AutoCloner

Multiple sequence alignment - TraesCS2A01G330300

Loading Multiple Alignment...

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	TraesCS2A01G330300	chr2A	100.000	2756	0	0	1	2756	562680363	562683118	0.000000e+00	5090.0
1	TraesCS2A01G330300	chr2A	96.460	904	17	7	1860	2756	702857299	702856404	0.000000e+00	1478.0
2	TraesCS2A01G330300	chr2D	92.180	1867	99	19	1	1834	425495537	425493685	0.000000e+00	2595.0
3	TraesCS2A01G330300	chr2B	91.525	1829	101	19	43	1834	500839353	500837542	0.000000e+00	2470.0
4	TraesCS2A01G330300	chr2B	91.304	46	4	0	4	49	500840734	500840689	2.290000e-06	63.9
5	TraesCS2A01G330300	chr4A	94.481	906	34	11	1860	2756	45375833	45374935	0.000000e+00	1382.0
6	TraesCS2A01G330300	chr3A	94.157	907	36	12	1860	2756	26581193	26582092	0.000000e+00	1365.0
7	TraesCS2A01G330300	chr5A	76.838	272	57	6	1100	1368	475525750	475525482	6.150000e-32	148.0
8	TraesCS2A01G330300	chr5D	76.471	272	58	6	1100	1368	372325198	372324930	2.860000e-30	143.0

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	TraesCS2A01G330300	chr2A	562680363	562683118	2755	False	5090.00	5090	100.0000	1	2756	1	chr2A.!!$F1	2755
1	TraesCS2A01G330300	chr2A	702856404	702857299	895	True	1478.00	1478	96.4600	1860	2756	1	chr2A.!!$R1	896
2	TraesCS2A01G330300	chr2D	425493685	425495537	1852	True	2595.00	2595	92.1800	1	1834	1	chr2D.!!$R1	1833
3	TraesCS2A01G330300	chr2B	500837542	500840734	3192	True	1266.95	2470	91.4145	4	1834	2	chr2B.!!$R1	1830
4	TraesCS2A01G330300	chr4A	45374935	45375833	898	True	1382.00	1382	94.4810	1860	2756	1	chr4A.!!$R1	896
5	TraesCS2A01G330300	chr3A	26581193	26582092	899	False	1365.00	1365	94.1570	1860	2756	1	chr3A.!!$F1	896

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
35	36	0.391528	TCAGCCGTGACATGGACATG	60.392	55.0	18.32	11.9	44.15	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1885	3269	0.106519	AGGGCGCTGCTATGGAAAAT	60.107	50.0	7.64	0.0	0.0	1.82	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
35	36	0.391528	TCAGCCGTGACATGGACATG	60.392	55.000	18.32	11.90	44.15	3.21
54	1397	6.093219	GGACATGTATGCTATTATCTGGCTTG	59.907	42.308	0.00	0.00	31.45	4.01
87	1430	2.265904	TACGTGCGCTGGTGAGACT	61.266	57.895	9.73	0.00	0.00	3.24
214	1564	1.859703	CGTGCATCAGAGATTCAGAGC	59.140	52.381	0.00	0.00	0.00	4.09
216	1566	1.479730	TGCATCAGAGATTCAGAGCGT	59.520	47.619	0.00	0.00	0.00	5.07
217	1567	1.859703	GCATCAGAGATTCAGAGCGTG	59.140	52.381	0.00	0.00	0.00	5.34
218	1568	2.738000	GCATCAGAGATTCAGAGCGTGT	60.738	50.000	0.00	0.00	0.00	4.49
219	1569	3.519579	CATCAGAGATTCAGAGCGTGTT	58.480	45.455	0.00	0.00	0.00	3.32
220	1570	4.676546	CATCAGAGATTCAGAGCGTGTTA	58.323	43.478	0.00	0.00	0.00	2.41
279	1649	7.611079	TCATCATTCATCATACCTGTGTTTTGA	59.389	33.333	0.00	0.00	0.00	2.69
298	1668	2.591429	TTGGCCGACACAGCACTG	60.591	61.111	0.00	0.00	0.00	3.66
381	1751	4.079253	TCTGCATTTTTGTAGAGGGTTCC	58.921	43.478	0.00	0.00	0.00	3.62
402	1772	2.742372	GTGCATTCCGTCGGTGCT	60.742	61.111	22.86	3.30	39.52	4.40
418	1788	4.080807	TCGGTGCTCCCATTTTAATACTCA	60.081	41.667	0.00	0.00	0.00	3.41
419	1789	4.821805	CGGTGCTCCCATTTTAATACTCAT	59.178	41.667	0.00	0.00	0.00	2.90
478	1848	9.733556	TGTACTATTCTATTTTGGAAAAGCTCA	57.266	29.630	0.00	0.00	0.00	4.26
541	1911	2.392181	CCGGCCGTGTAAATCGCAA	61.392	57.895	26.12	0.00	0.00	4.85
599	1969	6.478512	TCATCACAACATAGTACTATGCCA	57.521	37.500	33.26	17.98	45.06	4.92
613	1983	4.666512	ACTATGCCAGAAGGTTTTGACAT	58.333	39.130	0.00	0.00	37.19	3.06
615	1985	1.879380	TGCCAGAAGGTTTTGACATCG	59.121	47.619	0.00	0.00	37.19	3.84
650	2020	3.813724	AGCCCGAGAAAACTTTACTGAAC	59.186	43.478	0.00	0.00	0.00	3.18
682	2052	1.142474	CTGTTTGTTCCGACGTACCC	58.858	55.000	0.00	0.00	0.00	3.69
960	2332	3.842732	TGCTCATCATCTGCACTTTTG	57.157	42.857	0.00	0.00	0.00	2.44
961	2333	3.151554	TGCTCATCATCTGCACTTTTGT	58.848	40.909	0.00	0.00	0.00	2.83
962	2334	4.325972	TGCTCATCATCTGCACTTTTGTA	58.674	39.130	0.00	0.00	0.00	2.41

Showing 1 to 25 of 76 entries

Previous1 2 3 4Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	4.583871	AGCCAAGCCAGATAATAGCATAC	58.416	43.478	0.00	0.00	0.00	2.39
41	1384	4.621510	CGAGCATAGCCAAGCCAGATAATA	60.622	45.833	0.00	0.00	0.00	0.98
176	1526	1.205064	GTAGTTGTGCTGCACTGCG	59.795	57.895	30.43	0.00	35.11	5.18
252	1622	7.943079	AAACACAGGTATGATGAATGATGAA	57.057	32.000	0.00	0.00	0.00	2.57
253	1623	7.611079	TCAAAACACAGGTATGATGAATGATGA	59.389	33.333	0.00	0.00	0.00	2.92
254	1624	7.764331	TCAAAACACAGGTATGATGAATGATG	58.236	34.615	0.00	0.00	0.00	3.07
255	1625	7.613022	ACTCAAAACACAGGTATGATGAATGAT	59.387	33.333	0.00	0.00	0.00	2.45
271	1641	0.736053	TGTCGGCCAACTCAAAACAC	59.264	50.000	2.24	0.00	0.00	3.32
279	1649	2.591715	GTGCTGTGTCGGCCAACT	60.592	61.111	2.24	0.00	34.37	3.16
381	1751	3.853330	CCGACGGAATGCACAGCG	61.853	66.667	8.64	0.00	0.00	5.18
402	1772	6.494666	AGACCGATGAGTATTAAAATGGGA	57.505	37.500	0.00	0.00	0.00	4.37
418	1788	9.967451	TTATCTAGAGAATAGATCAAGACCGAT	57.033	33.333	0.00	0.00	35.95	4.18
419	1789	9.967451	ATTATCTAGAGAATAGATCAAGACCGA	57.033	33.333	10.87	0.00	35.95	4.69
468	1838	6.720012	TGTTTTTGAAAACTGAGCTTTTCC	57.280	33.333	17.33	3.84	46.37	3.13
525	1895	1.427819	CCTTGCGATTTACACGGCC	59.572	57.895	0.00	0.00	0.00	6.13
527	1897	0.519519	TTGCCTTGCGATTTACACGG	59.480	50.000	0.00	0.00	0.00	4.94
541	1911	0.322906	GCTTAGCCCTTCAGTTGCCT	60.323	55.000	0.00	0.00	0.00	4.75
599	1969	2.851195	ACAGCGATGTCAAAACCTTCT	58.149	42.857	0.00	0.00	0.00	2.85
633	2003	5.977725	GCTTTGGGTTCAGTAAAGTTTTCTC	59.022	40.000	0.00	0.00	34.69	2.87
650	2020	0.527565	CAAACAGGATCCGCTTTGGG	59.472	55.000	21.20	5.27	38.76	4.12
674	2044	3.177249	GAACGCTGCGGGTACGTC	61.177	66.667	26.95	9.32	43.45	4.34
697	2069	6.361748	GTGACTGCAATTTTGTTCTTCTGATC	59.638	38.462	0.00	0.00	0.00	2.92
960	2332	1.725164	GTGCGTTACAGGACTTGCTAC	59.275	52.381	0.00	0.00	0.00	3.58
961	2333	1.341852	TGTGCGTTACAGGACTTGCTA	59.658	47.619	0.00	0.00	33.42	3.49
962	2334	0.105964	TGTGCGTTACAGGACTTGCT	59.894	50.000	0.00	0.00	33.42	3.91

Showing 1 to 25 of 71 entries

Previous1 2 3Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.