AutoCloner

Multiple sequence alignment - TraesCS3B01G075800

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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	TraesCS3B01G075800	chr3B	100.000	4064	0	0	1	4064	46765151	46769214	0.000000e+00	7505
1	TraesCS3B01G075800	chr3B	89.261	4088	361	58	1	4064	543865295	543861262	0.000000e+00	5046
2	TraesCS3B01G075800	chr3B	94.084	2248	115	15	1	2241	708794887	708792651	0.000000e+00	3398
3	TraesCS3B01G075800	chr7B	94.869	4073	192	15	1	4064	16174979	16170915	0.000000e+00	6348
4	TraesCS3B01G075800	chr7B	89.605	4127	317	59	1	4064	655038968	655034891	0.000000e+00	5142
5	TraesCS3B01G075800	chr7B	90.340	3178	247	44	1	3166	331005211	331002082	0.000000e+00	4113
6	TraesCS3B01G075800	chr7B	83.747	1932	261	43	2159	4064	142426161	142424257	0.000000e+00	1779
7	TraesCS3B01G075800	chr7B	79.390	1936	288	68	2182	4058	147709029	147710912	0.000000e+00	1262
8	TraesCS3B01G075800	chr7B	86.933	551	63	8	3516	4064	630441228	630440685	9.660000e-171	610
9	TraesCS3B01G075800	chr2B	90.644	4083	328	42	1	4064	769026774	769022727	0.000000e+00	5374
10	TraesCS3B01G075800	chr2B	90.597	4084	310	43	1	4064	676187978	676183949	0.000000e+00	5347
11	TraesCS3B01G075800	chr2B	94.783	2607	113	17	1472	4064	67198290	67195693	0.000000e+00	4039
12	TraesCS3B01G075800	chr4B	90.375	4083	331	42	1	4064	195244829	195248868	0.000000e+00	5306
13	TraesCS3B01G075800	chr6B	89.809	4092	338	60	1	4064	510709373	510713413	0.000000e+00	5173
14	TraesCS3B01G075800	chr1B	94.737	2603	120	13	1472	4064	547572850	547570255	0.000000e+00	4032

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	TraesCS3B01G075800	chr3B	46765151	46769214	4063	False	7505	7505	100.000	1	4064	1	chr3B.!!$F1	4063
1	TraesCS3B01G075800	chr3B	543861262	543865295	4033	True	5046	5046	89.261	1	4064	1	chr3B.!!$R1	4063
2	TraesCS3B01G075800	chr3B	708792651	708794887	2236	True	3398	3398	94.084	1	2241	1	chr3B.!!$R2	2240
3	TraesCS3B01G075800	chr7B	16170915	16174979	4064	True	6348	6348	94.869	1	4064	1	chr7B.!!$R1	4063
4	TraesCS3B01G075800	chr7B	655034891	655038968	4077	True	5142	5142	89.605	1	4064	1	chr7B.!!$R5	4063
5	TraesCS3B01G075800	chr7B	331002082	331005211	3129	True	4113	4113	90.340	1	3166	1	chr7B.!!$R3	3165
6	TraesCS3B01G075800	chr7B	142424257	142426161	1904	True	1779	1779	83.747	2159	4064	1	chr7B.!!$R2	1905
7	TraesCS3B01G075800	chr7B	147709029	147710912	1883	False	1262	1262	79.390	2182	4058	1	chr7B.!!$F1	1876
8	TraesCS3B01G075800	chr7B	630440685	630441228	543	True	610	610	86.933	3516	4064	1	chr7B.!!$R4	548
9	TraesCS3B01G075800	chr2B	769022727	769026774	4047	True	5374	5374	90.644	1	4064	1	chr2B.!!$R3	4063
10	TraesCS3B01G075800	chr2B	676183949	676187978	4029	True	5347	5347	90.597	1	4064	1	chr2B.!!$R2	4063
11	TraesCS3B01G075800	chr2B	67195693	67198290	2597	True	4039	4039	94.783	1472	4064	1	chr2B.!!$R1	2592
12	TraesCS3B01G075800	chr4B	195244829	195248868	4039	False	5306	5306	90.375	1	4064	1	chr4B.!!$F1	4063
13	TraesCS3B01G075800	chr6B	510709373	510713413	4040	False	5173	5173	89.809	1	4064	1	chr6B.!!$F1	4063
14	TraesCS3B01G075800	chr1B	547570255	547572850	2595	True	4032	4032	94.737	1472	4064	1	chr1B.!!$R1	2592

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
905	929	1.021390	AGGAATCCGTTTCTGCGCTG	61.021	55.0	9.73	8.88	34.56	5.18	F
2215	2383	0.256752	TAGCTGATGGCCAAGCATGT	59.743	50.0	27.17	12.37	43.05	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2828	3006	0.033228	CTGCCCATCATCCTCTCGAC	59.967	60.0	0.0	0.0	0.00	4.20	R
3203	3389	0.250901	TGGCTTTCTCAAGTCTGGCC	60.251	55.0	0.0	0.0	35.44	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
47	49	3.770933	ACATGGCAATTTCAACCTAGCAT	59.229	39.130	0.00	0.00	0.00	3.79
98	100	1.357137	TGTTGCATGAGGACAGGGTA	58.643	50.000	0.00	0.00	0.00	3.69
275	279	9.566530	CCACATTTATGTTTTCGACAATCATAA	57.433	29.630	11.73	11.73	42.62	1.90
280	284	4.013728	TGTTTTCGACAATCATAAGGGGG	58.986	43.478	0.00	0.00	34.69	5.40
342	359	2.086869	CATTTTCACTCGAGCCCATGT	58.913	47.619	13.61	0.00	0.00	3.21
455	473	1.731709	CTCGCGGTGATCATCAAAACA	59.268	47.619	6.13	0.00	0.00	2.83
491	509	3.025322	TGGAACCACCACAACAGAATT	57.975	42.857	0.00	0.00	44.64	2.17
528	546	1.192428	AAAGAGGGCGACGAGGTAAT	58.808	50.000	0.00	0.00	0.00	1.89
576	594	2.666272	TGTTATTGGTTGCCACCTCA	57.334	45.000	8.65	0.00	44.61	3.86
583	603	1.662044	GTTGCCACCTCAAGCTTGG	59.338	57.895	25.73	13.76	0.00	3.61
592	612	1.819288	CCTCAAGCTTGGAGTCGTCTA	59.181	52.381	25.73	2.60	0.00	2.59
631	651	1.400142	TGACAGTGAAAACACGGCAAG	59.600	47.619	0.00	0.00	0.00	4.01
675	697	3.973657	TCGCAGAAGAAGAAACGTACTT	58.026	40.909	7.48	7.48	0.00	2.24
846	869	2.539277	TTATGACCCCGCCTCCAGGA	62.539	60.000	0.00	0.00	37.39	3.86
902	926	1.656652	ATGAGGAATCCGTTTCTGCG	58.343	50.000	0.00	0.00	34.56	5.18
905	929	1.021390	AGGAATCCGTTTCTGCGCTG	61.021	55.000	9.73	8.88	34.56	5.18
1018	1043	1.640428	CATGCCGAACACGTCTGTAT	58.360	50.000	0.00	0.00	0.00	2.29
1222	1248	3.339253	TGTCATGTGCAAGCTAGTCAT	57.661	42.857	0.00	0.00	0.00	3.06
1302	1332	0.829333	AAAATTGTGTGGTGCAGGCA	59.171	45.000	0.00	0.00	0.00	4.75
1754	1907	4.128925	ACATCAGCTCATGTACGTCAAT	57.871	40.909	0.00	0.00	35.10	2.57
1802	1957	2.039831	GGGATAGGAGGCCCACCA	60.040	66.667	17.23	5.52	44.07	4.17
1925	2080	6.557633	AGGTTAGTCCTGGTTTCTTTCTCTAA	59.442	38.462	0.00	0.00	46.19	2.10
1950	2106	7.172654	ACGACATTCTTTACAAATTTTTGCC	57.827	32.000	3.00	0.00	41.79	4.52
2033	2193	1.281577	TGTTATCCATGGCTGTCTGCA	59.718	47.619	6.96	0.00	45.15	4.41
2145	2308	7.382218	AGTTTTTGCAATACATGAACTGTTAGC	59.618	33.333	0.00	0.00	39.39	3.09
2215	2383	0.256752	TAGCTGATGGCCAAGCATGT	59.743	50.000	27.17	12.37	43.05	3.21
2329	2498	8.396390	CAAAGATATACATCTATGGCTGCATTC	58.604	37.037	0.50	0.00	40.81	2.67
2331	2500	2.916702	ACATCTATGGCTGCATTCGA	57.083	45.000	0.50	0.00	0.00	3.71
2332	2501	3.413846	ACATCTATGGCTGCATTCGAT	57.586	42.857	0.50	0.00	0.00	3.59
2465	2643	1.741770	GAATGACCGGCTTGCTCGT	60.742	57.895	0.00	0.00	0.00	4.18
2476	2654	1.334149	GCTTGCTCGTGAAGTTGGTTC	60.334	52.381	0.00	0.00	35.48	3.62
2717	2895	1.144969	GACGAACATGGCGAAGTTCA	58.855	50.000	15.51	0.00	43.20	3.18
2828	3006	2.003548	CCTCAAAGAGGGGGAGGGG	61.004	68.421	5.13	0.00	45.43	4.79
3061	3247	1.765314	GTGAGGTGATAGCTGGTGGAT	59.235	52.381	0.00	0.00	0.00	3.41
3106	3292	1.252904	AACGCCTACCCGTGCTTCTA	61.253	55.000	0.00	0.00	41.90	2.10
3170	3356	5.144159	TCCACTAGGTCATCTCCTTGTAT	57.856	43.478	0.00	0.00	40.42	2.29
3203	3389	2.184322	CGGGGATCCTGTCGTGTG	59.816	66.667	12.58	0.00	0.00	3.82
3234	3420	5.489792	TGAGAAAGCCAGTCAAGAAGTAT	57.510	39.130	0.00	0.00	0.00	2.12
3387	3598	4.808558	TGCATGGAAACTATTGCTTGTTC	58.191	39.130	0.00	0.00	35.38	3.18
3591	3838	4.149511	TGCATGGCAACTGCTAACTATA	57.850	40.909	13.68	0.00	40.34	1.31
3756	4014	1.339929	TGAAGAAGACTACTGCACGCA	59.660	47.619	0.00	0.00	0.00	5.24
3787	4045	1.146263	CCATTAGGGACCCACTCGC	59.854	63.158	14.60	0.00	40.01	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	7.450124	TGAAATTGCCATGTTAAAATGCAAT	57.550	28.000	16.29	16.29	36.61	3.56
98	100	1.842562	ACCTAAGATGTGGCAGCTCAT	59.157	47.619	0.00	0.00	0.00	2.90
280	284	2.127270	CATGAACACGCACGCACC	60.127	61.111	0.00	0.00	0.00	5.01
455	473	7.345132	TGGTGGTTCCATGAAATTATCATCATT	59.655	33.333	0.00	0.00	45.91	2.57
475	493	1.703411	CCCAATTCTGTTGTGGTGGT	58.297	50.000	0.00	0.00	0.00	4.16
484	502	1.133513	TGTCCAGTTGCCCAATTCTGT	60.134	47.619	0.00	0.00	0.00	3.41
491	509	0.843309	TTTCTCTGTCCAGTTGCCCA	59.157	50.000	0.00	0.00	0.00	5.36
528	546	1.415672	GGAGGAGGGTGTGTGGACAA	61.416	60.000	0.00	0.00	32.49	3.18
576	594	3.701542	TCATGATAGACGACTCCAAGCTT	59.298	43.478	0.00	0.00	0.00	3.74
655	677	3.489785	ACAAGTACGTTTCTTCTTCTGCG	59.510	43.478	0.00	0.00	0.00	5.18
675	697	1.923395	CCTGGGAGGCCCTGTTACA	60.923	63.158	0.00	0.00	45.70	2.41
846	869	2.227865	CACGTCCCGGAATCACAAAATT	59.772	45.455	0.73	0.00	0.00	1.82
873	896	2.301346	GGATTCCTCATTCAACGGCAT	58.699	47.619	0.00	0.00	0.00	4.40
1178	1204	3.366374	CGGAAGCCAAAAGATTGAAGGAC	60.366	47.826	0.00	0.00	38.94	3.85
1222	1248	4.734398	AAACATCAAAGAACACTGGCAA	57.266	36.364	0.00	0.00	0.00	4.52
1302	1332	7.999679	TCATGTTCTTCACATCTTTCAGTTTT	58.000	30.769	0.00	0.00	43.17	2.43
1337	1367	1.522668	CAGGAAGTCGGCAATGAACA	58.477	50.000	0.00	0.00	0.00	3.18
1636	1781	6.768483	TCCTACAATCATCAAGTTGAAGTGA	58.232	36.000	10.14	10.50	0.00	3.41
1754	1907	3.494924	CCACAGTGGACAGATCAAGACAA	60.495	47.826	15.35	0.00	40.96	3.18
1802	1957	2.361789	ACAACAAACTTGTGCGTAGGT	58.638	42.857	0.00	0.00	41.31	3.08
1925	2080	7.515998	CGGCAAAAATTTGTAAAGAATGTCGTT	60.516	33.333	7.64	0.00	40.24	3.85
1950	2106	7.587392	ACATCACGATTTTTCATATGTTATGCG	59.413	33.333	1.90	4.21	0.00	4.73
2033	2193	5.247110	GTGGAGTGAGACATGGATACCATAT	59.753	44.000	2.86	0.00	43.15	1.78
2145	2308	9.219603	TGTAAAAGAGAGAATGATTAACACTGG	57.780	33.333	0.00	0.00	0.00	4.00
2215	2383	5.011329	CCCCCAAACACGCTATAGTCTATAA	59.989	44.000	0.84	0.00	0.00	0.98
2349	2521	2.877786	CCATGTTACAGTCACTTGCACA	59.122	45.455	0.00	0.00	0.00	4.57
2465	2643	1.566703	TCCAACCCTGAACCAACTTCA	59.433	47.619	0.00	0.00	36.46	3.02
2512	2690	4.719369	GAACTGCCTCGCGACCGT	62.719	66.667	3.71	0.00	35.54	4.83
2690	2868	1.076533	GCCATGTTCGTCGTCATCGT	61.077	55.000	0.00	0.00	38.33	3.73
2717	2895	0.034089	GCCCTTCTTACCACCTGCAT	60.034	55.000	0.00	0.00	0.00	3.96
2828	3006	0.033228	CTGCCCATCATCCTCTCGAC	59.967	60.000	0.00	0.00	0.00	4.20
2857	3035	0.033991	TCGCTCCTAGACCTCTTGCT	60.034	55.000	0.00	0.00	0.00	3.91
3050	3236	1.279496	AACTGCTCATCCACCAGCTA	58.721	50.000	0.00	0.00	36.53	3.32
3061	3247	4.824537	TGCCTGTTTATTTGTAACTGCTCA	59.175	37.500	0.00	0.00	0.00	4.26
3106	3292	1.021968	GCACCTTTGTTCAACCGAGT	58.978	50.000	0.00	0.00	0.00	4.18
3170	3356	2.026445	CGGTGTTGGACGTCGTCA	59.974	61.111	25.64	10.15	33.68	4.35
3203	3389	0.250901	TGGCTTTCTCAAGTCTGGCC	60.251	55.000	0.00	0.00	35.44	5.36
3234	3420	4.022068	GGCAATGAGAGAACATGGAAAACA	60.022	41.667	0.00	0.00	0.00	2.83
3378	3589	2.613133	GCCATGCAAAAAGAACAAGCAA	59.387	40.909	0.00	0.00	38.85	3.91
3591	3838	3.245229	TGGAATAAGAGTTGCCATGTGGT	60.245	43.478	0.35	0.00	37.57	4.16
3756	4014	2.158813	CCCTAATGGTATGCTTGACCGT	60.159	50.000	0.00	0.00	40.09	4.83
3787	4045	5.155509	TGACAACTTTGAATGAAGACGTG	57.844	39.130	0.00	0.00	0.00	4.49
3937	4195	2.549992	GCTGATGTACGGATGCCCATTA	60.550	50.000	0.00	0.00	0.00	1.90
3940	4198	1.146041	GCTGATGTACGGATGCCCA	59.854	57.895	0.00	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.