AutoCloner

Multiple sequence alignment - TraesCS5D01G227200

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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	TraesCS5D01G227200	chr5D	100.000	2930	0	0	1	2930	335053979	335051050	0.000000e+00	5411.0
1	TraesCS5D01G227200	chr5D	79.734	301	31	15	1	276	16601147	16601442	1.070000e-44	191.0
2	TraesCS5D01G227200	chr5D	79.216	255	33	9	272	510	16614462	16614712	3.020000e-35	159.0
3	TraesCS5D01G227200	chr5D	81.132	159	24	4	1	158	228391486	228391639	3.970000e-24	122.0
4	TraesCS5D01G227200	chr5D	92.208	77	2	2	761	837	421908366	421908294	3.990000e-19	106.0
5	TraesCS5D01G227200	chr5A	93.320	1961	85	16	978	2930	436333551	436331629	0.000000e+00	2854.0
6	TraesCS5D01G227200	chr5A	89.850	867	48	8	1	837	262438197	262437341	0.000000e+00	1077.0
7	TraesCS5D01G227200	chr5A	78.782	542	76	15	1	511	254926099	254925566	7.830000e-86	327.0
8	TraesCS5D01G227200	chr5A	87.912	91	8	2	2741	2828	436331726	436331816	1.440000e-18	104.0
9	TraesCS5D01G227200	chr5B	96.032	1134	35	6	877	2009	391830847	391829723	0.000000e+00	1836.0
10	TraesCS5D01G227200	chr5B	91.593	797	32	10	1	768	446615283	446616073	0.000000e+00	1068.0
11	TraesCS5D01G227200	chr5B	83.742	449	30	21	2027	2467	391829734	391829321	4.580000e-103	385.0
12	TraesCS5D01G227200	chr5B	92.045	88	7	0	2741	2828	364139504	364139417	1.100000e-24	124.0
13	TraesCS5D01G227200	chr6A	89.836	915	46	6	1	878	567968188	567969092	0.000000e+00	1131.0
14	TraesCS5D01G227200	chr1A	88.828	546	39	10	1	544	278379325	278378800	0.000000e+00	651.0
15	TraesCS5D01G227200	chr2B	95.092	163	4	2	1	159	767911686	767911848	1.350000e-63	254.0
16	TraesCS5D01G227200	chr7B	94.479	163	5	2	1	159	729811840	729812002	6.270000e-62	248.0
17	TraesCS5D01G227200	chr7B	93.865	163	6	2	1	159	729763502	729763664	2.920000e-60	243.0
18	TraesCS5D01G227200	chr4B	90.741	108	6	3	2826	2930	512558912	512559018	1.090000e-29	141.0
19	TraesCS5D01G227200	chr4D	90.741	108	5	3	2826	2930	74079370	74079475	3.940000e-29	139.0
20	TraesCS5D01G227200	chr3D	89.815	108	6	3	2826	2930	288550592	288550487	1.830000e-27	134.0
21	TraesCS5D01G227200	chr3D	91.860	86	7	0	2742	2827	381989073	381989158	1.430000e-23	121.0
22	TraesCS5D01G227200	chr3D	90.805	87	8	0	2741	2827	429306328	429306242	1.840000e-22	117.0
23	TraesCS5D01G227200	chr3D	86.667	105	9	5	734	837	358330908	358331008	8.580000e-21	111.0
24	TraesCS5D01G227200	chr3D	90.789	76	3	2	762	837	405513406	405513335	6.680000e-17	99.0
25	TraesCS5D01G227200	chr3B	89.815	108	6	3	2826	2930	381481608	381481503	1.830000e-27	134.0
26	TraesCS5D01G227200	chr3B	88.889	108	8	2	2826	2930	447622327	447622221	2.370000e-26	130.0
27	TraesCS5D01G227200	chr3B	85.393	89	11	2	2742	2830	59446050	59445964	1.120000e-14	91.6
28	TraesCS5D01G227200	chr2D	89.815	108	5	3	2826	2930	14772025	14772129	1.830000e-27	134.0
29	TraesCS5D01G227200	chr3A	88.889	108	9	1	2826	2930	310692069	310691962	2.370000e-26	130.0
30	TraesCS5D01G227200	chr3A	81.690	142	19	6	727	862	644944417	644944557	8.580000e-21	111.0
31	TraesCS5D01G227200	chr3A	91.139	79	3	2	759	837	520491173	520491247	1.440000e-18	104.0
32	TraesCS5D01G227200	chr7D	88.889	108	7	3	2826	2930	436961929	436961824	8.520000e-26	128.0
33	TraesCS5D01G227200	chr1D	91.954	87	7	0	2742	2828	120537616	120537702	3.970000e-24	122.0
34	TraesCS5D01G227200	chr1D	85.714	98	10	4	2737	2830	287466115	287466212	1.860000e-17	100.0
35	TraesCS5D01G227200	chr6B	89.655	87	8	1	2741	2827	232168209	232168124	3.090000e-20	110.0
36	TraesCS5D01G227200	chr6D	92.208	77	2	2	761	837	291665498	291665426	3.990000e-19	106.0
37	TraesCS5D01G227200	chr7A	84.404	109	12	3	763	866	483279981	483279873	5.170000e-18	102.0
38	TraesCS5D01G227200	chr4A	83.784	111	14	2	727	837	298189787	298189893	5.170000e-18	102.0
39	TraesCS5D01G227200	chr1B	84.762	105	11	5	717	817	207374927	207375030	1.860000e-17	100.0
40	TraesCS5D01G227200	chr2A	87.500	72	7	2	727	797	631474718	631474788	6.730000e-12	82.4

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	TraesCS5D01G227200	chr5D	335051050	335053979	2929	True	5411.0	5411	100.000	1	2930	1	chr5D.!!$R1	2929
1	TraesCS5D01G227200	chr5A	436331629	436333551	1922	True	2854.0	2854	93.320	978	2930	1	chr5A.!!$R3	1952
2	TraesCS5D01G227200	chr5A	262437341	262438197	856	True	1077.0	1077	89.850	1	837	1	chr5A.!!$R2	836
3	TraesCS5D01G227200	chr5A	254925566	254926099	533	True	327.0	327	78.782	1	511	1	chr5A.!!$R1	510
4	TraesCS5D01G227200	chr5B	391829321	391830847	1526	True	1110.5	1836	89.887	877	2467	2	chr5B.!!$R2	1590
5	TraesCS5D01G227200	chr5B	446615283	446616073	790	False	1068.0	1068	91.593	1	768	1	chr5B.!!$F1	767
6	TraesCS5D01G227200	chr6A	567968188	567969092	904	False	1131.0	1131	89.836	1	878	1	chr6A.!!$F1	877
7	TraesCS5D01G227200	chr1A	278378800	278379325	525	True	651.0	651	88.828	1	544	1	chr1A.!!$R1	543

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
844	902	1.019278	AAGCGTATTGTGCCACGGAG	61.019	55.0	0.0	0.0	38.57	4.63	F
1296	1355	0.988678	GCCCCCTCACTTCCACCTAT	60.989	60.0	0.0	0.0	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1902	1970	1.003696	TCACCATTGCCATTGTACGGA	59.996	47.619	0.00	0.0	0.0	4.69	R
2309	2384	2.898729	ATAACTGACAGCTCATCGGG	57.101	50.000	1.25	0.0	0.0	5.14	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
421	456	1.202582	CTGGACGTCAACGAGGAGATT	59.797	52.381	18.91	0.00	43.02	2.40
479	515	4.057428	GATCTCGATCGGGGCGGG	62.057	72.222	16.43	0.00	0.00	6.13
540	576	2.892305	CAATCGCTCGGAGTGGATC	58.108	57.895	17.79	0.00	37.10	3.36
693	733	3.858877	GCCCAGCATAGAAGACGTATGAG	60.859	52.174	0.00	0.00	30.56	2.90
817	866	9.968870	TTTAAACTAAAAGCATAAATTCACGGT	57.031	25.926	0.00	0.00	0.00	4.83
844	902	1.019278	AAGCGTATTGTGCCACGGAG	61.019	55.000	0.00	0.00	38.57	4.63
861	919	3.460857	GGAGTCAATCCGTGCTCTATT	57.539	47.619	0.00	0.00	38.67	1.73
862	920	3.126831	GGAGTCAATCCGTGCTCTATTG	58.873	50.000	0.00	5.02	38.67	1.90
918	976	4.402616	TGGGAAAGTGGAAATGAAGGAT	57.597	40.909	0.00	0.00	0.00	3.24
919	977	4.750941	TGGGAAAGTGGAAATGAAGGATT	58.249	39.130	0.00	0.00	0.00	3.01
1296	1355	0.988678	GCCCCCTCACTTCCACCTAT	60.989	60.000	0.00	0.00	0.00	2.57
1463	1531	4.065281	CGTCGCCCGGGACTTCTT	62.065	66.667	29.31	0.00	34.75	2.52
1464	1532	2.125633	GTCGCCCGGGACTTCTTC	60.126	66.667	29.31	2.60	34.09	2.87
1465	1533	2.602267	TCGCCCGGGACTTCTTCA	60.602	61.111	29.31	0.00	0.00	3.02
1466	1534	2.125512	CGCCCGGGACTTCTTCAG	60.126	66.667	29.31	0.00	0.00	3.02
1467	1535	2.436824	GCCCGGGACTTCTTCAGC	60.437	66.667	29.31	0.00	0.00	4.26
1611	1679	2.665000	CTGCCGGAGCTCCAGAAA	59.335	61.111	31.67	13.24	40.80	2.52
1923	1991	1.132262	CCGTACAATGGCAATGGTGAC	59.868	52.381	7.57	1.40	0.00	3.67
2015	2083	7.510428	CGCAGCACATTACTGAATAATTTTT	57.490	32.000	0.00	0.00	37.32	1.94
2058	2133	8.737168	TGAATTCTTCTTGTCCCTATACATTG	57.263	34.615	7.05	0.00	0.00	2.82
2073	2148	7.339212	CCCTATACATTGTTGGAAGTCATTGAA	59.661	37.037	0.00	0.00	0.00	2.69
2202	2277	5.772393	TTTCTGTGGTATGGAACTATGGT	57.228	39.130	0.00	0.00	0.00	3.55
2216	2291	5.294552	GGAACTATGGTTAATGTCTGCTGAC	59.705	44.000	16.18	16.18	38.48	3.51
2256	2331	9.350951	AGATGATAAATCAATGTGTGTGATCAT	57.649	29.630	0.00	0.00	40.69	2.45
2296	2371	7.208225	AGAAAGAAAGATTCTAAAGGCACAC	57.792	36.000	0.00	0.00	39.61	3.82
2309	2384	2.508526	AGGCACACCAAGATTTCAGAC	58.491	47.619	0.00	0.00	39.06	3.51
2340	2417	6.447162	AGCTGTCAGTTATTTTAAAACCTGC	58.553	36.000	1.97	7.03	0.00	4.85
2457	2540	5.116882	GGAGTTCGTGCAACTAAATATCCT	58.883	41.667	0.00	0.00	46.10	3.24
2459	2542	5.730550	AGTTCGTGCAACTAAATATCCTCA	58.269	37.500	0.00	0.00	44.13	3.86
2470	2553	9.449719	CAACTAAATATCCTCACTTTACTGGTT	57.550	33.333	0.00	0.00	0.00	3.67
2483	2566	9.787435	TCACTTTACTGGTTTGTAGTTATTCAT	57.213	29.630	0.00	0.00	0.00	2.57
2604	2687	4.638421	TGATTTGGTATTTGCCGTCTAAGG	59.362	41.667	0.00	0.00	0.00	2.69
2626	2709	3.357823	GCGCAAACTTGTAGATTTTGACG	59.642	43.478	0.30	0.00	34.22	4.35
2672	2755	5.543507	TTTGGGATTTTTCAGCTGCTTTA	57.456	34.783	9.47	0.00	0.00	1.85
2684	2767	6.349973	TCAGCTGCTTTATCAATTAAGTCG	57.650	37.500	9.47	0.00	0.00	4.18
2751	2839	2.027561	CCGTTCACAAATACTCCCTCCA	60.028	50.000	0.00	0.00	0.00	3.86
2754	2842	4.383118	CGTTCACAAATACTCCCTCCATCT	60.383	45.833	0.00	0.00	0.00	2.90
2755	2843	5.119694	GTTCACAAATACTCCCTCCATCTC	58.880	45.833	0.00	0.00	0.00	2.75
2769	2857	5.178797	CCTCCATCTCAAAATAAGTGTCGT	58.821	41.667	0.00	0.00	0.00	4.34
2818	2909	4.082625	TCAGCGACACTTATTTTAGGACGA	60.083	41.667	0.00	0.00	0.00	4.20
2822	2913	5.166398	CGACACTTATTTTAGGACGAAGGT	58.834	41.667	0.00	0.00	0.00	3.50
2874	2965	6.812879	TGAATCGGATGTATATAGACACGT	57.187	37.500	1.52	0.00	30.52	4.49
2875	2966	7.210718	TGAATCGGATGTATATAGACACGTT	57.789	36.000	1.52	1.31	30.52	3.99
2901	2992	6.266168	AGTGTGTTTGTTCACTCATTTCAA	57.734	33.333	0.00	0.00	40.28	2.69
2906	2997	6.980397	GTGTTTGTTCACTCATTTCAATCCTT	59.020	34.615	0.00	0.00	35.68	3.36
2907	2998	8.134895	GTGTTTGTTCACTCATTTCAATCCTTA	58.865	33.333	0.00	0.00	35.68	2.69
2908	2999	8.859090	TGTTTGTTCACTCATTTCAATCCTTAT	58.141	29.630	0.00	0.00	0.00	1.73
2913	3004	7.792374	TCACTCATTTCAATCCTTATGTAGC	57.208	36.000	0.00	0.00	0.00	3.58
2914	3005	7.568349	TCACTCATTTCAATCCTTATGTAGCT	58.432	34.615	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
167	193	1.768112	CGCAAGTCGTTTCACGGGTT	61.768	55.000	0.00	0.00	42.81	4.11
179	205	2.956964	CGATCTCCGGCGCAAGTC	60.957	66.667	10.83	3.43	41.68	3.01
284	310	2.124942	GAGGCGAAGGAAGGGCAG	60.125	66.667	0.00	0.00	0.00	4.85
421	456	3.021695	CGCCCCCTCGTATAATCTATCA	58.978	50.000	0.00	0.00	0.00	2.15
537	573	2.101770	GTCCACGGGTCGTCGATC	59.898	66.667	0.00	0.00	38.32	3.69
538	574	3.807538	CGTCCACGGGTCGTCGAT	61.808	66.667	0.00	0.00	38.32	3.59
539	575	4.986645	TCGTCCACGGGTCGTCGA	62.987	66.667	0.00	0.00	38.32	4.20
540	576	4.748679	GTCGTCCACGGGTCGTCG	62.749	72.222	0.00	0.00	38.32	5.12
693	733	1.817209	CCGACTGGGCCTTCTCTAC	59.183	63.158	4.53	0.00	0.00	2.59
750	798	7.014230	ACGAGGTGGTACTAAAGTAAAGTTGTA	59.986	37.037	0.00	0.00	31.52	2.41
752	800	6.145048	CACGAGGTGGTACTAAAGTAAAGTTG	59.855	42.308	0.00	0.00	31.52	3.16
799	847	7.608761	TCTTACCTACCGTGAATTTATGCTTTT	59.391	33.333	0.00	0.00	0.00	2.27
805	853	5.751990	CGCTTCTTACCTACCGTGAATTTAT	59.248	40.000	0.00	0.00	0.00	1.40
815	864	3.554731	GCACAATACGCTTCTTACCTACC	59.445	47.826	0.00	0.00	0.00	3.18
816	865	3.554731	GGCACAATACGCTTCTTACCTAC	59.445	47.826	0.00	0.00	0.00	3.18
817	866	3.196039	TGGCACAATACGCTTCTTACCTA	59.804	43.478	0.00	0.00	31.92	3.08
818	867	2.027561	TGGCACAATACGCTTCTTACCT	60.028	45.455	0.00	0.00	31.92	3.08
844	902	6.604735	AATAACAATAGAGCACGGATTGAC	57.395	37.500	15.16	0.00	35.12	3.18
857	915	8.621286	ACGCAAATCTTTCCCTAATAACAATAG	58.379	33.333	0.00	0.00	0.00	1.73
860	918	6.827586	ACGCAAATCTTTCCCTAATAACAA	57.172	33.333	0.00	0.00	0.00	2.83
861	919	6.349777	CCAACGCAAATCTTTCCCTAATAACA	60.350	38.462	0.00	0.00	0.00	2.41
862	920	6.033966	CCAACGCAAATCTTTCCCTAATAAC	58.966	40.000	0.00	0.00	0.00	1.89
881	939	1.656818	CCCAAGCATACTGCCCAACG	61.657	60.000	0.00	0.00	46.52	4.10
1383	1442	0.106894	CCGGGTAGAAATGGAGGAGC	59.893	60.000	0.00	0.00	0.00	4.70
1608	1676	3.423154	CGCCAGGTGTCCGCTTTC	61.423	66.667	0.00	0.00	0.00	2.62
1902	1970	1.003696	TCACCATTGCCATTGTACGGA	59.996	47.619	0.00	0.00	0.00	4.69
1923	1991	7.177921	ACTGCATAATCCCCATCTATTCATTTG	59.822	37.037	0.00	0.00	0.00	2.32
1925	1993	6.662234	CACTGCATAATCCCCATCTATTCATT	59.338	38.462	0.00	0.00	0.00	2.57
2073	2148	2.158755	GGCATGCCCTGTTAGTCACTAT	60.159	50.000	27.24	0.00	0.00	2.12
2216	2291	9.939802	TGATTTATCATCTGGTCATTAGAGATG	57.060	33.333	0.00	0.00	43.01	2.90
2296	2371	3.201290	CTCATCGGGTCTGAAATCTTGG	58.799	50.000	0.00	0.00	0.00	3.61
2309	2384	2.898729	ATAACTGACAGCTCATCGGG	57.101	50.000	1.25	0.00	0.00	5.14
2457	2540	9.787435	ATGAATAACTACAAACCAGTAAAGTGA	57.213	29.630	0.00	0.00	0.00	3.41
2505	2588	9.929180	GTTCTGGATTGTATGCTATTATGAGTA	57.071	33.333	0.00	0.00	0.00	2.59
2507	2590	9.149225	GAGTTCTGGATTGTATGCTATTATGAG	57.851	37.037	0.00	0.00	0.00	2.90
2508	2591	8.874156	AGAGTTCTGGATTGTATGCTATTATGA	58.126	33.333	0.00	0.00	0.00	2.15
2509	2592	9.499479	AAGAGTTCTGGATTGTATGCTATTATG	57.501	33.333	0.00	0.00	0.00	1.90
2510	2593	9.717942	GAAGAGTTCTGGATTGTATGCTATTAT	57.282	33.333	0.00	0.00	0.00	1.28
2511	2594	8.928448	AGAAGAGTTCTGGATTGTATGCTATTA	58.072	33.333	0.00	0.00	38.91	0.98
2513	2596	7.372260	AGAAGAGTTCTGGATTGTATGCTAT	57.628	36.000	0.00	0.00	38.91	2.97
2514	2597	6.798427	AGAAGAGTTCTGGATTGTATGCTA	57.202	37.500	0.00	0.00	38.91	3.49
2515	2598	5.690464	AGAAGAGTTCTGGATTGTATGCT	57.310	39.130	0.00	0.00	38.91	3.79
2530	2613	6.710597	TCACTACAGTTTGTACAGAAGAGT	57.289	37.500	0.00	0.00	0.00	3.24
2563	2646	5.931441	AATCAGCACAACAGAAGTTACTC	57.069	39.130	0.00	0.00	35.85	2.59
2565	2648	5.215160	CCAAATCAGCACAACAGAAGTTAC	58.785	41.667	0.00	0.00	35.85	2.50
2604	2687	3.357823	CGTCAAAATCTACAAGTTTGCGC	59.642	43.478	0.00	0.00	41.53	6.09
2605	2688	3.906008	CCGTCAAAATCTACAAGTTTGCG	59.094	43.478	0.00	0.00	41.53	4.85
2626	2709	8.794335	AATATTTTCTCTTCCAGAACTGTACC	57.206	34.615	1.18	0.00	41.13	3.34
2709	2792	5.012354	ACGGAGGGTTGACATTAAAGTTAGA	59.988	40.000	0.00	0.00	0.00	2.10
2847	2938	8.974408	CGTGTCTATATACATCCGATTCAAAAA	58.026	33.333	0.00	0.00	0.00	1.94
2848	2939	8.139350	ACGTGTCTATATACATCCGATTCAAAA	58.861	33.333	7.85	0.00	0.00	2.44
2849	2940	7.654568	ACGTGTCTATATACATCCGATTCAAA	58.345	34.615	7.85	0.00	0.00	2.69
2850	2941	7.210718	ACGTGTCTATATACATCCGATTCAA	57.789	36.000	7.85	0.00	0.00	2.69
2859	2950	9.865321	AACACACTAAAACGTGTCTATATACAT	57.135	29.630	0.00	0.00	45.74	2.29
2874	2965	8.300286	TGAAATGAGTGAACAAACACACTAAAA	58.700	29.630	0.00	0.00	45.54	1.52
2875	2966	7.821652	TGAAATGAGTGAACAAACACACTAAA	58.178	30.769	0.00	0.00	45.54	1.85
2888	2979	8.049117	AGCTACATAAGGATTGAAATGAGTGAA	58.951	33.333	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.