AutoCloner

Multiple sequence alignment - TraesCS2D01G361500

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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	TraesCS2D01G361500	chr2D	100.000	3176	0	0	1	3176	466686745	466683570	0.000000e+00	5866
1	TraesCS2D01G361500	chr2B	92.533	2491	141	17	715	3176	545272198	545269724	0.000000e+00	3528
2	TraesCS2D01G361500	chr2A	91.501	2412	126	24	740	3105	607831996	607829618	0.000000e+00	3245
3	TraesCS2D01G361500	chr4D	96.084	715	26	1	1	713	505190932	505190218	0.000000e+00	1164
4	TraesCS2D01G361500	chr6A	96.197	710	27	0	1	710	33288749	33289458	0.000000e+00	1162
5	TraesCS2D01G361500	chr6D	94.191	723	34	6	1	717	16681258	16681978	0.000000e+00	1096
6	TraesCS2D01G361500	chr7D	92.629	719	49	4	1	717	26613142	26612426	0.000000e+00	1031
7	TraesCS2D01G361500	chr3A	92.340	718	53	2	1	716	67316577	67315860	0.000000e+00	1020
8	TraesCS2D01G361500	chr3A	91.678	721	56	3	1	720	366636101	366635384	0.000000e+00	996
9	TraesCS2D01G361500	chr5D	91.049	715	61	3	1	713	430539671	430538958	0.000000e+00	963
10	TraesCS2D01G361500	chr4A	91.434	502	41	2	212	712	5550708	5551208	0.000000e+00	688
11	TraesCS2D01G361500	chr4A	92.558	215	16	0	1	215	5550454	5550668	3.080000e-80	309
12	TraesCS2D01G361500	chr3D	92.781	471	29	5	238	704	476995730	476995261	0.000000e+00	676
13	TraesCS2D01G361500	chr3D	93.388	242	16	0	1	242	477006383	477006142	3.010000e-95	359
14	TraesCS2D01G361500	chr1D	88.103	580	40	16	2625	3176	211697983	211698561	0.000000e+00	662
15	TraesCS2D01G361500	chr3B	86.027	365	23	16	2840	3176	486885173	486884809	1.800000e-97	366
16	TraesCS2D01G361500	chr3B	90.521	211	20	0	2625	2835	486895421	486895211	2.410000e-71	279

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	TraesCS2D01G361500	chr2D	466683570	466686745	3175	True	5866.0	5866	100.000	1	3176	1	chr2D.!!$R1	3175
1	TraesCS2D01G361500	chr2B	545269724	545272198	2474	True	3528.0	3528	92.533	715	3176	1	chr2B.!!$R1	2461
2	TraesCS2D01G361500	chr2A	607829618	607831996	2378	True	3245.0	3245	91.501	740	3105	1	chr2A.!!$R1	2365
3	TraesCS2D01G361500	chr4D	505190218	505190932	714	True	1164.0	1164	96.084	1	713	1	chr4D.!!$R1	712
4	TraesCS2D01G361500	chr6A	33288749	33289458	709	False	1162.0	1162	96.197	1	710	1	chr6A.!!$F1	709
5	TraesCS2D01G361500	chr6D	16681258	16681978	720	False	1096.0	1096	94.191	1	717	1	chr6D.!!$F1	716
6	TraesCS2D01G361500	chr7D	26612426	26613142	716	True	1031.0	1031	92.629	1	717	1	chr7D.!!$R1	716
7	TraesCS2D01G361500	chr3A	67315860	67316577	717	True	1020.0	1020	92.340	1	716	1	chr3A.!!$R1	715
8	TraesCS2D01G361500	chr3A	366635384	366636101	717	True	996.0	996	91.678	1	720	1	chr3A.!!$R2	719
9	TraesCS2D01G361500	chr5D	430538958	430539671	713	True	963.0	963	91.049	1	713	1	chr5D.!!$R1	712
10	TraesCS2D01G361500	chr4A	5550454	5551208	754	False	498.5	688	91.996	1	712	2	chr4A.!!$F1	711
11	TraesCS2D01G361500	chr1D	211697983	211698561	578	False	662.0	662	88.103	2625	3176	1	chr1D.!!$F1	551

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
792	847	0.741221	GGCAACGAGATTTCTCCGCT	60.741	55.0	2.08	0.0	39.79	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2188	2268	0.179037	TCTGCAGCTCAGTTTGTGCT	60.179	50.0	9.47	0.2	46.71	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
33	34	9.845740	TCTATTTAGCATTAAAGTTGCCTCATA	57.154	29.630	0.00	0.00	41.06	2.15
249	294	7.505258	TGATGCTTAGTTGCCTACATACATTA	58.495	34.615	0.00	0.00	0.00	1.90
317	366	9.865321	TTGATAGGTAAATTCACTAGTACACAC	57.135	33.333	0.00	0.00	0.00	3.82
321	370	8.284945	AGGTAAATTCACTAGTACACACGATA	57.715	34.615	0.00	0.00	0.00	2.92
758	812	6.761242	GGCGGATGCTTTCCTTTTAAATTAAT	59.239	34.615	4.99	0.00	42.99	1.40
759	813	7.279981	GGCGGATGCTTTCCTTTTAAATTAATT	59.720	33.333	0.00	0.00	42.99	1.40
786	840	7.637709	AAAATAAAACTGGCAACGAGATTTC	57.362	32.000	0.00	0.00	42.51	2.17
792	847	0.741221	GGCAACGAGATTTCTCCGCT	60.741	55.000	2.08	0.00	39.79	5.52
796	851	3.242123	GCAACGAGATTTCTCCGCTAAAG	60.242	47.826	2.08	0.00	39.79	1.85
800	855	4.201970	ACGAGATTTCTCCGCTAAAGAGAG	60.202	45.833	2.08	0.00	41.26	3.20
810	865	6.732896	TCCGCTAAAGAGAGGAGATTTATT	57.267	37.500	0.00	0.00	45.80	1.40
812	867	6.551601	TCCGCTAAAGAGAGGAGATTTATTCT	59.448	38.462	0.00	0.00	45.80	2.40
817	872	4.942852	AGAGAGGAGATTTATTCTGCGTG	58.057	43.478	0.00	0.00	46.72	5.34
858	913	4.562757	GGATTCCGTTCCGATCCATGATTA	60.563	45.833	0.00	0.00	39.30	1.75
884	939	3.432588	CGCTCGACCTCCACGTCT	61.433	66.667	0.00	0.00	0.00	4.18
1386	1466	0.878961	GGTTCTTCTTCGTGTGCCGT	60.879	55.000	0.00	0.00	37.94	5.68
1770	1850	1.447838	CAGAATGTACGCCACGCCT	60.448	57.895	0.00	0.00	0.00	5.52
1896	1976	0.387929	AGAACGACGAGGACAAAGCA	59.612	50.000	0.00	0.00	0.00	3.91
2158	2238	5.296813	GTACAAGCTGTACCTGAAAATGG	57.703	43.478	12.68	0.00	45.52	3.16
2159	2239	2.558359	ACAAGCTGTACCTGAAAATGGC	59.442	45.455	0.00	0.00	0.00	4.40
2178	2258	2.125793	GGTCACCGGCGGTAGAAC	60.126	66.667	33.65	27.57	32.11	3.01
2179	2259	2.505557	GTCACCGGCGGTAGAACG	60.506	66.667	33.65	19.38	32.11	3.95
2189	2269	2.205307	CGGTAGAACGCCTCCTTTAG	57.795	55.000	0.00	0.00	0.00	1.85
2190	2270	1.801765	CGGTAGAACGCCTCCTTTAGC	60.802	57.143	0.00	0.00	0.00	3.09
2191	2271	1.206371	GGTAGAACGCCTCCTTTAGCA	59.794	52.381	0.00	0.00	0.00	3.49
2196	2278	1.235724	ACGCCTCCTTTAGCACAAAC	58.764	50.000	0.00	0.00	0.00	2.93
2200	2282	2.485814	GCCTCCTTTAGCACAAACTGAG	59.514	50.000	0.00	0.00	0.00	3.35
2237	2319	4.054780	TGCACGACTTAGACTGAAACTT	57.945	40.909	0.00	0.00	0.00	2.66
2346	2431	4.535781	TGGGGTTTGATGATATCACCAAG	58.464	43.478	12.32	0.00	39.39	3.61
2421	2518	1.035139	CAACAAGCCCTGAACTTGCT	58.965	50.000	3.52	0.00	46.81	3.91
2431	2530	3.191371	CCCTGAACTTGCTAAACATCCAC	59.809	47.826	0.00	0.00	0.00	4.02
2489	2588	5.631929	TCATGTAACACACTAACATGTCGAC	59.368	40.000	9.11	9.11	46.73	4.20
2516	2615	2.086054	ACTCGCAAACAGAGCTAAGG	57.914	50.000	0.00	0.00	39.23	2.69
2603	2702	0.954452	CCTCCCTTGTTCAGTGCAAC	59.046	55.000	0.00	0.00	0.00	4.17
2622	2721	3.883830	ACAGTATCTGCCACAGAAGAG	57.116	47.619	0.74	0.00	44.04	2.85
2900	3002	7.017254	TGGGTTAGTTCAATAAGAGTTTCTCCT	59.983	37.037	0.00	0.00	0.00	3.69
2946	3048	2.031069	GCAGAGCCAATACATGATGCAG	60.031	50.000	0.00	0.00	32.79	4.41
3007	3137	4.305769	AGATGAGTAGTAGCGTAGTACGG	58.694	47.826	23.29	6.33	42.82	4.02
3008	3138	2.826428	TGAGTAGTAGCGTAGTACGGG	58.174	52.381	23.29	0.00	42.82	5.28
3036	3169	7.040686	GGGAGCAGTCTAAAGAAACATGTTTTA	60.041	37.037	24.02	12.23	32.11	1.52
3061	3194	8.709386	ACTCATAGCATGTAAACACTAAAGAG	57.291	34.615	0.00	1.80	32.00	2.85
3145	3283	2.229792	TCTTGCGACCTCAATTGCTTT	58.770	42.857	0.00	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
249	294	8.628280	CATAAAAACCATGTGGGACAAAATTTT	58.372	29.630	3.77	0.00	44.16	1.82
317	366	3.997021	ACAGAAGCAACTTCCTTGTATCG	59.003	43.478	3.77	0.00	40.98	2.92
321	370	5.193679	ACTAAACAGAAGCAACTTCCTTGT	58.806	37.500	3.77	0.79	40.98	3.16
502	554	7.225538	GTCATCTCACATTATTCCGTCTCATTT	59.774	37.037	0.00	0.00	0.00	2.32
676	730	1.816679	CAGCTGCGCTATCTGGCAA	60.817	57.895	9.73	0.00	36.40	4.52
677	731	2.202974	CAGCTGCGCTATCTGGCA	60.203	61.111	9.73	0.00	36.40	4.92
727	781	0.533085	GGAAAGCATCCGCCCTCTAC	60.533	60.000	0.00	0.00	38.79	2.59
765	819	5.123979	GGAGAAATCTCGTTGCCAGTTTTAT	59.876	40.000	4.45	0.00	43.76	1.40
766	820	4.454504	GGAGAAATCTCGTTGCCAGTTTTA	59.545	41.667	4.45	0.00	43.76	1.52
792	847	6.980978	CACGCAGAATAAATCTCCTCTCTTTA	59.019	38.462	0.00	0.00	35.73	1.85
796	851	3.492756	GCACGCAGAATAAATCTCCTCTC	59.507	47.826	0.00	0.00	35.73	3.20
800	855	2.286654	GCTGCACGCAGAATAAATCTCC	60.287	50.000	22.81	0.00	46.30	3.71
809	864	0.953471	AAATACGGCTGCACGCAGAA	60.953	50.000	22.81	4.91	46.30	3.02
810	865	0.953471	AAAATACGGCTGCACGCAGA	60.953	50.000	22.81	1.77	46.30	4.26
812	867	1.208870	CAAAATACGGCTGCACGCA	59.791	52.632	0.50	0.00	41.67	5.24
817	872	0.523335	CCGAAGCAAAATACGGCTGC	60.523	55.000	0.00	0.00	40.93	5.25
906	961	4.452733	GTTCAGGTCCCCGAGGCG	62.453	72.222	0.00	0.00	0.00	5.52
1524	1604	2.650116	CCACTCGGTCTCCCTGGTG	61.650	68.421	0.00	0.00	33.49	4.17
1668	1748	3.458163	ATGTCCGGACGGTGCGAT	61.458	61.111	28.70	13.28	30.86	4.58
1680	1760	0.947244	CCTGCGGCTTATTCATGTCC	59.053	55.000	0.00	0.00	0.00	4.02
1947	2027	2.612567	GCCATTGCCGTTCACGACA	61.613	57.895	0.00	0.00	43.02	4.35
1988	2068	1.706443	GTCTTCCCGGTACAAGAACG	58.294	55.000	0.00	0.00	30.38	3.95
2037	2117	0.833287	ACTCCTCCATCCACCATTCG	59.167	55.000	0.00	0.00	0.00	3.34
2040	2120	1.414158	CGTACTCCTCCATCCACCAT	58.586	55.000	0.00	0.00	0.00	3.55
2097	2177	1.595093	CGTCCATTGTTGCCTTCCCC	61.595	60.000	0.00	0.00	0.00	4.81
2099	2179	1.200020	CTTCGTCCATTGTTGCCTTCC	59.800	52.381	0.00	0.00	0.00	3.46
2107	2187	1.202582	CTCCTCGTCTTCGTCCATTGT	59.797	52.381	0.00	0.00	38.33	2.71
2158	2238	4.814294	CTACCGCCGGTGACCAGC	62.814	72.222	21.20	0.00	36.19	4.85
2159	2239	2.642254	TTCTACCGCCGGTGACCAG	61.642	63.158	21.20	8.41	36.19	4.00
2178	2258	1.197721	CAGTTTGTGCTAAAGGAGGCG	59.802	52.381	0.00	0.00	0.00	5.52
2179	2259	2.485814	CTCAGTTTGTGCTAAAGGAGGC	59.514	50.000	0.00	0.00	0.00	4.70
2181	2261	3.188048	CAGCTCAGTTTGTGCTAAAGGAG	59.812	47.826	5.44	9.34	44.32	3.69
2182	2262	3.141398	CAGCTCAGTTTGTGCTAAAGGA	58.859	45.455	5.44	0.00	44.32	3.36
2183	2263	2.351157	GCAGCTCAGTTTGTGCTAAAGG	60.351	50.000	5.44	0.00	44.32	3.11
2184	2264	2.291465	TGCAGCTCAGTTTGTGCTAAAG	59.709	45.455	5.44	0.00	44.32	1.85
2185	2265	2.291465	CTGCAGCTCAGTTTGTGCTAAA	59.709	45.455	0.00	0.00	44.32	1.85
2186	2266	1.875514	CTGCAGCTCAGTTTGTGCTAA	59.124	47.619	0.00	0.00	44.32	3.09
2188	2268	0.179037	TCTGCAGCTCAGTTTGTGCT	60.179	50.000	9.47	0.20	46.71	4.40
2189	2269	0.879765	ATCTGCAGCTCAGTTTGTGC	59.120	50.000	9.47	0.00	43.32	4.57
2190	2270	2.812591	AGAATCTGCAGCTCAGTTTGTG	59.187	45.455	9.47	0.00	43.32	3.33
2191	2271	2.812591	CAGAATCTGCAGCTCAGTTTGT	59.187	45.455	9.47	7.21	43.32	2.83
2196	2278	0.392595	TGCCAGAATCTGCAGCTCAG	60.393	55.000	9.47	5.01	44.21	3.35
2200	2282	1.065928	GCATGCCAGAATCTGCAGC	59.934	57.895	9.47	4.65	34.77	5.25
2213	2295	1.996292	TCAGTCTAAGTCGTGCATGC	58.004	50.000	11.82	11.82	0.00	4.06
2237	2319	4.357142	CGTAGACGCTTAAGGCAGAATTA	58.643	43.478	4.29	0.00	41.91	1.40
2304	2387	5.009210	CCCCAAATTACTGTCGTTCTTTTGA	59.991	40.000	0.00	0.00	0.00	2.69
2421	2518	7.608376	TCATGAAATAACGAAGGTGGATGTTTA	59.392	33.333	0.00	0.00	0.00	2.01
2431	2530	3.063452	CCCGTGTCATGAAATAACGAAGG	59.937	47.826	17.91	10.65	0.00	3.46
2516	2615	0.313043	TTCGAAGACCACCGTCACTC	59.687	55.000	0.00	0.00	41.87	3.51
2576	2675	0.693049	GAACAAGGGAGGGAAGCTGA	59.307	55.000	0.00	0.00	0.00	4.26
2603	2702	3.883830	ACTCTTCTGTGGCAGATACTG	57.116	47.619	0.00	0.00	40.39	2.74
2900	3002	1.412710	GGATGATCGGCACAGGTCTTA	59.587	52.381	0.00	0.00	0.00	2.10
2946	3048	8.034058	ACATCAAGCATGTTCTAAGTTCTAAC	57.966	34.615	0.00	0.00	43.89	2.34
3007	3137	3.075148	GTTTCTTTAGACTGCTCCCACC	58.925	50.000	0.00	0.00	0.00	4.61
3008	3138	3.740115	TGTTTCTTTAGACTGCTCCCAC	58.260	45.455	0.00	0.00	0.00	4.61
3036	3169	8.531982	TCTCTTTAGTGTTTACATGCTATGAGT	58.468	33.333	0.00	0.00	0.00	3.41
3057	3190	7.690952	ACGTCAGATTAGTTACTCTTCTCTT	57.309	36.000	0.00	0.00	0.00	2.85
3058	3191	7.608761	AGAACGTCAGATTAGTTACTCTTCTCT	59.391	37.037	0.00	0.00	0.00	3.10
3059	3192	7.694784	CAGAACGTCAGATTAGTTACTCTTCTC	59.305	40.741	0.00	0.00	0.00	2.87
3060	3193	7.390996	TCAGAACGTCAGATTAGTTACTCTTCT	59.609	37.037	0.00	0.00	0.00	2.85
3061	3194	7.528307	TCAGAACGTCAGATTAGTTACTCTTC	58.472	38.462	0.00	0.00	0.00	2.87
3079	3217	7.862873	TGTAATCTAAGTGCTATCATCAGAACG	59.137	37.037	0.00	0.00	0.00	3.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.