AutoCloner

Multiple sequence alignment - TraesCS3A01G506600

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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	TraesCS3A01G506600	chr3A	100.000	3182	0	0	1	3182	728055588	728058769	0.000000e+00	5877.0
1	TraesCS3A01G506600	chr3A	89.086	1237	130	4	953	2186	729690612	729691846	0.000000e+00	1531.0
2	TraesCS3A01G506600	chr3A	89.856	1183	120	0	1004	2186	728018602	728017420	0.000000e+00	1520.0
3	TraesCS3A01G506600	chr3A	90.019	1062	106	0	1125	2186	728033572	728032511	0.000000e+00	1375.0
4	TraesCS3A01G506600	chr3A	86.921	1208	140	13	996	2187	728384618	728385823	0.000000e+00	1339.0
5	TraesCS3A01G506600	chr3A	84.050	1210	177	11	996	2191	728458187	728456980	0.000000e+00	1151.0
6	TraesCS3A01G506600	chr3D	95.528	1297	58	0	930	2226	598060818	598062114	0.000000e+00	2074.0
7	TraesCS3A01G506600	chr3D	90.372	1236	115	3	953	2186	598049273	598048040	0.000000e+00	1620.0
8	TraesCS3A01G506600	chr3D	92.308	65	5	0	2228	2292	275632080	275632016	3.380000e-15	93.5
9	TraesCS3A01G506600	chr4B	97.754	935	20	1	1	935	613038653	613037720	0.000000e+00	1609.0
10	TraesCS3A01G506600	chr4B	91.667	48	4	0	2228	2275	438418206	438418159	2.050000e-07	67.6
11	TraesCS3A01G506600	chr3B	89.334	1247	126	6	953	2196	805004700	805003458	0.000000e+00	1559.0
12	TraesCS3A01G506600	chr3B	96.674	932	31	0	1	932	188464614	188463683	0.000000e+00	1550.0
13	TraesCS3A01G506600	chr3B	96.375	938	29	1	1	933	188492682	188491745	0.000000e+00	1539.0
14	TraesCS3A01G506600	chr3B	84.380	1210	173	12	996	2191	805425853	805424646	0.000000e+00	1173.0
15	TraesCS3A01G506600	chr3B	79.894	378	60	12	2564	2932	59760061	59760431	2.430000e-66	263.0
16	TraesCS3A01G506600	chr3B	90.909	165	14	1	1	165	778556083	778556246	1.490000e-53	220.0
17	TraesCS3A01G506600	chr5B	96.567	932	32	0	1	932	418372425	418373356	0.000000e+00	1544.0
18	TraesCS3A01G506600	chr5B	97.368	342	8	1	592	932	430167087	430166746	5.920000e-162	580.0
19	TraesCS3A01G506600	chr1B	95.829	935	39	0	1	935	29269103	29268169	0.000000e+00	1511.0
20	TraesCS3A01G506600	chr1B	91.018	167	12	3	1	164	282111254	282111420	4.130000e-54	222.0
21	TraesCS3A01G506600	chr1B	84.753	223	31	3	2963	3182	42071174	42070952	1.490000e-53	220.0
22	TraesCS3A01G506600	chr1B	96.774	31	1	0	2253	2283	573290	573320	6.000000e-03	52.8
23	TraesCS3A01G506600	chr7D	90.252	595	57	1	1	594	220315833	220315239	0.000000e+00	776.0
24	TraesCS3A01G506600	chr6A	83.886	844	99	24	2368	3182	497397321	497396486	0.000000e+00	771.0
25	TraesCS3A01G506600	chr6A	88.000	575	44	9	2570	3122	585582719	585582148	0.000000e+00	656.0
26	TraesCS3A01G506600	chr6A	97.376	343	8	1	592	933	228523914	228524256	1.650000e-162	582.0
27	TraesCS3A01G506600	chr6A	82.967	182	25	6	2990	3168	445680684	445680506	3.290000e-35	159.0
28	TraesCS3A01G506600	chr6D	88.870	602	43	8	2581	3160	437348226	437347627	0.000000e+00	719.0
29	TraesCS3A01G506600	chr6D	85.986	421	28	16	2601	2998	61006528	61006940	3.790000e-114	422.0
30	TraesCS3A01G506600	chr6D	87.255	204	21	4	2365	2566	61006325	61006525	8.880000e-56	228.0
31	TraesCS3A01G506600	chr6D	94.483	145	7	1	3039	3182	61007139	61007283	4.130000e-54	222.0
32	TraesCS3A01G506600	chr6D	86.928	153	17	3	3033	3182	12668329	12668481	5.460000e-38	169.0
33	TraesCS3A01G506600	chr6D	86.928	153	17	3	3033	3182	12692674	12692826	5.460000e-38	169.0
34	TraesCS3A01G506600	chrUn	97.953	342	6	1	592	932	342507763	342508104	2.730000e-165	592.0
35	TraesCS3A01G506600	chrUn	97.953	342	6	1	592	932	399642414	399642073	2.730000e-165	592.0
36	TraesCS3A01G506600	chrUn	90.909	165	14	1	1	165	240411567	240411730	1.490000e-53	220.0
37	TraesCS3A01G506600	chr4A	80.651	584	79	18	2388	2949	583720096	583720667	3.790000e-114	422.0
38	TraesCS3A01G506600	chr1A	80.750	587	72	15	2388	2949	475298971	475299541	1.360000e-113	420.0
39	TraesCS3A01G506600	chr5D	85.556	180	24	2	3001	3179	480808377	480808555	1.510000e-43	187.0
40	TraesCS3A01G506600	chr5D	92.500	40	1	2	2254	2292	540574131	540574093	4.430000e-04	56.5
41	TraesCS3A01G506600	chr2D	74.702	336	54	26	2	324	14890360	14890677	1.550000e-23	121.0
42	TraesCS3A01G506600	chr6B	94.595	74	2	1	2368	2439	662128589	662128516	2.590000e-21	113.0
43	TraesCS3A01G506600	chr7A	93.750	48	3	0	2228	2275	1951461	1951508	4.400000e-09	73.1
44	TraesCS3A01G506600	chr5A	90.566	53	5	0	2228	2280	77750094	77750146	1.580000e-08	71.3
45	TraesCS3A01G506600	chr5A	77.876	113	17	8	2782	2891	632571736	632571843	2.650000e-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	TraesCS3A01G506600	chr3A	728055588	728058769	3181	False	5877.000000	5877	100.000000	1	3182	1	chr3A.!!$F1	3181
1	TraesCS3A01G506600	chr3A	729690612	729691846	1234	False	1531.000000	1531	89.086000	953	2186	1	chr3A.!!$F3	1233
2	TraesCS3A01G506600	chr3A	728017420	728018602	1182	True	1520.000000	1520	89.856000	1004	2186	1	chr3A.!!$R1	1182
3	TraesCS3A01G506600	chr3A	728032511	728033572	1061	True	1375.000000	1375	90.019000	1125	2186	1	chr3A.!!$R2	1061
4	TraesCS3A01G506600	chr3A	728384618	728385823	1205	False	1339.000000	1339	86.921000	996	2187	1	chr3A.!!$F2	1191
5	TraesCS3A01G506600	chr3A	728456980	728458187	1207	True	1151.000000	1151	84.050000	996	2191	1	chr3A.!!$R3	1195
6	TraesCS3A01G506600	chr3D	598060818	598062114	1296	False	2074.000000	2074	95.528000	930	2226	1	chr3D.!!$F1	1296
7	TraesCS3A01G506600	chr3D	598048040	598049273	1233	True	1620.000000	1620	90.372000	953	2186	1	chr3D.!!$R2	1233
8	TraesCS3A01G506600	chr4B	613037720	613038653	933	True	1609.000000	1609	97.754000	1	935	1	chr4B.!!$R2	934
9	TraesCS3A01G506600	chr3B	805003458	805004700	1242	True	1559.000000	1559	89.334000	953	2196	1	chr3B.!!$R3	1243
10	TraesCS3A01G506600	chr3B	188463683	188464614	931	True	1550.000000	1550	96.674000	1	932	1	chr3B.!!$R1	931
11	TraesCS3A01G506600	chr3B	188491745	188492682	937	True	1539.000000	1539	96.375000	1	933	1	chr3B.!!$R2	932
12	TraesCS3A01G506600	chr3B	805424646	805425853	1207	True	1173.000000	1173	84.380000	996	2191	1	chr3B.!!$R4	1195
13	TraesCS3A01G506600	chr5B	418372425	418373356	931	False	1544.000000	1544	96.567000	1	932	1	chr5B.!!$F1	931
14	TraesCS3A01G506600	chr1B	29268169	29269103	934	True	1511.000000	1511	95.829000	1	935	1	chr1B.!!$R1	934
15	TraesCS3A01G506600	chr7D	220315239	220315833	594	True	776.000000	776	90.252000	1	594	1	chr7D.!!$R1	593
16	TraesCS3A01G506600	chr6A	497396486	497397321	835	True	771.000000	771	83.886000	2368	3182	1	chr6A.!!$R2	814
17	TraesCS3A01G506600	chr6A	585582148	585582719	571	True	656.000000	656	88.000000	2570	3122	1	chr6A.!!$R3	552
18	TraesCS3A01G506600	chr6D	437347627	437348226	599	True	719.000000	719	88.870000	2581	3160	1	chr6D.!!$R1	579
19	TraesCS3A01G506600	chr6D	61006325	61007283	958	False	290.666667	422	89.241333	2365	3182	3	chr6D.!!$F3	817
20	TraesCS3A01G506600	chr4A	583720096	583720667	571	False	422.000000	422	80.651000	2388	2949	1	chr4A.!!$F1	561
21	TraesCS3A01G506600	chr1A	475298971	475299541	570	False	420.000000	420	80.750000	2388	2949	1	chr1A.!!$F1	561

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
776	778	0.611618	CAGCCTAACATGTGGGCCAA	60.612	55.0	28.48	0.0	46.31	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2335	2361	0.105224	TGTCAGTCGGCCGAAAGAAA	59.895	50.0	32.93	22.48	0.0	2.52	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	1.075482	CATGTCAGCCCCACACCTT	59.925	57.895	0.00	0.00	0.00	3.50
168	170	4.692475	GCGGCCGTACCCAACTGT	62.692	66.667	28.70	0.00	33.26	3.55
465	467	1.065926	TCTGCCTGCAACAATCGATCT	60.066	47.619	0.00	0.00	0.00	2.75
763	765	2.949177	TTCTTTGCCAAGTCAGCCTA	57.051	45.000	0.00	0.00	0.00	3.93
776	778	0.611618	CAGCCTAACATGTGGGCCAA	60.612	55.000	28.48	0.00	46.31	4.52
786	788	1.604593	GTGGGCCAAGCATGTCAGT	60.605	57.895	8.40	0.00	0.00	3.41
842	850	3.445450	TGCTTTTTGTTACTCACTTGCCA	59.555	39.130	0.00	0.00	0.00	4.92
897	905	6.403866	AAAGTGATGGTTTTGCAGTATTCA	57.596	33.333	0.00	0.00	0.00	2.57
959	967	1.163554	CTTCTCCTTGCTGCTTCACC	58.836	55.000	0.00	0.00	0.00	4.02
1077	1095	1.587054	CGCGTCCTCCTTTCAGAGT	59.413	57.895	0.00	0.00	31.53	3.24
1098	1116	3.210528	GCCCTCGTCGTCGGATCT	61.211	66.667	1.55	0.00	37.69	2.75
1237	1260	2.512286	CCGCCATCACGCATCTGT	60.512	61.111	0.00	0.00	0.00	3.41
1298	1321	1.807165	CACCGCTCACCGACATCAG	60.807	63.158	0.00	0.00	40.02	2.90
1299	1322	2.276116	ACCGCTCACCGACATCAGT	61.276	57.895	0.00	0.00	40.02	3.41
1614	1640	2.842462	TGGTCTGTGCACCGTCCT	60.842	61.111	21.17	0.00	39.62	3.85
1761	1787	3.001902	TTTCAGCGACGCCTCGGAT	62.002	57.895	17.79	0.00	40.53	4.18
1800	1826	2.202987	GAGATCTGGGCAGCCGTG	60.203	66.667	5.00	0.02	0.00	4.94
1818	1844	1.737793	GTGGATCCGTTCGCAAAGAAT	59.262	47.619	7.39	0.00	41.49	2.40
1922	1948	1.124477	GCAGGGTATGAGGGAGAGGG	61.124	65.000	0.00	0.00	0.00	4.30
2009	2035	0.670546	AATGAGCTTGTCACGACGGG	60.671	55.000	0.00	0.00	38.28	5.28
2016	2042	3.771160	GTCACGACGGGGCTCCAT	61.771	66.667	1.96	0.00	0.00	3.41
2196	2222	7.151999	TGTTCCGTGATGCTTTTATATTGTT	57.848	32.000	0.00	0.00	0.00	2.83
2202	2228	9.313323	CCGTGATGCTTTTATATTGTTTATACG	57.687	33.333	0.00	0.00	0.00	3.06
2203	2229	8.827599	CGTGATGCTTTTATATTGTTTATACGC	58.172	33.333	0.00	0.00	0.00	4.42
2213	2239	3.620427	TGTTTATACGCAGTCCCATGT	57.380	42.857	0.00	0.00	43.93	3.21

Showing 1 to 25 of 122 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
28	29	2.025793	AGAGATGTGAGGAGGAAGACGA	60.026	50.000	0.00	0.00	0.00	4.20
123	125	3.749064	GCCAGTCGTCGAGGAGCA	61.749	66.667	8.30	0.00	0.00	4.26
212	214	3.490759	GTCCTGCGCGACACCATG	61.491	66.667	12.10	0.00	32.74	3.66
300	302	3.364964	TCCCCATCGACCTCCCCT	61.365	66.667	0.00	0.00	0.00	4.79
360	362	0.950116	GGGTAGATCGATTCGTCCGT	59.050	55.000	5.89	0.00	0.00	4.69
416	418	1.293924	CAGAAGCAAGCGGATCGAAT	58.706	50.000	0.00	0.00	0.00	3.34
763	765	1.976898	CATGCTTGGCCCACATGTT	59.023	52.632	17.34	0.00	37.10	2.71
776	778	5.050091	CGACTAAGTGAAAAACTGACATGCT	60.050	40.000	0.00	0.00	39.81	3.79
786	788	1.796459	GAGCCGCGACTAAGTGAAAAA	59.204	47.619	8.23	0.00	0.00	1.94
1029	1038	1.004560	CTGGCTCTTCTTGACGGCA	60.005	57.895	0.00	0.00	0.00	5.69
1071	1089	2.282251	ACGAGGGCGACACTCTGA	60.282	61.111	7.37	0.00	41.64	3.27
1158	1176	2.590114	GGCGTACACCTTCCAGGGT	61.590	63.158	0.00	0.00	40.58	4.34
1225	1248	1.065701	GTCGAGGTACAGATGCGTGAT	59.934	52.381	0.00	0.00	0.00	3.06
1237	1260	2.753043	GTCGGCCAGGTCGAGGTA	60.753	66.667	18.83	0.00	41.35	3.08
1281	1304	2.214181	GACTGATGTCGGTGAGCGGT	62.214	60.000	3.57	0.00	35.19	5.68
1298	1321	1.472276	CGCGGCGTAGAAGACATGAC	61.472	60.000	15.36	0.00	0.00	3.06
1299	1322	1.226575	CGCGGCGTAGAAGACATGA	60.227	57.895	15.36	0.00	0.00	3.07
1614	1640	0.841289	AGAACCCAAAGACCACGGAA	59.159	50.000	0.00	0.00	0.00	4.30
1800	1826	2.006888	TCATTCTTTGCGAACGGATCC	58.993	47.619	0.00	0.00	33.72	3.36
1818	1844	3.455990	TTGCTGCAATTGAAAGCTTCA	57.544	38.095	25.09	12.65	37.82	3.02
2016	2042	3.173540	CCACCAATTGGCGATCTCA	57.826	52.632	24.79	0.00	39.07	3.27
2129	2155	1.098050	AATCCATGCGTTGAAGGAGC	58.902	50.000	0.00	0.00	32.91	4.70
2196	2222	7.903145	AGATTATAACATGGGACTGCGTATAA	58.097	34.615	0.00	0.00	0.00	0.98
2201	2227	6.025749	TCTAGATTATAACATGGGACTGCG	57.974	41.667	0.00	0.00	0.00	5.18
2202	2228	7.335422	CCATTCTAGATTATAACATGGGACTGC	59.665	40.741	8.83	0.00	0.00	4.40

Showing 1 to 25 of 108 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.