AutoCloner

Multiple sequence alignment - TraesCS1B01G239700

Loading Multiple Alignment...

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	TraesCS1B01G239700	chr1B	100.000	2162	0	0	1	2162	427650987	427653148	0.000000e+00	3993
1	TraesCS1B01G239700	chr1B	92.119	1345	56	19	1	1303	633716990	633715654	0.000000e+00	1851
2	TraesCS1B01G239700	chr1B	85.880	864	98	19	1304	2162	280815930	280816774	0.000000e+00	898
3	TraesCS1B01G239700	chr5D	92.582	1348	54	19	1	1303	6253257	6254603	0.000000e+00	1893
4	TraesCS1B01G239700	chr5D	92.193	1345	62	17	1	1303	329125888	329127231	0.000000e+00	1862
5	TraesCS1B01G239700	chr5D	91.970	1345	61	18	1	1303	503339459	503338120	0.000000e+00	1842
6	TraesCS1B01G239700	chr5D	92.089	1302	53	19	1	1260	299972489	299973782	0.000000e+00	1788
7	TraesCS1B01G239700	chr5D	85.714	861	95	23	1304	2155	252473349	252474190	0.000000e+00	883
8	TraesCS1B01G239700	chr5D	96.903	226	7	0	1078	1303	481593868	481593643	1.570000e-101	379
9	TraesCS1B01G239700	chr5D	96.903	226	7	0	1078	1303	503335546	503335321	1.570000e-101	379
10	TraesCS1B01G239700	chr3B	92.348	1346	54	17	1	1303	101924895	101923556	0.000000e+00	1869
11	TraesCS1B01G239700	chr3B	85.465	860	98	20	1304	2155	653617377	653616537	0.000000e+00	870
12	TraesCS1B01G239700	chr5B	92.279	1347	54	18	1	1303	57515106	57516446	0.000000e+00	1866
13	TraesCS1B01G239700	chr3A	92.142	1349	54	20	1	1303	105556938	105558280	0.000000e+00	1857
14	TraesCS1B01G239700	chr1D	92.090	1340	59	22	1	1303	254459427	254458098	0.000000e+00	1844
15	TraesCS1B01G239700	chr1D	91.660	1343	67	14	1	1303	51831941	51833278	0.000000e+00	1818
16	TraesCS1B01G239700	chr1D	96.903	226	7	0	1078	1303	254455542	254455317	1.570000e-101	379
17	TraesCS1B01G239700	chr7B	91.822	1345	60	15	1	1303	662755016	662756352	0.000000e+00	1829
18	TraesCS1B01G239700	chr7B	85.057	870	97	28	1298	2155	59702354	59703202	0.000000e+00	856
19	TraesCS1B01G239700	chr4A	90.497	1347	76	18	1	1303	309446389	309447727	0.000000e+00	1731
20	TraesCS1B01G239700	chr4A	87.889	867	84	15	1303	2162	697840444	697839592	0.000000e+00	1000
21	TraesCS1B01G239700	chrUn	91.987	911	37	12	1	881	445188126	445187222	0.000000e+00	1245
22	TraesCS1B01G239700	chrUn	92.934	835	35	8	485	1303	423337822	423338648	0.000000e+00	1194
23	TraesCS1B01G239700	chr7A	92.092	822	36	10	311	1112	706285495	706286307	0.000000e+00	1131
24	TraesCS1B01G239700	chr7A	87.237	854	80	21	1304	2146	430884355	430883520	0.000000e+00	946
25	TraesCS1B01G239700	chr3D	87.872	874	81	15	1301	2162	247346767	247347627	0.000000e+00	1003
26	TraesCS1B01G239700	chr6B	86.536	869	87	22	1304	2162	295203723	295202875	0.000000e+00	929
27	TraesCS1B01G239700	chr5A	85.006	867	101	22	1301	2155	381063196	381064045	0.000000e+00	854

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	TraesCS1B01G239700	chr1B	427650987	427653148	2161	False	3993.0	3993	100.0000	1	2162	1	chr1B.!!$F2	2161
1	TraesCS1B01G239700	chr1B	633715654	633716990	1336	True	1851.0	1851	92.1190	1	1303	1	chr1B.!!$R1	1302
2	TraesCS1B01G239700	chr1B	280815930	280816774	844	False	898.0	898	85.8800	1304	2162	1	chr1B.!!$F1	858
3	TraesCS1B01G239700	chr5D	6253257	6254603	1346	False	1893.0	1893	92.5820	1	1303	1	chr5D.!!$F1	1302
4	TraesCS1B01G239700	chr5D	329125888	329127231	1343	False	1862.0	1862	92.1930	1	1303	1	chr5D.!!$F4	1302
5	TraesCS1B01G239700	chr5D	299972489	299973782	1293	False	1788.0	1788	92.0890	1	1260	1	chr5D.!!$F3	1259
6	TraesCS1B01G239700	chr5D	503335321	503339459	4138	True	1110.5	1842	94.4365	1	1303	2	chr5D.!!$R2	1302
7	TraesCS1B01G239700	chr5D	252473349	252474190	841	False	883.0	883	85.7140	1304	2155	1	chr5D.!!$F2	851
8	TraesCS1B01G239700	chr3B	101923556	101924895	1339	True	1869.0	1869	92.3480	1	1303	1	chr3B.!!$R1	1302
9	TraesCS1B01G239700	chr3B	653616537	653617377	840	True	870.0	870	85.4650	1304	2155	1	chr3B.!!$R2	851
10	TraesCS1B01G239700	chr5B	57515106	57516446	1340	False	1866.0	1866	92.2790	1	1303	1	chr5B.!!$F1	1302
11	TraesCS1B01G239700	chr3A	105556938	105558280	1342	False	1857.0	1857	92.1420	1	1303	1	chr3A.!!$F1	1302
12	TraesCS1B01G239700	chr1D	51831941	51833278	1337	False	1818.0	1818	91.6600	1	1303	1	chr1D.!!$F1	1302
13	TraesCS1B01G239700	chr1D	254455317	254459427	4110	True	1111.5	1844	94.4965	1	1303	2	chr1D.!!$R1	1302
14	TraesCS1B01G239700	chr7B	662755016	662756352	1336	False	1829.0	1829	91.8220	1	1303	1	chr7B.!!$F2	1302
15	TraesCS1B01G239700	chr7B	59702354	59703202	848	False	856.0	856	85.0570	1298	2155	1	chr7B.!!$F1	857
16	TraesCS1B01G239700	chr4A	309446389	309447727	1338	False	1731.0	1731	90.4970	1	1303	1	chr4A.!!$F1	1302
17	TraesCS1B01G239700	chr4A	697839592	697840444	852	True	1000.0	1000	87.8890	1303	2162	1	chr4A.!!$R1	859
18	TraesCS1B01G239700	chrUn	445187222	445188126	904	True	1245.0	1245	91.9870	1	881	1	chrUn.!!$R1	880
19	TraesCS1B01G239700	chrUn	423337822	423338648	826	False	1194.0	1194	92.9340	485	1303	1	chrUn.!!$F1	818
20	TraesCS1B01G239700	chr7A	706285495	706286307	812	False	1131.0	1131	92.0920	311	1112	1	chr7A.!!$F1	801
21	TraesCS1B01G239700	chr7A	430883520	430884355	835	True	946.0	946	87.2370	1304	2146	1	chr7A.!!$R1	842
22	TraesCS1B01G239700	chr3D	247346767	247347627	860	False	1003.0	1003	87.8720	1301	2162	1	chr3D.!!$F1	861
23	TraesCS1B01G239700	chr6B	295202875	295203723	848	True	929.0	929	86.5360	1304	2162	1	chr6B.!!$R1	858
24	TraesCS1B01G239700	chr5A	381063196	381064045	849	False	854.0	854	85.0060	1301	2155	1	chr5A.!!$F1	854

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
296	313	2.618816	CCAGGTCCAATAGAAGCAAGCA	60.619	50.0	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1562	7216	0.251386	ACTCGAGACTCTTCTGGCCA	60.251	55.0	21.68	4.71	29.47	5.36	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
67	71	6.934561	GCAGAAGCAACCAATTTACTAAAG	57.065	37.500	0.00	0.00	41.58	1.85
220	236	8.258708	AGTACCTCGTATTTTATCTTCTGCTTT	58.741	33.333	0.00	0.00	0.00	3.51
224	240	7.148239	CCTCGTATTTTATCTTCTGCTTTTGGT	60.148	37.037	0.00	0.00	0.00	3.67
237	253	3.058293	TGCTTTTGGTTGTCTCGCAATAG	60.058	43.478	0.00	0.00	39.55	1.73
296	313	2.618816	CCAGGTCCAATAGAAGCAAGCA	60.619	50.000	0.00	0.00	0.00	3.91
302	319	3.194755	TCCAATAGAAGCAAGCACTACGA	59.805	43.478	0.00	0.00	0.00	3.43
312	344	3.428999	GCAAGCACTACGACCAATCTAGA	60.429	47.826	0.00	0.00	0.00	2.43
322	354	4.141937	ACGACCAATCTAGAAGCAGCAATA	60.142	41.667	0.00	0.00	0.00	1.90
323	355	4.447054	CGACCAATCTAGAAGCAGCAATAG	59.553	45.833	0.00	0.00	0.00	1.73
324	356	5.363939	GACCAATCTAGAAGCAGCAATAGT	58.636	41.667	0.00	0.00	0.00	2.12
325	357	6.485830	ACCAATCTAGAAGCAGCAATAGTA	57.514	37.500	0.00	0.00	0.00	1.82
419	455	6.898521	AGTCTTACTTCTAAGCTCTATTGGGT	59.101	38.462	0.00	0.00	30.85	4.51
425	461	5.793030	TCTAAGCTCTATTGGGTAGAAGC	57.207	43.478	0.00	0.00	38.91	3.86
439	475	8.700439	TTGGGTAGAAGCAAAGTAACTAAAAT	57.300	30.769	0.00	0.00	0.00	1.82
488	524	8.908786	ATGATAATGTGAATTGTCCGAACTAT	57.091	30.769	0.00	0.00	0.00	2.12
502	538	8.258850	TGTCCGAACTATATAGAAGGGAATTT	57.741	34.615	16.79	0.00	0.00	1.82
853	909	7.442364	GCAACCAAGCAGATTATCTAGAACATA	59.558	37.037	0.00	0.00	0.00	2.29
868	924	9.926158	ATCTAGAACATACATGAATTGAGCTAG	57.074	33.333	0.00	9.69	0.00	3.42
925	984	4.801521	ATTCAATGATGACCCTCCATGA	57.198	40.909	0.00	0.00	34.61	3.07
1049	1108	7.317390	GGGACTAAAGAAACAAGAACAACAAA	58.683	34.615	0.00	0.00	0.00	2.83
1050	1109	7.815549	GGGACTAAAGAAACAAGAACAACAAAA	59.184	33.333	0.00	0.00	0.00	2.44
1539	7193	5.335976	GGTGATTTTTGATGGACCAGAAGAC	60.336	44.000	0.00	0.00	0.00	3.01
1541	7195	3.762407	TTTTGATGGACCAGAAGACGA	57.238	42.857	0.00	0.00	0.00	4.20
1542	7196	3.762407	TTTGATGGACCAGAAGACGAA	57.238	42.857	0.00	0.00	0.00	3.85
1543	7197	3.319137	TTGATGGACCAGAAGACGAAG	57.681	47.619	0.00	0.00	0.00	3.79
1546	7200	1.446272	GGACCAGAAGACGAAGCCG	60.446	63.158	0.00	0.00	42.50	5.52
1576	7230	2.334023	AGAGTTTGGCCAGAAGAGTCT	58.666	47.619	5.11	8.63	32.85	3.24
1585	7239	2.165437	GCCAGAAGAGTCTCGAGTCAAT	59.835	50.000	13.13	0.00	33.26	2.57
1678	7338	0.324943	CCCACCCTTGACGTGAATCT	59.675	55.000	0.00	0.00	32.77	2.40
1693	7353	5.047802	ACGTGAATCTGATGCCAAAAATTCT	60.048	36.000	0.00	0.00	0.00	2.40
1695	7355	6.183360	CGTGAATCTGATGCCAAAAATTCTTG	60.183	38.462	0.00	0.00	0.00	3.02
1759	7419	2.359230	GCCGCAAGCCTCTGAGTT	60.359	61.111	3.66	0.00	34.35	3.01
1764	7424	1.093159	GCAAGCCTCTGAGTTCATGG	58.907	55.000	3.66	0.00	0.00	3.66
1775	7435	5.634118	TCTGAGTTCATGGAAAACCAATCT	58.366	37.500	0.00	0.00	0.00	2.40
1919	7580	5.275067	AGCTATGTGTTTGATCTCTCTCC	57.725	43.478	0.00	0.00	0.00	3.71
1944	7617	4.218200	TCGTGTTCTTGATTTGGCATGATT	59.782	37.500	0.00	0.00	0.00	2.57
2098	7773	2.416547	ACACTTGATGTATGTCTTGCGC	59.583	45.455	0.00	0.00	40.88	6.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	9.750125	CTTTTCTTTAGTAAATTGGTTGCTTCT	57.250	29.630	0.00	0.00	33.71	2.85
210	226	2.872245	CGAGACAACCAAAAGCAGAAGA	59.128	45.455	0.00	0.00	0.00	2.87
220	236	2.472695	AGCTATTGCGAGACAACCAA	57.527	45.000	0.00	0.00	42.27	3.67
224	240	2.995939	CTGTGAAGCTATTGCGAGACAA	59.004	45.455	0.00	0.00	45.42	3.18
237	253	1.168407	TGCAGGACAAGCTGTGAAGC	61.168	55.000	0.00	0.00	0.00	3.86
296	313	3.181485	GCTGCTTCTAGATTGGTCGTAGT	60.181	47.826	0.00	0.00	0.00	2.73
302	319	5.365021	ACTATTGCTGCTTCTAGATTGGT	57.635	39.130	0.00	0.00	0.00	3.67
312	344	5.500234	TGAATCCACTTACTATTGCTGCTT	58.500	37.500	0.00	0.00	0.00	3.91
322	354	5.721960	ACTACTCACCATGAATCCACTTACT	59.278	40.000	0.00	0.00	0.00	2.24
323	355	5.978814	ACTACTCACCATGAATCCACTTAC	58.021	41.667	0.00	0.00	0.00	2.34
324	356	6.351881	GGAACTACTCACCATGAATCCACTTA	60.352	42.308	0.00	0.00	0.00	2.24
325	357	5.491982	GAACTACTCACCATGAATCCACTT	58.508	41.667	0.00	0.00	0.00	3.16
395	431	7.114866	ACCCAATAGAGCTTAGAAGTAAGAC	57.885	40.000	0.00	0.00	38.39	3.01
584	630	9.859427	TGAGAAAATATGCAAACAAAATAGAGG	57.141	29.630	0.00	0.00	0.00	3.69
623	671	9.227777	ACTTTAAGCAATAGTTTTAGAATCCGT	57.772	29.630	0.00	0.00	0.00	4.69
636	684	4.674362	GCGGGTTTCCACTTTAAGCAATAG	60.674	45.833	0.00	0.00	0.00	1.73
637	685	3.191791	GCGGGTTTCCACTTTAAGCAATA	59.808	43.478	0.00	0.00	0.00	1.90
714	762	1.473434	GCATTAAGGAGGGTGGAGTCG	60.473	57.143	0.00	0.00	0.00	4.18
770	823	6.946009	GCCTAGAGTTGTAGGAGAGAGAATAT	59.054	42.308	6.53	0.00	42.18	1.28
771	824	6.102027	AGCCTAGAGTTGTAGGAGAGAGAATA	59.898	42.308	6.53	0.00	42.18	1.75
772	825	5.103686	AGCCTAGAGTTGTAGGAGAGAGAAT	60.104	44.000	6.53	0.00	42.18	2.40
773	826	4.228666	AGCCTAGAGTTGTAGGAGAGAGAA	59.771	45.833	6.53	0.00	42.18	2.87
774	827	3.783642	AGCCTAGAGTTGTAGGAGAGAGA	59.216	47.826	6.53	0.00	42.18	3.10
853	909	2.295885	GCAGCCTAGCTCAATTCATGT	58.704	47.619	0.00	0.00	36.40	3.21
897	956	5.762218	GGAGGGTCATCATTGAATTGACTAG	59.238	44.000	16.17	0.00	39.70	2.57
955	1014	8.115490	AGCAGTATTCAAGCTCTTATTTTTGT	57.885	30.769	0.00	0.00	32.05	2.83
1005	1064	7.918579	AGTCCCCTTAGTAATCCCTATACTA	57.081	40.000	0.00	0.00	35.34	1.82
1006	1065	6.817119	AGTCCCCTTAGTAATCCCTATACT	57.183	41.667	0.00	0.00	37.39	2.12
1049	1108	9.174166	GGAATATATTGGCGGATGTATTAGTTT	57.826	33.333	1.78	0.00	0.00	2.66
1050	1109	8.548877	AGGAATATATTGGCGGATGTATTAGTT	58.451	33.333	1.78	0.00	0.00	2.24
1057	1116	3.009473	AGCAGGAATATATTGGCGGATGT	59.991	43.478	1.78	0.00	0.00	3.06
1236	6887	1.949525	GCAGTGCCCACGAATGATATT	59.050	47.619	2.85	0.00	36.20	1.28
1340	6991	9.625747	TCCAAAACAGATAATATAACAGCATGA	57.374	29.630	0.00	0.00	39.69	3.07
1539	7193	3.635734	CTTGTGCTTCGCGGCTTCG	62.636	63.158	6.13	0.00	0.00	3.79
1541	7195	2.280797	TCTTGTGCTTCGCGGCTT	60.281	55.556	6.13	0.00	0.00	4.35
1542	7196	2.740055	CTCTTGTGCTTCGCGGCT	60.740	61.111	6.13	0.00	0.00	5.52
1543	7197	2.117941	AAACTCTTGTGCTTCGCGGC	62.118	55.000	6.13	2.62	0.00	6.53
1546	7200	0.661483	GCCAAACTCTTGTGCTTCGC	60.661	55.000	0.00	0.00	0.00	4.70
1562	7216	0.251386	ACTCGAGACTCTTCTGGCCA	60.251	55.000	21.68	4.71	29.47	5.36
1576	7230	1.001974	CCACCCTTGTCATTGACTCGA	59.998	52.381	17.26	3.67	33.15	4.04
1585	7239	2.449518	TGCCCTCCACCCTTGTCA	60.450	61.111	0.00	0.00	0.00	3.58
1662	7321	2.936993	GCATCAGATTCACGTCAAGGGT	60.937	50.000	0.00	0.00	0.00	4.34
1663	7322	1.667724	GCATCAGATTCACGTCAAGGG	59.332	52.381	0.00	0.00	0.00	3.95
1664	7323	1.667724	GGCATCAGATTCACGTCAAGG	59.332	52.381	0.00	0.00	0.00	3.61
1665	7324	2.349590	TGGCATCAGATTCACGTCAAG	58.650	47.619	0.00	0.00	0.00	3.02
1666	7325	2.470983	TGGCATCAGATTCACGTCAA	57.529	45.000	0.00	0.00	0.00	3.18
1678	7338	7.448420	TGGATTTACAAGAATTTTTGGCATCA	58.552	30.769	12.83	1.95	32.32	3.07
1693	7353	3.399644	TCTGGGGGTTTCTGGATTTACAA	59.600	43.478	0.00	0.00	0.00	2.41
1695	7355	3.732048	TCTGGGGGTTTCTGGATTTAC	57.268	47.619	0.00	0.00	0.00	2.01
1764	7424	3.119602	GGAACGGGCTTAGATTGGTTTTC	60.120	47.826	0.00	0.00	0.00	2.29
1919	7580	1.879380	TGCCAAATCAAGAACACGAGG	59.121	47.619	0.00	0.00	0.00	4.63
1944	7617	1.463056	CAAAGCTCGCGGTACATCAAA	59.537	47.619	6.13	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.