AutoCloner

Multiple sequence alignment - TraesCS1D01G310900

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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	TraesCS1D01G310900	chr1D	100.000	3065	0	0	1	3065	406972036	406975100	0.000000e+00	5661.0
1	TraesCS1D01G310900	chr1B	94.998	2439	73	24	521	2934	547281324	547283738	0.000000e+00	3783.0
2	TraesCS1D01G310900	chr1B	86.689	293	18	10	14	286	547280349	547280640	3.840000e-79	305.0
3	TraesCS1D01G310900	chr1B	81.466	232	20	13	271	485	547281101	547281326	5.260000e-38	169.0
4	TraesCS1D01G310900	chr1B	93.269	104	3	1	2966	3065	547283828	547283931	1.900000e-32	150.0
5	TraesCS1D01G310900	chr1A	95.294	2040	50	19	912	2929	502677635	502679650	0.000000e+00	3193.0
6	TraesCS1D01G310900	chr1A	91.715	688	27	22	186	854	502676650	502677326	0.000000e+00	928.0
7	TraesCS1D01G310900	chr1A	92.571	175	12	1	1	174	502674867	502675041	1.820000e-62	250.0
8	TraesCS1D01G310900	chr1A	97.561	82	2	0	2984	3065	502679853	502679934	1.150000e-29	141.0
9	TraesCS1D01G310900	chr3D	90.655	1038	92	5	1029	2063	437779397	437778362	0.000000e+00	1375.0
10	TraesCS1D01G310900	chr3B	89.368	1091	111	4	997	2083	572936930	572935841	0.000000e+00	1367.0
11	TraesCS1D01G310900	chr3A	89.674	1075	101	9	997	2063	575949006	575947934	0.000000e+00	1362.0
12	TraesCS1D01G310900	chr5A	83.333	942	142	11	1052	1981	308376769	308375831	0.000000e+00	856.0
13	TraesCS1D01G310900	chr5D	82.777	958	148	12	1037	1981	243219947	243220900	0.000000e+00	839.0
14	TraesCS1D01G310900	chr5B	82.997	941	147	9	1052	1981	255200464	255199526	0.000000e+00	839.0
15	TraesCS1D01G310900	chr7B	100.000	30	0	0	1298	1327	508981759	508981730	4.270000e-04	56.5

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	TraesCS1D01G310900	chr1D	406972036	406975100	3064	False	5661.00	5661	100.00000	1	3065	1	chr1D.!!$F1	3064
1	TraesCS1D01G310900	chr1B	547280349	547283931	3582	False	1101.75	3783	89.10550	14	3065	4	chr1B.!!$F1	3051
2	TraesCS1D01G310900	chr1A	502674867	502679934	5067	False	1128.00	3193	94.28525	1	3065	4	chr1A.!!$F1	3064
3	TraesCS1D01G310900	chr3D	437778362	437779397	1035	True	1375.00	1375	90.65500	1029	2063	1	chr3D.!!$R1	1034
4	TraesCS1D01G310900	chr3B	572935841	572936930	1089	True	1367.00	1367	89.36800	997	2083	1	chr3B.!!$R1	1086
5	TraesCS1D01G310900	chr3A	575947934	575949006	1072	True	1362.00	1362	89.67400	997	2063	1	chr3A.!!$R1	1066
6	TraesCS1D01G310900	chr5A	308375831	308376769	938	True	856.00	856	83.33300	1052	1981	1	chr5A.!!$R1	929
7	TraesCS1D01G310900	chr5D	243219947	243220900	953	False	839.00	839	82.77700	1037	1981	1	chr5D.!!$F1	944
8	TraesCS1D01G310900	chr5B	255199526	255200464	938	True	839.00	839	82.99700	1052	1981	1	chr5B.!!$R1	929

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
512	2607	0.038435	TGGACACGTATTTTCGCGGA	60.038	50.0	6.13	0.0	0.0	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2167	4555	3.565764	TCCTCTACCATGGCAAATCAG	57.434	47.619	13.04	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
50	52	2.119457	CTTTCGTTTGAAACTGGCAGC	58.881	47.619	15.89	0.00	39.13	5.25
57	59	4.382754	CGTTTGAAACTGGCAGCTTAATTC	59.617	41.667	15.89	11.69	0.00	2.17
76	78	1.562942	TCTCGAGCTACCCTGTCCTAA	59.437	52.381	7.81	0.00	0.00	2.69
175	1752	8.786898	CATCCCCATCAACAAATTACATACTAG	58.213	37.037	0.00	0.00	0.00	2.57
176	1753	7.867921	TCCCCATCAACAAATTACATACTAGT	58.132	34.615	0.00	0.00	0.00	2.57
178	1755	9.621629	CCCCATCAACAAATTACATACTAGTAA	57.378	33.333	6.70	0.00	38.25	2.24
240	1839	0.608640	CCTTGCCGAACCACTAGAGT	59.391	55.000	0.00	0.00	0.00	3.24
405	2481	0.612732	CATTGCCACCCCATGACACT	60.613	55.000	0.00	0.00	0.00	3.55
418	2494	5.590259	CCCCATGACACTAACTATTTTCTGG	59.410	44.000	0.00	0.00	0.00	3.86
451	2546	6.267699	CCATAACCTATCTATCCTCACACACA	59.732	42.308	0.00	0.00	0.00	3.72
497	2592	3.056322	ACGGTAGGTGATGTAACTTGGAC	60.056	47.826	0.00	0.00	0.00	4.02
510	2605	1.458064	ACTTGGACACGTATTTTCGCG	59.542	47.619	0.00	0.00	0.00	5.87
512	2607	0.038435	TGGACACGTATTTTCGCGGA	60.038	50.000	6.13	0.00	0.00	5.54
513	2608	1.070038	GGACACGTATTTTCGCGGAA	58.930	50.000	6.13	0.00	0.00	4.30
517	2612	3.547601	ACACGTATTTTCGCGGAAAAAG	58.452	40.909	17.96	13.14	43.32	2.27
519	2614	4.212911	CACGTATTTTCGCGGAAAAAGAA	58.787	39.130	17.96	0.00	43.32	2.52
520	2615	4.317291	CACGTATTTTCGCGGAAAAAGAAG	59.683	41.667	17.96	13.30	43.32	2.85
521	2616	4.024641	ACGTATTTTCGCGGAAAAAGAAGT	60.025	37.500	17.96	13.91	43.32	3.01
523	2618	2.766970	TTTCGCGGAAAAAGAAGTGG	57.233	45.000	6.13	0.00	0.00	4.00
563	2660	1.798223	CACACACACATGGAGTTACCG	59.202	52.381	0.00	0.00	42.61	4.02
743	2845	2.619013	AGAAAAGGAAAGCAATCGCG	57.381	45.000	0.00	0.00	45.49	5.87
778	2880	3.706373	GCGCCCAGTCCTCTCCAA	61.706	66.667	0.00	0.00	0.00	3.53
779	2881	2.581354	CGCCCAGTCCTCTCCAAG	59.419	66.667	0.00	0.00	0.00	3.61
780	2882	2.270527	GCCCAGTCCTCTCCAAGC	59.729	66.667	0.00	0.00	0.00	4.01
781	2883	2.596851	GCCCAGTCCTCTCCAAGCA	61.597	63.158	0.00	0.00	0.00	3.91
785	2887	1.152030	AGTCCTCTCCAAGCACCCA	60.152	57.895	0.00	0.00	0.00	4.51
793	2896	2.615465	CCAAGCACCCATCCCCTCA	61.615	63.158	0.00	0.00	0.00	3.86
903	3028	4.410400	CCCGAGCCCAAGTCCACC	62.410	72.222	0.00	0.00	0.00	4.61
904	3029	4.410400	CCGAGCCCAAGTCCACCC	62.410	72.222	0.00	0.00	0.00	4.61
905	3030	4.410400	CGAGCCCAAGTCCACCCC	62.410	72.222	0.00	0.00	0.00	4.95
906	3031	2.936032	GAGCCCAAGTCCACCCCT	60.936	66.667	0.00	0.00	0.00	4.79
2076	4464	1.969208	CAGGCATAGAGCTCCAGATCA	59.031	52.381	10.93	0.00	44.79	2.92
2167	4555	6.162777	TGCACAATAGGCTTGTTATTTTTCC	58.837	36.000	0.00	0.00	0.00	3.13
2251	4640	2.352388	GCGATGTACTTTGCCCACTTA	58.648	47.619	9.38	0.00	0.00	2.24
2252	4641	2.095372	GCGATGTACTTTGCCCACTTAC	59.905	50.000	9.38	0.00	0.00	2.34
2286	4682	8.893563	AGTAAAATTGTAAAGATCAATGGGGA	57.106	30.769	0.00	0.00	35.95	4.81
2287	4683	9.492730	AGTAAAATTGTAAAGATCAATGGGGAT	57.507	29.630	0.00	0.00	35.95	3.85
2413	4817	9.141400	AGATAGAAACATGAAAGTACTCGAAAC	57.859	33.333	0.00	0.00	0.00	2.78
2722	5126	1.753649	CTTCCTCTCTCGCTCATTCCA	59.246	52.381	0.00	0.00	0.00	3.53
2893	5297	2.704725	ATGTGTCGGTTTGTTGCATC	57.295	45.000	0.00	0.00	0.00	3.91
2895	5299	0.385473	GTGTCGGTTTGTTGCATCGG	60.385	55.000	0.00	0.00	0.00	4.18
2913	5317	2.099405	CGGTGGGTGAATATTTGCCTT	58.901	47.619	8.51	0.00	0.00	4.35
2914	5318	2.159254	CGGTGGGTGAATATTTGCCTTG	60.159	50.000	8.51	0.00	0.00	3.61
2915	5319	2.418609	GGTGGGTGAATATTTGCCTTGC	60.419	50.000	8.51	0.00	0.00	4.01
2919	5323	3.261580	GGTGAATATTTGCCTTGCCAAC	58.738	45.455	0.00	0.00	0.00	3.77
2930	5334	2.242043	CCTTGCCAACTTTCACCTGAT	58.758	47.619	0.00	0.00	0.00	2.90
2931	5335	2.229784	CCTTGCCAACTTTCACCTGATC	59.770	50.000	0.00	0.00	0.00	2.92
2933	5337	2.942804	TGCCAACTTTCACCTGATCAA	58.057	42.857	0.00	0.00	0.00	2.57
2945	5415	6.358974	TCACCTGATCAATTTGTCACTAGA	57.641	37.500	0.00	0.00	0.00	2.43
2948	5418	6.037940	CACCTGATCAATTTGTCACTAGATGG	59.962	42.308	0.00	0.00	0.00	3.51
2956	5426	7.181305	TCAATTTGTCACTAGATGGGGTAACTA	59.819	37.037	0.00	0.00	0.00	2.24
2957	5427	6.540438	TTTGTCACTAGATGGGGTAACTAG	57.460	41.667	0.00	0.00	39.32	2.57
2958	5428	4.543689	TGTCACTAGATGGGGTAACTAGG	58.456	47.826	0.00	0.00	38.20	3.02
2959	5429	4.016851	TGTCACTAGATGGGGTAACTAGGT	60.017	45.833	0.00	0.00	38.20	3.08
2960	5430	4.341520	GTCACTAGATGGGGTAACTAGGTG	59.658	50.000	0.00	0.00	38.20	4.00
2961	5431	3.641906	CACTAGATGGGGTAACTAGGTGG	59.358	52.174	0.00	0.00	38.20	4.61
2962	5432	2.963654	AGATGGGGTAACTAGGTGGT	57.036	50.000	0.00	0.00	0.00	4.16
2963	5433	3.216230	AGATGGGGTAACTAGGTGGTT	57.784	47.619	0.00	0.00	0.00	3.67
2964	5434	2.844348	AGATGGGGTAACTAGGTGGTTG	59.156	50.000	0.00	0.00	0.00	3.77
2967	5437	1.339727	GGGGTAACTAGGTGGTTGCTG	60.340	57.143	0.00	0.00	33.47	4.41
3052	5619	8.855279	GCATTATTATCTTCAGAGTACTTAGCG	58.145	37.037	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	6.939622	AGGAAAGGATTTAATGGCTTTTGAG	58.060	36.000	0.00	0.00	39.27	3.02
15	16	7.375053	TCAAACGAAAGGAAAGGATTTAATGG	58.625	34.615	0.00	0.00	39.27	3.16
50	52	4.500035	GGACAGGGTAGCTCGAGAATTAAG	60.500	50.000	18.75	2.05	0.00	1.85
57	59	1.950909	CTTAGGACAGGGTAGCTCGAG	59.049	57.143	8.45	8.45	0.00	4.04
76	78	9.461312	TGTTACTATTAATTGGTTGCTTGATCT	57.539	29.630	0.00	0.00	0.00	2.75
175	1752	6.986231	CCCTTATCATTTTCCAGCCAATTTAC	59.014	38.462	0.00	0.00	0.00	2.01
176	1753	6.407979	GCCCTTATCATTTTCCAGCCAATTTA	60.408	38.462	0.00	0.00	0.00	1.40
178	1755	4.141642	GCCCTTATCATTTTCCAGCCAATT	60.142	41.667	0.00	0.00	0.00	2.32
179	1756	3.389002	GCCCTTATCATTTTCCAGCCAAT	59.611	43.478	0.00	0.00	0.00	3.16
181	1758	2.292126	TGCCCTTATCATTTTCCAGCCA	60.292	45.455	0.00	0.00	0.00	4.75
182	1759	2.363359	CTGCCCTTATCATTTTCCAGCC	59.637	50.000	0.00	0.00	0.00	4.85
183	1760	3.026694	ACTGCCCTTATCATTTTCCAGC	58.973	45.455	0.00	0.00	0.00	4.85
240	1839	2.030628	GCGCCTTGGCAGTAAAGTTTAA	60.031	45.455	12.45	0.00	0.00	1.52
307	2383	4.856487	CACGCAAAAACACTGAAAGAAGAA	59.144	37.500	0.00	0.00	37.43	2.52
308	2384	4.083003	ACACGCAAAAACACTGAAAGAAGA	60.083	37.500	0.00	0.00	37.43	2.87
309	2385	4.165779	ACACGCAAAAACACTGAAAGAAG	58.834	39.130	0.00	0.00	37.43	2.85
429	2507	5.298527	CGTGTGTGTGAGGATAGATAGGTTA	59.701	44.000	0.00	0.00	0.00	2.85
451	2546	0.324614	TGACATGGTCAATGAGCCGT	59.675	50.000	10.13	7.12	39.78	5.68
497	2592	3.801293	TCTTTTTCCGCGAAAATACGTG	58.199	40.909	8.23	0.00	40.50	4.49
510	2605	1.613925	GCCTCCACCACTTCTTTTTCC	59.386	52.381	0.00	0.00	0.00	3.13
512	2607	1.318576	CGCCTCCACCACTTCTTTTT	58.681	50.000	0.00	0.00	0.00	1.94
513	2608	0.182775	ACGCCTCCACCACTTCTTTT	59.817	50.000	0.00	0.00	0.00	2.27
517	2612	0.606604	TTCTACGCCTCCACCACTTC	59.393	55.000	0.00	0.00	0.00	3.01
519	2614	0.320697	GTTTCTACGCCTCCACCACT	59.679	55.000	0.00	0.00	0.00	4.00
520	2615	1.012486	CGTTTCTACGCCTCCACCAC	61.012	60.000	0.00	0.00	41.41	4.16
521	2616	1.290955	CGTTTCTACGCCTCCACCA	59.709	57.895	0.00	0.00	41.41	4.17
563	2660	2.095919	GCCACCGTTTTGTACTGTCATC	60.096	50.000	0.00	0.00	0.00	2.92
651	2750	1.134250	GCTGGATTCCCACCTCTCTTC	60.134	57.143	0.00	0.00	37.58	2.87
743	2845	3.050275	GCTGGCCACGTGGAGAAC	61.050	66.667	38.30	22.79	37.39	3.01
772	2874	2.308722	GGGGATGGGTGCTTGGAGA	61.309	63.158	0.00	0.00	0.00	3.71
773	2875	2.276309	GAGGGGATGGGTGCTTGGAG	62.276	65.000	0.00	0.00	0.00	3.86
774	2876	2.204291	AGGGGATGGGTGCTTGGA	60.204	61.111	0.00	0.00	0.00	3.53
776	2878	1.379044	GTGAGGGGATGGGTGCTTG	60.379	63.158	0.00	0.00	0.00	4.01
777	2879	2.616458	GGTGAGGGGATGGGTGCTT	61.616	63.158	0.00	0.00	0.00	3.91
778	2880	3.017581	GGTGAGGGGATGGGTGCT	61.018	66.667	0.00	0.00	0.00	4.40
779	2881	3.017581	AGGTGAGGGGATGGGTGC	61.018	66.667	0.00	0.00	0.00	5.01
780	2882	1.616327	TGAGGTGAGGGGATGGGTG	60.616	63.158	0.00	0.00	0.00	4.61
781	2883	1.616628	GTGAGGTGAGGGGATGGGT	60.617	63.158	0.00	0.00	0.00	4.51
785	2887	2.197465	GTTTAGGTGAGGTGAGGGGAT	58.803	52.381	0.00	0.00	0.00	3.85
856	2965	0.839946	CGGATCTGAGGATTTGGGGT	59.160	55.000	0.00	0.00	31.46	4.95
892	3017	3.339093	GGGAGGGGTGGACTTGGG	61.339	72.222	0.00	0.00	0.00	4.12
980	3340	3.028921	GCTCCCTCCTGCTGACCTG	62.029	68.421	0.00	0.00	0.00	4.00
981	3341	2.686835	GCTCCCTCCTGCTGACCT	60.687	66.667	0.00	0.00	0.00	3.85
983	3343	2.430610	ATCGCTCCCTCCTGCTGAC	61.431	63.158	0.00	0.00	0.00	3.51
984	3344	2.042537	ATCGCTCCCTCCTGCTGA	60.043	61.111	0.00	0.00	0.00	4.26
985	3345	2.108566	CATCGCTCCCTCCTGCTG	59.891	66.667	0.00	0.00	0.00	4.41
986	3346	3.160047	CCATCGCTCCCTCCTGCT	61.160	66.667	0.00	0.00	0.00	4.24
2167	4555	3.565764	TCCTCTACCATGGCAAATCAG	57.434	47.619	13.04	0.00	0.00	2.90
2285	4681	6.956299	ACTTAATTGTGCAAAAGCATCATC	57.044	33.333	0.00	0.00	0.00	2.92
2286	4682	6.347888	GCAACTTAATTGTGCAAAAGCATCAT	60.348	34.615	0.00	0.00	40.77	2.45
2287	4683	5.050227	GCAACTTAATTGTGCAAAAGCATCA	60.050	36.000	0.00	0.00	40.77	3.07
2722	5126	7.234988	ACCTAGGCTACTCGACCAAATAAATAT	59.765	37.037	9.30	0.00	0.00	1.28
2841	5245	8.398665	ACGATATTAAAAGCTAAAAGAGGCAAG	58.601	33.333	0.00	0.00	0.00	4.01
2877	5281	0.816018	ACCGATGCAACAAACCGACA	60.816	50.000	0.00	0.00	0.00	4.35
2878	5282	0.385473	CACCGATGCAACAAACCGAC	60.385	55.000	0.00	0.00	0.00	4.79
2893	5297	1.762708	AGGCAAATATTCACCCACCG	58.237	50.000	3.64	0.00	0.00	4.94
2895	5299	2.418609	GGCAAGGCAAATATTCACCCAC	60.419	50.000	3.64	0.00	0.00	4.61
2913	5317	2.655090	TGATCAGGTGAAAGTTGGCA	57.345	45.000	0.00	0.00	0.00	4.92
2914	5318	4.525912	AATTGATCAGGTGAAAGTTGGC	57.474	40.909	0.00	0.00	0.00	4.52
2915	5319	5.846203	ACAAATTGATCAGGTGAAAGTTGG	58.154	37.500	0.00	0.00	0.00	3.77
2919	5323	6.323203	AGTGACAAATTGATCAGGTGAAAG	57.677	37.500	0.00	0.00	0.00	2.62
2930	5334	4.927267	ACCCCATCTAGTGACAAATTGA	57.073	40.909	0.00	0.00	0.00	2.57
2931	5335	6.180472	AGTTACCCCATCTAGTGACAAATTG	58.820	40.000	0.00	0.00	0.00	2.32
2933	5337	6.099845	CCTAGTTACCCCATCTAGTGACAAAT	59.900	42.308	0.00	0.00	32.01	2.32
2945	5415	1.283905	GCAACCACCTAGTTACCCCAT	59.716	52.381	0.00	0.00	0.00	4.00
2948	5418	1.626825	TCAGCAACCACCTAGTTACCC	59.373	52.381	0.00	0.00	0.00	3.69
2956	5426	0.395586	TGCAACTTCAGCAACCACCT	60.396	50.000	0.00	0.00	39.39	4.00
2957	5427	0.675633	ATGCAACTTCAGCAACCACC	59.324	50.000	0.00	0.00	46.27	4.61
2958	5428	2.129607	CAATGCAACTTCAGCAACCAC	58.870	47.619	0.00	0.00	46.27	4.16
2959	5429	1.755959	ACAATGCAACTTCAGCAACCA	59.244	42.857	0.00	0.00	46.27	3.67
2960	5430	2.223782	TGACAATGCAACTTCAGCAACC	60.224	45.455	0.00	0.00	46.27	3.77
2961	5431	3.082698	TGACAATGCAACTTCAGCAAC	57.917	42.857	0.00	0.00	46.27	4.17
2962	5432	3.068448	ACATGACAATGCAACTTCAGCAA	59.932	39.130	0.00	0.00	46.27	3.91
2964	5434	3.293311	ACATGACAATGCAACTTCAGC	57.707	42.857	0.00	0.00	37.29	4.26
2967	5437	6.032094	CCTGAATACATGACAATGCAACTTC	58.968	40.000	0.00	0.00	37.29	3.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.