AutoCloner

Multiple sequence alignment - TraesCS2D01G463900

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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	TraesCS2D01G463900	chr2D	100.000	2643	0	0	1	2643	569308541	569311183	0.000000e+00	4881
1	TraesCS2D01G463900	chr2B	87.936	2611	120	68	12	2506	682137781	682140312	0.000000e+00	2896
2	TraesCS2D01G463900	chr2A	86.116	2096	111	60	9	2011	709048045	709050053	0.000000e+00	2093
3	TraesCS2D01G463900	chr2A	92.632	190	13	1	2013	2202	709051407	709051595	3.350000e-69	272
4	TraesCS2D01G463900	chr2A	94.737	76	4	0	2295	2370	709051602	709051677	4.620000e-23	119

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	TraesCS2D01G463900	chr2D	569308541	569311183	2642	False	4881	4881	100.000000	1	2643	1	chr2D.!!$F1	2642
1	TraesCS2D01G463900	chr2B	682137781	682140312	2531	False	2896	2896	87.936000	12	2506	1	chr2B.!!$F1	2494
2	TraesCS2D01G463900	chr2A	709048045	709051677	3632	False	828	2093	91.161667	9	2370	3	chr2A.!!$F1	2361

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
167	169	0.16923	CGTGACTTGACCTCGAGGAG	59.831	60.0	37.69	25.59	38.94	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1979	2133	0.727398	GCATCCGTCAGTTGGCTTAC	59.273	55.0	0.0	0.0	0.0	2.34	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)

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	2.876581	TTACCACTCGCCTGATCGA	58.123	52.632	0.00	0.00	36.94	3.59
19	20	1.399714	TTACCACTCGCCTGATCGAT	58.600	50.000	0.00	0.00	37.87	3.59
20	21	0.952280	TACCACTCGCCTGATCGATC	59.048	55.000	18.72	18.72	37.87	3.69
21	22	1.371022	CCACTCGCCTGATCGATCG	60.371	63.158	20.03	9.36	37.87	3.69
22	23	1.649267	CACTCGCCTGATCGATCGA	59.351	57.895	21.86	21.86	37.87	3.59
23	24	4.836892	CTCGCCTGATCGATCGAG	57.163	61.111	23.84	18.18	41.66	4.04
24	25	4.456806	TCGCCTGATCGATCGAGA	57.543	55.556	23.84	11.01	33.02	4.04
51	52	1.721487	CCAATGGCGATCAACCGTC	59.279	57.895	0.00	0.00	34.30	4.79
109	110	4.753662	AGGACGGCCCTGCTCGTA	62.754	66.667	1.76	0.00	45.61	3.43
110	111	4.509737	GGACGGCCCTGCTCGTAC	62.510	72.222	0.00	0.80	36.12	3.67
114	115	4.874977	GGCCCTGCTCGTACTCGC	62.875	72.222	0.00	0.00	36.96	5.03
136	137	3.726517	CAACCAGCAGGCGAACGG	61.727	66.667	0.00	0.00	39.06	4.44
166	168	1.863662	GCGTGACTTGACCTCGAGGA	61.864	60.000	37.69	14.23	38.94	3.71
167	169	0.169230	CGTGACTTGACCTCGAGGAG	59.831	60.000	37.69	25.59	38.94	3.69
168	170	1.249407	GTGACTTGACCTCGAGGAGT	58.751	55.000	37.69	28.62	38.94	3.85
169	171	2.434428	GTGACTTGACCTCGAGGAGTA	58.566	52.381	37.69	19.34	38.94	2.59
176	209	4.708576	TGACCTCGAGGAGTAGTATGAT	57.291	45.455	37.69	11.29	38.94	2.45
213	246	2.104111	TGAGCTAATTATGGTCACCGGG	59.896	50.000	6.32	0.00	37.07	5.73
268	307	4.656117	TGAAGCGCGGCTCGTGAA	62.656	61.111	8.83	0.00	38.25	3.18
269	308	4.135493	GAAGCGCGGCTCGTGAAC	62.135	66.667	8.83	0.00	38.25	3.18
338	377	2.162208	CGGAGTACAGTAACCGTAGCAA	59.838	50.000	15.37	0.00	40.42	3.91
365	408	1.151450	GGCACGGGATGGATGGATT	59.849	57.895	0.00	0.00	0.00	3.01
388	431	1.129998	CGGTGGTACTGTACGAGACTG	59.870	57.143	11.52	9.15	0.00	3.51
440	483	1.178276	AGCCGACAGAGAGGTTAGTG	58.822	55.000	0.00	0.00	0.00	2.74
666	760	2.390225	AGGGTTCTCACTCACTCACT	57.610	50.000	0.00	0.00	0.00	3.41

Showing 1 to 25 of 161 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	1.337071	GATCGATCAGGCGAGTGGTAA	59.663	52.381	20.52	0.00	44.26	2.85
2	3	1.736586	GATCGATCAGGCGAGTGGT	59.263	57.895	20.52	0.00	44.26	4.16
3	4	1.371022	CGATCGATCAGGCGAGTGG	60.371	63.158	24.40	1.69	44.26	4.00
5	6	1.945522	CTCGATCGATCAGGCGAGT	59.054	57.895	24.40	0.00	44.26	4.18
6	7	4.836892	CTCGATCGATCAGGCGAG	57.163	61.111	24.40	20.20	44.26	5.03
7	8	0.533085	ACTCTCGATCGATCAGGCGA	60.533	55.000	24.40	15.25	45.22	5.54
8	9	0.110419	GACTCTCGATCGATCAGGCG	60.110	60.000	24.40	11.72	0.00	5.52
9	10	0.947960	TGACTCTCGATCGATCAGGC	59.052	55.000	24.40	19.25	0.00	4.85
11	12	1.070242	CGGTGACTCTCGATCGATCAG	60.070	57.143	24.40	18.83	0.00	2.90
13	14	0.236187	CCGGTGACTCTCGATCGATC	59.764	60.000	19.78	15.68	0.00	3.69
14	15	1.787057	GCCGGTGACTCTCGATCGAT	61.787	60.000	19.78	3.36	0.00	3.59
15	16	2.470362	GCCGGTGACTCTCGATCGA	61.470	63.158	18.32	18.32	0.00	3.59
16	17	2.024871	GCCGGTGACTCTCGATCG	59.975	66.667	9.36	9.36	0.00	3.69
17	18	1.945354	TTGGCCGGTGACTCTCGATC	61.945	60.000	1.90	0.00	0.00	3.69
18	19	1.330655	ATTGGCCGGTGACTCTCGAT	61.331	55.000	1.90	0.00	0.00	3.59
19	20	1.982395	ATTGGCCGGTGACTCTCGA	60.982	57.895	1.90	0.00	0.00	4.04
20	21	1.811266	CATTGGCCGGTGACTCTCG	60.811	63.158	1.90	0.00	0.00	4.04
21	22	1.450312	CCATTGGCCGGTGACTCTC	60.450	63.158	1.90	0.00	0.00	3.20
22	23	2.671070	CCATTGGCCGGTGACTCT	59.329	61.111	1.90	0.00	0.00	3.24
23	24	3.134127	GCCATTGGCCGGTGACTC	61.134	66.667	17.28	0.00	44.06	3.36
72	73	3.433031	CCTCGAGTCCTGAGAGATGTACT	60.433	52.174	12.31	0.00	35.43	2.73
102	103	2.089887	TTGTTGGGCGAGTACGAGCA	62.090	55.000	15.48	0.00	42.66	4.26
105	106	1.005867	GGTTGTTGGGCGAGTACGA	60.006	57.895	0.00	0.00	42.66	3.43
109	110	2.594592	GCTGGTTGTTGGGCGAGT	60.595	61.111	0.00	0.00	0.00	4.18
110	111	2.594303	TGCTGGTTGTTGGGCGAG	60.594	61.111	0.00	0.00	0.00	5.03

Showing 1 to 25 of 184 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.