AutoCloner

Multiple sequence alignment - TraesCS1D01G221400

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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	TraesCS1D01G221400	chr1D	100.000	5291	0	0	1	5291	309077568	309082858	0.000000e+00	9771.0
1	TraesCS1D01G221400	chr1D	91.379	58	5	0	5214	5271	408239826	408239883	4.390000e-11	80.5
2	TraesCS1D01G221400	chr1A	97.792	4711	84	7	1	4710	388837841	388842532	0.000000e+00	8106.0
3	TraesCS1D01G221400	chr1A	94.203	483	28	0	4719	5201	388842740	388843222	0.000000e+00	737.0
4	TraesCS1D01G221400	chr1B	95.794	4636	145	22	99	4714	418809490	418814095	0.000000e+00	7435.0
5	TraesCS1D01G221400	chr1B	97.358	265	5	1	4709	4971	418814311	418814575	2.910000e-122	449.0
6	TraesCS1D01G221400	chr1B	93.981	216	11	1	5002	5217	418814575	418814788	5.110000e-85	326.0
7	TraesCS1D01G221400	chr1B	90.756	119	10	1	1	118	418809257	418809375	1.970000e-34	158.0
8	TraesCS1D01G221400	chr1B	91.379	58	5	0	5213	5270	53414837	53414894	4.390000e-11	80.5
9	TraesCS1D01G221400	chr2A	87.044	3396	425	11	916	4304	95991724	95995111	0.000000e+00	3819.0
10	TraesCS1D01G221400	chr2B	87.267	3330	414	7	978	4304	148237503	148240825	0.000000e+00	3792.0
11	TraesCS1D01G221400	chr3D	86.847	3368	426	14	944	4304	147817813	147821170	0.000000e+00	3749.0
12	TraesCS1D01G221400	chr3A	86.863	3357	423	15	956	4304	165420136	165416790	0.000000e+00	3740.0
13	TraesCS1D01G221400	chr2D	86.993	3329	424	6	978	4304	97220116	97223437	0.000000e+00	3740.0
14	TraesCS1D01G221400	chr3B	86.796	3355	427	13	956	4304	214563663	214560319	0.000000e+00	3727.0
15	TraesCS1D01G221400	chr5D	80.754	3315	584	35	993	4283	46319055	46322339	0.000000e+00	2538.0

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	TraesCS1D01G221400	chr1D	309077568	309082858	5290	False	9771.0	9771	100.00000	1	5291	1	chr1D.!!$F1	5290
1	TraesCS1D01G221400	chr1A	388837841	388843222	5381	False	4421.5	8106	95.99750	1	5201	2	chr1A.!!$F1	5200
2	TraesCS1D01G221400	chr1B	418809257	418814788	5531	False	2092.0	7435	94.47225	1	5217	4	chr1B.!!$F2	5216
3	TraesCS1D01G221400	chr2A	95991724	95995111	3387	False	3819.0	3819	87.04400	916	4304	1	chr2A.!!$F1	3388
4	TraesCS1D01G221400	chr2B	148237503	148240825	3322	False	3792.0	3792	87.26700	978	4304	1	chr2B.!!$F1	3326
5	TraesCS1D01G221400	chr3D	147817813	147821170	3357	False	3749.0	3749	86.84700	944	4304	1	chr3D.!!$F1	3360
6	TraesCS1D01G221400	chr3A	165416790	165420136	3346	True	3740.0	3740	86.86300	956	4304	1	chr3A.!!$R1	3348
7	TraesCS1D01G221400	chr2D	97220116	97223437	3321	False	3740.0	3740	86.99300	978	4304	1	chr2D.!!$F1	3326
8	TraesCS1D01G221400	chr3B	214560319	214563663	3344	True	3727.0	3727	86.79600	956	4304	1	chr3B.!!$R1	3348
9	TraesCS1D01G221400	chr5D	46319055	46322339	3284	False	2538.0	2538	80.75400	993	4283	1	chr5D.!!$F1	3290

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
43	44	2.953466	ACATGATTGTGGCATGCTTC	57.047	45.000	18.92	11.37	45.32	3.86	F
152	288	3.084039	TGATTGCTTTTCTTCGAGCCAT	58.916	40.909	0.00	0.00	38.11	4.40	F
1479	1636	1.072173	TCTAAGGCTGCTGCAAAGACA	59.928	47.619	17.89	0.00	41.91	3.41	F
1741	1898	2.028930	GTCAAGGACCTGAGGTACACAG	60.029	54.545	17.74	5.23	46.47	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1479	1636	1.822990	CATTGGAACTTCTGCATGCCT	59.177	47.619	16.68	0.0	0.00	4.75	R
1682	1839	3.361281	TGAGCTTTCTCATCTGCCATT	57.639	42.857	0.00	0.0	43.95	3.16	R
3898	4061	4.272504	ACGTGTTTGGCTATCATAATTCGG	59.727	41.667	0.00	0.0	0.00	4.30	R
4323	4489	2.030007	GCTGCAAACATGTAAGGCAAGA	60.030	45.455	16.57	0.0	33.58	3.02	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
43	44	2.953466	ACATGATTGTGGCATGCTTC	57.047	45.000	18.92	11.37	45.32	3.86
152	288	3.084039	TGATTGCTTTTCTTCGAGCCAT	58.916	40.909	0.00	0.00	38.11	4.40
572	717	6.459573	GCTCCAGTTGTTATTGTTCTTGTCAA	60.460	38.462	0.00	0.00	0.00	3.18
580	725	6.094742	TGTTATTGTTCTTGTCAAGTTGCTGA	59.905	34.615	12.30	0.00	0.00	4.26
581	726	4.355543	TTGTTCTTGTCAAGTTGCTGAC	57.644	40.909	12.30	0.00	45.01	3.51
582	727	3.609853	TGTTCTTGTCAAGTTGCTGACT	58.390	40.909	12.30	0.00	45.03	3.41
954	1107	8.690203	ATTCCGGAATAATGTACATGAAATCA	57.310	30.769	28.25	0.00	0.00	2.57
1423	1580	3.517100	TGATAGAGAAGTTGAGCAGGCTT	59.483	43.478	0.00	0.00	0.00	4.35
1479	1636	1.072173	TCTAAGGCTGCTGCAAAGACA	59.928	47.619	17.89	0.00	41.91	3.41
1682	1839	7.707624	ATCCTTTCTATGATGCTTTTGTTCA	57.292	32.000	0.00	0.00	0.00	3.18
1741	1898	2.028930	GTCAAGGACCTGAGGTACACAG	60.029	54.545	17.74	5.23	46.47	3.66
2169	2326	3.549794	GCTTCCCATGCTCACTATCTTT	58.450	45.455	0.00	0.00	0.00	2.52
3658	3815	4.773323	CTAAGGAAGGAAGGTTTTGCAG	57.227	45.455	0.00	0.00	0.00	4.41
3898	4061	1.251251	ATGCTTGAGGGTGCTTCAAC	58.749	50.000	0.00	0.00	31.66	3.18
4314	4480	3.695816	TCAGCTTCATCGATGTAAGTCG	58.304	45.455	24.09	18.00	42.74	4.18
4425	4591	1.334869	CACTGTTGTGGCCTGAAACTC	59.665	52.381	3.32	0.00	40.33	3.01
4506	4672	5.994668	TGTGTTTAGTCAGATTACATGCACA	59.005	36.000	0.00	0.00	0.00	4.57
4507	4673	6.654582	TGTGTTTAGTCAGATTACATGCACAT	59.345	34.615	0.00	0.00	0.00	3.21
4508	4674	6.963242	GTGTTTAGTCAGATTACATGCACATG	59.037	38.462	9.06	9.06	44.15	3.21
4509	4675	5.739752	TTAGTCAGATTACATGCACATGC	57.260	39.130	10.50	0.00	42.39	4.06
4578	4744	7.736447	AACCAAGTTCTAGAATGTTCAGAAG	57.264	36.000	8.75	0.00	30.61	2.85
4674	4841	1.196808	CGTGGCAATCCTGTGTGTTAC	59.803	52.381	0.00	0.00	0.00	2.50
4973	5562	3.515502	TCATGGGAGTGACTTCGAATTCT	59.484	43.478	15.49	4.54	0.00	2.40
4981	5570	4.563184	AGTGACTTCGAATTCTTCATACGC	59.437	41.667	15.49	0.00	0.00	4.42
5001	5590	2.843701	CAAGAACTGAGGAAGTGCAGT	58.156	47.619	0.00	0.00	46.59	4.40
5029	5618	5.065859	TGGGAAATTGTATCATACTTGCACG	59.934	40.000	0.00	0.00	0.00	5.34
5119	5708	5.499047	GTTTCCTGTGTTTAGACTTGAACG	58.501	41.667	0.00	0.00	0.00	3.95
5139	5728	2.727798	CGTACTGTTTAACCTCGTGTGG	59.272	50.000	0.00	0.00	0.00	4.17
5174	5763	0.036010	AGGTTGATGCGTGAGAAGGG	60.036	55.000	0.00	0.00	0.00	3.95
5217	5806	4.399618	TGTACAAGCTGATCCTGTCTACTC	59.600	45.833	0.00	0.00	0.00	2.59
5218	5807	3.707316	ACAAGCTGATCCTGTCTACTCT	58.293	45.455	0.00	0.00	0.00	3.24
5219	5808	3.699038	ACAAGCTGATCCTGTCTACTCTC	59.301	47.826	0.00	0.00	0.00	3.20
5220	5809	3.951563	AGCTGATCCTGTCTACTCTCT	57.048	47.619	0.00	0.00	0.00	3.10
5221	5810	3.820557	AGCTGATCCTGTCTACTCTCTC	58.179	50.000	0.00	0.00	0.00	3.20
5222	5811	2.884639	GCTGATCCTGTCTACTCTCTCC	59.115	54.545	0.00	0.00	0.00	3.71
5223	5812	3.138304	CTGATCCTGTCTACTCTCTCCG	58.862	54.545	0.00	0.00	0.00	4.63
5224	5813	2.506231	TGATCCTGTCTACTCTCTCCGT	59.494	50.000	0.00	0.00	0.00	4.69
5225	5814	3.054287	TGATCCTGTCTACTCTCTCCGTT	60.054	47.826	0.00	0.00	0.00	4.44
5226	5815	4.163649	TGATCCTGTCTACTCTCTCCGTTA	59.836	45.833	0.00	0.00	0.00	3.18
5227	5816	4.564782	TCCTGTCTACTCTCTCCGTTAA	57.435	45.455	0.00	0.00	0.00	2.01
5228	5817	4.914983	TCCTGTCTACTCTCTCCGTTAAA	58.085	43.478	0.00	0.00	0.00	1.52
5229	5818	5.319453	TCCTGTCTACTCTCTCCGTTAAAA	58.681	41.667	0.00	0.00	0.00	1.52
5230	5819	5.771666	TCCTGTCTACTCTCTCCGTTAAAAA	59.228	40.000	0.00	0.00	0.00	1.94
5280	5869	9.857957	AAGTTAGTATAAAGTTACTGTCAGCTC	57.142	33.333	0.00	0.00	34.35	4.09
5281	5870	9.021807	AGTTAGTATAAAGTTACTGTCAGCTCA	57.978	33.333	0.00	0.00	34.35	4.26
5282	5871	9.635520	GTTAGTATAAAGTTACTGTCAGCTCAA	57.364	33.333	0.00	0.00	34.35	3.02
5285	5874	9.726438	AGTATAAAGTTACTGTCAGCTCAAAAT	57.274	29.630	0.00	0.00	31.25	1.82
5286	5875	9.760660	GTATAAAGTTACTGTCAGCTCAAAATG	57.239	33.333	0.00	0.00	0.00	2.32
5287	5876	4.756084	AGTTACTGTCAGCTCAAAATGC	57.244	40.909	0.00	0.00	0.00	3.56
5288	5877	4.392940	AGTTACTGTCAGCTCAAAATGCT	58.607	39.130	0.00	0.00	42.06	3.79
5289	5878	4.453819	AGTTACTGTCAGCTCAAAATGCTC	59.546	41.667	0.00	0.00	38.92	4.26
5290	5879	3.137446	ACTGTCAGCTCAAAATGCTCT	57.863	42.857	0.00	0.00	38.92	4.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	6.492429	AGCATGCCACAATCATGTTATATTCT	59.508	34.615	15.66	0.00	42.34	2.40
18	19	6.659745	AGCATGCCACAATCATGTTATATT	57.340	33.333	15.66	0.00	42.34	1.28
22	23	4.018490	AGAAGCATGCCACAATCATGTTA	58.982	39.130	15.66	0.00	42.34	2.41
29	30	4.523943	TGAACTAAAGAAGCATGCCACAAT	59.476	37.500	15.66	0.72	0.00	2.71
152	288	4.305539	TCATTCTCAAATCCCAAGCTCA	57.694	40.909	0.00	0.00	0.00	4.26
242	378	2.543848	TCTGAACTACGCAAGCAACAAG	59.456	45.455	0.00	0.00	45.62	3.16
291	435	1.467342	CGAATTTCCCCGTCCAAACTC	59.533	52.381	0.00	0.00	0.00	3.01
331	475	2.586648	AAGTTCCACATCCTTGACCC	57.413	50.000	0.00	0.00	0.00	4.46
572	717	2.158900	ACAGTACAGCAAGTCAGCAACT	60.159	45.455	0.00	0.00	41.10	3.16
580	725	4.826274	ATATCCACACAGTACAGCAAGT	57.174	40.909	0.00	0.00	0.00	3.16
581	726	7.661968	ACTATATATCCACACAGTACAGCAAG	58.338	38.462	0.00	0.00	0.00	4.01
582	727	7.597288	ACTATATATCCACACAGTACAGCAA	57.403	36.000	0.00	0.00	0.00	3.91
583	728	7.597288	AACTATATATCCACACAGTACAGCA	57.403	36.000	0.00	0.00	0.00	4.41
584	729	7.095607	GCAAACTATATATCCACACAGTACAGC	60.096	40.741	0.00	0.00	0.00	4.40
585	730	7.114953	CGCAAACTATATATCCACACAGTACAG	59.885	40.741	0.00	0.00	0.00	2.74
586	731	6.921307	CGCAAACTATATATCCACACAGTACA	59.079	38.462	0.00	0.00	0.00	2.90
587	732	6.921857	ACGCAAACTATATATCCACACAGTAC	59.078	38.462	0.00	0.00	0.00	2.73
878	1031	2.088950	GCATGGTGCAATCTGCTTTT	57.911	45.000	8.04	0.00	45.31	2.27
954	1107	2.843113	AGGTATCAGAGGCAAGCTTCTT	59.157	45.455	3.75	0.00	29.56	2.52
1372	1529	7.093814	TGCCACTTCAGCACTTGAATTATTATT	60.094	33.333	0.00	0.00	44.48	1.40
1373	1530	6.377996	TGCCACTTCAGCACTTGAATTATTAT	59.622	34.615	0.00	0.00	44.48	1.28
1374	1531	5.709631	TGCCACTTCAGCACTTGAATTATTA	59.290	36.000	0.00	0.00	44.48	0.98
1423	1580	1.868713	TTATCTGGGGTAACGGCAGA	58.131	50.000	0.00	0.00	37.60	4.26
1479	1636	1.822990	CATTGGAACTTCTGCATGCCT	59.177	47.619	16.68	0.00	0.00	4.75
1682	1839	3.361281	TGAGCTTTCTCATCTGCCATT	57.639	42.857	0.00	0.00	43.95	3.16
2169	2326	6.070481	TCACAATGCCAGTACCTTTATCTGTA	60.070	38.462	0.00	0.00	0.00	2.74
3898	4061	4.272504	ACGTGTTTGGCTATCATAATTCGG	59.727	41.667	0.00	0.00	0.00	4.30
4323	4489	2.030007	GCTGCAAACATGTAAGGCAAGA	60.030	45.455	16.57	0.00	33.58	3.02
4400	4566	0.319211	CAGGCCACAACAGTGCAATG	60.319	55.000	13.51	13.51	31.87	2.82
4425	4591	2.185004	AACCATCACAAGGAGGAACG	57.815	50.000	0.00	0.00	0.00	3.95
4510	4676	3.476552	CAGAACTTGTGTACACATGGGT	58.523	45.455	32.93	25.31	41.52	4.51
4511	4677	2.226437	GCAGAACTTGTGTACACATGGG	59.774	50.000	32.93	24.95	41.52	4.00
4578	4744	3.414549	TTCGGTGCAGAACTTGTTTTC	57.585	42.857	0.00	0.00	0.00	2.29
4674	4841	6.889301	ATACATGATTTCCCAAGCTACATG	57.111	37.500	0.00	0.00	39.27	3.21
4973	5562	3.953712	TCCTCAGTTCTTGCGTATGAA	57.046	42.857	0.00	0.00	0.00	2.57
4981	5570	2.805099	GACTGCACTTCCTCAGTTCTTG	59.195	50.000	0.00	0.00	42.97	3.02
5001	5590	7.341512	TGCAAGTATGATACAATTTCCCAATGA	59.658	33.333	5.28	0.00	0.00	2.57
5041	5630	2.680352	ACTGATCGTGGGCGTCCT	60.680	61.111	7.97	0.00	39.49	3.85
5119	5708	3.981211	TCCACACGAGGTTAAACAGTAC	58.019	45.455	0.00	0.00	0.00	2.73
5139	5728	8.230486	CGCATCAACCTATTCCTTTGTAATATC	58.770	37.037	0.00	0.00	0.00	1.63
5254	5843	9.857957	GAGCTGACAGTAACTTTATACTAACTT	57.142	33.333	3.99	0.00	34.40	2.66
5255	5844	9.021807	TGAGCTGACAGTAACTTTATACTAACT	57.978	33.333	3.99	0.00	34.40	2.24
5256	5845	9.635520	TTGAGCTGACAGTAACTTTATACTAAC	57.364	33.333	3.99	0.00	34.40	2.34
5259	5848	9.726438	ATTTTGAGCTGACAGTAACTTTATACT	57.274	29.630	3.99	0.00	36.57	2.12
5260	5849	9.760660	CATTTTGAGCTGACAGTAACTTTATAC	57.239	33.333	3.99	0.00	0.00	1.47
5261	5850	8.450964	GCATTTTGAGCTGACAGTAACTTTATA	58.549	33.333	3.99	0.00	0.00	0.98
5262	5851	7.175641	AGCATTTTGAGCTGACAGTAACTTTAT	59.824	33.333	3.99	0.00	41.61	1.40
5263	5852	6.486657	AGCATTTTGAGCTGACAGTAACTTTA	59.513	34.615	3.99	0.00	41.61	1.85
5264	5853	5.300286	AGCATTTTGAGCTGACAGTAACTTT	59.700	36.000	3.99	0.00	41.61	2.66
5265	5854	4.823989	AGCATTTTGAGCTGACAGTAACTT	59.176	37.500	3.99	0.00	41.61	2.66
5266	5855	4.392940	AGCATTTTGAGCTGACAGTAACT	58.607	39.130	3.99	0.00	41.61	2.24
5267	5856	4.453819	AGAGCATTTTGAGCTGACAGTAAC	59.546	41.667	3.99	0.00	43.58	2.50
5268	5857	4.645535	AGAGCATTTTGAGCTGACAGTAA	58.354	39.130	3.99	0.00	43.58	2.24
5269	5858	4.277515	AGAGCATTTTGAGCTGACAGTA	57.722	40.909	3.99	0.00	43.58	2.74
5270	5859	3.137446	AGAGCATTTTGAGCTGACAGT	57.863	42.857	3.99	0.00	43.58	3.55

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.