AutoCloner

Multiple sequence alignment - TraesCS4D01G086700

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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	TraesCS4D01G086700	chr4D	100.000	2981	0	0	1	2981	62095216	62098196	0.000000e+00	5505.0
1	TraesCS4D01G086700	chr4B	94.419	3010	105	24	1	2981	90507696	90504721	0.000000e+00	4569.0
2	TraesCS4D01G086700	chr4A	93.214	3006	122	30	1	2981	535424677	535427625	0.000000e+00	4346.0
3	TraesCS4D01G086700	chr4A	83.054	537	75	12	218	740	464770623	464770089	9.670000e-130	473.0
4	TraesCS4D01G086700	chr3D	79.356	528	84	19	228	745	25138751	25139263	6.120000e-92	348.0
5	TraesCS4D01G086700	chr1D	82.524	309	44	6	215	513	347220829	347221137	2.280000e-66	263.0
6	TraesCS4D01G086700	chr1D	82.353	85	14	1	654	737	347253224	347253308	4.120000e-09	73.1
7	TraesCS4D01G086700	chr5A	84.348	115	11	4	656	764	44606127	44606014	4.060000e-19	106.0
8	TraesCS4D01G086700	chr5D	85.227	88	10	3	522	607	170264849	170264763	1.470000e-13	87.9
9	TraesCS4D01G086700	chr5B	82.955	88	12	3	522	607	162449662	162449576	3.190000e-10	76.8

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	TraesCS4D01G086700	chr4D	62095216	62098196	2980	False	5505	5505	100.000	1	2981	1	chr4D.!!$F1	2980
1	TraesCS4D01G086700	chr4B	90504721	90507696	2975	True	4569	4569	94.419	1	2981	1	chr4B.!!$R1	2980
2	TraesCS4D01G086700	chr4A	535424677	535427625	2948	False	4346	4346	93.214	1	2981	1	chr4A.!!$F1	2980
3	TraesCS4D01G086700	chr4A	464770089	464770623	534	True	473	473	83.054	218	740	1	chr4A.!!$R1	522
4	TraesCS4D01G086700	chr3D	25138751	25139263	512	False	348	348	79.356	228	745	1	chr3D.!!$F1	517

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
722	748	1.308998	AAGCCGGTGACAACTCTTTG	58.691	50.0	1.90	0.0	38.83	2.77	F
1627	1657	0.855598	CCCACCCAAGGATCATCCAT	59.144	55.0	6.42	0.0	39.61	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1762	1792	0.391130	ATGTATATCGCGCCGCCAAT	60.391	50.0	2.28	0.0	0.0	3.16	R
2583	2632	0.591659	CATGATGCTGCTGGGAATCG	59.408	55.0	0.00	0.0	0.0	3.34	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
97	98	2.457366	AAAGGAGTTGACTACAGCGG	57.543	50.000	0.00	0.00	32.59	5.52
263	264	6.277605	ACAAATGTTACTTTTACAAGGTGCC	58.722	36.000	0.00	0.00	33.82	5.01
350	362	5.088680	TGCATGTATGTGATCTCAACTCA	57.911	39.130	0.90	2.61	0.00	3.41
351	363	5.490159	TGCATGTATGTGATCTCAACTCAA	58.510	37.500	0.90	0.00	0.00	3.02
383	397	5.805994	GTCTTGATTGTAGTTTCTCTACCCG	59.194	44.000	3.15	0.00	45.99	5.28
642	662	7.816640	ACATGATTTTTCACTATAGTTTGCGT	58.183	30.769	1.56	0.00	0.00	5.24
643	663	8.296713	ACATGATTTTTCACTATAGTTTGCGTT	58.703	29.630	1.56	0.00	0.00	4.84
667	689	2.084610	TCTTCTCGTGAACCATGCAG	57.915	50.000	0.00	0.00	0.00	4.41
722	748	1.308998	AAGCCGGTGACAACTCTTTG	58.691	50.000	1.90	0.00	38.83	2.77
756	782	2.101082	TCATAGTAACGCACGGGCATTA	59.899	45.455	11.77	0.52	41.24	1.90
772	798	5.807520	CGGGCATTATGCTAGTAATAGTGAG	59.192	44.000	17.13	2.69	44.28	3.51
778	808	3.845860	TGCTAGTAATAGTGAGGGGAGG	58.154	50.000	0.00	0.00	0.00	4.30
780	810	2.797285	AGTAATAGTGAGGGGAGGGG	57.203	55.000	0.00	0.00	0.00	4.79
800	830	3.584733	GGTAGCTCCCAATCAAATCCT	57.415	47.619	0.00	0.00	0.00	3.24
859	889	3.750922	GCCCACCAAACTTTAGGTCTCTT	60.751	47.826	0.00	0.00	35.52	2.85
1542	1572	2.064581	GTCCCACCAGGTCGCCTAT	61.065	63.158	0.00	0.00	36.75	2.57
1627	1657	0.855598	CCCACCCAAGGATCATCCAT	59.144	55.000	6.42	0.00	39.61	3.41
1722	1752	1.754803	GAGTGGGACGTGATCATGGTA	59.245	52.381	18.97	0.00	0.00	3.25
1731	1761	1.664965	GATCATGGTAGACGCGCCC	60.665	63.158	5.73	1.19	0.00	6.13
1734	1764	4.157120	ATGGTAGACGCGCCCACC	62.157	66.667	5.73	11.57	0.00	4.61
1764	1794	2.003548	GGAGGCACCAGGGAGGATT	61.004	63.158	0.00	0.00	41.22	3.01
1783	1813	1.445410	GGCGGCGCGATATACATGA	60.445	57.895	26.95	0.00	0.00	3.07
1845	1875	1.227999	CGGAAGTGTTGGTGCACGAT	61.228	55.000	11.45	0.00	43.61	3.73
2000	2030	7.137426	CCTTGAGAGCAAAACATAAGCATATC	58.863	38.462	0.00	0.00	32.73	1.63
2171	2217	1.673920	TGTTGTTTTCGAACTCCAGGC	59.326	47.619	0.00	0.00	0.00	4.85
2200	2246	2.233431	TCCCTGTGGCATTAATTTGTGC	59.767	45.455	6.27	6.27	40.55	4.57
2234	2280	8.954950	TCCTGAATTTCAGTGATCTATCTTTC	57.045	34.615	21.75	0.00	42.80	2.62
2448	2497	5.781210	TGTTAGCAGGATCAGATCTACAG	57.219	43.478	10.36	0.00	0.00	2.74
2478	2527	2.554893	TGTTTTCAAGATACGGGGCAAC	59.445	45.455	0.00	0.00	0.00	4.17
2485	2534	1.761500	GATACGGGGCAACGGGGTAT	61.761	60.000	5.83	0.00	38.39	2.73
2486	2535	0.471591	ATACGGGGCAACGGGGTATA	60.472	55.000	5.83	0.00	38.39	1.47
2487	2536	0.471591	TACGGGGCAACGGGGTATAT	60.472	55.000	5.83	0.00	38.39	0.86
2488	2537	0.471591	ACGGGGCAACGGGGTATATA	60.472	55.000	5.83	0.00	38.39	0.86
2489	2538	0.906775	CGGGGCAACGGGGTATATAT	59.093	55.000	0.00	0.00	37.60	0.86
2490	2539	2.109774	CGGGGCAACGGGGTATATATA	58.890	52.381	0.00	0.00	37.60	0.86
2583	2632	2.017049	ACCAATTGCAGCTATCGTTCC	58.983	47.619	0.00	0.00	0.00	3.62
2717	2767	5.653507	GCATAATGCATATACCATGGGTTG	58.346	41.667	18.09	8.77	44.26	3.77
2720	2770	3.222173	TGCATATACCATGGGTTGTCC	57.778	47.619	18.09	0.61	37.09	4.02
2767	2817	6.982141	TGCTTTATCATGAGAAATTTGCCATC	59.018	34.615	15.44	0.57	0.00	3.51
2812	2862	8.777865	TCAGAACTATGTTCTTTATGTTCAGG	57.222	34.615	9.89	0.00	37.03	3.86
2845	2895	7.268586	ACTAGAGCAATCTGTGGTATTTGTAG	58.731	38.462	0.00	0.00	38.34	2.74
2848	2898	5.560724	AGCAATCTGTGGTATTTGTAGTGT	58.439	37.500	0.00	0.00	35.75	3.55
2849	2899	6.707290	AGCAATCTGTGGTATTTGTAGTGTA	58.293	36.000	0.00	0.00	35.75	2.90
2850	2900	6.594159	AGCAATCTGTGGTATTTGTAGTGTAC	59.406	38.462	0.00	0.00	35.75	2.90
2876	2926	6.248433	ACATCCTTCCTTGCAAATCTTCTTA	58.752	36.000	0.00	0.00	0.00	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	1.002087	CCCGCTGTAGTCAACTCCTTT	59.998	52.381	0.00	0.00	0.00	3.11
97	98	1.450312	CCCTGCGGTGAGACAATCC	60.450	63.158	0.00	0.00	0.00	3.01
114	115	5.857822	ACACGAACTAACTTTAAGCATCC	57.142	39.130	0.00	0.00	0.00	3.51
350	362	8.695456	AGAAACTACAATCAAGACCATGTTTTT	58.305	29.630	0.00	0.00	0.00	1.94
351	363	8.237811	AGAAACTACAATCAAGACCATGTTTT	57.762	30.769	0.00	0.00	0.00	2.43
460	477	6.517529	GCACAAGATGGTAGATTAGGTAGGAG	60.518	46.154	0.00	0.00	0.00	3.69
649	671	0.445436	GCTGCATGGTTCACGAGAAG	59.555	55.000	0.00	0.00	33.63	2.85
667	689	0.319900	ATGATGGTATCTCGTGCCGC	60.320	55.000	0.00	0.00	34.92	6.53
672	694	5.043903	CGTCAAAAGATGATGGTATCTCGT	58.956	41.667	0.00	0.00	40.72	4.18
673	695	5.281727	TCGTCAAAAGATGATGGTATCTCG	58.718	41.667	0.00	0.00	43.93	4.04
756	782	4.421131	CCTCCCCTCACTATTACTAGCAT	58.579	47.826	0.00	0.00	0.00	3.79
780	810	3.584733	AGGATTTGATTGGGAGCTACC	57.415	47.619	8.55	8.55	38.08	3.18
800	830	1.409427	CCGCCTTTGTGGGTGTTTAAA	59.591	47.619	0.00	0.00	38.56	1.52
859	889	0.608130	CTTGATGGGTGACGAGGACA	59.392	55.000	0.00	0.00	0.00	4.02
1611	1641	2.105477	CGAGAATGGATGATCCTTGGGT	59.895	50.000	13.44	0.00	37.46	4.51
1627	1657	2.654877	GAAGTGGTCCGGCGAGAA	59.345	61.111	9.30	0.00	0.00	2.87
1746	1776	2.003548	AATCCTCCCTGGTGCCTCC	61.004	63.158	0.00	0.00	37.07	4.30
1752	1782	3.411517	CCGCCAATCCTCCCTGGT	61.412	66.667	0.00	0.00	34.97	4.00
1762	1792	0.391130	ATGTATATCGCGCCGCCAAT	60.391	50.000	2.28	0.00	0.00	3.16
1764	1794	1.736282	CATGTATATCGCGCCGCCA	60.736	57.895	2.28	0.00	0.00	5.69
1845	1875	2.123208	TCCACCGTCCTGTCCACA	60.123	61.111	0.00	0.00	0.00	4.17
2187	2233	6.311200	AGGAAAGAATTCGCACAAATTAATGC	59.689	34.615	0.00	4.17	36.36	3.56
2234	2280	7.543868	TGGCATGAAAATTTAAAATGTACTCCG	59.456	33.333	0.00	0.00	0.00	4.63
2281	2330	3.605749	CTGGGTGGGTGGCACTACG	62.606	68.421	18.45	1.73	0.00	3.51
2316	2365	0.905337	GTGACTCCCTACCTGGCTGT	60.905	60.000	0.00	0.00	0.00	4.40
2448	2497	4.679654	CGTATCTTGAAAACAAAAGGTGGC	59.320	41.667	0.00	0.00	0.00	5.01
2583	2632	0.591659	CATGATGCTGCTGGGAATCG	59.408	55.000	0.00	0.00	0.00	3.34
2634	2684	6.064060	CCTGCCTCAGTCATATAATTTTCCA	58.936	40.000	0.00	0.00	0.00	3.53
2635	2685	5.048434	GCCTGCCTCAGTCATATAATTTTCC	60.048	44.000	0.00	0.00	0.00	3.13
2645	2695	2.207501	CTTGGGCCTGCCTCAGTCAT	62.208	60.000	4.53	0.00	36.10	3.06
2705	2755	1.284785	CACCAGGACAACCCATGGTAT	59.715	52.381	11.73	0.00	41.46	2.73
2706	2756	0.695924	CACCAGGACAACCCATGGTA	59.304	55.000	11.73	0.00	41.46	3.25
2720	2770	2.747177	TGTAGTCCAGTATCCCACCAG	58.253	52.381	0.00	0.00	0.00	4.00
2767	2817	7.019774	TCTGAACAAACATTGAGTTGAGAAG	57.980	36.000	10.43	5.89	41.19	2.85
2773	2823	8.225603	ACATAGTTCTGAACAAACATTGAGTT	57.774	30.769	21.50	0.17	43.89	3.01
2774	2824	7.807977	ACATAGTTCTGAACAAACATTGAGT	57.192	32.000	21.50	5.10	0.00	3.41
2812	2862	8.894768	ACCACAGATTGCTCTAGTAAATTATC	57.105	34.615	0.00	0.00	0.00	1.75
2824	2874	5.643777	ACACTACAAATACCACAGATTGCTC	59.356	40.000	0.00	0.00	0.00	4.26
2845	2895	4.202245	TGCAAGGAAGGATGTAGTACAC	57.798	45.455	4.80	0.00	0.00	2.90
2848	2898	6.313519	AGATTTGCAAGGAAGGATGTAGTA	57.686	37.500	0.00	0.00	0.00	1.82
2849	2899	5.184892	AGATTTGCAAGGAAGGATGTAGT	57.815	39.130	0.00	0.00	0.00	2.73
2850	2900	5.884792	AGAAGATTTGCAAGGAAGGATGTAG	59.115	40.000	0.00	0.00	0.00	2.74
2876	2926	9.599866	TTGTCTTCGTGATGATATTTGAAGTAT	57.400	29.630	0.00	0.00	35.51	2.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.