AutoCloner

Multiple sequence alignment - TraesCS2D01G458100

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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	TraesCS2D01G458100	chr2D	100.000	2441	0	0	1	2441	565184127	565181687	0.000000e+00	4508.0
1	TraesCS2D01G458100	chr2B	93.974	2041	88	13	1	2033	677220038	677218025	0.000000e+00	3055.0
2	TraesCS2D01G458100	chr2B	93.252	163	10	1	2059	2221	677211211	677211050	3.140000e-59	239.0
3	TraesCS2D01G458100	chr2A	91.817	2053	92	24	1	2030	705785294	705783295	0.000000e+00	2791.0
4	TraesCS2D01G458100	chr2A	94.087	389	15	6	2053	2441	705782744	705782364	3.500000e-163	584.0
5	TraesCS2D01G458100	chr2A	91.228	57	4	1	2054	2109	705759622	705759566	2.600000e-10	76.8
6	TraesCS2D01G458100	chr2A	100.000	28	0	0	2022	2049	628686654	628686681	4.000000e-03	52.8
7	TraesCS2D01G458100	chr4A	79.155	1396	191	49	426	1774	712966642	712965300	0.000000e+00	874.0
8	TraesCS2D01G458100	chr7A	82.394	869	102	30	919	1774	20402174	20401344	0.000000e+00	710.0
9	TraesCS2D01G458100	chr7A	85.874	446	48	9	927	1362	20226161	20225721	6.150000e-126	460.0
10	TraesCS2D01G458100	chr7D	87.179	546	58	5	919	1462	20516221	20515686	5.770000e-171	610.0
11	TraesCS2D01G458100	chr7D	86.621	441	52	6	927	1362	20117609	20117171	4.720000e-132	481.0
12	TraesCS2D01G458100	chr7D	81.707	246	29	12	673	905	20516635	20516393	8.910000e-45	191.0
13	TraesCS2D01G458100	chr7D	100.000	29	0	0	2023	2051	542092265	542092293	1.000000e-03	54.7
14	TraesCS2D01G458100	chr6A	100.000	30	0	0	2022	2051	6436030	6436059	3.390000e-04	56.5
15	TraesCS2D01G458100	chr6A	94.118	34	2	0	2024	2057	580286212	580286179	4.000000e-03	52.8
16	TraesCS2D01G458100	chr5D	100.000	30	0	0	2022	2051	380084985	380084956	3.390000e-04	56.5
17	TraesCS2D01G458100	chr3B	100.000	30	0	0	2022	2051	59757324	59757353	3.390000e-04	56.5
18	TraesCS2D01G458100	chr1B	100.000	29	0	0	2023	2051	57440265	57440293	1.000000e-03	54.7
19	TraesCS2D01G458100	chr1B	94.118	34	2	0	2018	2051	659333431	659333464	4.000000e-03	52.8
20	TraesCS2D01G458100	chr3A	100.000	28	0	0	2024	2051	737824666	737824639	4.000000e-03	52.8

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	TraesCS2D01G458100	chr2D	565181687	565184127	2440	True	4508.0	4508	100.000	1	2441	1	chr2D.!!$R1	2440
1	TraesCS2D01G458100	chr2B	677218025	677220038	2013	True	3055.0	3055	93.974	1	2033	1	chr2B.!!$R2	2032
2	TraesCS2D01G458100	chr2A	705782364	705785294	2930	True	1687.5	2791	92.952	1	2441	2	chr2A.!!$R2	2440
3	TraesCS2D01G458100	chr4A	712965300	712966642	1342	True	874.0	874	79.155	426	1774	1	chr4A.!!$R1	1348
4	TraesCS2D01G458100	chr7A	20401344	20402174	830	True	710.0	710	82.394	919	1774	1	chr7A.!!$R2	855
5	TraesCS2D01G458100	chr7D	20515686	20516635	949	True	400.5	610	84.443	673	1462	2	chr7D.!!$R2	789

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
422	425	0.18135	GGGTAGGTTGCTATGCTGCT	59.819	55.0	0.0	0.0	0.0	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2047	2259	0.24912	TGATCCGTCGGTTTGCTCAT	59.751	50.0	11.88	0.0	0.0	2.9	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
87	88	3.155167	GCTCGGTTCCGGGGAGAT	61.155	66.667	13.13	0.00	0.00	2.75
157	158	3.917760	GGATCGGCGTCTCCCCTG	61.918	72.222	16.79	0.00	0.00	4.45
171	173	0.758685	CCCCTGTCTAGGCCTCTCTG	60.759	65.000	9.68	5.10	43.16	3.35
261	263	1.742768	CCGCTAGGTCATCTCCACC	59.257	63.158	0.00	0.00	0.00	4.61
288	290	0.389687	GGCAGATGATCCTAGCGCTC	60.390	60.000	16.34	0.00	0.00	5.03
306	308	0.535335	TCGGGGAGAAGGATTTCGTG	59.465	55.000	0.00	0.00	38.38	4.35
345	347	0.603065	GAATTGGGGCGCAAACTCTT	59.397	50.000	21.22	10.64	0.00	2.85
346	348	0.318120	AATTGGGGCGCAAACTCTTG	59.682	50.000	21.22	0.00	35.49	3.02
347	349	0.539438	ATTGGGGCGCAAACTCTTGA	60.539	50.000	21.22	0.00	34.14	3.02
348	350	0.539438	TTGGGGCGCAAACTCTTGAT	60.539	50.000	15.15	0.00	34.14	2.57
350	352	1.017387	GGGGCGCAAACTCTTGATAG	58.983	55.000	10.83	0.00	34.14	2.08
355	357	3.492756	GGCGCAAACTCTTGATAGATCTC	59.507	47.826	10.83	0.00	34.14	2.75
422	425	0.181350	GGGTAGGTTGCTATGCTGCT	59.819	55.000	0.00	0.00	0.00	4.24
542	547	4.275936	GTGTTGCCTTGTAGTTGAATCAGT	59.724	41.667	0.00	0.00	0.00	3.41
543	548	4.515191	TGTTGCCTTGTAGTTGAATCAGTC	59.485	41.667	0.00	0.00	0.00	3.51
547	552	4.390297	GCCTTGTAGTTGAATCAGTCTGAC	59.610	45.833	4.21	0.00	0.00	3.51
553	558	4.626042	AGTTGAATCAGTCTGACAGTGTC	58.374	43.478	16.68	16.68	0.00	3.67
555	560	4.248691	TGAATCAGTCTGACAGTGTCTG	57.751	45.455	23.29	21.98	37.52	3.51
557	562	4.827284	TGAATCAGTCTGACAGTGTCTGTA	59.173	41.667	23.29	10.60	45.44	2.74
558	563	4.775058	ATCAGTCTGACAGTGTCTGTAC	57.225	45.455	23.29	19.57	45.44	2.90
566	571	3.889538	TGACAGTGTCTGTACTAGCAACT	59.110	43.478	23.29	0.00	45.44	3.16
841	865	4.457603	GGTGATTATTGCCAACTGTGTGTA	59.542	41.667	0.00	0.00	0.00	2.90
842	866	5.390613	GTGATTATTGCCAACTGTGTGTAC	58.609	41.667	0.00	0.00	0.00	2.90
846	877	0.394938	TGCCAACTGTGTGTACGGAT	59.605	50.000	0.00	0.00	36.65	4.18
974	1171	3.409026	TCTCTCTGCAGGTTTCTTTCC	57.591	47.619	15.13	0.00	0.00	3.13
985	1182	4.022849	CAGGTTTCTTTCCTTGCTGTTAGG	60.023	45.833	0.00	0.00	32.37	2.69
1427	1628	0.468029	CAGGGTGTTCTTGTTGGCCT	60.468	55.000	3.32	0.00	0.00	5.19
1450	1651	0.179034	GGGCCAGTAGAGCAGAATGG	60.179	60.000	4.39	0.00	35.86	3.16
1537	1744	2.951642	ACAGTGATTGTGTGTTTCTGGG	59.048	45.455	0.00	0.00	38.99	4.45
1558	1765	3.065371	GGTGCAGTTTATCATGCTACACC	59.935	47.826	4.51	4.51	42.98	4.16
1679	1887	2.762745	GCGTGTCTTTTGTCTCCCTTA	58.237	47.619	0.00	0.00	0.00	2.69
1760	1970	5.751509	AGTTTCAAAGAAATTTTACCGCACC	59.248	36.000	0.00	0.00	0.00	5.01
2027	2239	5.193679	AGGAAAATGATGGTACCTTGCTAC	58.806	41.667	14.36	0.00	0.00	3.58
2030	2242	6.183360	GGAAAATGATGGTACCTTGCTACTTC	60.183	42.308	14.36	7.80	0.00	3.01
2033	2245	3.451178	TGATGGTACCTTGCTACTTCCTC	59.549	47.826	14.36	0.00	0.00	3.71
2034	2246	2.185387	TGGTACCTTGCTACTTCCTCC	58.815	52.381	14.36	0.00	0.00	4.30
2035	2247	1.136500	GGTACCTTGCTACTTCCTCCG	59.864	57.143	4.06	0.00	0.00	4.63
2036	2248	1.823610	GTACCTTGCTACTTCCTCCGT	59.176	52.381	0.00	0.00	0.00	4.69
2038	2250	1.275573	ACCTTGCTACTTCCTCCGTTC	59.724	52.381	0.00	0.00	0.00	3.95
2040	2252	1.275291	CTTGCTACTTCCTCCGTTCCA	59.725	52.381	0.00	0.00	0.00	3.53
2041	2253	1.344065	TGCTACTTCCTCCGTTCCAA	58.656	50.000	0.00	0.00	0.00	3.53
2042	2254	1.695242	TGCTACTTCCTCCGTTCCAAA	59.305	47.619	0.00	0.00	0.00	3.28
2043	2255	2.105134	TGCTACTTCCTCCGTTCCAAAA	59.895	45.455	0.00	0.00	0.00	2.44
2044	2256	3.244770	TGCTACTTCCTCCGTTCCAAAAT	60.245	43.478	0.00	0.00	0.00	1.82
2045	2257	4.020039	TGCTACTTCCTCCGTTCCAAAATA	60.020	41.667	0.00	0.00	0.00	1.40
2046	2258	4.571176	GCTACTTCCTCCGTTCCAAAATAG	59.429	45.833	0.00	0.00	0.00	1.73
2047	2259	4.903045	ACTTCCTCCGTTCCAAAATAGA	57.097	40.909	0.00	0.00	0.00	1.98
2048	2260	5.437191	ACTTCCTCCGTTCCAAAATAGAT	57.563	39.130	0.00	0.00	0.00	1.98
2050	2262	5.045869	ACTTCCTCCGTTCCAAAATAGATGA	60.046	40.000	0.00	0.00	0.00	2.92
2051	2263	5.023533	TCCTCCGTTCCAAAATAGATGAG	57.976	43.478	0.00	0.00	0.00	2.90
2058	2798	4.963276	TCCAAAATAGATGAGCAAACCG	57.037	40.909	0.00	0.00	0.00	4.44
2101	2841	4.673441	CAACGTGTAGAAGATACTCTGGG	58.327	47.826	0.00	0.00	0.00	4.45
2131	2871	4.885325	ACAAACATAAACCAAAGAGACCGT	59.115	37.500	0.00	0.00	0.00	4.83
2140	2880	2.928116	CCAAAGAGACCGTCGATAAACC	59.072	50.000	0.00	0.00	0.00	3.27
2226	2966	3.226537	GCCCGCATCCAAATCCCC	61.227	66.667	0.00	0.00	0.00	4.81
2302	3042	2.813179	GCTCACCGCGCAACCATAG	61.813	63.158	8.75	0.00	0.00	2.23
2310	3050	1.746615	CGCAACCATAGCAGCCAGT	60.747	57.895	0.00	0.00	0.00	4.00
2311	3051	1.709147	CGCAACCATAGCAGCCAGTC	61.709	60.000	0.00	0.00	0.00	3.51
2312	3052	0.677731	GCAACCATAGCAGCCAGTCA	60.678	55.000	0.00	0.00	0.00	3.41
2313	3053	1.089920	CAACCATAGCAGCCAGTCAC	58.910	55.000	0.00	0.00	0.00	3.67
2314	3054	0.692476	AACCATAGCAGCCAGTCACA	59.308	50.000	0.00	0.00	0.00	3.58
2315	3055	0.251354	ACCATAGCAGCCAGTCACAG	59.749	55.000	0.00	0.00	0.00	3.66
2328	3068	0.603569	GTCACAGGACGACACCTCAT	59.396	55.000	0.00	0.00	38.32	2.90
2333	3073	0.320771	AGGACGACACCTCATGTTGC	60.321	55.000	0.00	0.00	45.64	4.17
2335	3075	1.298859	GACGACACCTCATGTTGCCC	61.299	60.000	0.00	0.00	45.64	5.36
2426	3166	3.691342	CCTCGGTCCGTGGCTCAA	61.691	66.667	18.86	0.00	33.90	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
171	173	2.034053	CGCATCTGAGAGGACTAAGGAC	59.966	54.545	0.00	0.00	0.00	3.85
213	215	2.684843	CGCAACAGCAGCTCTTCCC	61.685	63.158	0.00	0.00	0.00	3.97
261	263	1.134580	AGGATCATCTGCCTGACAACG	60.135	52.381	0.00	0.00	32.06	4.10
288	290	1.090052	GCACGAAATCCTTCTCCCCG	61.090	60.000	0.00	0.00	0.00	5.73
306	308	3.444916	TCGTCTATTTCAGAACATCGGC	58.555	45.455	0.00	0.00	34.17	5.54
542	547	3.751518	TGCTAGTACAGACACTGTCAGA	58.248	45.455	11.80	0.00	41.21	3.27
543	548	4.022762	AGTTGCTAGTACAGACACTGTCAG	60.023	45.833	11.80	6.01	41.21	3.51
547	552	5.753438	TGAAAAGTTGCTAGTACAGACACTG	59.247	40.000	0.00	0.00	37.52	3.66
553	558	8.827677	ACTAAGTTTGAAAAGTTGCTAGTACAG	58.172	33.333	6.19	0.00	33.79	2.74
555	560	8.823818	TGACTAAGTTTGAAAAGTTGCTAGTAC	58.176	33.333	6.19	0.00	33.79	2.73
557	562	7.012421	CCTGACTAAGTTTGAAAAGTTGCTAGT	59.988	37.037	6.19	2.56	33.79	2.57
558	563	7.355778	CCTGACTAAGTTTGAAAAGTTGCTAG	58.644	38.462	6.19	0.00	33.79	3.42
566	571	3.317993	GCTGCCCTGACTAAGTTTGAAAA	59.682	43.478	0.00	0.00	0.00	2.29
748	769	0.318120	AAGGGCATCAAAGGCAAACG	59.682	50.000	0.00	0.00	35.46	3.60
841	865	9.705290	AAGCAAAGAAAACAAATAATAATCCGT	57.295	25.926	0.00	0.00	0.00	4.69
974	1171	1.825090	TGTGATGCCCTAACAGCAAG	58.175	50.000	0.00	0.00	44.83	4.01
985	1182	1.275856	TGCCATTTTCCTTGTGATGCC	59.724	47.619	0.00	0.00	0.00	4.40
1427	1628	3.315142	CTGCTCTACTGGCCCGCAA	62.315	63.158	0.00	0.00	0.00	4.85
1450	1651	3.993535	CAAGTCTCCTTGCCCTGC	58.006	61.111	0.00	0.00	41.51	4.85
1470	1677	5.728898	GCAATCTGGCTTCGATAAAGAACTG	60.729	44.000	0.00	0.00	37.12	3.16
1537	1744	3.941483	AGGTGTAGCATGATAAACTGCAC	59.059	43.478	10.99	9.92	43.61	4.57
1558	1765	4.742167	CGAGGATTCAACAGTACTGCATAG	59.258	45.833	22.90	10.06	0.00	2.23
1679	1887	1.949525	AGTTCTGAAGCGCAACAACAT	59.050	42.857	11.47	0.00	0.00	2.71
1760	1970	2.580589	CCAACACGCCTTAACATTTCG	58.419	47.619	0.00	0.00	0.00	3.46
1803	2013	5.468540	TCCGACTCTGATCAAGAAGAAAA	57.531	39.130	10.61	0.00	33.37	2.29
1865	2075	4.202141	GGTATTGCAAGCCATAATTCAGCA	60.202	41.667	15.50	0.00	0.00	4.41
2013	2225	2.772515	GGAGGAAGTAGCAAGGTACCAT	59.227	50.000	15.94	0.00	0.00	3.55
2027	2239	5.428253	TCATCTATTTTGGAACGGAGGAAG	58.572	41.667	0.00	0.00	0.00	3.46
2030	2242	3.561725	GCTCATCTATTTTGGAACGGAGG	59.438	47.826	0.00	0.00	0.00	4.30
2033	2245	4.963276	TTGCTCATCTATTTTGGAACGG	57.037	40.909	0.00	0.00	0.00	4.44
2034	2246	5.095490	GGTTTGCTCATCTATTTTGGAACG	58.905	41.667	0.00	0.00	0.00	3.95
2035	2247	5.095490	CGGTTTGCTCATCTATTTTGGAAC	58.905	41.667	0.00	0.00	0.00	3.62
2036	2248	5.007034	TCGGTTTGCTCATCTATTTTGGAA	58.993	37.500	0.00	0.00	0.00	3.53
2038	2250	4.662145	GTCGGTTTGCTCATCTATTTTGG	58.338	43.478	0.00	0.00	0.00	3.28
2040	2252	3.374058	CCGTCGGTTTGCTCATCTATTTT	59.626	43.478	2.08	0.00	0.00	1.82
2041	2253	2.936498	CCGTCGGTTTGCTCATCTATTT	59.064	45.455	2.08	0.00	0.00	1.40
2042	2254	2.167693	TCCGTCGGTTTGCTCATCTATT	59.832	45.455	11.88	0.00	0.00	1.73
2043	2255	1.754803	TCCGTCGGTTTGCTCATCTAT	59.245	47.619	11.88	0.00	0.00	1.98
2044	2256	1.179152	TCCGTCGGTTTGCTCATCTA	58.821	50.000	11.88	0.00	0.00	1.98
2045	2257	0.537188	ATCCGTCGGTTTGCTCATCT	59.463	50.000	11.88	0.00	0.00	2.90
2046	2258	0.931005	GATCCGTCGGTTTGCTCATC	59.069	55.000	11.88	0.99	0.00	2.92
2047	2259	0.249120	TGATCCGTCGGTTTGCTCAT	59.751	50.000	11.88	0.00	0.00	2.90
2048	2260	0.389817	CTGATCCGTCGGTTTGCTCA	60.390	55.000	11.88	7.04	0.00	4.26
2050	2262	1.741770	GCTGATCCGTCGGTTTGCT	60.742	57.895	11.88	0.00	33.06	3.91
2051	2263	2.032634	TGCTGATCCGTCGGTTTGC	61.033	57.895	11.88	11.83	33.06	3.68
2058	2798	1.734465	CTTCTTTGGTGCTGATCCGTC	59.266	52.381	0.00	0.00	0.00	4.79
2131	2871	2.997986	GGCGACTCTTTTGGTTTATCGA	59.002	45.455	0.00	0.00	0.00	3.59
2140	2880	2.556287	GTGGCGGCGACTCTTTTG	59.444	61.111	16.45	0.00	0.00	2.44
2210	2950	2.906897	CGGGGATTTGGATGCGGG	60.907	66.667	0.00	0.00	0.00	6.13
2281	3021	4.090057	GGTTGCGCGGTGAGCTTC	62.090	66.667	8.83	0.00	45.59	3.86
2292	3032	1.709147	GACTGGCTGCTATGGTTGCG	61.709	60.000	0.00	0.00	0.00	4.85
2302	3042	2.740055	CGTCCTGTGACTGGCTGC	60.740	66.667	3.33	0.00	39.47	5.25
2310	3050	0.603065	CATGAGGTGTCGTCCTGTGA	59.397	55.000	0.00	0.00	38.02	3.58
2311	3051	0.318441	ACATGAGGTGTCGTCCTGTG	59.682	55.000	0.00	3.96	35.77	3.66
2312	3052	1.048601	AACATGAGGTGTCGTCCTGT	58.951	50.000	0.00	0.00	41.14	4.00
2313	3053	1.432514	CAACATGAGGTGTCGTCCTG	58.567	55.000	0.00	0.00	41.14	3.86
2314	3054	0.320771	GCAACATGAGGTGTCGTCCT	60.321	55.000	0.00	0.00	41.14	3.85
2315	3055	1.298859	GGCAACATGAGGTGTCGTCC	61.299	60.000	0.00	0.00	41.14	4.79
2414	3154	2.280797	TGCTGTTGAGCCACGGAC	60.281	61.111	0.00	0.00	45.57	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.