AutoCloner

Multiple sequence alignment - TraesCS1D01G442400

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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	TraesCS1D01G442400	chr1D	100.000	4750	0	0	1	4750	486875302	486880051	0.000000e+00	8772.0
1	TraesCS1D01G442400	chr1D	85.663	279	29	6	141	418	418405083	418404815	2.800000e-72	283.0
2	TraesCS1D01G442400	chr1D	93.204	103	7	0	38	140	417625917	417626019	8.230000e-33	152.0
3	TraesCS1D01G442400	chr1D	89.189	111	12	0	38	148	296894396	296894506	6.410000e-29	139.0
4	TraesCS1D01G442400	chr1D	97.778	45	0	1	1	45	249721482	249721439	5.100000e-10	76.8
5	TraesCS1D01G442400	chr1D	100.000	41	0	0	1	41	425378643	425378683	5.100000e-10	76.8
6	TraesCS1D01G442400	chr1D	100.000	30	0	0	4270	4299	71606474	71606445	6.640000e-04	56.5
7	TraesCS1D01G442400	chr1B	89.352	1991	155	33	2133	4105	678047981	678049932	0.000000e+00	2449.0
8	TraesCS1D01G442400	chr1B	91.982	1771	81	21	446	2187	678046243	678047981	0.000000e+00	2427.0
9	TraesCS1D01G442400	chr1B	87.407	135	14	2	4324	4456	610318485	610318352	8.230000e-33	152.0
10	TraesCS1D01G442400	chr1A	88.621	2030	155	39	2210	4206	584507957	584509943	0.000000e+00	2399.0
11	TraesCS1D01G442400	chr1A	91.627	1684	92	16	523	2187	584506064	584507717	0.000000e+00	2283.0
12	TraesCS1D01G442400	chr1A	97.590	83	2	0	2133	2215	584507717	584507799	4.960000e-30	143.0
13	TraesCS1D01G442400	chr6A	85.714	280	30	6	141	418	592431611	592431882	2.160000e-73	287.0
14	TraesCS1D01G442400	chr6D	85.461	282	31	5	141	421	27033893	27034165	7.780000e-73	285.0
15	TraesCS1D01G442400	chr6D	85.305	279	31	5	141	418	121158655	121158386	3.620000e-71	279.0
16	TraesCS1D01G442400	chr6D	93.204	103	7	0	38	140	42959764	42959866	8.230000e-33	152.0
17	TraesCS1D01G442400	chr6D	100.000	28	0	0	4247	4274	419881893	419881920	9.000000e-03	52.8
18	TraesCS1D01G442400	chr3D	86.296	270	27	5	151	418	29810468	29810207	7.780000e-73	285.0
19	TraesCS1D01G442400	chr5D	85.560	277	31	6	143	418	520111437	520111705	1.010000e-71	281.0
20	TraesCS1D01G442400	chr5D	85.357	280	32	4	141	419	548674931	548675202	1.010000e-71	281.0
21	TraesCS1D01G442400	chr5D	87.931	58	5	2	4245	4301	57849792	57849848	3.070000e-07	67.6
22	TraesCS1D01G442400	chr5D	100.000	28	0	0	4245	4272	380481930	380481903	9.000000e-03	52.8
23	TraesCS1D01G442400	chr2B	85.305	279	32	4	141	418	688429773	688430043	3.620000e-71	279.0
24	TraesCS1D01G442400	chr2B	85.106	282	31	6	141	420	162860565	162860837	1.300000e-70	278.0
25	TraesCS1D01G442400	chr2B	86.957	138	15	2	4317	4452	798146552	798146688	8.230000e-33	152.0
26	TraesCS1D01G442400	chr2B	95.833	48	0	1	1	46	786306442	786306395	5.100000e-10	76.8
27	TraesCS1D01G442400	chr2B	95.833	48	0	1	1	46	786311622	786311575	5.100000e-10	76.8
28	TraesCS1D01G442400	chr2B	95.833	48	0	1	1	46	786312992	786312945	5.100000e-10	76.8
29	TraesCS1D01G442400	chr2B	95.833	48	0	1	1	46	786318352	786318305	5.100000e-10	76.8
30	TraesCS1D01G442400	chr2B	97.143	35	1	0	4247	4281	210846221	210846255	5.130000e-05	60.2
31	TraesCS1D01G442400	chr2B	100.000	31	0	0	4251	4281	427571765	427571795	1.850000e-04	58.4
32	TraesCS1D01G442400	chrUn	80.100	402	54	13	3854	4244	45529825	45530211	4.680000e-70	276.0
33	TraesCS1D01G442400	chrUn	91.667	108	9	0	38	145	27663951	27664058	2.960000e-32	150.0
34	TraesCS1D01G442400	chr3B	89.437	142	12	2	4317	4456	12407537	12407677	4.890000e-40	176.0
35	TraesCS1D01G442400	chr3B	87.407	135	14	2	4324	4456	125703630	125703763	8.230000e-33	152.0
36	TraesCS1D01G442400	chr3B	86.957	138	14	3	4322	4456	696715402	696715266	8.230000e-33	152.0
37	TraesCS1D01G442400	chr3B	86.420	81	8	2	1001	1078	520330384	520330464	8.470000e-13	86.1
38	TraesCS1D01G442400	chr3B	100.000	43	0	0	1	43	151507657	151507615	3.940000e-11	80.5
39	TraesCS1D01G442400	chr4B	92.727	110	8	0	38	147	16060510	16060401	4.920000e-35	159.0
40	TraesCS1D01G442400	chr4B	97.778	45	0	1	1	45	396597548	396597505	5.100000e-10	76.8
41	TraesCS1D01G442400	chr5A	87.681	138	13	3	4322	4456	598251897	598251761	1.770000e-34	158.0
42	TraesCS1D01G442400	chr5A	89.474	114	10	2	42	153	4076501	4076388	4.960000e-30	143.0
43	TraesCS1D01G442400	chr4D	92.661	109	8	0	38	146	258893546	258893654	1.770000e-34	158.0
44	TraesCS1D01G442400	chr4D	95.238	42	2	0	4245	4286	483092884	483092925	3.070000e-07	67.6
45	TraesCS1D01G442400	chr6B	86.957	138	14	3	4322	4456	445408403	445408267	8.230000e-33	152.0
46	TraesCS1D01G442400	chr6B	97.143	35	1	0	4247	4281	73158877	73158911	5.130000e-05	60.2
47	TraesCS1D01G442400	chr5B	91.743	109	9	0	38	146	357161075	357161183	8.230000e-33	152.0
48	TraesCS1D01G442400	chr5B	87.407	135	14	2	4324	4456	472929617	472929484	8.230000e-33	152.0
49	TraesCS1D01G442400	chr5B	91.743	109	9	0	38	146	634998952	634998844	8.230000e-33	152.0
50	TraesCS1D01G442400	chr5B	86.014	143	15	4	4317	4456	665813107	665813247	1.070000e-31	148.0
51	TraesCS1D01G442400	chr7B	86.861	137	14	4	4328	4461	156421913	156421778	2.960000e-32	150.0
52	TraesCS1D01G442400	chr7B	92.683	41	2	1	4266	4306	699906177	699906216	1.850000e-04	58.4
53	TraesCS1D01G442400	chr4A	89.256	121	10	3	38	155	683610133	683610253	1.070000e-31	148.0
54	TraesCS1D01G442400	chr4A	86.239	109	15	0	38	146	626072455	626072563	8.350000e-23	119.0
55	TraesCS1D01G442400	chr4A	95.000	40	1	1	4250	4289	358069207	358069169	1.430000e-05	62.1
56	TraesCS1D01G442400	chr2D	89.565	115	12	0	38	152	558072225	558072111	3.830000e-31	147.0
57	TraesCS1D01G442400	chr2D	100.000	33	0	0	4267	4299	323417680	323417712	1.430000e-05	62.1
58	TraesCS1D01G442400	chr3A	90.000	70	7	0	1009	1078	515244680	515244749	1.820000e-14	91.6
59	TraesCS1D01G442400	chr7A	97.826	46	0	1	1	45	315742611	315742656	1.420000e-10	78.7
60	TraesCS1D01G442400	chr7A	100.000	29	0	0	4245	4273	583165753	583165781	2.000000e-03	54.7
61	TraesCS1D01G442400	chr7D	100.000	28	0	0	4271	4298	480003116	480003089	9.000000e-03	52.8
62	TraesCS1D01G442400	chr7D	100.000	28	0	0	4270	4297	558158314	558158287	9.000000e-03	52.8

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	TraesCS1D01G442400	chr1D	486875302	486880051	4749	False	8772.000000	8772	100.000000	1	4750	1	chr1D.!!$F4	4749
1	TraesCS1D01G442400	chr1B	678046243	678049932	3689	False	2438.000000	2449	90.667000	446	4105	2	chr1B.!!$F1	3659
2	TraesCS1D01G442400	chr1A	584506064	584509943	3879	False	1608.333333	2399	92.612667	523	4206	3	chr1A.!!$F1	3683

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	End Stability	Orientation
190	191	0.034337	GTTCTGGTGCGTTGGTCCTA	59.966	55.0	0.00	0.00	2.94	F
311	312	0.037326	TCCCTTCAGCGCTTGTAGTG	60.037	55.0	7.50	0.00	2.74	F
2072	2120	0.106167	CCAGATACTCCCTCCGGTCA	60.106	60.0	0.00	0.00	4.02	F
3061	3349	0.809385	CCTCTGGCATGCTTGAACTG	59.191	55.0	18.92	4.58	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1220	1247	0.305922	GAAATGGAAGCTCGCATCGG	59.694	55.000	0.00	0.00	0.00	4.18	R
2110	2167	1.343821	CGCAACCTCGATACAACGC	59.656	57.895	0.00	0.00	0.00	4.84	R
3133	3428	0.105224	CCTGTACAACGGTGGTGACA	59.895	55.000	4.97	5.11	38.70	3.58	R
4711	5022	0.035056	ATGTGCAGGGCCTGTCTAAC	60.035	55.000	32.80	24.27	33.43	2.34	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	Hairpin	End Stability
25	26	8.256611	GCTATTACACATATTACATCCACTGG	57.743	38.462	0.00	4.00
26	27	7.334421	GCTATTACACATATTACATCCACTGGG	59.666	40.741	0.00	4.45
27	28	3.820557	ACACATATTACATCCACTGGGC	58.179	45.455	0.00	5.36
28	29	3.201930	ACACATATTACATCCACTGGGCA	59.798	43.478	0.00	5.36
29	30	4.141181	ACACATATTACATCCACTGGGCAT	60.141	41.667	0.00	4.40
30	31	4.456911	CACATATTACATCCACTGGGCATC	59.543	45.833	0.00	3.91
31	32	4.104579	ACATATTACATCCACTGGGCATCA	59.895	41.667	0.00	3.07
32	33	3.668141	ATTACATCCACTGGGCATCAA	57.332	42.857	0.00	2.57
33	34	3.448093	TTACATCCACTGGGCATCAAA	57.552	42.857	0.00	2.69
34	35	1.843368	ACATCCACTGGGCATCAAAG	58.157	50.000	0.00	2.77
35	36	1.076024	ACATCCACTGGGCATCAAAGT	59.924	47.619	0.00	2.66
36	37	2.173519	CATCCACTGGGCATCAAAGTT	58.826	47.619	0.00	2.66
37	38	1.909700	TCCACTGGGCATCAAAGTTC	58.090	50.000	0.00	3.01
38	39	0.523072	CCACTGGGCATCAAAGTTCG	59.477	55.000	0.00	3.95
39	40	0.109597	CACTGGGCATCAAAGTTCGC	60.110	55.000	0.00	4.70
40	41	1.244019	ACTGGGCATCAAAGTTCGCC	61.244	55.000	44.10	5.54
41	42	0.962356	CTGGGCATCAAAGTTCGCCT	60.962	55.000	44.27	5.52
42	43	0.326595	TGGGCATCAAAGTTCGCCTA	59.673	50.000	44.27	3.93
43	44	1.017387	GGGCATCAAAGTTCGCCTAG	58.983	55.000	44.27	3.02
44	45	1.679032	GGGCATCAAAGTTCGCCTAGT	60.679	52.381	44.27	2.57
45	46	2.084546	GGCATCAAAGTTCGCCTAGTT	58.915	47.619	41.50	2.24
46	47	3.267483	GGCATCAAAGTTCGCCTAGTTA	58.733	45.455	41.50	2.24
47	48	3.687698	GGCATCAAAGTTCGCCTAGTTAA	59.312	43.478	41.50	2.01
48	49	4.201822	GGCATCAAAGTTCGCCTAGTTAAG	60.202	45.833	41.50	1.85
49	50	4.728021	GCATCAAAGTTCGCCTAGTTAAGC	60.728	45.833	0.00	3.09

Showing 1 to 25 of 750 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	7.334421	CCCAGTGGATGTAATATGTGTAATAGC	59.666	40.741	11.95	0.00	0.00	2.97
1	2	7.334421	GCCCAGTGGATGTAATATGTGTAATAG	59.666	40.741	11.95	0.00	0.00	1.73
3	4	6.003950	GCCCAGTGGATGTAATATGTGTAAT	58.996	40.000	11.95	0.00	0.00	1.89
5	6	4.410555	TGCCCAGTGGATGTAATATGTGTA	59.589	41.667	11.95	0.00	0.00	2.90
6	7	3.201930	TGCCCAGTGGATGTAATATGTGT	59.798	43.478	11.95	0.00	0.00	3.72
7	8	3.819368	TGCCCAGTGGATGTAATATGTG	58.181	45.455	11.95	0.00	0.00	3.21
8	9	4.104579	TGATGCCCAGTGGATGTAATATGT	59.895	41.667	11.95	0.00	0.00	2.29
9	10	4.654915	TGATGCCCAGTGGATGTAATATG	58.345	43.478	11.95	0.00	0.00	1.78
10	11	4.999469	TGATGCCCAGTGGATGTAATAT	57.001	40.909	11.95	0.00	0.00	1.28
11	12	4.787135	TTGATGCCCAGTGGATGTAATA	57.213	40.909	11.95	0.00	0.00	0.98
12	13	3.668141	TTGATGCCCAGTGGATGTAAT	57.332	42.857	11.95	0.00	0.00	1.89
13	14	3.245229	ACTTTGATGCCCAGTGGATGTAA	60.245	43.478	11.95	0.00	0.00	2.41
14	15	2.308570	ACTTTGATGCCCAGTGGATGTA	59.691	45.455	11.95	0.00	0.00	2.29
15	16	1.076024	ACTTTGATGCCCAGTGGATGT	59.924	47.619	11.95	0.00	0.00	3.06
16	17	1.843368	ACTTTGATGCCCAGTGGATG	58.157	50.000	11.95	0.00	0.00	3.51
17	18	2.450476	GAACTTTGATGCCCAGTGGAT	58.550	47.619	11.95	0.00	0.00	3.41
18	19	1.881925	CGAACTTTGATGCCCAGTGGA	60.882	52.381	11.95	0.00	0.00	4.02
19	20	0.523072	CGAACTTTGATGCCCAGTGG	59.477	55.000	0.63	0.63	0.00	4.00
20	21	0.109597	GCGAACTTTGATGCCCAGTG	60.110	55.000	0.00	0.00	0.00	3.66
21	22	1.244019	GGCGAACTTTGATGCCCAGT	61.244	55.000	0.00	0.00	41.70	4.00
22	23	1.508088	GGCGAACTTTGATGCCCAG	59.492	57.895	0.00	0.00	41.70	4.45
23	24	3.680156	GGCGAACTTTGATGCCCA	58.320	55.556	0.00	0.00	41.70	5.36
26	27	4.728021	GCTTAACTAGGCGAACTTTGATGC	60.728	45.833	0.00	0.00	0.00	3.91
27	28	4.898370	GCTTAACTAGGCGAACTTTGATG	58.102	43.478	0.00	0.00	0.00	3.07
38	39	3.318557	ACAGGATAGACGCTTAACTAGGC	59.681	47.826	0.00	0.00	0.00	3.93

Showing 1 to 25 of 773 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.