AutoCloner

Multiple sequence alignment - TraesCS7D01G418300

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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	TraesCS7D01G418300	chr7D	100.000	2055	0	0	1	2055	537678646	537680700	0.000000e+00	3795.0
1	TraesCS7D01G418300	chr7D	100.000	440	0	0	2365	2804	537681010	537681449	0.000000e+00	813.0
2	TraesCS7D01G418300	chr7A	90.353	1047	57	15	369	1413	619037873	619038877	0.000000e+00	1334.0
3	TraesCS7D01G418300	chr7A	93.145	496	26	3	1563	2054	619038875	619039366	0.000000e+00	721.0
4	TraesCS7D01G418300	chr7A	91.985	262	12	4	2514	2766	619039684	619039945	2.660000e-95	359.0
5	TraesCS7D01G418300	chr7A	81.892	370	43	13	1466	1827	43043834	43043481	9.830000e-75	291.0
6	TraesCS7D01G418300	chr7A	99.315	146	1	0	2365	2510	619039408	619039553	5.960000e-67	265.0
7	TraesCS7D01G418300	chr7A	91.525	177	12	2	33	208	619037678	619037852	1.000000e-59	241.0
8	TraesCS7D01G418300	chr7B	92.609	690	45	4	517	1201	580166498	580167186	0.000000e+00	987.0
9	TraesCS7D01G418300	chr7B	93.715	541	30	3	1297	1835	580182445	580182983	0.000000e+00	808.0
10	TraesCS7D01G418300	chr7B	87.215	438	20	13	2365	2766	580183539	580183976	1.520000e-127	466.0
11	TraesCS7D01G418300	chr7B	86.410	390	20	14	154	526	580164688	580165061	2.020000e-106	396.0
12	TraesCS7D01G418300	chr7B	91.150	113	10	0	1193	1305	580167207	580167319	1.350000e-33	154.0
13	TraesCS7D01G418300	chr7B	97.561	41	1	0	2764	2804	580184008	580184048	1.390000e-08	71.3
14	TraesCS7D01G418300	chr4A	79.668	1205	158	53	869	2031	651343398	651342239	0.000000e+00	787.0
15	TraesCS7D01G418300	chr2B	80.632	759	101	24	1258	1986	97188035	97188777	1.900000e-151	545.0
16	TraesCS7D01G418300	chr2B	82.645	121	12	2	2520	2631	97189122	97189242	6.390000e-17	99.0
17	TraesCS7D01G418300	chr2B	98.039	51	1	0	1141	1191	781006155	781006205	3.850000e-14	89.8
18	TraesCS7D01G418300	chr2A	79.630	756	96	29	1257	1986	62297034	62297757	9.030000e-135	490.0
19	TraesCS7D01G418300	chr2D	80.048	421	44	19	1589	1986	61978100	61978503	2.750000e-70	276.0

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	TraesCS7D01G418300	chr7D	537678646	537681449	2803	False	2304.000000	3795	100.000000	1	2804	2	chr7D.!!$F1	2803
1	TraesCS7D01G418300	chr7A	619037678	619039945	2267	False	584.000000	1334	93.264600	33	2766	5	chr7A.!!$F1	2733
2	TraesCS7D01G418300	chr7B	580164688	580167319	2631	False	512.333333	987	90.056333	154	1305	3	chr7B.!!$F1	1151
3	TraesCS7D01G418300	chr7B	580182445	580184048	1603	False	448.433333	808	92.830333	1297	2804	3	chr7B.!!$F2	1507
4	TraesCS7D01G418300	chr4A	651342239	651343398	1159	True	787.000000	787	79.668000	869	2031	1	chr4A.!!$R1	1162
5	TraesCS7D01G418300	chr2B	97188035	97189242	1207	False	322.000000	545	81.638500	1258	2631	2	chr2B.!!$F2	1373
6	TraesCS7D01G418300	chr2A	62297034	62297757	723	False	490.000000	490	79.630000	1257	1986	1	chr2A.!!$F1	729

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
939	2428	0.169672	CTGTGCGCTGCTAGCAATTT	59.83	50.0	19.86	0.0	46.97	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	3904	1.683385	GGTGCTGGGATTAAGGATTGC	59.317	52.381	0.0	0.0	0.0	3.56	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
17	18	3.915575	CTCTGCTGGTCATTGCCC	58.084	61.111	0.00	0.00	0.00	5.36
18	19	1.001764	CTCTGCTGGTCATTGCCCA	60.002	57.895	0.00	0.00	0.00	5.36
22	23	3.599584	CTGGTCATTGCCCAGCTG	58.400	61.111	6.78	6.78	42.81	4.24
23	24	2.677524	TGGTCATTGCCCAGCTGC	60.678	61.111	8.66	0.00	0.00	5.25
24	25	2.677524	GGTCATTGCCCAGCTGCA	60.678	61.111	8.66	0.19	40.07	4.41
25	26	2.707849	GGTCATTGCCCAGCTGCAG	61.708	63.158	10.11	10.11	43.21	4.41
26	27	3.066190	TCATTGCCCAGCTGCAGC	61.066	61.111	31.53	31.53	43.21	5.25
45	46	2.558617	TGCTCATGCATGGTGTGAC	58.441	52.632	25.97	10.05	45.31	3.67
49	50	2.936553	GCTCATGCATGGTGTGACTGTA	60.937	50.000	25.97	2.08	39.41	2.74
85	86	4.009370	AGGTCGAAAAGAGGGAGAAAAG	57.991	45.455	0.00	0.00	0.00	2.27
90	91	5.296035	GTCGAAAAGAGGGAGAAAAGTGAAA	59.704	40.000	0.00	0.00	0.00	2.69
93	94	5.948992	AAAGAGGGAGAAAAGTGAAATCG	57.051	39.130	0.00	0.00	0.00	3.34
98	99	6.717084	AGAGGGAGAAAAGTGAAATCGAAAAT	59.283	34.615	0.00	0.00	0.00	1.82
108	109	7.202016	AGTGAAATCGAAAATGCTTTACAGA	57.798	32.000	0.00	0.00	0.00	3.41
111	112	8.578769	GTGAAATCGAAAATGCTTTACAGATTC	58.421	33.333	0.00	0.00	29.98	2.52
225	226	4.108299	CCTGGCGCACCCATACCA	62.108	66.667	10.83	0.00	44.33	3.25
226	227	2.824041	CTGGCGCACCCATACCAC	60.824	66.667	10.83	0.00	44.33	4.16
227	228	4.418328	TGGCGCACCCATACCACC	62.418	66.667	10.83	0.00	39.18	4.61
228	229	4.109675	GGCGCACCCATACCACCT	62.110	66.667	10.83	0.00	0.00	4.00
229	230	2.513897	GCGCACCCATACCACCTC	60.514	66.667	0.30	0.00	0.00	3.85
339	340	1.067582	GATCGGCGGAATTCGGTCT	59.932	57.895	14.68	0.00	39.69	3.85
579	2043	4.436998	CCGTGGAGACCGAGCACC	62.437	72.222	0.00	0.00	0.00	5.01
580	2044	4.778415	CGTGGAGACCGAGCACCG	62.778	72.222	0.00	0.00	38.18	4.94
584	2048	4.373116	GAGACCGAGCACCGCCAA	62.373	66.667	0.00	0.00	36.84	4.52
585	2049	3.876589	GAGACCGAGCACCGCCAAA	62.877	63.158	0.00	0.00	36.84	3.28
586	2050	2.975799	GACCGAGCACCGCCAAAA	60.976	61.111	0.00	0.00	36.84	2.44
587	2051	2.966309	GACCGAGCACCGCCAAAAG	61.966	63.158	0.00	0.00	36.84	2.27
588	2052	4.404654	CCGAGCACCGCCAAAAGC	62.405	66.667	0.00	0.00	36.84	3.51
589	2053	4.404654	CGAGCACCGCCAAAAGCC	62.405	66.667	0.00	0.00	38.78	4.35
617	2101	3.358076	CTCTCCGCCGACAGGTTCC	62.358	68.421	0.00	0.00	40.50	3.62
628	2112	1.068352	ACAGGTTCCCTCCTTTGCCT	61.068	55.000	0.00	0.00	35.37	4.75
689	2173	2.059756	TCCACCTCTGATTTCCCCTT	57.940	50.000	0.00	0.00	0.00	3.95
809	2296	2.595386	GCTCGGTTATTTGTGGCTTTG	58.405	47.619	0.00	0.00	0.00	2.77
939	2428	0.169672	CTGTGCGCTGCTAGCAATTT	59.830	50.000	19.86	0.00	46.97	1.82
940	2429	0.597568	TGTGCGCTGCTAGCAATTTT	59.402	45.000	19.86	0.00	46.97	1.82
1004	2494	3.500343	CCTCTTGGACAGGAAAAATGGT	58.500	45.455	0.00	0.00	31.91	3.55
1031	2521	6.523840	AGCATCTCTTTGAGGATATCTTCAC	58.476	40.000	16.48	3.79	31.40	3.18
1033	2523	6.991531	GCATCTCTTTGAGGATATCTTCACTT	59.008	38.462	16.48	0.00	31.40	3.16
1070	2560	3.369892	CCTGATGGGAAGAAGTTCGACAT	60.370	47.826	0.00	1.24	35.09	3.06
1106	2596	2.424956	GGCTGTTCCACCTGATGAATTC	59.575	50.000	0.00	0.00	34.01	2.17
1113	2603	6.173339	GTTCCACCTGATGAATTCTGAGTTA	58.827	40.000	7.05	0.00	0.00	2.24
1124	2614	1.776662	TCTGAGTTATGCTAGGCCGT	58.223	50.000	0.00	0.00	0.00	5.68
1138	2628	1.671054	GCCGTGCTTTACTCTGCCA	60.671	57.895	0.00	0.00	0.00	4.92
1249	2783	8.329502	ACTATGTAAATATTTAGATCCTGGGGC	58.670	37.037	18.30	0.92	30.45	5.80
1279	2814	4.740268	TCATAGCTACACTTACACAACCG	58.260	43.478	0.00	0.00	0.00	4.44
1280	2815	4.219070	TCATAGCTACACTTACACAACCGT	59.781	41.667	0.00	0.00	0.00	4.83
1424	2964	4.855340	ACCCGATTCATACTGGTGAAAAT	58.145	39.130	2.61	0.00	41.09	1.82
1488	3029	4.576216	CCAGACACTGGCTACTATACAG	57.424	50.000	4.84	0.00	45.13	2.74
1557	3099	4.080687	TGGCAACTGAATGATGTGAATGA	58.919	39.130	0.00	0.00	37.61	2.57
1715	3260	1.203001	TGGTAGGAAAACCCTTGCTGG	60.203	52.381	0.00	0.00	44.85	4.85
1779	3327	1.625818	GAGGACAGTTCCAGTGGTCAT	59.374	52.381	9.54	0.00	45.72	3.06
1898	3465	3.868077	GTGAGGTTGATTCCTGATCTTCG	59.132	47.826	0.00	0.00	38.02	3.79
1945	3859	7.382898	TCTGTAACATGTTGCTGAAGTACATA	58.617	34.615	26.08	9.80	32.34	2.29
1986	3900	7.922382	AGTGATTCTCTTATTTTCCCTTCAGA	58.078	34.615	0.00	0.00	0.00	3.27
1990	3904	7.944729	TTCTCTTATTTTCCCTTCAGATTGG	57.055	36.000	0.00	0.00	0.00	3.16
2041	3955	5.437060	TGTCTACATAATCTTTTCTGGCCC	58.563	41.667	0.00	0.00	0.00	5.80
2043	3957	3.366052	ACATAATCTTTTCTGGCCCGT	57.634	42.857	0.00	0.00	0.00	5.28
2621	4822	3.891366	ACAAAGAACAAGGTTCCATCTGG	59.109	43.478	5.54	0.00	0.00	3.86
2640	4841	1.215423	GGTGAATGGCTACCCCTCAAT	59.785	52.381	0.00	0.00	0.00	2.57
2749	4959	7.112565	CGCTTAAATATTTGCAAGATGCTACAG	59.887	37.037	11.05	0.00	45.31	2.74
2800	5044	8.863049	GTTATTTACATTTTCTCACAATGCCTG	58.137	33.333	0.00	0.00	35.36	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.001764	TGGGCAATGACCAGCAGAG	60.002	57.895	2.27	0.00	34.69	3.35
1	2	3.169378	TGGGCAATGACCAGCAGA	58.831	55.556	2.27	0.00	34.69	4.26
6	7	2.677524	GCAGCTGGGCAATGACCA	60.678	61.111	17.12	7.95	39.14	4.02
7	8	2.677524	TGCAGCTGGGCAATGACC	60.678	61.111	17.12	0.00	41.65	4.02
8	9	2.882876	CTGCAGCTGGGCAATGAC	59.117	61.111	17.12	0.00	44.40	3.06
9	10	3.066190	GCTGCAGCTGGGCAATGA	61.066	61.111	31.33	0.00	44.40	2.57
28	29	0.450583	CAGTCACACCATGCATGAGC	59.549	55.000	28.31	10.44	42.57	4.26
29	30	1.817357	ACAGTCACACCATGCATGAG	58.183	50.000	28.31	20.73	0.00	2.90
30	31	2.302733	ACTACAGTCACACCATGCATGA	59.697	45.455	28.31	5.43	0.00	3.07
31	32	2.417586	CACTACAGTCACACCATGCATG	59.582	50.000	20.19	20.19	0.00	4.06
45	46	3.764434	ACCTACTGGTCATGACACTACAG	59.236	47.826	26.47	23.51	44.78	2.74
85	86	8.452989	AATCTGTAAAGCATTTTCGATTTCAC	57.547	30.769	0.00	0.00	40.09	3.18
90	91	5.065218	AGCGAATCTGTAAAGCATTTTCGAT	59.935	36.000	9.01	0.97	40.60	3.59
93	94	5.631026	TCAGCGAATCTGTAAAGCATTTTC	58.369	37.500	0.00	0.00	43.32	2.29
98	99	2.742053	GGTTCAGCGAATCTGTAAAGCA	59.258	45.455	0.00	0.00	43.32	3.91
108	109	0.179073	CCATCGGAGGTTCAGCGAAT	60.179	55.000	0.00	0.00	0.00	3.34
111	112	2.892425	GCCATCGGAGGTTCAGCG	60.892	66.667	0.00	0.00	0.00	5.18
118	119	2.388890	GACATCAGGGCCATCGGAGG	62.389	65.000	6.18	1.71	0.00	4.30
180	181	3.524606	CTCCGGACGTATGGCCGT	61.525	66.667	27.23	1.35	45.85	5.68
181	182	4.944372	GCTCCGGACGTATGGCCG	62.944	72.222	23.08	23.08	46.80	6.13
216	217	4.157120	GCGCGAGGTGGTATGGGT	62.157	66.667	12.10	0.00	0.00	4.51
217	218	4.910585	GGCGCGAGGTGGTATGGG	62.911	72.222	12.10	0.00	0.00	4.00
339	340	3.725459	CATGCAACAGCGACGGCA	61.725	61.111	0.00	0.00	43.41	5.69
378	380	3.391665	CTCACATCCGACCCCCTGC	62.392	68.421	0.00	0.00	0.00	4.85
385	387	1.142748	CCTCAGCCTCACATCCGAC	59.857	63.158	0.00	0.00	0.00	4.79
412	426	0.038166	ACCACAACAGCCCATACAGG	59.962	55.000	0.00	0.00	37.03	4.00
494	512	2.358247	TTTGGTCGCGAGGGCTTC	60.358	61.111	10.24	0.00	36.88	3.86
572	2036	4.404654	GGCTTTTGGCGGTGCTCG	62.405	66.667	0.00	0.00	42.94	5.03
617	2101	1.304617	GGGAAGGAGGCAAAGGAGG	59.695	63.158	0.00	0.00	0.00	4.30
689	2173	7.093289	TGGAATCAGTTGGGTTTAGAAAACAAA	60.093	33.333	5.03	0.00	0.00	2.83
848	2336	5.630069	GCCTCCTAATTCATGTTCTCCAAGA	60.630	44.000	0.00	0.00	0.00	3.02
855	2343	4.702131	ACAAGTGCCTCCTAATTCATGTTC	59.298	41.667	0.00	0.00	0.00	3.18
1004	2494	6.744175	AGATATCCTCAAAGAGATGCTCAA	57.256	37.500	0.00	0.00	32.06	3.02
1070	2560	4.141846	GGAACAGCCAGAGAGAATCACATA	60.142	45.833	0.00	0.00	34.80	2.29
1106	2596	1.858091	CACGGCCTAGCATAACTCAG	58.142	55.000	0.00	0.00	0.00	3.35
1113	2603	0.541863	AGTAAAGCACGGCCTAGCAT	59.458	50.000	17.16	3.77	0.00	3.79
1124	2614	1.234821	CGGTTTGGCAGAGTAAAGCA	58.765	50.000	0.00	0.00	34.82	3.91
1138	2628	1.739466	CATACATGAGCAGCACGGTTT	59.261	47.619	0.00	0.00	0.00	3.27
1201	2730	5.817816	AGTGCAGTGTAAAATGCCTAGATAC	59.182	40.000	2.30	0.00	41.85	2.24
1203	2732	4.848357	AGTGCAGTGTAAAATGCCTAGAT	58.152	39.130	2.30	0.00	41.85	1.98
1249	2783	7.062956	TGTGTAAGTGTAGCTATGATTTGAACG	59.937	37.037	0.00	0.00	0.00	3.95
1372	2912	5.301805	TCAGTAGCGACATCTAATTCCATCA	59.698	40.000	0.00	0.00	0.00	3.07
1424	2964	3.909732	AGGAGTCAAAACCATGGTGAAA	58.090	40.909	20.60	1.39	0.00	2.69
1440	2981	3.708631	CCATCCAGATTCAGTGTAGGAGT	59.291	47.826	0.00	0.00	0.00	3.85
1488	3029	7.435784	GGAAGAAGAATTAGATCACGTTACCTC	59.564	40.741	0.00	0.00	0.00	3.85
1557	3099	5.804639	TCAACTGTAACACATAATGAGCCT	58.195	37.500	0.00	0.00	0.00	4.58
1587	3130	4.391830	GCACGTCCATCTGAGAATAACAAA	59.608	41.667	0.00	0.00	0.00	2.83
1779	3327	7.881775	TCAGAGATCATACACTTTAGTAGCA	57.118	36.000	0.00	0.00	0.00	3.49
1871	3438	2.029020	TCAGGAATCAACCTCACACGAG	60.029	50.000	0.00	0.00	38.32	4.18
1945	3859	9.474313	AGAGAATCACTATTTACTCTCAGACTT	57.526	33.333	0.00	0.00	37.82	3.01
1986	3900	2.967887	GCTGGGATTAAGGATTGCCAAT	59.032	45.455	0.00	0.00	32.55	3.16
1990	3904	1.683385	GGTGCTGGGATTAAGGATTGC	59.317	52.381	0.00	0.00	0.00	3.56
2621	4822	2.736670	ATTGAGGGGTAGCCATTCAC	57.263	50.000	14.06	0.00	0.00	3.18
2648	4855	3.094572	CCTTCAATCAGCCATTCACCTT	58.905	45.455	0.00	0.00	0.00	3.50
2649	4856	2.622452	CCCTTCAATCAGCCATTCACCT	60.622	50.000	0.00	0.00	0.00	4.00
2722	4932	4.998295	GCATCTTGCAAATATTTAAGCGC	58.002	39.130	0.00	0.00	44.26	5.92
2749	4959	4.960938	TCCCAGCACACTATCAATACATC	58.039	43.478	0.00	0.00	0.00	3.06

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.