AutoCloner

Multiple sequence alignment - TraesCS7D01G178300

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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	TraesCS7D01G178300	chr7D	100.000	1661	0	0	802	2462	131597775	131599435	0.000000e+00	3068
1	TraesCS7D01G178300	chr7D	100.000	487	0	0	1	487	131596974	131597460	0.000000e+00	900
2	TraesCS7D01G178300	chr7A	86.827	1207	87	39	808	1973	130292532	130293707	0.000000e+00	1282
3	TraesCS7D01G178300	chr7A	88.068	352	22	8	66	405	130239924	130240267	1.370000e-107	399
4	TraesCS7D01G178300	chr7A	82.218	478	34	13	1994	2462	130293759	130294194	5.000000e-97	364
5	TraesCS7D01G178300	chr7A	98.684	76	1	0	1	76	130239827	130239902	4.270000e-28	135
6	TraesCS7D01G178300	chr7B	93.205	883	29	9	802	1675	92554807	92555667	0.000000e+00	1269
7	TraesCS7D01G178300	chr7B	93.919	296	14	1	1	292	92552623	92552918	6.250000e-121	444
8	TraesCS7D01G178300	chr7B	81.048	496	45	26	1994	2462	92556095	92556568	1.400000e-92	350
9	TraesCS7D01G178300	chr7B	91.262	206	13	4	1705	1907	92555666	92555869	2.410000e-70	276

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	TraesCS7D01G178300	chr7D	131596974	131599435	2461	False	1984.00	3068	100.0000	1	2462	2	chr7D.!!$F1	2461
1	TraesCS7D01G178300	chr7A	130292532	130294194	1662	False	823.00	1282	84.5225	808	2462	2	chr7A.!!$F2	1654
2	TraesCS7D01G178300	chr7B	92552623	92556568	3945	False	584.75	1269	89.8585	1	2462	4	chr7B.!!$F1	2461

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
357	370	0.303493	GACGCGCACAAGACTTTTGA	59.697	50.0	5.73	0.0	0.0	2.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1873	3317	0.033228	GCAGACTCAGCTGTCAGTGT	59.967	55.0	14.67	6.5	39.27	3.55	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
76	77	0.376852	AACGTGCATGTGTGTGTGTC	59.623	50.000	13.39	0.00	0.00	3.67
83	88	0.750249	ATGTGTGTGTGTCGAGGTGA	59.250	50.000	0.00	0.00	0.00	4.02
118	123	2.438795	CCGGGGTGGTGGAAATGT	59.561	61.111	0.00	0.00	0.00	2.71
132	137	2.609459	GGAAATGTGTGATGCTACGAGG	59.391	50.000	0.00	0.00	0.00	4.63
183	188	0.974383	ACTTTGGGTCCTCTGTACGG	59.026	55.000	0.00	0.00	0.00	4.02
187	192	1.982938	GGGTCCTCTGTACGGCTGT	60.983	63.158	2.42	2.42	0.00	4.40
216	221	2.502492	CCAGCCAGGACCGATCGAT	61.502	63.158	18.66	0.00	41.22	3.59
217	222	1.443407	CAGCCAGGACCGATCGATT	59.557	57.895	18.66	2.17	0.00	3.34
231	236	4.031652	CCGATCGATTTGGCATTGTTTTTC	59.968	41.667	18.66	0.00	0.00	2.29
238	243	2.621338	TGGCATTGTTTTTCGCACAAA	58.379	38.095	0.00	0.00	37.67	2.83
292	297	3.440872	ACGAACACTTTGCAAGTTGGTAA	59.559	39.130	13.53	0.00	40.46	2.85
293	298	4.097286	ACGAACACTTTGCAAGTTGGTAAT	59.903	37.500	13.53	0.00	40.46	1.89
294	299	5.040635	CGAACACTTTGCAAGTTGGTAATT	58.959	37.500	7.23	0.00	40.46	1.40
295	300	5.173131	CGAACACTTTGCAAGTTGGTAATTC	59.827	40.000	7.23	4.53	40.46	2.17
296	301	4.606961	ACACTTTGCAAGTTGGTAATTCG	58.393	39.130	4.75	0.00	40.46	3.34
297	302	3.425193	CACTTTGCAAGTTGGTAATTCGC	59.575	43.478	4.75	0.00	40.46	4.70
298	303	2.715737	TTGCAAGTTGGTAATTCGCC	57.284	45.000	4.75	0.00	0.00	5.54
300	305	1.268352	TGCAAGTTGGTAATTCGCCAC	59.732	47.619	4.75	0.00	35.46	5.01
302	307	2.745281	GCAAGTTGGTAATTCGCCACTA	59.255	45.455	4.75	0.00	35.46	2.74
304	309	4.495844	GCAAGTTGGTAATTCGCCACTATC	60.496	45.833	4.75	0.00	35.46	2.08
305	310	4.755266	AGTTGGTAATTCGCCACTATCT	57.245	40.909	1.57	0.00	35.46	1.98
306	311	4.442706	AGTTGGTAATTCGCCACTATCTG	58.557	43.478	1.57	0.00	35.46	2.90
308	313	4.322080	TGGTAATTCGCCACTATCTGAG	57.678	45.455	0.00	0.00	0.00	3.35
309	314	3.958147	TGGTAATTCGCCACTATCTGAGA	59.042	43.478	0.00	0.00	0.00	3.27
310	315	4.404394	TGGTAATTCGCCACTATCTGAGAA	59.596	41.667	0.00	0.00	0.00	2.87

Showing 1 to 25 of 170 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
114	119	1.743772	GCCCTCGTAGCATCACACATT	60.744	52.381	0.00	0.00	0.00	2.71
118	123	1.987306	TGGCCCTCGTAGCATCACA	60.987	57.895	0.00	0.00	0.00	3.58
132	137	1.450134	TGCACAGATCATCGTGGCC	60.450	57.895	0.00	0.00	33.62	5.36
187	192	3.626996	CTGGCTGGAACCGATGGCA	62.627	63.158	0.00	0.00	0.00	4.92
216	221	2.621338	TGTGCGAAAAACAATGCCAAA	58.379	38.095	0.00	0.00	0.00	3.28
217	222	2.299993	TGTGCGAAAAACAATGCCAA	57.700	40.000	0.00	0.00	0.00	4.52
231	236	3.963340	AAAGAAAAACGTGTTTGTGCG	57.037	38.095	8.82	0.00	32.36	5.34
238	243	4.090786	CCGCAAAAGAAAAGAAAAACGTGT	59.909	37.500	0.00	0.00	0.00	4.49
292	297	3.070734	AGCATTCTCAGATAGTGGCGAAT	59.929	43.478	0.00	0.00	31.11	3.34
293	298	2.432146	AGCATTCTCAGATAGTGGCGAA	59.568	45.455	0.00	0.00	0.00	4.70
294	299	2.034878	AGCATTCTCAGATAGTGGCGA	58.965	47.619	0.00	0.00	0.00	5.54
295	300	2.133553	CAGCATTCTCAGATAGTGGCG	58.866	52.381	0.00	0.00	0.00	5.69
296	301	2.492012	CCAGCATTCTCAGATAGTGGC	58.508	52.381	0.00	0.00	0.00	5.01
297	302	2.437281	ACCCAGCATTCTCAGATAGTGG	59.563	50.000	0.00	0.00	0.00	4.00
298	303	3.834489	ACCCAGCATTCTCAGATAGTG	57.166	47.619	0.00	0.00	0.00	2.74
300	305	4.133078	GGAAACCCAGCATTCTCAGATAG	58.867	47.826	0.00	0.00	0.00	2.08
302	307	2.309755	TGGAAACCCAGCATTCTCAGAT	59.690	45.455	0.00	0.00	0.00	2.90
304	309	2.089980	CTGGAAACCCAGCATTCTCAG	58.910	52.381	0.00	0.00	44.11	3.35
305	310	2.205022	CTGGAAACCCAGCATTCTCA	57.795	50.000	0.00	0.00	44.11	3.27
322	335	1.190984	GCGTCGTGCACATATCATCTG	59.809	52.381	18.64	0.00	45.45	2.90
323	336	1.491670	GCGTCGTGCACATATCATCT	58.508	50.000	18.64	0.00	45.45	2.90
337	350	0.986874	CAAAAGTCTTGTGCGCGTCG	60.987	55.000	8.43	0.00	0.00	5.12
339	352	0.944386	ATCAAAAGTCTTGTGCGCGT	59.056	45.000	8.43	0.00	0.00	6.01
340	353	1.595609	GATCAAAAGTCTTGTGCGCG	58.404	50.000	0.00	0.00	0.00	6.86
341	354	1.537202	AGGATCAAAAGTCTTGTGCGC	59.463	47.619	0.00	0.00	0.00	6.09

Showing 1 to 25 of 154 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.