AutoCloner

Multiple sequence alignment - TraesCS2A01G345700

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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	TraesCS2A01G345700	chr2A	100.000	2718	0	0	1	2718	584054317	584051600	0.000000e+00	5020.0
1	TraesCS2A01G345700	chr2D	90.607	1778	69	34	708	2412	440592103	440590351	0.000000e+00	2268.0
2	TraesCS2A01G345700	chr2D	87.302	567	71	1	1	567	440592710	440592145	0.000000e+00	647.0
3	TraesCS2A01G345700	chr2D	78.615	650	119	15	1	642	132063950	132064587	1.950000e-111	412.0
4	TraesCS2A01G345700	chr2D	78.818	406	65	12	4	407	65659480	65659094	1.250000e-63	254.0
5	TraesCS2A01G345700	chr2D	97.931	145	2	1	2574	2718	440590205	440590062	1.620000e-62	250.0
6	TraesCS2A01G345700	chr2D	97.638	127	2	1	2448	2573	440590366	440590240	1.640000e-52	217.0
7	TraesCS2A01G345700	chr2D	95.833	48	2	0	2573	2620	440590208	440590255	8.070000e-11	78.7
8	TraesCS2A01G345700	chr2D	89.831	59	5	1	568	625	622305120	622305178	1.040000e-09	75.0
9	TraesCS2A01G345700	chr2B	92.205	898	60	5	34	922	518383785	518382889	0.000000e+00	1262.0
10	TraesCS2A01G345700	chr2B	90.309	939	34	15	924	1814	518382728	518381799	0.000000e+00	1177.0
11	TraesCS2A01G345700	chr2B	89.696	592	50	3	1832	2412	518375686	518375095	0.000000e+00	745.0
12	TraesCS2A01G345700	chr2B	90.722	97	7	2	2623	2718	518374985	518374890	7.900000e-26	128.0
13	TraesCS2A01G345700	chr2B	94.231	52	2	1	2573	2623	793544213	793544162	8.070000e-11	78.7
14	TraesCS2A01G345700	chr2B	95.122	41	2	0	2413	2453	174365320	174365280	6.280000e-07	65.8
15	TraesCS2A01G345700	chr5B	78.214	560	103	12	31	587	272003662	272003119	9.320000e-90	340.0
16	TraesCS2A01G345700	chr5B	78.981	157	21	7	458	613	506933511	506933366	2.230000e-16	97.1
17	TraesCS2A01G345700	chr7A	75.828	604	117	17	4	601	403359203	403358623	2.060000e-71	279.0
18	TraesCS2A01G345700	chr7A	94.231	52	2	1	2573	2623	572189054	572189105	8.070000e-11	78.7
19	TraesCS2A01G345700	chr5A	76.383	470	81	22	177	640	507962352	507961907	2.720000e-55	226.0
20	TraesCS2A01G345700	chr3A	75.579	475	91	16	6	472	67117178	67116721	7.620000e-51	211.0
21	TraesCS2A01G345700	chr3A	79.273	275	51	6	6	278	508152070	508152340	1.280000e-43	187.0
22	TraesCS2A01G345700	chr3A	82.659	173	21	7	226	395	65307827	65307661	7.840000e-31	145.0
23	TraesCS2A01G345700	chr3A	81.287	171	24	5	524	692	487454260	487454096	6.110000e-27	132.0
24	TraesCS2A01G345700	chr5D	73.702	597	125	20	21	611	459079409	459078839	1.280000e-48	204.0
25	TraesCS2A01G345700	chr5D	79.699	133	17	3	564	694	420717102	420716978	1.340000e-13	87.9
26	TraesCS2A01G345700	chr5D	95.000	40	2	0	2413	2452	65995646	65995607	2.260000e-06	63.9
27	TraesCS2A01G345700	chr5D	95.000	40	2	0	2413	2452	130412045	130412006	2.260000e-06	63.9
28	TraesCS2A01G345700	chr5D	100.000	34	0	0	2413	2446	217916201	217916234	2.260000e-06	63.9
29	TraesCS2A01G345700	chr3D	77.133	293	60	7	6	296	386401046	386401333	2.170000e-36	163.0
30	TraesCS2A01G345700	chr3D	93.023	43	3	0	2413	2455	85066854	85066812	2.260000e-06	63.9
31	TraesCS2A01G345700	chr4D	94.231	52	3	0	2572	2623	385735050	385734999	2.240000e-11	80.5
32	TraesCS2A01G345700	chr4A	94.118	51	3	0	2573	2623	67170223	67170173	8.070000e-11	78.7
33	TraesCS2A01G345700	chr1A	94.231	52	2	1	2573	2623	23020333	23020384	8.070000e-11	78.7
34	TraesCS2A01G345700	chr1A	91.489	47	4	0	2413	2459	576370398	576370444	6.280000e-07	65.8
35	TraesCS2A01G345700	chr1A	100.000	34	0	0	2413	2446	557198168	557198201	2.260000e-06	63.9
36	TraesCS2A01G345700	chr7D	92.453	53	4	0	2569	2621	263044781	263044833	2.900000e-10	76.8
37	TraesCS2A01G345700	chr7B	92.453	53	4	0	2569	2621	240489755	240489703	2.900000e-10	76.8
38	TraesCS2A01G345700	chr6D	95.122	41	2	0	2413	2453	25730089	25730049	6.280000e-07	65.8
39	TraesCS2A01G345700	chr1D	95.000	40	2	0	2413	2452	26678439	26678400	2.260000e-06	63.9

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	TraesCS2A01G345700	chr2A	584051600	584054317	2717	True	5020.0	5020	100.0000	1	2718	1	chr2A.!!$R1	2717
1	TraesCS2A01G345700	chr2D	440590062	440592710	2648	True	845.5	2268	93.3695	1	2718	4	chr2D.!!$R2	2717
2	TraesCS2A01G345700	chr2D	132063950	132064587	637	False	412.0	412	78.6150	1	642	1	chr2D.!!$F1	641
3	TraesCS2A01G345700	chr2B	518381799	518383785	1986	True	1219.5	1262	91.2570	34	1814	2	chr2B.!!$R4	1780
4	TraesCS2A01G345700	chr2B	518374890	518375686	796	True	436.5	745	90.2090	1832	2718	2	chr2B.!!$R3	886
5	TraesCS2A01G345700	chr5B	272003119	272003662	543	True	340.0	340	78.2140	31	587	1	chr5B.!!$R1	556
6	TraesCS2A01G345700	chr7A	403358623	403359203	580	True	279.0	279	75.8280	4	601	1	chr7A.!!$R1	597
7	TraesCS2A01G345700	chr5D	459078839	459079409	570	True	204.0	204	73.7020	21	611	1	chr5D.!!$R4	590

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
922	951	0.381445	TTCAATCCATGCGCGATTGG	59.619	50.0	26.01	21.37	44.41	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2426	2680	0.907837	CTCGAATACGCACGAGTGTG	59.092	55.0	14.4	14.4	46.9	3.82	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
59	60	6.070656	TCCCATTAATCAATTGGACTGGATC	58.929	40.000	5.42	0.00	32.41	3.36
62	63	1.586422	ATCAATTGGACTGGATCGCG	58.414	50.000	5.42	0.00	0.00	5.87
120	121	5.220931	GCTATCATGCAAAAGAGAAACCGAT	60.221	40.000	0.00	0.00	0.00	4.18
313	315	5.507985	GGGTGAAAGAGAAGTTGAACATTGG	60.508	44.000	0.00	0.00	0.00	3.16
340	342	5.163457	GGGAGAGAATAGACTTGGAGAAGTG	60.163	48.000	0.00	0.00	42.80	3.16
451	458	5.314529	ACGGAGGAGTCGAAGATCATATTA	58.685	41.667	0.00	0.00	40.67	0.98
452	459	5.768662	ACGGAGGAGTCGAAGATCATATTAA	59.231	40.000	0.00	0.00	40.67	1.40
458	465	8.919145	AGGAGTCGAAGATCATATTAAAAGACT	58.081	33.333	0.00	0.00	40.67	3.24
540	550	1.268352	GCACAACAATGGAGGCGTTTA	59.732	47.619	0.00	0.00	0.00	2.01
625	635	6.478344	TGTTGAATTGTTGAAGCATGGTTTAC	59.522	34.615	12.13	13.10	0.00	2.01
645	655	9.673454	GGTTTACTCTGTTTTGTCGAATTATTT	57.327	29.630	0.00	0.00	0.00	1.40
652	662	9.872757	TCTGTTTTGTCGAATTATTTAAGTGAC	57.127	29.630	0.00	0.00	0.00	3.67
750	768	9.975218	AAGGTTTATATATGAAAAGTGTGGTCT	57.025	29.630	0.00	0.00	0.00	3.85
754	772	9.967451	TTTATATATGAAAAGTGTGGTCTTCCA	57.033	29.630	0.00	0.00	42.05	3.53
758	776	2.938956	AAAGTGTGGTCTTCCAGGAG	57.061	50.000	0.00	0.00	45.24	3.69
759	787	2.103153	AAGTGTGGTCTTCCAGGAGA	57.897	50.000	0.00	0.00	45.24	3.71
765	793	2.123589	TGGTCTTCCAGGAGAACAACA	58.876	47.619	4.61	0.00	40.26	3.33
771	799	6.231211	GTCTTCCAGGAGAACAACATTTAGA	58.769	40.000	0.00	0.00	0.00	2.10
803	831	1.308998	CCGAATGGGTTGTAGATGCC	58.691	55.000	0.00	0.00	0.00	4.40
824	852	2.852748	CTTGTAGTCCAAGTCGTCTCG	58.147	52.381	0.00	0.00	44.64	4.04
852	880	0.605319	ATGAACATGCGGTCCGTTGT	60.605	50.000	13.94	13.99	0.00	3.32
922	951	0.381445	TTCAATCCATGCGCGATTGG	59.619	50.000	26.01	21.37	44.41	3.16
935	1123	1.136305	GCGATTGGCTAGTGGAGTACA	59.864	52.381	0.00	0.00	39.11	2.90
972	1161	5.049828	AGGTTTACATTTCAAAACAGCTGC	58.950	37.500	15.27	0.00	37.33	5.25
1516	1745	3.848347	CTATGTGCGCGGCCTCGAT	62.848	63.158	21.43	6.15	39.00	3.59
1702	1931	0.107848	ACTATTACCGTGGTGCTGGC	60.108	55.000	0.72	0.00	0.00	4.85
1930	2173	7.858052	AATTTCAGTTTACATCAAAGCTTCG	57.142	32.000	0.00	0.00	0.00	3.79
1949	2192	2.060284	CGAAGCTCAGCTGCTGATATC	58.940	52.381	30.50	24.52	43.24	1.63
2111	2354	1.139058	AGGTAGCAAATGGGCTAGTCG	59.861	52.381	0.00	0.00	46.34	4.18
2131	2374	6.464222	AGTCGTCTGGAAACTTCAATGATAA	58.536	36.000	0.00	0.00	0.00	1.75
2336	2590	6.973843	TCAAAGACAACTTCATCAAGAATGG	58.026	36.000	0.00	0.00	35.25	3.16
2401	2655	7.041508	GCAGATAGAGGTGATGTATTCCAAAAG	60.042	40.741	0.00	0.00	0.00	2.27
2402	2656	7.443575	CAGATAGAGGTGATGTATTCCAAAAGG	59.556	40.741	0.00	0.00	0.00	3.11
2403	2657	4.860022	AGAGGTGATGTATTCCAAAAGGG	58.140	43.478	0.00	0.00	38.37	3.95
2404	2658	4.540099	AGAGGTGATGTATTCCAAAAGGGA	59.460	41.667	0.00	0.00	46.61	4.20
2434	2688	7.664082	AGTAATATATAGTACGCACACTCGT	57.336	36.000	13.17	0.00	45.49	4.18
2435	2689	7.516481	AGTAATATATAGTACGCACACTCGTG	58.484	38.462	13.17	0.00	46.56	4.35
2444	2698	3.010088	CACACTCGTGCGTATTCGA	57.990	52.632	0.00	0.00	36.06	3.71
2448	2702	3.598678	CTCGTGCGTATTCGAGTCA	57.401	52.632	5.55	0.00	45.37	3.41
2449	2703	1.891178	CTCGTGCGTATTCGAGTCAA	58.109	50.000	5.55	0.00	45.37	3.18
2450	2704	2.247637	CTCGTGCGTATTCGAGTCAAA	58.752	47.619	5.55	0.00	45.37	2.69
2451	2705	2.659757	CTCGTGCGTATTCGAGTCAAAA	59.340	45.455	5.55	0.00	45.37	2.44
2473	2727	4.666512	AGGGAAAATAAGCTCAGCAGAAA	58.333	39.130	0.00	0.00	0.00	2.52
2661	2954	6.294010	GGTTTTACTGTAGCTTCTTTTGGGAG	60.294	42.308	0.00	0.00	0.00	4.30

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	2.026262	TGGGAGCTAGGGTCATTGTTTC	60.026	50.000	0.00	0.00	0.00	2.78
120	121	3.830178	TCCCAGTTGTTTCTCGTCATCTA	59.170	43.478	0.00	0.00	0.00	1.98
210	212	2.260822	CTCCTTCTTCACCTCCTTGGA	58.739	52.381	0.00	0.00	39.71	3.53
263	265	3.653344	TCAGTCAAACTTCATCACCTCG	58.347	45.455	0.00	0.00	0.00	4.63
313	315	3.895041	CTCCAAGTCTATTCTCTCCCTCC	59.105	52.174	0.00	0.00	0.00	4.30
340	342	6.434018	AGCTCTTGTTTTGCATATTCTCTC	57.566	37.500	0.00	0.00	0.00	3.20
451	458	7.686615	GCATCATCTAAGAGGCTAGAGTCTTTT	60.687	40.741	11.14	0.00	41.71	2.27
452	459	6.239289	GCATCATCTAAGAGGCTAGAGTCTTT	60.239	42.308	11.14	0.00	41.71	2.52
458	465	4.522405	GTCTGCATCATCTAAGAGGCTAGA	59.478	45.833	0.00	0.00	44.93	2.43
540	550	9.836076	CATAGATTTGCGATACATGAATGAATT	57.164	29.630	0.00	0.00	0.00	2.17
645	655	9.974980	TTATATAGCACAAATCATCGTCACTTA	57.025	29.630	0.00	0.00	0.00	2.24
648	658	8.171196	CCATTATATAGCACAAATCATCGTCAC	58.829	37.037	0.00	0.00	0.00	3.67
652	662	8.255394	TGTCCATTATATAGCACAAATCATCG	57.745	34.615	0.00	0.00	0.00	3.84
732	745	6.214615	TCCTGGAAGACCACACTTTTCATATA	59.785	38.462	0.00	0.00	41.77	0.86
750	768	5.003804	GCTCTAAATGTTGTTCTCCTGGAA	58.996	41.667	0.00	0.00	0.00	3.53
754	772	8.691661	TTTAAAGCTCTAAATGTTGTTCTCCT	57.308	30.769	0.00	0.00	0.00	3.69
758	776	9.797473	GCAAATTTAAAGCTCTAAATGTTGTTC	57.203	29.630	18.31	8.05	32.92	3.18
759	787	8.773645	GGCAAATTTAAAGCTCTAAATGTTGTT	58.226	29.630	18.31	5.78	32.92	2.83
765	793	7.492344	CCATTCGGCAAATTTAAAGCTCTAAAT	59.508	33.333	0.00	0.00	33.78	1.40
771	799	3.260632	ACCCATTCGGCAAATTTAAAGCT	59.739	39.130	0.00	0.00	33.26	3.74
824	852	1.269206	CCGCATGTTCATGGGTAATGC	60.269	52.381	21.91	11.27	40.14	3.56
852	880	0.396435	ATCAACAAGTGGCCACGAGA	59.604	50.000	29.68	22.20	36.20	4.04
922	951	6.313164	GTGGAAATTACTTGTACTCCACTAGC	59.687	42.308	15.70	0.00	46.09	3.42
935	1123	9.758651	GAAATGTAAACCTTGTGGAAATTACTT	57.241	29.630	0.00	0.00	34.64	2.24
972	1161	0.911769	TCTATGGCTTGTGGGGACAG	59.088	55.000	0.00	0.00	44.46	3.51
975	1164	1.215173	CCAATCTATGGCTTGTGGGGA	59.785	52.381	0.00	0.00	43.80	4.81
1026	1217	5.298276	TCCCTTCCAATAATGCAACGAATAC	59.702	40.000	0.00	0.00	0.00	1.89
1186	1386	2.144952	TGGAGCTTGAAGCCACAGA	58.855	52.632	14.45	0.00	43.77	3.41
1511	1738	1.663379	TACCTCCACGCCACATCGAG	61.663	60.000	0.00	0.00	0.00	4.04
1516	1745	3.687102	CGGTACCTCCACGCCACA	61.687	66.667	10.90	0.00	35.57	4.17
1642	1871	0.817634	TCAAGTCCTGCCCAAACACG	60.818	55.000	0.00	0.00	0.00	4.49
1732	1964	8.266392	AGATCATGCTGTTTTTGTTTGAAAAA	57.734	26.923	0.00	0.00	30.95	1.94
1733	1965	7.846644	AGATCATGCTGTTTTTGTTTGAAAA	57.153	28.000	0.00	0.00	0.00	2.29
1828	2071	6.426937	CCCGCAGTAAAGCATTGTATTATACT	59.573	38.462	3.92	0.00	0.00	2.12
1930	2173	3.061322	CAGATATCAGCAGCTGAGCTTC	58.939	50.000	28.60	22.56	44.08	3.86
1934	2177	3.794717	ACAACAGATATCAGCAGCTGAG	58.205	45.455	28.60	17.49	44.08	3.35
2111	2354	6.500684	TGCTTATCATTGAAGTTTCCAGAC	57.499	37.500	0.00	0.00	0.00	3.51
2312	2563	6.547141	ACCATTCTTGATGAAGTTGTCTTTGA	59.453	34.615	0.00	0.00	38.03	2.69
2336	2590	4.065789	ACAAACCTAGTTAGCTCTGCAAC	58.934	43.478	0.00	0.00	0.00	4.17
2408	2662	9.208022	ACGAGTGTGCGTACTATATATTACTTA	57.792	33.333	4.97	0.00	43.61	2.24
2409	2663	8.013947	CACGAGTGTGCGTACTATATATTACTT	58.986	37.037	4.97	0.00	43.59	2.24
2410	2664	7.516481	CACGAGTGTGCGTACTATATATTACT	58.484	38.462	4.97	0.00	43.59	2.24
2411	2665	7.702069	CACGAGTGTGCGTACTATATATTAC	57.298	40.000	4.97	1.13	43.59	1.89
2426	2680	0.907837	CTCGAATACGCACGAGTGTG	59.092	55.000	14.40	14.40	46.90	3.82
2427	2681	3.307829	CTCGAATACGCACGAGTGT	57.692	52.632	4.12	4.12	46.90	3.55
2431	2685	2.334971	TTTGACTCGAATACGCACGA	57.665	45.000	0.00	0.00	39.58	4.35
2432	2686	2.222508	CCTTTTGACTCGAATACGCACG	60.223	50.000	0.00	0.00	39.58	5.34
2433	2687	2.093783	CCCTTTTGACTCGAATACGCAC	59.906	50.000	0.00	0.00	39.58	5.34
2434	2688	2.028839	TCCCTTTTGACTCGAATACGCA	60.029	45.455	0.00	0.00	39.58	5.24
2435	2689	2.613691	TCCCTTTTGACTCGAATACGC	58.386	47.619	0.00	0.00	39.58	4.42
2436	2690	5.600908	TTTTCCCTTTTGACTCGAATACG	57.399	39.130	0.00	0.00	41.26	3.06
2437	2691	7.696872	GCTTATTTTCCCTTTTGACTCGAATAC	59.303	37.037	0.00	0.00	0.00	1.89
2438	2692	7.610305	AGCTTATTTTCCCTTTTGACTCGAATA	59.390	33.333	0.00	0.00	0.00	1.75
2439	2693	6.434340	AGCTTATTTTCCCTTTTGACTCGAAT	59.566	34.615	0.00	0.00	0.00	3.34
2440	2694	5.768164	AGCTTATTTTCCCTTTTGACTCGAA	59.232	36.000	0.00	0.00	0.00	3.71
2441	2695	5.313712	AGCTTATTTTCCCTTTTGACTCGA	58.686	37.500	0.00	0.00	0.00	4.04
2442	2696	5.181245	TGAGCTTATTTTCCCTTTTGACTCG	59.819	40.000	0.00	0.00	0.00	4.18
2443	2697	6.575162	TGAGCTTATTTTCCCTTTTGACTC	57.425	37.500	0.00	0.00	0.00	3.36
2444	2698	5.047731	GCTGAGCTTATTTTCCCTTTTGACT	60.048	40.000	0.00	0.00	0.00	3.41
2445	2699	5.164233	GCTGAGCTTATTTTCCCTTTTGAC	58.836	41.667	0.00	0.00	0.00	3.18
2446	2700	4.832266	TGCTGAGCTTATTTTCCCTTTTGA	59.168	37.500	5.83	0.00	0.00	2.69
2447	2701	5.047802	TCTGCTGAGCTTATTTTCCCTTTTG	60.048	40.000	5.83	0.00	0.00	2.44
2448	2702	5.079643	TCTGCTGAGCTTATTTTCCCTTTT	58.920	37.500	5.83	0.00	0.00	2.27
2449	2703	4.666512	TCTGCTGAGCTTATTTTCCCTTT	58.333	39.130	5.83	0.00	0.00	3.11
2450	2704	4.307032	TCTGCTGAGCTTATTTTCCCTT	57.693	40.909	5.83	0.00	0.00	3.95
2451	2705	4.307032	TTCTGCTGAGCTTATTTTCCCT	57.693	40.909	5.83	0.00	0.00	4.20
2473	2727	4.887071	TGCAAGTCATTCTGGTAGTTTTGT	59.113	37.500	0.00	0.00	0.00	2.83
2503	2762	7.230913	TGTTTACGATTTGATTTTCCCACCTAA	59.769	33.333	0.00	0.00	0.00	2.69
2661	2954	2.860136	GCTTCGCATTGCTTTTAATCCC	59.140	45.455	7.12	0.00	0.00	3.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.