AutoCloner

Multiple sequence alignment - TraesCS7D01G302000

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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	TraesCS7D01G302000	chr7D	100.000	4494	0	0	1	4494	382254410	382258903	0.000000e+00	8299.0
1	TraesCS7D01G302000	chr7D	84.211	228	31	5	1655	1881	438368655	438368878	2.720000e-52	217.0
2	TraesCS7D01G302000	chr7D	88.281	128	13	2	1632	1758	215096309	215096183	7.790000e-33	152.0
3	TraesCS7D01G302000	chr7A	92.002	2013	103	26	2402	4401	430241427	430243394	0.000000e+00	2772.0
4	TraesCS7D01G302000	chr7A	90.412	1043	57	23	1320	2351	430240420	430241430	0.000000e+00	1332.0
5	TraesCS7D01G302000	chr7A	91.868	455	9	4	818	1268	430239976	430240406	1.070000e-170	610.0
6	TraesCS7D01G302000	chr7A	79.245	583	81	18	6	576	430239305	430239859	1.970000e-98	370.0
7	TraesCS7D01G302000	chr7A	83.772	228	32	5	1655	1881	489163240	489163463	1.270000e-50	211.0
8	TraesCS7D01G302000	chr7A	95.413	109	5	0	4386	4494	430271883	430271991	1.660000e-39	174.0
9	TraesCS7D01G302000	chr7A	92.308	65	3	2	2342	2405	360611190	360611253	1.720000e-14	91.6
10	TraesCS7D01G302000	chr7B	93.442	1540	62	12	2402	3925	376432281	376433797	0.000000e+00	2248.0
11	TraesCS7D01G302000	chr7B	90.650	877	41	22	1493	2351	376431427	376432280	0.000000e+00	1127.0
12	TraesCS7D01G302000	chr7B	88.058	762	32	16	684	1431	376430678	376431394	0.000000e+00	848.0
13	TraesCS7D01G302000	chr7B	88.862	413	27	10	4087	4494	376436044	376436442	1.450000e-134	490.0
14	TraesCS7D01G302000	chr7B	80.032	621	84	26	6	617	376430072	376430661	1.490000e-114	424.0
15	TraesCS7D01G302000	chr7B	84.211	228	31	5	1655	1881	455272016	455271793	2.720000e-52	217.0
16	TraesCS7D01G302000	chr7B	95.652	46	2	0	3913	3958	376435279	376435324	1.730000e-09	75.0
17	TraesCS7D01G302000	chr2D	87.747	253	28	3	1629	1881	568801800	568802049	4.400000e-75	292.0
18	TraesCS7D01G302000	chr2D	79.894	189	26	3	1004	1180	568801320	568801508	1.310000e-25	128.0
19	TraesCS7D01G302000	chr2D	82.222	90	14	2	1794	1882	398086987	398086899	4.820000e-10	76.8
20	TraesCS7D01G302000	chr2A	87.352	253	29	2	1629	1881	708059137	708059386	2.050000e-73	287.0
21	TraesCS7D01G302000	chr2A	95.918	49	1	1	627	674	377135607	377135559	1.340000e-10	78.7
22	TraesCS7D01G302000	chr2B	87.805	246	27	2	1629	1874	681409271	681409513	7.360000e-73	285.0
23	TraesCS7D01G302000	chr2B	82.320	181	27	4	1004	1180	681408801	681408980	7.790000e-33	152.0
24	TraesCS7D01G302000	chr2B	91.429	70	2	4	2344	2410	38218223	38218291	4.790000e-15	93.5
25	TraesCS7D01G302000	chr6A	96.552	58	1	1	2349	2405	454654059	454654002	1.330000e-15	95.3
26	TraesCS7D01G302000	chr6A	87.692	65	5	3	613	674	17700407	17700343	6.240000e-09	73.1
27	TraesCS7D01G302000	chr5B	96.552	58	1	1	2349	2405	69548107	69548050	1.330000e-15	95.3
28	TraesCS7D01G302000	chr5D	93.651	63	3	1	2344	2405	273117881	273117943	4.790000e-15	93.5
29	TraesCS7D01G302000	chr3A	95.000	60	2	1	2347	2405	466806948	466807007	4.790000e-15	93.5
30	TraesCS7D01G302000	chr3A	95.918	49	1	1	627	674	620767136	620767184	1.340000e-10	78.7
31	TraesCS7D01G302000	chr3A	92.593	54	3	1	622	674	594510490	594510543	4.820000e-10	76.8
32	TraesCS7D01G302000	chr3B	92.308	65	4	1	2348	2411	525999187	525999123	1.720000e-14	91.6
33	TraesCS7D01G302000	chr1A	88.158	76	7	2	2350	2424	137852083	137852009	6.190000e-14	89.8
34	TraesCS7D01G302000	chr3D	90.769	65	6	0	2341	2405	74197494	74197558	2.230000e-13	87.9
35	TraesCS7D01G302000	chr4D	76.506	166	32	7	1018	1181	46293024	46292864	2.880000e-12	84.2
36	TraesCS7D01G302000	chr4D	90.909	55	3	2	627	679	360102137	360102191	6.240000e-09	73.1
37	TraesCS7D01G302000	chr4B	76.647	167	30	9	1015	1178	67771414	67771574	2.880000e-12	84.2
38	TraesCS7D01G302000	chr4B	95.918	49	1	1	627	674	387795129	387795177	1.340000e-10	78.7
39	TraesCS7D01G302000	chr4B	92.727	55	2	2	627	679	629952328	629952382	1.340000e-10	78.7
40	TraesCS7D01G302000	chr4A	76.506	166	32	7	1015	1178	552698531	552698691	2.880000e-12	84.2
41	TraesCS7D01G302000	chr5A	90.000	60	4	2	622	679	461871459	461871400	4.820000e-10	76.8
42	TraesCS7D01G302000	chr6B	90.909	55	3	2	627	679	601049784	601049838	6.240000e-09	73.1

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	TraesCS7D01G302000	chr7D	382254410	382258903	4493	False	8299.000000	8299	100.000000	1	4494	1	chr7D.!!$F1	4493
1	TraesCS7D01G302000	chr7A	430239305	430243394	4089	False	1271.000000	2772	88.381750	6	4401	4	chr7A.!!$F4	4395
2	TraesCS7D01G302000	chr7B	376430072	376436442	6370	False	868.666667	2248	89.449333	6	4494	6	chr7B.!!$F1	4488
3	TraesCS7D01G302000	chr2D	568801320	568802049	729	False	210.000000	292	83.820500	1004	1881	2	chr2D.!!$F1	877
4	TraesCS7D01G302000	chr2B	681408801	681409513	712	False	218.500000	285	85.062500	1004	1874	2	chr2B.!!$F2	870

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	Hairpin	End Stability	Orientation
506	509	0.040692	CATGCTCGATGGCGATTTGG	60.041	55.0	0.00	46.80	3.28	F
958	979	0.178935	CCCTCCATCTCTCCCTCTCC	60.179	65.0	0.00	0.00	3.71	F
1209	1245	0.248289	TTCCTACTTGCTACGTGCCC	59.752	55.0	0.00	42.00	5.36	F
1490	1543	0.313987	CCCGGGTTTGAACTTTGAGC	59.686	55.0	14.18	0.00	4.26	F
2707	2879	0.319900	CAGGTCAACTCCACAGTCCG	60.320	60.0	0.00	29.93	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1467	1510	0.538746	AAAGTTCAAACCCGGGCGAT	60.539	50.0	24.08	3.77	0.00	4.58	R
2227	2395	0.584876	CACTTTGGGGAACGAACGTC	59.415	55.0	0.00	0.00	28.11	4.34	R
2723	2895	0.872388	CTGGCGTAAACACTGGAACC	59.128	55.0	0.00	0.00	0.00	3.62	R
3242	3426	0.036765	TCAAAGGCGATGTAGGCGTT	60.037	50.0	0.00	0.00	39.89	4.84	R
3969	5654	0.606401	TGCCGCTTTTTCTCTCCTGG	60.606	55.0	0.00	0.00	0.00	4.45	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
34	35	2.048597	GACGCATGTGGGTGTCGA	60.049	61.111	11.65	0.00	41.50	4.20
38	39	1.741770	GCATGTGGGTGTCGAGTCC	60.742	63.158	0.00	0.00	0.00	3.85
72	74	3.190738	TTGTGGCCTTCCTCCCGTG	62.191	63.158	3.32	0.00	0.00	4.94
85	87	4.463879	CCGTGCCAGAGCTCCCAG	62.464	72.222	10.93	0.00	40.80	4.45
87	89	2.046507	GTGCCAGAGCTCCCAGTG	60.047	66.667	10.93	1.41	40.80	3.66
120	122	0.536460	ATCTTGTTGGTTTCGGCGGT	60.536	50.000	7.21	0.00	0.00	5.68
133	136	3.497879	GCGGTAGCAATGTGTCCC	58.502	61.111	0.00	0.00	44.35	4.46
165	168	1.836999	TTGGGGTGTCATCGTGGAGG	61.837	60.000	0.00	0.00	0.00	4.30
167	170	1.218316	GGGTGTCATCGTGGAGGTC	59.782	63.158	0.00	0.00	0.00	3.85
171	174	1.000955	GTGTCATCGTGGAGGTCAGTT	59.999	52.381	0.00	0.00	0.00	3.16
172	175	2.230508	GTGTCATCGTGGAGGTCAGTTA	59.769	50.000	0.00	0.00	0.00	2.24
182	185	3.437746	GGTCAGTTACCTTCCGAGC	57.562	57.895	0.00	0.00	45.75	5.03
183	186	0.458025	GGTCAGTTACCTTCCGAGCG	60.458	60.000	0.00	0.00	45.75	5.03
184	187	1.077089	GTCAGTTACCTTCCGAGCGC	61.077	60.000	0.00	0.00	0.00	5.92
185	188	1.080093	CAGTTACCTTCCGAGCGCA	60.080	57.895	11.47	0.00	0.00	6.09
186	189	0.460284	CAGTTACCTTCCGAGCGCAT	60.460	55.000	11.47	0.00	0.00	4.73
187	190	0.460284	AGTTACCTTCCGAGCGCATG	60.460	55.000	11.47	0.00	0.00	4.06
188	191	1.813753	TTACCTTCCGAGCGCATGC	60.814	57.895	11.47	7.91	43.24	4.06
215	218	4.058817	GCGTATATAGGCAAGCTTGACTT	58.941	43.478	38.46	26.30	46.60	3.01
226	229	3.601443	AGCTTGACTTGTAGCTCGAAT	57.399	42.857	0.00	0.00	44.05	3.34
230	233	5.521735	AGCTTGACTTGTAGCTCGAATATTG	59.478	40.000	0.00	0.00	44.05	1.90
233	236	7.624344	GCTTGACTTGTAGCTCGAATATTGTTT	60.624	37.037	0.00	0.00	34.57	2.83
234	237	7.290857	TGACTTGTAGCTCGAATATTGTTTC	57.709	36.000	0.00	0.00	0.00	2.78
245	248	4.553429	CGAATATTGTTTCGCTTTGGTGTC	59.447	41.667	0.00	0.00	41.61	3.67
251	254	0.817634	TTCGCTTTGGTGTCAGGTGG	60.818	55.000	0.00	0.00	0.00	4.61

Showing 1 to 25 of 275 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
13	14	3.422303	CACCCACATGCGTCACCG	61.422	66.667	0.00	0.00	37.07	4.94
22	23	3.388841	GGGACTCGACACCCACAT	58.611	61.111	14.98	0.00	44.96	3.21
54	55	2.852075	ACGGGAGGAAGGCCACAA	60.852	61.111	5.01	0.00	36.29	3.33
62	64	3.706373	GCTCTGGCACGGGAGGAA	61.706	66.667	0.00	0.00	38.54	3.36
63	65	4.704103	AGCTCTGGCACGGGAGGA	62.704	66.667	0.00	0.00	41.70	3.71
65	67	4.154347	GGAGCTCTGGCACGGGAG	62.154	72.222	14.64	0.00	41.70	4.30
72	74	2.129555	TTTCCACTGGGAGCTCTGGC	62.130	60.000	14.64	0.00	46.01	4.85
84	86	2.065799	AGATGGACTTGGGTTTCCACT	58.934	47.619	0.00	0.00	44.80	4.00
85	87	2.586648	AGATGGACTTGGGTTTCCAC	57.413	50.000	0.00	0.00	44.80	4.02
131	134	1.549203	CCCAAGAGGTTGACAATGGG	58.451	55.000	8.98	8.98	41.38	4.00
132	135	1.203050	ACCCCAAGAGGTTGACAATGG	60.203	52.381	0.00	0.00	36.44	3.16
133	136	1.888512	CACCCCAAGAGGTTGACAATG	59.111	52.381	0.00	0.00	38.39	2.82
154	157	1.822990	GGTAACTGACCTCCACGATGA	59.177	52.381	0.00	0.00	45.89	2.92
171	174	2.202878	GCATGCGCTCGGAAGGTA	60.203	61.111	9.73	0.00	34.30	3.08
174	177	3.918220	GACGCATGCGCTCGGAAG	61.918	66.667	38.15	11.72	44.19	3.46
183	186	1.920574	CCTATATACGCTGACGCATGC	59.079	52.381	7.91	7.91	45.53	4.06
184	187	1.920574	GCCTATATACGCTGACGCATG	59.079	52.381	0.00	0.00	45.53	4.06
185	188	1.544246	TGCCTATATACGCTGACGCAT	59.456	47.619	5.49	0.00	45.53	4.73
186	189	0.955905	TGCCTATATACGCTGACGCA	59.044	50.000	5.49	0.00	45.53	5.24
187	190	1.986378	CTTGCCTATATACGCTGACGC	59.014	52.381	5.49	0.00	45.53	5.19
189	192	3.305398	AGCTTGCCTATATACGCTGAC	57.695	47.619	5.49	0.00	0.00	3.51
190	193	3.320826	TCAAGCTTGCCTATATACGCTGA	59.679	43.478	21.99	0.00	0.00	4.26
191	194	3.430218	GTCAAGCTTGCCTATATACGCTG	59.570	47.826	21.99	0.00	0.00	5.18
192	195	3.322254	AGTCAAGCTTGCCTATATACGCT	59.678	43.478	21.99	3.91	0.00	5.07
193	196	3.654414	AGTCAAGCTTGCCTATATACGC	58.346	45.455	21.99	0.00	0.00	4.42

Showing 1 to 25 of 233 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.