	913	3.844804	GGATCGGATCCCTAGGGTAAATT	59.155	47.826	27.58	9.45	43.88	1.82
985	1027	1.972660	ATCCTCCCTACCGCTGCAAC	61.973	60.000	0.00	0.00	0.00	4.17
1003	1046	1.459450	ACCCAAATCGACGGAAATGG	58.541	50.000	0.00	0.00	33.81	3.16
1366	1439	4.394712	GGGTGTACCTGCGCTGCT	62.395	66.667	9.73	0.00	35.85	4.24
1369	1442	4.312941	TGTACCTGCGCTGCTGCA	62.313	61.111	16.29	15.89	43.95	4.41
1602	1678	2.417933	CTCGCTCAAGAAATTGGTCCTG	59.582	50.000	0.00	0.00	0.00	3.86
1781	1857	0.533531	CAGCTATCCATTGGCTGCGA	60.534	55.000	0.00	0.00	45.04	5.10
1806	1882	0.734942	CCACAACCGCGTACGAATCT	60.735	55.000	21.65	0.00	43.93	2.40
1878	1954	1.349688	GGGGTCACTGTATGTTCCACA	59.650	52.381	0.00	0.00	30.77	4.17
2005	2081	1.638529	ACCTGAGGACCTTGTCTCTG	58.361	55.000	4.99	0.00	32.47	3.35
2092	2168	0.249489	AGAAGCTCACTTTGCGTCGT	60.249	50.000	0.00	0.00	42.20	4.34
2238	2314	1.210478	CACCTTGATGACCCTTCCGAT	59.790	52.381	0.00	0.00	0.00	4.18
2336	2412	1.981256	TTGGTCAAGTTTCTGGAGGC	58.019	50.000	0.00	0.00	0.00	4.70
2383	2459	6.085555	ACAAGATCGAACTCACTAAAGTCA	57.914	37.500	0.00	0.00	0.00	3.41
2439	2515	7.416664	CGTGGTGAGGATAATTCATTTTGGAAT	60.417	37.037	0.00	0.00	39.11	3.01
2510	2586	1.099879	GGGACCATCTGAGCATGTGC	61.100	60.000	0.00	0.00	42.49	4.57
2537	2613	8.436200	GGCTACACGAAATTCATACTCATATTC	58.564	37.037	0.00	0.00	0.00	1.75
2647	2723	6.869206	TTGAGAAATAGTGGCTTACTAGGT	57.131	37.500	0.00	0.00	44.69	3.08
2749	2825	7.923414	ACAAGGTGATATTGTTTAGGAAGAC	57.077	36.000	0.00	0.00	37.61	3.01
2824	2900	6.164176	AGTTTTTAACGGAGGAGTATGACAG	58.836	40.000	0.00	0.00	36.23	3.51
2931	3007	9.807921	AGGTTTGGAATAAGAAAGAGATTACAA	57.192	29.630	0.00	0.00	32.72	2.41
2946	3022	6.041523	AGAGATTACAACTAAGCAGAGATCCC	59.958	42.308	0.00	0.00	0.00	3.85
2980	3056	2.705658	TCATGGAAGGCGATAGGAACAT	59.294	45.455	0.00	0.00	0.00	2.71
3064	3140	6.645884	TGGTCCTAATAAACCAGGTAATGT	57.354	37.500	0.00	0.00	40.60	2.71
3079	3155	5.065731	CAGGTAATGTGGAGATGAAGAAAGC	59.934	44.000	0.00	0.00	0.00	3.51
3244	3320	7.701539	ACCAAGCATGTTATCTTTCATACAA	57.298	32.000	0.00	0.00	0.00	2.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
233	234	2.071526	GTCGTCGTCGTTGTCGTCC	61.072	63.158	1.33	0.00	38.33	4.79
456	482	0.813610	CCAAGTCGCCGCCAATATCA	60.814	55.000	0.00	0.00	0.00	2.15
579	612	7.371159	GGTGAAAAATGGACTTCTTTCTTAGG	58.629	38.462	0.00	0.00	0.00	2.69
594	627	3.747529	GCCACATTTGAGGGTGAAAAATG	59.252	43.478	5.95	5.95	43.64	2.32
637	670	7.277539	GTCAAAATCACACCAAATTGAAGTTCA	59.722	33.333	0.08	0.08	0.00	3.18
683	716	8.956446	TGAAAGATTTAGGGGAAAGATTTTCT	57.044	30.769	2.03	0.00	31.93	2.52
795	833	0.981183	ACGTATTGGGTTCAGCTGGA	59.019	50.000	15.13	0.46	0.00	3.86
869	907	3.699038	CGGAATGGAAGCAAGGGAATTTA	59.301	43.478	0.00	0.00	0.00	1.40
874	913	0.035439	GACGGAATGGAAGCAAGGGA	60.035	55.000	0.00	0.00	0.00	4.20
985	1027	1.400494	GACCATTTCCGTCGATTTGGG	59.600	52.381	0.00	0.00	0.00	4.12
1017	1060	3.948719	GCGTCAGTGGGGGTGGAA	61.949	66.667	0.00	0.00	0.00	3.53
1146	1219	1.142748	CAGGATGTCGTGGAGGAGC	59.857	63.158	0.00	0.00	0.00	4.70
1267	1340	4.711949	AGGCTGCTTGGCGGTGAG	62.712	66.667	0.00	0.00	46.88	3.51
1366	1439	3.399181	GGACCACCCGAGGATGCA	61.399	66.667	0.00	0.00	0.00	3.96
1602	1678	1.412710	TCCTCATCATAGTTGCCGTCC	59.587	52.381	0.00	0.00	0.00	4.79
1801	1877	0.729690	GCGGCAAGAAGACCAGATTC	59.270	55.000	0.00	0.00	0.00	2.52
1806	1882	1.188219	AGAGAGCGGCAAGAAGACCA	61.188	55.000	1.45	0.00	0.00	4.02
1878	1954	6.267014	CAGGATAAAATGGATGCCAAGAAGAT	59.733	38.462	0.00	0.00	36.95	2.40
2005	2081	3.306166	CGTTGGAAATATGACACTCGTCC	59.694	47.826	0.00	0.00	41.85	4.79
2024	2100	2.354805	GCTCCAGACCCATAAAGTCGTT	60.355	50.000	0.00	0.00	39.31	3.85
2224	2300	1.123928	AGGTCATCGGAAGGGTCATC	58.876	55.000	0.00	0.00	0.00	2.92
2238	2314	2.862541	CACTTGAAATCCACCAGGTCA	58.137	47.619	0.00	0.00	35.89	4.02
2336	2412	0.256752	TGGCAGATTCCTCCACATGG	59.743	55.000	0.00	0.00	0.00	3.66
2383	2459	1.079681	TCACGCGGTTCGGCTAATT	60.080	52.632	12.47	0.00	43.86	1.40
2510	2586	4.109766	TGAGTATGAATTTCGTGTAGCCG	58.890	43.478	1.25	0.00	0.00	5.52
2515	2591	8.420374	AACGAATATGAGTATGAATTTCGTGT	57.580	30.769	8.34	0.00	0.00	4.49
2663	2739	9.710818	AGACCAATCCTTAAATACTACTCTGTA	57.289	33.333	0.00	0.00	0.00	2.74
2664	2740	8.611051	AGACCAATCCTTAAATACTACTCTGT	57.389	34.615	0.00	0.00	0.00	3.41
2665	2741	9.968870	GTAGACCAATCCTTAAATACTACTCTG	57.031	37.037	0.00	0.00	0.00	3.35
2666	2742	9.939424	AGTAGACCAATCCTTAAATACTACTCT	57.061	33.333	0.00	0.00	34.88	3.24
2748	2824	0.036875	GCACTCCACCCTTTAGCAGT	59.963	55.000	0.00	0.00	0.00	4.40
2749	2825	0.678048	GGCACTCCACCCTTTAGCAG	60.678	60.000	0.00	0.00	0.00	4.24
2824	2900	7.148086	TGCTAGACACAATTTGGATATCAAACC	60.148	37.037	4.83	0.00	46.72	3.27
2918	2994	8.940768	ATCTCTGCTTAGTTGTAATCTCTTTC	57.059	34.615	0.00	0.00	0.00	2.62
2931	3007	2.856760	TCCAGGGATCTCTGCTTAGT	57.143	50.000	17.80	0.00	33.64	2.24
2935	3011	2.323999	CCTATCCAGGGATCTCTGCT	57.676	55.000	17.80	8.97	38.41	4.24
2946	3022	3.008813	CCTTCCATGATGTCCCTATCCAG	59.991	52.174	0.00	0.00	0.00	3.86
3064	3140	2.816087	GCAACAGCTTTCTTCATCTCCA	59.184	45.455	0.00	0.00	0.00	3.86
3079	3155	7.369803	ACATCTTTGTAGTAATCTGCAACAG	57.630	36.000	0.00	0.00	43.67	3.16
3225	3301	8.668353	TCAGAGTTTGTATGAAAGATAACATGC	58.332	33.333	0.00	0.00	0.00	4.06
3244	3320	0.038744	CCAGGGGCACAATCAGAGTT	59.961	55.000	0.00	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.