AutoCloner

Multiple sequence alignment - TraesCS1D01G316700

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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	TraesCS1D01G316700	chr1D	100.000	2731	0	0	1	2731	411743427	411746157	0.000000e+00	5044
1	TraesCS1D01G316700	chr1D	90.969	1982	126	22	2	1971	411700287	411702227	0.000000e+00	2619
2	TraesCS1D01G316700	chr1D	91.349	1653	117	13	533	2179	411694488	411696120	0.000000e+00	2237
3	TraesCS1D01G316700	chr1D	87.605	476	36	4	2278	2731	411696135	411696609	5.180000e-147	531
4	TraesCS1D01G316700	chr1B	88.439	2768	242	27	2	2731	555059538	555062265	0.000000e+00	3267
5	TraesCS1D01G316700	chr1B	88.395	2766	244	31	4	2731	555064898	555067624	0.000000e+00	3258
6	TraesCS1D01G316700	chr1B	88.299	2769	243	36	2	2731	555011615	555014341	0.000000e+00	3243
7	TraesCS1D01G316700	chr1B	88.263	2769	236	31	2	2731	555070249	555072967	0.000000e+00	3230
8	TraesCS1D01G316700	chr1B	89.394	2574	217	25	2	2558	555075592	555078126	0.000000e+00	3190
9	TraesCS1D01G316700	chr1B	89.239	2574	221	26	2	2558	555016968	555019502	0.000000e+00	3168
10	TraesCS1D01G316700	chr1B	87.738	2520	251	29	2	2517	555031181	555033646	0.000000e+00	2889
11	TraesCS1D01G316700	chr1B	88.906	1938	161	14	828	2729	555057027	555058946	0.000000e+00	2338
12	TraesCS1D01G316700	chr1B	87.326	1649	156	11	1115	2729	555004090	555005719	0.000000e+00	1838
13	TraesCS1D01G316700	chr1B	85.185	972	105	12	1798	2731	555008014	555008984	0.000000e+00	961
14	TraesCS1D01G316700	chr1A	89.168	1994	172	19	2	1984	508314697	508316657	0.000000e+00	2446
15	TraesCS1D01G316700	chr1A	89.034	1997	171	21	2	1984	508282573	508284535	0.000000e+00	2431
16	TraesCS1D01G316700	chr1A	87.738	1998	178	25	2	1970	508213298	508215257	0.000000e+00	2270
17	TraesCS1D01G316700	chr1A	89.249	1265	118	9	2	1260	508182211	508183463	0.000000e+00	1567
18	TraesCS1D01G316700	chr1A	86.083	1509	145	20	1252	2731	508205748	508207220	0.000000e+00	1563
19	TraesCS1D01G316700	chr1A	90.190	897	81	6	2	897	508160412	508161302	0.000000e+00	1162
20	TraesCS1D01G316700	chr1A	88.299	923	102	5	2	923	508335994	508336911	0.000000e+00	1101
21	TraesCS1D01G316700	chr1A	88.191	923	103	5	2	923	508277070	508277987	0.000000e+00	1096
22	TraesCS1D01G316700	chr1A	88.191	923	103	5	2	923	508304099	508305016	0.000000e+00	1096
23	TraesCS1D01G316700	chrUn	88.047	594	47	3	2160	2731	423066746	423066155	0.000000e+00	682
24	TraesCS1D01G316700	chrUn	91.429	105	9	0	2627	2731	11273030	11272926	7.880000e-31	145

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	TraesCS1D01G316700	chr1D	411743427	411746157	2730	False	5044.000000	5044	100.000000	1	2731	1	chr1D.!!$F1	2730
1	TraesCS1D01G316700	chr1D	411694488	411702227	7739	False	1795.666667	2619	89.974333	2	2731	3	chr1D.!!$F2	2729
2	TraesCS1D01G316700	chr1B	555057027	555078126	21099	False	3056.600000	3267	88.679400	2	2731	5	chr1B.!!$F3	2729
3	TraesCS1D01G316700	chr1B	555031181	555033646	2465	False	2889.000000	2889	87.738000	2	2517	1	chr1B.!!$F1	2515
4	TraesCS1D01G316700	chr1B	555004090	555019502	15412	False	2302.500000	3243	87.512250	2	2731	4	chr1B.!!$F2	2729
5	TraesCS1D01G316700	chr1A	508314697	508316657	1960	False	2446.000000	2446	89.168000	2	1984	1	chr1A.!!$F8	1982
6	TraesCS1D01G316700	chr1A	508282573	508284535	1962	False	2431.000000	2431	89.034000	2	1984	1	chr1A.!!$F6	1982
7	TraesCS1D01G316700	chr1A	508213298	508215257	1959	False	2270.000000	2270	87.738000	2	1970	1	chr1A.!!$F4	1968
8	TraesCS1D01G316700	chr1A	508182211	508183463	1252	False	1567.000000	1567	89.249000	2	1260	1	chr1A.!!$F2	1258
9	TraesCS1D01G316700	chr1A	508205748	508207220	1472	False	1563.000000	1563	86.083000	1252	2731	1	chr1A.!!$F3	1479
10	TraesCS1D01G316700	chr1A	508160412	508161302	890	False	1162.000000	1162	90.190000	2	897	1	chr1A.!!$F1	895
11	TraesCS1D01G316700	chr1A	508335994	508336911	917	False	1101.000000	1101	88.299000	2	923	1	chr1A.!!$F9	921
12	TraesCS1D01G316700	chr1A	508277070	508277987	917	False	1096.000000	1096	88.191000	2	923	1	chr1A.!!$F5	921
13	TraesCS1D01G316700	chr1A	508304099	508305016	917	False	1096.000000	1096	88.191000	2	923	1	chr1A.!!$F7	921
14	TraesCS1D01G316700	chrUn	423066155	423066746	591	True	682.000000	682	88.047000	2160	2731	1	chrUn.!!$R2	571

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
81	5986	0.324738	TGGATCTCTCCTTGCCGTCT	60.325	55.0	0.0	0.0	42.59	4.18	F
1362	17987	0.250467	GACTCCTGCAACAGCTCCAA	60.250	55.0	0.0	0.0	0.00	3.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1555	23534	0.248743	TCGTGGCCGAGCTTAATACG	60.249	55.0	0.00	0.0	38.40	3.06	R
2572	35299	0.249073	GACACCGCGATGCTGTATCT	60.249	55.0	8.23	0.0	33.44	1.98	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
81	5986	0.324738	TGGATCTCTCCTTGCCGTCT	60.325	55.000	0.00	0.00	42.59	4.18
186	6091	1.192428	GTGACGGTGGGTATTCCTCT	58.808	55.000	0.00	0.00	36.20	3.69
276	6182	4.505556	GCATTTTTAGCATTCTTGGCTAGC	59.494	41.667	6.04	6.04	44.03	3.42
297	6203	9.204570	GCTAGCATTACCGATTTTCTTTAGATA	57.795	33.333	10.63	0.00	0.00	1.98
328	6245	3.330701	AGGTTCTCCTCAATGCCTTGTAA	59.669	43.478	1.49	0.00	40.58	2.41
343	6260	4.379082	GCCTTGTAACGGGTCATTTTGTAG	60.379	45.833	0.00	0.00	0.00	2.74
347	6264	3.495434	AACGGGTCATTTTGTAGTGGA	57.505	42.857	0.00	0.00	0.00	4.02
364	6281	3.075884	GTGGATTGGTTGTTTACGCCTA	58.924	45.455	0.00	0.00	0.00	3.93
369	6286	5.761234	GGATTGGTTGTTTACGCCTATATCA	59.239	40.000	0.00	0.00	0.00	2.15
375	6292	9.175312	TGGTTGTTTACGCCTATATCAATAAAA	57.825	29.630	0.00	0.00	0.00	1.52
380	6297	8.843262	GTTTACGCCTATATCAATAAAAAGGGT	58.157	33.333	0.00	0.00	0.00	4.34
486	6411	3.417069	TGACCAAATCAGTCGACCAAT	57.583	42.857	13.01	2.92	37.04	3.16
521	6446	5.190677	CCCTTCTTGTATTTGTTATCCCGT	58.809	41.667	0.00	0.00	0.00	5.28
525	6450	7.120726	CCTTCTTGTATTTGTTATCCCGTCTTT	59.879	37.037	0.00	0.00	0.00	2.52
656	6608	2.235155	TGTGGTAGGAATATGCACACGT	59.765	45.455	0.00	0.00	0.00	4.49
1052	12316	3.134458	GCAACTTCCTTGGATCCTATCG	58.866	50.000	14.23	0.00	0.00	2.92
1058	12322	7.374975	ACTTCCTTGGATCCTATCGAATTTA	57.625	36.000	14.23	0.00	0.00	1.40
1225	17850	3.640407	CCGGCCGGATCATGGGAT	61.640	66.667	41.82	0.00	37.50	3.85
1362	17987	0.250467	GACTCCTGCAACAGCTCCAA	60.250	55.000	0.00	0.00	0.00	3.53
1414	18039	1.078497	CGTCCCACTTGCAGCCATA	60.078	57.895	0.00	0.00	0.00	2.74
1692	34376	0.231279	TTTTCTTCTTGACGCGTCGC	59.769	50.000	31.88	12.97	0.00	5.19
1791	34475	7.865706	ATCTTCTTGCAAAACCGAACTATAT	57.134	32.000	0.00	0.00	0.00	0.86
1792	34476	8.958119	ATCTTCTTGCAAAACCGAACTATATA	57.042	30.769	0.00	0.00	0.00	0.86
1834	34518	7.341769	TCATGTAATAAATAAAGGGCAGTGCTT	59.658	33.333	16.11	4.07	0.00	3.91
1840	34524	2.934363	AAAGGGCAGTGCTTGGTGCT	62.934	55.000	16.11	0.00	43.37	4.40
1847	34531	3.555324	TGCTTGGTGCTGGTCGGA	61.555	61.111	0.00	0.00	43.37	4.55
1921	34605	1.159285	CGTCTGATTTGGCTGCTCAA	58.841	50.000	0.00	0.00	0.00	3.02
1937	34621	1.192146	TCAACTCCTTCCTCCCCACG	61.192	60.000	0.00	0.00	0.00	4.94
1938	34622	1.918800	AACTCCTTCCTCCCCACGG	60.919	63.158	0.00	0.00	0.00	4.94
1971	34655	2.160171	CCCAACACCCTTCCCCTCA	61.160	63.158	0.00	0.00	0.00	3.86
1972	34656	1.074951	CCAACACCCTTCCCCTCAC	59.925	63.158	0.00	0.00	0.00	3.51
2006	34705	3.200593	GCAGCATCGCACCTCCTG	61.201	66.667	0.00	0.00	0.00	3.86
2010	34709	2.887568	CATCGCACCTCCTGTCGC	60.888	66.667	0.00	0.00	0.00	5.19
2011	34710	4.148825	ATCGCACCTCCTGTCGCC	62.149	66.667	0.00	0.00	0.00	5.54
2033	34732	2.687200	TCCCTAGCACCGTGCCAT	60.687	61.111	19.96	5.18	46.52	4.40
2036	34735	3.204827	CTAGCACCGTGCCATGCC	61.205	66.667	19.96	0.00	46.52	4.40
2043	34742	4.758251	CGTGCCATGCCGGTGAGA	62.758	66.667	1.90	0.00	36.97	3.27
2047	34746	3.274586	CCATGCCGGTGAGATGCG	61.275	66.667	1.90	0.00	0.00	4.73
2058	34757	1.532868	GTGAGATGCGGTATCAATGGC	59.467	52.381	8.78	0.00	38.31	4.40
2061	34760	2.481952	GAGATGCGGTATCAATGGCTTC	59.518	50.000	8.78	0.00	38.31	3.86
2062	34761	1.537202	GATGCGGTATCAATGGCTTCC	59.463	52.381	0.89	0.00	35.78	3.46
2090	34789	1.733912	TGATGCTCGCAATTGACACTC	59.266	47.619	10.34	0.00	0.00	3.51
2101	34800	3.944055	ATTGACACTCGCACTAGTTCT	57.056	42.857	0.00	0.00	0.00	3.01
2106	34805	2.162608	ACACTCGCACTAGTTCTAGCAG	59.837	50.000	6.75	0.00	0.00	4.24
2118	34817	7.551262	CACTAGTTCTAGCAGAAACTCTCTCTA	59.449	40.741	6.75	0.00	35.75	2.43
2181	34880	2.407616	CGGTGCTCATCGTCGCTA	59.592	61.111	0.00	0.00	0.00	4.26
2200	34899	5.105513	TCGCTAATTCCAACATCTACAGTCA	60.106	40.000	0.00	0.00	0.00	3.41
2249	34948	1.610624	CCAGCAAAAGGACTTCGCCTA	60.611	52.381	0.00	0.00	37.26	3.93
2324	35023	2.424557	ACTCTGATGACTGCTTGCAAG	58.575	47.619	22.44	22.44	0.00	4.01
2325	35024	2.224475	ACTCTGATGACTGCTTGCAAGT	60.224	45.455	26.55	8.92	0.00	3.16
2344	35043	4.688770	TTTTTGCCAACGGGTCCT	57.311	50.000	0.00	0.00	36.17	3.85
2472	35177	1.076559	CTGCCCCATTCCAGCATCA	60.077	57.895	0.00	0.00	35.64	3.07
2533	35238	1.523032	CTATTGCCGTCGGGTTCCC	60.523	63.158	14.38	0.00	34.97	3.97
2572	35299	1.607178	CCAGCAAGAACCATGGCCA	60.607	57.895	13.04	8.56	0.00	5.36
2576	35303	1.565759	AGCAAGAACCATGGCCAGATA	59.434	47.619	13.05	0.00	0.00	1.98
2619	35346	0.593128	GCTTTTCTCTTTGGCGAGCA	59.407	50.000	0.00	0.00	0.00	4.26
2635	35362	1.137086	GAGCATAGCTTTCCTCCGTCA	59.863	52.381	0.00	0.00	39.88	4.35
2636	35363	1.555075	AGCATAGCTTTCCTCCGTCAA	59.445	47.619	0.00	0.00	33.89	3.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	5971	2.093106	GAGTTAGACGGCAAGGAGAGA	58.907	52.381	0.00	0.00	0.00	3.10
81	5986	6.697641	ATAAAGGTTTCACCCTGAGAGTTA	57.302	37.500	0.00	0.00	39.75	2.24
171	6076	0.251916	TGCAAGAGGAATACCCACCG	59.748	55.000	0.00	0.00	37.41	4.94
179	6084	0.032813	CACCCCCATGCAAGAGGAAT	60.033	55.000	5.16	0.00	0.00	3.01
186	6091	1.535202	GAAACCCACCCCCATGCAA	60.535	57.895	0.00	0.00	0.00	4.08
328	6245	3.713826	ATCCACTACAAAATGACCCGT	57.286	42.857	0.00	0.00	0.00	5.28
343	6260	1.883926	AGGCGTAAACAACCAATCCAC	59.116	47.619	0.00	0.00	0.00	4.02
347	6264	7.817418	ATTGATATAGGCGTAAACAACCAAT	57.183	32.000	0.00	0.00	0.00	3.16
364	6281	8.815912	ACAAGCTTTCACCCTTTTTATTGATAT	58.184	29.630	0.00	0.00	0.00	1.63
369	6286	6.478673	CGAAACAAGCTTTCACCCTTTTTATT	59.521	34.615	0.00	0.00	0.00	1.40
375	6292	2.618709	CTCGAAACAAGCTTTCACCCTT	59.381	45.455	0.00	0.00	0.00	3.95
380	6297	4.038042	TCTCTCTCTCGAAACAAGCTTTCA	59.962	41.667	0.00	0.00	0.00	2.69
486	6411	7.685849	AATACAAGAAGGGTAGTAATAGGCA	57.314	36.000	0.00	0.00	0.00	4.75
656	6608	2.623535	AGTTATGAACGTATTGGCGCA	58.376	42.857	10.83	0.00	36.23	6.09
822	6782	3.425713	CGTGCATGCTTGGCTCGT	61.426	61.111	20.33	0.00	41.66	4.18
1058	12322	5.768164	GGAGCTAGAAGTTAGCACTAGAGAT	59.232	44.000	8.69	0.00	42.68	2.75
1225	17850	0.685097	GGGTGTAGTTGGTCTGCAGA	59.315	55.000	13.74	13.74	39.29	4.26
1255	17880	3.677976	CGCCGATGGTAAACCTAGTTCTT	60.678	47.826	0.02	0.00	36.82	2.52
1288	17913	3.873801	GCATGGTGGTGGAGTACTGAAAT	60.874	47.826	0.00	0.00	0.00	2.17
1362	17987	4.446413	GGAACGTCGCGATGGGGT	62.446	66.667	30.24	16.13	0.00	4.95
1414	18039	0.683504	AGATGAAGTACCGCGTCCCT	60.684	55.000	4.92	0.00	0.00	4.20
1470	23449	2.727777	TCGACTTCACGTTGACTTGAG	58.272	47.619	0.00	0.00	30.94	3.02
1495	23474	1.300311	CCGTTGTACTGTCCGCACA	60.300	57.895	0.00	0.00	0.00	4.57
1555	23534	0.248743	TCGTGGCCGAGCTTAATACG	60.249	55.000	0.00	0.00	38.40	3.06
1584	23563	1.812922	GCCACCGCAGACTGATCAG	60.813	63.158	21.37	21.37	34.03	2.90
1605	23584	0.320697	GACAACGGCCAGACCTAGTT	59.679	55.000	2.24	0.00	35.61	2.24
1813	34497	5.955355	ACCAAGCACTGCCCTTTATTTATTA	59.045	36.000	0.00	0.00	0.00	0.98
1840	34524	2.700407	AAATTTGGGCCGTCCGACCA	62.700	55.000	0.00	0.00	38.76	4.02
1847	34531	2.329614	CGACCGAAATTTGGGCCGT	61.330	57.895	17.60	0.52	0.00	5.68
1878	34562	2.789917	GCAGCTTGCATCTGACGG	59.210	61.111	17.55	0.00	44.26	4.79
1921	34605	2.284699	CCGTGGGGAGGAAGGAGT	60.285	66.667	0.00	0.00	34.06	3.85
1989	34688	3.200593	CAGGAGGTGCGATGCTGC	61.201	66.667	0.00	0.00	29.03	5.25
1992	34691	2.887568	CGACAGGAGGTGCGATGC	60.888	66.667	0.00	0.00	0.00	3.91
2028	34727	2.124612	CATCTCACCGGCATGGCA	60.125	61.111	20.37	0.00	43.94	4.92
2036	34735	1.794701	CATTGATACCGCATCTCACCG	59.205	52.381	0.00	0.00	34.46	4.94
2039	34738	1.417517	AGCCATTGATACCGCATCTCA	59.582	47.619	0.00	0.00	34.46	3.27
2043	34742	1.609208	GGAAGCCATTGATACCGCAT	58.391	50.000	0.00	0.00	0.00	4.73
2068	34767	0.448990	TGTCAATTGCGAGCATCAGC	59.551	50.000	0.00	0.00	42.56	4.26
2074	34773	1.225854	GCGAGTGTCAATTGCGAGC	60.226	57.895	0.00	0.00	0.00	5.03
2083	34782	2.161808	GCTAGAACTAGTGCGAGTGTCA	59.838	50.000	12.15	0.00	35.65	3.58
2090	34789	3.839293	AGTTTCTGCTAGAACTAGTGCG	58.161	45.455	0.00	0.00	33.26	5.34
2101	34800	5.571285	TGGAACTAGAGAGAGTTTCTGCTA	58.429	41.667	0.00	0.00	39.79	3.49
2106	34805	4.792521	TGCTGGAACTAGAGAGAGTTTC	57.207	45.455	0.00	0.00	39.79	2.78
2118	34817	0.108992	CGCATGCAAATGCTGGAACT	60.109	50.000	19.57	0.00	44.90	3.01
2173	34872	3.520290	AGATGTTGGAATTAGCGACGA	57.480	42.857	0.00	0.00	0.00	4.20
2181	34880	5.221925	ACCAGTGACTGTAGATGTTGGAATT	60.222	40.000	12.15	0.00	0.00	2.17
2249	34948	4.096003	CTGGAACGGACGGGCCAT	62.096	66.667	4.39	0.00	36.31	4.40
2298	34997	4.501229	GCAAGCAGTCATCAGAGTAGCTAT	60.501	45.833	0.00	0.00	33.43	2.97
2362	35061	1.024271	GAATGGCGGCATGCTTCTAA	58.976	50.000	26.50	0.16	45.43	2.10
2533	35238	3.129502	CAGCTGTGGTGCATCCCG	61.130	66.667	5.25	0.00	34.77	5.14
2561	35288	1.312815	GCTGTATCTGGCCATGGTTC	58.687	55.000	14.67	6.95	0.00	3.62
2572	35299	0.249073	GACACCGCGATGCTGTATCT	60.249	55.000	8.23	0.00	33.44	1.98
2576	35303	3.939837	CTGGACACCGCGATGCTGT	62.940	63.158	8.23	2.62	0.00	4.40
2593	35320	3.251004	CGCCAAAGAGAAAAGCTACAACT	59.749	43.478	0.00	0.00	0.00	3.16
2619	35346	5.501156	AGAAAATTGACGGAGGAAAGCTAT	58.499	37.500	0.00	0.00	0.00	2.97
2661	35388	8.951243	CCCTTTATAGCTGCTAAGATAAAATCC	58.049	37.037	14.13	0.00	0.00	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.