AutoCloner

Multiple sequence alignment - TraesCS7B01G146200

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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	TraesCS7B01G146200	chr7B	100.000	2729	0	0	1	2729	190117664	190114936	0.000000e+00	5040.0
1	TraesCS7B01G146200	chr7B	87.842	329	22	6	1859	2169	190101635	190101307	1.190000e-98	370.0
2	TraesCS7B01G146200	chr7B	92.920	113	8	0	1745	1857	190101288	190101176	6.050000e-37	165.0
3	TraesCS7B01G146200	chr7B	96.970	33	0	1	676	707	608210640	608210608	1.000000e-03	54.7
4	TraesCS7B01G146200	chr7D	92.193	1883	76	32	2	1857	211404988	211406826	0.000000e+00	2597.0
5	TraesCS7B01G146200	chr7D	81.341	895	120	30	1865	2729	296635295	296634418	0.000000e+00	684.0
6	TraesCS7B01G146200	chr7A	90.441	1883	91	42	2	1857	223471015	223472835	0.000000e+00	2398.0
7	TraesCS7B01G146200	chr1D	86.502	889	97	16	1859	2729	154022311	154023194	0.000000e+00	955.0
8	TraesCS7B01G146200	chr4B	84.710	896	106	20	1860	2729	12076754	12077644	0.000000e+00	867.0
9	TraesCS7B01G146200	chr4B	82.556	900	126	24	1856	2729	236311874	236312768	0.000000e+00	763.0
10	TraesCS7B01G146200	chr3B	84.351	901	108	22	1856	2729	157664959	157665853	0.000000e+00	852.0
11	TraesCS7B01G146200	chr3B	83.204	899	117	25	1859	2729	520619267	520618375	0.000000e+00	793.0
12	TraesCS7B01G146200	chr2B	83.964	898	111	26	1859	2729	400457927	400457036	0.000000e+00	830.0
13	TraesCS7B01G146200	chr2B	82.941	170	19	9	2038	2203	401284181	401284344	7.880000e-31	145.0
14	TraesCS7B01G146200	chr1A	79.426	836	133	29	1915	2721	292565321	292566146	3.070000e-154	555.0
15	TraesCS7B01G146200	chr2A	81.579	646	94	24	2038	2671	560781735	560781103	6.740000e-141	510.0
16	TraesCS7B01G146200	chr2D	75.773	194	25	18	552	737	323650066	323649887	8.100000e-11	78.7
17	TraesCS7B01G146200	chr5A	89.362	47	5	0	677	723	640408902	640408856	2.930000e-05	60.2

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	TraesCS7B01G146200	chr7B	190114936	190117664	2728	True	5040	5040	100.000	1	2729	1	chr7B.!!$R1	2728
1	TraesCS7B01G146200	chr7D	211404988	211406826	1838	False	2597	2597	92.193	2	1857	1	chr7D.!!$F1	1855
2	TraesCS7B01G146200	chr7D	296634418	296635295	877	True	684	684	81.341	1865	2729	1	chr7D.!!$R1	864
3	TraesCS7B01G146200	chr7A	223471015	223472835	1820	False	2398	2398	90.441	2	1857	1	chr7A.!!$F1	1855
4	TraesCS7B01G146200	chr1D	154022311	154023194	883	False	955	955	86.502	1859	2729	1	chr1D.!!$F1	870
5	TraesCS7B01G146200	chr4B	12076754	12077644	890	False	867	867	84.710	1860	2729	1	chr4B.!!$F1	869
6	TraesCS7B01G146200	chr4B	236311874	236312768	894	False	763	763	82.556	1856	2729	1	chr4B.!!$F2	873
7	TraesCS7B01G146200	chr3B	157664959	157665853	894	False	852	852	84.351	1856	2729	1	chr3B.!!$F1	873
8	TraesCS7B01G146200	chr3B	520618375	520619267	892	True	793	793	83.204	1859	2729	1	chr3B.!!$R1	870
9	TraesCS7B01G146200	chr2B	400457036	400457927	891	True	830	830	83.964	1859	2729	1	chr2B.!!$R1	870
10	TraesCS7B01G146200	chr1A	292565321	292566146	825	False	555	555	79.426	1915	2721	1	chr1A.!!$F1	806
11	TraesCS7B01G146200	chr2A	560781103	560781735	632	True	510	510	81.579	2038	2671	1	chr2A.!!$R1	633

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
805	826	0.806868	CTGGTGCTGTGCGAATCAAT	59.193	50.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2164	2235	0.11714	ACCAGATGTGAGGGTGGAGA	59.883	55.0	0.0	0.0	32.6	3.71	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
168	170	8.878769	GTCCATTTTATAAATTTGCGAACCAAT	58.121	29.630	0.00	0.00	32.49	3.16
180	182	2.794631	GCGAACCAATATTCAAAGGCGG	60.795	50.000	0.00	0.00	0.00	6.13
277	280	6.367695	GGGAAGTAATTTTGAAATTGGGAACG	59.632	38.462	11.02	0.00	38.90	3.95
333	336	9.741647	TTTGGGAAAACAATTAAAATGCAAATC	57.258	25.926	0.00	0.00	0.00	2.17
555	570	5.830799	AAATGAGGAAAGCAAAGGGAAAT	57.169	34.783	0.00	0.00	0.00	2.17
567	582	8.978874	AAGCAAAGGGAAATAAACAAAGAAAT	57.021	26.923	0.00	0.00	0.00	2.17
666	687	3.606687	ACATAAACCGGTTCATGTCCTC	58.393	45.455	27.39	0.00	0.00	3.71
727	748	4.236147	GACTGGAACCTTCTAGAACGTTC	58.764	47.826	26.47	26.47	37.94	3.95
728	749	3.243336	CTGGAACCTTCTAGAACGTTCG	58.757	50.000	26.89	17.42	37.94	3.95
739	760	1.068055	AGAACGTTCGCATAACCGTCT	60.068	47.619	21.87	0.00	32.30	4.18
805	826	0.806868	CTGGTGCTGTGCGAATCAAT	59.193	50.000	0.00	0.00	0.00	2.57
816	837	6.252967	TGTGCGAATCAATAACAATCTGTT	57.747	33.333	0.00	0.00	43.88	3.16
819	840	4.500477	GCGAATCAATAACAATCTGTTGCC	59.500	41.667	2.30	0.00	41.30	4.52
822	843	3.417101	TCAATAACAATCTGTTGCCGGT	58.583	40.909	1.90	0.00	41.30	5.28
839	866	2.432444	CGGTTGCAAAGATTGTCCCTA	58.568	47.619	0.00	0.00	0.00	3.53
946	974	4.656117	CGCGCAAAAACCACCCCC	62.656	66.667	8.75	0.00	0.00	5.40
947	975	3.541713	GCGCAAAAACCACCCCCA	61.542	61.111	0.30	0.00	0.00	4.96
948	976	2.419620	CGCAAAAACCACCCCCAC	59.580	61.111	0.00	0.00	0.00	4.61
949	977	2.825982	GCAAAAACCACCCCCACC	59.174	61.111	0.00	0.00	0.00	4.61
950	978	2.066999	GCAAAAACCACCCCCACCA	61.067	57.895	0.00	0.00	0.00	4.17
951	979	1.826709	CAAAAACCACCCCCACCAC	59.173	57.895	0.00	0.00	0.00	4.16
952	980	1.383386	AAAAACCACCCCCACCACC	60.383	57.895	0.00	0.00	0.00	4.61
953	981	3.742248	AAAACCACCCCCACCACCG	62.742	63.158	0.00	0.00	0.00	4.94
1029	1057	1.687493	CGCTTCCCTCTTCTCCCCT	60.687	63.158	0.00	0.00	0.00	4.79
1464	1492	2.280797	GTGCTGGACAACCTCGCA	60.281	61.111	0.00	0.00	39.50	5.10
1596	1624	2.186384	GCGCACAGCCTCATCTCT	59.814	61.111	0.30	0.00	40.81	3.10
1769	1810	2.103537	AAGCGGTTTTGTATAGGCGT	57.896	45.000	0.00	0.00	0.00	5.68
1779	1820	6.201425	GGTTTTGTATAGGCGTTATCATCGAA	59.799	38.462	0.00	0.00	0.00	3.71
1787	1828	2.473235	GCGTTATCATCGAAGAAGAGGC	59.527	50.000	0.00	0.36	43.58	4.70
1853	1894	8.862325	TTGATCTGTAAATTGCTTTCTTCCTA	57.138	30.769	0.00	0.00	0.00	2.94
1857	1898	8.635765	TCTGTAAATTGCTTTCTTCCTATGTT	57.364	30.769	0.00	0.00	0.00	2.71
1967	2008	3.574074	AAGCGTCATTGGGCTGGCT	62.574	57.895	0.00	0.00	39.93	4.75
2047	2106	0.524862	ACGACGACACGGCTCTTATT	59.475	50.000	0.00	0.00	37.61	1.40
2084	2146	0.318784	CGCCACGAACCCTAGCTATC	60.319	60.000	0.00	0.00	0.00	2.08
2085	2147	0.033642	GCCACGAACCCTAGCTATCC	59.966	60.000	0.00	0.00	0.00	2.59
2121	2188	4.649674	TCTTCCTGTAATCGCTACCAGATT	59.350	41.667	0.00	0.00	40.88	2.40
2129	2197	3.695830	TCGCTACCAGATTGAACCTTT	57.304	42.857	0.00	0.00	0.00	3.11
2130	2198	4.811969	TCGCTACCAGATTGAACCTTTA	57.188	40.909	0.00	0.00	0.00	1.85
2154	2224	6.096673	TGAGTGAAGTGTTGCTAGTAATCA	57.903	37.500	0.00	0.00	0.00	2.57
2155	2225	6.701340	TGAGTGAAGTGTTGCTAGTAATCAT	58.299	36.000	0.00	0.00	0.00	2.45
2164	2235	5.604231	TGTTGCTAGTAATCATGAGATCCCT	59.396	40.000	0.09	0.00	31.90	4.20
2283	2360	0.179100	CACTTCGTCGCCATGGATCT	60.179	55.000	18.40	0.00	0.00	2.75
2311	2388	1.878656	AAGCCTTCCTCGACCGACTG	61.879	60.000	0.00	0.00	0.00	3.51
2332	2409	1.152567	CAACACCCTCAAGGCCCAA	60.153	57.895	0.00	0.00	40.58	4.12
2419	2496	1.034838	ATCTGGAGAAGCGCGTCTCT	61.035	55.000	39.14	25.94	43.14	3.10
2474	2553	4.250305	AGCCGCCGTCCAACAAGT	62.250	61.111	0.00	0.00	0.00	3.16
2599	2678	2.050442	GGCCACGGCGTTTTCAAG	60.050	61.111	11.19	0.00	43.06	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
56	58	7.706179	GTCTGTGAATTCAAAAATTGTTCAGGA	59.294	33.333	10.35	0.00	35.21	3.86
119	121	8.905850	GGACGGGAATTTTACTTTCCAAATATA	58.094	33.333	4.96	0.00	43.72	0.86
257	260	7.471657	AACACGTTCCCAATTTCAAAATTAC	57.528	32.000	0.63	0.00	36.52	1.89
666	687	5.167303	AGGAACCTTCTAGCCTTACTTTG	57.833	43.478	0.00	0.00	0.00	2.77
727	748	2.546778	ACAATACCAGACGGTTATGCG	58.453	47.619	0.00	0.00	46.31	4.73
728	749	3.493503	GCTACAATACCAGACGGTTATGC	59.506	47.826	0.00	0.00	46.31	3.14
739	760	6.720748	TCAGTATATAACGGGCTACAATACCA	59.279	38.462	0.00	0.00	0.00	3.25
744	765	9.647797	CAATTATCAGTATATAACGGGCTACAA	57.352	33.333	0.00	0.00	0.00	2.41
805	826	1.268352	GCAACCGGCAACAGATTGTTA	59.732	47.619	0.00	0.00	38.77	2.41
819	840	1.247567	AGGGACAATCTTTGCAACCG	58.752	50.000	0.00	0.00	0.00	4.44
822	843	3.244422	ACGAGTAGGGACAATCTTTGCAA	60.244	43.478	0.00	0.00	0.00	4.08
826	847	2.165845	CCGACGAGTAGGGACAATCTTT	59.834	50.000	0.00	0.00	0.00	2.52
827	848	1.749634	CCGACGAGTAGGGACAATCTT	59.250	52.381	0.00	0.00	0.00	2.40
828	849	1.340795	ACCGACGAGTAGGGACAATCT	60.341	52.381	7.28	0.00	0.00	2.40
839	866	2.264794	GGCATTCCACCGACGAGT	59.735	61.111	0.00	0.00	0.00	4.18
1029	1057	1.229529	GGTGGTGAGGAGAGGGGAA	60.230	63.158	0.00	0.00	0.00	3.97
1196	1224	2.094338	CCGTAGTACACCTTGAACTCCC	60.094	54.545	0.38	0.00	0.00	4.30
1452	1480	1.079750	GGAGAGTGCGAGGTTGTCC	60.080	63.158	0.00	0.00	0.00	4.02
1747	1788	3.619929	ACGCCTATACAAAACCGCTTAAG	59.380	43.478	0.00	0.00	0.00	1.85
1769	1810	6.348498	TCAATTGCCTCTTCTTCGATGATAA	58.652	36.000	0.00	0.00	0.00	1.75
1779	1820	4.165565	TCATCCAGATCAATTGCCTCTTCT	59.834	41.667	0.00	0.00	0.00	2.85
1787	1828	9.894783	GTTCTGAATAATCATCCAGATCAATTG	57.105	33.333	0.00	0.00	35.39	2.32
1853	1894	2.233271	CTGTCAGGGCTGTTGAAACAT	58.767	47.619	0.00	0.00	38.41	2.71
1901	1942	4.451150	GGAGCCGTGGTGATGCGA	62.451	66.667	0.00	0.00	0.00	5.10
1963	2004	1.616159	GCTTCAGTTTACCCAAGCCA	58.384	50.000	0.00	0.00	36.11	4.75
1967	2008	0.250989	CCGGGCTTCAGTTTACCCAA	60.251	55.000	0.00	0.00	42.97	4.12
2034	2093	1.209747	GGAAGGGAATAAGAGCCGTGT	59.790	52.381	0.00	0.00	0.00	4.49
2047	2106	1.939082	CGAGAGAGGAGGGGAAGGGA	61.939	65.000	0.00	0.00	0.00	4.20
2084	2146	4.860022	ACAGGAAGATTACAAGAATGGGG	58.140	43.478	0.00	0.00	0.00	4.96
2085	2147	7.041780	CGATTACAGGAAGATTACAAGAATGGG	60.042	40.741	0.00	0.00	0.00	4.00
2121	2188	5.008613	GCAACACTTCACTCATAAAGGTTCA	59.991	40.000	0.00	0.00	0.00	3.18
2129	2197	7.836842	TGATTACTAGCAACACTTCACTCATA	58.163	34.615	0.00	0.00	0.00	2.15
2130	2198	6.701340	TGATTACTAGCAACACTTCACTCAT	58.299	36.000	0.00	0.00	0.00	2.90
2154	2224	0.948050	AGGGTGGAGAGGGATCTCAT	59.052	55.000	7.51	0.00	42.34	2.90
2155	2225	0.263172	GAGGGTGGAGAGGGATCTCA	59.737	60.000	7.51	0.00	42.34	3.27
2164	2235	0.117140	ACCAGATGTGAGGGTGGAGA	59.883	55.000	0.00	0.00	32.60	3.71
2311	2388	1.603739	GGCCTTGAGGGTGTTGTCC	60.604	63.158	0.00	0.00	37.43	4.02
2332	2409	2.489938	TCTCCGCTATTGCCTTGTTT	57.510	45.000	0.00	0.00	35.36	2.83
2419	2496	2.994995	ACCGCGTCACCCAGATCA	60.995	61.111	4.92	0.00	0.00	2.92
2469	2548	2.126812	GCTCGTCGCTCGACTTGT	60.127	61.111	18.51	0.00	44.01	3.16
2474	2553	3.500642	CTGAGGCTCGTCGCTCGA	61.501	66.667	10.42	2.98	46.83	4.04
2491	2570	0.675522	TTTGCTTCGGATTCGTCCCC	60.676	55.000	0.00	0.00	37.69	4.81
2511	2590	4.052229	CGGTCGTCGCAGAAGGGT	62.052	66.667	0.00	0.00	39.69	4.34
2593	2672	2.574450	GTTCCCCGTGGTAACTTGAAA	58.426	47.619	0.00	0.00	37.61	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.