AutoCloner

Multiple sequence alignment - TraesCS1B01G197100

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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	TraesCS1B01G197100	chr1B	100.000	6389	0	0	1	6389	354546549	354540161	0.000000e+00	11799.0
1	TraesCS1B01G197100	chr1B	88.817	769	54	21	988	1732	354660688	354659928	0.000000e+00	915.0
2	TraesCS1B01G197100	chr1B	85.490	827	80	19	2394	3206	354657937	354657137	0.000000e+00	826.0
3	TraesCS1B01G197100	chr1B	86.684	751	82	9	3915	4653	354656532	354655788	0.000000e+00	817.0
4	TraesCS1B01G197100	chr1B	89.157	498	47	5	3270	3763	354657135	354656641	1.180000e-171	614.0
5	TraesCS1B01G197100	chr1B	78.835	704	74	37	1732	2402	354659982	354659321	7.710000e-109	405.0
6	TraesCS1B01G197100	chr1B	83.855	415	37	13	60	449	640878528	640878119	1.010000e-97	368.0
7	TraesCS1B01G197100	chr1B	86.905	336	32	10	4762	5097	354655760	354655437	3.640000e-97	366.0
8	TraesCS1B01G197100	chr1B	81.731	416	53	15	48	453	688981976	688981574	6.180000e-85	326.0
9	TraesCS1B01G197100	chr1B	93.671	158	9	1	454	610	688981545	688981388	1.070000e-57	235.0
10	TraesCS1B01G197100	chr1B	91.837	147	12	0	791	937	200649087	200649233	8.400000e-49	206.0
11	TraesCS1B01G197100	chr1D	93.859	1726	50	20	981	2671	258356294	258357998	0.000000e+00	2549.0
12	TraesCS1B01G197100	chr1D	95.432	1226	42	9	2698	3917	258357985	258359202	0.000000e+00	1941.0
13	TraesCS1B01G197100	chr1D	92.378	1207	52	11	3915	5121	258359244	258360410	0.000000e+00	1683.0
14	TraesCS1B01G197100	chr1D	94.802	1058	51	4	5332	6387	45714649	45713594	0.000000e+00	1646.0
15	TraesCS1B01G197100	chr1D	88.586	771	58	19	985	1732	258346049	258346812	0.000000e+00	909.0
16	TraesCS1B01G197100	chr1D	87.408	683	75	9	3975	4653	258351582	258352257	0.000000e+00	774.0
17	TraesCS1B01G197100	chr1D	84.556	777	75	20	2464	3225	258349996	258350742	0.000000e+00	728.0
18	TraesCS1B01G197100	chr1D	88.145	523	55	5	3227	3745	258350860	258351379	3.270000e-172	616.0
19	TraesCS1B01G197100	chr1D	95.122	82	4	0	5147	5228	258360397	258360478	5.200000e-26	130.0
20	TraesCS1B01G197100	chr1A	93.468	1730	63	17	981	2671	342878950	342877232	0.000000e+00	2523.0
21	TraesCS1B01G197100	chr1A	95.673	1225	39	4	2698	3917	342877245	342876030	0.000000e+00	1956.0
22	TraesCS1B01G197100	chr1A	95.130	965	44	3	4264	5228	342875710	342874749	0.000000e+00	1519.0
23	TraesCS1B01G197100	chr1A	88.457	771	53	18	991	1732	343394994	343394231	0.000000e+00	898.0
24	TraesCS1B01G197100	chr1A	86.613	747	86	9	3915	4653	343391029	343390289	0.000000e+00	813.0
25	TraesCS1B01G197100	chr1A	88.668	653	67	5	3270	3917	343391721	343391071	0.000000e+00	789.0
26	TraesCS1B01G197100	chr1A	84.401	827	84	19	2394	3206	343392518	343391723	0.000000e+00	771.0
27	TraesCS1B01G197100	chr1A	80.552	689	78	25	1732	2402	343394285	343393635	4.480000e-131	479.0
28	TraesCS1B01G197100	chr1A	88.251	383	33	7	4762	5144	343390261	343389891	1.260000e-121	448.0
29	TraesCS1B01G197100	chr1A	87.460	311	17	4	3915	4224	342875997	342875708	7.930000e-89	339.0
30	TraesCS1B01G197100	chr4D	95.377	1060	43	6	5332	6389	375436050	375437105	0.000000e+00	1681.0
31	TraesCS1B01G197100	chr5B	94.712	1059	50	4	5332	6389	84886361	84887414	0.000000e+00	1640.0
32	TraesCS1B01G197100	chr5B	80.361	443	53	23	188	603	487910836	487911271	8.050000e-79	305.0
33	TraesCS1B01G197100	chr5B	89.032	155	17	0	786	940	486034099	486033945	6.540000e-45	193.0
34	TraesCS1B01G197100	chr7D	94.334	1059	57	3	5332	6389	442769980	442768924	0.000000e+00	1620.0
35	TraesCS1B01G197100	chr7D	90.604	149	11	2	466	611	549364844	549364992	1.820000e-45	195.0
36	TraesCS1B01G197100	chr7D	94.382	89	4	1	516	603	147991680	147991768	1.120000e-27	135.0
37	TraesCS1B01G197100	chr7B	94.173	1064	53	5	5332	6389	460546783	460545723	0.000000e+00	1613.0
38	TraesCS1B01G197100	chr7B	94.085	1065	54	4	5332	6389	511318785	511317723	0.000000e+00	1609.0
39	TraesCS1B01G197100	chr7B	90.698	129	9	2	790	915	633320191	633320063	1.100000e-37	169.0
40	TraesCS1B01G197100	chr3A	93.703	1064	59	4	5332	6389	749157769	749156708	0.000000e+00	1587.0
41	TraesCS1B01G197100	chrUn	93.691	1062	56	9	5332	6389	33158435	33159489	0.000000e+00	1580.0
42	TraesCS1B01G197100	chr4A	93.591	1061	63	4	5332	6389	12191773	12192831	0.000000e+00	1578.0
43	TraesCS1B01G197100	chr4A	91.558	154	13	0	787	940	725273571	725273418	5.020000e-51	213.0
44	TraesCS1B01G197100	chr4A	92.537	67	5	0	5271	5337	544409814	544409880	5.270000e-16	97.1
45	TraesCS1B01G197100	chr2B	90.330	455	20	10	1	453	706566356	706566788	5.560000e-160	575.0
46	TraesCS1B01G197100	chr2B	96.226	159	5	1	455	612	706566971	706567129	6.350000e-65	259.0
47	TraesCS1B01G197100	chr2B	93.421	152	10	0	786	937	774368948	774369099	6.450000e-55	226.0
48	TraesCS1B01G197100	chr2B	91.447	152	13	0	786	937	38372862	38373013	6.490000e-50	209.0
49	TraesCS1B01G197100	chr2B	96.330	109	4	0	829	937	606482923	606483031	5.090000e-41	180.0
50	TraesCS1B01G197100	chr6A	87.309	457	45	9	1	449	86535012	86535463	1.590000e-140	510.0
51	TraesCS1B01G197100	chr6A	90.123	162	15	1	456	616	86535498	86535659	6.490000e-50	209.0
52	TraesCS1B01G197100	chr6A	88.462	130	15	0	3519	3648	233345052	233345181	2.380000e-34	158.0
53	TraesCS1B01G197100	chr6A	88.991	109	12	0	5229	5337	97696136	97696244	1.120000e-27	135.0
54	TraesCS1B01G197100	chr6B	84.165	461	49	13	1	438	682667143	682667602	5.920000e-115	425.0
55	TraesCS1B01G197100	chr6B	85.025	394	46	10	68	453	309271851	309272239	7.770000e-104	388.0
56	TraesCS1B01G197100	chr6B	91.304	161	11	3	451	610	309272265	309272423	3.880000e-52	217.0
57	TraesCS1B01G197100	chr6B	92.308	65	4	1	1	65	309271823	309271886	2.450000e-14	91.6
58	TraesCS1B01G197100	chr5D	78.315	641	88	34	1	603	406833900	406834527	3.640000e-97	366.0
59	TraesCS1B01G197100	chr5D	88.073	109	7	6	5232	5337	552376395	552376290	2.420000e-24	124.0
60	TraesCS1B01G197100	chr5A	77.513	587	86	36	49	603	512445202	512445774	1.730000e-80	311.0
61	TraesCS1B01G197100	chr5A	93.506	154	10	0	610	763	313581364	313581517	4.980000e-56	230.0
62	TraesCS1B01G197100	chr5A	93.750	112	7	0	829	940	343767300	343767189	1.100000e-37	169.0
63	TraesCS1B01G197100	chr5A	82.000	150	10	3	788	937	313581504	313581636	1.880000e-20	111.0
64	TraesCS1B01G197100	chr3D	76.535	635	87	45	10	603	102647503	102648116	2.250000e-74	291.0
65	TraesCS1B01G197100	chr3B	78.824	340	49	21	1	329	506731863	506732190	2.330000e-49	207.0
66	TraesCS1B01G197100	chr3B	89.103	156	7	1	822	967	568561111	568560956	1.090000e-42	185.0
67	TraesCS1B01G197100	chr3B	86.364	110	13	2	5229	5337	534174592	534174700	1.130000e-22	119.0
68	TraesCS1B01G197100	chr3B	92.537	67	4	1	5272	5337	14696106	14696040	1.900000e-15	95.3
69	TraesCS1B01G197100	chr3B	92.537	67	4	1	5272	5337	14701440	14701374	1.900000e-15	95.3
70	TraesCS1B01G197100	chr6D	90.789	152	12	2	612	763	50203186	50203037	1.090000e-47	202.0
71	TraesCS1B01G197100	chr2A	86.207	116	12	4	5225	5337	543604954	543605068	8.700000e-24	122.0
72	TraesCS1B01G197100	chr2A	86.607	112	11	4	5229	5337	543619226	543619336	3.130000e-23	121.0
73	TraesCS1B01G197100	chr4B	92.537	67	4	1	5272	5337	114569937	114569871	1.900000e-15	95.3
74	TraesCS1B01G197100	chr7A	96.970	33	1	0	1847	1879	148481500	148481468	8.950000e-04	56.5

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	TraesCS1B01G197100	chr1B	354540161	354546549	6388	True	11799.000000	11799	100.000000	1	6389	1	chr1B.!!$R1	6388
1	TraesCS1B01G197100	chr1B	354655437	354660688	5251	True	657.166667	915	85.981333	988	5097	6	chr1B.!!$R3	4109
2	TraesCS1B01G197100	chr1B	688981388	688981976	588	True	280.500000	326	87.701000	48	610	2	chr1B.!!$R4	562
3	TraesCS1B01G197100	chr1D	45713594	45714649	1055	True	1646.000000	1646	94.802000	5332	6387	1	chr1D.!!$R1	1055
4	TraesCS1B01G197100	chr1D	258356294	258360478	4184	False	1575.750000	2549	94.197750	981	5228	4	chr1D.!!$F2	4247
5	TraesCS1B01G197100	chr1D	258346049	258352257	6208	False	756.750000	909	87.173750	985	4653	4	chr1D.!!$F1	3668
6	TraesCS1B01G197100	chr1A	342874749	342878950	4201	True	1584.250000	2523	92.932750	981	5228	4	chr1A.!!$R1	4247
7	TraesCS1B01G197100	chr1A	343389891	343394994	5103	True	699.666667	898	86.157000	991	5144	6	chr1A.!!$R2	4153
8	TraesCS1B01G197100	chr4D	375436050	375437105	1055	False	1681.000000	1681	95.377000	5332	6389	1	chr4D.!!$F1	1057
9	TraesCS1B01G197100	chr5B	84886361	84887414	1053	False	1640.000000	1640	94.712000	5332	6389	1	chr5B.!!$F1	1057
10	TraesCS1B01G197100	chr7D	442768924	442769980	1056	True	1620.000000	1620	94.334000	5332	6389	1	chr7D.!!$R1	1057
11	TraesCS1B01G197100	chr7B	460545723	460546783	1060	True	1613.000000	1613	94.173000	5332	6389	1	chr7B.!!$R1	1057
12	TraesCS1B01G197100	chr7B	511317723	511318785	1062	True	1609.000000	1609	94.085000	5332	6389	1	chr7B.!!$R2	1057
13	TraesCS1B01G197100	chr3A	749156708	749157769	1061	True	1587.000000	1587	93.703000	5332	6389	1	chr3A.!!$R1	1057
14	TraesCS1B01G197100	chrUn	33158435	33159489	1054	False	1580.000000	1580	93.691000	5332	6389	1	chrUn.!!$F1	1057
15	TraesCS1B01G197100	chr4A	12191773	12192831	1058	False	1578.000000	1578	93.591000	5332	6389	1	chr4A.!!$F1	1057
16	TraesCS1B01G197100	chr2B	706566356	706567129	773	False	417.000000	575	93.278000	1	612	2	chr2B.!!$F4	611
17	TraesCS1B01G197100	chr6A	86535012	86535659	647	False	359.500000	510	88.716000	1	616	2	chr6A.!!$F3	615
18	TraesCS1B01G197100	chr6B	309271823	309272423	600	False	232.200000	388	89.545667	1	610	3	chr6B.!!$F2	609
19	TraesCS1B01G197100	chr5D	406833900	406834527	627	False	366.000000	366	78.315000	1	603	1	chr5D.!!$F1	602
20	TraesCS1B01G197100	chr5A	512445202	512445774	572	False	311.000000	311	77.513000	49	603	1	chr5A.!!$F1	554
21	TraesCS1B01G197100	chr3D	102647503	102648116	613	False	291.000000	291	76.535000	10	603	1	chr3D.!!$F1	593

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
750	1183	0.034337	ACAAAAGCCCTCGTTCGCTA	59.966	50.000	0.00	0.00	34.11	4.26	F
822	1255	0.108520	TCGTATGAGGCGTTTGTCCC	60.109	55.000	0.00	0.00	0.00	4.46	F
1671	2140	0.175302	CAGCAGAAGTCCAGCGAGAT	59.825	55.000	0.00	0.00	0.00	2.75	F
1719	2189	0.744414	TCAGCGTGCATTTCTAGCCC	60.744	55.000	0.00	0.00	0.00	5.19	F
2678	6929	1.079612	GGGCTGTTTCAAGCATGCC	60.080	57.895	15.66	6.27	45.43	4.40	F
4116	8628	1.302366	TGTCAGCTCAACTTGCAGTG	58.698	50.000	0.00	0.00	0.00	3.66	F
5202	9764	0.454957	CCGTGTATGCACTTGCTTGC	60.455	55.000	12.30	0.58	43.16	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1739	2209	0.107508	CGCTGAATCAGACCATGGGT	60.108	55.000	18.09	0.99	39.44	4.51	R
2677	6928	0.901827	GTTAAAACCATGGGCCAGGG	59.098	55.000	34.29	34.29	41.50	4.45	R
3512	7888	1.005215	ACAATCAGAGGGGCAGAAAGG	59.995	52.381	0.00	0.00	0.00	3.11	R
3691	8068	3.074412	GGTCAGTGATGTTAACACAGGG	58.926	50.000	11.22	6.57	40.25	4.45	R
4123	8635	0.038744	CAACAGAAGGATGGCCCACT	59.961	55.000	0.00	0.00	37.41	4.00	R
5323	9885	0.035056	GCATACCTGCTCAACACCCT	60.035	55.000	0.00	0.00	45.32	4.34	R
6115	10685	1.463444	GATGCTTACGTTCAGCGGTTT	59.537	47.619	13.13	0.95	46.52	3.27	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
52	54	6.793479	TTGAAAAACGTTCACGGATAAAAC	57.207	33.333	0.00	0.00	44.95	2.43
181	341	8.567221	GTTCATCGATTTTCATAAAAGTTCACG	58.433	33.333	0.00	0.00	33.22	4.35
359	587	8.267183	AGAAAAAGTTCATCAAACCAGGAAAAT	58.733	29.630	0.00	0.00	38.76	1.82
438	685	0.759959	TTGAGAGGCGTGGTGGTTAA	59.240	50.000	0.00	0.00	0.00	2.01
449	849	3.241701	GTGGTGGTTAATTCATTGCGTG	58.758	45.455	0.00	0.00	0.00	5.34
487	915	8.229811	GCACTTGTTTTTCTCTTTTGAAAACAT	58.770	29.630	12.58	0.00	43.09	2.71
529	960	5.559770	TGCAGTCTGAAACAGATAAATGGA	58.440	37.500	3.32	1.85	42.73	3.41
544	976	0.844661	ATGGACCAGCCCACCTAACA	60.845	55.000	0.00	0.00	39.34	2.41
612	1045	0.586802	GCCGAATAGGAAATGCCGTC	59.413	55.000	0.00	0.00	45.00	4.79
616	1049	2.034001	CGAATAGGAAATGCCGTCGTTC	60.034	50.000	0.00	0.00	43.43	3.95
617	1050	1.567504	ATAGGAAATGCCGTCGTTCG	58.432	50.000	0.00	0.00	43.43	3.95
618	1051	1.079875	TAGGAAATGCCGTCGTTCGC	61.080	55.000	0.00	0.00	43.43	4.70
619	1052	2.275812	GAAATGCCGTCGTTCGCG	60.276	61.111	0.00	0.00	42.98	5.87
620	1053	4.439472	AAATGCCGTCGTTCGCGC	62.439	61.111	0.00	0.00	41.05	6.86
627	1060	4.191485	GTCGTTCGCGCACGGATG	62.191	66.667	29.35	3.22	40.74	3.51
628	1061	4.407694	TCGTTCGCGCACGGATGA	62.408	61.111	29.35	8.91	40.57	2.92
629	1062	3.902063	CGTTCGCGCACGGATGAG	61.902	66.667	23.39	0.00	35.69	2.90
630	1063	3.554692	GTTCGCGCACGGATGAGG	61.555	66.667	8.75	0.00	40.63	3.86
631	1064	3.754530	TTCGCGCACGGATGAGGA	61.755	61.111	8.75	0.00	40.63	3.71
632	1065	3.076258	TTCGCGCACGGATGAGGAT	62.076	57.895	8.75	0.00	40.63	3.24
633	1066	3.333189	CGCGCACGGATGAGGATG	61.333	66.667	8.75	0.00	34.97	3.51
634	1067	3.643978	GCGCACGGATGAGGATGC	61.644	66.667	0.30	0.00	34.66	3.91
635	1068	2.107750	CGCACGGATGAGGATGCT	59.892	61.111	0.00	0.00	35.88	3.79
636	1069	1.953138	CGCACGGATGAGGATGCTC	60.953	63.158	7.39	7.39	35.88	4.26
637	1070	1.953138	GCACGGATGAGGATGCTCG	60.953	63.158	9.88	0.42	35.16	5.03

Showing 1 to 25 of 335 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
487	915	8.204836	AGACTGCAGTAGTTTTTCTTCTTCTTA	58.795	33.333	21.73	0.00	40.53	2.10
529	960	2.747686	CGTGTTAGGTGGGCTGGT	59.252	61.111	0.00	0.00	0.00	4.00
612	1045	3.902063	CTCATCCGTGCGCGAACG	61.902	66.667	32.41	32.41	43.20	3.95
616	1049	3.333189	CATCCTCATCCGTGCGCG	61.333	66.667	13.88	13.88	37.95	6.86
617	1050	3.643978	GCATCCTCATCCGTGCGC	61.644	66.667	0.00	0.00	0.00	6.09
618	1051	1.953138	GAGCATCCTCATCCGTGCG	60.953	63.158	0.00	0.00	42.18	5.34
619	1052	1.953138	CGAGCATCCTCATCCGTGC	60.953	63.158	0.00	0.00	38.00	5.34
620	1053	0.179100	AACGAGCATCCTCATCCGTG	60.179	55.000	0.00	0.00	38.00	4.94
621	1054	0.179100	CAACGAGCATCCTCATCCGT	60.179	55.000	0.00	0.00	38.00	4.69
622	1055	0.179100	ACAACGAGCATCCTCATCCG	60.179	55.000	0.00	0.00	38.00	4.18
623	1056	1.137872	AGACAACGAGCATCCTCATCC	59.862	52.381	0.00	0.00	38.00	3.51
624	1057	2.468831	GAGACAACGAGCATCCTCATC	58.531	52.381	0.00	0.00	38.00	2.92
625	1058	1.202348	CGAGACAACGAGCATCCTCAT	60.202	52.381	0.00	0.00	38.00	2.90
626	1059	0.171231	CGAGACAACGAGCATCCTCA	59.829	55.000	0.00	0.00	38.00	3.86
627	1060	0.171455	ACGAGACAACGAGCATCCTC	59.829	55.000	0.00	0.00	37.03	3.71
628	1061	1.402259	CTACGAGACAACGAGCATCCT	59.598	52.381	0.00	0.00	37.03	3.24
629	1062	1.828832	CTACGAGACAACGAGCATCC	58.171	55.000	0.00	0.00	37.03	3.51
630	1063	1.192793	GCTACGAGACAACGAGCATC	58.807	55.000	0.00	0.00	36.88	3.91
631	1064	0.526211	TGCTACGAGACAACGAGCAT	59.474	50.000	0.00	0.00	39.41	3.79
632	1065	0.109735	CTGCTACGAGACAACGAGCA	60.110	55.000	0.00	0.00	40.70	4.26
633	1066	0.109689	ACTGCTACGAGACAACGAGC	60.110	55.000	0.00	0.00	37.15	5.03
634	1067	2.788407	GCTACTGCTACGAGACAACGAG	60.788	54.545	0.00	0.00	35.25	4.18
635	1068	1.129998	GCTACTGCTACGAGACAACGA	59.870	52.381	0.00	0.00	35.25	3.85
636	1069	1.536149	GCTACTGCTACGAGACAACG	58.464	55.000	0.00	0.00	36.40	4.10
637	1070	1.536149	CGCTACTGCTACGAGACAAC	58.464	55.000	0.00	0.00	36.97	3.32

Showing 1 to 25 of 313 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.