AutoCloner

Multiple sequence alignment - TraesCS7A01G561400

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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	TraesCS7A01G561400	chr7A	100.000	3293	0	0	1	3293	732589567	732586275	0.000000e+00	6082.0
1	TraesCS7A01G561400	chr7A	92.701	137	6	2	742	874	732588694	732588558	9.320000e-46	195.0
2	TraesCS7A01G561400	chr7A	92.701	137	6	2	874	1010	732588826	732588694	9.320000e-46	195.0
3	TraesCS7A01G561400	chr7B	94.533	3329	133	17	1	3293	741998621	742001936	0.000000e+00	5094.0
4	TraesCS7A01G561400	chr7B	91.078	2320	121	22	1	2294	750571678	750569419	0.000000e+00	3059.0
5	TraesCS7A01G561400	chr7B	92.857	644	35	6	83	717	741994207	741994848	0.000000e+00	924.0
6	TraesCS7A01G561400	chr7B	82.256	727	53	29	2625	3293	750569081	750568373	2.870000e-155	558.0
7	TraesCS7A01G561400	chr7B	90.404	396	28	5	2908	3293	741963034	741963429	2.270000e-141	512.0
8	TraesCS7A01G561400	chr7B	92.199	141	3	3	742	874	750570820	750570680	3.350000e-45	193.0
9	TraesCS7A01G561400	chr7B	91.971	137	7	2	742	874	741999510	741999646	4.340000e-44	189.0
10	TraesCS7A01G561400	chr7B	89.781	137	10	2	874	1010	750570952	750570820	4.370000e-39	172.0
11	TraesCS7A01G561400	chr7B	85.714	147	6	6	874	1010	741999369	741999510	1.230000e-29	141.0
12	TraesCS7A01G561400	chr7D	93.161	3363	123	31	1	3293	633872943	633876268	0.000000e+00	4837.0
13	TraesCS7A01G561400	chr7D	94.891	137	3	2	742	874	633873833	633873969	9.260000e-51	211.0
14	TraesCS7A01G561400	chr7D	85.315	143	5	7	874	1010	633873701	633873833	2.060000e-27	134.0
15	TraesCS7A01G561400	chrUn	93.923	1843	79	11	653	2479	308271442	308273267	0.000000e+00	2752.0
16	TraesCS7A01G561400	chrUn	92.893	788	44	4	2516	3293	308273265	308274050	0.000000e+00	1134.0
17	TraesCS7A01G561400	chrUn	92.610	433	30	2	1	431	88895831	88895399	3.610000e-174	621.0
18	TraesCS7A01G561400	chrUn	93.418	395	25	1	25	418	308271050	308271444	4.740000e-163	584.0
19	TraesCS7A01G561400	chrUn	95.783	166	7	0	562	727	88895394	88895229	5.420000e-68	268.0
20	TraesCS7A01G561400	chrUn	94.161	137	4	2	742	874	308271675	308271811	4.310000e-49	206.0
21	TraesCS7A01G561400	chrUn	96.471	85	3	0	643	727	335070421	335070505	1.230000e-29	141.0
22	TraesCS7A01G561400	chr1B	75.333	150	32	4	1185	1333	23978811	23978666	2.120000e-07	67.6

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	TraesCS7A01G561400	chr7A	732586275	732589567	3292	True	2157.333333	6082	95.134000	1	3293	3	chr7A.!!$R1	3292
1	TraesCS7A01G561400	chr7B	741994207	742001936	7729	False	1587.000000	5094	91.268750	1	3293	4	chr7B.!!$F2	3292
2	TraesCS7A01G561400	chr7B	750568373	750571678	3305	True	995.500000	3059	88.828500	1	3293	4	chr7B.!!$R1	3292
3	TraesCS7A01G561400	chr7D	633872943	633876268	3325	False	1727.333333	4837	91.122333	1	3293	3	chr7D.!!$F1	3292
4	TraesCS7A01G561400	chrUn	308271050	308274050	3000	False	1169.000000	2752	93.598750	25	3293	4	chrUn.!!$F2	3268
5	TraesCS7A01G561400	chrUn	88895229	88895831	602	True	444.500000	621	94.196500	1	727	2	chrUn.!!$R1	726

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
908	5366	0.390124	ACAGCACACCAATTGCAAGG	59.610	50.000	4.94	3.99	42.83	3.61	F
964	5426	1.906574	CCGGGCCTCTATAAATGGCTA	59.093	52.381	0.84	0.00	45.45	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1830	6310	0.036164	CACCGTTCTGGATCACCCAA	59.964	55.0	0.0	0.0	46.07	4.12	R
2873	7502	0.178992	CCGCTCTCATCTCCTCTCCT	60.179	60.0	0.0	0.0	0.00	3.69	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
19	4434	3.801997	CCCGGGAGCTTGCAGGAT	61.802	66.667	18.48	0.00	0.00	3.24
109	4533	6.239317	GGGGTTAATAATGAAAGAGCCATTCC	60.239	42.308	0.00	0.00	35.94	3.01
155	4583	2.093658	GGAGAAACGAGATACAAGCCCA	60.094	50.000	0.00	0.00	0.00	5.36
167	4595	3.428413	ACAAGCCCACTAACCGTAATT	57.572	42.857	0.00	0.00	0.00	1.40
174	4602	2.485038	CCACTAACCGTAATTGGCGTTT	59.515	45.455	0.00	0.00	0.00	3.60
237	4665	1.279271	CTCCCAAGATCCAACCTCGTT	59.721	52.381	0.00	0.00	0.00	3.85
257	4685	2.038007	AGGCGGAGAAGGAGCTCA	59.962	61.111	17.19	0.00	36.62	4.26
287	4715	1.139853	GATTGGCAAGAGGAGGACGAT	59.860	52.381	5.96	0.00	0.00	3.73
382	4811	7.187824	AGAAGATAAACCAGCAAGTCTGATA	57.812	36.000	0.00	0.00	45.72	2.15
806	5254	5.184096	ACGTCAATCAGTAGTGAGATCTGTT	59.816	40.000	0.00	0.00	35.66	3.16
908	5366	0.390124	ACAGCACACCAATTGCAAGG	59.610	50.000	4.94	3.99	42.83	3.61
964	5426	1.906574	CCGGGCCTCTATAAATGGCTA	59.093	52.381	0.84	0.00	45.45	3.93
974	5436	7.528881	GCCTCTATAAATGGCTATACCCAAAGA	60.529	40.741	0.00	0.00	43.05	2.52
1017	5479	2.104267	CATGGCTTTCATGCGCTCT	58.896	52.632	9.73	0.00	45.58	4.09
1215	5677	4.443266	GAGGAGAAGCTGCGCCGT	62.443	66.667	9.10	0.00	32.50	5.68
1616	6093	2.349886	GTCGTACGTCGTCTACTCCATT	59.650	50.000	16.05	0.00	40.80	3.16
1617	6094	3.551890	GTCGTACGTCGTCTACTCCATTA	59.448	47.826	16.05	0.00	40.80	1.90
1618	6095	3.551890	TCGTACGTCGTCTACTCCATTAC	59.448	47.826	16.05	0.00	40.80	1.89
1619	6096	3.306973	CGTACGTCGTCTACTCCATTACA	59.693	47.826	7.22	0.00	34.52	2.41
1725	6202	4.854784	GCGACGATGGAGAGCGCA	62.855	66.667	11.47	0.00	46.19	6.09
1830	6310	0.181350	GGATGGACAAGGCCTTCGAT	59.819	55.000	17.29	8.50	33.99	3.59
1868	6348	4.082523	CATCACCACGGAGGCGGT	62.083	66.667	0.00	0.00	43.14	5.68
1966	6446	1.174078	TACACCGTCTGGCAACGAGA	61.174	55.000	19.00	0.00	45.37	4.04
1970	6450	2.338984	GTCTGGCAACGAGACGGT	59.661	61.111	0.00	0.00	42.51	4.83
2306	6786	4.864334	CTGATGACCCAGCCGCCC	62.864	72.222	0.00	0.00	0.00	6.13
2352	6912	5.238868	TGACTCCGTGCATCTCTACTTATAC	59.761	44.000	0.00	0.00	0.00	1.47
2444	7004	2.071540	GTAAAGGTTCGGGTGCTACAC	58.928	52.381	0.00	0.00	0.00	2.90
2445	7005	0.470766	AAAGGTTCGGGTGCTACACA	59.529	50.000	0.00	0.00	35.86	3.72
2446	7006	0.690762	AAGGTTCGGGTGCTACACAT	59.309	50.000	0.00	0.00	35.86	3.21
2447	7007	0.036388	AGGTTCGGGTGCTACACATG	60.036	55.000	0.00	0.00	35.86	3.21
2459	7019	2.287427	GCTACACATGCATGCATCCTTC	60.287	50.000	30.07	13.19	33.90	3.46
2632	7212	2.477845	AATGACTTGCAATTTGGGGC	57.522	45.000	0.00	0.00	0.00	5.80
2659	7239	7.147461	GGAGGAAGTATCTCCCTTCTGTTTTAT	60.147	40.741	0.00	0.00	43.71	1.40
2660	7240	8.164057	AGGAAGTATCTCCCTTCTGTTTTATT	57.836	34.615	0.00	0.00	38.66	1.40
2661	7241	8.615705	AGGAAGTATCTCCCTTCTGTTTTATTT	58.384	33.333	0.00	0.00	38.66	1.40
2662	7242	9.901172	GGAAGTATCTCCCTTCTGTTTTATTTA	57.099	33.333	0.00	0.00	38.66	1.40
2704	7289	1.068741	GCGGTACATGAACTAGGGAGG	59.931	57.143	0.00	0.00	0.00	4.30
2743	7328	3.084039	TCTCCTGAAATGCACATTGGAC	58.916	45.455	0.00	0.00	0.00	4.02
2756	7341	4.651778	CACATTGGACTCCCTAAACTTGA	58.348	43.478	0.00	0.00	0.00	3.02
2855	7465	0.540923	ATGGAGAGCAAGAGAGGCAC	59.459	55.000	0.00	0.00	0.00	5.01
2863	7492	3.547787	AAGAGAGGCACGAGGGGGT	62.548	63.158	0.00	0.00	0.00	4.95
2873	7502	2.297895	CGAGGGGGTTGACCATGGA	61.298	63.158	21.47	0.00	42.91	3.41
2881	7510	1.573108	GTTGACCATGGAGGAGAGGA	58.427	55.000	21.47	0.00	41.22	3.71
2882	7511	1.484240	GTTGACCATGGAGGAGAGGAG	59.516	57.143	21.47	0.00	41.22	3.69
2919	7550	2.745492	GAGCTCTGGTGGTGCTGC	60.745	66.667	6.43	0.00	43.67	5.25
2984	7623	4.388499	GGACGGGGCGAGCTTTGA	62.388	66.667	0.00	0.00	0.00	2.69
2985	7624	2.125106	GACGGGGCGAGCTTTGAT	60.125	61.111	0.00	0.00	0.00	2.57
3097	7760	1.585297	GCATGCCATTTAACATGGGC	58.415	50.000	6.36	0.00	43.13	5.36
3202	7865	5.392767	TGACACTCTCTACCAAGTTCATC	57.607	43.478	0.00	0.00	0.00	2.92
3221	7885	3.222173	TCTACCGCCCATGCATTTTAT	57.778	42.857	0.00	0.00	37.32	1.40
3277	7941	1.544724	ACCAACGCCAAATGCTATGT	58.455	45.000	0.00	0.00	38.05	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
69	4493	1.280457	ACCCCTTTGCTTCTCGATCT	58.720	50.000	0.00	0.00	0.00	2.75
109	4533	0.033366	TCATGGTATCACGCGGGATG	59.967	55.000	33.27	18.27	0.00	3.51
155	4583	3.401182	TCAAACGCCAATTACGGTTAGT	58.599	40.909	3.31	0.00	38.65	2.24
167	4595	2.350964	GCCGAACTTTTATCAAACGCCA	60.351	45.455	0.00	0.00	0.00	5.69
174	4602	6.873997	TCTCTCTATTGCCGAACTTTTATCA	58.126	36.000	0.00	0.00	0.00	2.15
237	4665	3.077556	GCTCCTTCTCCGCCTCCA	61.078	66.667	0.00	0.00	0.00	3.86
287	4715	2.109128	TCCCCTACACCTGAATTTTGCA	59.891	45.455	0.00	0.00	0.00	4.08
382	4811	5.063880	GGTACTCCTTTGTCTCACAACAAT	58.936	41.667	0.00	0.00	37.90	2.71
577	5019	6.039717	CACACCAGCCATTTATAAGTGCTTAT	59.960	38.462	9.13	9.13	39.02	1.73
806	5254	0.400213	CCATTTATAGAGGCCCGGCA	59.600	55.000	12.58	0.00	0.00	5.69
908	5366	2.100989	ACTACTGATTCACGTCCTCCC	58.899	52.381	0.00	0.00	0.00	4.30
964	5426	7.885399	GGATGATGTTTAGCTATCTTTGGGTAT	59.115	37.037	0.00	0.00	0.00	2.73
974	5436	7.423844	TCCGATATGGATGATGTTTAGCTAT	57.576	36.000	0.00	0.00	43.74	2.97
1017	5479	0.465705	GAGCCATGGATGAGGACGAA	59.534	55.000	18.40	0.00	0.00	3.85
1215	5677	1.180456	TGCTCCGGTACACCTCGAAA	61.180	55.000	0.00	0.00	0.00	3.46
1830	6310	0.036164	CACCGTTCTGGATCACCCAA	59.964	55.000	0.00	0.00	46.07	4.12
1868	6348	0.974010	CTTGCCGGTGTAGGGGTAGA	60.974	60.000	1.90	0.00	0.00	2.59
2306	6786	1.065636	ACACAGATGATGGAGGTGCAG	60.066	52.381	0.00	0.00	32.89	4.41
2444	7004	2.281539	TAGGGAAGGATGCATGCATG	57.718	50.000	36.73	22.70	36.70	4.06
2445	7005	4.662966	TTATAGGGAAGGATGCATGCAT	57.337	40.909	32.66	32.66	39.69	3.96
2446	7006	4.662966	ATTATAGGGAAGGATGCATGCA	57.337	40.909	25.04	25.04	0.00	3.96
2447	7007	7.651027	ATTTATTATAGGGAAGGATGCATGC	57.349	36.000	11.82	11.82	0.00	4.06
2615	7195	1.664873	CGCCCCAAATTGCAAGTCA	59.335	52.632	4.94	0.00	0.00	3.41
2659	7239	9.849166	GCTGGTGTATTTTACTGCTTAAATAAA	57.151	29.630	0.00	0.00	30.46	1.40
2660	7240	8.178964	CGCTGGTGTATTTTACTGCTTAAATAA	58.821	33.333	0.00	0.00	30.46	1.40
2661	7241	7.201661	CCGCTGGTGTATTTTACTGCTTAAATA	60.202	37.037	0.00	0.00	29.47	1.40
2662	7242	6.404293	CCGCTGGTGTATTTTACTGCTTAAAT	60.404	38.462	0.00	0.00	29.47	1.40
2663	7243	5.106475	CCGCTGGTGTATTTTACTGCTTAAA	60.106	40.000	0.00	0.00	0.00	1.52
2669	7254	4.247258	TGTACCGCTGGTGTATTTTACTG	58.753	43.478	10.01	0.00	36.19	2.74
2704	7289	2.627699	GAGATGAGAGACCTGGATGACC	59.372	54.545	0.00	0.00	0.00	4.02
2743	7328	6.598064	ACGAACCAATTATCAAGTTTAGGGAG	59.402	38.462	0.00	0.00	0.00	4.30
2756	7341	4.637276	TGAGTGTCACACGAACCAATTAT	58.363	39.130	1.22	0.00	39.64	1.28
2855	7465	2.257409	CTCCATGGTCAACCCCCTCG	62.257	65.000	12.58	0.00	34.29	4.63
2863	7492	1.362584	TCTCCTCTCCTCCATGGTCAA	59.637	52.381	12.58	0.00	37.07	3.18
2873	7502	0.178992	CCGCTCTCATCTCCTCTCCT	60.179	60.000	0.00	0.00	0.00	3.69
2881	7510	0.257328	TCCTGTCTCCGCTCTCATCT	59.743	55.000	0.00	0.00	0.00	2.90
2882	7511	0.383949	GTCCTGTCTCCGCTCTCATC	59.616	60.000	0.00	0.00	0.00	2.92
2919	7550	4.253257	GCGCCGACCTCGACCTAG	62.253	72.222	0.00	0.00	43.02	3.02
2984	7623	2.024918	CGCCCAAATCTTGCGCTAT	58.975	52.632	9.73	0.00	41.95	2.97
2985	7624	3.496711	CGCCCAAATCTTGCGCTA	58.503	55.556	9.73	0.00	41.95	4.26
2991	7630	1.003839	TCGCACTCGCCCAAATCTT	60.004	52.632	0.00	0.00	35.26	2.40
3202	7865	3.569701	AGAATAAAATGCATGGGCGGTAG	59.430	43.478	0.00	0.00	45.35	3.18
3221	7885	6.311735	AGGACAAGCCAAACCTTATAAAGAA	58.688	36.000	0.00	0.00	40.02	2.52
3240	7904	7.361894	GCGTTGGTTTAGTTTAATTTAGGACA	58.638	34.615	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.