AutoCloner

Multiple sequence alignment - TraesCS5A01G208300

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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	TraesCS5A01G208300	chr5A	100.000	3182	0	0	1	3182	421830932	421827751	0.000000e+00	5877.0
1	TraesCS5A01G208300	chr5D	97.038	3207	61	12	1	3182	323914053	323910856	0.000000e+00	5365.0
2	TraesCS5A01G208300	chr5B	97.407	2507	62	3	1	2506	375641116	375638612	0.000000e+00	4266.0
3	TraesCS5A01G208300	chr5B	92.982	342	14	5	2675	3016	375638567	375638236	1.030000e-134	490.0
4	TraesCS5A01G208300	chr5B	91.209	182	11	4	3006	3182	375620415	375620234	3.170000e-60	243.0
5	TraesCS5A01G208300	chr3D	91.074	2364	193	14	1	2350	340890558	340888199	0.000000e+00	3181.0
6	TraesCS5A01G208300	chr3D	87.952	83	7	1	2402	2481	340888196	340888114	9.400000e-16	95.3
7	TraesCS5A01G208300	chr3D	94.872	39	2	0	2354	2392	69500642	69500680	9.530000e-06	62.1
8	TraesCS5A01G208300	chr3A	91.536	2304	180	9	1	2291	462333091	462335392	0.000000e+00	3160.0
9	TraesCS5A01G208300	chr3B	90.101	2384	198	21	1	2350	439858990	439856611	0.000000e+00	3061.0
10	TraesCS5A01G208300	chr3B	86.905	84	7	3	2402	2481	439856608	439856525	1.220000e-14	91.6
11	TraesCS5A01G208300	chr4B	72.966	381	92	10	1388	1763	660195944	660195570	4.310000e-24	122.0
12	TraesCS5A01G208300	chr7D	95.745	47	1	1	2347	2392	634214349	634214303	1.220000e-09	75.0
13	TraesCS5A01G208300	chr6B	97.619	42	1	0	2351	2392	494088511	494088552	4.400000e-09	73.1
14	TraesCS5A01G208300	chr1D	89.286	56	4	2	2338	2392	296168370	296168316	5.700000e-08	69.4
15	TraesCS5A01G208300	chr1D	92.857	42	3	0	2351	2392	450055840	450055881	9.530000e-06	62.1
16	TraesCS5A01G208300	chr6D	93.182	44	3	0	2349	2392	10677228	10677271	7.370000e-07	65.8
17	TraesCS5A01G208300	chrUn	90.698	43	4	0	2346	2388	155025677	155025635	1.230000e-04	58.4

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	TraesCS5A01G208300	chr5A	421827751	421830932	3181	True	5877.00	5877	100.0000	1	3182	1	chr5A.!!$R1	3181
1	TraesCS5A01G208300	chr5D	323910856	323914053	3197	True	5365.00	5365	97.0380	1	3182	1	chr5D.!!$R1	3181
2	TraesCS5A01G208300	chr5B	375638236	375641116	2880	True	2378.00	4266	95.1945	1	3016	2	chr5B.!!$R2	3015
3	TraesCS5A01G208300	chr3D	340888114	340890558	2444	True	1638.15	3181	89.5130	1	2481	2	chr3D.!!$R1	2480
4	TraesCS5A01G208300	chr3A	462333091	462335392	2301	False	3160.00	3160	91.5360	1	2291	1	chr3A.!!$F1	2290
5	TraesCS5A01G208300	chr3B	439856525	439858990	2465	True	1576.30	3061	88.5030	1	2481	2	chr3B.!!$R1	2480

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
277	278	0.398318	AACAGACACCTTGCTCCCTC	59.602	55.000	0.00	0.00	0.0	4.30	F
1612	1619	1.374947	CTCGGTTGGAGCCAAAGGA	59.625	57.895	3.05	3.75	37.7	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1900	1907	4.165372	ACTTGAAACCCTAGTTCCAGTCAA	59.835	41.667	0.0	0.0	34.19	3.18	R
3061	3120	0.033699	AGCAAGGAAAGGAGGGATGC	60.034	55.000	0.0	0.0	0.00	3.91	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
253	254	2.857186	TGTATGGCAGAGCTTTCACA	57.143	45.000	0.00	0.00	0.00	3.58
277	278	0.398318	AACAGACACCTTGCTCCCTC	59.602	55.000	0.00	0.00	0.00	4.30
339	340	7.339466	GGTTACCATCACCTCTATTTTGACAAT	59.661	37.037	0.00	0.00	0.00	2.71
867	869	8.728833	GGCTCTAATCAATCCATCTCATTTAAG	58.271	37.037	0.00	0.00	0.00	1.85
991	993	3.434596	GGTGTACCCATATTTCCCAGGAC	60.435	52.174	0.00	0.00	0.00	3.85
1521	1528	4.279169	TGCTCAGAAGGGAAAAACAGATTG	59.721	41.667	0.00	0.00	0.00	2.67
1612	1619	1.374947	CTCGGTTGGAGCCAAAGGA	59.625	57.895	3.05	3.75	37.70	3.36
1857	1864	3.251487	CACTGAATATGCCGATCAATGCA	59.749	43.478	4.29	4.29	42.52	3.96
1900	1907	2.368548	GGGGTTGTGCTTCTGGAAATTT	59.631	45.455	0.00	0.00	0.00	1.82
1946	1966	2.845967	GCATAATTGCCAACGAAAGACG	59.154	45.455	0.00	0.00	43.38	4.18
2508	2562	0.695347	AGAGAAGGGGGCAACTCTTG	59.305	55.000	0.00	0.00	36.50	3.02
2571	2625	3.744942	TCGAGTCTACACTCTACACACAC	59.255	47.826	0.00	0.00	46.31	3.82
2572	2626	3.747010	CGAGTCTACACTCTACACACACT	59.253	47.826	0.00	0.00	46.31	3.55
2610	2664	8.286800	CAGACGAAAATAAACACCACATTAAGA	58.713	33.333	0.00	0.00	0.00	2.10
2670	2724	3.108144	GTTAAATGCACCAGCTATTGCG	58.892	45.455	12.71	0.00	45.42	4.85
2671	2725	1.176527	AAATGCACCAGCTATTGCGT	58.823	45.000	12.71	10.19	45.42	5.24
2704	2758	6.599244	AGCTGGAATGATTTAACGATTCAGAA	59.401	34.615	0.00	0.00	0.00	3.02
2796	2850	8.186821	GCTATAGTTTGAATCAACATCTGCTTT	58.813	33.333	0.00	0.00	0.00	3.51
2804	2858	3.819368	TCAACATCTGCTTTGTTCCAGA	58.181	40.909	0.00	0.00	41.81	3.86
2845	2899	4.095610	GGAAACAGATAAAACAATCGCCG	58.904	43.478	0.00	0.00	0.00	6.46
2846	2900	3.757745	AACAGATAAAACAATCGCCGG	57.242	42.857	0.00	0.00	0.00	6.13
2847	2901	1.400494	ACAGATAAAACAATCGCCGGC	59.600	47.619	19.07	19.07	0.00	6.13
2848	2902	1.021968	AGATAAAACAATCGCCGGCC	58.978	50.000	23.46	2.84	0.00	6.13
2849	2903	0.736053	GATAAAACAATCGCCGGCCA	59.264	50.000	23.46	9.24	0.00	5.36
2850	2904	0.738389	ATAAAACAATCGCCGGCCAG	59.262	50.000	23.46	8.15	0.00	4.85
2851	2905	1.928706	TAAAACAATCGCCGGCCAGC	61.929	55.000	23.46	0.55	0.00	4.85
2945	3001	3.705072	ACGGGAAGTAGGAAGTATTCTGG	59.295	47.826	0.00	0.00	46.56	3.86
2993	3049	4.330944	TTCTCTAGTTTCCGTTTGAGCA	57.669	40.909	0.00	0.00	0.00	4.26
2995	3051	5.654603	TCTCTAGTTTCCGTTTGAGCATA	57.345	39.130	0.00	0.00	0.00	3.14
3015	3072	5.221382	GCATAATTGAGAGGGATGCAAATGT	60.221	40.000	0.00	0.00	41.98	2.71
3028	3085	2.288961	CAAATGTTGCAGCCCATCTC	57.711	50.000	0.00	0.00	0.00	2.75
3040	3099	1.401905	GCCCATCTCTGTAAAAAGGCG	59.598	52.381	0.00	0.00	0.00	5.52
3044	3103	4.382685	CCCATCTCTGTAAAAAGGCGTAGA	60.383	45.833	0.00	0.00	0.00	2.59
3061	3120	4.612259	GCGTAGATGCTTATGGCTCAATTG	60.612	45.833	0.00	0.00	42.39	2.32
3144	3203	3.207474	AGCTCATTGAATCGCAACAAC	57.793	42.857	0.02	0.00	39.78	3.32
3147	3211	3.120121	GCTCATTGAATCGCAACAACAAC	59.880	43.478	0.00	0.00	39.78	3.32
3151	3215	5.578336	TCATTGAATCGCAACAACAACAAAA	59.422	32.000	0.00	0.00	39.78	2.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
253	254	0.255890	AGCAAGGTGTCTGTTGGTGT	59.744	50.000	0.00	0.00	33.25	4.16
277	278	2.223157	TGTCTTTCGTCAAGTTTTGCCG	60.223	45.455	0.00	0.00	33.66	5.69
764	766	2.896044	TGTGGTTGATTGCTGCCAATTA	59.104	40.909	0.00	0.00	41.60	1.40
991	993	7.226720	ACTCTTTGGTACTTTCATGTAGTTGTG	59.773	37.037	8.20	0.00	0.00	3.33
1521	1528	8.367911	TCATTCTCCACATACTCATATACCAAC	58.632	37.037	0.00	0.00	0.00	3.77
1857	1864	4.876107	CCATAGCTGTAAACATCGACCTTT	59.124	41.667	0.00	0.00	0.00	3.11
1900	1907	4.165372	ACTTGAAACCCTAGTTCCAGTCAA	59.835	41.667	0.00	0.00	34.19	3.18
1946	1966	4.645136	GGATAAAGTCTGGAAACCCCATTC	59.355	45.833	0.00	0.00	45.57	2.67
2335	2367	6.235664	GGAGGGAGTACTGTTTATTTGTTGA	58.764	40.000	0.00	0.00	0.00	3.18
2430	2464	5.222079	TGCTGTTATGAGAACACTTGGTA	57.778	39.130	0.00	0.00	0.00	3.25
2508	2562	1.548986	GCAATTGTGCGTGATAAGCC	58.451	50.000	7.40	0.00	41.93	4.35
2571	2625	2.561733	TCGTCTGCGTTAAGATGGAG	57.438	50.000	4.87	0.00	39.49	3.86
2572	2626	3.306917	TTTCGTCTGCGTTAAGATGGA	57.693	42.857	4.87	0.00	39.49	3.41
2637	2691	7.518211	GCTGGTGCATTTAACGAAATTTCTTTT	60.518	33.333	14.31	10.31	39.41	2.27
2655	2709	2.039974	CCACGCAATAGCTGGTGCA	61.040	57.895	19.70	0.00	40.94	4.57
2670	2724	5.391312	AAATCATTCCAGCTAAACACCAC	57.609	39.130	0.00	0.00	0.00	4.16
2671	2725	6.348950	CGTTAAATCATTCCAGCTAAACACCA	60.349	38.462	0.00	0.00	0.00	4.17
2716	2770	3.579586	TCGTTGGTACAGACTAATGGGTT	59.420	43.478	0.00	0.00	42.39	4.11
2804	2858	9.492973	CTGTTTCCTTATGAAATGAACCAAATT	57.507	29.630	0.00	0.00	44.44	1.82
2849	2903	3.825160	TTTTGTCTGCCTCGCCGCT	62.825	57.895	0.00	0.00	0.00	5.52
2850	2904	3.353836	TTTTGTCTGCCTCGCCGC	61.354	61.111	0.00	0.00	0.00	6.53
2851	2905	2.175184	CTGTTTTGTCTGCCTCGCCG	62.175	60.000	0.00	0.00	0.00	6.46
2921	2977	4.159879	CAGAATACTTCCTACTTCCCGTGT	59.840	45.833	0.00	0.00	0.00	4.49
2945	3001	4.518249	CCCACTAAATCCTGAACTTCCTC	58.482	47.826	0.00	0.00	0.00	3.71
2993	3049	6.812998	CAACATTTGCATCCCTCTCAATTAT	58.187	36.000	0.00	0.00	0.00	1.28
2995	3051	5.080969	CAACATTTGCATCCCTCTCAATT	57.919	39.130	0.00	0.00	0.00	2.32
3015	3072	2.877097	TTTACAGAGATGGGCTGCAA	57.123	45.000	0.50	0.00	36.86	4.08
3024	3081	4.811557	GCATCTACGCCTTTTTACAGAGAT	59.188	41.667	0.00	0.00	0.00	2.75
3028	3085	4.946784	AAGCATCTACGCCTTTTTACAG	57.053	40.909	0.00	0.00	0.00	2.74
3061	3120	0.033699	AGCAAGGAAAGGAGGGATGC	60.034	55.000	0.00	0.00	0.00	3.91
3151	3215	5.359860	GCCCATAATGTACTGGCTTTAGTTT	59.640	40.000	0.00	0.00	39.05	2.66
3153	3217	4.080015	TGCCCATAATGTACTGGCTTTAGT	60.080	41.667	0.00	0.00	42.62	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.