AutoCloner

Multiple sequence alignment - TraesCS1D01G163200

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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	TraesCS1D01G163200	chr1D	100.000	2399	0	0	1	2399	233902602	233900204	0.000000e+00	4431
1	TraesCS1D01G163200	chr1D	100.000	221	0	0	2648	2868	233899955	233899735	2.660000e-110	409
2	TraesCS1D01G163200	chr1A	93.207	2429	97	25	1	2399	313743388	313745778	0.000000e+00	3509
3	TraesCS1D01G163200	chr1A	86.099	223	20	2	2648	2868	313745853	313746066	2.220000e-56	230
4	TraesCS1D01G163200	chr1B	93.272	2081	86	31	341	2399	368551239	368549191	0.000000e+00	3018
5	TraesCS1D01G163200	chr1B	90.385	364	16	6	1	351	368551621	368551264	7.240000e-126	460
6	TraesCS1D01G163200	chr1B	86.547	223	22	3	2648	2868	368549116	368548900	3.690000e-59	239
7	TraesCS1D01G163200	chr5A	90.984	244	18	2	2153	2392	402121622	402121865	2.760000e-85	326
8	TraesCS1D01G163200	chr5A	87.204	211	25	2	2659	2868	402121959	402122168	3.690000e-59	239
9	TraesCS1D01G163200	chr2A	89.919	248	24	1	2153	2399	665683610	665683857	4.610000e-83	318
10	TraesCS1D01G163200	chr2A	88.950	181	15	2	1046	1226	573418644	573418819	4.810000e-53	219
11	TraesCS1D01G163200	chr2A	85.417	192	23	2	1035	1226	98887946	98887760	8.110000e-46	195
12	TraesCS1D01G163200	chr2A	86.614	127	16	1	1035	1161	98888771	98888646	3.850000e-29	139
13	TraesCS1D01G163200	chr5D	90.123	243	22	1	2152	2392	313155938	313156180	5.970000e-82	315
14	TraesCS1D01G163200	chr5D	89.216	204	20	2	2666	2868	313156282	313156484	1.320000e-63	254
15	TraesCS1D01G163200	chr5D	87.500	192	19	2	1035	1226	58253556	58253370	1.730000e-52	217
16	TraesCS1D01G163200	chr5D	90.780	141	13	0	1086	1226	17818171	17818031	3.770000e-44	189
17	TraesCS1D01G163200	chr2D	90.041	241	21	2	2155	2392	561060598	561060358	2.780000e-80	309
18	TraesCS1D01G163200	chr2D	87.678	211	24	2	2659	2868	561060263	561060054	7.940000e-61	244
19	TraesCS1D01G163200	chr2D	88.021	192	18	2	1035	1226	234337205	234337019	3.720000e-54	222
20	TraesCS1D01G163200	chr7B	89.256	242	22	2	2155	2392	621768194	621767953	1.670000e-77	300
21	TraesCS1D01G163200	chr4B	88.843	242	24	2	2154	2392	317152367	317152608	7.770000e-76	294
22	TraesCS1D01G163200	chr7D	88.750	240	23	3	2152	2388	106365366	106365604	1.010000e-74	291
23	TraesCS1D01G163200	chr3B	86.730	211	26	2	2659	2868	279666385	279666176	1.720000e-57	233
24	TraesCS1D01G163200	chr3B	88.950	181	15	2	1046	1226	5770054	5769879	4.810000e-53	219

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	TraesCS1D01G163200	chr1D	233899735	233902602	2867	True	2420.0	4431	100.0000	1	2868	2	chr1D.!!$R1	2867
1	TraesCS1D01G163200	chr1A	313743388	313746066	2678	False	1869.5	3509	89.6530	1	2868	2	chr1A.!!$F1	2867
2	TraesCS1D01G163200	chr1B	368548900	368551621	2721	True	1239.0	3018	90.0680	1	2868	3	chr1B.!!$R1	2867
3	TraesCS1D01G163200	chr5A	402121622	402122168	546	False	282.5	326	89.0940	2153	2868	2	chr5A.!!$F1	715
4	TraesCS1D01G163200	chr5D	313155938	313156484	546	False	284.5	315	89.6695	2152	2868	2	chr5D.!!$F1	716
5	TraesCS1D01G163200	chr2D	561060054	561060598	544	True	276.5	309	88.8595	2155	2868	2	chr2D.!!$R2	713

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
498	547	1.064946	GATGACCTGAGAGACGGCG	59.935	63.158	4.8	4.8	0.00	6.46	F
832	891	1.069049	GCAGAAAATGCGGCCCAATAT	59.931	47.619	0.0	0.0	46.99	1.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1653	1714	0.105709	CCCTCTTCCTCCTCTCCTCC	60.106	65.0	0.0	0.0	0.0	4.30	R
2654	2738	0.528684	CTTCTTCAGGTCCGGCGATC	60.529	60.0	9.3	0.0	0.0	3.69	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
74	75	9.102757	CATATAATGCAGGTACCAAGATATCAC	57.897	37.037	15.94	0.00	0.00	3.06
97	98	2.501723	AGTGCCATCAGAACTAATCGGT	59.498	45.455	0.00	0.00	0.00	4.69
149	150	6.679327	ACGAAAGAAAAGCCTATTATCACC	57.321	37.500	0.00	0.00	0.00	4.02
257	271	2.417719	CCACAGACTTCACTGCTTACC	58.582	52.381	0.00	0.00	41.06	2.85
264	278	2.304180	ACTTCACTGCTTACCTCTGCAT	59.696	45.455	0.00	0.00	38.59	3.96
323	337	1.968017	CACAGGTGCAATGAGCCGT	60.968	57.895	7.15	0.00	44.83	5.68
498	547	1.064946	GATGACCTGAGAGACGGCG	59.935	63.158	4.80	4.80	0.00	6.46
504	553	1.517257	CTGAGAGACGGCGCGAAAT	60.517	57.895	12.10	0.00	0.00	2.17
525	574	2.126307	CACTGAGACCAGCGACCG	60.126	66.667	0.00	0.00	44.16	4.79
539	588	1.712018	CGACCGAGCTACGATGGTGA	61.712	60.000	7.07	0.00	45.77	4.02
569	618	1.673168	GGCCAGGAGCACAGAATAAG	58.327	55.000	0.00	0.00	46.50	1.73
716	765	2.746277	GGCACCGCCGATTTCAGT	60.746	61.111	0.00	0.00	39.62	3.41
786	836	2.359975	CTTGAACCCCAGGACGGC	60.360	66.667	0.00	0.00	0.00	5.68
787	837	3.172106	TTGAACCCCAGGACGGCA	61.172	61.111	0.00	0.00	0.00	5.69
821	880	6.327934	AGAATTTCGAATCTGGCAGAAAATG	58.672	36.000	22.84	11.74	36.39	2.32
830	889	1.218854	GCAGAAAATGCGGCCCAAT	59.781	52.632	0.00	0.00	46.99	3.16
832	891	1.069049	GCAGAAAATGCGGCCCAATAT	59.931	47.619	0.00	0.00	46.99	1.28
1566	1627	3.074412	CTGGTACATGTCGAAGCCTTTT	58.926	45.455	0.00	0.00	38.20	2.27
1653	1714	4.394729	AGAAGAGTATCGAGGAGCTTAGG	58.605	47.826	0.00	0.00	42.67	2.69
1805	1866	9.584839	GCAGTTGTTGTGATTTCATTAATTTTC	57.415	29.630	0.00	0.00	0.00	2.29
1918	1979	7.228314	CAGGATCTGCAATGGATGATTATTT	57.772	36.000	0.00	0.00	0.00	1.40
1925	1986	7.946219	TCTGCAATGGATGATTATTTGAGGTAT	59.054	33.333	0.00	0.00	0.00	2.73
2017	2084	6.677431	GCAGTCCAAGCAAAGAGAATCATTAG	60.677	42.308	0.00	0.00	37.82	1.73
2039	2106	6.287107	AGTTGTTCATGTTTTACTCTGACG	57.713	37.500	0.00	0.00	0.00	4.35
2040	2107	5.815740	AGTTGTTCATGTTTTACTCTGACGT	59.184	36.000	0.00	0.00	0.00	4.34
2041	2108	5.651172	TGTTCATGTTTTACTCTGACGTG	57.349	39.130	0.00	0.00	0.00	4.49
2042	2109	4.025229	TGTTCATGTTTTACTCTGACGTGC	60.025	41.667	0.00	0.00	31.91	5.34
2044	2111	4.377021	TCATGTTTTACTCTGACGTGCTT	58.623	39.130	0.00	0.00	31.91	3.91
2045	2112	4.814234	TCATGTTTTACTCTGACGTGCTTT	59.186	37.500	0.00	0.00	31.91	3.51
2046	2113	5.986741	TCATGTTTTACTCTGACGTGCTTTA	59.013	36.000	0.00	0.00	31.91	1.85
2047	2114	5.900339	TGTTTTACTCTGACGTGCTTTAG	57.100	39.130	0.00	0.00	0.00	1.85
2048	2115	4.210537	TGTTTTACTCTGACGTGCTTTAGC	59.789	41.667	0.00	0.00	42.50	3.09
2073	2140	9.716507	GCAAAACTGTTATATGTATTGTACTGG	57.283	33.333	0.00	0.00	0.00	4.00
2181	2261	0.096802	CGAATACGCACAAGCATGCA	59.903	50.000	21.98	0.00	46.47	3.96
2368	2452	1.228245	GGACAGAGCAAACAGGCCA	60.228	57.895	5.01	0.00	0.00	5.36
2394	2478	0.464735	TACCGTTGCAAGCCACAACT	60.465	50.000	0.00	0.00	44.15	3.16
2679	2763	2.355209	GCCGGACCTGAAGAAGAAGATT	60.355	50.000	5.05	0.00	0.00	2.40
2721	2805	0.471971	ATACATAGCGCCCTGGAGGT	60.472	55.000	2.29	0.00	38.26	3.85
2755	2840	0.173708	GCAACCCACACCAAAACGAA	59.826	50.000	0.00	0.00	0.00	3.85
2770	2855	1.247567	ACGAAATGCCCCAAACTCTG	58.752	50.000	0.00	0.00	0.00	3.35
2773	2858	1.194121	AAATGCCCCAAACTCTGGCC	61.194	55.000	0.00	0.00	44.90	5.36
2801	2886	2.192861	CCACGAACAGCCAAGGCAA	61.193	57.895	14.40	0.00	44.88	4.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	7.557358	TCCACTATGCATGTGAGTTTTTGATAT	59.443	33.333	22.76	0.00	37.60	1.63
74	75	2.868583	CGATTAGTTCTGATGGCACTGG	59.131	50.000	0.00	0.00	0.00	4.00
257	271	5.389859	TTTGTTCCAAACCATATGCAGAG	57.610	39.130	0.00	0.00	0.00	3.35
264	278	6.601332	AGAGAGAGTTTTGTTCCAAACCATA	58.399	36.000	0.00	0.00	0.00	2.74
426	475	2.121506	AAGGACAAGGGGAGGGCA	60.122	61.111	0.00	0.00	0.00	5.36
470	519	3.842923	AGGTCATCGGCGAGCTGG	61.843	66.667	17.22	5.00	42.01	4.85
498	547	1.291132	GGTCTCAGTGGCTATTTCGC	58.709	55.000	0.00	0.00	0.00	4.70
504	553	3.288484	CGCTGGTCTCAGTGGCTA	58.712	61.111	0.00	0.00	45.14	3.93
525	574	2.541999	GCACTAGTCACCATCGTAGCTC	60.542	54.545	0.00	0.00	0.00	4.09
533	582	2.367202	CCGGGGCACTAGTCACCAT	61.367	63.158	12.46	0.00	0.00	3.55
716	765	1.269448	GCTTTTGTTTCCATGGAGCGA	59.731	47.619	15.53	9.23	0.00	4.93
766	816	2.843545	GTCCTGGGGTTCAAGGCA	59.156	61.111	0.00	0.00	0.00	4.75
786	836	2.985896	TCGAAATTCTAGGCCCAACTG	58.014	47.619	0.00	0.00	0.00	3.16
787	837	3.713826	TTCGAAATTCTAGGCCCAACT	57.286	42.857	0.00	0.00	0.00	3.16
821	880	0.685097	TCCTCACTATATTGGGCCGC	59.315	55.000	0.00	0.00	0.00	6.53
822	881	3.485463	TTTCCTCACTATATTGGGCCG	57.515	47.619	0.00	0.00	0.00	6.13
830	889	3.069158	GCCTACGGCTTTTCCTCACTATA	59.931	47.826	0.00	0.00	46.69	1.31
832	891	1.206371	GCCTACGGCTTTTCCTCACTA	59.794	52.381	0.00	0.00	46.69	2.74
1653	1714	0.105709	CCCTCTTCCTCCTCTCCTCC	60.106	65.000	0.00	0.00	0.00	4.30
1701	1762	1.397672	TTGCTGTAGTGGCAAGCAAA	58.602	45.000	19.04	5.95	43.50	3.68
1746	1807	2.614779	TGACACTACCTCGACGAGTAG	58.385	52.381	22.61	22.32	0.00	2.57
1820	1881	6.373779	CAAGGAATACACAGACAACAATCAC	58.626	40.000	0.00	0.00	0.00	3.06
1918	1979	8.624670	AGGGATTACTATGACTATCATACCTCA	58.375	37.037	0.00	0.00	38.26	3.86
1925	1986	7.347222	ACCAAACAGGGATTACTATGACTATCA	59.653	37.037	0.00	0.00	43.89	2.15
1930	1991	7.462571	AAAACCAAACAGGGATTACTATGAC	57.537	36.000	0.00	0.00	43.89	3.06
1937	1998	9.343539	CCAAAATTTAAAACCAAACAGGGATTA	57.656	29.630	0.00	0.00	43.89	1.75
1941	2005	7.815840	ATCCAAAATTTAAAACCAAACAGGG	57.184	32.000	0.00	0.00	43.89	4.45
2017	2084	5.901884	CACGTCAGAGTAAAACATGAACAAC	59.098	40.000	0.00	0.00	0.00	3.32
2047	2114	9.716507	CCAGTACAATACATATAACAGTTTTGC	57.283	33.333	0.00	0.00	32.32	3.68
2049	2116	8.899771	GCCCAGTACAATACATATAACAGTTTT	58.100	33.333	0.00	0.00	0.00	2.43
2050	2117	8.050325	TGCCCAGTACAATACATATAACAGTTT	58.950	33.333	0.00	0.00	0.00	2.66
2051	2118	7.570132	TGCCCAGTACAATACATATAACAGTT	58.430	34.615	0.00	0.00	0.00	3.16
2052	2119	7.131907	TGCCCAGTACAATACATATAACAGT	57.868	36.000	0.00	0.00	0.00	3.55
2053	2120	7.497579	TGTTGCCCAGTACAATACATATAACAG	59.502	37.037	0.00	0.00	0.00	3.16
2054	2121	7.339482	TGTTGCCCAGTACAATACATATAACA	58.661	34.615	0.00	0.00	0.00	2.41
2055	2122	7.795482	TGTTGCCCAGTACAATACATATAAC	57.205	36.000	0.00	0.00	0.00	1.89
2073	2140	6.165577	ACATGAATTAATCCAACTTGTTGCC	58.834	36.000	0.00	0.00	0.00	4.52
2647	2731	2.416260	GTCCGGCGATCCTACCAC	59.584	66.667	9.30	0.00	0.00	4.16
2648	2732	2.836360	GGTCCGGCGATCCTACCA	60.836	66.667	9.30	0.00	36.56	3.25
2649	2733	2.521224	AGGTCCGGCGATCCTACC	60.521	66.667	18.10	12.42	36.71	3.18
2650	2734	1.389609	TTCAGGTCCGGCGATCCTAC	61.390	60.000	18.85	5.41	0.00	3.18
2651	2735	1.076559	TTCAGGTCCGGCGATCCTA	60.077	57.895	18.85	5.82	0.00	2.94
2652	2736	2.363795	TTCAGGTCCGGCGATCCT	60.364	61.111	9.30	12.93	0.00	3.24
2653	2737	1.956629	TTCTTCAGGTCCGGCGATCC	61.957	60.000	9.30	10.54	0.00	3.36
2654	2738	0.528684	CTTCTTCAGGTCCGGCGATC	60.529	60.000	9.30	0.00	0.00	3.69
2655	2739	0.970937	TCTTCTTCAGGTCCGGCGAT	60.971	55.000	9.30	0.00	0.00	4.58
2656	2740	1.183030	TTCTTCTTCAGGTCCGGCGA	61.183	55.000	9.30	0.00	0.00	5.54
2657	2741	0.737715	CTTCTTCTTCAGGTCCGGCG	60.738	60.000	0.00	0.00	0.00	6.46
2721	2805	1.559682	GGTTGCCTCTTAGGACATGGA	59.440	52.381	0.00	0.00	37.67	3.41
2773	2858	2.214181	CTGTTCGTGGAGTCCTCGGG	62.214	65.000	28.14	14.91	40.35	5.14
2837	2922	2.115266	CTCCCCAAAACAGGCGGT	59.885	61.111	0.00	0.00	0.00	5.68

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.