AutoCloner

Multiple sequence alignment - TraesCS2A01G334000

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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	TraesCS2A01G334000	chr2A	100.000	2839	0	0	1	2839	567734201	567737039	0.000000e+00	5243.0
1	TraesCS2A01G334000	chr2A	95.205	292	10	2	1338	1629	546771202	546770915	2.580000e-125	459.0
2	TraesCS2A01G334000	chr2A	93.985	266	16	0	2236	2501	546743003	546742738	1.220000e-108	403.0
3	TraesCS2A01G334000	chr2A	95.455	154	7	0	157	310	546771352	546771199	2.180000e-61	246.0
4	TraesCS2A01G334000	chr2A	95.833	120	5	0	1	120	546773819	546773700	8.030000e-46	195.0
5	TraesCS2A01G334000	chr2A	97.938	97	2	0	1	97	568283400	568283496	4.860000e-38	169.0
6	TraesCS2A01G334000	chr2A	96.341	82	3	0	2758	2839	546742739	546742658	4.930000e-28	135.0
7	TraesCS2A01G334000	chr2B	90.665	2346	109	32	522	2839	493987200	493989463	0.000000e+00	3018.0
8	TraesCS2A01G334000	chr2B	95.745	94	3	1	1	93	494260736	494260829	1.760000e-32	150.0
9	TraesCS2A01G334000	chr2B	93.878	98	5	1	1	97	493986467	493986564	2.280000e-31	147.0
10	TraesCS2A01G334000	chr2B	96.053	76	2	1	157	231	493986862	493986937	3.840000e-24	122.0
11	TraesCS2A01G334000	chr2B	85.965	114	5	4	306	416	493987045	493987150	8.310000e-21	111.0
12	TraesCS2A01G334000	chr2B	95.455	66	3	0	94	159	494260889	494260954	3.870000e-19	106.0
13	TraesCS2A01G334000	chr2B	90.909	66	3	2	94	157	493986631	493986695	5.040000e-13	86.1
14	TraesCS2A01G334000	chr2D	90.102	1475	78	28	522	1982	421479951	421481371	0.000000e+00	1853.0
15	TraesCS2A01G334000	chr2D	91.171	521	36	3	1981	2499	421481418	421481930	0.000000e+00	699.0
16	TraesCS2A01G334000	chr2D	95.633	229	10	0	2611	2839	421481985	421482213	4.470000e-98	368.0
17	TraesCS2A01G334000	chr2D	90.728	151	5	8	162	305	421477402	421477550	2.890000e-45	193.0
18	TraesCS2A01G334000	chr2D	88.961	154	6	6	306	456	421477609	421477754	2.250000e-41	180.0
19	TraesCS2A01G334000	chr2D	95.876	97	4	0	1	97	421477044	421477140	1.050000e-34	158.0
20	TraesCS2A01G334000	chr2D	93.814	97	6	0	1	97	421792296	421792392	2.280000e-31	147.0
21	TraesCS2A01G334000	chr2D	97.059	68	2	0	2524	2591	421481925	421481992	6.430000e-22	115.0
22	TraesCS2A01G334000	chr2D	92.208	77	4	2	94	168	421792461	421792537	1.080000e-19	108.0
23	TraesCS2A01G334000	chr3B	88.030	944	57	10	1838	2780	9687474	9688362	0.000000e+00	1066.0
24	TraesCS2A01G334000	chr4D	84.146	164	17	7	1	157	323927632	323927793	1.760000e-32	150.0
25	TraesCS2A01G334000	chr4A	93.814	97	6	0	1	97	147567102	147567006	2.280000e-31	147.0
26	TraesCS2A01G334000	chr4A	87.931	58	7	0	100	157	147566933	147566876	5.080000e-08	69.4
27	TraesCS2A01G334000	chr4B	95.000	60	3	0	1	60	404512696	404512755	8.370000e-16	95.3
28	TraesCS2A01G334000	chr1D	94.737	38	1	1	114	151	376281604	376281568	1.100000e-04	58.4

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	TraesCS2A01G334000	chr2A	567734201	567737039	2838	False	5243.000000	5243	100.000000	1	2839	1	chr2A.!!$F1	2838
1	TraesCS2A01G334000	chr2A	546770915	546773819	2904	True	300.000000	459	95.497667	1	1629	3	chr2A.!!$R2	1628
2	TraesCS2A01G334000	chr2B	493986467	493989463	2996	False	696.820000	3018	91.494000	1	2839	5	chr2B.!!$F1	2838
3	TraesCS2A01G334000	chr2D	421477044	421482213	5169	False	509.428571	1853	92.790000	1	2839	7	chr2D.!!$F1	2838
4	TraesCS2A01G334000	chr3B	9687474	9688362	888	False	1066.000000	1066	88.030000	1838	2780	1	chr3B.!!$F1	942

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
506	5154	0.036306	GAGGTGCTCCCTTTTTCGGA	59.964	55.0	0.0	0.0	46.51	4.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2209	6943	0.03759	TTGTTTGTCATCCCCTCCGG	59.962	55.0	0.0	0.0	0.0	5.14	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
35	36	4.100808	GCTGAAGATCAAGGAGTCCAGTAT	59.899	45.833	12.86	0.56	0.00	2.12
278	2690	7.719193	TGAAGATGTTGGTTCAAAGATCTGTTA	59.281	33.333	0.00	0.00	30.29	2.41
279	2691	8.463930	AAGATGTTGGTTCAAAGATCTGTTAA	57.536	30.769	0.00	0.00	30.29	2.01
344	2818	1.616725	GCTTGGGGATGATGTGGTGAA	60.617	52.381	0.00	0.00	0.00	3.18
345	2819	2.094675	CTTGGGGATGATGTGGTGAAC	58.905	52.381	0.00	0.00	0.00	3.18
346	2820	1.371467	TGGGGATGATGTGGTGAACT	58.629	50.000	0.00	0.00	0.00	3.01
347	2821	1.004628	TGGGGATGATGTGGTGAACTG	59.995	52.381	0.00	0.00	0.00	3.16
348	2822	1.683011	GGGGATGATGTGGTGAACTGG	60.683	57.143	0.00	0.00	0.00	4.00
349	2823	1.004745	GGGATGATGTGGTGAACTGGT	59.995	52.381	0.00	0.00	0.00	4.00
350	2824	2.086869	GGATGATGTGGTGAACTGGTG	58.913	52.381	0.00	0.00	0.00	4.17
351	2825	2.290260	GGATGATGTGGTGAACTGGTGA	60.290	50.000	0.00	0.00	0.00	4.02
352	2826	3.614092	GATGATGTGGTGAACTGGTGAT	58.386	45.455	0.00	0.00	0.00	3.06
353	2827	2.781923	TGATGTGGTGAACTGGTGATG	58.218	47.619	0.00	0.00	0.00	3.07
354	2828	1.470098	GATGTGGTGAACTGGTGATGC	59.530	52.381	0.00	0.00	0.00	3.91
355	2829	0.182299	TGTGGTGAACTGGTGATGCA	59.818	50.000	0.00	0.00	0.00	3.96
356	2830	1.202915	TGTGGTGAACTGGTGATGCAT	60.203	47.619	0.00	0.00	0.00	3.96
359	2833	1.098050	GTGAACTGGTGATGCATCCC	58.902	55.000	23.67	22.16	0.00	3.85
411	2887	4.338964	TCTCTTTGCAAGCTGATTTGTTCA	59.661	37.500	0.00	0.00	0.00	3.18
480	5128	3.778619	CCGTGGGCATCACTTGATA	57.221	52.632	7.64	0.00	43.94	2.15
481	5129	1.586422	CCGTGGGCATCACTTGATAG	58.414	55.000	7.64	0.00	43.94	2.08
482	5130	1.138859	CCGTGGGCATCACTTGATAGA	59.861	52.381	7.64	0.00	43.94	1.98
483	5131	2.477825	CGTGGGCATCACTTGATAGAG	58.522	52.381	7.64	0.00	43.94	2.43
484	5132	2.804572	CGTGGGCATCACTTGATAGAGG	60.805	54.545	7.64	0.00	43.94	3.69
485	5133	1.141657	TGGGCATCACTTGATAGAGGC	59.858	52.381	0.00	0.00	40.52	4.70
486	5134	1.419387	GGGCATCACTTGATAGAGGCT	59.581	52.381	0.00	0.00	40.98	4.58

Showing 1 to 25 of 115 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
202	2608	2.423538	CCCTGATTAAGCCGGAAAGTTG	59.576	50.000	5.05	0.00	0.00	3.16
235	2647	2.917701	TCAATAAGTAACGACGCGGA	57.082	45.000	12.47	0.00	0.00	5.54
278	2690	5.063880	GTCAGACCAAAGGTATCACACTTT	58.936	41.667	0.00	0.00	35.25	2.66
279	2691	4.102524	TGTCAGACCAAAGGTATCACACTT	59.897	41.667	0.00	0.00	35.25	3.16
346	2820	1.303948	CACCTGGGATGCATCACCA	59.696	57.895	25.88	25.89	0.00	4.17
347	2821	1.454479	CCACCTGGGATGCATCACC	60.454	63.158	25.88	23.09	40.01	4.02
348	2822	1.033746	CACCACCTGGGATGCATCAC	61.034	60.000	27.25	25.01	41.15	3.06
349	2823	1.303948	CACCACCTGGGATGCATCA	59.696	57.895	27.25	8.45	41.15	3.07
350	2824	1.454479	CCACCACCTGGGATGCATC	60.454	63.158	18.81	18.81	41.15	3.91
351	2825	1.291459	ATCCACCACCTGGGATGCAT	61.291	55.000	0.00	0.00	42.24	3.96
352	2826	1.930133	ATCCACCACCTGGGATGCA	60.930	57.895	0.00	0.00	42.24	3.96
353	2827	3.010144	ATCCACCACCTGGGATGC	58.990	61.111	0.00	0.00	42.24	3.91
355	2829	2.693871	GCCATCCACCACCTGGGAT	61.694	63.158	0.00	0.00	44.65	3.85
356	2830	3.338250	GCCATCCACCACCTGGGA	61.338	66.667	0.00	0.00	41.06	4.37
359	2833	2.273449	GAGGCCATCCACCACCTG	59.727	66.667	5.01	0.00	30.95	4.00
386	2860	7.630458	TGAACAAATCAGCTTGCAAAGAGAGA	61.630	38.462	0.00	0.00	38.88	3.10
388	2862	4.338964	TGAACAAATCAGCTTGCAAAGAGA	59.661	37.500	0.00	0.00	38.88	3.10
448	2924	3.418047	GCCCACGGCCATAGTATTTTAT	58.582	45.455	2.24	0.00	44.06	1.40
480	5128	2.686835	GGGAGCACCTCAGCCTCT	60.687	66.667	0.00	0.00	35.85	3.69
489	5137	1.324383	TTTCCGAAAAAGGGAGCACC	58.676	50.000	0.00	0.00	40.67	5.01
490	5138	3.446310	TTTTTCCGAAAAAGGGAGCAC	57.554	42.857	13.84	0.00	35.84	4.40
517	5165	9.362539	GTAGAAACAACAGGAGTCGATTATTTA	57.637	33.333	0.00	0.00	0.00	1.40
518	5166	7.876068	TGTAGAAACAACAGGAGTCGATTATTT	59.124	33.333	0.00	0.00	30.91	1.40
519	5167	7.383687	TGTAGAAACAACAGGAGTCGATTATT	58.616	34.615	0.00	0.00	30.91	1.40
520	5168	6.931838	TGTAGAAACAACAGGAGTCGATTAT	58.068	36.000	0.00	0.00	30.91	1.28

Showing 1 to 25 of 91 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.