AutoCloner

Multiple sequence alignment - TraesCS6D01G227700

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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	TraesCS6D01G227700	chr6D	100.000	3372	0	0	1	3372	318957389	318960760	0.000000e+00	6228
1	TraesCS6D01G227700	chr6A	93.464	2861	100	16	153	2982	456759361	456762165	0.000000e+00	4167
2	TraesCS6D01G227700	chr6A	93.684	570	28	4	1	562	456757601	456758170	0.000000e+00	846
3	TraesCS6D01G227700	chr6A	94.915	354	10	3	3027	3372	456762161	456762514	6.360000e-152	547
4	TraesCS6D01G227700	chr6B	93.677	1550	88	3	940	2479	504310566	504309017	0.000000e+00	2311
5	TraesCS6D01G227700	chr6B	90.698	817	34	16	153	942	504311518	504310717	0.000000e+00	1050
6	TraesCS6D01G227700	chr5A	88.848	538	52	3	969	1506	609611385	609610856	0.000000e+00	654
7	TraesCS6D01G227700	chr5A	90.476	336	28	3	605	939	609611883	609611551	1.110000e-119	440
8	TraesCS6D01G227700	chr2B	88.043	92	11	0	2767	2858	765923121	765923030	3.560000e-20	110

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	TraesCS6D01G227700	chr6D	318957389	318960760	3371	False	6228.000000	6228	100.0000	1	3372	1	chr6D.!!$F1	3371
1	TraesCS6D01G227700	chr6A	456757601	456762514	4913	False	1853.333333	4167	94.0210	1	3372	3	chr6A.!!$F1	3371
2	TraesCS6D01G227700	chr6B	504309017	504311518	2501	True	1680.500000	2311	92.1875	153	2479	2	chr6B.!!$R1	2326
3	TraesCS6D01G227700	chr5A	609610856	609611883	1027	True	547.000000	654	89.6620	605	1506	2	chr5A.!!$R1	901

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	Hairpin	End Stability	Orientation
43	45	0.249238	GGTCAGCCAGTCGCATCTAG	60.249	60.0	0.0	41.38	2.43	F
683	2291	0.324830	AGGAAAGGAGGAGGAGACCG	60.325	60.0	0.0	34.73	4.79	F
1884	3667	0.249868	CCTGAAGCTTGGTCGTGTCA	60.250	55.0	2.1	0.00	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1535	3318	0.179100	CTGATCTCGTGCCCGATGTT	60.179	55.0	43.27	2.71	R
1922	3705	0.460109	TCTGTTCGATCACCGGCATG	60.460	55.0	39.14	4.06	R
3016	4815	0.322997	CGTGGACTCACCTCCTCTCT	60.323	60.0	40.65	3.10	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	32	2.570181	GCAGCAACCATGGTCAGC	59.430	61.111	26.54	26.54	34.35	4.26
43	45	0.249238	GGTCAGCCAGTCGCATCTAG	60.249	60.000	0.00	0.00	41.38	2.43
53	55	1.032794	TCGCATCTAGTACCAGCAGG	58.967	55.000	0.00	0.00	42.21	4.85
66	68	1.341209	CCAGCAGGCGATATACTGTCA	59.659	52.381	0.00	0.00	37.07	3.58
73	75	5.528870	CAGGCGATATACTGTCACATACAA	58.471	41.667	0.00	0.00	37.74	2.41
101	103	2.416202	CACGAGCATGCTTTGTGTATCA	59.584	45.455	30.76	0.00	32.07	2.15
113	115	6.880529	TGCTTTGTGTATCATCTCAGATTGAA	59.119	34.615	0.00	0.00	0.00	2.69
151	153	8.221965	TCTGAGAAGAAAATCATCAATCATGG	57.778	34.615	0.00	0.00	32.64	3.66
216	220	5.648033	ACATGATTGATGATTCGAGAACG	57.352	39.130	0.00	0.00	37.02	3.95
273	277	3.978718	TTCAACGTGCACATTGATCAA	57.021	38.095	26.95	11.46	34.87	2.57
290	297	6.545504	TGATCAAGAAGCAAAGACAAGTAC	57.454	37.500	0.00	0.00	0.00	2.73
323	330	5.626142	AGGAAGACCTTTCTTTCTTTCTCC	58.374	41.667	0.00	0.00	44.38	3.71
342	354	6.089249	TCTCCCTTTTTCTTCATTTTCAGC	57.911	37.500	0.00	0.00	0.00	4.26
682	2290	1.273324	TGAGGAAAGGAGGAGGAGACC	60.273	57.143	0.00	0.00	0.00	3.85
683	2291	0.324830	AGGAAAGGAGGAGGAGACCG	60.325	60.000	0.00	0.00	34.73	4.79
685	2293	1.341778	GGAAAGGAGGAGGAGACCGTA	60.342	57.143	0.00	0.00	34.73	4.02
898	2528	1.079543	AGCATCCACTCTCGTGTGC	60.080	57.895	0.00	0.00	41.11	4.57
924	2554	3.345808	GCGCGCCAGTTGAGTTCA	61.346	61.111	23.24	0.00	0.00	3.18
1045	2828	2.649034	GAGTCGTGCGTGGGAGAA	59.351	61.111	0.00	0.00	0.00	2.87
1063	2846	2.743928	CTGAACCGCTGGTGAGGC	60.744	66.667	0.94	0.00	35.34	4.70
1080	2863	2.575993	CCTGTGCGTCCTCTCAGG	59.424	66.667	0.00	0.00	40.83	3.86
1414	3197	3.488489	CGATGCAGGTAAAAGGAAAACG	58.512	45.455	0.00	0.00	0.00	3.60
1417	3200	3.018149	TGCAGGTAAAAGGAAAACGTGT	58.982	40.909	0.00	0.00	32.92	4.49
1441	3224	4.190772	CACCCCAATGGCAATGTAATTTC	58.809	43.478	1.30	0.00	37.83	2.17
1535	3318	1.663379	CTCGGAGGTGCACATCGGTA	61.663	60.000	29.99	19.21	0.00	4.02

Showing 1 to 25 of 77 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	1.592400	CTGACCATGGTTGCTGCCAG	61.592	60.000	20.85	16.17	42.47	4.85
14	15	1.604308	TGGCTGACCATGGTTGCTG	60.604	57.895	29.93	19.49	42.67	4.41
30	32	1.269309	GCTGGTACTAGATGCGACTGG	60.269	57.143	10.90	0.00	0.00	4.00
43	45	2.296471	ACAGTATATCGCCTGCTGGTAC	59.704	50.000	11.69	5.48	35.27	3.34
53	55	6.475727	AGTTGTTGTATGTGACAGTATATCGC	59.524	38.462	0.00	0.00	39.88	4.58
66	68	3.985008	TGCTCGTGTAGTTGTTGTATGT	58.015	40.909	0.00	0.00	0.00	2.29
73	75	2.169832	AAGCATGCTCGTGTAGTTGT	57.830	45.000	22.93	0.00	0.00	3.32
141	143	4.166246	ACACAGAGCATCCATGATTGAT	57.834	40.909	0.00	0.00	33.66	2.57
151	153	5.261209	ACTGAGAAGATACACAGAGCATC	57.739	43.478	0.00	0.00	33.86	3.91
216	220	1.135699	CGATGTTCGCTGGCATTTGC	61.136	55.000	0.00	0.00	34.72	3.68
273	277	5.918608	TCTTCAGTACTTGTCTTTGCTTCT	58.081	37.500	0.00	0.00	0.00	2.85
323	330	4.919754	CGAGGCTGAAAATGAAGAAAAAGG	59.080	41.667	0.00	0.00	0.00	3.11
682	2290	3.689649	CCCCAGAGTCCAGAAAAATTACG	59.310	47.826	0.00	0.00	0.00	3.18
683	2291	4.663334	ACCCCAGAGTCCAGAAAAATTAC	58.337	43.478	0.00	0.00	0.00	1.89
685	2293	3.903530	ACCCCAGAGTCCAGAAAAATT	57.096	42.857	0.00	0.00	0.00	1.82
924	2554	0.320771	AAGGCGATTTGACGAGCAGT	60.321	50.000	0.00	0.00	35.09	4.40
983	2766	2.350388	GGCATTTCATCGAACACGTTGT	60.350	45.455	0.00	0.00	0.00	3.32
1045	2828	2.743718	CCTCACCAGCGGTTCAGT	59.256	61.111	0.00	0.00	31.02	3.41
1063	2846	2.575993	CCTGAGAGGACGCACAGG	59.424	66.667	5.31	5.31	42.71	4.00
1371	3154	3.329889	ACCGGGATGGCAGCTTCA	61.330	61.111	6.32	0.00	43.94	3.02
1414	3197	1.204467	CATTGCCATTGGGGTGTACAC	59.796	52.381	18.01	18.01	39.65	2.90
1417	3200	3.458044	TTACATTGCCATTGGGGTGTA	57.542	42.857	4.53	0.00	39.65	2.90
1441	3224	0.896940	AGACCATGGCTGTGCAAAGG	60.897	55.000	13.04	0.00	0.00	3.11
1535	3318	0.179100	CTGATCTCGTGCCCGATGTT	60.179	55.000	0.00	0.00	43.27	2.71
1573	3356	0.752009	AGGAGTTCCTCGATGCGCTA	60.752	55.000	9.73	0.00	44.77	4.26

Showing 1 to 25 of 71 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.