AutoCloner

Multiple sequence alignment - TraesCS2A01G416600

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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	TraesCS2A01G416600	chr2A	100.000	4775	0	0	1	4775	672835708	672840482	0.000000e+00	8818
1	TraesCS2A01G416600	chr2D	92.345	3070	230	4	969	4034	528077072	528080140	0.000000e+00	4362
2	TraesCS2A01G416600	chr2D	90.528	549	35	10	4039	4582	528080206	528080742	0.000000e+00	710
3	TraesCS2A01G416600	chr2D	90.000	190	18	1	4586	4775	528081229	528081417	1.330000e-60	244
4	TraesCS2A01G416600	chr2B	92.234	2923	222	5	969	3889	625917066	625919985	0.000000e+00	4135
5	TraesCS2A01G416600	chr2B	87.113	613	41	16	4036	4630	625926875	625927467	0.000000e+00	660
6	TraesCS2A01G416600	chr2B	93.421	152	8	1	3885	4034	625926662	625926813	1.730000e-54	224
7	TraesCS2A01G416600	chr2B	89.167	120	11	1	4658	4775	625927550	625927669	1.070000e-31	148
8	TraesCS2A01G416600	chr7D	87.515	817	95	6	1	812	611664817	611665631	0.000000e+00	937
9	TraesCS2A01G416600	chr5B	87.408	818	95	7	1	813	614364903	614364089	0.000000e+00	933
10	TraesCS2A01G416600	chr5B	86.603	836	99	10	5	831	356688426	356687595	0.000000e+00	911
11	TraesCS2A01G416600	chr3D	87.132	816	99	5	1	812	528948105	528948918	0.000000e+00	920
12	TraesCS2A01G416600	chr1D	86.651	839	98	11	1	829	461901110	461900276	0.000000e+00	917
13	TraesCS2A01G416600	chr3B	86.603	836	101	7	5	832	554961534	554960702	0.000000e+00	913
14	TraesCS2A01G416600	chr4B	86.499	837	103	6	1	828	81362354	81363189	0.000000e+00	911
15	TraesCS2A01G416600	chr4B	86.483	836	103	7	1	829	67923544	67922712	0.000000e+00	909
16	TraesCS2A01G416600	chr6B	86.499	837	101	9	1	829	696644531	696643699	0.000000e+00	909

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	TraesCS2A01G416600	chr2A	672835708	672840482	4774	False	8818	8818	100.000000	1	4775	1	chr2A.!!$F1	4774
1	TraesCS2A01G416600	chr2D	528077072	528081417	4345	False	1772	4362	90.957667	969	4775	3	chr2D.!!$F1	3806
2	TraesCS2A01G416600	chr2B	625917066	625919985	2919	False	4135	4135	92.234000	969	3889	1	chr2B.!!$F1	2920
3	TraesCS2A01G416600	chr2B	625926662	625927669	1007	False	344	660	89.900333	3885	4775	3	chr2B.!!$F2	890
4	TraesCS2A01G416600	chr7D	611664817	611665631	814	False	937	937	87.515000	1	812	1	chr7D.!!$F1	811
5	TraesCS2A01G416600	chr5B	614364089	614364903	814	True	933	933	87.408000	1	813	1	chr5B.!!$R2	812
6	TraesCS2A01G416600	chr5B	356687595	356688426	831	True	911	911	86.603000	5	831	1	chr5B.!!$R1	826
7	TraesCS2A01G416600	chr3D	528948105	528948918	813	False	920	920	87.132000	1	812	1	chr3D.!!$F1	811
8	TraesCS2A01G416600	chr1D	461900276	461901110	834	True	917	917	86.651000	1	829	1	chr1D.!!$R1	828
9	TraesCS2A01G416600	chr3B	554960702	554961534	832	True	913	913	86.603000	5	832	1	chr3B.!!$R1	827
10	TraesCS2A01G416600	chr4B	81362354	81363189	835	False	911	911	86.499000	1	828	1	chr4B.!!$F1	827
11	TraesCS2A01G416600	chr4B	67922712	67923544	832	True	909	909	86.483000	1	829	1	chr4B.!!$R1	828
12	TraesCS2A01G416600	chr6B	696643699	696644531	832	True	909	909	86.499000	1	829	1	chr6B.!!$R1	828

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
958	968	0.036732	TGCCGCCAGTCAAAGAGAAT	59.963	50.0	0.00	0.0	0.00	2.40	F
1548	1558	0.112606	TCACGGAGGACCTTGACTCT	59.887	55.0	0.00	0.0	39.09	3.24	F
1552	1562	0.323542	GGAGGACCTTGACTCTCGGA	60.324	60.0	0.00	0.0	34.22	4.55	F
2883	2893	0.178068	CCATGGTCCAGAGGTTACCG	59.822	60.0	2.57	0.0	35.98	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2353	2363	0.041684	CCCTGGCCCTTTTCCTCAAT	59.958	55.0	0.0	0.0	0.00	2.57	R
2462	2472	0.393402	ATGAATGCAGAGCCGCTTCA	60.393	50.0	0.0	0.0	35.24	3.02	R
3160	3170	0.443869	CGACTGACAATTCCCAAGCG	59.556	55.0	0.0	0.0	0.00	4.68	R
4640	5207	0.241213	TCAGTTCGCTCCGTCTTCTG	59.759	55.0	0.0	0.0	0.00	3.02	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
65	66	6.991531	ACGTAAGGACCAACATAACAAAACTA	59.008	34.615	0.00	0.00	46.39	2.24
117	118	2.086869	CCAACGAATGTCATCTGCCTT	58.913	47.619	0.00	0.00	0.00	4.35
138	139	1.039233	GGCACAACCATAGCAGCCAT	61.039	55.000	0.00	0.00	41.63	4.40
140	141	1.753930	CACAACCATAGCAGCCATCA	58.246	50.000	0.00	0.00	0.00	3.07
151	152	4.248691	AGCAGCCATCAAAGAAAAGAAC	57.751	40.909	0.00	0.00	0.00	3.01
165	166	1.254026	AAGAACGACGGATCACCTCA	58.746	50.000	0.00	0.00	0.00	3.86
170	171	0.741326	CGACGGATCACCTCATCACT	59.259	55.000	0.00	0.00	0.00	3.41
256	257	0.383949	GAAGCCTTTGCCGTTGAACA	59.616	50.000	0.00	0.00	38.69	3.18
264	265	4.549458	CTTTGCCGTTGAACAAATCAGAT	58.451	39.130	0.00	0.00	39.77	2.90
286	287	1.228552	GGCAACACCCCAGACACAT	60.229	57.895	0.00	0.00	0.00	3.21
298	299	2.167281	CCAGACACATCATCGAACTCCT	59.833	50.000	0.00	0.00	0.00	3.69
376	378	0.398696	AACCACGAACCCAGCACATA	59.601	50.000	0.00	0.00	0.00	2.29
380	382	2.491693	CCACGAACCCAGCACATATTTT	59.508	45.455	0.00	0.00	0.00	1.82
389	391	5.304101	ACCCAGCACATATTTTGTCTTTCAA	59.696	36.000	0.00	0.00	36.00	2.69
428	430	1.558294	ACAATCTGCATCAGCTCCTGA	59.442	47.619	0.00	0.00	44.99	3.86
429	431	1.941294	CAATCTGCATCAGCTCCTGAC	59.059	52.381	0.00	0.00	43.63	3.51
441	443	1.952621	CTCCTGACCTACCTCCCAAA	58.047	55.000	0.00	0.00	0.00	3.28
455	457	2.317609	CCAAACTCCACGCCGACAG	61.318	63.158	0.00	0.00	0.00	3.51
509	511	2.148916	GACACATGTCCACAACGAGA	57.851	50.000	0.00	0.00	39.07	4.04
522	527	2.745884	CGAGAATGCCACCGCCAA	60.746	61.111	0.00	0.00	0.00	4.52
616	621	8.267894	AGAAGGATCCGAAGAATCTTTATTCAA	58.732	33.333	5.98	0.00	43.44	2.69
626	631	5.354234	AGAATCTTTATTCAACGCCGTCATT	59.646	36.000	0.00	0.00	43.44	2.57
655	660	3.057019	CCGAAGTCAAGACGATGAACAA	58.943	45.455	0.00	0.00	36.20	2.83
660	665	3.809832	AGTCAAGACGATGAACAAACCTG	59.190	43.478	0.00	0.00	36.20	4.00
702	707	1.500108	AAAAACGATCCACACGCGTA	58.500	45.000	13.44	0.00	37.26	4.42

Showing 1 to 25 of 311 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	8.603242	ACGTGACTTGTACTTTGATCTTTATT	57.397	30.769	0.00	0.00	0.00	1.40
70	71	7.939039	TGTCAACCTCAGAGATGTTTTTCTATT	59.061	33.333	0.00	0.00	0.00	1.73
75	76	4.580580	GGTGTCAACCTCAGAGATGTTTTT	59.419	41.667	0.00	0.00	43.84	1.94
117	118	1.745115	GCTGCTATGGTTGTGCCGA	60.745	57.895	0.00	0.00	41.21	5.54
124	125	3.370840	TCTTTGATGGCTGCTATGGTT	57.629	42.857	2.27	0.00	0.00	3.67
129	130	4.083324	CGTTCTTTTCTTTGATGGCTGCTA	60.083	41.667	0.00	0.00	0.00	3.49
138	139	4.210537	GTGATCCGTCGTTCTTTTCTTTGA	59.789	41.667	0.00	0.00	0.00	2.69
140	141	3.497262	GGTGATCCGTCGTTCTTTTCTTT	59.503	43.478	0.00	0.00	0.00	2.52
151	152	0.741326	AGTGATGAGGTGATCCGTCG	59.259	55.000	0.00	0.00	39.05	5.12
229	230	1.066908	CGGCAAAGGCTTCACTTTTGA	59.933	47.619	0.00	0.00	38.56	2.69
243	244	4.545610	GATCTGATTTGTTCAACGGCAAA	58.454	39.130	0.00	0.00	38.68	3.68
256	257	1.463674	GTGTTGCCCCGATCTGATTT	58.536	50.000	0.00	0.00	0.00	2.17
286	287	1.410517	GCCAGATCAGGAGTTCGATGA	59.589	52.381	8.61	0.00	0.00	2.92
298	299	2.531428	TGGTGGGGTGCCAGATCA	60.531	61.111	0.00	0.00	0.00	2.92
338	339	0.464036	TCGTGGATGCAGGTATGGTC	59.536	55.000	6.81	0.00	0.00	4.02
380	382	3.120683	GCATCGACGACATTTGAAAGACA	60.121	43.478	0.00	0.00	0.00	3.41
389	391	0.246360	TGGTCTGCATCGACGACATT	59.754	50.000	0.00	0.00	34.75	2.71
428	430	1.359168	GTGGAGTTTGGGAGGTAGGT	58.641	55.000	0.00	0.00	0.00	3.08
429	431	0.249398	CGTGGAGTTTGGGAGGTAGG	59.751	60.000	0.00	0.00	0.00	3.18
455	457	4.072088	CGACGGCGTTTGCTCCAC	62.072	66.667	16.19	0.00	42.25	4.02
477	479	4.436998	GTGTCCTCGGGCTCCACG	62.437	72.222	0.00	0.00	0.00	4.94
479	481	2.284625	ATGTGTCCTCGGGCTCCA	60.285	61.111	0.00	0.00	0.00	3.86
503	505	2.746277	GGCGGTGGCATTCTCGTT	60.746	61.111	0.00	0.00	42.47	3.85
509	511	4.992740	TGGCTTGGCGGTGGCATT	62.993	61.111	0.00	0.00	42.47	3.56
522	527	5.374921	CAGTCTATTCAATCAAGGATGGCT	58.625	41.667	0.00	0.00	0.00	4.75

Showing 1 to 25 of 317 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.