AutoCloner

Multiple sequence alignment - TraesCS2A01G243700

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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	TraesCS2A01G243700	chr2A	100.000	2834	0	0	1	2834	343446803	343443970	0.000000e+00	5234
1	TraesCS2A01G243700	chr2A	86.833	2719	297	44	25	2710	679108876	679106186	0.000000e+00	2981
2	TraesCS2A01G243700	chr2A	84.252	254	22	13	2423	2664	586826725	586826972	6.110000e-57	231
3	TraesCS2A01G243700	chr2A	83.730	252	27	10	2423	2664	441444896	441444649	2.840000e-55	226
4	TraesCS2A01G243700	chr7D	88.685	2775	255	38	1	2741	149136387	149139136	0.000000e+00	3330
5	TraesCS2A01G243700	chr5B	86.615	2839	327	41	24	2832	333648036	333650851	0.000000e+00	3088
6	TraesCS2A01G243700	chr5B	86.559	2842	331	39	13	2826	373340087	373342905	0.000000e+00	3085
7	TraesCS2A01G243700	chr5B	86.348	2842	337	39	13	2826	373348186	373351004	0.000000e+00	3051
8	TraesCS2A01G243700	chr2B	86.721	2824	316	45	35	2826	388225728	388228524	0.000000e+00	3083
9	TraesCS2A01G243700	chr2B	84.430	1201	139	32	1655	2826	337501588	337502769	0.000000e+00	1138
10	TraesCS2A01G243700	chr2B	86.752	936	83	31	1912	2834	272993515	272992608	0.000000e+00	1003
11	TraesCS2A01G243700	chr2B	88.175	389	34	7	2449	2826	426926128	426926515	1.200000e-123	453
12	TraesCS2A01G243700	chr3D	87.263	2740	286	44	35	2741	213697085	213694376	0.000000e+00	3068
13	TraesCS2A01G243700	chr3A	87.375	2709	277	45	38	2710	91713300	91710621	0.000000e+00	3048
14	TraesCS2A01G243700	chr3A	87.371	2708	278	45	38	2710	91717927	91715249	0.000000e+00	3048
15	TraesCS2A01G243700	chr1D	88.261	2530	255	26	13	2511	481789101	481786583	0.000000e+00	2988
16	TraesCS2A01G243700	chr1B	84.501	1684	209	39	1170	2826	106888419	106890077	0.000000e+00	1616
17	TraesCS2A01G243700	chr7A	85.047	1284	157	29	1576	2834	582572757	582574030	0.000000e+00	1275
18	TraesCS2A01G243700	chr7A	83.069	1199	147	40	1665	2832	555908841	555907668	0.000000e+00	1038
19	TraesCS2A01G243700	chr7A	85.849	106	9	3	2735	2834	592897215	592897320	1.070000e-19	108
20	TraesCS2A01G243700	chr4B	90.441	408	29	3	2436	2834	241673954	241674360	1.930000e-146	529

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	TraesCS2A01G243700	chr2A	343443970	343446803	2833	True	5234	5234	100.000	1	2834	1	chr2A.!!$R1	2833
1	TraesCS2A01G243700	chr2A	679106186	679108876	2690	True	2981	2981	86.833	25	2710	1	chr2A.!!$R3	2685
2	TraesCS2A01G243700	chr7D	149136387	149139136	2749	False	3330	3330	88.685	1	2741	1	chr7D.!!$F1	2740
3	TraesCS2A01G243700	chr5B	333648036	333650851	2815	False	3088	3088	86.615	24	2832	1	chr5B.!!$F1	2808
4	TraesCS2A01G243700	chr5B	373340087	373342905	2818	False	3085	3085	86.559	13	2826	1	chr5B.!!$F2	2813
5	TraesCS2A01G243700	chr5B	373348186	373351004	2818	False	3051	3051	86.348	13	2826	1	chr5B.!!$F3	2813
6	TraesCS2A01G243700	chr2B	388225728	388228524	2796	False	3083	3083	86.721	35	2826	1	chr2B.!!$F2	2791
7	TraesCS2A01G243700	chr2B	337501588	337502769	1181	False	1138	1138	84.430	1655	2826	1	chr2B.!!$F1	1171
8	TraesCS2A01G243700	chr2B	272992608	272993515	907	True	1003	1003	86.752	1912	2834	1	chr2B.!!$R1	922
9	TraesCS2A01G243700	chr3D	213694376	213697085	2709	True	3068	3068	87.263	35	2741	1	chr3D.!!$R1	2706
10	TraesCS2A01G243700	chr3A	91710621	91717927	7306	True	3048	3048	87.373	38	2710	2	chr3A.!!$R1	2672
11	TraesCS2A01G243700	chr1D	481786583	481789101	2518	True	2988	2988	88.261	13	2511	1	chr1D.!!$R1	2498
12	TraesCS2A01G243700	chr1B	106888419	106890077	1658	False	1616	1616	84.501	1170	2826	1	chr1B.!!$F1	1656
13	TraesCS2A01G243700	chr7A	582572757	582574030	1273	False	1275	1275	85.047	1576	2834	1	chr7A.!!$F1	1258
14	TraesCS2A01G243700	chr7A	555907668	555908841	1173	True	1038	1038	83.069	1665	2832	1	chr7A.!!$R1	1167

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
141	151	0.384309	AGAACACGACACTCGCAGAA	59.616	50.0	0.0	0.0	45.12	3.02	F
1820	1847	0.698818	GGTGACATTCCTTGGGACCT	59.301	55.0	0.0	0.0	31.23	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1829	1856	0.323816	TCCTCATCTCCGTGCTCAGT	60.324	55.000	0.00	0.0	0.0	3.41	R
2774	2876	2.178580	CCTAGAGAGAGCATGATCCCC	58.821	57.143	7.49	0.0	0.0	4.81	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
108	117	0.586802	CCGAGCATAGTCGTCATCGA	59.413	55.000	0.00	0.00	44.12	3.59
141	151	0.384309	AGAACACGACACTCGCAGAA	59.616	50.000	0.00	0.00	45.12	3.02
223	237	3.475774	GTGCGACCGTGTTAGGCG	61.476	66.667	0.00	0.00	35.18	5.52
241	255	3.532542	GGCGATAGACTAGGTTTTGCTT	58.467	45.455	0.00	0.00	44.90	3.91
242	256	3.556365	GGCGATAGACTAGGTTTTGCTTC	59.444	47.826	0.00	0.00	44.90	3.86
248	262	7.412020	CGATAGACTAGGTTTTGCTTCTGTTTC	60.412	40.741	0.00	0.00	39.76	2.78
254	270	9.569122	ACTAGGTTTTGCTTCTGTTTCTATTTA	57.431	29.630	0.00	0.00	0.00	1.40
409	430	3.063452	CGAGCAACAGTACAAACAACACT	59.937	43.478	0.00	0.00	0.00	3.55
413	434	4.557301	GCAACAGTACAAACAACACTGAAC	59.443	41.667	7.88	0.00	41.80	3.18
492	513	6.758886	CAGCGAGAAGTAGTTTTTGAGGATAT	59.241	38.462	0.00	0.00	0.00	1.63
664	690	6.828273	AGCATAGCTCATACCAAAACAATACA	59.172	34.615	0.00	0.00	30.62	2.29
693	719	3.381590	GGTGGCCTGAAAACCAGAATATC	59.618	47.826	3.32	0.00	45.78	1.63
747	773	9.494271	TCACCATTTGCTTCTAGTAATCATATC	57.506	33.333	0.00	0.00	0.00	1.63
831	857	5.597182	TCCTACTCATATACCTCAACACCAC	59.403	44.000	0.00	0.00	0.00	4.16
1025	1051	5.471456	TGAAGAAGATCAAGAGTGGAAAAGC	59.529	40.000	0.00	0.00	0.00	3.51
1051	1077	7.416438	CGCTAGTGGAAGAAGTAAGGAAGATTA	60.416	40.741	0.00	0.00	0.00	1.75
1135	1161	4.927267	TCCCTTGATACATGTGAGGTTT	57.073	40.909	9.11	0.00	0.00	3.27
1139	1165	5.476599	CCCTTGATACATGTGAGGTTTCAAA	59.523	40.000	9.11	0.00	36.34	2.69
1306	1332	5.479375	TCTCCCGAAGAAGTAAAAGAAGCTA	59.521	40.000	0.00	0.00	0.00	3.32
1329	1355	4.530161	ACTGTAGCTGAAGATGAAGAACCT	59.470	41.667	0.00	0.00	0.00	3.50
1332	1358	4.205065	AGCTGAAGATGAAGAACCTGAG	57.795	45.455	0.00	0.00	0.00	3.35
1361	1387	7.884354	TCATTTGCCTATTATCATACATGAGCA	59.116	33.333	0.00	0.00	40.64	4.26
1368	1394	8.827677	CCTATTATCATACATGAGCATGATGTG	58.172	37.037	21.68	11.28	44.51	3.21
1369	1395	9.379791	CTATTATCATACATGAGCATGATGTGT	57.620	33.333	21.68	6.35	44.51	3.72
1389	1415	5.119694	GTGTCAGGTTTATCCAATCCTCTC	58.880	45.833	0.00	0.00	39.02	3.20
1390	1416	4.164221	TGTCAGGTTTATCCAATCCTCTCC	59.836	45.833	0.00	0.00	39.02	3.71
1400	1426	2.422377	CCAATCCTCTCCATGACATGCA	60.422	50.000	10.10	0.00	0.00	3.96
1417	1443	7.709947	TGACATGCATCCTTATGATTTCTTTC	58.290	34.615	0.00	0.00	34.84	2.62
1464	1490	6.599244	TGCCATCTGTTAAAGTAGATTTGAGG	59.401	38.462	0.00	0.00	31.53	3.86
1530	1556	7.040617	GGCATTACTCTCATTTGTGATGATCAT	60.041	37.037	8.25	8.25	33.71	2.45
1535	1561	8.434733	ACTCTCATTTGTGATGATCATAGTTG	57.565	34.615	8.54	1.70	0.00	3.16
1560	1586	2.105993	TCCTCGTGCTAGTCCTATGCTA	59.894	50.000	0.00	0.00	0.00	3.49
1600	1626	4.284490	CCCATGCTAGTCCTGAGCTTAATA	59.716	45.833	0.00	0.00	40.76	0.98
1635	1661	3.146066	TCATGTTAGTGTTGACCTTGCC	58.854	45.455	0.00	0.00	0.00	4.52
1764	1791	3.733337	TGAGTGCTCTTTCAGGTTCTTC	58.267	45.455	0.68	0.00	0.00	2.87
1776	1803	0.868406	GGTTCTTCCTTGTGCACGAG	59.132	55.000	24.97	24.97	0.00	4.18
1820	1847	0.698818	GGTGACATTCCTTGGGACCT	59.301	55.000	0.00	0.00	31.23	3.85
1828	1855	2.221299	CCTTGGGACCTCGGTGGAA	61.221	63.158	2.59	0.00	39.71	3.53
1829	1856	1.758592	CTTGGGACCTCGGTGGAAA	59.241	57.895	2.59	0.00	39.71	3.13
1902	1929	0.110678	ATGGAGCAGGCATGAGGATG	59.889	55.000	0.62	0.00	0.00	3.51
1915	1942	4.439837	GCATGAGGATGGAGAAGAAAAAGC	60.440	45.833	0.00	0.00	0.00	3.51
1917	1944	4.728772	TGAGGATGGAGAAGAAAAAGCAA	58.271	39.130	0.00	0.00	0.00	3.91
1984	2029	1.308069	CCCGGTGAGCTGTTTCATGG	61.308	60.000	0.00	0.00	0.00	3.66
2014	2063	6.354130	TCCGAGTATATCATCCGATACATGA	58.646	40.000	0.00	0.00	36.94	3.07
2267	2323	9.147732	TGATACACCTAGATCATTAAGTGTCAT	57.852	33.333	9.38	4.43	39.12	3.06
2294	2350	4.203226	TGAGTTTGTGCCTATTGTGTTCA	58.797	39.130	0.00	0.00	0.00	3.18
2313	2370	5.152097	GTTCACATTCAGAGCAATCACTTG	58.848	41.667	0.00	0.00	35.36	3.16
2396	2453	7.990541	TGAGTGATGATTCTTGTTTTTGTTG	57.009	32.000	0.00	0.00	0.00	3.33
2491	2560	1.066002	GGATCGGTGGCATGTGAAATG	59.934	52.381	0.00	0.00	0.00	2.32
2495	2564	1.255882	GGTGGCATGTGAAATGTGGA	58.744	50.000	0.00	0.00	0.00	4.02
2505	2575	1.879380	TGAAATGTGGAAGCTTGGACG	59.121	47.619	2.10	0.00	0.00	4.79
2507	2577	1.244019	AATGTGGAAGCTTGGACGGC	61.244	55.000	2.10	0.00	0.00	5.68
2590	2676	3.704061	TCCTTTGGGGAGACAAACAAAAG	59.296	43.478	0.00	0.00	39.58	2.27
2593	2679	5.337975	CCTTTGGGGAGACAAACAAAAGAAA	60.338	40.000	0.00	0.00	35.57	2.52
2594	2680	4.729227	TGGGGAGACAAACAAAAGAAAC	57.271	40.909	0.00	0.00	0.00	2.78
2595	2681	4.349365	TGGGGAGACAAACAAAAGAAACT	58.651	39.130	0.00	0.00	0.00	2.66
2731	2826	4.681744	TCAACTGCAATGTTTTGTTCCTC	58.318	39.130	0.00	0.00	35.17	3.71
2743	2838	7.181143	TGTTTTGTTCCTCGTAATAAGTGAC	57.819	36.000	0.00	0.00	0.00	3.67
2790	2892	2.948315	GTTTTGGGGATCATGCTCTCTC	59.052	50.000	0.00	0.00	0.00	3.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	3.676093	AGGTTGTTCCCGAAGATCTTTC	58.324	45.455	9.87	2.35	36.75	2.62
9	10	3.790089	AGGTTGTTCCCGAAGATCTTT	57.210	42.857	9.87	0.00	36.75	2.52
11	12	2.372172	ACAAGGTTGTTCCCGAAGATCT	59.628	45.455	0.00	0.00	38.47	2.75
108	117	3.008813	TCGTGTTCTCCTCAGGTACTAGT	59.991	47.826	0.00	0.00	36.02	2.57
114	123	0.674534	GTGTCGTGTTCTCCTCAGGT	59.325	55.000	0.00	0.00	0.00	4.00
157	168	8.514594	CCAAAATGATCATGTGTAAGTACAGTT	58.485	33.333	9.46	0.00	36.78	3.16
223	237	7.604545	AGAAACAGAAGCAAAACCTAGTCTATC	59.395	37.037	0.00	0.00	0.00	2.08
323	340	9.415544	GAAGACAATTCAAGCTACAAAATGAAT	57.584	29.630	3.70	3.70	42.61	2.57
336	355	5.636543	GCCATTTCCAAGAAGACAATTCAAG	59.363	40.000	0.00	0.00	0.00	3.02
396	417	6.707711	TGAATACGTTCAGTGTTGTTTGTAC	58.292	36.000	0.00	0.00	39.36	2.90
409	430	9.917129	TTACTTATCAGTTCTTGAATACGTTCA	57.083	29.630	0.00	0.00	39.77	3.18
492	513	7.019388	AGAATAAGGATCATAAGAGGTAGGCA	58.981	38.462	0.00	0.00	0.00	4.75
498	519	7.147742	GGCCTCTAGAATAAGGATCATAAGAGG	60.148	44.444	9.65	9.65	46.74	3.69
664	690	0.105760	TTTTCAGGCCACCCATGTGT	60.106	50.000	5.01	0.00	41.09	3.72
693	719	4.101585	TCAGGGTTGTTGCTCCTATATGAG	59.898	45.833	0.92	0.92	35.40	2.90
747	773	6.270927	TCTCCTCTTCATACATAAATCCCTGG	59.729	42.308	0.00	0.00	0.00	4.45
758	784	4.284490	AGTTGTTGCTCTCCTCTTCATACA	59.716	41.667	0.00	0.00	0.00	2.29
831	857	6.618287	TTTAACTCCATTGGCAATATCTCG	57.382	37.500	13.23	0.00	0.00	4.04
871	897	4.156922	CACTTGTGTTGAAGGTGTTGGTTA	59.843	41.667	0.00	0.00	0.00	2.85
1025	1051	4.158025	TCTTCCTTACTTCTTCCACTAGCG	59.842	45.833	0.00	0.00	0.00	4.26
1051	1077	1.537202	GCCAGCGTTGATGTTCTTCTT	59.463	47.619	0.00	0.00	0.00	2.52
1135	1161	4.206375	TCAGCTGAATGTGAAGGTTTTGA	58.794	39.130	15.67	0.00	0.00	2.69
1139	1165	2.157738	GCTCAGCTGAATGTGAAGGTT	58.842	47.619	18.85	0.00	0.00	3.50
1194	1220	7.402054	TGGCTTCAAGTATTTCTTCTTGGATA	58.598	34.615	0.00	0.00	40.67	2.59
1306	1332	4.530161	AGGTTCTTCATCTTCAGCTACAGT	59.470	41.667	0.00	0.00	0.00	3.55
1313	1339	6.404708	TGAATCTCAGGTTCTTCATCTTCAG	58.595	40.000	0.00	0.00	0.00	3.02
1356	1382	2.865119	AACCTGACACATCATGCTCA	57.135	45.000	0.00	0.00	33.22	4.26
1361	1387	5.829924	GGATTGGATAAACCTGACACATCAT	59.170	40.000	0.00	0.00	39.86	2.45
1368	1394	4.164221	TGGAGAGGATTGGATAAACCTGAC	59.836	45.833	0.00	0.00	38.99	3.51
1369	1395	4.370776	TGGAGAGGATTGGATAAACCTGA	58.629	43.478	0.00	0.00	38.99	3.86
1389	1415	5.977489	AATCATAAGGATGCATGTCATGG	57.023	39.130	14.64	0.00	36.02	3.66
1390	1416	7.215719	AGAAATCATAAGGATGCATGTCATG	57.784	36.000	2.46	8.56	36.02	3.07
1400	1426	9.453830	AGGTAGTAGGAAAGAAATCATAAGGAT	57.546	33.333	0.00	0.00	38.05	3.24
1417	1443	3.544684	TCATGCAATGCAAGGTAGTAGG	58.455	45.455	13.45	0.00	46.21	3.18
1530	1556	2.561419	ACTAGCACGAGGAAAGCAACTA	59.439	45.455	0.00	0.00	0.00	2.24
1535	1561	0.533032	AGGACTAGCACGAGGAAAGC	59.467	55.000	0.00	0.00	0.00	3.51
1560	1586	7.369551	AGCATGGGAATGATATGTTTCATTT	57.630	32.000	0.00	0.00	44.35	2.32
1635	1661	6.511767	GCACATGTTTAGGATGGTAGAAATCG	60.512	42.308	0.00	0.00	0.00	3.34
1764	1791	1.269569	TGTAGTGACTCGTGCACAAGG	60.270	52.381	18.64	8.34	38.70	3.61
1776	1803	1.276421	ACCTGGTCAGCATGTAGTGAC	59.724	52.381	13.54	13.54	42.06	3.67
1820	1847	1.300620	CGTGCTCAGTTTCCACCGA	60.301	57.895	0.00	0.00	0.00	4.69
1828	1855	0.534412	CCTCATCTCCGTGCTCAGTT	59.466	55.000	0.00	0.00	0.00	3.16
1829	1856	0.323816	TCCTCATCTCCGTGCTCAGT	60.324	55.000	0.00	0.00	0.00	3.41
1902	1929	4.936891	TGCTCTTTTGCTTTTTCTTCTCC	58.063	39.130	0.00	0.00	0.00	3.71
1963	2008	2.281484	GAAACAGCTCACCGGGCA	60.281	61.111	6.32	0.00	0.00	5.36
1984	2029	3.738281	CGGATGATATACTCGGAATGGGC	60.738	52.174	0.00	0.00	0.00	5.36
2014	2063	7.884354	AGCAACCCAAATAACATTTGATTTCAT	59.116	29.630	12.13	0.00	0.00	2.57
2167	2221	7.386299	AGCACTCAAAACTAATAGTTCTCACTG	59.614	37.037	6.09	1.81	37.47	3.66
2267	2323	4.395854	CACAATAGGCACAAACTCAGCATA	59.604	41.667	0.00	0.00	0.00	3.14
2294	2350	2.490903	GGCAAGTGATTGCTCTGAATGT	59.509	45.455	12.25	0.00	46.56	2.71
2313	2370	2.787994	AGCATGCTAATCCATAGTGGC	58.212	47.619	21.21	0.00	37.47	5.01
2491	2560	1.244019	ATTGCCGTCCAAGCTTCCAC	61.244	55.000	0.00	0.00	36.76	4.02
2525	2611	3.132289	ACATGGTATACACCTGGTTCGAG	59.868	47.826	5.01	0.00	45.98	4.04
2590	2676	7.628235	GGCTCGACCAATTATTAGTTAGTTTC	58.372	38.462	0.00	0.00	38.86	2.78
2743	2838	9.023967	CAAAAAGAACTTAAACTTGTGATCAGG	57.976	33.333	0.00	0.00	0.00	3.86
2774	2876	2.178580	CCTAGAGAGAGCATGATCCCC	58.821	57.143	7.49	0.00	0.00	4.81
2790	2892	3.826157	TGATTGTGCCAAAAGGTTCCTAG	59.174	43.478	0.00	0.00	0.00	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.