AutoCloner

Multiple sequence alignment - TraesCS5D01G372200

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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	TraesCS5D01G372200	chr5D	100.000	2211	0	0	1	2211	446179180	446176970	0.000000e+00	4084
1	TraesCS5D01G372200	chr5D	98.840	1897	20	1	317	2211	503222786	503220890	0.000000e+00	3380
2	TraesCS5D01G372200	chr5D	98.522	1894	28	0	318	2211	6193505	6191612	0.000000e+00	3343
3	TraesCS5D01G372200	chrUn	98.997	1895	19	0	317	2211	216514037	216515931	0.000000e+00	3395
4	TraesCS5D01G372200	chrUn	98.997	1895	19	0	317	2211	286269346	286267452	0.000000e+00	3395
5	TraesCS5D01G372200	chr3B	98.948	1901	13	3	317	2211	101915746	101913847	0.000000e+00	3393
6	TraesCS5D01G372200	chr3D	98.945	1895	19	1	317	2211	589272390	589274283	0.000000e+00	3387
7	TraesCS5D01G372200	chr3D	95.610	205	8	1	16	220	175949463	175949260	5.890000e-86	327
8	TraesCS5D01G372200	chr3D	95.610	205	8	1	16	220	176220768	176220565	5.890000e-86	327
9	TraesCS5D01G372200	chr3D	95.122	205	9	1	16	220	175819429	175819226	2.740000e-84	322
10	TraesCS5D01G372200	chr3D	94.634	205	10	1	16	220	175811389	175811186	1.270000e-82	316
11	TraesCS5D01G372200	chr1D	98.680	1894	25	0	317	2210	254393546	254395439	0.000000e+00	3360
12	TraesCS5D01G372200	chr1A	98.579	1900	21	2	317	2211	554516818	554514920	0.000000e+00	3354
13	TraesCS5D01G372200	chr3A	98.417	1895	28	2	317	2211	594895061	594896953	0.000000e+00	3332
14	TraesCS5D01G372200	chr7D	94.098	305	16	1	1	305	208870920	208870618	1.550000e-126	462
15	TraesCS5D01G372200	chr7D	95.610	205	8	1	16	220	540701160	540701363	5.890000e-86	327
16	TraesCS5D01G372200	chr7D	95.122	205	9	1	16	220	500374502	500374299	2.740000e-84	322
17	TraesCS5D01G372200	chr4D	92.810	306	19	2	1	305	230795992	230795689	7.250000e-120	440
18	TraesCS5D01G372200	chr6D	96.585	205	6	1	16	220	112903913	112903710	2.720000e-89	339

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	TraesCS5D01G372200	chr5D	446176970	446179180	2210	True	4084	4084	100.000	1	2211	1	chr5D.!!$R2	2210
1	TraesCS5D01G372200	chr5D	503220890	503222786	1896	True	3380	3380	98.840	317	2211	1	chr5D.!!$R3	1894
2	TraesCS5D01G372200	chr5D	6191612	6193505	1893	True	3343	3343	98.522	318	2211	1	chr5D.!!$R1	1893
3	TraesCS5D01G372200	chrUn	216514037	216515931	1894	False	3395	3395	98.997	317	2211	1	chrUn.!!$F1	1894
4	TraesCS5D01G372200	chrUn	286267452	286269346	1894	True	3395	3395	98.997	317	2211	1	chrUn.!!$R1	1894
5	TraesCS5D01G372200	chr3B	101913847	101915746	1899	True	3393	3393	98.948	317	2211	1	chr3B.!!$R1	1894
6	TraesCS5D01G372200	chr3D	589272390	589274283	1893	False	3387	3387	98.945	317	2211	1	chr3D.!!$F1	1894
7	TraesCS5D01G372200	chr1D	254393546	254395439	1893	False	3360	3360	98.680	317	2210	1	chr1D.!!$F1	1893
8	TraesCS5D01G372200	chr1A	554514920	554516818	1898	True	3354	3354	98.579	317	2211	1	chr1A.!!$R1	1894
9	TraesCS5D01G372200	chr3A	594895061	594896953	1892	False	3332	3332	98.417	317	2211	1	chr3A.!!$F1	1894

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
313	314	1.019278	AATTCGTCGCGTGAGGCAAT	61.019	50.0	13.6	10.95	43.84	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1631	1633	0.384353	GTCACTTTTTCCTGTCGCGC	60.384	55.0	0.0	0.0	0.0	6.86	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
17	18	2.829592	GGGGGCTTAGTGGATCGG	59.170	66.667	0.00	0.00	0.00	4.18
18	19	2.819284	GGGGGCTTAGTGGATCGGG	61.819	68.421	0.00	0.00	0.00	5.14
19	20	2.111251	GGGCTTAGTGGATCGGGC	59.889	66.667	0.00	0.00	0.00	6.13
20	21	2.280186	GGCTTAGTGGATCGGGCG	60.280	66.667	0.00	0.00	0.00	6.13
21	22	2.967615	GCTTAGTGGATCGGGCGC	60.968	66.667	0.00	0.00	0.00	6.53
22	23	2.815308	CTTAGTGGATCGGGCGCT	59.185	61.111	7.64	0.00	0.00	5.92
23	24	1.592669	CTTAGTGGATCGGGCGCTG	60.593	63.158	7.64	0.00	0.00	5.18
24	25	2.978452	CTTAGTGGATCGGGCGCTGG	62.978	65.000	7.64	0.00	0.00	4.85
38	39	3.726517	CTGGCGAAACGGGTGCAG	61.727	66.667	0.00	0.00	0.00	4.41
42	43	4.025401	CGAAACGGGTGCAGGCAC	62.025	66.667	15.78	15.78	45.49	5.01
66	67	4.643387	GCTCGGTTGCTGGGGTGT	62.643	66.667	0.00	0.00	0.00	4.16
67	68	2.669569	CTCGGTTGCTGGGGTGTG	60.670	66.667	0.00	0.00	0.00	3.82
68	69	4.947147	TCGGTTGCTGGGGTGTGC	62.947	66.667	0.00	0.00	0.00	4.57
140	141	3.450115	GGGGTCGACGACAGGGAG	61.450	72.222	27.77	0.00	33.68	4.30
141	142	3.450115	GGGTCGACGACAGGGAGG	61.450	72.222	27.77	0.00	33.68	4.30
142	143	4.131088	GGTCGACGACAGGGAGGC	62.131	72.222	27.77	6.38	33.68	4.70
172	173	3.673484	GGACGGACCCGAACGACA	61.673	66.667	16.07	0.00	42.83	4.35
173	174	2.429739	GACGGACCCGAACGACAC	60.430	66.667	16.07	0.00	42.83	3.67
174	175	3.903932	GACGGACCCGAACGACACC	62.904	68.421	16.07	0.00	42.83	4.16
182	183	4.047059	GAACGACACCGCGGAGGA	62.047	66.667	35.90	0.00	45.00	3.71
183	184	3.562779	GAACGACACCGCGGAGGAA	62.563	63.158	35.90	0.00	45.00	3.36
184	185	3.569049	AACGACACCGCGGAGGAAG	62.569	63.158	35.90	21.06	45.00	3.46
204	205	4.117661	GCGAGCGACGAGGAGGTT	62.118	66.667	0.00	0.00	45.77	3.50
205	206	2.100603	CGAGCGACGAGGAGGTTC	59.899	66.667	0.00	0.00	45.77	3.62
206	207	2.100603	GAGCGACGAGGAGGTTCG	59.899	66.667	0.00	0.00	45.70	3.95
207	208	3.398353	GAGCGACGAGGAGGTTCGG	62.398	68.421	0.00	0.00	44.57	4.30
208	209	3.745803	GCGACGAGGAGGTTCGGT	61.746	66.667	0.00	0.00	44.57	4.69
209	210	2.178521	CGACGAGGAGGTTCGGTG	59.821	66.667	0.00	0.00	44.57	4.94
210	211	2.572284	GACGAGGAGGTTCGGTGG	59.428	66.667	0.00	0.00	44.57	4.61
211	212	3.644399	GACGAGGAGGTTCGGTGGC	62.644	68.421	0.00	0.00	44.57	5.01
212	213	4.796231	CGAGGAGGTTCGGTGGCG	62.796	72.222	0.00	0.00	36.95	5.69
232	233	4.161295	CGCGCAGAGGGATGGGAA	62.161	66.667	8.75	0.00	35.25	3.97
233	234	2.514824	GCGCAGAGGGATGGGAAC	60.515	66.667	0.30	0.00	35.25	3.62
234	235	2.202932	CGCAGAGGGATGGGAACG	60.203	66.667	0.00	0.00	35.25	3.95
235	236	2.514824	GCAGAGGGATGGGAACGC	60.515	66.667	0.00	0.00	0.00	4.84
236	237	2.202932	CAGAGGGATGGGAACGCG	60.203	66.667	3.53	3.53	0.00	6.01
237	238	3.470888	AGAGGGATGGGAACGCGG	61.471	66.667	12.47	0.00	0.00	6.46
257	258	4.883354	GGGCGATGGCAGGGAAGG	62.883	72.222	1.01	0.00	42.47	3.46
258	259	4.883354	GGCGATGGCAGGGAAGGG	62.883	72.222	1.01	0.00	42.47	3.95
259	260	4.883354	GCGATGGCAGGGAAGGGG	62.883	72.222	0.00	0.00	39.62	4.79
260	261	3.089874	CGATGGCAGGGAAGGGGA	61.090	66.667	0.00	0.00	0.00	4.81
261	262	2.597903	GATGGCAGGGAAGGGGAC	59.402	66.667	0.00	0.00	0.00	4.46
262	263	3.406595	GATGGCAGGGAAGGGGACG	62.407	68.421	0.00	0.00	0.00	4.79
266	267	4.760047	CAGGGAAGGGGACGCGTG	62.760	72.222	20.70	0.00	0.00	5.34
269	270	4.754667	GGAAGGGGACGCGTGGAC	62.755	72.222	20.70	6.55	0.00	4.02
298	299	2.408835	CGTGGGGCATCGCAATTC	59.591	61.111	0.00	0.00	37.58	2.17
299	300	2.408835	GTGGGGCATCGCAATTCG	59.591	61.111	0.00	0.00	37.58	3.34
300	301	2.045438	TGGGGCATCGCAATTCGT	60.045	55.556	0.00	0.00	39.67	3.85
301	302	2.112198	TGGGGCATCGCAATTCGTC	61.112	57.895	0.00	0.00	39.67	4.20
302	303	2.324477	GGGCATCGCAATTCGTCG	59.676	61.111	0.00	0.00	39.67	5.12
303	304	2.351210	GGCATCGCAATTCGTCGC	60.351	61.111	0.00	0.00	39.67	5.19
308	309	2.018670	CGCAATTCGTCGCGTGAG	59.981	61.111	5.77	0.00	46.23	3.51
309	310	2.395690	GCAATTCGTCGCGTGAGG	59.604	61.111	12.30	12.30	0.00	3.86
310	311	2.395690	CAATTCGTCGCGTGAGGC	59.604	61.111	13.60	0.00	38.69	4.70
311	312	2.048597	AATTCGTCGCGTGAGGCA	60.049	55.556	13.60	3.48	43.84	4.75
312	313	1.666553	AATTCGTCGCGTGAGGCAA	60.667	52.632	13.60	9.30	43.84	4.52
313	314	1.019278	AATTCGTCGCGTGAGGCAAT	61.019	50.000	13.60	10.95	43.84	3.56
314	315	1.695893	ATTCGTCGCGTGAGGCAATG	61.696	55.000	13.60	0.00	43.84	2.82
315	316	3.112075	CGTCGCGTGAGGCAATGT	61.112	61.111	5.77	0.00	43.84	2.71
482	483	8.281893	ACGAGCGTTCTTTCTATCTACTATTAC	58.718	37.037	0.00	0.00	0.00	1.89
640	641	8.275187	ACTATACCAGGAATATCAATGAACCA	57.725	34.615	0.00	0.00	0.00	3.67
1113	1115	4.814234	GTGTCCTACGGATAATGCAAATCA	59.186	41.667	12.84	0.00	32.73	2.57
2116	2126	5.131308	TCCAAAAATGGGTACTATCGGATCA	59.869	40.000	0.00	0.00	0.00	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.819284	CCCGATCCACTAAGCCCCC	61.819	68.421	0.00	0.00	0.00	5.40
1	2	2.829592	CCCGATCCACTAAGCCCC	59.170	66.667	0.00	0.00	0.00	5.80
2	3	2.111251	GCCCGATCCACTAAGCCC	59.889	66.667	0.00	0.00	0.00	5.19
3	4	2.280186	CGCCCGATCCACTAAGCC	60.280	66.667	0.00	0.00	0.00	4.35
4	5	2.967615	GCGCCCGATCCACTAAGC	60.968	66.667	0.00	0.00	0.00	3.09
5	6	1.592669	CAGCGCCCGATCCACTAAG	60.593	63.158	2.29	0.00	0.00	2.18
6	7	2.499205	CAGCGCCCGATCCACTAA	59.501	61.111	2.29	0.00	0.00	2.24
7	8	3.536917	CCAGCGCCCGATCCACTA	61.537	66.667	2.29	0.00	0.00	2.74
21	22	3.726517	CTGCACCCGTTTCGCCAG	61.727	66.667	0.00	0.00	0.00	4.85
25	26	4.025401	GTGCCTGCACCCGTTTCG	62.025	66.667	11.16	0.00	40.79	3.46
49	50	4.643387	ACACCCCAGCAACCGAGC	62.643	66.667	0.00	0.00	0.00	5.03
50	51	2.669569	CACACCCCAGCAACCGAG	60.670	66.667	0.00	0.00	0.00	4.63
51	52	4.947147	GCACACCCCAGCAACCGA	62.947	66.667	0.00	0.00	0.00	4.69
123	124	3.450115	CTCCCTGTCGTCGACCCC	61.450	72.222	22.05	0.67	0.00	4.95
124	125	3.450115	CCTCCCTGTCGTCGACCC	61.450	72.222	22.05	1.07	0.00	4.46
125	126	4.131088	GCCTCCCTGTCGTCGACC	62.131	72.222	22.05	5.49	0.00	4.79
126	127	4.477975	CGCCTCCCTGTCGTCGAC	62.478	72.222	18.51	18.51	0.00	4.20
129	130	3.827898	CTCCGCCTCCCTGTCGTC	61.828	72.222	0.00	0.00	0.00	4.20
155	156	3.673484	TGTCGTTCGGGTCCGTCC	61.673	66.667	9.36	0.74	40.74	4.79
156	157	2.429739	GTGTCGTTCGGGTCCGTC	60.430	66.667	9.36	3.74	40.74	4.79
157	158	3.982241	GGTGTCGTTCGGGTCCGT	61.982	66.667	9.36	0.00	40.74	4.69
165	166	3.562779	TTCCTCCGCGGTGTCGTTC	62.563	63.158	27.15	0.00	38.89	3.95
166	167	3.569049	CTTCCTCCGCGGTGTCGTT	62.569	63.158	27.15	0.00	38.89	3.85
167	168	4.052229	CTTCCTCCGCGGTGTCGT	62.052	66.667	27.15	0.00	38.89	4.34
187	188	4.117661	AACCTCCTCGTCGCTCGC	62.118	66.667	0.00	0.00	39.67	5.03
188	189	2.100603	GAACCTCCTCGTCGCTCG	59.899	66.667	0.00	0.00	41.41	5.03
189	190	2.100603	CGAACCTCCTCGTCGCTC	59.899	66.667	0.00	0.00	34.08	5.03
190	191	3.441290	CCGAACCTCCTCGTCGCT	61.441	66.667	0.00	0.00	37.11	4.93
191	192	3.745803	ACCGAACCTCCTCGTCGC	61.746	66.667	0.00	0.00	37.11	5.19
192	193	2.178521	CACCGAACCTCCTCGTCG	59.821	66.667	0.00	0.00	37.11	5.12
193	194	2.572284	CCACCGAACCTCCTCGTC	59.428	66.667	0.00	0.00	37.11	4.20
194	195	3.692406	GCCACCGAACCTCCTCGT	61.692	66.667	0.00	0.00	37.11	4.18
195	196	4.796231	CGCCACCGAACCTCCTCG	62.796	72.222	0.00	0.00	38.58	4.63
215	216	4.161295	TTCCCATCCCTCTGCGCG	62.161	66.667	0.00	0.00	0.00	6.86
216	217	2.514824	GTTCCCATCCCTCTGCGC	60.515	66.667	0.00	0.00	0.00	6.09
217	218	2.202932	CGTTCCCATCCCTCTGCG	60.203	66.667	0.00	0.00	0.00	5.18
218	219	2.514824	GCGTTCCCATCCCTCTGC	60.515	66.667	0.00	0.00	0.00	4.26
219	220	2.202932	CGCGTTCCCATCCCTCTG	60.203	66.667	0.00	0.00	0.00	3.35
220	221	3.470888	CCGCGTTCCCATCCCTCT	61.471	66.667	4.92	0.00	0.00	3.69
240	241	4.883354	CCTTCCCTGCCATCGCCC	62.883	72.222	0.00	0.00	0.00	6.13
241	242	4.883354	CCCTTCCCTGCCATCGCC	62.883	72.222	0.00	0.00	0.00	5.54
242	243	4.883354	CCCCTTCCCTGCCATCGC	62.883	72.222	0.00	0.00	0.00	4.58
243	244	3.089874	TCCCCTTCCCTGCCATCG	61.090	66.667	0.00	0.00	0.00	3.84
244	245	2.597903	GTCCCCTTCCCTGCCATC	59.402	66.667	0.00	0.00	0.00	3.51
245	246	3.411517	CGTCCCCTTCCCTGCCAT	61.412	66.667	0.00	0.00	0.00	4.40
249	250	4.760047	CACGCGTCCCCTTCCCTG	62.760	72.222	9.86	0.00	0.00	4.45
252	253	4.754667	GTCCACGCGTCCCCTTCC	62.755	72.222	9.86	0.00	0.00	3.46
281	282	2.408835	GAATTGCGATGCCCCACG	59.591	61.111	0.00	0.00	0.00	4.94
282	283	2.322999	GACGAATTGCGATGCCCCAC	62.323	60.000	0.00	0.00	44.57	4.61
283	284	2.045438	ACGAATTGCGATGCCCCA	60.045	55.556	0.00	0.00	44.57	4.96
284	285	2.715624	GACGAATTGCGATGCCCC	59.284	61.111	0.00	0.00	44.57	5.80
285	286	2.324477	CGACGAATTGCGATGCCC	59.676	61.111	0.00	0.00	44.57	5.36
286	287	2.351210	GCGACGAATTGCGATGCC	60.351	61.111	0.00	0.00	44.57	4.40
292	293	2.395690	CCTCACGCGACGAATTGC	59.604	61.111	15.93	0.00	0.00	3.56
293	294	1.896339	TTGCCTCACGCGACGAATTG	61.896	55.000	15.93	0.00	42.08	2.32
294	295	1.019278	ATTGCCTCACGCGACGAATT	61.019	50.000	15.93	0.00	42.08	2.17
295	296	1.447838	ATTGCCTCACGCGACGAAT	60.448	52.632	15.93	0.00	42.08	3.34
296	297	2.048597	ATTGCCTCACGCGACGAA	60.049	55.556	15.93	0.00	42.08	3.85
297	298	2.809174	CATTGCCTCACGCGACGA	60.809	61.111	15.93	8.11	42.08	4.20
298	299	3.071459	GACATTGCCTCACGCGACG	62.071	63.158	15.93	2.89	42.08	5.12
299	300	1.291877	AAGACATTGCCTCACGCGAC	61.292	55.000	15.93	0.00	42.08	5.19
300	301	0.602638	AAAGACATTGCCTCACGCGA	60.603	50.000	15.93	0.00	42.08	5.87
301	302	0.238289	AAAAGACATTGCCTCACGCG	59.762	50.000	3.53	3.53	42.08	6.01
302	303	2.422276	AAAAAGACATTGCCTCACGC	57.578	45.000	0.00	0.00	38.31	5.34
434	435	6.070424	TCGTAAGGAGTCCTATTGAAACCAAT	60.070	38.462	13.43	0.00	36.66	3.16
640	641	3.159472	TCCTGAGCAATTGCAAGAATGT	58.841	40.909	30.89	9.54	45.16	2.71
1113	1115	5.879223	CCTGAGTCAGACATCAAATAGCTTT	59.121	40.000	22.09	0.00	32.44	3.51
1429	1431	7.051623	TGGCTTTTACTGTCTACTTTTCTCAA	58.948	34.615	0.00	0.00	0.00	3.02
1631	1633	0.384353	GTCACTTTTTCCTGTCGCGC	60.384	55.000	0.00	0.00	0.00	6.86
2033	2043	7.016072	TCACCAATCCAATACCTTTGACAAATT	59.984	33.333	0.05	0.00	0.00	1.82
2116	2126	7.129425	ACCTCTGTCTATTCTCTAATTCACCT	58.871	38.462	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.