AutoCloner

Multiple sequence alignment - TraesCS2D01G050200

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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	TraesCS2D01G050200	chr2D	100.000	3366	0	0	1	3366	18610770	18614135	0.000000e+00	6216.0
1	TraesCS2D01G050200	chr2D	81.620	1148	168	26	1467	2583	18374114	18375249	0.000000e+00	911.0
2	TraesCS2D01G050200	chr2D	88.785	749	77	6	1	745	19607010	19606265	0.000000e+00	911.0
3	TraesCS2D01G050200	chr2D	88.188	745	86	2	1	745	186331414	186330672	0.000000e+00	887.0
4	TraesCS2D01G050200	chr2D	89.323	665	41	10	771	1429	18373469	18374109	0.000000e+00	808.0
5	TraesCS2D01G050200	chr2D	74.757	721	119	38	2670	3364	18375294	18375977	7.160000e-67	265.0
6	TraesCS2D01G050200	chr2A	95.914	2472	90	7	902	3364	19586999	19589468	0.000000e+00	3995.0
7	TraesCS2D01G050200	chr2A	88.410	742	83	3	1	742	426717507	426718245	0.000000e+00	891.0
8	TraesCS2D01G050200	chr2A	88.070	746	85	4	1	745	423781547	423780805	0.000000e+00	881.0
9	TraesCS2D01G050200	chr2A	88.626	633	42	7	803	1429	19566696	19567304	0.000000e+00	743.0
10	TraesCS2D01G050200	chr2A	75.559	581	95	28	2670	3226	19568489	19569046	3.360000e-60	243.0
11	TraesCS2D01G050200	chr2A	100.000	30	0	0	771	800	19566640	19566669	4.690000e-04	56.5
12	TraesCS2D01G050200	chr2B	83.244	2250	254	54	1176	3364	30468098	30470285	0.000000e+00	1953.0
13	TraesCS2D01G050200	chr2B	89.530	745	73	4	1	745	418961753	418961014	0.000000e+00	939.0
14	TraesCS2D01G050200	chr7D	89.086	733	76	3	1	732	69077917	69078646	0.000000e+00	907.0
15	TraesCS2D01G050200	chr7D	81.382	854	143	14	900	1746	621172804	621173648	0.000000e+00	682.0
16	TraesCS2D01G050200	chr3D	89.306	720	70	5	26	742	173712165	173712880	0.000000e+00	896.0
17	TraesCS2D01G050200	chr4A	88.322	745	84	2	1	745	678372334	678371593	0.000000e+00	891.0
18	TraesCS2D01G050200	chr3B	88.204	746	81	6	1	742	252592648	252593390	0.000000e+00	883.0

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	TraesCS2D01G050200	chr2D	18610770	18614135	3365	False	6216.000000	6216	100.000000	1	3366	1	chr2D.!!$F1	3365
1	TraesCS2D01G050200	chr2D	19606265	19607010	745	True	911.000000	911	88.785000	1	745	1	chr2D.!!$R1	744
2	TraesCS2D01G050200	chr2D	186330672	186331414	742	True	887.000000	887	88.188000	1	745	1	chr2D.!!$R2	744
3	TraesCS2D01G050200	chr2D	18373469	18375977	2508	False	661.333333	911	81.900000	771	3364	3	chr2D.!!$F2	2593
4	TraesCS2D01G050200	chr2A	19586999	19589468	2469	False	3995.000000	3995	95.914000	902	3364	1	chr2A.!!$F1	2462
5	TraesCS2D01G050200	chr2A	426717507	426718245	738	False	891.000000	891	88.410000	1	742	1	chr2A.!!$F2	741
6	TraesCS2D01G050200	chr2A	423780805	423781547	742	True	881.000000	881	88.070000	1	745	1	chr2A.!!$R1	744
7	TraesCS2D01G050200	chr2A	19566640	19569046	2406	False	347.500000	743	88.061667	771	3226	3	chr2A.!!$F3	2455
8	TraesCS2D01G050200	chr2B	30468098	30470285	2187	False	1953.000000	1953	83.244000	1176	3364	1	chr2B.!!$F1	2188
9	TraesCS2D01G050200	chr2B	418961014	418961753	739	True	939.000000	939	89.530000	1	745	1	chr2B.!!$R1	744
10	TraesCS2D01G050200	chr7D	69077917	69078646	729	False	907.000000	907	89.086000	1	732	1	chr7D.!!$F1	731
11	TraesCS2D01G050200	chr7D	621172804	621173648	844	False	682.000000	682	81.382000	900	1746	1	chr7D.!!$F2	846
12	TraesCS2D01G050200	chr3D	173712165	173712880	715	False	896.000000	896	89.306000	26	742	1	chr3D.!!$F1	716
13	TraesCS2D01G050200	chr4A	678371593	678372334	741	True	891.000000	891	88.322000	1	745	1	chr4A.!!$R1	744
14	TraesCS2D01G050200	chr3B	252592648	252593390	742	False	883.000000	883	88.204000	1	742	1	chr3B.!!$F1	741

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
470	476	0.391263	GCCGACTAGTCAACCTTGGG	60.391	60.0	22.37	13.84	0.00	4.12	F
847	880	0.868406	GCCTCATACGCATTACTGCC	59.132	55.0	0.00	0.00	46.07	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1615	1663	2.887463	TTACGGTACCACGCGCCATC	62.887	60.000	13.54	0.0	37.37	3.51	R
2490	2567	4.940046	AGAAACTATGTGGCAAGTCATGAG	59.060	41.667	0.00	0.0	0.00	2.90	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
155	156	2.685897	CCCAAAAGAGAAAACGACACCA	59.314	45.455	0.00	0.00	0.00	4.17
202	203	4.286813	AGATCAGATCCTAGGGTTTCCA	57.713	45.455	9.46	0.00	34.83	3.53
237	239	2.565834	AGTTGGTCGGCAGTAGTTACAT	59.434	45.455	0.00	0.00	0.00	2.29
246	248	3.941483	GGCAGTAGTTACATGACAATGCT	59.059	43.478	0.00	0.00	37.29	3.79
331	336	1.592400	ATGTCTTCCCGACTCGCGAA	61.592	55.000	11.33	0.00	44.57	4.70
344	349	1.063616	CTCGCGAACGGAACTAGATGA	59.936	52.381	11.33	0.00	40.63	2.92
350	355	3.372954	GAACGGAACTAGATGACGGATG	58.627	50.000	0.00	0.00	0.00	3.51
388	393	2.997315	CTCAGGCCGACCACCTCA	60.997	66.667	0.00	0.00	39.06	3.86
466	472	3.003113	GCCGCCGACTAGTCAACCT	62.003	63.158	22.37	0.00	0.00	3.50
470	476	0.391263	GCCGACTAGTCAACCTTGGG	60.391	60.000	22.37	13.84	0.00	4.12
471	477	1.263356	CCGACTAGTCAACCTTGGGA	58.737	55.000	22.37	0.00	0.00	4.37
475	481	3.400255	GACTAGTCAACCTTGGGAACAC	58.600	50.000	18.20	0.00	42.67	3.32
487	495	2.398919	GGAACACCCCCTCCTGATT	58.601	57.895	0.00	0.00	0.00	2.57
662	670	2.750637	TCTCTGGGGACGACGAGC	60.751	66.667	0.00	0.00	0.00	5.03
742	751	2.646143	GAGGGAGCGATACGAGGC	59.354	66.667	0.00	0.00	0.00	4.70
745	754	2.336809	GGAGCGATACGAGGCAGG	59.663	66.667	0.00	0.00	0.00	4.85
746	755	2.336809	GAGCGATACGAGGCAGGG	59.663	66.667	0.00	0.00	0.00	4.45
747	756	2.442272	AGCGATACGAGGCAGGGT	60.442	61.111	0.00	0.00	0.00	4.34
748	757	1.152819	AGCGATACGAGGCAGGGTA	60.153	57.895	0.00	0.00	0.00	3.69
749	758	1.007618	GCGATACGAGGCAGGGTAC	60.008	63.158	0.00	0.00	0.00	3.34
750	759	1.453762	GCGATACGAGGCAGGGTACT	61.454	60.000	0.00	0.00	0.00	2.73
752	761	1.400737	GATACGAGGCAGGGTACTGT	58.599	55.000	0.00	0.00	46.62	3.55
753	762	1.755380	GATACGAGGCAGGGTACTGTT	59.245	52.381	0.00	0.00	46.62	3.16
754	763	2.512692	TACGAGGCAGGGTACTGTTA	57.487	50.000	0.00	0.00	46.62	2.41
755	764	1.861982	ACGAGGCAGGGTACTGTTAT	58.138	50.000	0.00	0.00	46.62	1.89
756	765	2.185387	ACGAGGCAGGGTACTGTTATT	58.815	47.619	0.00	0.00	46.62	1.40
757	766	2.570302	ACGAGGCAGGGTACTGTTATTT	59.430	45.455	0.00	0.00	46.62	1.40
758	767	3.008704	ACGAGGCAGGGTACTGTTATTTT	59.991	43.478	0.00	0.00	46.62	1.82
759	768	4.007659	CGAGGCAGGGTACTGTTATTTTT	58.992	43.478	0.00	0.00	46.62	1.94
845	878	4.094887	AGTTTTGCCTCATACGCATTACTG	59.905	41.667	0.00	0.00	35.83	2.74
846	879	1.581934	TGCCTCATACGCATTACTGC	58.418	50.000	0.00	0.00	45.31	4.40
847	880	0.868406	GCCTCATACGCATTACTGCC	59.132	55.000	0.00	0.00	46.07	4.85
889	928	3.430042	AGACTGATGCATGGTTTGTCT	57.570	42.857	2.46	7.33	0.00	3.41
890	929	3.341823	AGACTGATGCATGGTTTGTCTC	58.658	45.455	2.46	0.00	0.00	3.36
891	930	3.008813	AGACTGATGCATGGTTTGTCTCT	59.991	43.478	2.46	0.00	0.00	3.10
892	931	3.755378	GACTGATGCATGGTTTGTCTCTT	59.245	43.478	2.46	0.00	0.00	2.85
893	932	3.755378	ACTGATGCATGGTTTGTCTCTTC	59.245	43.478	2.46	0.00	0.00	2.87
894	933	3.084039	TGATGCATGGTTTGTCTCTTCC	58.916	45.455	2.46	0.00	0.00	3.46
895	934	2.655090	TGCATGGTTTGTCTCTTCCA	57.345	45.000	0.00	0.00	0.00	3.53
896	935	3.159213	TGCATGGTTTGTCTCTTCCAT	57.841	42.857	0.00	0.00	40.73	3.41
897	936	3.499338	TGCATGGTTTGTCTCTTCCATT	58.501	40.909	0.00	0.00	38.43	3.16
898	937	3.507233	TGCATGGTTTGTCTCTTCCATTC	59.493	43.478	0.00	0.00	38.43	2.67
899	938	3.507233	GCATGGTTTGTCTCTTCCATTCA	59.493	43.478	0.00	0.00	38.43	2.57
900	939	4.380233	GCATGGTTTGTCTCTTCCATTCAG	60.380	45.833	0.00	0.00	38.43	3.02
974	1015	8.768957	ATATGTTGTCTCTTCCATTCATATCG	57.231	34.615	0.00	0.00	0.00	2.92
1051	1092	2.487934	CAAGAATCCTAGTGATGGCCG	58.512	52.381	0.00	0.00	32.68	6.13
1126	1167	1.420430	CGCCACCCCTCCTATCTTAA	58.580	55.000	0.00	0.00	0.00	1.85
1174	1218	5.717178	AGTAGTTGTGAGGAAGAGCTCAATA	59.283	40.000	17.77	0.00	0.00	1.90
1236	1280	4.452455	CGCAACCAAGAAGTAATTCTCAGT	59.548	41.667	5.80	4.09	0.00	3.41
1260	1304	1.810755	GGCTTTCCTAACTCGTTTGGG	59.189	52.381	9.74	3.60	36.37	4.12
1297	1341	1.153188	TGGACTATGCATGCCACCG	60.153	57.895	16.68	3.49	0.00	4.94
1384	1428	1.874872	CCAATGGCTTTGCTTGGTTTG	59.125	47.619	7.56	0.00	35.70	2.93
1440	1484	6.071952	GGTATATCCATGCAGGTTTAACCATG	60.072	42.308	17.10	10.89	37.10	3.66
1534	1579	2.047002	ACACCGTTTACAGCTTTGGT	57.953	45.000	0.00	0.00	0.00	3.67
2490	2567	4.025480	AGTTTAATTGTCGACGACCACAAC	60.025	41.667	24.33	17.82	35.37	3.32
2514	2595	4.696877	TCATGACTTGCCACATAGTTTCTG	59.303	41.667	0.00	0.00	0.00	3.02
2517	2598	5.237815	TGACTTGCCACATAGTTTCTGTAG	58.762	41.667	0.00	0.00	0.00	2.74
2526	2607	8.552034	GCCACATAGTTTCTGTAGATTTCATAC	58.448	37.037	0.00	0.00	0.00	2.39
2639	2721	9.413048	GGTGATAAAGAGAGTATCGAATTAAGG	57.587	37.037	0.00	0.00	42.67	2.69
2713	2795	0.923729	TGGTGGCCCACTTATCCCAT	60.924	55.000	14.71	0.00	35.17	4.00
2802	2884	9.681062	AATTAATAGTATGCTTGTAACCACAGT	57.319	29.630	0.00	0.00	35.67	3.55
3131	3258	3.309600	TTACTCTAGACCCCTAGTGCC	57.690	52.381	0.00	0.00	42.33	5.01
3194	3321	9.855021	ATTTTACGTCTTTCAAAGGATAAATGG	57.145	29.630	0.00	0.00	0.00	3.16
3364	3492	9.125026	GGAAGATCAAGAAGGCAAAATCTAATA	57.875	33.333	0.00	0.00	0.00	0.98
3365	3493	9.943163	GAAGATCAAGAAGGCAAAATCTAATAC	57.057	33.333	0.00	0.00	0.00	1.89

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	2.048603	GTCAAGTCATGCCTGGCCC	61.049	63.158	17.53	1.27	0.00	5.80
155	156	1.153901	CGAACGATGGCGGTACTGT	60.154	57.895	3.10	0.00	37.73	3.55
184	185	2.478292	GGTGGAAACCCTAGGATCTGA	58.522	52.381	11.48	0.00	0.00	3.27
202	203	2.932663	CAACTCATGTTGCTCCGGT	58.067	52.632	0.00	0.00	45.57	5.28
225	227	5.551760	AAGCATTGTCATGTAACTACTGC	57.448	39.130	0.00	0.00	32.28	4.40
237	239	5.334802	CGTTACCTTGATGAAAGCATTGTCA	60.335	40.000	0.00	0.00	34.11	3.58
246	248	2.734606	CTGCGTCGTTACCTTGATGAAA	59.265	45.455	0.00	0.00	0.00	2.69
300	303	1.369625	GAAGACATAGTTGGCGGTGG	58.630	55.000	0.00	0.00	35.32	4.61
331	336	2.358267	GACATCCGTCATCTAGTTCCGT	59.642	50.000	0.00	0.00	42.13	4.69
344	349	1.025812	GGTCAGATCTCGACATCCGT	58.974	55.000	19.98	0.00	39.75	4.69
350	355	1.269517	GCTGGATGGTCAGATCTCGAC	60.270	57.143	13.69	13.69	36.93	4.20
388	393	1.059006	GGTGGCCATCTCCTCCATCT	61.059	60.000	9.72	0.00	39.10	2.90
432	438	4.593864	GCGCCTCCGGTCAGATCC	62.594	72.222	0.00	0.00	34.32	3.36
457	463	2.943036	GGTGTTCCCAAGGTTGACTA	57.057	50.000	0.00	0.00	0.00	2.59
470	476	0.107654	CGAATCAGGAGGGGGTGTTC	60.108	60.000	0.00	0.00	0.00	3.18
471	477	1.991230	CGAATCAGGAGGGGGTGTT	59.009	57.895	0.00	0.00	0.00	3.32
475	481	3.878667	GGGCGAATCAGGAGGGGG	61.879	72.222	0.00	0.00	0.00	5.40
527	535	0.319405	TTCGGTCTTCGTCTTTCCCC	59.681	55.000	0.00	0.00	40.32	4.81
587	595	2.844839	GGCGGGGATCTAGGCTGT	60.845	66.667	0.00	0.00	0.00	4.40
756	765	1.133407	GTTCTGTGTGTCCCGCAAAAA	59.867	47.619	0.00	0.00	32.02	1.94
757	766	0.736053	GTTCTGTGTGTCCCGCAAAA	59.264	50.000	0.00	0.00	32.02	2.44
758	767	0.393132	TGTTCTGTGTGTCCCGCAAA	60.393	50.000	0.00	0.00	32.02	3.68
759	768	0.393132	TTGTTCTGTGTGTCCCGCAA	60.393	50.000	0.00	0.00	32.02	4.85
760	769	0.813610	CTTGTTCTGTGTGTCCCGCA	60.814	55.000	0.00	0.00	0.00	5.69
761	770	0.814010	ACTTGTTCTGTGTGTCCCGC	60.814	55.000	0.00	0.00	0.00	6.13
762	771	0.937304	CACTTGTTCTGTGTGTCCCG	59.063	55.000	0.00	0.00	0.00	5.14
763	772	1.308998	CCACTTGTTCTGTGTGTCCC	58.691	55.000	0.00	0.00	33.92	4.46
764	773	1.670811	CACCACTTGTTCTGTGTGTCC	59.329	52.381	0.00	0.00	33.92	4.02
765	774	1.064060	GCACCACTTGTTCTGTGTGTC	59.936	52.381	0.00	0.00	33.92	3.67
766	775	1.094785	GCACCACTTGTTCTGTGTGT	58.905	50.000	0.00	0.00	33.92	3.72
767	776	0.381801	GGCACCACTTGTTCTGTGTG	59.618	55.000	0.00	0.00	33.92	3.82
768	777	0.034574	TGGCACCACTTGTTCTGTGT	60.035	50.000	0.00	0.00	33.92	3.72
769	778	1.066002	CTTGGCACCACTTGTTCTGTG	59.934	52.381	0.00	0.00	35.39	3.66
845	878	1.692519	AGATCACGGGTATACAAGGGC	59.307	52.381	5.01	0.00	0.00	5.19
846	879	4.150359	AGTAGATCACGGGTATACAAGGG	58.850	47.826	5.01	0.00	0.00	3.95
847	880	6.149142	GTCTAGTAGATCACGGGTATACAAGG	59.851	46.154	2.51	0.00	0.00	3.61
889	928	6.837312	TCACTTTCCTTTACTGAATGGAAGA	58.163	36.000	5.50	0.00	45.01	2.87
890	929	7.693969	ATCACTTTCCTTTACTGAATGGAAG	57.306	36.000	5.50	4.03	45.01	3.46
891	930	8.477419	AAATCACTTTCCTTTACTGAATGGAA	57.523	30.769	1.94	1.94	43.58	3.53
892	931	8.477419	AAAATCACTTTCCTTTACTGAATGGA	57.523	30.769	0.00	0.00	37.16	3.41
920	960	3.254166	AGTTAGTTTTCGACTCTGCCGTA	59.746	43.478	0.00	0.00	39.86	4.02
921	961	2.035576	AGTTAGTTTTCGACTCTGCCGT	59.964	45.455	0.00	0.00	39.86	5.68
922	962	2.662156	GAGTTAGTTTTCGACTCTGCCG	59.338	50.000	0.00	0.00	39.86	5.69
974	1015	4.575885	TCAGGTATGAGTTTTGGTACTGC	58.424	43.478	0.00	0.00	0.00	4.40
1051	1092	1.815421	CCACGACATGGCTAGCACC	60.815	63.158	18.24	0.00	43.24	5.01
1174	1218	5.179452	ACTTGGTGCAGGTACAAAGATAT	57.821	39.130	11.00	0.00	35.57	1.63
1214	1258	5.106515	GGACTGAGAATTACTTCTTGGTTGC	60.107	44.000	0.00	0.00	41.87	4.17
1236	1280	0.901580	ACGAGTTAGGAAAGCCGGGA	60.902	55.000	2.18	0.00	39.96	5.14
1297	1341	6.204359	CAATGATACTTGCAGTGGAATTAGC	58.796	40.000	0.00	0.00	0.00	3.09
1384	1428	3.569701	TCAAAGACCATGCTGAAAGGAAC	59.430	43.478	0.00	0.00	38.32	3.62
1502	1547	9.903682	GCTGTAAACGGTGTATCTATAATTAGA	57.096	33.333	0.00	0.00	38.79	2.10
1534	1579	4.080582	CCCATCACTTGTAATGTAGACCCA	60.081	45.833	0.00	0.00	0.00	4.51
1615	1663	2.887463	TTACGGTACCACGCGCCATC	62.887	60.000	13.54	0.00	37.37	3.51
1765	1814	7.206981	ACCAAACTTCACAGAACTTCATATG	57.793	36.000	0.00	0.00	0.00	1.78
2490	2567	4.940046	AGAAACTATGTGGCAAGTCATGAG	59.060	41.667	0.00	0.00	0.00	2.90
2639	2721	7.862873	CCTTGTTCAGTTTTCCTATTTGTCTTC	59.137	37.037	0.00	0.00	0.00	2.87
2713	2795	8.160765	TGGAGATGAACTATTTGGTAAGTTTCA	58.839	33.333	0.00	0.00	36.10	2.69
2968	3094	2.358957	TCTCGTTTGCATGGATCTTGG	58.641	47.619	0.00	0.00	0.00	3.61
3131	3258	6.743575	ATCTTGGATTTTAGTTTGTCTCCG	57.256	37.500	0.00	0.00	0.00	4.63
3194	3321	7.484007	CACTTTTCTCTTGATCATATGCAACAC	59.516	37.037	0.00	0.00	0.00	3.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.