AutoCloner

Multiple sequence alignment - TraesCS3B01G266400

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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	TraesCS3B01G266400	chr3B	100.000	3017	0	0	1	3017	427008221	427005205	0.000000e+00	5572
1	TraesCS3B01G266400	chr3A	91.321	1590	82	20	661	2223	444547027	444545467	0.000000e+00	2121
2	TraesCS3B01G266400	chr3A	88.609	676	60	10	2353	3017	444545379	444544710	0.000000e+00	806
3	TraesCS3B01G266400	chr3D	93.327	1019	48	8	725	1735	329520027	329519021	0.000000e+00	1487
4	TraesCS3B01G266400	chr3D	83.377	764	71	33	1816	2556	329519021	329518291	0.000000e+00	656
5	TraesCS3B01G266400	chr3D	88.281	384	28	8	2645	3017	329518224	329517847	7.670000e-121	444
6	TraesCS3B01G266400	chr2D	91.030	602	36	8	40	631	612335935	612335342	0.000000e+00	797
7	TraesCS3B01G266400	chr5D	93.165	278	19	0	1	278	50879266	50878989	2.800000e-110	409
8	TraesCS3B01G266400	chr5D	89.474	304	23	3	331	634	50878984	50878690	2.840000e-100	375
9	TraesCS3B01G266400	chr2A	92.580	283	21	0	1	283	656956190	656955908	1.010000e-109	407

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	TraesCS3B01G266400	chr3B	427005205	427008221	3016	True	5572.000000	5572	100.000000	1	3017	1	chr3B.!!$R1	3016
1	TraesCS3B01G266400	chr3A	444544710	444547027	2317	True	1463.500000	2121	89.965000	661	3017	2	chr3A.!!$R1	2356
2	TraesCS3B01G266400	chr3D	329517847	329520027	2180	True	862.333333	1487	88.328333	725	3017	3	chr3D.!!$R1	2292
3	TraesCS3B01G266400	chr2D	612335342	612335935	593	True	797.000000	797	91.030000	40	631	1	chr2D.!!$R1	591
4	TraesCS3B01G266400	chr5D	50878690	50879266	576	True	392.000000	409	91.319500	1	634	2	chr5D.!!$R1	633

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
690	701	0.168128	ATTGCTTTAACCACGCTCGC	59.832	50.0	0.0	0.0	0.0	5.03	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2100	2144	0.035056	CCTCGCCCCTTCAATCAGTT	60.035	55.0	0.0	0.0	0.0	3.16	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
28	29	4.662961	CTCACCAGCCGCACACGA	62.663	66.667	0.00	0.00	43.93	4.35
110	111	4.169696	CGGGCCATAGGAACGCCA	62.170	66.667	4.39	0.00	44.90	5.69
144	145	4.514577	ACAGATCGAAGCGCCCCG	62.515	66.667	2.29	8.46	0.00	5.73
207	208	3.551496	CTCCAACAGCCAGGCGGAA	62.551	63.158	19.66	0.00	0.00	4.30
283	284	3.697439	ATGGCAACCCGCGCATAGT	62.697	57.895	8.75	0.00	43.84	2.12
286	287	2.244651	GCAACCCGCGCATAGTAGG	61.245	63.158	8.75	0.00	0.00	3.18
287	288	2.108362	AACCCGCGCATAGTAGGC	59.892	61.111	8.75	0.00	0.00	3.93
288	289	3.456105	AACCCGCGCATAGTAGGCC	62.456	63.158	8.75	0.00	0.00	5.19
290	291	4.681978	CCGCGCATAGTAGGCCCC	62.682	72.222	8.75	0.00	0.00	5.80
483	484	1.604278	GAAGCGGCTGTAATTGGATCC	59.396	52.381	1.81	4.20	0.00	3.36
635	646	4.570663	CGACACGGGAGCGGGATC	62.571	72.222	0.00	0.00	0.00	3.36
636	647	4.222847	GACACGGGAGCGGGATCC	62.223	72.222	1.92	1.92	38.76	3.36
637	648	4.779733	ACACGGGAGCGGGATCCT	62.780	66.667	12.58	0.00	39.50	3.24
638	649	3.917760	CACGGGAGCGGGATCCTC	61.918	72.222	12.58	0.76	39.50	3.71
642	653	3.568578	GGAGCGGGATCCTCCAAT	58.431	61.111	12.58	0.00	46.51	3.16
643	654	1.839894	GGAGCGGGATCCTCCAATT	59.160	57.895	12.58	0.00	46.51	2.32
644	655	0.250510	GGAGCGGGATCCTCCAATTC	60.251	60.000	12.58	1.62	46.51	2.17
645	656	0.761802	GAGCGGGATCCTCCAATTCT	59.238	55.000	12.58	0.00	38.64	2.40
646	657	0.471617	AGCGGGATCCTCCAATTCTG	59.528	55.000	12.58	0.00	38.64	3.02
647	658	0.536006	GCGGGATCCTCCAATTCTGG	60.536	60.000	12.58	0.00	45.08	3.86
690	701	0.168128	ATTGCTTTAACCACGCTCGC	59.832	50.000	0.00	0.00	0.00	5.03
708	719	1.070615	CCGTGTGGTGTGTGGATCA	59.929	57.895	0.00	0.00	0.00	2.92
781	792	7.709182	CCATAGTATCGTTGGAATTACTTCACA	59.291	37.037	0.00	0.00	32.70	3.58
884	895	1.599542	GCCCTGCGAGTTCATACATTC	59.400	52.381	0.00	0.00	0.00	2.67
946	969	0.178992	CCACTCACCCTCTTGCCAAA	60.179	55.000	0.00	0.00	0.00	3.28

Showing 1 to 25 of 145 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	4.626081	GTGTGCGGCTGGTGAGGT	62.626	66.667	0.00	0.00	0.00	3.85
110	111	2.527624	TCTCTGGGCAGGTGCTGT	60.528	61.111	1.26	0.00	41.70	4.40
123	124	1.435515	GGCGCTTCGATCTGTCTCT	59.564	57.895	7.64	0.00	0.00	3.10
144	145	2.750237	CCGTTTAGGTGCTGGCCC	60.750	66.667	0.00	0.00	34.51	5.80
207	208	0.689080	AGATGCGGGTGGATGTCTCT	60.689	55.000	0.00	0.00	0.00	3.10
232	233	3.622514	GAGATGGCTCGGTCCTGT	58.377	61.111	0.00	0.00	0.00	4.00
306	307	3.716539	TTTCTCCAGATCCGCGCGG	62.717	63.158	42.13	42.13	0.00	6.46
307	308	2.202743	TTTCTCCAGATCCGCGCG	60.203	61.111	25.67	25.67	0.00	6.86
308	309	1.884926	CCTTTCTCCAGATCCGCGC	60.885	63.158	0.00	0.00	0.00	6.86
387	388	2.705821	CGCGGTCTCTGCCTTCTCT	61.706	63.158	0.00	0.00	0.00	3.10
391	392	4.379243	CCACGCGGTCTCTGCCTT	62.379	66.667	12.47	0.00	0.00	4.35
416	417	1.974875	TCGTCTTGCTCTACGGGCA	60.975	57.895	5.66	0.00	39.52	5.36
418	419	1.226323	CGTCGTCTTGCTCTACGGG	60.226	63.158	5.66	0.00	39.52	5.28
429	430	2.976350	TGTCCTGCGTCGTCGTCT	60.976	61.111	3.66	0.00	39.49	4.18
473	474	2.609747	CTCTCCCTCCGGATCCAATTA	58.390	52.381	13.41	0.00	37.60	1.40
483	484	4.504916	CACGCAGCTCTCCCTCCG	62.505	72.222	0.00	0.00	0.00	4.63
638	649	5.749462	ACCTATCAGAAAGTCCAGAATTGG	58.251	41.667	0.00	0.00	46.49	3.16
639	650	6.648192	AGACCTATCAGAAAGTCCAGAATTG	58.352	40.000	0.00	0.00	0.00	2.32
640	651	6.882768	AGACCTATCAGAAAGTCCAGAATT	57.117	37.500	0.00	0.00	0.00	2.17
641	652	8.560124	AATAGACCTATCAGAAAGTCCAGAAT	57.440	34.615	0.00	0.00	0.00	2.40
642	653	7.979786	AATAGACCTATCAGAAAGTCCAGAA	57.020	36.000	0.00	0.00	0.00	3.02
643	654	7.619698	TCAAATAGACCTATCAGAAAGTCCAGA	59.380	37.037	0.00	0.00	0.00	3.86
644	655	7.786030	TCAAATAGACCTATCAGAAAGTCCAG	58.214	38.462	0.00	0.00	0.00	3.86
645	656	7.619698	TCTCAAATAGACCTATCAGAAAGTCCA	59.380	37.037	0.00	0.00	0.00	4.02
646	657	8.012957	TCTCAAATAGACCTATCAGAAAGTCC	57.987	38.462	0.00	0.00	0.00	3.85

Showing 1 to 25 of 153 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.