AutoCloner

Multiple sequence alignment - TraesCS4D01G167100

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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	TraesCS4D01G167100	chr4D	100.000	5948	0	0	1	5948	286397971	286392024	0.000000e+00	10984.0
1	TraesCS4D01G167100	chr4D	100.000	28	0	0	4570	4597	286393282	286393255	1.100000e-02	52.8
2	TraesCS4D01G167100	chr4D	100.000	28	0	0	4690	4717	286393402	286393375	1.100000e-02	52.8
3	TraesCS4D01G167100	chr4A	93.930	6063	158	54	1	5948	207983305	207977338	0.000000e+00	8964.0
4	TraesCS4D01G167100	chr4A	100.000	28	0	0	4570	4597	207978554	207978527	1.100000e-02	52.8
5	TraesCS4D01G167100	chr4A	100.000	28	0	0	4690	4717	207978674	207978647	1.100000e-02	52.8
6	TraesCS4D01G167100	chr4B	97.153	2880	65	8	3078	5948	276962349	276965220	0.000000e+00	4848.0
7	TraesCS4D01G167100	chr4B	92.935	1826	33	24	289	2051	276958131	276959923	0.000000e+00	2569.0
8	TraesCS4D01G167100	chr4B	98.577	984	14	0	2038	3021	276961366	276962349	0.000000e+00	1740.0
9	TraesCS4D01G167100	chr4B	93.897	213	13	0	80	292	276957807	276958019	7.440000e-84	322.0
10	TraesCS4D01G167100	chr4B	97.753	89	2	0	1	89	276957536	276957624	2.870000e-33	154.0
11	TraesCS4D01G167100	chr4B	100.000	28	0	0	4690	4717	276963844	276963871	1.100000e-02	52.8
12	TraesCS4D01G167100	chr7A	85.155	741	88	12	3016	3750	613776524	613777248	0.000000e+00	739.0
13	TraesCS4D01G167100	chr7A	83.712	749	104	13	3016	3756	613778343	613779081	0.000000e+00	691.0
14	TraesCS4D01G167100	chr7A	83.423	742	110	10	3016	3755	614595490	614596220	0.000000e+00	676.0
15	TraesCS4D01G167100	chr7D	84.367	742	98	12	3016	3755	534072083	534072808	0.000000e+00	712.0
16	TraesCS4D01G167100	chr7D	83.578	749	105	13	3016	3756	534194022	534194760	0.000000e+00	686.0
17	TraesCS4D01G167100	chr7D	83.693	742	104	11	3016	3754	534171382	534172109	0.000000e+00	684.0
18	TraesCS4D01G167100	chr7D	83.266	741	110	9	3016	3754	534192068	534192796	0.000000e+00	669.0

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	TraesCS4D01G167100	chr4D	286392024	286397971	5947	True	10984.0	10984	100.000000	1	5948	1	chr4D.!!$R1	5947
1	TraesCS4D01G167100	chr4A	207977338	207983305	5967	True	8964.0	8964	93.930000	1	5948	1	chr4A.!!$R1	5947
2	TraesCS4D01G167100	chr4B	276957536	276965220	7684	False	1614.3	4848	96.719167	1	5948	6	chr4B.!!$F1	5947
3	TraesCS4D01G167100	chr7A	613776524	613779081	2557	False	715.0	739	84.433500	3016	3756	2	chr7A.!!$F2	740
4	TraesCS4D01G167100	chr7A	614595490	614596220	730	False	676.0	676	83.423000	3016	3755	1	chr7A.!!$F1	739
5	TraesCS4D01G167100	chr7D	534072083	534072808	725	False	712.0	712	84.367000	3016	3755	1	chr7D.!!$F1	739
6	TraesCS4D01G167100	chr7D	534171382	534172109	727	False	684.0	684	83.693000	3016	3754	1	chr7D.!!$F2	738
7	TraesCS4D01G167100	chr7D	534192068	534194760	2692	False	677.5	686	83.422000	3016	3756	2	chr7D.!!$F3	740

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
941	1287	0.462759	CCCAGCCAAGAGAATCGTCC	60.463	60.000	0.00	0.00	42.67	4.79	F
1219	1566	0.386352	CGACGGTGTTTGCGTCTCTA	60.386	55.000	0.00	0.00	0.00	2.43	F
1274	1621	0.956902	ATGGGGTTTGGTTCGTACGC	60.957	55.000	11.24	0.00	0.00	4.42	F
2350	4227	2.293122	TCCACAGTTGCAAGTTACATGC	59.707	45.455	3.38	5.56	44.08	4.06	F
3336	5217	0.322008	GGTCTTTGGGCTCTGACCTG	60.322	60.000	14.02	0.00	43.91	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2726	4603	2.266055	GAGAGCACCTCCCCAACG	59.734	66.667	0.00	0.00	35.87	4.10	R
3189	5069	1.002792	CTGCACAATCATGATCAGCGG	60.003	52.381	9.06	13.83	0.00	5.52	R
3336	5217	7.064016	GTGAAGACACATTCCTCTAAAGATGTC	59.936	40.741	0.00	0.00	45.32	3.06	R
3397	5279	2.483014	TTACCAATCCCAACGACCTG	57.517	50.000	0.00	0.00	0.00	4.00	R
5222	7111	0.108520	CACCAATCACCAATGCCTGC	60.109	55.000	0.00	0.00	0.00	4.85	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
41	42	0.546122	AATGGATCTTGGCGCCACTA	59.454	50.000	32.95	21.27	33.93	2.74
52	53	2.960129	GCCACTATCGAACCCGCG	60.960	66.667	0.00	0.00	35.37	6.46
173	366	1.512156	GGGTGCGACAAACGTCCATT	61.512	55.000	0.00	0.00	44.60	3.16
221	414	3.452990	TGGCATTAGTCTCGAACCCATAA	59.547	43.478	0.00	0.00	0.00	1.90
227	420	7.063544	GCATTAGTCTCGAACCCATAACATATC	59.936	40.741	0.00	0.00	0.00	1.63
250	443	7.008440	TCTCTCATGATTAATGCAAAAGACG	57.992	36.000	0.00	0.00	36.11	4.18
251	444	6.818142	TCTCTCATGATTAATGCAAAAGACGA	59.182	34.615	0.00	0.00	36.11	4.20
299	622	5.590259	CACCCATCTTTCATACTTCCGATTT	59.410	40.000	0.00	0.00	0.00	2.17
321	644	1.001815	ACGGATTTTGTTTCAGCGGTG	60.002	47.619	8.67	8.67	0.00	4.94
369	692	5.640357	TGATTAATGTAGGACGTGTGTTTCC	59.360	40.000	0.00	0.00	0.00	3.13
375	698	6.534475	TGTAGGACGTGTGTTTCCTATAAT	57.466	37.500	0.00	0.00	44.57	1.28
379	702	7.838771	AGGACGTGTGTTTCCTATAATAAAC	57.161	36.000	0.00	0.00	40.70	2.01
380	703	7.388437	AGGACGTGTGTTTCCTATAATAAACA	58.612	34.615	0.00	7.77	40.70	2.83
382	705	8.671028	GGACGTGTGTTTCCTATAATAAACAAT	58.329	33.333	11.77	2.35	44.64	2.71
505	832	1.588139	GAACCTACGGCGTGGATCG	60.588	63.158	25.47	10.69	43.12	3.69
559	886	4.322349	CGAGAGACTCCTCAAGGAAATTGT	60.322	45.833	0.00	0.00	44.91	2.71
590	918	2.203015	AGCAAGCACCACGACGTT	60.203	55.556	0.00	0.00	0.00	3.99
634	970	2.619074	CCAATTTCTCTCTCCGCCCTTT	60.619	50.000	0.00	0.00	0.00	3.11
884	1230	1.032114	CCCAGATTCTTTCACCCCGC	61.032	60.000	0.00	0.00	0.00	6.13
897	1243	4.712425	CCCGCTCGTCGTTCCGTT	62.712	66.667	0.00	0.00	36.19	4.44
941	1287	0.462759	CCCAGCCAAGAGAATCGTCC	60.463	60.000	0.00	0.00	42.67	4.79
945	1291	1.517832	CCAAGAGAATCGTCCGCCT	59.482	57.895	0.00	0.00	42.67	5.52
1200	1547	3.953766	TCACGTCATCTCTAGATTTCGC	58.046	45.455	0.00	0.00	34.07	4.70
1219	1566	0.386352	CGACGGTGTTTGCGTCTCTA	60.386	55.000	0.00	0.00	0.00	2.43
1274	1621	0.956902	ATGGGGTTTGGTTCGTACGC	60.957	55.000	11.24	0.00	0.00	4.42
1514	1899	2.299993	TTCGTCAGGCTGATGTGATC	57.700	50.000	30.27	12.63	35.03	2.92
1753	2167	6.183360	GCTGCTCAAAACATATAAGCCACTTA	60.183	38.462	0.00	0.00	31.96	2.24
1970	2386	5.532025	CATGTAGATATGCATGTGAGCTG	57.468	43.478	10.16	0.00	38.06	4.24
2350	4227	2.293122	TCCACAGTTGCAAGTTACATGC	59.707	45.455	3.38	5.56	44.08	4.06
2726	4603	3.628032	GCAAGTTTATAGGGAGCAAGACC	59.372	47.826	0.00	0.00	0.00	3.85
3163	5040	3.385755	AGAACAGCCAAATTTCAGCTTGT	59.614	39.130	9.09	8.48	33.70	3.16
3336	5217	0.322008	GGTCTTTGGGCTCTGACCTG	60.322	60.000	14.02	0.00	43.91	4.00
3397	5279	4.746611	CCATTGGAGCAGAAACTTTTGTTC	59.253	41.667	0.00	0.00	42.67	3.18
3524	5407	5.987347	GCATAAATTGTTCCATGCTTGCTAT	59.013	36.000	0.00	0.00	40.46	2.97
3577	5460	2.028385	TCCAGGAGAAGTAAGGCGAAAC	60.028	50.000	0.00	0.00	0.00	2.78
4512	6398	0.329261	TGAAGGGGAAGCCATGTGAG	59.671	55.000	0.00	0.00	0.00	3.51
4549	6435	0.804933	GAAGCCTACTACCAACGGCG	60.805	60.000	4.80	4.80	46.85	6.46
4760	6646	3.884037	AGTTCCTGATGTTTTGGAGGT	57.116	42.857	0.00	0.00	0.00	3.85
4761	6647	3.756117	AGTTCCTGATGTTTTGGAGGTC	58.244	45.455	0.00	0.00	0.00	3.85
4898	6784	2.359975	CAAGGGGGACGCCAGAAC	60.360	66.667	11.16	0.00	44.92	3.01
5171	7060	2.514824	GCCATCCGAAGCTGTCCC	60.515	66.667	0.00	0.00	0.00	4.46
5214	7103	2.355513	GCTCACTGTTCCCTCATCATGT	60.356	50.000	0.00	0.00	0.00	3.21
5215	7104	3.871463	GCTCACTGTTCCCTCATCATGTT	60.871	47.826	0.00	0.00	0.00	2.71
5216	7105	3.937706	CTCACTGTTCCCTCATCATGTTC	59.062	47.826	0.00	0.00	0.00	3.18
5217	7106	3.327464	TCACTGTTCCCTCATCATGTTCA	59.673	43.478	0.00	0.00	0.00	3.18
5218	7107	3.438087	CACTGTTCCCTCATCATGTTCAC	59.562	47.826	0.00	0.00	0.00	3.18
5219	7108	3.072915	ACTGTTCCCTCATCATGTTCACA	59.927	43.478	0.00	0.00	0.00	3.58
5220	7109	4.263639	ACTGTTCCCTCATCATGTTCACAT	60.264	41.667	0.00	0.00	36.96	3.21
5221	7110	4.665451	TGTTCCCTCATCATGTTCACATT	58.335	39.130	0.00	0.00	33.61	2.71
5222	7111	4.460034	TGTTCCCTCATCATGTTCACATTG	59.540	41.667	0.00	0.00	33.61	2.82
5223	7112	3.018856	TCCCTCATCATGTTCACATTGC	58.981	45.455	0.00	0.00	33.61	3.56
5224	7113	2.756207	CCCTCATCATGTTCACATTGCA	59.244	45.455	0.00	0.00	33.61	4.08
5225	7114	3.181490	CCCTCATCATGTTCACATTGCAG	60.181	47.826	0.00	0.00	33.61	4.41
5226	7115	3.181490	CCTCATCATGTTCACATTGCAGG	60.181	47.826	0.00	0.00	33.61	4.85
5227	7116	2.164827	TCATCATGTTCACATTGCAGGC	59.835	45.455	0.00	0.00	33.61	4.85
5228	7117	1.618487	TCATGTTCACATTGCAGGCA	58.382	45.000	0.00	0.00	33.61	4.75
5229	7118	2.172679	TCATGTTCACATTGCAGGCAT	58.827	42.857	0.00	0.00	33.61	4.40
5230	7119	2.563620	TCATGTTCACATTGCAGGCATT	59.436	40.909	0.00	0.00	33.61	3.56
5231	7120	2.442212	TGTTCACATTGCAGGCATTG	57.558	45.000	13.00	13.00	34.58	2.82
5232	7121	1.001068	TGTTCACATTGCAGGCATTGG	59.999	47.619	17.37	8.79	33.22	3.16
5233	7122	1.001181	GTTCACATTGCAGGCATTGGT	59.999	47.619	17.37	4.60	33.22	3.67
5234	7123	0.604073	TCACATTGCAGGCATTGGTG	59.396	50.000	17.37	14.43	33.22	4.17
5235	7124	0.604073	CACATTGCAGGCATTGGTGA	59.396	50.000	17.37	0.00	33.22	4.02
5279	7190	6.407525	CCCTTTCTTTCTAGAATCTCGGATGT	60.408	42.308	5.89	0.00	40.01	3.06
5351	7262	2.380064	AGGGTTTCATGTCCAGCAAA	57.620	45.000	0.00	0.00	0.00	3.68
5352	7263	2.893424	AGGGTTTCATGTCCAGCAAAT	58.107	42.857	0.00	0.00	0.00	2.32
5666	7585	4.955925	TTTGTAACATGGCTATCAACGG	57.044	40.909	0.00	0.00	0.00	4.44
5706	7674	3.030291	AGTCATGCCAACAAAAACTGGA	58.970	40.909	0.00	0.00	34.35	3.86
5710	7678	4.278170	TCATGCCAACAAAAACTGGAGTAG	59.722	41.667	0.00	0.00	34.35	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	0.100146	GTAGAAGACGCGGGTTCGAT	59.900	55.000	12.47	0.45	39.00	3.59
52	53	7.972277	TGTTGTATTAATCACGAGGTAGAAGAC	59.028	37.037	0.00	0.00	0.00	3.01
122	315	2.959275	GTCCACTGCTTATCGGACG	58.041	57.895	0.00	0.00	38.68	4.79
173	366	4.574892	TCTGTTGCATCGGATGTAAAAGA	58.425	39.130	27.56	27.56	43.84	2.52
227	420	7.008440	TCGTCTTTTGCATTAATCATGAGAG	57.992	36.000	0.09	0.00	34.31	3.20
250	443	3.002348	CGGCGAATCCCTGAAAAAGTATC	59.998	47.826	0.00	0.00	0.00	2.24
251	444	2.943033	CGGCGAATCCCTGAAAAAGTAT	59.057	45.455	0.00	0.00	0.00	2.12
299	622	2.879646	ACCGCTGAAACAAAATCCGTTA	59.120	40.909	0.00	0.00	0.00	3.18
321	644	7.933577	TCATGAGATATACATTCAGGGTTTGAC	59.066	37.037	0.00	0.00	34.94	3.18
472	795	1.626654	GGTTCATCTGACGTGCGTGG	61.627	60.000	0.67	0.00	0.00	4.94
505	832	1.212751	GCCGTTGGATGCCACTTTC	59.787	57.895	0.00	0.00	30.78	2.62
590	918	0.312729	TGTGTTGAGAACGCTCGCTA	59.687	50.000	0.00	0.00	44.33	4.26
634	970	4.322049	CCTTTAAAGACGAGAGAGCAGGAA	60.322	45.833	16.98	0.00	0.00	3.36
732	1068	1.204312	GGTTTGTTCGCTCGCAGTC	59.796	57.895	0.00	0.00	0.00	3.51
897	1243	1.539496	CGGGAAACAGAAGACGGTGAA	60.539	52.381	0.00	0.00	0.00	3.18
958	1304	2.494918	CCCCTACTGGACGAAGCG	59.505	66.667	0.00	0.00	35.39	4.68
1039	1385	4.189231	AGAACGAATGTACTAACATGGGC	58.811	43.478	0.00	0.00	45.79	5.36
1083	1429	2.031919	ATCACCGAAACGCCAGCA	59.968	55.556	0.00	0.00	0.00	4.41
1295	1642	1.763770	CAAACCTGGAGGCTGGAGT	59.236	57.895	0.00	0.00	39.32	3.85
1514	1899	3.069016	TGCACCATAACTAGGACGTATGG	59.931	47.826	16.48	16.48	42.39	2.74
1608	2010	8.166066	TGATGTTTAAGATTTATCGTGTTCACG	58.834	33.333	17.57	17.57	0.00	4.35
2726	4603	2.266055	GAGAGCACCTCCCCAACG	59.734	66.667	0.00	0.00	35.87	4.10
3189	5069	1.002792	CTGCACAATCATGATCAGCGG	60.003	52.381	9.06	13.83	0.00	5.52
3336	5217	7.064016	GTGAAGACACATTCCTCTAAAGATGTC	59.936	40.741	0.00	0.00	45.32	3.06
3397	5279	2.483014	TTACCAATCCCAACGACCTG	57.517	50.000	0.00	0.00	0.00	4.00
3524	5407	8.645814	TGTTAAGGTGTTGACTATCTCTTCTA	57.354	34.615	0.00	0.00	0.00	2.10
3577	5460	6.071728	ACAGCTTCCCAAAACAGATCATTTAG	60.072	38.462	0.00	0.00	0.00	1.85
4512	6398	2.010145	TCGCAACCTCTGTTATCTGC	57.990	50.000	0.00	0.00	32.09	4.26
4603	6489	2.483877	TGGCTACTGCATCAAACTTTCG	59.516	45.455	0.00	0.00	41.91	3.46
4760	6646	2.933906	GTTAGATCATGTTTTCCGGCGA	59.066	45.455	9.30	0.00	0.00	5.54
4761	6647	2.936498	AGTTAGATCATGTTTTCCGGCG	59.064	45.455	0.00	0.00	0.00	6.46
4938	6827	2.306805	AGATGCCCACATTCAGTCTTCA	59.693	45.455	0.00	0.00	36.35	3.02
5171	7060	1.453155	CTCCACAAGAAATGGACCGG	58.547	55.000	0.00	0.00	41.47	5.28
5214	7103	1.001068	CACCAATGCCTGCAATGTGAA	59.999	47.619	6.45	0.00	0.00	3.18
5215	7104	0.604073	CACCAATGCCTGCAATGTGA	59.396	50.000	6.45	0.00	0.00	3.58
5216	7105	0.604073	TCACCAATGCCTGCAATGTG	59.396	50.000	6.45	8.93	0.00	3.21
5217	7106	1.563924	ATCACCAATGCCTGCAATGT	58.436	45.000	6.45	0.00	0.00	2.71
5218	7107	2.276201	CAATCACCAATGCCTGCAATG	58.724	47.619	0.00	0.00	0.00	2.82
5219	7108	1.208535	CCAATCACCAATGCCTGCAAT	59.791	47.619	0.00	0.00	0.00	3.56
5220	7109	0.609151	CCAATCACCAATGCCTGCAA	59.391	50.000	0.00	0.00	0.00	4.08
5221	7110	0.542467	ACCAATCACCAATGCCTGCA	60.542	50.000	0.00	0.00	0.00	4.41
5222	7111	0.108520	CACCAATCACCAATGCCTGC	60.109	55.000	0.00	0.00	0.00	4.85
5223	7112	1.203052	GTCACCAATCACCAATGCCTG	59.797	52.381	0.00	0.00	0.00	4.85
5224	7113	1.203038	TGTCACCAATCACCAATGCCT	60.203	47.619	0.00	0.00	0.00	4.75
5225	7114	1.067635	GTGTCACCAATCACCAATGCC	60.068	52.381	0.00	0.00	0.00	4.40
5226	7115	2.352503	GTGTCACCAATCACCAATGC	57.647	50.000	0.00	0.00	0.00	3.56
5232	7121	1.537202	GAGCAAGGTGTCACCAATCAC	59.463	52.381	24.02	8.38	41.95	3.06
5233	7122	1.421268	AGAGCAAGGTGTCACCAATCA	59.579	47.619	24.02	0.00	41.95	2.57
5234	7123	2.079925	GAGAGCAAGGTGTCACCAATC	58.920	52.381	24.02	14.54	41.95	2.67
5235	7124	1.271597	GGAGAGCAAGGTGTCACCAAT	60.272	52.381	24.02	9.55	41.95	3.16
5369	7280	7.679783	TGGTGTTCATCTTTCTTCTCTATTCA	58.320	34.615	0.00	0.00	0.00	2.57
5370	7281	8.610896	CATGGTGTTCATCTTTCTTCTCTATTC	58.389	37.037	0.00	0.00	32.92	1.75
5666	7585	4.028852	ACTTGCCTTTTTCTTGTCGTTC	57.971	40.909	0.00	0.00	0.00	3.95
5710	7678	7.363268	CGGGGTGGAGGTAATACTATTATACAC	60.363	44.444	0.00	0.00	0.00	2.90
5731	7699	4.457949	GTGACAAGACAATTAATTCGGGGT	59.542	41.667	0.00	0.00	0.00	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.