AutoCloner

Multiple sequence alignment - TraesCS2A01G542300

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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	TraesCS2A01G542300	chr2A	100.000	2516	0	0	1	2516	753054193	753051678	0.000000e+00	4647.0
1	TraesCS2A01G542300	chr2A	95.816	741	25	3	1	737	70696216	70695478	0.000000e+00	1192.0
2	TraesCS2A01G542300	chr2A	88.704	602	44	9	1890	2472	753040798	753040202	0.000000e+00	713.0
3	TraesCS2A01G542300	chr2A	78.659	328	64	6	2029	2354	145392633	145392310	1.960000e-51	213.0
4	TraesCS2A01G542300	chr2B	93.674	1154	69	3	739	1888	762072014	762070861	0.000000e+00	1724.0
5	TraesCS2A01G542300	chr2B	89.515	639	46	7	1895	2514	762070620	762069984	0.000000e+00	789.0
6	TraesCS2A01G542300	chr2B	92.118	406	29	2	1	403	608537109	608537514	1.010000e-158	569.0
7	TraesCS2A01G542300	chrUn	93.414	1154	72	3	739	1888	342645067	342643914	0.000000e+00	1707.0
8	TraesCS2A01G542300	chrUn	92.374	1154	74	5	739	1888	343020617	343019474	0.000000e+00	1631.0
9	TraesCS2A01G542300	chrUn	89.356	1071	103	9	825	1885	338975305	338976374	0.000000e+00	1336.0
10	TraesCS2A01G542300	chrUn	89.356	1071	103	9	825	1885	342893158	342894227	0.000000e+00	1336.0
11	TraesCS2A01G542300	chrUn	88.792	919	93	8	831	1740	329049457	329048540	0.000000e+00	1118.0
12	TraesCS2A01G542300	chrUn	88.649	925	95	8	825	1740	417387713	417388636	0.000000e+00	1118.0
13	TraesCS2A01G542300	chrUn	90.167	600	39	7	1890	2472	342643677	342643081	0.000000e+00	763.0
14	TraesCS2A01G542300	chrUn	90.167	600	39	7	1890	2472	343019237	343018641	0.000000e+00	763.0
15	TraesCS2A01G542300	chrUn	90.050	603	40	7	1887	2472	440176539	440177138	0.000000e+00	763.0
16	TraesCS2A01G542300	chrUn	84.233	463	33	23	281	737	75238558	75238130	5.010000e-112	414.0
17	TraesCS2A01G542300	chr2D	94.369	1101	60	2	789	1888	621140962	621139863	0.000000e+00	1688.0
18	TraesCS2A01G542300	chr2D	89.292	1130	101	11	770	1888	621265656	621264536	0.000000e+00	1399.0
19	TraesCS2A01G542300	chr2D	85.116	645	65	12	1890	2514	621139626	621138993	4.570000e-177	630.0
20	TraesCS2A01G542300	chr2D	100.000	34	0	0	756	789	621141088	621141055	2.090000e-06	63.9
21	TraesCS2A01G542300	chr6B	91.142	429	32	4	1	426	4499701	4499276	6.030000e-161	577.0
22	TraesCS2A01G542300	chr6B	93.333	150	8	2	590	738	4499193	4499045	1.170000e-53	220.0
23	TraesCS2A01G542300	chr1B	90.783	434	34	2	1	431	329956504	329956934	2.170000e-160	575.0
24	TraesCS2A01G542300	chr1B	92.462	398	27	1	1	395	578042914	578043311	1.310000e-157	566.0
25	TraesCS2A01G542300	chr1B	89.091	165	13	4	575	738	578043460	578043620	1.530000e-47	200.0
26	TraesCS2A01G542300	chr5B	90.000	450	36	7	1	446	61062646	61062202	7.810000e-160	573.0
27	TraesCS2A01G542300	chr3B	92.677	396	26	1	1	393	31365512	31365907	3.630000e-158	568.0
28	TraesCS2A01G542300	chr3B	86.957	161	18	2	577	737	31366049	31366206	7.150000e-41	178.0
29	TraesCS2A01G542300	chr1A	92.462	398	27	1	1	395	9215049	9214652	1.310000e-157	566.0
30	TraesCS2A01G542300	chr1A	88.957	163	15	2	575	737	576789603	576789762	5.490000e-47	198.0
31	TraesCS2A01G542300	chr1A	88.272	162	16	2	576	737	52222896	52222738	9.190000e-45	191.0
32	TraesCS2A01G542300	chr5A	87.002	477	52	9	3	472	644331132	644330659	1.710000e-146	529.0
33	TraesCS2A01G542300	chr5A	77.944	467	78	20	1978	2425	520241499	520241959	4.130000e-68	268.0
34	TraesCS2A01G542300	chr5A	79.052	401	76	8	2021	2419	672842671	672843065	4.130000e-68	268.0
35	TraesCS2A01G542300	chr7B	90.909	165	9	4	576	737	672989111	672988950	1.520000e-52	217.0
36	TraesCS2A01G542300	chr7B	91.156	147	9	2	591	737	228828974	228828832	1.970000e-46	196.0
37	TraesCS2A01G542300	chr7B	93.750	64	4	0	1974	2037	502692644	502692581	2.060000e-16	97.1
38	TraesCS2A01G542300	chr4A	88.462	52	6	0	2272	2323	634528432	634528483	2.090000e-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	TraesCS2A01G542300	chr2A	753051678	753054193	2515	True	4647.000000	4647	100.000000	1	2516	1	chr2A.!!$R4	2515
1	TraesCS2A01G542300	chr2A	70695478	70696216	738	True	1192.000000	1192	95.816000	1	737	1	chr2A.!!$R1	736
2	TraesCS2A01G542300	chr2A	753040202	753040798	596	True	713.000000	713	88.704000	1890	2472	1	chr2A.!!$R3	582
3	TraesCS2A01G542300	chr2B	762069984	762072014	2030	True	1256.500000	1724	91.594500	739	2514	2	chr2B.!!$R1	1775
4	TraesCS2A01G542300	chrUn	338975305	338976374	1069	False	1336.000000	1336	89.356000	825	1885	1	chrUn.!!$F1	1060
5	TraesCS2A01G542300	chrUn	342893158	342894227	1069	False	1336.000000	1336	89.356000	825	1885	1	chrUn.!!$F2	1060
6	TraesCS2A01G542300	chrUn	342643081	342645067	1986	True	1235.000000	1707	91.790500	739	2472	2	chrUn.!!$R3	1733
7	TraesCS2A01G542300	chrUn	343018641	343020617	1976	True	1197.000000	1631	91.270500	739	2472	2	chrUn.!!$R4	1733
8	TraesCS2A01G542300	chrUn	329048540	329049457	917	True	1118.000000	1118	88.792000	831	1740	1	chrUn.!!$R2	909
9	TraesCS2A01G542300	chrUn	417387713	417388636	923	False	1118.000000	1118	88.649000	825	1740	1	chrUn.!!$F3	915
10	TraesCS2A01G542300	chrUn	440176539	440177138	599	False	763.000000	763	90.050000	1887	2472	1	chrUn.!!$F4	585
11	TraesCS2A01G542300	chr2D	621264536	621265656	1120	True	1399.000000	1399	89.292000	770	1888	1	chr2D.!!$R1	1118
12	TraesCS2A01G542300	chr2D	621138993	621141088	2095	True	793.966667	1688	93.161667	756	2514	3	chr2D.!!$R2	1758
13	TraesCS2A01G542300	chr6B	4499045	4499701	656	True	398.500000	577	92.237500	1	738	2	chr6B.!!$R1	737
14	TraesCS2A01G542300	chr1B	578042914	578043620	706	False	383.000000	566	90.776500	1	738	2	chr1B.!!$F2	737
15	TraesCS2A01G542300	chr3B	31365512	31366206	694	False	373.000000	568	89.817000	1	737	2	chr3B.!!$F1	736

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
933	1161	0.179189	GAAGCAAACGCATTCTCCGG	60.179	55.0	0.0	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2094	2581	0.039074	CCGGATCGAGGAGGAAATCG	60.039	60.0	0.0	0.0	40.26	3.34	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
236	237	1.219124	GAAGCACCGGAGAGATGCA	59.781	57.895	9.46	0.00	43.63	3.96
253	254	1.447838	CATCACGGTGAGGGTTCGG	60.448	63.158	16.84	0.00	0.00	4.30
277	278	2.435938	GGGAAGTTGCCGCGATCA	60.436	61.111	8.23	1.40	0.00	2.92
279	280	1.582610	GGGAAGTTGCCGCGATCAAA	61.583	55.000	8.23	0.00	0.00	2.69
549	649	0.523546	AGTTGCGCGTACGATCTGAG	60.524	55.000	21.65	3.31	43.93	3.35
585	709	1.286501	GAATATGTGCGGCTTCGACA	58.713	50.000	0.00	0.00	35.61	4.35
823	1041	3.568007	GTCCAAAATCAAGCAGGTACACA	59.432	43.478	0.00	0.00	0.00	3.72
933	1161	0.179189	GAAGCAAACGCATTCTCCGG	60.179	55.000	0.00	0.00	0.00	5.14
949	1177	3.772572	TCTCCGGTCAAGGATCAATACAA	59.227	43.478	0.00	0.00	39.96	2.41
955	1183	4.636206	GGTCAAGGATCAATACAACACCTC	59.364	45.833	0.00	0.00	0.00	3.85
1006	1234	1.476085	CATTTCCAACCGCAATGGCTA	59.524	47.619	0.00	0.00	43.94	3.93
1077	1305	1.290203	CGTCTGCGGCAATCTACAAT	58.710	50.000	3.44	0.00	0.00	2.71
1124	1352	0.391661	CTCAGCACCAACTACGGCAT	60.392	55.000	0.00	0.00	0.00	4.40
1180	1408	4.039973	ACCAAATCGTCTTCAAGTACTCCA	59.960	41.667	0.00	0.00	0.00	3.86
1182	1410	3.870633	ATCGTCTTCAAGTACTCCACC	57.129	47.619	0.00	0.00	0.00	4.61
1194	1422	2.927856	TCCACCCAGGCACACGAT	60.928	61.111	0.00	0.00	37.29	3.73
1197	1425	1.600636	CACCCAGGCACACGATGTT	60.601	57.895	0.00	0.00	0.00	2.71
1200	1428	0.606401	CCCAGGCACACGATGTTCTT	60.606	55.000	0.00	0.00	0.00	2.52
1278	1506	3.262151	TCAACTCCGGGAATGATGTTGTA	59.738	43.478	19.48	8.88	36.93	2.41
1285	1513	2.943033	GGGAATGATGTTGTAACCCTCG	59.057	50.000	0.00	0.00	33.79	4.63
1286	1514	3.606687	GGAATGATGTTGTAACCCTCGT	58.393	45.455	0.00	0.00	0.00	4.18
1311	1539	1.449601	CGGCACCCGCTACTTCATT	60.450	57.895	0.00	0.00	41.17	2.57
1324	1552	3.149005	ACTTCATTTGCGGTTTCCCTA	57.851	42.857	0.00	0.00	0.00	3.53
1421	1649	2.727544	CCCAAGTGCAACCAACGG	59.272	61.111	0.00	0.00	37.80	4.44
1500	1728	0.804156	CCGTTTTGCTTGCCGTTGTT	60.804	50.000	0.00	0.00	0.00	2.83
1532	1762	3.340928	CTTGAGTGCATCTCCACATTCA	58.659	45.455	11.99	0.00	42.12	2.57
1559	1789	6.027749	GGCACATGTGTACTTTATGTTTAGC	58.972	40.000	26.01	6.42	33.06	3.09
1596	1826	9.692749	TTACTAGCAATTATCTGTGTGTATAGC	57.307	33.333	0.00	0.00	0.00	2.97
1653	1884	6.584563	GGCTTTGCGTTTTACTGATTCATTTA	59.415	34.615	0.00	0.00	0.00	1.40
1666	1897	8.286191	ACTGATTCATTTAGGAGGATTTGTTC	57.714	34.615	0.00	0.00	0.00	3.18
1714	1945	3.692101	ACATTTGTCCTGAAACACGTTCA	59.308	39.130	0.00	0.00	44.20	3.18
1740	1971	3.636153	AACCATAAGAGCCCAGACTTC	57.364	47.619	0.00	0.00	0.00	3.01
1747	1978	0.606604	GAGCCCAGACTTCCGTAACA	59.393	55.000	0.00	0.00	0.00	2.41
1818	2051	3.632145	GTCTGCCCCGATTGTAAATGAAT	59.368	43.478	0.00	0.00	0.00	2.57
1885	2120	2.587889	CCCGCCCCGAACATACTT	59.412	61.111	0.00	0.00	0.00	2.24
1888	2123	0.810031	CCGCCCCGAACATACTTGAG	60.810	60.000	0.00	0.00	0.00	3.02
1890	2125	0.107654	GCCCCGAACATACTTGAGCT	60.108	55.000	0.00	0.00	0.00	4.09
1892	2127	2.224305	GCCCCGAACATACTTGAGCTAT	60.224	50.000	0.00	0.00	0.00	2.97
1894	2129	4.502604	GCCCCGAACATACTTGAGCTATAA	60.503	45.833	0.00	0.00	0.00	0.98
1895	2130	5.607477	CCCCGAACATACTTGAGCTATAAA	58.393	41.667	0.00	0.00	0.00	1.40
1896	2131	6.053005	CCCCGAACATACTTGAGCTATAAAA	58.947	40.000	0.00	0.00	0.00	1.52
1897	2132	6.540914	CCCCGAACATACTTGAGCTATAAAAA	59.459	38.462	0.00	0.00	0.00	1.94
1898	2133	7.228706	CCCCGAACATACTTGAGCTATAAAAAT	59.771	37.037	0.00	0.00	0.00	1.82
1917	2385	4.859304	AATATACATGCAGCATTGGGTG	57.141	40.909	4.69	0.00	45.24	4.61
1924	2392	0.675633	GCAGCATTGGGTGAAAGTGT	59.324	50.000	0.00	0.00	45.29	3.55
1932	2400	1.780309	TGGGTGAAAGTGTTCCATCCT	59.220	47.619	0.00	0.00	32.28	3.24
2147	2634	2.800881	CGTGAGCATAGCATAGGTCA	57.199	50.000	0.00	0.00	39.66	4.02
2217	2704	3.071580	GGAGAGAAATGTGCTCCGG	57.928	57.895	0.00	0.00	38.88	5.14
2228	2715	2.281484	GCTCCGGCTGGAACAACA	60.281	61.111	16.91	0.00	45.87	3.33
2373	2861	1.021202	CGTTGAGCTGTTGGGTTTCA	58.979	50.000	0.00	0.00	0.00	2.69
2374	2862	1.268539	CGTTGAGCTGTTGGGTTTCAC	60.269	52.381	0.00	0.00	0.00	3.18
2375	2863	2.024414	GTTGAGCTGTTGGGTTTCACT	58.976	47.619	0.00	0.00	0.00	3.41
2391	2879	1.006825	CACTGCGATTTCCGTGTCGA	61.007	55.000	0.00	0.00	40.11	4.20
2446	2934	1.473434	GGACGTCTCAGGCCTATTTGG	60.473	57.143	16.46	0.00	39.35	3.28
2491	2983	0.470456	ACCACTAACTGACCGGACCA	60.470	55.000	9.46	4.56	0.00	4.02
2514	3006	1.674057	CCCGGATGTATCAGAGGGC	59.326	63.158	0.73	0.00	33.22	5.19
2515	3007	0.833834	CCCGGATGTATCAGAGGGCT	60.834	60.000	0.73	0.00	33.22	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	108	2.762360	CGTATGCAACGTGGTGGAT	58.238	52.632	11.62	0.00	46.72	3.41
193	194	2.829458	GGCTACCTCGACGGCTCT	60.829	66.667	0.00	0.00	35.61	4.09
236	237	2.978824	CCGAACCCTCACCGTGAT	59.021	61.111	0.62	0.00	0.00	3.06
253	254	2.823829	CGGCAACTTCCCGCTATGC	61.824	63.158	0.00	0.00	39.22	3.14
277	278	2.933928	GCCTTCCCTTGACGTACGATTT	60.934	50.000	24.41	0.00	0.00	2.17
279	280	0.175073	GCCTTCCCTTGACGTACGAT	59.825	55.000	24.41	6.13	0.00	3.73
287	288	2.125147	CATCGCGCCTTCCCTTGA	60.125	61.111	0.00	0.00	0.00	3.02
344	345	2.620115	CGATGCAACTGATTATTGGCCT	59.380	45.455	3.32	0.00	0.00	5.19
349	350	2.286595	CGCAGCGATGCAACTGATTATT	60.287	45.455	26.87	0.00	35.90	1.40
536	636	2.289375	CGCTGCTCAGATCGTACGC	61.289	63.158	11.24	0.00	0.00	4.42
823	1041	2.023414	TTGGTGGAAGCGTCGAGTGT	62.023	55.000	0.00	0.00	36.92	3.55
933	1161	4.636206	GGAGGTGTTGTATTGATCCTTGAC	59.364	45.833	0.00	0.00	0.00	3.18
949	1177	5.151454	CAGAGGAGATTATAAGGGAGGTGT	58.849	45.833	0.00	0.00	0.00	4.16
955	1183	4.041444	AGCTTGCAGAGGAGATTATAAGGG	59.959	45.833	0.00	0.00	0.00	3.95
1006	1234	3.866449	GCGAGAAGAATGGTTCTCCTTGT	60.866	47.826	10.36	0.00	46.73	3.16
1124	1352	0.611714	GTTCCTAGAGGACGCCCAAA	59.388	55.000	0.00	0.00	45.39	3.28
1180	1408	1.302511	GAACATCGTGTGCCTGGGT	60.303	57.895	0.00	0.00	0.00	4.51
1182	1410	0.518636	CAAGAACATCGTGTGCCTGG	59.481	55.000	0.00	0.00	0.00	4.45
1194	1422	1.815408	GCCTTGCTGACCTCAAGAACA	60.815	52.381	4.48	0.00	42.52	3.18
1197	1425	1.376466	GGCCTTGCTGACCTCAAGA	59.624	57.895	0.00	0.00	42.52	3.02
1200	1428	2.922503	TCGGCCTTGCTGACCTCA	60.923	61.111	0.00	0.00	39.19	3.86
1250	1478	1.003118	CATTCCCGGAGTTGAAGGTGA	59.997	52.381	0.73	0.00	0.00	4.02
1532	1762	4.651778	ACATAAAGTACACATGTGCCTGT	58.348	39.130	25.68	17.93	31.83	4.00
1596	1826	6.035650	CGTCCAACATACACATAACTACTTGG	59.964	42.308	0.00	0.00	0.00	3.61
1653	1884	8.670521	AATAATCCTTTTGAACAAATCCTCCT	57.329	30.769	0.82	0.00	0.00	3.69
1714	1945	5.430089	AGTCTGGGCTCTTATGGTTTAGAAT	59.570	40.000	0.00	0.00	0.00	2.40
1885	2120	8.620116	TGCTGCATGTATATTTTTATAGCTCA	57.380	30.769	0.00	0.00	0.00	4.26
1888	2123	9.079833	CCAATGCTGCATGTATATTTTTATAGC	57.920	33.333	17.00	0.00	0.00	2.97
1890	2125	9.087871	ACCCAATGCTGCATGTATATTTTTATA	57.912	29.630	17.00	0.00	0.00	0.98
1892	2127	7.069208	TCACCCAATGCTGCATGTATATTTTTA	59.931	33.333	17.00	0.00	0.00	1.52
1894	2129	5.363292	TCACCCAATGCTGCATGTATATTTT	59.637	36.000	17.00	0.00	0.00	1.82
1895	2130	4.894705	TCACCCAATGCTGCATGTATATTT	59.105	37.500	17.00	0.00	0.00	1.40
1896	2131	4.472496	TCACCCAATGCTGCATGTATATT	58.528	39.130	17.00	0.00	0.00	1.28
1897	2132	4.103013	TCACCCAATGCTGCATGTATAT	57.897	40.909	17.00	0.00	0.00	0.86
1898	2133	3.574354	TCACCCAATGCTGCATGTATA	57.426	42.857	17.00	0.00	0.00	1.47
1907	2375	1.963515	GGAACACTTTCACCCAATGCT	59.036	47.619	0.00	0.00	32.80	3.79
1932	2400	2.551270	GGCCATGACCTATCTATCCCA	58.449	52.381	0.00	0.00	0.00	4.37
1961	2429	3.737172	GGTGAAATGCTGCGCCGT	61.737	61.111	4.18	0.00	0.00	5.68
2094	2581	0.039074	CCGGATCGAGGAGGAAATCG	60.039	60.000	0.00	0.00	40.26	3.34
2098	2585	1.392710	GCTTCCGGATCGAGGAGGAA	61.393	60.000	18.05	14.76	39.22	3.36
2147	2634	2.158608	CCCTGGCCCGATAAAAGAAGAT	60.159	50.000	0.00	0.00	0.00	2.40
2217	2704	0.957888	GCCCTCTCTGTTGTTCCAGC	60.958	60.000	0.00	0.00	32.32	4.85
2228	2715	1.274712	CAACCTCTTCTGCCCTCTCT	58.725	55.000	0.00	0.00	0.00	3.10
2373	2861	0.319211	TTCGACACGGAAATCGCAGT	60.319	50.000	0.00	0.00	43.89	4.40
2374	2862	0.093026	GTTCGACACGGAAATCGCAG	59.907	55.000	0.00	0.00	43.89	5.18
2375	2863	1.286354	GGTTCGACACGGAAATCGCA	61.286	55.000	0.00	0.00	43.89	5.10
2391	2879	3.677648	CGGACTGACGACCGGGTT	61.678	66.667	6.32	0.00	43.23	4.11
2432	2920	4.587056	GCCCCAAATAGGCCTGAG	57.413	61.111	17.99	1.69	45.16	3.35
2472	2962	0.470456	TGGTCCGGTCAGTTAGTGGT	60.470	55.000	0.00	0.00	0.00	4.16
2473	2963	0.902531	ATGGTCCGGTCAGTTAGTGG	59.097	55.000	0.00	0.00	0.00	4.00
2474	2964	1.134788	GGATGGTCCGGTCAGTTAGTG	60.135	57.143	0.00	0.00	0.00	2.74
2475	2965	1.192428	GGATGGTCCGGTCAGTTAGT	58.808	55.000	0.00	0.00	0.00	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.