AutoCloner

Multiple sequence alignment - TraesCS1D01G046100

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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	TraesCS1D01G046100	chr1D	100.000	6320	0	0	1	6320	25742700	25736381	0.000000e+00	11671
1	TraesCS1D01G046100	chr1D	100.000	660	0	0	6661	7320	25736040	25735381	0.000000e+00	1219
2	TraesCS1D01G046100	chr1B	93.403	4320	167	38	914	5181	41097580	41093327	0.000000e+00	6290
3	TraesCS1D01G046100	chr1B	96.290	1213	31	2	5122	6320	41093329	41092117	0.000000e+00	1978
4	TraesCS1D01G046100	chr1B	92.285	674	37	8	6661	7320	41092051	41091379	0.000000e+00	942
5	TraesCS1D01G046100	chr1B	89.362	188	15	2	14	197	41097825	41097639	1.590000e-56	231
6	TraesCS1D01G046100	chr1A	92.470	2656	135	24	891	3503	26971407	26968774	0.000000e+00	3736
7	TraesCS1D01G046100	chr1A	90.698	2849	148	35	3502	6320	26968698	26965937	0.000000e+00	3685
8	TraesCS1D01G046100	chr1A	94.570	663	32	3	6661	7320	26965871	26965210	0.000000e+00	1022
9	TraesCS1D01G046100	chr1A	84.942	259	32	7	1	256	26973378	26973124	9.420000e-64	255

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	TraesCS1D01G046100	chr1D	25735381	25742700	7319	True	6445.00	11671	100.000	1	7320	2	chr1D.!!$R1	7319
1	TraesCS1D01G046100	chr1B	41091379	41097825	6446	True	2360.25	6290	92.835	14	7320	4	chr1B.!!$R1	7306
2	TraesCS1D01G046100	chr1A	26965210	26973378	8168	True	2174.50	3736	90.670	1	7320	4	chr1A.!!$R1	7319

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
780	1771	0.322456	TGTCAACCCCAGCATGCTAC	60.322	55.000	22.19	13.68	31.97	3.58	F
1480	2685	0.252197	GTAAGGGCTCGGGTGTGATT	59.748	55.000	0.00	0.00	0.00	2.57	F
1481	2686	0.988832	TAAGGGCTCGGGTGTGATTT	59.011	50.000	0.00	0.00	0.00	2.17	F
1878	3114	1.750778	ACACAAACTCTGGGCACAAAG	59.249	47.619	0.00	0.00	0.00	2.77	F
2110	3346	2.636647	TGCACAGGTTCTGACAATGA	57.363	45.000	1.59	0.00	35.18	2.57	F
3869	5194	1.067354	CCCATTTGTCCTTTGCTCTGC	60.067	52.381	0.00	0.00	0.00	4.26	F
4758	6097	0.895100	TGGCAGTTCTGGGACATTGC	60.895	55.000	1.97	0.00	38.20	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2200	3436	0.539051	AGCCTCAGTGACACTATGCC	59.461	55.000	8.02	0.0	0.00	4.40	R
2733	3969	0.957395	AATGCCTTGAGGTGTCTGCG	60.957	55.000	0.00	0.0	37.57	5.18	R
3002	4238	2.621338	CGTGCATCTTCCACTGTGTAT	58.379	47.619	7.08	0.0	0.00	2.29	R
3859	5184	4.092383	GTGCATAAATTTGGCAGAGCAAAG	59.908	41.667	16.64	0.0	38.38	2.77	R
4069	5395	9.078990	CCATCTATGGTATTAGTCAGTAAGACA	57.921	37.037	0.49	0.0	45.13	3.41	R
5265	6662	1.707989	TGGGGTGTTAGATTCCAGCAA	59.292	47.619	0.00	0.0	0.00	3.91	R
6756	8183	0.606096	TCGGATCGAACAAAGCTGGA	59.394	50.000	0.00	0.0	31.06	3.86	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
162	167	3.691342	TGAAGACCCCCTGCGTCG	61.691	66.667	0.00	0.00	35.33	5.12
179	186	1.072116	TCGTCCGTATTTGCGTTCCG	61.072	55.000	0.00	0.00	0.00	4.30
187	194	0.608035	ATTTGCGTTCCGGTCCATGT	60.608	50.000	0.00	0.00	0.00	3.21
188	195	1.511318	TTTGCGTTCCGGTCCATGTG	61.511	55.000	0.00	0.00	0.00	3.21
237	249	2.559440	TGTTTTGCATTTGAGGTTGCC	58.441	42.857	0.00	0.00	38.08	4.52
238	250	2.170187	TGTTTTGCATTTGAGGTTGCCT	59.830	40.909	0.00	0.00	38.08	4.75
256	268	3.436700	CCTTTGGCACGAGTTCTTTTT	57.563	42.857	0.00	0.00	0.00	1.94
257	269	3.115554	CCTTTGGCACGAGTTCTTTTTG	58.884	45.455	0.00	0.00	0.00	2.44
258	270	3.428862	CCTTTGGCACGAGTTCTTTTTGT	60.429	43.478	0.00	0.00	0.00	2.83
259	271	3.414549	TTGGCACGAGTTCTTTTTGTC	57.585	42.857	0.00	0.00	0.00	3.18
260	272	2.360844	TGGCACGAGTTCTTTTTGTCA	58.639	42.857	0.00	0.00	0.00	3.58
261	273	2.096819	TGGCACGAGTTCTTTTTGTCAC	59.903	45.455	0.00	0.00	0.00	3.67
262	274	2.363220	GCACGAGTTCTTTTTGTCACG	58.637	47.619	0.00	0.00	0.00	4.35
263	275	2.849502	GCACGAGTTCTTTTTGTCACGG	60.850	50.000	0.00	0.00	0.00	4.94
264	276	2.605818	CACGAGTTCTTTTTGTCACGGA	59.394	45.455	0.00	0.00	0.00	4.69
265	277	3.247648	CACGAGTTCTTTTTGTCACGGAT	59.752	43.478	0.00	0.00	0.00	4.18
266	278	4.446385	CACGAGTTCTTTTTGTCACGGATA	59.554	41.667	0.00	0.00	0.00	2.59
267	279	5.120208	CACGAGTTCTTTTTGTCACGGATAT	59.880	40.000	0.00	0.00	0.00	1.63
268	280	5.120208	ACGAGTTCTTTTTGTCACGGATATG	59.880	40.000	0.00	0.00	0.00	1.78
269	281	5.347635	CGAGTTCTTTTTGTCACGGATATGA	59.652	40.000	0.00	0.00	0.00	2.15
270	282	6.036083	CGAGTTCTTTTTGTCACGGATATGAT	59.964	38.462	0.00	0.00	0.00	2.45
271	283	7.413000	CGAGTTCTTTTTGTCACGGATATGATT	60.413	37.037	0.00	0.00	0.00	2.57
272	284	8.786826	AGTTCTTTTTGTCACGGATATGATTA	57.213	30.769	0.00	0.00	0.00	1.75
273	285	8.883731	AGTTCTTTTTGTCACGGATATGATTAG	58.116	33.333	0.00	0.00	0.00	1.73
274	286	8.665685	GTTCTTTTTGTCACGGATATGATTAGT	58.334	33.333	0.00	0.00	0.00	2.24

Showing 1 to 25 of 278 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
179	186	2.548920	GCCATAGAGCTACACATGGACC	60.549	54.545	15.83	0.00	40.37	4.46
187	194	2.694397	AGGAATGGCCATAGAGCTACA	58.306	47.619	21.15	0.00	40.02	2.74
188	195	4.223923	ACATAGGAATGGCCATAGAGCTAC	59.776	45.833	21.15	3.03	40.02	3.58
217	229	2.170187	AGGCAACCTCAAATGCAAAACA	59.830	40.909	0.00	0.00	44.32	2.83
237	249	3.769536	ACAAAAAGAACTCGTGCCAAAG	58.230	40.909	0.00	0.00	0.00	2.77
238	250	3.191581	TGACAAAAAGAACTCGTGCCAAA	59.808	39.130	0.00	0.00	0.00	3.28
245	257	5.347635	TCATATCCGTGACAAAAAGAACTCG	59.652	40.000	0.00	0.00	0.00	4.18
249	261	8.664798	CACTAATCATATCCGTGACAAAAAGAA	58.335	33.333	0.00	0.00	0.00	2.52
250	262	7.822334	ACACTAATCATATCCGTGACAAAAAGA	59.178	33.333	0.00	0.00	0.00	2.52
251	263	7.974675	ACACTAATCATATCCGTGACAAAAAG	58.025	34.615	0.00	0.00	0.00	2.27
254	266	8.201464	ACATACACTAATCATATCCGTGACAAA	58.799	33.333	0.00	0.00	0.00	2.83
255	267	7.722363	ACATACACTAATCATATCCGTGACAA	58.278	34.615	0.00	0.00	0.00	3.18
256	268	7.284919	ACATACACTAATCATATCCGTGACA	57.715	36.000	0.00	0.00	0.00	3.58
257	269	9.343103	CTTACATACACTAATCATATCCGTGAC	57.657	37.037	0.00	0.00	0.00	3.67
258	270	8.520351	CCTTACATACACTAATCATATCCGTGA	58.480	37.037	0.00	0.00	0.00	4.35
259	271	8.520351	TCCTTACATACACTAATCATATCCGTG	58.480	37.037	0.00	0.00	0.00	4.94
260	272	8.645814	TCCTTACATACACTAATCATATCCGT	57.354	34.615	0.00	0.00	0.00	4.69
272	284	7.980099	GCTAACACAACTATCCTTACATACACT	59.020	37.037	0.00	0.00	0.00	3.55
273	285	7.762615	TGCTAACACAACTATCCTTACATACAC	59.237	37.037	0.00	0.00	0.00	2.90
274	286	7.842982	TGCTAACACAACTATCCTTACATACA	58.157	34.615	0.00	0.00	0.00	2.29
275	287	8.765219	CATGCTAACACAACTATCCTTACATAC	58.235	37.037	0.00	0.00	0.00	2.39
276	288	7.931407	CCATGCTAACACAACTATCCTTACATA	59.069	37.037	0.00	0.00	0.00	2.29
277	289	6.767902	CCATGCTAACACAACTATCCTTACAT	59.232	38.462	0.00	0.00	0.00	2.29
278	290	6.112734	CCATGCTAACACAACTATCCTTACA	58.887	40.000	0.00	0.00	0.00	2.41
279	291	5.527582	CCCATGCTAACACAACTATCCTTAC	59.472	44.000	0.00	0.00	0.00	2.34

Showing 1 to 25 of 255 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.