AutoCloner

Multiple sequence alignment - TraesCS1B01G156300

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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	TraesCS1B01G156300	chr1B	100.000	3296	0	0	1	3296	263949470	263946175	0.000000e+00	6087.0
1	TraesCS1B01G156300	chr1D	94.131	2658	94	17	653	3278	190481038	190478411	0.000000e+00	3988.0
2	TraesCS1B01G156300	chr1A	91.475	1736	88	37	653	2357	212018171	212019877	0.000000e+00	2331.0
3	TraesCS1B01G156300	chr1A	91.760	983	47	11	2340	3296	212021720	212022694	0.000000e+00	1336.0
4	TraesCS1B01G156300	chr3B	96.716	609	18	2	3	610	246495819	246495212	0.000000e+00	1013.0
5	TraesCS1B01G156300	chr3B	72.742	620	158	8	1	610	177490085	177490703	7.210000e-47	198.0
6	TraesCS1B01G156300	chrUn	97.425	466	12	0	1	466	108309200	108309665	0.000000e+00	795.0
7	TraesCS1B01G156300	chrUn	94.444	54	2	1	558	610	108309970	108310023	7.580000e-12	82.4
8	TraesCS1B01G156300	chr7A	92.762	525	37	1	1	525	430316765	430317288	0.000000e+00	758.0
9	TraesCS1B01G156300	chr2A	91.434	537	30	3	65	599	705538722	705538200	0.000000e+00	723.0
10	TraesCS1B01G156300	chr2A	72.852	291	56	19	1739	2016	716488109	716487829	9.810000e-11	78.7
11	TraesCS1B01G156300	chr2D	89.624	559	24	10	65	608	565096923	565096384	0.000000e+00	680.0
12	TraesCS1B01G156300	chr2D	73.568	227	41	15	1739	1954	578937062	578936844	5.900000e-08	69.4
13	TraesCS1B01G156300	chr2B	90.466	451	34	6	79	524	676758769	676758323	1.320000e-163	586.0
14	TraesCS1B01G156300	chr2B	74.336	226	41	16	1739	1954	695859716	695859498	2.730000e-11	80.5
15	TraesCS1B01G156300	chr6D	73.879	513	132	1	100	610	47890	48402	1.550000e-48	204.0
16	TraesCS1B01G156300	chr5B	90.385	52	5	0	1258	1309	136018626	136018677	5.900000e-08	69.4
17	TraesCS1B01G156300	chr5A	90.385	52	5	0	1258	1309	135154552	135154603	5.900000e-08	69.4

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	TraesCS1B01G156300	chr1B	263946175	263949470	3295	True	6087.0	6087	100.0000	1	3296	1	chr1B.!!$R1	3295
1	TraesCS1B01G156300	chr1D	190478411	190481038	2627	True	3988.0	3988	94.1310	653	3278	1	chr1D.!!$R1	2625
2	TraesCS1B01G156300	chr1A	212018171	212022694	4523	False	1833.5	2331	91.6175	653	3296	2	chr1A.!!$F1	2643
3	TraesCS1B01G156300	chr3B	246495212	246495819	607	True	1013.0	1013	96.7160	3	610	1	chr3B.!!$R1	607
4	TraesCS1B01G156300	chrUn	108309200	108310023	823	False	438.7	795	95.9345	1	610	2	chrUn.!!$F1	609
5	TraesCS1B01G156300	chr7A	430316765	430317288	523	False	758.0	758	92.7620	1	525	1	chr7A.!!$F1	524
6	TraesCS1B01G156300	chr2A	705538200	705538722	522	True	723.0	723	91.4340	65	599	1	chr2A.!!$R1	534
7	TraesCS1B01G156300	chr2D	565096384	565096923	539	True	680.0	680	89.6240	65	608	1	chr2D.!!$R1	543
8	TraesCS1B01G156300	chr6D	47890	48402	512	False	204.0	204	73.8790	100	610	1	chr6D.!!$F1	510

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
746	988	0.093026	GACAATGCTCACACGTACGC	59.907	55.0	16.72	0.0	0.00	4.42	F
1397	1681	1.324740	GCATTTGATCCTGCCAGCCA	61.325	55.0	0.00	0.0	32.15	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2241	2557	0.834687	TGAGGAGGTTGTAGCCCGTT	60.835	55.0	0.0	0.0	0.00	4.44	R
3067	5256	1.192803	AACAAGACCCCTCTCCGGAC	61.193	60.0	0.0	0.0	33.16	4.79	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
115	116	4.337177	TCCGGCGTGGATGGCAAA	62.337	61.111	6.01	0.00	43.74	3.68
201	216	1.005037	TGTTAGTGCAGTCTGCCGG	60.005	57.895	21.99	0.00	44.23	6.13
207	222	3.695606	GCAGTCTGCCGGGACTCA	61.696	66.667	14.27	0.00	43.75	3.41
231	246	0.955428	GCACGTTCCTTGGAGCATCA	60.955	55.000	4.50	0.00	36.25	3.07
343	372	2.037902	TCCAAGTTACAGATTGCCACGA	59.962	45.455	0.00	0.00	0.00	4.35
350	379	1.603802	ACAGATTGCCACGAACTGTTG	59.396	47.619	0.00	0.00	38.41	3.33
467	496	8.372459	AGTATCTATTAGTCATGAGTCTCGAGT	58.628	37.037	13.13	0.00	0.00	4.18
572	814	7.285401	CACCAATAGCTTGTATTCCCATAAACT	59.715	37.037	0.00	0.00	0.00	2.66
708	950	6.147656	GCACGAAAATTTCCATTCCAAGATTT	59.852	34.615	0.00	0.00	0.00	2.17
709	951	7.307930	GCACGAAAATTTCCATTCCAAGATTTT	60.308	33.333	0.00	0.00	31.55	1.82
710	952	8.223100	CACGAAAATTTCCATTCCAAGATTTTC	58.777	33.333	0.00	0.00	38.84	2.29
712	954	7.411804	CGAAAATTTCCATTCCAAGATTTTCCG	60.412	37.037	11.50	5.76	38.94	4.30
713	955	3.866883	TTCCATTCCAAGATTTTCCGC	57.133	42.857	0.00	0.00	0.00	5.54
714	956	2.099405	TCCATTCCAAGATTTTCCGCC	58.901	47.619	0.00	0.00	0.00	6.13
716	958	2.233431	CCATTCCAAGATTTTCCGCCAA	59.767	45.455	0.00	0.00	0.00	4.52
717	959	3.514645	CATTCCAAGATTTTCCGCCAAG	58.485	45.455	0.00	0.00	0.00	3.61
718	960	1.544724	TCCAAGATTTTCCGCCAAGG	58.455	50.000	0.00	0.00	42.97	3.61
742	984	1.139989	CGAAGACAATGCTCACACGT	58.860	50.000	0.00	0.00	0.00	4.49
746	988	0.093026	GACAATGCTCACACGTACGC	59.907	55.000	16.72	0.00	0.00	4.42
748	990	2.092291	AATGCTCACACGTACGCGG	61.092	57.895	16.72	10.71	43.45	6.46
809	1051	3.074412	AGGTAGCCGAAACTTGTGAATG	58.926	45.455	0.00	0.00	0.00	2.67
812	1054	2.297701	AGCCGAAACTTGTGAATGTGT	58.702	42.857	0.00	0.00	0.00	3.72
813	1055	2.290641	AGCCGAAACTTGTGAATGTGTC	59.709	45.455	0.00	0.00	0.00	3.67
933	1176	1.387295	ATCGATCGGACAGAGCAGCA	61.387	55.000	16.41	0.00	34.30	4.41
935	1178	1.882167	GATCGGACAGAGCAGCAGC	60.882	63.158	0.00	0.00	42.56	5.25
939	1182	2.661399	GACAGAGCAGCAGCAGGA	59.339	61.111	3.17	0.00	45.49	3.86
941	1184	2.125065	CAGAGCAGCAGCAGGAGG	60.125	66.667	3.17	0.00	45.49	4.30
942	1185	2.284478	AGAGCAGCAGCAGGAGGA	60.284	61.111	3.17	0.00	45.49	3.71
943	1186	2.187424	GAGCAGCAGCAGGAGGAG	59.813	66.667	3.17	0.00	45.49	3.69
944	1187	3.388703	GAGCAGCAGCAGGAGGAGG	62.389	68.421	3.17	0.00	45.49	4.30
947	1190	2.365370	AGCAGCAGGAGGAGGAGG	60.365	66.667	0.00	0.00	0.00	4.30
964	1207	2.048127	GAGGAGGCGTGGTGTGAC	60.048	66.667	0.00	0.00	0.00	3.67
1030	1276	3.799755	GTGAATGCACGCCCGGAC	61.800	66.667	0.73	0.00	34.94	4.79
1310	1559	2.025727	CGGCGACATCCTCGGTAC	59.974	66.667	0.00	0.00	43.18	3.34
1397	1681	1.324740	GCATTTGATCCTGCCAGCCA	61.325	55.000	0.00	0.00	32.15	4.75
1405	1689	3.479203	CTGCCAGCCACCCGGATA	61.479	66.667	0.73	0.00	0.00	2.59
1857	2173	2.437359	ATCCAGAAGCTGCACGGC	60.437	61.111	1.02	0.00	0.00	5.68
2005	2321	3.452786	CGGCGCTGGAGAAGGAGA	61.453	66.667	8.83	0.00	0.00	3.71
2173	2489	2.661537	TGACGCTCACCTGCAACG	60.662	61.111	0.00	0.00	0.00	4.10
2174	2490	4.077188	GACGCTCACCTGCAACGC	62.077	66.667	0.00	0.00	0.00	4.84
2175	2491	4.908687	ACGCTCACCTGCAACGCA	62.909	61.111	0.00	0.00	36.92	5.24
2241	2557	0.470456	ACACCTACCACCTCACCGAA	60.470	55.000	0.00	0.00	0.00	4.30
2300	2616	2.541178	GCTACGGTCTGTGGTAGATTCG	60.541	54.545	2.60	0.00	38.69	3.34
2320	2636	5.041951	TCGGCATCATCAAACTTTACAAC	57.958	39.130	0.00	0.00	0.00	3.32
2399	4575	7.048629	TGATAAGCAGACACCAATTTTGAAA	57.951	32.000	0.00	0.00	0.00	2.69
2401	4577	4.734398	AGCAGACACCAATTTTGAAACA	57.266	36.364	0.00	0.00	0.00	2.83
2402	4578	4.432712	AGCAGACACCAATTTTGAAACAC	58.567	39.130	0.00	0.00	0.00	3.32
2403	4579	4.160252	AGCAGACACCAATTTTGAAACACT	59.840	37.500	0.00	0.00	0.00	3.55
2405	4581	5.687285	GCAGACACCAATTTTGAAACACTAG	59.313	40.000	0.00	0.00	0.00	2.57
2406	4582	6.680378	GCAGACACCAATTTTGAAACACTAGT	60.680	38.462	0.00	0.00	0.00	2.57
2408	4584	8.567948	CAGACACCAATTTTGAAACACTAGTAT	58.432	33.333	0.00	0.00	0.00	2.12
2409	4585	8.784043	AGACACCAATTTTGAAACACTAGTATC	58.216	33.333	0.00	0.00	0.00	2.24
2488	4667	1.271379	ACTTTGGTCCTTATGCGCAGT	60.271	47.619	18.32	6.92	0.00	4.40
2554	4733	6.661777	TGACCATGATTATCCAAGATGACAA	58.338	36.000	0.00	0.00	0.00	3.18
2556	4735	7.283807	TGACCATGATTATCCAAGATGACAAAG	59.716	37.037	0.00	0.00	0.00	2.77
2558	4737	7.284034	ACCATGATTATCCAAGATGACAAAGAC	59.716	37.037	0.00	0.00	0.00	3.01
2618	4798	7.935755	ACCCAGAGACATGACATAAATGATAAG	59.064	37.037	0.00	0.00	0.00	1.73
2658	4838	4.823989	TGAGATGAGACATGAGAAGCGATA	59.176	41.667	0.00	0.00	0.00	2.92
2663	4843	5.284864	TGAGACATGAGAAGCGATATCAAC	58.715	41.667	0.00	0.00	31.99	3.18
2758	4947	1.846712	AAACTCTGGGAGAGGCTGCC	61.847	60.000	11.65	11.65	46.45	4.85
2875	5064	0.732880	GCTTCACGTCGAGCAGCTTA	60.733	55.000	13.30	0.00	0.00	3.09
2920	5109	0.112412	TTGGAGCCTTTGGGGTTCTC	59.888	55.000	0.00	0.00	44.22	2.87
2982	5171	7.593875	TGAAAATTCAGTGGTTTTCAAACAG	57.406	32.000	23.26	0.00	45.85	3.16
3041	5230	7.724490	TGAGGGTAATCATGATAGGTATGAG	57.276	40.000	9.04	0.00	37.91	2.90
3060	5249	3.274288	GAGTAACCTCATGAAAGGCCAG	58.726	50.000	5.01	0.00	40.34	4.85
3067	5256	0.809385	CATGAAAGGCCAGTGCTCAG	59.191	55.000	5.01	0.00	37.74	3.35
3260	5463	7.095439	CGCTACAGAAAGATTTGGAATCCTATC	60.095	40.741	0.00	3.97	0.00	2.08
3261	5464	7.174080	GCTACAGAAAGATTTGGAATCCTATCC	59.826	40.741	0.00	0.00	40.10	2.59
3262	5465	7.218314	ACAGAAAGATTTGGAATCCTATCCT	57.782	36.000	0.00	0.00	40.35	3.24
3263	5466	8.337118	ACAGAAAGATTTGGAATCCTATCCTA	57.663	34.615	0.00	0.00	40.35	2.94
3264	5467	8.953665	ACAGAAAGATTTGGAATCCTATCCTAT	58.046	33.333	0.00	0.00	40.35	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
201	216	2.665185	AACGTGCCGCTTGAGTCC	60.665	61.111	0.00	0.00	0.00	3.85
207	222	2.978010	CCAAGGAACGTGCCGCTT	60.978	61.111	7.01	0.00	36.24	4.68
231	246	1.378762	CCCCTCAAACACCACCGAT	59.621	57.895	0.00	0.00	0.00	4.18
343	372	2.366266	TCCGTACTACTTGCCAACAGTT	59.634	45.455	0.00	0.00	0.00	3.16
350	379	3.592059	TCAATGTTCCGTACTACTTGCC	58.408	45.455	0.00	0.00	0.00	4.52
467	496	9.462174	CAAGATTGTGTGCTTCTAAATTACAAA	57.538	29.630	0.00	0.00	31.39	2.83
572	814	7.902087	ACACCAAATAGCTTTATTTAGGCAAA	58.098	30.769	0.00	0.00	0.00	3.68
648	890	4.553330	TCGCCACCTTCTAGAGATTTTT	57.447	40.909	0.00	0.00	0.00	1.94
649	891	4.254492	GTTCGCCACCTTCTAGAGATTTT	58.746	43.478	0.00	0.00	0.00	1.82
650	892	3.676324	CGTTCGCCACCTTCTAGAGATTT	60.676	47.826	0.00	0.00	0.00	2.17
651	893	2.159226	CGTTCGCCACCTTCTAGAGATT	60.159	50.000	0.00	0.00	0.00	2.40
709	951	0.107081	TCTTCGTTTTCCTTGGCGGA	59.893	50.000	0.00	0.00	41.06	5.54
710	952	0.237498	GTCTTCGTTTTCCTTGGCGG	59.763	55.000	0.00	0.00	0.00	6.13
712	954	3.308530	CATTGTCTTCGTTTTCCTTGGC	58.691	45.455	0.00	0.00	0.00	4.52
713	955	3.004734	AGCATTGTCTTCGTTTTCCTTGG	59.995	43.478	0.00	0.00	0.00	3.61
714	956	4.222114	GAGCATTGTCTTCGTTTTCCTTG	58.778	43.478	0.00	0.00	0.00	3.61
716	958	3.251004	GTGAGCATTGTCTTCGTTTTCCT	59.749	43.478	0.00	0.00	0.00	3.36
717	959	3.003275	TGTGAGCATTGTCTTCGTTTTCC	59.997	43.478	0.00	0.00	0.00	3.13
718	960	3.968724	GTGTGAGCATTGTCTTCGTTTTC	59.031	43.478	0.00	0.00	0.00	2.29
742	984	1.904865	AAGTGAGGTGACCCGCGTA	60.905	57.895	4.92	0.00	35.12	4.42
746	988	1.372997	CGTCAAGTGAGGTGACCCG	60.373	63.158	0.00	0.00	42.00	5.28
748	990	1.865340	GTTTCGTCAAGTGAGGTGACC	59.135	52.381	0.00	0.00	42.00	4.02
809	1051	3.059884	TCTTGCAAGATTGAGACGACAC	58.940	45.455	25.16	0.00	0.00	3.67
812	1054	4.154737	CCATTTCTTGCAAGATTGAGACGA	59.845	41.667	28.89	9.49	34.49	4.20
813	1055	4.409570	CCATTTCTTGCAAGATTGAGACG	58.590	43.478	28.89	13.17	34.49	4.18
933	1176	1.938596	TCCTCCTCCTCCTCCTGCT	60.939	63.158	0.00	0.00	0.00	4.24
935	1178	1.232792	CCTCCTCCTCCTCCTCCTG	59.767	68.421	0.00	0.00	0.00	3.86
939	1182	3.351885	ACGCCTCCTCCTCCTCCT	61.352	66.667	0.00	0.00	0.00	3.69
941	1184	3.151022	CCACGCCTCCTCCTCCTC	61.151	72.222	0.00	0.00	0.00	3.71
942	1185	3.999285	ACCACGCCTCCTCCTCCT	61.999	66.667	0.00	0.00	0.00	3.69
943	1186	3.775654	CACCACGCCTCCTCCTCC	61.776	72.222	0.00	0.00	0.00	4.30
944	1187	2.997897	ACACCACGCCTCCTCCTC	60.998	66.667	0.00	0.00	0.00	3.71
947	1190	2.048127	GTCACACCACGCCTCCTC	60.048	66.667	0.00	0.00	0.00	3.71
1310	1559	3.985925	GCTTGAACCTTACGATATACCCG	59.014	47.826	0.00	0.00	0.00	5.28
1320	1569	2.736400	GCCATGCATGCTTGAACCTTAC	60.736	50.000	29.52	9.94	0.00	2.34
1352	1636	1.927487	TCAGTTTCAATGCCTGCCAT	58.073	45.000	0.00	0.00	35.06	4.40
1353	1637	1.546923	CATCAGTTTCAATGCCTGCCA	59.453	47.619	0.00	0.00	0.00	4.92
1354	1638	1.134907	CCATCAGTTTCAATGCCTGCC	60.135	52.381	0.00	0.00	0.00	4.85
1355	1639	1.547372	ACCATCAGTTTCAATGCCTGC	59.453	47.619	0.00	0.00	0.00	4.85
1356	1640	3.581755	CAACCATCAGTTTCAATGCCTG	58.418	45.455	0.00	0.00	36.18	4.85
1397	1681	2.444256	GCTTCAGGCCTATCCGGGT	61.444	63.158	3.98	0.00	40.77	5.28
1405	1689	1.293498	CACGTACTGCTTCAGGCCT	59.707	57.895	0.00	0.00	40.92	5.19
1519	1803	2.125952	TGAGCGCTCACCACGATG	60.126	61.111	35.30	0.00	34.14	3.84
2196	2512	1.134438	AGAGGAACTTGGTGGGGTCC	61.134	60.000	0.00	0.00	41.55	4.46
2202	2518	1.699634	TCCCAGAAGAGGAACTTGGTG	59.300	52.381	0.00	0.00	41.55	4.17
2241	2557	0.834687	TGAGGAGGTTGTAGCCCGTT	60.835	55.000	0.00	0.00	0.00	4.44
2286	2602	2.107366	TGATGCCGAATCTACCACAGA	58.893	47.619	0.00	0.00	36.15	3.41
2300	2616	5.183904	AGAGGTTGTAAAGTTTGATGATGCC	59.816	40.000	0.00	0.00	0.00	4.40
2320	2636	8.581253	TGTCCATACATACACAGATATAGAGG	57.419	38.462	0.00	0.00	0.00	3.69
2331	2647	7.766219	AATTCGTACTTGTCCATACATACAC	57.234	36.000	0.00	0.00	34.97	2.90
2399	4575	8.964533	ATATCTTGGAAGGATGATACTAGTGT	57.035	34.615	5.39	0.00	0.00	3.55
2401	4577	9.607333	TGAATATCTTGGAAGGATGATACTAGT	57.393	33.333	0.00	0.00	0.00	2.57
2405	4581	7.118390	CGGTTGAATATCTTGGAAGGATGATAC	59.882	40.741	0.00	0.00	0.00	2.24
2406	4582	7.161404	CGGTTGAATATCTTGGAAGGATGATA	58.839	38.462	0.00	0.00	0.00	2.15
2408	4584	5.368145	CGGTTGAATATCTTGGAAGGATGA	58.632	41.667	0.00	0.00	0.00	2.92
2409	4585	4.023707	GCGGTTGAATATCTTGGAAGGATG	60.024	45.833	0.00	0.00	0.00	3.51
2488	4667	7.230913	GGTTAGTCATTAGCCTGTCATACTCTA	59.769	40.741	0.00	0.00	30.44	2.43
2588	4767	6.806668	TTTATGTCATGTCTCTGGGTATGA	57.193	37.500	0.00	0.00	0.00	2.15
2644	4824	3.134623	TGGGTTGATATCGCTTCTCATGT	59.865	43.478	0.00	0.00	0.00	3.21
2658	4838	3.833559	AAAGAAGTGGGATGGGTTGAT	57.166	42.857	0.00	0.00	0.00	2.57
2758	4947	1.303317	AAGGCCTGTACCCAAAGCG	60.303	57.895	5.69	0.00	0.00	4.68
2875	5064	1.599797	CCCTCGGCCTTCACGTTTT	60.600	57.895	0.00	0.00	0.00	2.43
3041	5230	2.749621	CACTGGCCTTTCATGAGGTTAC	59.250	50.000	3.32	0.00	39.11	2.50
3060	5249	2.716017	CCCTCTCCGGACTGAGCAC	61.716	68.421	13.92	0.00	33.16	4.40
3067	5256	1.192803	AACAAGACCCCTCTCCGGAC	61.193	60.000	0.00	0.00	33.16	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.