AutoCloner

Multiple sequence alignment - TraesCS7D01G054000

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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	TraesCS7D01G054000	chr7D	100.000	3533	0	0	1	3533	28579569	28576037	0.000000e+00	6525.0
1	TraesCS7D01G054000	chr7D	92.701	274	14	3	3265	3533	28613751	28613479	1.190000e-104	390.0
2	TraesCS7D01G054000	chr7D	92.336	274	15	3	3265	3533	28633777	28634049	5.530000e-103	385.0
3	TraesCS7D01G054000	chr7D	82.432	444	48	11	3109	3533	28543559	28543127	9.320000e-96	361.0
4	TraesCS7D01G054000	chr7D	86.331	139	19	0	318	456	28594851	28594713	6.110000e-33	152.0
5	TraesCS7D01G054000	chr7D	86.331	139	19	0	318	456	28651672	28651810	6.110000e-33	152.0
6	TraesCS7D01G054000	chr7D	86.022	93	8	3	1	88	28651336	28651428	1.040000e-15	95.3
7	TraesCS7D01G054000	chr7D	89.474	76	3	3	18	88	28595170	28595095	1.350000e-14	91.6
8	TraesCS7D01G054000	chr7A	89.463	2420	216	27	578	2976	29009671	29007270	0.000000e+00	3020.0
9	TraesCS7D01G054000	chr7A	87.631	2288	225	31	744	2997	28809201	28806938	0.000000e+00	2604.0
10	TraesCS7D01G054000	chr7A	87.626	2287	226	31	744	2997	28969298	28967036	0.000000e+00	2603.0
11	TraesCS7D01G054000	chr7A	87.500	2288	228	32	744	2997	28846002	28843739	0.000000e+00	2588.0
12	TraesCS7D01G054000	chr7A	87.441	1919	228	9	989	2901	563246827	563244916	0.000000e+00	2196.0
13	TraesCS7D01G054000	chr7A	93.607	219	14	0	1	219	29010181	29009963	9.460000e-86	327.0
14	TraesCS7D01G054000	chr7A	84.343	198	15	1	1	198	29011734	29011553	2.800000e-41	180.0
15	TraesCS7D01G054000	chr4A	88.751	2338	211	31	576	2887	702328223	702325912	0.000000e+00	2813.0
16	TraesCS7D01G054000	chr4A	87.053	2155	247	26	750	2878	702299073	702296925	0.000000e+00	2405.0
17	TraesCS7D01G054000	chr4A	86.311	2177	249	32	1017	3169	702353126	702350975	0.000000e+00	2324.0
18	TraesCS7D01G054000	chr4A	86.842	228	20	7	572	799	702368908	702368691	2.720000e-61	246.0
19	TraesCS7D01G054000	chr4A	80.321	249	34	13	3273	3519	11733855	11734090	1.300000e-39	174.0
20	TraesCS7D01G054000	chr4A	85.235	149	9	6	3	146	702328739	702328599	1.320000e-29	141.0
21	TraesCS7D01G054000	chr4A	100.000	33	0	0	20	52	702127875	702127843	1.060000e-05	62.1
22	TraesCS7D01G054000	chrUn	87.500	2288	224	34	744	2997	313533646	313531387	0.000000e+00	2584.0
23	TraesCS7D01G054000	chrUn	80.366	820	82	27	2723	3492	459694202	459694992	1.850000e-152	549.0
24	TraesCS7D01G054000	chr7B	86.018	2167	253	27	747	2901	525598724	525596596	0.000000e+00	2278.0
25	TraesCS7D01G054000	chr7B	76.471	136	32	0	294	429	3894116	3894251	1.360000e-09	75.0
26	TraesCS7D01G054000	chr5B	80.274	365	51	13	3171	3518	338935198	338934838	4.530000e-64	255.0
27	TraesCS7D01G054000	chr5B	77.410	332	47	17	3144	3453	674489589	674489264	4.690000e-39	172.0
28	TraesCS7D01G054000	chr1A	77.887	407	64	14	3141	3527	124346722	124347122	2.740000e-56	230.0
29	TraesCS7D01G054000	chr1B	83.117	231	34	5	3295	3522	331583947	331584175	4.620000e-49	206.0
30	TraesCS7D01G054000	chr1D	81.081	185	32	3	3315	3498	114116170	114116352	1.020000e-30	145.0
31	TraesCS7D01G054000	chr1D	79.845	129	24	2	3398	3525	272550986	272550859	3.760000e-15	93.5
32	TraesCS7D01G054000	chr3A	88.136	59	5	2	384	440	505225094	505225152	6.330000e-08	69.4

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	TraesCS7D01G054000	chr7D	28576037	28579569	3532	True	6525.000000	6525	100.000000	1	3533	1	chr7D.!!$R2	3532
1	TraesCS7D01G054000	chr7A	28806938	28809201	2263	True	2604.000000	2604	87.631000	744	2997	1	chr7A.!!$R1	2253
2	TraesCS7D01G054000	chr7A	28967036	28969298	2262	True	2603.000000	2603	87.626000	744	2997	1	chr7A.!!$R3	2253
3	TraesCS7D01G054000	chr7A	28843739	28846002	2263	True	2588.000000	2588	87.500000	744	2997	1	chr7A.!!$R2	2253
4	TraesCS7D01G054000	chr7A	563244916	563246827	1911	True	2196.000000	2196	87.441000	989	2901	1	chr7A.!!$R4	1912
5	TraesCS7D01G054000	chr7A	29007270	29011734	4464	True	1175.666667	3020	89.137667	1	2976	3	chr7A.!!$R5	2975
6	TraesCS7D01G054000	chr4A	702296925	702299073	2148	True	2405.000000	2405	87.053000	750	2878	1	chr4A.!!$R2	2128
7	TraesCS7D01G054000	chr4A	702350975	702353126	2151	True	2324.000000	2324	86.311000	1017	3169	1	chr4A.!!$R3	2152
8	TraesCS7D01G054000	chr4A	702325912	702328739	2827	True	1477.000000	2813	86.993000	3	2887	2	chr4A.!!$R5	2884
9	TraesCS7D01G054000	chrUn	313531387	313533646	2259	True	2584.000000	2584	87.500000	744	2997	1	chrUn.!!$R1	2253
10	TraesCS7D01G054000	chrUn	459694202	459694992	790	False	549.000000	549	80.366000	2723	3492	1	chrUn.!!$F1	769
11	TraesCS7D01G054000	chr7B	525596596	525598724	2128	True	2278.000000	2278	86.018000	747	2901	1	chr7B.!!$R1	2154

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
187	1746	0.250727	ACAGCTTTAAGCAGCCGGAA	60.251	50.0	19.63	0.0	45.56	4.30	F
228	1787	0.392863	AGCATGCATAACAGGTGCGA	60.393	50.0	21.98	0.0	45.37	5.10	F
709	2337	0.466124	GACCTCTACCTGCCCATGAC	59.534	60.0	0.00	0.0	0.00	3.06	F
2415	4083	0.321564	AGGCTTATCTTGCGCACACA	60.322	50.0	11.12	0.0	0.00	3.72	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1233	2896	0.179936	CCCTGAGCTCCTTCATGGTC	59.820	60.0	12.15	0.0	37.07	4.02	R
1644	3307	0.881118	GCCGACATGCCTTGAAGAAA	59.119	50.0	0.00	0.0	0.00	2.52	R
2449	4117	0.327924	TCCTGCAATGACGACCCAAT	59.672	50.0	0.00	0.0	0.00	3.16	R
3502	5280	0.109319	CCGCACAAGGGCACAATAAC	60.109	55.0	0.00	0.0	0.00	1.89	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
71	1629	6.487668	TGCCATCAGATTCATATTGGTACTTG	59.512	38.462	0.00	0.00	0.00	3.16
90	1648	3.107642	TGAAAGAACGGTCTGAAGTCC	57.892	47.619	2.28	0.00	33.05	3.85
100	1658	2.444421	GTCTGAAGTCCGAACCCTAGA	58.556	52.381	0.00	0.00	0.00	2.43
108	1666	6.664816	TGAAGTCCGAACCCTAGATACTTTTA	59.335	38.462	0.00	0.00	0.00	1.52
132	1691	1.608590	ACCGGCTGTTCAATCAAAGTG	59.391	47.619	0.00	0.00	0.00	3.16
159	1718	1.452833	GCTTAAGCAGCCCTCCAGG	60.453	63.158	22.59	0.00	43.65	4.45
171	1730	2.297315	GCCCTCCAGGAAAAAGAAACAG	59.703	50.000	0.00	0.00	38.24	3.16
187	1746	0.250727	ACAGCTTTAAGCAGCCGGAA	60.251	50.000	19.63	0.00	45.56	4.30
202	1761	1.540267	CGGAAGGTGGCCAATTAACA	58.460	50.000	7.24	0.00	0.00	2.41
228	1787	0.392863	AGCATGCATAACAGGTGCGA	60.393	50.000	21.98	0.00	45.37	5.10
279	1838	1.141053	ACTTGCCGGTTCTCACTTTCT	59.859	47.619	1.90	0.00	0.00	2.52
280	1839	2.222027	CTTGCCGGTTCTCACTTTCTT	58.778	47.619	1.90	0.00	0.00	2.52
282	1841	2.218603	TGCCGGTTCTCACTTTCTTTC	58.781	47.619	1.90	0.00	0.00	2.62
283	1842	2.218603	GCCGGTTCTCACTTTCTTTCA	58.781	47.619	1.90	0.00	0.00	2.69
284	1843	2.224314	GCCGGTTCTCACTTTCTTTCAG	59.776	50.000	1.90	0.00	0.00	3.02
285	1844	3.467803	CCGGTTCTCACTTTCTTTCAGT	58.532	45.455	0.00	0.00	0.00	3.41
286	1845	3.248602	CCGGTTCTCACTTTCTTTCAGTG	59.751	47.826	0.00	0.00	42.74	3.66
288	1847	5.047847	CGGTTCTCACTTTCTTTCAGTGTA	58.952	41.667	0.24	0.00	42.12	2.90
289	1848	5.522460	CGGTTCTCACTTTCTTTCAGTGTAA	59.478	40.000	0.24	0.00	42.12	2.41
290	1849	6.202954	CGGTTCTCACTTTCTTTCAGTGTAAT	59.797	38.462	0.24	0.00	42.12	1.89
291	1850	7.355778	GGTTCTCACTTTCTTTCAGTGTAATG	58.644	38.462	0.24	0.00	42.12	1.90
293	1852	7.715265	TCTCACTTTCTTTCAGTGTAATGTC	57.285	36.000	0.24	0.00	42.12	3.06
297	1856	9.554395	TCACTTTCTTTCAGTGTAATGTCATTA	57.446	29.630	0.89	0.89	42.12	1.90
299	1858	9.561069	ACTTTCTTTCAGTGTAATGTCATTACT	57.439	29.630	27.80	14.13	44.17	2.24
310	1869	9.554724	GTGTAATGTCATTACTTTTGGTACATG	57.445	33.333	27.80	0.00	44.17	3.21

Showing 1 to 25 of 161 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
71	1629	2.059541	CGGACTTCAGACCGTTCTTTC	58.940	52.381	9.25	0.00	45.60	2.62
90	1648	6.474751	CGGTTTCTAAAAGTATCTAGGGTTCG	59.525	42.308	0.00	0.00	0.00	3.95
100	1658	5.310451	TGAACAGCCGGTTTCTAAAAGTAT	58.690	37.500	1.90	0.00	40.63	2.12
108	1666	2.270352	TGATTGAACAGCCGGTTTCT	57.730	45.000	1.90	0.00	40.63	2.52
157	1716	6.220726	TGCTTAAAGCTGTTTCTTTTTCCT	57.779	33.333	0.00	0.00	42.97	3.36
159	1718	5.050769	GGCTGCTTAAAGCTGTTTCTTTTTC	60.051	40.000	0.00	0.00	42.97	2.29
171	1730	0.960861	ACCTTCCGGCTGCTTAAAGC	60.961	55.000	0.00	0.00	42.82	3.51
187	1746	1.616374	CCGTTTGTTAATTGGCCACCT	59.384	47.619	3.88	0.00	0.00	4.00
191	1750	1.708822	CTGCCGTTTGTTAATTGGCC	58.291	50.000	0.00	0.00	45.12	5.36
202	1761	0.887247	TGTTATGCATGCTGCCGTTT	59.113	45.000	20.33	0.00	44.23	3.60
254	1813	1.289380	GAGAACCGGCAAGTCTCGT	59.711	57.895	0.00	0.00	0.00	4.18
255	1814	1.009389	GTGAGAACCGGCAAGTCTCG	61.009	60.000	0.00	0.00	0.00	4.04
259	1818	1.141053	AGAAAGTGAGAACCGGCAAGT	59.859	47.619	0.00	0.00	0.00	3.16
279	1838	8.908903	ACCAAAAGTAATGACATTACACTGAAA	58.091	29.630	30.57	0.63	45.80	2.69
280	1839	8.458573	ACCAAAAGTAATGACATTACACTGAA	57.541	30.769	30.57	1.32	45.80	3.02
282	1841	8.779303	TGTACCAAAAGTAATGACATTACACTG	58.221	33.333	30.57	23.83	45.80	3.66
283	1842	8.911918	TGTACCAAAAGTAATGACATTACACT	57.088	30.769	30.57	19.02	45.80	3.55
284	1843	9.554724	CATGTACCAAAAGTAATGACATTACAC	57.445	33.333	30.57	21.09	45.80	2.90
285	1844	8.240682	GCATGTACCAAAAGTAATGACATTACA	58.759	33.333	30.57	15.95	45.80	2.41
286	1845	8.458843	AGCATGTACCAAAAGTAATGACATTAC	58.541	33.333	24.78	24.78	44.18	1.89
288	1847	7.466746	AGCATGTACCAAAAGTAATGACATT	57.533	32.000	5.87	5.87	31.05	2.71
289	1848	8.046708	TCTAGCATGTACCAAAAGTAATGACAT	58.953	33.333	0.00	0.00	31.05	3.06
290	1849	7.390823	TCTAGCATGTACCAAAAGTAATGACA	58.609	34.615	0.00	0.00	31.05	3.58
291	1850	7.843490	TCTAGCATGTACCAAAAGTAATGAC	57.157	36.000	0.00	0.00	31.05	3.06
299	1858	9.914834	AGGTAATTATTCTAGCATGTACCAAAA	57.085	29.630	11.50	0.00	33.63	2.44

Showing 1 to 25 of 188 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.