AutoCloner

Multiple sequence alignment - TraesCS3A01G096600

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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	TraesCS3A01G096600	chr3A	100.000	4822	0	0	1	4822	61477511	61482332	0.000000e+00	8905.0
1	TraesCS3A01G096600	chr3A	84.390	615	65	18	842	1451	61434225	61434813	4.190000e-160	575.0
2	TraesCS3A01G096600	chr3A	87.059	85	10	1	842	925	61433210	61433294	1.430000e-15	95.3
3	TraesCS3A01G096600	chr3B	93.039	4626	232	43	46	4638	78594152	78598720	0.000000e+00	6676.0
4	TraesCS3A01G096600	chr3D	94.725	3943	167	26	903	4819	49005238	49009165	0.000000e+00	6091.0
5	TraesCS3A01G096600	chr3D	88.815	599	45	13	254	846	49004661	49005243	0.000000e+00	715.0

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	TraesCS3A01G096600	chr3A	61477511	61482332	4821	False	8905.00	8905	100.0000	1	4822	1	chr3A.!!$F1	4821
1	TraesCS3A01G096600	chr3A	61433210	61434813	1603	False	335.15	575	85.7245	842	1451	2	chr3A.!!$F2	609
2	TraesCS3A01G096600	chr3B	78594152	78598720	4568	False	6676.00	6676	93.0390	46	4638	1	chr3B.!!$F1	4592
3	TraesCS3A01G096600	chr3D	49004661	49009165	4504	False	3403.00	6091	91.7700	254	4819	2	chr3D.!!$F1	4565

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
955	1132	0.462047	CCTCGATTGGGGGAACGAAG	60.462	60.000	0.00	0.0	34.50	3.79	F
1247	1428	0.249741	ACGCCGTGTACAAGAAGCTT	60.250	50.000	10.61	0.0	0.00	3.74	F
1960	2147	0.970427	GGTTGATGGGGTTGGCGAAT	60.970	55.000	0.00	0.0	0.00	3.34	F
2416	2603	1.004277	TCATACAGTTGGGGTTCTGCC	59.996	52.381	0.00	0.0	35.37	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2605	2792	1.073923	ACAACCCATCTGAGACCAACC	59.926	52.381	0.0	0.0	0.00	3.77	R
3030	3217	0.599558	CACTACGGACCTTTCCACGA	59.400	55.000	0.0	0.0	43.00	4.35	R
3497	3684	0.175760	TACATTCGCCTCTGGAGCAC	59.824	55.000	0.0	0.0	0.00	4.40	R
4306	4513	0.246635	CTGGGAGTAACCACCAGTCG	59.753	60.000	0.0	0.0	45.21	4.18	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
24	25	7.129109	CATAGTTTGTATTCAACACGGAGTT	57.871	36.000	0.00	0.00	41.61	3.01
38	39	1.730064	CGGAGTTGTATTTGTCCGTGG	59.270	52.381	1.43	0.00	45.62	4.94
39	40	2.610976	CGGAGTTGTATTTGTCCGTGGA	60.611	50.000	1.43	0.00	45.62	4.02
69	70	5.123344	CCACAAATCGGAAGTAAAGTTAGGG	59.877	44.000	0.00	0.00	0.00	3.53
90	91	3.270877	GAATGTTTGCGGTAGTCTGGAT	58.729	45.455	0.00	0.00	0.00	3.41
118	119	3.951775	TCACCAATTAAATGCCACCAC	57.048	42.857	0.00	0.00	0.00	4.16
131	132	1.401409	GCCACCACACACAATTGATCG	60.401	52.381	13.59	2.59	0.00	3.69
142	143	6.206634	ACACACAATTGATCGGTTATTTGACT	59.793	34.615	13.59	0.00	0.00	3.41
161	162	0.622136	TGGAGGATTGCAGCTCACAT	59.378	50.000	0.00	0.00	0.00	3.21
180	181	9.787532	GCTCACATGCTATTTTAAAGTTGATAA	57.212	29.630	0.00	0.00	0.00	1.75
213	216	9.184523	CATTTAAGGTATAAAGTTGGATGACCA	57.815	33.333	0.00	0.00	45.34	4.02
226	229	2.540101	GGATGACCAGCTTTCGTATTCG	59.460	50.000	0.00	0.00	35.97	3.34
252	255	5.375417	TTGTGAACACAATCATGGACATC	57.625	39.130	15.04	0.00	45.42	3.06
262	265	1.520120	ATGGACATCTGCGCTGTCG	60.520	57.895	18.52	11.72	43.16	4.35
296	299	1.000052	GCGTAGGAGATGCCCTAACTC	60.000	57.143	0.00	0.00	40.24	3.01
298	301	3.752665	CGTAGGAGATGCCCTAACTCTA	58.247	50.000	0.00	0.00	40.24	2.43
299	302	4.337145	CGTAGGAGATGCCCTAACTCTAT	58.663	47.826	0.00	0.00	40.24	1.98
301	304	5.944599	CGTAGGAGATGCCCTAACTCTATTA	59.055	44.000	0.00	0.00	40.24	0.98
303	306	7.122948	CGTAGGAGATGCCCTAACTCTATTATT	59.877	40.741	0.00	0.00	40.24	1.40
304	307	7.880265	AGGAGATGCCCTAACTCTATTATTT	57.120	36.000	0.00	0.00	37.37	1.40
305	308	7.912719	AGGAGATGCCCTAACTCTATTATTTC	58.087	38.462	0.00	0.00	37.37	2.17
306	309	7.737149	AGGAGATGCCCTAACTCTATTATTTCT	59.263	37.037	0.00	0.00	37.37	2.52
307	310	9.036980	GGAGATGCCCTAACTCTATTATTTCTA	57.963	37.037	0.00	0.00	0.00	2.10
340	343	7.895975	TTCATCTAGACACAACTTCTGAATG	57.104	36.000	0.00	0.00	0.00	2.67
346	349	2.942376	ACACAACTTCTGAATGTTCGCA	59.058	40.909	0.00	0.00	0.00	5.10

Showing 1 to 25 of 118 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	6.721571	ACTCCGTGTTGAATACAAACTATG	57.278	37.500	0.00	0.00	38.80	2.23
14	15	2.803956	CGGACAAATACAACTCCGTGTT	59.196	45.455	0.00	0.00	40.71	3.32
15	16	2.409975	CGGACAAATACAACTCCGTGT	58.590	47.619	0.00	0.00	40.71	4.49
19	20	2.740447	GTCCACGGACAAATACAACTCC	59.260	50.000	11.43	0.00	44.02	3.85
38	39	1.459592	CTTCCGATTTGTGGACGTGTC	59.540	52.381	0.00	0.00	34.56	3.67
39	40	1.202604	ACTTCCGATTTGTGGACGTGT	60.203	47.619	0.00	0.00	36.70	4.49
41	42	3.389925	TTACTTCCGATTTGTGGACGT	57.610	42.857	0.00	0.00	40.63	4.34
42	43	3.744426	ACTTTACTTCCGATTTGTGGACG	59.256	43.478	0.00	0.00	34.56	4.79
43	44	5.684550	AACTTTACTTCCGATTTGTGGAC	57.315	39.130	0.00	0.00	34.56	4.02
44	45	5.935789	CCTAACTTTACTTCCGATTTGTGGA	59.064	40.000	0.00	0.00	0.00	4.02
69	70	2.695359	TCCAGACTACCGCAAACATTC	58.305	47.619	0.00	0.00	0.00	2.67
90	91	3.366883	GCATTTAATTGGTGAAGCGGACA	60.367	43.478	0.00	0.00	0.00	4.02
118	119	6.524239	CAGTCAAATAACCGATCAATTGTGTG	59.476	38.462	5.13	0.00	0.00	3.82
131	132	4.016444	TGCAATCCTCCAGTCAAATAACC	58.984	43.478	0.00	0.00	0.00	2.85
142	143	0.622136	ATGTGAGCTGCAATCCTCCA	59.378	50.000	1.02	4.99	0.00	3.86
192	193	5.044846	AGCTGGTCATCCAACTTTATACCTT	60.045	40.000	0.00	0.00	43.81	3.50
208	211	2.288579	ACACGAATACGAAAGCTGGTCA	60.289	45.455	0.00	0.00	42.66	4.02
209	212	2.334838	ACACGAATACGAAAGCTGGTC	58.665	47.619	0.00	0.00	42.66	4.02
213	216	3.805422	TCACAAACACGAATACGAAAGCT	59.195	39.130	0.00	0.00	42.66	3.74
250	253	1.662629	CTCAAAATCGACAGCGCAGAT	59.337	47.619	11.47	5.99	37.46	2.90
252	255	0.095935	CCTCAAAATCGACAGCGCAG	59.904	55.000	11.47	3.33	37.46	5.18
262	265	3.541632	TCCTACGCAATCCCTCAAAATC	58.458	45.455	0.00	0.00	0.00	2.17
373	376	8.950210	AGTAAGGAAATGACTAAATGACACATG	58.050	33.333	0.00	0.00	0.00	3.21
385	388	4.705507	TCAGCGTCTAGTAAGGAAATGACT	59.294	41.667	0.00	0.00	0.00	3.41
390	393	4.280174	AGTGTTCAGCGTCTAGTAAGGAAA	59.720	41.667	0.00	0.00	0.00	3.13

Showing 1 to 25 of 99 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.