AutoCloner

Multiple sequence alignment - TraesCS3A01G367700

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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	TraesCS3A01G367700	chr3A	100.000	4224	0	0	1	4224	616703493	616707716	0.000000e+00	7801
1	TraesCS3A01G367700	chr3A	94.156	770	42	3	1	769	509556506	509555739	0.000000e+00	1170
2	TraesCS3A01G367700	chr3A	96.354	192	4	3	627	817	616667169	616667358	3.170000e-81	313
3	TraesCS3A01G367700	chr3A	93.782	193	8	4	627	817	509560611	509560421	1.920000e-73	287
4	TraesCS3A01G367700	chr3D	96.292	3425	106	10	816	4224	474427569	474430988	0.000000e+00	5602
5	TraesCS3A01G367700	chr3B	94.160	3356	126	28	934	4224	630586751	630590101	0.000000e+00	5048
6	TraesCS3A01G367700	chr1D	94.110	815	45	3	1	814	66351637	66352449	0.000000e+00	1236
7	TraesCS3A01G367700	chr1D	92.708	192	11	3	627	817	66347517	66347706	1.500000e-69	274
8	TraesCS3A01G367700	chrUn	93.168	805	49	4	1	804	238513594	238512795	0.000000e+00	1177
9	TraesCS3A01G367700	chrUn	94.359	195	8	3	624	817	336880367	336880559	3.190000e-76	296
10	TraesCS3A01G367700	chr1B	93.971	763	44	2	1	762	62279677	62280438	0.000000e+00	1153
11	TraesCS3A01G367700	chr1B	95.361	194	7	2	626	817	62253895	62254088	1.480000e-79	307
12	TraesCS3A01G367700	chr6D	93.447	702	42	2	1	701	31713502	31714200	0.000000e+00	1038
13	TraesCS3A01G367700	chr7B	88.226	637	72	3	1	635	714610430	714611065	0.000000e+00	758
14	TraesCS3A01G367700	chr7B	84.965	705	99	7	1	701	714679931	714680632	0.000000e+00	708
15	TraesCS3A01G367700	chr7B	85.120	625	88	5	81	702	714671485	714672107	5.960000e-178	634
16	TraesCS3A01G367700	chr7B	74.560	625	146	12	18	635	125017925	125017307	1.160000e-65	261
17	TraesCS3A01G367700	chr7A	87.660	235	27	2	1	234	114108085	114107852	5.380000e-69	272

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	TraesCS3A01G367700	chr3A	616703493	616707716	4223	False	7801.0	7801	100.000	1	4224	1	chr3A.!!$F2	4223
1	TraesCS3A01G367700	chr3A	509555739	509560611	4872	True	728.5	1170	93.969	1	817	2	chr3A.!!$R1	816
2	TraesCS3A01G367700	chr3D	474427569	474430988	3419	False	5602.0	5602	96.292	816	4224	1	chr3D.!!$F1	3408
3	TraesCS3A01G367700	chr3B	630586751	630590101	3350	False	5048.0	5048	94.160	934	4224	1	chr3B.!!$F1	3290
4	TraesCS3A01G367700	chr1D	66347517	66352449	4932	False	755.0	1236	93.409	1	817	2	chr1D.!!$F1	816
5	TraesCS3A01G367700	chrUn	238512795	238513594	799	True	1177.0	1177	93.168	1	804	1	chrUn.!!$R1	803
6	TraesCS3A01G367700	chr1B	62279677	62280438	761	False	1153.0	1153	93.971	1	762	1	chr1B.!!$F2	761
7	TraesCS3A01G367700	chr6D	31713502	31714200	698	False	1038.0	1038	93.447	1	701	1	chr6D.!!$F1	700
8	TraesCS3A01G367700	chr7B	714610430	714611065	635	False	758.0	758	88.226	1	635	1	chr7B.!!$F1	634
9	TraesCS3A01G367700	chr7B	714679931	714680632	701	False	708.0	708	84.965	1	701	1	chr7B.!!$F3	700
10	TraesCS3A01G367700	chr7B	714671485	714672107	622	False	634.0	634	85.120	81	702	1	chr7B.!!$F2	621
11	TraesCS3A01G367700	chr7B	125017307	125017925	618	True	261.0	261	74.560	18	635	1	chr7B.!!$R1	617

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	Hairpin	End Stability	Orientation
809	4935	0.307760	GCCGCCCAGTTTATCAATCG	59.692	55.0	0.00	0.00	3.34	F
1751	5904	0.036858	GAGAGGCCGTTCTCAAAGCT	60.037	55.0	15.42	42.53	3.74	F
2222	6375	0.391661	CGTGCAGCCATAGTGGTCTT	60.392	55.0	0.00	40.46	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2303	6456	0.179073	ATCGCCCAAGAAGATCCACG	60.179	55.0	0.00	0.00	4.94	R
3182	7363	1.326328	TGAGGATCAGAGATCCAGCG	58.674	55.0	23.74	42.56	5.18	R
4186	8387	0.393267	CGTCCCGGCCCTTTTATTCA	60.393	55.0	0.00	0.00	2.57	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
128	4253	2.329379	GTCTCTCTTTACACCGCACTG	58.671	52.381	0.00	0.00	0.00	3.66
187	4312	0.388649	CTAGATGCCCGGATACACGC	60.389	60.000	0.73	0.00	0.00	5.34
234	4359	8.951243	CATGTATCTTGGAGATAATCTCGTCTA	58.049	37.037	0.00	0.00	44.28	2.59
433	4559	2.932187	GCTAACCCGGTACAACATCGTT	60.932	50.000	0.00	0.00	0.00	3.85
517	4643	2.542178	CGTGTTCTTCATGTTCCGTCAA	59.458	45.455	0.00	0.00	0.00	3.18
546	4672	2.198827	TTGCGGACATCTTCACCAAT	57.801	45.000	0.00	0.00	0.00	3.16
577	4703	1.734465	CAGCTCTCTTCCGCGATTTTT	59.266	47.619	8.23	0.00	0.00	1.94
586	4712	0.596082	CCGCGATTTTTGGTCCAGTT	59.404	50.000	8.23	0.00	0.00	3.16
591	4717	3.489416	GCGATTTTTGGTCCAGTTTTCAC	59.511	43.478	0.00	0.00	0.00	3.18
598	4724	1.597663	GGTCCAGTTTTCACGTCACTG	59.402	52.381	6.70	6.70	38.14	3.66
809	4935	0.307760	GCCGCCCAGTTTATCAATCG	59.692	55.000	0.00	0.00	0.00	3.34
814	4940	3.245284	CGCCCAGTTTATCAATCGTACAG	59.755	47.826	0.00	0.00	0.00	2.74
820	4946	1.847818	TATCAATCGTACAGGTGCGC	58.152	50.000	0.00	0.00	38.56	6.09
878	5004	6.215121	TGCTCCTTGTTGTAATTTTCATGTG	58.785	36.000	0.00	0.00	0.00	3.21
883	5009	9.442047	TCCTTGTTGTAATTTTCATGTGTTTTT	57.558	25.926	0.00	0.00	0.00	1.94
990	5117	2.817834	GCATTGCCAGTCGCGGTA	60.818	61.111	6.13	0.00	42.08	4.02
1164	5317	4.257810	TCCACCACCCCTTCCGGA	62.258	66.667	0.00	0.00	0.00	5.14
1204	5357	2.125912	CCTCTTCGCCCACGTCTG	60.126	66.667	0.00	0.00	41.18	3.51
1442	5595	1.569479	GAAGCGCTCGGAAGCTGTTT	61.569	55.000	12.06	0.00	46.91	2.83
1520	5673	1.630126	ATGCAGGGCTTGACGAGGAT	61.630	55.000	0.00	0.00	0.00	3.24
1538	5691	1.141858	GATAGCCTGGGGTTCTTCCTG	59.858	57.143	0.00	0.00	36.25	3.86
1628	5781	1.680735	CTCTCCGATCTTGTCTCTGGG	59.319	57.143	0.00	0.00	0.00	4.45
1649	5802	1.696063	GCCAGGTCCATGCATATGTT	58.304	50.000	0.00	0.00	32.21	2.71
1652	5805	2.620115	CCAGGTCCATGCATATGTTGTC	59.380	50.000	0.00	0.00	32.21	3.18
1712	5865	1.353103	GGCTCACATGTACATGCGC	59.647	57.895	31.19	27.80	42.39	6.09
1751	5904	0.036858	GAGAGGCCGTTCTCAAAGCT	60.037	55.000	15.42	0.00	42.53	3.74
1831	5984	2.172293	GAGATTCTGAGGGAGCATTGGT	59.828	50.000	0.00	0.00	0.00	3.67
1838	5991	3.620488	TGAGGGAGCATTGGTGTATTTC	58.380	45.455	0.00	0.00	0.00	2.17
1901	6054	6.700081	TCACATTCGTCAGTATTATTACCTGC	59.300	38.462	0.00	0.00	0.00	4.85
1910	6063	5.694006	CAGTATTATTACCTGCTGCTCAGAC	59.306	44.000	0.00	0.00	45.72	3.51
2222	6375	0.391661	CGTGCAGCCATAGTGGTCTT	60.392	55.000	0.00	0.00	40.46	3.01
2271	6424	6.100279	TGAGCTTATGACCAAGACTTATGGAT	59.900	38.462	0.00	0.00	40.56	3.41
2356	6509	1.487976	TGAAGCAGAGGCCCTTATCTG	59.512	52.381	13.99	13.99	44.70	2.90
2357	6510	1.488393	GAAGCAGAGGCCCTTATCTGT	59.512	52.381	18.16	2.74	43.94	3.41
2486	6639	1.266178	TTGACCCTCGAGATTCTGCA	58.734	50.000	15.71	0.14	0.00	4.41
2552	6705	2.102252	GGGAGATGTCAGTGAGCTAAGG	59.898	54.545	0.00	0.00	0.00	2.69
2588	6741	2.150397	AGAACGTGAGAAAGGAACCG	57.850	50.000	0.00	0.00	0.00	4.44
2838	6991	5.888982	TCTGAGTTTACCTGAAGGAGTTT	57.111	39.130	2.62	0.00	38.94	2.66
3182	7363	9.178758	ACCTGTACTCTGGAAATCATAAAATTC	57.821	33.333	7.04	0.00	36.65	2.17
3192	7373	7.080724	GGAAATCATAAAATTCGCTGGATCTC	58.919	38.462	0.00	0.00	0.00	2.75
3208	7389	6.941436	GCTGGATCTCTGATCCTCAAAAATAT	59.059	38.462	22.36	0.00	38.95	1.28
3256	7439	7.989826	ACAAATCATTGCCTTCTATAAGTGAC	58.010	34.615	0.00	0.00	40.34	3.67
3272	7455	4.002906	AGTGACGGACTAGCATTTTTCA	57.997	40.909	0.00	0.00	30.86	2.69
3330	7524	6.544038	TGATATGAATATTTGTGGACAGCG	57.456	37.500	0.00	0.00	0.00	5.18
3401	7595	4.916041	TGTCCCATCTTTCATCTCTTGT	57.084	40.909	0.00	0.00	0.00	3.16
3469	7668	5.220931	GGTCATAAAGCTGGATCATGTGTTC	60.221	44.000	0.00	0.00	0.00	3.18
3695	7896	4.284550	GCCAGGGTCCACAGGCAA	62.285	66.667	12.21	0.00	46.26	4.52
3731	7932	7.123997	TGCATTGTACAATAGTCCCATTGAATT	59.876	33.333	20.39	0.00	38.01	2.17
3800	8001	6.089954	GCTGTGCTTGGTTTTGAATAAGATTC	59.910	38.462	0.00	0.00	0.00	2.52
3863	8064	5.752472	TGTACAAATTGACAGCATTGTTTGG	59.248	36.000	0.00	0.00	37.76	3.28
3911	8112	3.508793	CCTCTTGTTGCTCATCCATTTGT	59.491	43.478	0.00	0.00	0.00	2.83
3958	8159	4.578105	GCTGAAAGGTTATTATGCTGCTCT	59.422	41.667	0.00	0.00	0.00	4.09
3959	8160	5.067023	GCTGAAAGGTTATTATGCTGCTCTT	59.933	40.000	0.00	0.00	0.00	2.85
3999	8200	3.073946	TGAGGGTTTCTTTACCTTGGGAG	59.926	47.826	0.00	0.00	38.30	4.30
4067	8268	5.635700	GTCTTCAGACACATTCAGGTTCTAC	59.364	44.000	1.86	0.00	44.18	2.59
4111	8312	5.534278	TGCCAGATTTTTGTGTCAAGTCATA	59.466	36.000	0.00	0.00	0.00	2.15
4149	8350	2.125512	CCGTGCTTCTAAGGCGCT	60.126	61.111	7.64	0.00	37.96	5.92
4186	8387	0.538516	TTTGGCCTGGCACAATACGT	60.539	50.000	22.05	0.00	38.70	3.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
128	4253	2.159085	AGGCGGTAAGAGAATGTGTAGC	60.159	50.000	0.00	0.00	0.00	3.58
170	4295	2.421739	GCGTGTATCCGGGCATCT	59.578	61.111	0.00	0.00	0.00	2.90
187	4312	0.676782	AAAATCCCGAAGTGGAGCGG	60.677	55.000	0.00	0.00	46.80	5.52
322	4448	3.119388	TCCTGTAATAACTGACGAACCCG	60.119	47.826	0.00	0.00	42.50	5.28
433	4559	4.796830	GTCTAACTCGATATGTTTCGTGCA	59.203	41.667	0.00	0.00	40.03	4.57
517	4643	0.899717	ATGTCCGCAAATTGCAGGGT	60.900	50.000	18.65	7.40	45.36	4.34
546	4672	3.514309	GGAAGAGAGCTGTAGGTAAACCA	59.486	47.826	0.00	0.00	38.89	3.67
577	4703	1.208535	AGTGACGTGAAAACTGGACCA	59.791	47.619	0.00	0.00	0.00	4.02
710	4836	9.396022	CAGAGTTTGGTATAAATACAATGAGGT	57.604	33.333	2.74	0.00	34.98	3.85
711	4837	9.396022	ACAGAGTTTGGTATAAATACAATGAGG	57.604	33.333	2.74	0.00	34.98	3.86
792	4918	3.191669	TGTACGATTGATAAACTGGGCG	58.808	45.455	0.00	0.00	0.00	6.13
878	5004	8.627487	TCAACAATACAAGACATGTCAAAAAC	57.373	30.769	27.02	0.00	42.70	2.43
883	5009	7.800155	TCTTTCAACAATACAAGACATGTCA	57.200	32.000	27.02	7.35	42.70	3.58
913	5039	7.344352	AGCAATAGGCCTTGGATTTGTATAAAA	59.656	33.333	12.58	0.00	46.50	1.52
990	5117	0.975887	AGCATGGCGAATTTGGGTTT	59.024	45.000	0.00	0.00	0.00	3.27
1343	5496	2.941453	TCGGAATTCTCTCGAACAGG	57.059	50.000	5.23	0.00	30.67	4.00
1366	5519	1.414550	TGTTCCAGGACATGACGTTCA	59.585	47.619	0.00	0.00	0.00	3.18
1442	5595	1.375396	CCTCGTGGGCATTTCGTCA	60.375	57.895	0.00	0.00	0.00	4.35
1520	5673	0.914417	CCAGGAAGAACCCCAGGCTA	60.914	60.000	0.00	0.00	40.05	3.93
1538	5691	4.883354	CCCTCCCTTCGCATGGCC	62.883	72.222	0.00	0.00	0.00	5.36
1628	5781	1.601759	ATATGCATGGACCTGGCGC	60.602	57.895	10.16	0.00	0.00	6.53
1649	5802	0.766288	TGTCCATCCCACACCTGACA	60.766	55.000	0.00	0.00	0.00	3.58
1652	5805	1.004628	TCAATGTCCATCCCACACCTG	59.995	52.381	0.00	0.00	0.00	4.00
1712	5865	1.521450	CTTCTGCAAGGCACCCACAG	61.521	60.000	0.00	0.00	33.79	3.66
1751	5904	5.362717	TGACACAACTGTAAGAGAAGGAAGA	59.637	40.000	0.00	0.00	37.43	2.87
1814	5967	1.067295	ACACCAATGCTCCCTCAGAA	58.933	50.000	0.00	0.00	0.00	3.02
1817	5970	3.266772	AGAAATACACCAATGCTCCCTCA	59.733	43.478	0.00	0.00	0.00	3.86
1831	5984	7.862274	ATACCTCTCATCATGGAGAAATACA	57.138	36.000	5.05	0.00	42.99	2.29
1838	5991	3.558746	GCCCAATACCTCTCATCATGGAG	60.559	52.174	0.00	0.00	36.21	3.86
1886	6039	5.694006	GTCTGAGCAGCAGGTAATAATACTG	59.306	44.000	6.74	0.00	44.98	2.74
2190	6343	2.132300	TGCACGCATATAGCAGGGA	58.868	52.632	0.00	0.00	46.13	4.20
2222	6375	5.505181	AGAACTCCAAGCCTTCATCTTTA	57.495	39.130	0.00	0.00	0.00	1.85
2271	6424	2.953020	GTGTTTCACACTTGGTTGCAA	58.047	42.857	0.00	0.00	45.27	4.08
2303	6456	0.179073	ATCGCCCAAGAAGATCCACG	60.179	55.000	0.00	0.00	0.00	4.94
2356	6509	1.135972	CAGCACGTACAGGCATTGAAC	60.136	52.381	8.29	0.00	0.00	3.18
2357	6510	1.155889	CAGCACGTACAGGCATTGAA	58.844	50.000	8.29	0.00	0.00	2.69
2486	6639	8.993121	CGAATATTTGATAGCAGAACATAAGGT	58.007	33.333	0.00	0.00	0.00	3.50
2552	6705	4.515567	ACGTTCTTCTCCCTCATGTTTTTC	59.484	41.667	0.00	0.00	0.00	2.29
2588	6741	1.901085	CTCTACCCAGCTGACACCC	59.099	63.158	17.39	0.00	0.00	4.61
2822	6975	5.718130	TCGGATAGAAACTCCTTCAGGTAAA	59.282	40.000	0.00	0.00	36.40	2.01
2838	6991	9.011095	ACGTAGATTCTTCATTATTCGGATAGA	57.989	33.333	0.00	0.00	0.00	1.98
2915	7068	2.095461	TCTCTGACCACAATCTCTCGG	58.905	52.381	0.00	0.00	0.00	4.63
3071	7224	3.857157	AGACCAAAACCTGCTGACTTA	57.143	42.857	0.00	0.00	0.00	2.24
3182	7363	1.326328	TGAGGATCAGAGATCCAGCG	58.674	55.000	23.74	0.00	42.56	5.18
3256	7439	6.910536	ATTCTACTGAAAAATGCTAGTCCG	57.089	37.500	0.00	0.00	35.63	4.79
3330	7524	8.084684	AGAGAAAACCAAATCTTGTATTTCAGC	58.915	33.333	12.64	7.34	36.55	4.26
3469	7668	1.614824	AGAACCTCCAGGCTCCAGG	60.615	63.158	6.70	6.70	39.32	4.45
3721	7922	5.178996	TCAATGCAAAACGAAATTCAATGGG	59.821	36.000	0.00	0.00	0.00	4.00
3731	7932	9.443283	CCAAAATTAATTTCAATGCAAAACGAA	57.557	25.926	13.68	0.00	0.00	3.85
3863	8064	3.935828	CAGAAAGAAACCCGAGGAATCTC	59.064	47.826	0.00	0.00	36.69	2.75
3911	8112	6.405065	GCATAATTGCCAGTGAATCAAGAGAA	60.405	38.462	0.00	0.00	43.38	2.87
3937	8138	7.466746	AAAAGAGCAGCATAATAACCTTTCA	57.533	32.000	0.00	0.00	0.00	2.69
3972	8173	5.130350	CAAGGTAAAGAAACCCTCACAAGA	58.870	41.667	0.00	0.00	40.71	3.02
3999	8200	1.497722	CTTCTTTCAACGAGCCCGC	59.502	57.895	0.00	0.00	39.95	6.13
4056	8257	2.039879	GGGCCAAAGAGTAGAACCTGAA	59.960	50.000	4.39	0.00	0.00	3.02
4067	8268	1.805254	CAATCTGCGGGCCAAAGAG	59.195	57.895	4.39	0.00	0.00	2.85
4186	8387	0.393267	CGTCCCGGCCCTTTTATTCA	60.393	55.000	0.00	0.00	0.00	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.