AutoCloner

Multiple sequence alignment - TraesCS3A01G425100

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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	TraesCS3A01G425100	chr3A	100.000	2634	0	0	1	2634	667506732	667504099	0.000000e+00	4865.0
1	TraesCS3A01G425100	chr3A	80.670	388	54	15	2009	2388	667486951	667486577	5.550000e-72	281.0
2	TraesCS3A01G425100	chr3D	92.031	1669	71	23	518	2143	532239970	532238321	0.000000e+00	2289.0
3	TraesCS3A01G425100	chr3D	97.505	521	11	1	2114	2634	532238320	532237802	0.000000e+00	889.0
4	TraesCS3A01G425100	chr3D	86.713	286	32	3	2114	2394	532191751	532191467	1.970000e-81	313.0
5	TraesCS3A01G425100	chr3B	88.897	1333	72	36	605	1878	704573823	704572508	0.000000e+00	1572.0
6	TraesCS3A01G425100	chr3B	86.538	104	10	2	510	609	704574071	704573968	7.710000e-21	111.0
7	TraesCS3A01G425100	chr3B	85.714	91	10	1	2544	2634	704568301	704568214	2.790000e-15	93.5
8	TraesCS3A01G425100	chr2D	91.732	508	40	2	1	507	552138515	552138009	0.000000e+00	704.0
9	TraesCS3A01G425100	chr2D	90.310	516	41	2	1	507	487936697	487937212	0.000000e+00	667.0
10	TraesCS3A01G425100	chr2D	83.523	352	31	14	603	939	361421501	361421840	1.180000e-78	303.0
11	TraesCS3A01G425100	chr5D	93.446	473	30	1	36	507	510829737	510829265	0.000000e+00	701.0
12	TraesCS3A01G425100	chr5D	90.716	517	35	10	1	507	525764561	525764048	0.000000e+00	676.0
13	TraesCS3A01G425100	chr7D	90.909	517	37	3	1	508	159701320	159700805	0.000000e+00	686.0
14	TraesCS3A01G425100	chr7D	90.522	517	39	7	1	508	402317388	402317903	0.000000e+00	675.0
15	TraesCS3A01G425100	chr5A	90.716	517	39	3	1	508	119576533	119577049	0.000000e+00	680.0
16	TraesCS3A01G425100	chr5A	83.668	349	36	14	603	939	34524168	34524507	2.550000e-80	309.0
17	TraesCS3A01G425100	chr2A	90.522	517	38	8	1	507	571450885	571450370	0.000000e+00	673.0
18	TraesCS3A01G425100	chr5B	89.412	510	51	3	1	508	80676110	80675602	7.950000e-180	640.0
19	TraesCS3A01G425100	chr1A	84.104	346	36	12	603	939	516645054	516644719	1.520000e-82	316.0

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	TraesCS3A01G425100	chr3A	667504099	667506732	2633	True	4865.0	4865	100.0000	1	2634	1	chr3A.!!$R2	2633
1	TraesCS3A01G425100	chr3D	532237802	532239970	2168	True	1589.0	2289	94.7680	518	2634	2	chr3D.!!$R2	2116
2	TraesCS3A01G425100	chr3B	704572508	704574071	1563	True	841.5	1572	87.7175	510	1878	2	chr3B.!!$R2	1368
3	TraesCS3A01G425100	chr2D	552138009	552138515	506	True	704.0	704	91.7320	1	507	1	chr2D.!!$R1	506
4	TraesCS3A01G425100	chr2D	487936697	487937212	515	False	667.0	667	90.3100	1	507	1	chr2D.!!$F2	506
5	TraesCS3A01G425100	chr5D	525764048	525764561	513	True	676.0	676	90.7160	1	507	1	chr5D.!!$R2	506
6	TraesCS3A01G425100	chr7D	159700805	159701320	515	True	686.0	686	90.9090	1	508	1	chr7D.!!$R1	507
7	TraesCS3A01G425100	chr7D	402317388	402317903	515	False	675.0	675	90.5220	1	508	1	chr7D.!!$F1	507
8	TraesCS3A01G425100	chr5A	119576533	119577049	516	False	680.0	680	90.7160	1	508	1	chr5A.!!$F2	507
9	TraesCS3A01G425100	chr2A	571450370	571450885	515	True	673.0	673	90.5220	1	507	1	chr2A.!!$R1	506
10	TraesCS3A01G425100	chr5B	80675602	80676110	508	True	640.0	640	89.4120	1	508	1	chr5B.!!$R1	507

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
958	1160	0.17902	CTTCCCTTGCACTCCACACA	60.179	55.0	0.0	0.0	0.0	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1850	2111	0.798771	GAGATCTCCGTGCGTGACAC	60.799	60.0	12.0	0.0	46.45	3.67	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	118	0.608035	GCCGGACAAGAAACCCATGA	60.608	55.000	5.05	0.00	0.00	3.07
261	272	3.948719	GTCCAAGGTGGGCGGTCA	61.949	66.667	0.00	0.00	38.32	4.02
296	307	3.476031	CTGTGACGGTTGGGTGGCT	62.476	63.158	0.00	0.00	0.00	4.75
439	450	4.595538	TCGACGCGTTGGGCAGTT	62.596	61.111	25.66	0.00	43.84	3.16
491	502	0.462047	GCGGACGAAATGGATCACCT	60.462	55.000	0.00	0.00	37.04	4.00
508	519	3.196469	TCACCTCATTGGAGTTGCTCTAG	59.804	47.826	0.00	0.00	39.64	2.43
513	524	4.682589	CTCATTGGAGTTGCTCTAGCATGA	60.683	45.833	5.33	3.98	40.66	3.07
515	526	8.795342	CTCATTGGAGTTGCTCTAGCATGACT	62.795	46.154	5.33	7.23	42.76	3.41
540	551	1.522092	CGGGCATCCACTCAGCTTA	59.478	57.895	0.00	0.00	0.00	3.09
556	571	1.656652	CTTATCCCAGTTGAGCCACG	58.343	55.000	0.00	0.00	0.00	4.94
557	572	1.207089	CTTATCCCAGTTGAGCCACGA	59.793	52.381	0.00	0.00	0.00	4.35
576	591	2.162408	CGAATGGAGAGAGGCCAAAAAC	59.838	50.000	5.01	0.00	39.21	2.43
646	811	3.736996	AACCCCAGCAGTGCAGCAA	62.737	57.895	19.20	0.00	36.85	3.91
649	814	2.337532	CCAGCAGTGCAGCAAACC	59.662	61.111	19.20	0.00	36.85	3.27
662	827	3.426695	GCAGCAAACCTGTACTTAGCATG	60.427	47.826	0.00	0.00	43.71	4.06
666	839	3.350219	AACCTGTACTTAGCATGGTGG	57.650	47.619	7.89	0.26	0.00	4.61
680	853	2.616458	GGTGGCATCCCAGGACCTT	61.616	63.158	0.00	0.00	43.18	3.50
696	869	1.135373	ACCTTATGTCGCTGACTCACG	60.135	52.381	9.49	0.00	33.15	4.35
838	1040	2.754658	CACTCCGCTCTACCCGGT	60.755	66.667	0.00	0.00	45.71	5.28
841	1043	2.124403	TCCGCTCTACCCGGTCTC	60.124	66.667	0.00	0.00	45.71	3.36
958	1160	0.179020	CTTCCCTTGCACTCCACACA	60.179	55.000	0.00	0.00	0.00	3.72
977	1179	8.004801	TCCACACATCCTCTCTCTATATAACAA	58.995	37.037	0.00	0.00	0.00	2.83
1069	1296	0.032678	ATCGATGATCAGCACGGACC	59.967	55.000	12.15	0.00	0.00	4.46
1073	1300	0.179037	ATGATCAGCACGGACCATGG	60.179	55.000	11.19	11.19	0.00	3.66
1102	1329	3.188786	GCCATGTCGACGCTCCAC	61.189	66.667	11.62	0.00	0.00	4.02
1104	1331	1.517257	CCATGTCGACGCTCCACTC	60.517	63.158	11.62	0.00	0.00	3.51
1153	1381	3.773860	TCTCTCTCGCACAATTCTCTC	57.226	47.619	0.00	0.00	0.00	3.20
1154	1382	2.096657	TCTCTCTCGCACAATTCTCTCG	59.903	50.000	0.00	0.00	0.00	4.04
1155	1383	2.084546	TCTCTCGCACAATTCTCTCGA	58.915	47.619	0.00	0.00	0.00	4.04
1156	1384	2.685388	TCTCTCGCACAATTCTCTCGAT	59.315	45.455	0.00	0.00	0.00	3.59
1370	1598	1.186200	CCTGTCCCACATCTTCGAGA	58.814	55.000	0.00	0.00	0.00	4.04
1384	1612	3.754850	TCTTCGAGATGTACAAGGACGAA	59.245	43.478	20.30	20.30	36.94	3.85
1534	1762	1.912043	CTCTCCACCAACATCTCCCTT	59.088	52.381	0.00	0.00	0.00	3.95
1558	1786	2.032634	GTTCGAGTTCGCCATGGCA	61.033	57.895	34.93	19.88	42.06	4.92
1684	1912	7.465245	GCACGTACGTTCTACTAGTTCTTCTAT	60.465	40.741	20.23	0.00	0.00	1.98
1699	1936	1.522355	CTATCCCACTGGCGCTGTG	60.522	63.158	21.14	21.14	33.98	3.66
1719	1956	1.070914	GTAGCCTACATGCTCTTCCCC	59.929	57.143	0.00	0.00	41.68	4.81
1720	1957	1.227674	GCCTACATGCTCTTCCCCG	60.228	63.158	0.00	0.00	0.00	5.73
1725	1962	1.299648	CATGCTCTTCCCCGTTCCA	59.700	57.895	0.00	0.00	0.00	3.53
1758	1995	1.081442	GCCACTACGCCAAAACAGC	60.081	57.895	0.00	0.00	0.00	4.40
1850	2111	2.006888	GGGACGTGAATGTACATGGTG	58.993	52.381	9.63	2.77	0.00	4.17
1870	2131	1.583967	GTCACGCACGGAGATCTCG	60.584	63.158	16.46	13.62	0.00	4.04
1916	2177	8.478775	AAAACAGCTTCCTTAGATTAACCTTT	57.521	30.769	0.00	0.00	0.00	3.11
1917	2178	8.478775	AAACAGCTTCCTTAGATTAACCTTTT	57.521	30.769	0.00	0.00	0.00	2.27
1918	2179	8.478775	AACAGCTTCCTTAGATTAACCTTTTT	57.521	30.769	0.00	0.00	0.00	1.94
1950	2211	9.135843	GGCAACAATTTTACTTACTTAATGGTC	57.864	33.333	0.00	0.00	0.00	4.02
1951	2212	8.846607	GCAACAATTTTACTTACTTAATGGTCG	58.153	33.333	0.00	0.00	0.00	4.79
1952	2213	8.846607	CAACAATTTTACTTACTTAATGGTCGC	58.153	33.333	0.00	0.00	0.00	5.19
1953	2214	8.101654	ACAATTTTACTTACTTAATGGTCGCA	57.898	30.769	0.00	0.00	0.00	5.10
1954	2215	8.569641	ACAATTTTACTTACTTAATGGTCGCAA	58.430	29.630	0.00	0.00	0.00	4.85
1958	2219	9.968870	TTTTACTTACTTAATGGTCGCAAAAAT	57.031	25.926	0.00	0.00	0.00	1.82
2040	2301	0.843343	AATAACCGAGGGTGGGGTGT	60.843	55.000	0.00	0.00	35.34	4.16
2041	2302	0.843343	ATAACCGAGGGTGGGGTGTT	60.843	55.000	0.00	0.00	35.34	3.32
2044	2305	1.061324	ACCGAGGGTGGGGTGTTAAA	61.061	55.000	0.00	0.00	34.58	1.52
2045	2306	0.330267	CCGAGGGTGGGGTGTTAAAT	59.670	55.000	0.00	0.00	0.00	1.40
2046	2307	1.272258	CCGAGGGTGGGGTGTTAAATT	60.272	52.381	0.00	0.00	0.00	1.82
2056	2317	6.944290	GGTGGGGTGTTAAATTAAGAACTACT	59.056	38.462	0.00	0.00	0.00	2.57
2060	2321	7.881751	GGGGTGTTAAATTAAGAACTACTCAGT	59.118	37.037	0.00	0.00	36.19	3.41
2142	2433	0.871057	CACACACACACACACACACA	59.129	50.000	0.00	0.00	0.00	3.72
2150	2441	3.119884	ACACACACACACACATGAGTTTG	60.120	43.478	7.74	7.74	34.43	2.93
2172	2463	6.211587	TGCCAAATCAAATGGTCTATCAAG	57.788	37.500	0.00	0.00	40.23	3.02
2245	2536	9.369904	ACAAATTTCATACATTTATTGTCAGGC	57.630	29.630	0.00	0.00	39.87	4.85
2315	2606	4.347360	AAACCGCTGTAGTTCTTTACCT	57.653	40.909	0.00	0.00	0.00	3.08
2357	2648	4.271291	TCTCATCGATGTCTCTCGTTACTG	59.729	45.833	24.09	0.00	39.62	2.74
2384	2675	2.930826	TCTCCTTTCCATTATCGGGC	57.069	50.000	0.00	0.00	0.00	6.13
2583	2874	4.324402	CGTGCATTTGTTTCTTTGCCTATC	59.676	41.667	0.00	0.00	34.20	2.08
2600	2891	1.516110	ATCCCTCCTTCTCCCATGTG	58.484	55.000	0.00	0.00	0.00	3.21

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	2.046335	ATTTCCCCTCCCTCCCCC	59.954	66.667	0.00	0.00	0.00	5.40
95	105	0.457035	CCGCCATCATGGGTTTCTTG	59.543	55.000	5.62	0.00	38.19	3.02
108	118	3.015145	AACCCTAGCCACCGCCAT	61.015	61.111	0.00	0.00	34.57	4.40
261	272	7.552687	ACCGTCACAGTCAACATAATTTATGAT	59.447	33.333	20.54	8.19	39.45	2.45
279	290	3.484806	AGCCACCCAACCGTCACA	61.485	61.111	0.00	0.00	0.00	3.58
524	535	1.544314	GGGATAAGCTGAGTGGATGCC	60.544	57.143	0.00	0.00	0.00	4.40
540	551	0.620556	ATTCGTGGCTCAACTGGGAT	59.379	50.000	0.00	0.00	0.00	3.85
556	571	2.162408	CGTTTTTGGCCTCTCTCCATTC	59.838	50.000	3.32	0.00	32.92	2.67
557	572	2.162681	CGTTTTTGGCCTCTCTCCATT	58.837	47.619	3.32	0.00	32.92	3.16
576	591	0.595053	ACGCTCGGTAGATTGCATCG	60.595	55.000	0.00	0.00	0.00	3.84
646	811	2.618045	GCCACCATGCTAAGTACAGGTT	60.618	50.000	0.00	0.00	0.00	3.50
649	814	2.401583	TGCCACCATGCTAAGTACAG	57.598	50.000	0.00	0.00	0.00	2.74
655	820	0.106569	CTGGGATGCCACCATGCTAA	60.107	55.000	0.00	0.00	39.49	3.09
662	827	1.279025	TAAGGTCCTGGGATGCCACC	61.279	60.000	0.00	1.93	0.00	4.61
666	839	1.541233	CGACATAAGGTCCTGGGATGC	60.541	57.143	0.00	0.00	43.95	3.91
680	853	1.138883	GGCGTGAGTCAGCGACATA	59.861	57.895	16.04	0.00	35.95	2.29
696	869	0.897621	AATTTAGTGCAGGGCTTGGC	59.102	50.000	0.00	0.00	0.00	4.52
838	1040	1.032657	GTAGTGCCTCTGCCTCGAGA	61.033	60.000	15.71	0.00	36.33	4.04
841	1043	0.737715	GTTGTAGTGCCTCTGCCTCG	60.738	60.000	0.00	0.00	36.33	4.63
958	1160	9.308000	CTGGTCTTTGTTATATAGAGAGAGGAT	57.692	37.037	0.00	0.00	0.00	3.24
977	1179	2.158755	CCTCAGTTTGGTGTCTGGTCTT	60.159	50.000	0.00	0.00	33.13	3.01
1011	1238	4.083862	GAGGCGAGGCGGGAAAGT	62.084	66.667	0.00	0.00	0.00	2.66
1069	1296	3.857854	GCTCGTCGCAGCACCATG	61.858	66.667	10.53	0.00	39.43	3.66
1073	1300	3.857854	CATGGCTCGTCGCAGCAC	61.858	66.667	15.35	7.94	41.65	4.40
1102	1329	2.035632	GATCCACACTCTACCTGGGAG	58.964	57.143	0.00	0.00	36.92	4.30
1104	1331	2.166907	AGATCCACACTCTACCTGGG	57.833	55.000	0.00	0.00	0.00	4.45
1153	1381	3.864686	CCTTTGGGCGCACGATCG	61.865	66.667	14.88	14.88	0.00	3.69
1154	1382	1.776034	GATCCTTTGGGCGCACGATC	61.776	60.000	10.83	9.77	0.00	3.69
1155	1383	1.819632	GATCCTTTGGGCGCACGAT	60.820	57.895	10.83	3.00	0.00	3.73
1156	1384	2.435938	GATCCTTTGGGCGCACGA	60.436	61.111	10.83	0.63	0.00	4.35
1370	1598	2.761208	CCTCCTCTTCGTCCTTGTACAT	59.239	50.000	0.00	0.00	0.00	2.29
1384	1612	1.078285	GTCGTCGTCCTCCTCCTCT	60.078	63.158	0.00	0.00	0.00	3.69
1534	1762	1.372997	GGCGAACTCGAACTGCTGA	60.373	57.895	2.69	0.00	43.02	4.26
1558	1786	4.607325	TCATGCGCGGCGATGGAT	62.607	61.111	28.54	5.82	0.00	3.41
1684	1912	2.920384	TACACAGCGCCAGTGGGA	60.920	61.111	27.52	16.10	41.21	4.37
1699	1936	1.070914	GGGGAAGAGCATGTAGGCTAC	59.929	57.143	17.76	17.76	45.99	3.58
1719	1956	2.703798	CCAGCATTGGCCTGGAACG	61.704	63.158	3.32	0.00	42.56	3.95
1720	1957	3.291611	CCAGCATTGGCCTGGAAC	58.708	61.111	3.32	0.00	42.56	3.62
1758	1995	6.595326	ACATTATATACACCATCTGCCAATCG	59.405	38.462	0.00	0.00	0.00	3.34
1794	2055	6.983890	AGTTGGCGTCTCAAATTACAAAAATT	59.016	30.769	0.00	0.00	0.00	1.82
1850	2111	0.798771	GAGATCTCCGTGCGTGACAC	60.799	60.000	12.00	0.00	46.45	3.67
1924	2185	9.135843	GACCATTAAGTAAGTAAAATTGTTGCC	57.864	33.333	0.00	0.00	0.00	4.52
1968	2229	9.927668	AAAAGTCCCACATATGATGTTAAAAAG	57.072	29.630	10.38	0.00	42.70	2.27
2012	2273	2.170607	ACCCTCGGTTATTGATGTCAGG	59.829	50.000	0.00	0.00	27.29	3.86
2040	2301	8.911918	TTGCCACTGAGTAGTTCTTAATTTAA	57.088	30.769	0.00	0.00	34.07	1.52
2041	2302	8.946085	CATTGCCACTGAGTAGTTCTTAATTTA	58.054	33.333	0.00	0.00	34.07	1.40
2044	2305	5.882557	CCATTGCCACTGAGTAGTTCTTAAT	59.117	40.000	0.00	0.00	34.07	1.40
2045	2306	5.245531	CCATTGCCACTGAGTAGTTCTTAA	58.754	41.667	0.00	0.00	34.07	1.85
2046	2307	4.832248	CCATTGCCACTGAGTAGTTCTTA	58.168	43.478	0.00	0.00	34.07	2.10
2056	2317	2.359850	GTCCGCCATTGCCACTGA	60.360	61.111	0.00	0.00	0.00	3.41
2060	2321	2.203552	TTTGGTCCGCCATTGCCA	60.204	55.556	0.00	0.00	45.56	4.92
2142	2433	5.012354	AGACCATTTGATTTGGCAAACTCAT	59.988	36.000	16.00	0.00	40.23	2.90
2150	2441	6.038356	CACTTGATAGACCATTTGATTTGGC	58.962	40.000	0.00	0.00	37.81	4.52
2172	2463	2.202295	TTTGCTTCTTCAAACGCCAC	57.798	45.000	0.00	0.00	31.64	5.01
2274	2565	7.095816	GCGGTTTAAGTAATTTTTGATGTGCTT	60.096	33.333	0.00	0.00	0.00	3.91
2275	2566	6.364976	GCGGTTTAAGTAATTTTTGATGTGCT	59.635	34.615	0.00	0.00	0.00	4.40
2315	2606	7.148188	CGATGAGATTTTCAATTCTTGGGAAGA	60.148	37.037	0.00	0.00	39.77	2.87
2345	2636	5.335740	GGAGATTGACAACAGTAACGAGAGA	60.336	44.000	0.00	0.00	0.00	3.10
2357	2648	6.238484	CCGATAATGGAAAGGAGATTGACAAC	60.238	42.308	0.00	0.00	0.00	3.32
2384	2675	3.326747	CTCAAAGTTTCCGTCACTAGGG	58.673	50.000	0.00	0.00	0.00	3.53
2502	2793	1.376942	CTCCCAGCAGCACCTTGAG	60.377	63.158	0.00	0.00	0.00	3.02
2583	2874	0.995024	AACACATGGGAGAAGGAGGG	59.005	55.000	0.00	0.00	0.00	4.30
2600	2891	1.021968	AGGAAACGGTGTCAGCAAAC	58.978	50.000	0.00	0.00	0.00	2.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.