AutoCloner

Multiple sequence alignment - TraesCS1D01G198000

Loading Multiple Alignment...

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	TraesCS1D01G198000	chr1D	100.000	3241	0	0	1	3241	279105780	279102540	0.000000e+00	5986.0
1	TraesCS1D01G198000	chr1D	83.948	542	83	2	1	538	272535909	272536450	1.720000e-142	516.0
2	TraesCS1D01G198000	chr1D	83.829	538	79	7	5	538	472292473	472291940	3.730000e-139	505.0
3	TraesCS1D01G198000	chr1A	95.364	2718	89	14	546	3241	351351215	351348513	0.000000e+00	4287.0
4	TraesCS1D01G198000	chr1B	97.347	2488	46	6	761	3240	378839261	378836786	0.000000e+00	4211.0
5	TraesCS1D01G198000	chr3B	84.926	544	74	5	5	541	186089663	186089121	7.910000e-151	544.0
6	TraesCS1D01G198000	chr3B	84.375	544	78	4	5	541	184958161	184957618	7.960000e-146	527.0
7	TraesCS1D01G198000	chr5B	84.416	539	76	5	1	533	467374681	467374145	1.030000e-144	523.0
8	TraesCS1D01G198000	chr3D	84.191	544	79	5	1	538	47748642	47748100	3.710000e-144	521.0
9	TraesCS1D01G198000	chr2A	84.162	543	80	6	1	538	2741777	2742318	3.710000e-144	521.0
10	TraesCS1D01G198000	chr6D	83.764	542	82	4	1	538	407203947	407203408	2.880000e-140	508.0
11	TraesCS1D01G198000	chr5D	83.700	546	79	7	1	541	498465111	498464571	1.040000e-139	507.0
12	TraesCS1D01G198000	chr5A	74.519	208	39	11	546	746	411836009	411835809	9.640000e-11	78.7
13	TraesCS1D01G198000	chr3A	88.462	52	6	0	605	656	523156627	523156576	2.700000e-06	63.9

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	TraesCS1D01G198000	chr1D	279102540	279105780	3240	True	5986	5986	100.000	1	3241	1	chr1D.!!$R1	3240
1	TraesCS1D01G198000	chr1D	272535909	272536450	541	False	516	516	83.948	1	538	1	chr1D.!!$F1	537
2	TraesCS1D01G198000	chr1D	472291940	472292473	533	True	505	505	83.829	5	538	1	chr1D.!!$R2	533
3	TraesCS1D01G198000	chr1A	351348513	351351215	2702	True	4287	4287	95.364	546	3241	1	chr1A.!!$R1	2695
4	TraesCS1D01G198000	chr1B	378836786	378839261	2475	True	4211	4211	97.347	761	3240	1	chr1B.!!$R1	2479
5	TraesCS1D01G198000	chr3B	186089121	186089663	542	True	544	544	84.926	5	541	1	chr3B.!!$R2	536
6	TraesCS1D01G198000	chr3B	184957618	184958161	543	True	527	527	84.375	5	541	1	chr3B.!!$R1	536
7	TraesCS1D01G198000	chr5B	467374145	467374681	536	True	523	523	84.416	1	533	1	chr5B.!!$R1	532
8	TraesCS1D01G198000	chr3D	47748100	47748642	542	True	521	521	84.191	1	538	1	chr3D.!!$R1	537
9	TraesCS1D01G198000	chr2A	2741777	2742318	541	False	521	521	84.162	1	538	1	chr2A.!!$F1	537
10	TraesCS1D01G198000	chr6D	407203408	407203947	539	True	508	508	83.764	1	538	1	chr6D.!!$R1	537
11	TraesCS1D01G198000	chr5D	498464571	498465111	540	True	507	507	83.700	1	541	1	chr5D.!!$R1	540

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
73	74	0.034059	GTCCATGGATCACCTAGCGG	59.966	60.0	19.62	0.0	37.04	5.52	F
670	682	0.390492	TATGCATGCCCAGTCTCTCG	59.610	55.0	16.68	0.0	0.00	4.04	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1019	1035	1.222567	TAAAGGAAGGGGAGGGATGC	58.777	55.0	0.0	0.0	0.0	3.91	R
2270	2299	0.392998	CCAGAACCTGTTGATCCCCG	60.393	60.0	0.0	0.0	0.0	5.73	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
34	35	5.023533	AGCAGTACAAAGAACAACAGAGA	57.976	39.130	0.00	0.00	0.00	3.10
39	40	7.959651	GCAGTACAAAGAACAACAGAGATAATG	59.040	37.037	0.00	0.00	0.00	1.90
63	64	6.098552	TGCAAATTACAATCATGTCCATGGAT	59.901	34.615	19.62	0.00	41.05	3.41
73	74	0.034059	GTCCATGGATCACCTAGCGG	59.966	60.000	19.62	0.00	37.04	5.52
76	77	2.134287	ATGGATCACCTAGCGGCGT	61.134	57.895	9.37	0.00	37.04	5.68
93	95	1.135373	GCGTCTACAAGCACTAGAGCA	60.135	52.381	14.80	0.00	36.85	4.26
156	161	9.298250	TCGGAGCTAGACAAATCTTATAATAGT	57.702	33.333	0.00	0.00	36.29	2.12
167	172	9.542462	CAAATCTTATAATAGTCAGTCGGGAAA	57.458	33.333	0.00	0.00	0.00	3.13
176	181	1.548719	TCAGTCGGGAAATCATCGTGT	59.451	47.619	0.00	0.00	0.00	4.49
229	237	1.369625	ACCATCGCCGATGAAGAAAC	58.630	50.000	27.59	0.00	42.09	2.78
235	243	2.095110	TCGCCGATGAAGAAACTCGTAA	60.095	45.455	0.00	0.00	0.00	3.18
252	261	7.962964	ACTCGTAAATCAGAAGAATCAAACA	57.037	32.000	0.00	0.00	0.00	2.83
264	273	5.371115	AGAATCAAACATGTAAACACCCG	57.629	39.130	0.00	0.00	0.00	5.28
284	293	3.235195	CGAACGAAGACGAATGAAGACT	58.765	45.455	0.00	0.00	42.66	3.24
300	309	4.533707	TGAAGACTGGATCCAAACAGATCT	59.466	41.667	17.00	8.87	42.02	2.75
318	327	0.673644	CTACCAAAGACCAGCACCGG	60.674	60.000	0.00	0.00	0.00	5.28
319	328	1.412453	TACCAAAGACCAGCACCGGT	61.412	55.000	0.00	0.00	43.91	5.28
328	337	3.000819	AGCACCGGTCGAATCCCA	61.001	61.111	2.59	0.00	0.00	4.37
347	356	1.352404	CGAGATCCGACGGAGACAC	59.648	63.158	22.99	15.19	41.76	3.67
363	372	3.168528	ACACCTCCACACGCCCTT	61.169	61.111	0.00	0.00	0.00	3.95
386	395	1.824852	ACGATGCTAGACACACCATCA	59.175	47.619	0.00	0.00	35.08	3.07
398	407	2.707791	CACACCATCAGGACAGGGATAT	59.292	50.000	0.00	0.00	38.69	1.63
420	432	9.490379	GATATAACGTGGGAGACATTATTTCTT	57.510	33.333	0.00	0.00	0.00	2.52
542	554	2.321720	CCTCCATGGCCTAGGGTTT	58.678	57.895	11.72	0.00	0.00	3.27
543	555	0.631212	CCTCCATGGCCTAGGGTTTT	59.369	55.000	11.72	0.00	0.00	2.43
544	556	1.007118	CCTCCATGGCCTAGGGTTTTT	59.993	52.381	11.72	0.00	0.00	1.94
598	610	5.335269	CGATGCTCGTTAAGTGAGAGGATAT	60.335	44.000	8.48	0.00	41.89	1.63
602	614	5.688176	GCTCGTTAAGTGAGAGGATATGTTC	59.312	44.000	8.48	0.00	35.43	3.18
604	616	5.068723	TCGTTAAGTGAGAGGATATGTTCCC	59.931	44.000	0.00	0.00	46.81	3.97
635	647	2.684001	AGACGTTTGTGGTGACTTCA	57.316	45.000	0.00	0.00	0.00	3.02
636	648	3.194005	AGACGTTTGTGGTGACTTCAT	57.806	42.857	0.00	0.00	0.00	2.57
638	650	1.864711	ACGTTTGTGGTGACTTCATCG	59.135	47.619	0.00	0.00	0.00	3.84
649	661	6.535150	GTGGTGACTTCATCGATCTCAAAATA	59.465	38.462	0.00	0.00	0.00	1.40
656	668	9.276590	ACTTCATCGATCTCAAAATAATATGCA	57.723	29.630	0.00	0.00	0.00	3.96
660	672	6.845302	TCGATCTCAAAATAATATGCATGCC	58.155	36.000	16.68	0.00	0.00	4.40
670	682	0.390492	TATGCATGCCCAGTCTCTCG	59.610	55.000	16.68	0.00	0.00	4.04
671	683	2.202987	GCATGCCCAGTCTCTCGG	60.203	66.667	6.36	0.00	0.00	4.63
673	685	1.440893	CATGCCCAGTCTCTCGGAG	59.559	63.158	0.00	0.00	0.00	4.63
674	686	1.039785	CATGCCCAGTCTCTCGGAGA	61.040	60.000	7.60	7.60	36.22	3.71
686	698	1.757118	TCTCGGAGATGCTTACAAGGG	59.243	52.381	2.97	0.00	33.89	3.95
687	699	1.482593	CTCGGAGATGCTTACAAGGGT	59.517	52.381	0.00	0.00	33.89	4.34
688	700	2.693591	CTCGGAGATGCTTACAAGGGTA	59.306	50.000	0.00	0.00	33.89	3.69
689	701	3.101437	TCGGAGATGCTTACAAGGGTAA	58.899	45.455	0.00	0.00	37.15	2.85
693	705	9.669065	CTCGGAGATGCTTACAAGGGTAAGAAA	62.669	44.444	16.45	6.01	45.95	2.52
745	757	2.783832	CGTATGTATGAGTGTCTGCGTG	59.216	50.000	0.00	0.00	0.00	5.34
758	770	2.488952	TCTGCGTGCAGATTGTGTTTA	58.511	42.857	19.99	0.00	46.80	2.01
759	771	2.875317	TCTGCGTGCAGATTGTGTTTAA	59.125	40.909	19.99	0.00	46.80	1.52
1019	1035	6.049149	TCTGTTTATAAAAGAGAGGGCATCG	58.951	40.000	0.00	0.00	0.00	3.84
1058	1074	1.075301	CCACCCCATCCAAATCCCC	60.075	63.158	0.00	0.00	0.00	4.81
1763	1792	2.823147	AGCCTACCGGACGTCTCG	60.823	66.667	16.46	16.43	0.00	4.04
2048	2077	1.143183	GAAGATGCCCGGCTACGAA	59.857	57.895	11.61	0.00	44.60	3.85
2061	2090	4.440525	CCGGCTACGAAATTGTCCTTACTA	60.441	45.833	0.00	0.00	44.60	1.82
2270	2299	3.555966	CAACCAATTAGGATGGGGAGAC	58.444	50.000	0.00	0.00	42.48	3.36
2277	2306	2.217745	GGATGGGGAGACGGGGATC	61.218	68.421	0.00	0.00	0.00	3.36
2455	2485	2.227626	GGAAGCCAAGTTCTGAAGAAGC	59.772	50.000	0.00	0.00	34.27	3.86
2800	2835	2.807967	TGGAGAAACTCTCATTTGCACG	59.192	45.455	6.05	0.00	45.12	5.34
2984	3022	6.150140	GGACTCTGTGCAACTTCAGATTATTT	59.850	38.462	5.32	0.00	39.48	1.40
3118	3156	4.245660	TGAAAGAGTGAACAAGATAGCCG	58.754	43.478	0.00	0.00	0.00	5.52
3177	3215	2.395367	TTTTGTTTTCCGGCCGCTCG	62.395	55.000	22.85	6.58	0.00	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	7.364522	TGTTCTTTGTACTGCTATGATTGAC	57.635	36.000	0.00	0.00	0.00	3.18
12	13	5.023533	TCTCTGTTGTTCTTTGTACTGCT	57.976	39.130	0.00	0.00	0.00	4.24
34	35	9.483916	CATGGACATGATTGTAATTTGCATTAT	57.516	29.630	6.44	0.00	41.20	1.28
39	40	5.904941	TCCATGGACATGATTGTAATTTGC	58.095	37.500	11.44	0.00	41.20	3.68
73	74	1.135373	TGCTCTAGTGCTTGTAGACGC	60.135	52.381	17.08	0.00	0.00	5.19
76	77	2.093973	GGCTTGCTCTAGTGCTTGTAGA	60.094	50.000	17.08	0.00	0.00	2.59
122	124	1.063942	TGTCTAGCTCCGATGAGGGAA	60.064	52.381	0.00	0.00	41.52	3.97
156	161	1.548719	ACACGATGATTTCCCGACTGA	59.451	47.619	0.00	0.00	0.00	3.41
167	172	1.213296	AGGGGCCTTAACACGATGAT	58.787	50.000	0.84	0.00	0.00	2.45
176	181	0.986550	GCTGGTCCTAGGGGCCTTAA	60.987	60.000	19.47	4.10	32.49	1.85
229	237	8.446273	ACATGTTTGATTCTTCTGATTTACGAG	58.554	33.333	0.00	0.00	0.00	4.18
235	243	9.683069	GTGTTTACATGTTTGATTCTTCTGATT	57.317	29.630	2.30	0.00	0.00	2.57
252	261	3.062042	GTCTTCGTTCGGGTGTTTACAT	58.938	45.455	0.00	0.00	0.00	2.29
264	273	3.365220	CCAGTCTTCATTCGTCTTCGTTC	59.635	47.826	0.00	0.00	38.33	3.95
284	293	5.250543	TCTTTGGTAGATCTGTTTGGATCCA	59.749	40.000	11.44	11.44	42.02	3.41
300	309	1.373435	CCGGTGCTGGTCTTTGGTA	59.627	57.895	0.00	0.00	0.00	3.25
318	327	0.317938	CGGATCTCGTGGGATTCGAC	60.318	60.000	4.33	0.00	44.78	4.20
319	328	2.030551	CGGATCTCGTGGGATTCGA	58.969	57.895	4.33	0.00	44.78	3.71
328	337	1.078637	TGTCTCCGTCGGATCTCGT	60.079	57.895	15.81	0.00	40.32	4.18
347	356	2.113139	AAAGGGCGTGTGGAGGTG	59.887	61.111	0.00	0.00	0.00	4.00
363	372	1.616374	TGGTGTGTCTAGCATCGTCAA	59.384	47.619	0.00	0.00	0.00	3.18
386	395	2.090943	TCCCACGTTATATCCCTGTCCT	60.091	50.000	0.00	0.00	0.00	3.85
398	407	6.942976	AGAAGAAATAATGTCTCCCACGTTA	58.057	36.000	0.00	0.00	40.17	3.18
420	432	2.792947	GGCGGCGATGTCCCTTAGA	61.793	63.158	12.98	0.00	0.00	2.10
455	467	5.555818	CGTTCTTGTTAGGTTCAACGTCTTC	60.556	44.000	0.00	0.00	33.61	2.87
619	631	2.131972	TCGATGAAGTCACCACAAACG	58.868	47.619	0.00	0.00	0.00	3.60
622	634	3.258123	TGAGATCGATGAAGTCACCACAA	59.742	43.478	0.54	0.00	0.00	3.33
635	647	7.415989	GGGCATGCATATTATTTTGAGATCGAT	60.416	37.037	21.36	0.00	0.00	3.59
636	648	6.127925	GGGCATGCATATTATTTTGAGATCGA	60.128	38.462	21.36	0.00	0.00	3.59
638	650	6.927416	TGGGCATGCATATTATTTTGAGATC	58.073	36.000	21.36	0.00	0.00	2.75
649	661	2.549563	CGAGAGACTGGGCATGCATATT	60.550	50.000	21.36	1.16	0.00	1.28
656	668	0.105760	ATCTCCGAGAGACTGGGCAT	60.106	55.000	4.07	0.00	41.76	4.40
657	669	1.039785	CATCTCCGAGAGACTGGGCA	61.040	60.000	4.07	0.00	41.76	5.36
660	672	1.110442	AAGCATCTCCGAGAGACTGG	58.890	55.000	4.07	1.75	41.76	4.00
710	722	9.489084	ACTCATACATACGCACATACATTTATT	57.511	29.630	0.00	0.00	0.00	1.40
713	725	6.761242	ACACTCATACATACGCACATACATTT	59.239	34.615	0.00	0.00	0.00	2.32
715	727	5.842907	ACACTCATACATACGCACATACAT	58.157	37.500	0.00	0.00	0.00	2.29
721	733	2.535984	GCAGACACTCATACATACGCAC	59.464	50.000	0.00	0.00	0.00	5.34
723	735	1.781429	CGCAGACACTCATACATACGC	59.219	52.381	0.00	0.00	0.00	4.42
730	742	0.887933	TCTGCACGCAGACACTCATA	59.112	50.000	17.54	0.00	46.80	2.15
767	779	0.234884	GTCCTTTTCACGCGAGTTGG	59.765	55.000	15.93	7.21	46.40	3.77
768	780	1.217882	AGTCCTTTTCACGCGAGTTG	58.782	50.000	15.93	0.00	46.40	3.16
797	809	4.274950	TGCTGTTCTAGTTTTTCCTTTCCG	59.725	41.667	0.00	0.00	0.00	4.30
884	900	4.049376	GGCTGGCTGCATTTGTTAACAAA	61.049	43.478	30.29	30.29	45.15	2.83
1019	1035	1.222567	TAAAGGAAGGGGAGGGATGC	58.777	55.000	0.00	0.00	0.00	3.91
1058	1074	1.527370	GGAGGGTTGGAGGAATCGG	59.473	63.158	0.00	0.00	0.00	4.18
2048	2077	8.390921	TCCCAGAAGAAATTAGTAAGGACAATT	58.609	33.333	0.00	0.00	0.00	2.32
2061	2090	6.493166	TGTGAACCATATCCCAGAAGAAATT	58.507	36.000	0.00	0.00	0.00	1.82
2270	2299	0.392998	CCAGAACCTGTTGATCCCCG	60.393	60.000	0.00	0.00	0.00	5.73
2277	2306	4.218417	CCCAAGTAAATCCAGAACCTGTTG	59.782	45.833	0.00	0.00	0.00	3.33
2455	2485	8.627403	AGATTTGCACATCCAGAACAAATATAG	58.373	33.333	9.23	0.00	40.13	1.31
2800	2835	9.896645	ATCCATGTTCACATAGGATAATCATAC	57.103	33.333	16.22	0.00	39.83	2.39
2984	3022	0.899019	AAACATGCCATGATGCAGCA	59.101	45.000	12.53	7.31	45.93	4.41
3101	3139	3.552294	GCTTACGGCTATCTTGTTCACTC	59.448	47.826	0.00	0.00	38.06	3.51
3162	3200	3.045492	TTCGAGCGGCCGGAAAAC	61.045	61.111	29.38	9.78	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.