AutoCloner

Multiple sequence alignment - TraesCS5D01G320000

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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	TraesCS5D01G320000	chr5D	100.000	2657	0	0	1	2657	412447821	412450477	0.000000e+00	4907.0
1	TraesCS5D01G320000	chr5A	92.920	1356	51	13	314	1665	524308735	524310049	0.000000e+00	1930.0
2	TraesCS5D01G320000	chr5A	90.226	1105	75	18	643	1743	524388941	524390016	0.000000e+00	1411.0
3	TraesCS5D01G320000	chr5A	90.281	926	32	13	1785	2657	524390238	524391158	0.000000e+00	1158.0
4	TraesCS5D01G320000	chr5A	93.462	413	21	2	2214	2620	524317677	524318089	2.260000e-170	608.0
5	TraesCS5D01G320000	chr5A	85.032	314	16	15	1	314	524298125	524298407	9.300000e-75	291.0
6	TraesCS5D01G320000	chr5A	94.340	53	2	1	2068	2119	524312313	524312365	2.190000e-11	80.5
7	TraesCS5D01G320000	chr5B	91.386	1277	60	24	629	1871	496549375	496550635	0.000000e+00	1703.0
8	TraesCS5D01G320000	chr5B	89.327	1115	77	23	643	1743	496569085	496570171	0.000000e+00	1362.0
9	TraesCS5D01G320000	chr5B	89.702	1039	76	13	643	1665	496805686	496806709	0.000000e+00	1297.0
10	TraesCS5D01G320000	chr5B	91.814	904	26	17	1781	2657	496570339	496571221	0.000000e+00	1216.0
11	TraesCS5D01G320000	chr5B	92.593	594	25	9	2068	2657	496807262	496807840	0.000000e+00	835.0
12	TraesCS5D01G320000	chr5B	96.885	321	9	1	314	634	496549009	496549328	1.080000e-148	536.0
13	TraesCS5D01G320000	chr5B	92.675	314	18	4	1	314	496547795	496548103	5.220000e-122	448.0
14	TraesCS5D01G320000	chr4A	81.818	968	137	16	715	1660	601177938	601178888	0.000000e+00	776.0
15	TraesCS5D01G320000	chr4A	78.292	972	157	32	704	1660	601172850	601173782	6.380000e-161	577.0
16	TraesCS5D01G320000	chr4A	82.953	657	82	17	1000	1653	601194762	601194133	1.380000e-157	566.0
17	TraesCS5D01G320000	chr4A	87.654	81	5	4	705	780	601156182	601156262	3.640000e-14	89.8
18	TraesCS5D01G320000	chrUn	81.856	959	139	20	715	1660	60943090	60944026	0.000000e+00	774.0
19	TraesCS5D01G320000	chrUn	79.589	681	126	10	991	1669	60935682	60936351	2.390000e-130	475.0
20	TraesCS5D01G320000	chrUn	90.244	82	6	2	704	783	60939706	60939787	3.620000e-19	106.0
21	TraesCS5D01G320000	chrUn	90.698	43	4	0	155	197	293984491	293984449	1.030000e-04	58.4
22	TraesCS5D01G320000	chr4B	81.218	969	145	16	715	1660	5531714	5532668	0.000000e+00	747.0
23	TraesCS5D01G320000	chr3A	91.429	70	2	3	67	134	95131501	95131568	2.820000e-15	93.5

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	TraesCS5D01G320000	chr5D	412447821	412450477	2656	False	4907.000000	4907	100.000000	1	2657	1	chr5D.!!$F1	2656
1	TraesCS5D01G320000	chr5A	524388941	524391158	2217	False	1284.500000	1411	90.253500	643	2657	2	chr5A.!!$F4	2014
2	TraesCS5D01G320000	chr5A	524308735	524312365	3630	False	1005.250000	1930	93.630000	314	2119	2	chr5A.!!$F3	1805
3	TraesCS5D01G320000	chr5B	496569085	496571221	2136	False	1289.000000	1362	90.570500	643	2657	2	chr5B.!!$F2	2014
4	TraesCS5D01G320000	chr5B	496805686	496807840	2154	False	1066.000000	1297	91.147500	643	2657	2	chr5B.!!$F3	2014
5	TraesCS5D01G320000	chr5B	496547795	496550635	2840	False	895.666667	1703	93.648667	1	1871	3	chr5B.!!$F1	1870
6	TraesCS5D01G320000	chr4A	601177938	601178888	950	False	776.000000	776	81.818000	715	1660	1	chr4A.!!$F3	945
7	TraesCS5D01G320000	chr4A	601172850	601173782	932	False	577.000000	577	78.292000	704	1660	1	chr4A.!!$F2	956
8	TraesCS5D01G320000	chr4A	601194133	601194762	629	True	566.000000	566	82.953000	1000	1653	1	chr4A.!!$R1	653
9	TraesCS5D01G320000	chrUn	60935682	60944026	8344	False	451.666667	774	83.896333	704	1669	3	chrUn.!!$F1	965
10	TraesCS5D01G320000	chr4B	5531714	5532668	954	False	747.000000	747	81.218000	715	1660	1	chr4B.!!$F1	945

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
702	1662	0.318699	TCCGCGATGCATACTGTAGC	60.319	55.0	8.23	0.0	0.0	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2356	11267	1.458777	TGGGAGGACGTGTTCAGGT	60.459	57.895	0.0	0.0	0.0	4.0	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	64	1.106285	GTTAGCAAGCCCCATTCAGG	58.894	55.000	0.00	0.00	37.03	3.86
87	88	4.141597	GGGGGAGAGAGAGAATTAGTTTGG	60.142	50.000	0.00	0.00	0.00	3.28
128	129	9.708092	GTTTTGTAGATTCTTTGTAGGTCTAGT	57.292	33.333	0.00	0.00	0.00	2.57
155	156	8.721019	TTATTGTTTTTCCCGTATTAGATCGT	57.279	30.769	0.00	0.00	0.00	3.73
156	157	6.411630	TTGTTTTTCCCGTATTAGATCGTG	57.588	37.500	0.00	0.00	0.00	4.35
158	159	2.410785	TTCCCGTATTAGATCGTGCG	57.589	50.000	0.00	0.00	0.00	5.34
178	179	6.461698	CGTGCGATTAGTTTGAGTTAATGAAC	59.538	38.462	0.00	0.00	35.64	3.18
606	1513	6.377996	TCAGATTAATGAAGTTGGGAATGTGG	59.622	38.462	0.00	0.00	0.00	4.17
670	1628	9.357652	CACACCAAAGTTTTCATTATAATGGAG	57.642	33.333	22.31	8.31	37.03	3.86
689	1647	4.456222	TGGAGACAAAAATAAATTCCGCGA	59.544	37.500	8.23	0.00	37.44	5.87
695	1655	6.269315	ACAAAAATAAATTCCGCGATGCATA	58.731	32.000	8.23	0.00	0.00	3.14
696	1656	6.198216	ACAAAAATAAATTCCGCGATGCATAC	59.802	34.615	8.23	0.00	0.00	2.39
697	1657	5.689383	AAATAAATTCCGCGATGCATACT	57.311	34.783	8.23	0.00	0.00	2.12
698	1658	4.668576	ATAAATTCCGCGATGCATACTG	57.331	40.909	8.23	0.00	0.00	2.74
699	1659	1.953559	AATTCCGCGATGCATACTGT	58.046	45.000	8.23	0.00	0.00	3.55
701	1661	2.134201	TTCCGCGATGCATACTGTAG	57.866	50.000	8.23	0.00	0.00	2.74
702	1662	0.318699	TCCGCGATGCATACTGTAGC	60.319	55.000	8.23	0.00	0.00	3.58
1629	8373	1.962822	CGTGCAGAAGCTCAAGGCA	60.963	57.895	0.00	0.00	44.79	4.75
1677	8423	7.329499	AGTGATTCATGTGAGATATATGCTCC	58.671	38.462	0.00	0.00	0.00	4.70
1678	8424	7.180587	AGTGATTCATGTGAGATATATGCTCCT	59.819	37.037	0.00	0.00	0.00	3.69
1679	8425	7.278203	GTGATTCATGTGAGATATATGCTCCTG	59.722	40.741	0.00	0.00	0.00	3.86
1688	8434	2.338577	ATATGCTCCTGTGTTGCTCC	57.661	50.000	0.00	0.00	0.00	4.70
1708	8454	5.877012	GCTCCTCTTTTTCATGAGTGTATCA	59.123	40.000	0.00	0.00	43.70	2.15
1719	8477	2.009774	GAGTGTATCAACGCTGCCATT	58.990	47.619	0.00	0.00	46.40	3.16
1840	8801	2.481952	GCTTATGAGATCCATCCGTTGC	59.518	50.000	0.59	0.00	36.71	4.17
1841	8802	2.839486	TATGAGATCCATCCGTTGCC	57.161	50.000	0.59	0.00	36.71	4.52
1916	10741	9.119418	TGTAGTACTAGTACAACTTAACACACA	57.881	33.333	29.87	11.97	38.48	3.72
1919	10744	7.917505	AGTACTAGTACAACTTAACACACACAC	59.082	37.037	29.87	4.00	38.48	3.82
1925	10770	4.457603	ACAACTTAACACACACACACACAT	59.542	37.500	0.00	0.00	0.00	3.21
1963	10808	3.375299	CCTAATTTCCTTCAAGCGTCCTG	59.625	47.826	0.00	0.00	0.00	3.86
1964	10809	1.168714	ATTTCCTTCAAGCGTCCTGC	58.831	50.000	0.00	0.00	46.98	4.85
2219	11127	1.150536	GTGGTGGTGATGGTGGTGT	59.849	57.895	0.00	0.00	0.00	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	0.098552	TGTGCACAAAGACGCAACAG	59.901	50.000	19.28	0.00	40.44	3.16
27	28	3.637694	GCTAACCCCCACAACAGTAAAAA	59.362	43.478	0.00	0.00	0.00	1.94
148	149	5.244785	ACTCAAACTAATCGCACGATCTA	57.755	39.130	5.94	1.28	33.08	1.98
155	156	7.667043	AGTTCATTAACTCAAACTAATCGCA	57.333	32.000	0.00	0.00	42.42	5.10
321	1228	5.480281	GTTGCACGTAATGATTGTGAAAC	57.520	39.130	4.37	4.37	42.94	2.78
606	1513	0.748005	ACTTGGGTGTGTGAGTGTGC	60.748	55.000	0.00	0.00	0.00	4.57
670	1628	4.560819	TGCATCGCGGAATTTATTTTTGTC	59.439	37.500	6.13	0.00	0.00	3.18
689	1647	7.126061	TGGATATACCTAGCTACAGTATGCAT	58.874	38.462	16.75	3.79	38.77	3.96
695	1655	7.358263	AGCATATGGATATACCTAGCTACAGT	58.642	38.462	4.56	0.00	39.86	3.55
696	1656	7.831691	AGCATATGGATATACCTAGCTACAG	57.168	40.000	4.56	0.00	39.86	2.74
697	1657	7.069950	CCAAGCATATGGATATACCTAGCTACA	59.930	40.741	4.56	0.00	43.54	2.74
698	1658	7.287927	TCCAAGCATATGGATATACCTAGCTAC	59.712	40.741	4.56	0.00	44.52	3.58
699	1659	7.362234	TCCAAGCATATGGATATACCTAGCTA	58.638	38.462	4.56	0.00	44.52	3.32
701	1661	6.485830	TCCAAGCATATGGATATACCTAGC	57.514	41.667	4.56	0.00	44.52	3.42
1404	8147	2.434359	GCCAGGTCCTGCGTGTAC	60.434	66.667	13.99	0.00	0.00	2.90
1629	8373	3.386237	GGAGGTGGAGTGAGCGCT	61.386	66.667	11.27	11.27	0.00	5.92
1677	8423	4.276678	TCATGAAAAAGAGGAGCAACACAG	59.723	41.667	0.00	0.00	0.00	3.66
1678	8424	4.206375	TCATGAAAAAGAGGAGCAACACA	58.794	39.130	0.00	0.00	0.00	3.72
1679	8425	4.276926	ACTCATGAAAAAGAGGAGCAACAC	59.723	41.667	0.00	0.00	36.20	3.32
1688	8434	6.017933	GCGTTGATACACTCATGAAAAAGAG	58.982	40.000	0.00	0.00	37.87	2.85
1708	8454	4.036380	GCCTTATTAGTTAATGGCAGCGTT	59.964	41.667	0.00	0.00	35.69	4.84
1713	8471	6.655003	GCTCATAGCCTTATTAGTTAATGGCA	59.345	38.462	12.87	0.00	36.94	4.92
1719	8477	9.233649	GAGACTAGCTCATAGCCTTATTAGTTA	57.766	37.037	0.00	0.00	43.77	2.24
1840	8801	5.792741	TCTTTTACAATGCATTTGGGAAGG	58.207	37.500	9.83	0.00	39.80	3.46
1841	8802	6.930722	AGTTCTTTTACAATGCATTTGGGAAG	59.069	34.615	9.83	11.70	39.80	3.46
1913	10738	1.864082	TGCGACTTATGTGTGTGTGTG	59.136	47.619	0.00	0.00	0.00	3.82
1914	10739	2.232756	TGCGACTTATGTGTGTGTGT	57.767	45.000	0.00	0.00	0.00	3.72
1915	10740	2.659023	CGTTGCGACTTATGTGTGTGTG	60.659	50.000	1.84	0.00	0.00	3.82
1916	10741	1.525197	CGTTGCGACTTATGTGTGTGT	59.475	47.619	1.84	0.00	0.00	3.72
1919	10744	2.058798	ACTCGTTGCGACTTATGTGTG	58.941	47.619	1.84	0.00	0.00	3.82
1925	10770	3.921119	TTAGGAACTCGTTGCGACTTA	57.079	42.857	1.84	0.00	41.75	2.24
1963	10808	6.582672	CGGTCGATGGATATATATATGTGTGC	59.417	42.308	10.03	0.00	0.00	4.57
1964	10809	7.084486	CCGGTCGATGGATATATATATGTGTG	58.916	42.308	10.03	0.00	0.00	3.82
1966	10811	6.093404	GCCGGTCGATGGATATATATATGTG	58.907	44.000	10.03	0.00	0.00	3.21
1968	10813	6.267496	TGCCGGTCGATGGATATATATATG	57.733	41.667	10.03	0.00	0.00	1.78
2356	11267	1.458777	TGGGAGGACGTGTTCAGGT	60.459	57.895	0.00	0.00	0.00	4.00
2359	11270	2.099652	CTGCTGGGAGGACGTGTTCA	62.100	60.000	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.