AutoCloner

Multiple sequence alignment - TraesCS1A01G324200

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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	TraesCS1A01G324200	chr1A	100.000	2315	0	0	1	2315	514868968	514871282	0.000000e+00	4276
1	TraesCS1A01G324200	chr1A	99.258	1347	8	2	970	2315	515126132	515127477	0.000000e+00	2431
2	TraesCS1A01G324200	chr1A	99.258	943	7	0	1	943	515125211	515126153	0.000000e+00	1703
3	TraesCS1A01G324200	chr2A	90.769	585	49	3	1364	1944	3514501	3515084	0.000000e+00	776
4	TraesCS1A01G324200	chr2A	86.768	393	43	9	305	691	764335459	764335848	1.640000e-116	429
5	TraesCS1A01G324200	chr5B	89.116	588	58	6	1361	1944	87289223	87289808	0.000000e+00	726
6	TraesCS1A01G324200	chr3A	88.660	582	60	5	1364	1944	321109676	321109100	0.000000e+00	704
7	TraesCS1A01G324200	chr3A	88.738	515	50	8	1364	1872	602855589	602856101	7.020000e-175	623
8	TraesCS1A01G324200	chr3A	86.832	524	56	7	1365	1885	374441944	374442457	7.170000e-160	573
9	TraesCS1A01G324200	chr3A	84.407	590	83	8	1364	1947	740092745	740092159	2.580000e-159	571
10	TraesCS1A01G324200	chr3A	85.536	401	47	10	302	698	700606438	700606831	2.140000e-110	409
11	TraesCS1A01G324200	chr3A	89.121	239	26	0	1034	1272	23877476	23877238	4.840000e-77	298
12	TraesCS1A01G324200	chr3A	84.848	99	13	2	6	103	474681653	474681556	5.260000e-17	99
13	TraesCS1A01G324200	chr1D	89.313	524	53	3	1364	1885	416664990	416665512	0.000000e+00	654
14	TraesCS1A01G324200	chr1D	84.938	405	52	9	295	694	336370350	336370750	3.580000e-108	401
15	TraesCS1A01G324200	chr3D	84.497	587	80	9	1364	1944	30421606	30421025	9.280000e-159	569
16	TraesCS1A01G324200	chr3D	87.744	359	36	2	922	1272	13218967	13219325	1.660000e-111	412
17	TraesCS1A01G324200	chr1B	94.357	319	16	2	957	1273	565300798	565301116	2.670000e-134	488
18	TraesCS1A01G324200	chr1B	95.769	260	10	1	694	953	565300574	565300832	3.560000e-113	418
19	TraesCS1A01G324200	chr1B	96.407	167	6	0	135	301	565300404	565300570	2.270000e-70	276
20	TraesCS1A01G324200	chr2D	85.678	391	47	9	307	692	197037460	197037846	9.960000e-109	403
21	TraesCS1A01G324200	chr2D	86.010	386	43	8	305	686	485642417	485642039	9.960000e-109	403
22	TraesCS1A01G324200	chr2D	85.751	386	43	8	305	686	485599218	485598841	4.630000e-107	398
23	TraesCS1A01G324200	chr2D	85.567	388	44	9	305	688	485606103	485605724	1.670000e-106	396
24	TraesCS1A01G324200	chr3B	85.677	384	48	6	307	687	650058780	650059159	4.630000e-107	398
25	TraesCS1A01G324200	chr3B	84.848	330	38	3	943	1272	19077916	19078233	2.870000e-84	322
26	TraesCS1A01G324200	chr7B	90.476	105	8	2	1	104	213828305	213828408	1.120000e-28	137
27	TraesCS1A01G324200	chr7B	88.889	90	10	0	1	90	648731749	648731660	6.760000e-21	111
28	TraesCS1A01G324200	chr5A	90.196	102	10	0	3	104	14851925	14852026	1.440000e-27	134
29	TraesCS1A01G324200	chr4A	87.255	102	11	2	3	104	1734299	1734200	5.230000e-22	115

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	TraesCS1A01G324200	chr1A	514868968	514871282	2314	False	4276	4276	100.000	1	2315	1	chr1A.!!$F1	2314
1	TraesCS1A01G324200	chr1A	515125211	515127477	2266	False	2067	2431	99.258	1	2315	2	chr1A.!!$F2	2314
2	TraesCS1A01G324200	chr2A	3514501	3515084	583	False	776	776	90.769	1364	1944	1	chr2A.!!$F1	580
3	TraesCS1A01G324200	chr5B	87289223	87289808	585	False	726	726	89.116	1361	1944	1	chr5B.!!$F1	583
4	TraesCS1A01G324200	chr3A	321109100	321109676	576	True	704	704	88.660	1364	1944	1	chr3A.!!$R2	580
5	TraesCS1A01G324200	chr3A	602855589	602856101	512	False	623	623	88.738	1364	1872	1	chr3A.!!$F2	508
6	TraesCS1A01G324200	chr3A	374441944	374442457	513	False	573	573	86.832	1365	1885	1	chr3A.!!$F1	520
7	TraesCS1A01G324200	chr3A	740092159	740092745	586	True	571	571	84.407	1364	1947	1	chr3A.!!$R4	583
8	TraesCS1A01G324200	chr1D	416664990	416665512	522	False	654	654	89.313	1364	1885	1	chr1D.!!$F2	521
9	TraesCS1A01G324200	chr3D	30421025	30421606	581	True	569	569	84.497	1364	1944	1	chr3D.!!$R1	580
10	TraesCS1A01G324200	chr1B	565300404	565301116	712	False	394	488	95.511	135	1273	3	chr1B.!!$F1	1138

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
216	217	2.665165	GCCCACCATTATCATCCAACA	58.335	47.619	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1547	1565	4.356405	AAATGCAAGAAAAGAAAGGGGG	57.644	40.909	0.0	0.0	0.0	5.4	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	3.245668	AAGCACCCGTCTCCTGCAG	62.246	63.158	6.78	6.78	33.06	4.41
216	217	2.665165	GCCCACCATTATCATCCAACA	58.335	47.619	0.00	0.00	0.00	3.33
525	526	9.688592	AAGATCAGAATTTGTCTTTTTCACATC	57.311	29.630	0.00	0.00	32.70	3.06
541	542	4.637276	TCACATCCGACACATAAGTTGTT	58.363	39.130	0.00	0.00	36.00	2.83
780	781	3.446161	TCAGTCTAACTTGGTATCGGTGG	59.554	47.826	0.00	0.00	0.00	4.61
931	941	4.141274	CCCCTCAGTCAATAGAGAGAGAGA	60.141	50.000	0.00	0.00	33.74	3.10
932	942	5.065914	CCCTCAGTCAATAGAGAGAGAGAG	58.934	50.000	0.00	0.00	33.74	3.20
933	943	5.163205	CCCTCAGTCAATAGAGAGAGAGAGA	60.163	48.000	0.00	0.00	33.74	3.10
934	944	5.994054	CCTCAGTCAATAGAGAGAGAGAGAG	59.006	48.000	0.00	0.00	33.74	3.20
935	945	6.183361	CCTCAGTCAATAGAGAGAGAGAGAGA	60.183	46.154	0.00	0.00	33.74	3.10
936	946	6.820335	TCAGTCAATAGAGAGAGAGAGAGAG	58.180	44.000	0.00	0.00	0.00	3.20
937	947	6.611236	TCAGTCAATAGAGAGAGAGAGAGAGA	59.389	42.308	0.00	0.00	0.00	3.10
938	948	6.927936	CAGTCAATAGAGAGAGAGAGAGAGAG	59.072	46.154	0.00	0.00	0.00	3.20
939	949	6.841229	AGTCAATAGAGAGAGAGAGAGAGAGA	59.159	42.308	0.00	0.00	0.00	3.10
940	950	7.015098	AGTCAATAGAGAGAGAGAGAGAGAGAG	59.985	44.444	0.00	0.00	0.00	3.20
941	951	7.014711	GTCAATAGAGAGAGAGAGAGAGAGAGA	59.985	44.444	0.00	0.00	0.00	3.10
942	952	7.232330	TCAATAGAGAGAGAGAGAGAGAGAGAG	59.768	44.444	0.00	0.00	0.00	3.20
943	953	5.136068	AGAGAGAGAGAGAGAGAGAGAGA	57.864	47.826	0.00	0.00	0.00	3.10
944	954	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
945	955	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
946	956	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
947	957	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
948	958	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
949	959	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
950	960	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
951	961	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
952	962	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
953	963	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
954	964	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
955	965	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
956	966	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
957	967	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
958	968	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
959	969	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
960	970	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
961	971	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
962	972	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
963	973	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
964	974	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
965	975	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
966	976	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
967	977	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
968	978	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
969	979	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
970	980	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
971	981	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
972	982	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
973	983	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
974	984	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
975	985	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
976	986	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
977	987	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
978	988	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
1547	1565	5.007626	TGAAAGCATGCCTCAATACGATTAC	59.992	40.000	15.66	0.00	0.00	1.89
1799	1826	3.188873	ACGTATCGCAGAAGTATCCTAGC	59.811	47.826	0.00	0.00	43.58	3.42

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	0.825840	AGTAGAGCAGCGGGATCCTC	60.826	60.000	12.58	4.01	30.22	3.71
216	217	1.102978	GGGCTGTGTTTGAGTGTTGT	58.897	50.000	0.00	0.00	0.00	3.32
371	372	9.029243	TGTATGCGCCAAATTATTTTAGAAATG	57.971	29.630	4.18	0.00	0.00	2.32
525	526	4.561735	AAACCAACAACTTATGTGTCGG	57.438	40.909	0.00	0.00	42.99	4.79
541	542	4.809426	ACAACGTTGTTTTGTGAAAAACCA	59.191	33.333	27.70	0.00	40.84	3.67
931	941	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
932	942	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
933	943	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
934	944	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
935	945	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
936	946	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
937	947	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
938	948	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
939	949	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
940	950	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
941	951	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
942	952	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
943	953	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
944	954	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
945	955	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
946	956	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
947	957	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
948	958	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
949	959	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
950	960	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
951	961	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
952	962	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
953	963	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
954	964	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
955	965	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
956	966	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
957	967	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
958	968	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
959	969	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
960	970	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
961	971	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
962	972	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
963	973	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
964	974	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
965	975	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
966	976	5.136828	TCTCTCTCTCTCTCTCTCTCTCTC	58.863	50.000	0.00	0.00	0.00	3.20
967	977	5.136068	TCTCTCTCTCTCTCTCTCTCTCT	57.864	47.826	0.00	0.00	0.00	3.10
968	978	4.280677	CCTCTCTCTCTCTCTCTCTCTCTC	59.719	54.167	0.00	0.00	0.00	3.20
969	979	4.222336	CCTCTCTCTCTCTCTCTCTCTCT	58.778	52.174	0.00	0.00	0.00	3.10
970	980	3.244044	GCCTCTCTCTCTCTCTCTCTCTC	60.244	56.522	0.00	0.00	0.00	3.20
971	981	2.703007	GCCTCTCTCTCTCTCTCTCTCT	59.297	54.545	0.00	0.00	0.00	3.10
972	982	2.224402	GGCCTCTCTCTCTCTCTCTCTC	60.224	59.091	0.00	0.00	0.00	3.20
973	983	1.771255	GGCCTCTCTCTCTCTCTCTCT	59.229	57.143	0.00	0.00	0.00	3.10
974	984	1.490490	TGGCCTCTCTCTCTCTCTCTC	59.510	57.143	3.32	0.00	0.00	3.20
975	985	1.212935	GTGGCCTCTCTCTCTCTCTCT	59.787	57.143	3.32	0.00	0.00	3.10
976	986	1.064758	TGTGGCCTCTCTCTCTCTCTC	60.065	57.143	3.32	0.00	0.00	3.20
977	987	0.998928	TGTGGCCTCTCTCTCTCTCT	59.001	55.000	3.32	0.00	0.00	3.10
978	988	1.392589	CTGTGGCCTCTCTCTCTCTC	58.607	60.000	3.32	0.00	0.00	3.20
1547	1565	4.356405	AAATGCAAGAAAAGAAAGGGGG	57.644	40.909	0.00	0.00	0.00	5.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.