AutoCloner

Multiple sequence alignment - TraesCS7D01G136300

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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	TraesCS7D01G136300	chr7D	100.000	4061	0	0	427	4487	87481854	87477794	0.000000e+00	7500.0
1	TraesCS7D01G136300	chr7D	100.000	109	0	0	1	109	87482280	87482172	7.610000e-48	202.0
2	TraesCS7D01G136300	chr7A	87.294	3148	206	82	766	3821	88989898	88986853	0.000000e+00	3419.0
3	TraesCS7D01G136300	chr7A	86.726	113	9	5	648	758	88990043	88989935	2.190000e-23	121.0
4	TraesCS7D01G136300	chr7B	86.526	2323	146	78	629	2846	36458854	36456594	0.000000e+00	2401.0
5	TraesCS7D01G136300	chr7B	89.398	1179	71	20	2916	4050	36456606	36455438	0.000000e+00	1435.0
6	TraesCS7D01G136300	chr7B	86.797	462	37	12	4048	4487	36455411	36454952	1.120000e-135	494.0
7	TraesCS7D01G136300	chr7B	100.000	31	0	0	4137	4167	16131055	16131025	1.740000e-04	58.4
8	TraesCS7D01G136300	chr5B	87.912	91	10	1	4336	4425	234314350	234314440	6.140000e-19	106.0
9	TraesCS7D01G136300	chr4B	89.706	68	7	0	4417	4484	25793464	25793531	2.220000e-13	87.9
10	TraesCS7D01G136300	chr4D	93.182	44	1	2	498	540	222970857	222970815	3.750000e-06	63.9
11	TraesCS7D01G136300	chr4A	76.923	117	24	3	498	611	738135183	738135067	3.750000e-06	63.9
12	TraesCS7D01G136300	chr5A	89.362	47	3	2	498	543	668766711	668766666	1.740000e-04	58.4
13	TraesCS7D01G136300	chr2B	100.000	28	0	0	498	525	529764069	529764096	8.000000e-03	52.8

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	TraesCS7D01G136300	chr7D	87477794	87482280	4486	True	3851.000000	7500	100.000000	1	4487	2	chr7D.!!$R1	4486
1	TraesCS7D01G136300	chr7A	88986853	88990043	3190	True	1770.000000	3419	87.010000	648	3821	2	chr7A.!!$R1	3173
2	TraesCS7D01G136300	chr7B	36454952	36458854	3902	True	1443.333333	2401	87.573667	629	4487	3	chr7B.!!$R2	3858

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
480	481	0.519961	CCGAAACTTTTACCGGCTGG	59.480	55.0	11.02	11.02	42.84	4.85	F
1720	1809	0.034198	TCGGTCACCTCGAATTGCAA	59.966	50.0	0.00	0.00	33.42	4.08	F
2445	2567	0.473755	AACATGCAGTGGTCTGTGGA	59.526	50.0	0.00	0.00	43.05	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1911	2010	0.535335	CTTAGCAACGAGGTGGGCTA	59.465	55.0	0.00	37.79	3.93	R
3319	3479	0.109132	GGTTGAAAAGGCAGCCGATG	60.109	55.0	5.55	29.40	3.84	R
3849	4033	0.031449	CGTGCCGGGTGAAACAAAAT	59.969	50.0	2.18	39.98	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	Hairpin	End Stability
20	21	3.492102	ATAACATATGCCGCCAGAAGT	57.508	42.857	1.58	0.00	3.01
21	22	2.128771	AACATATGCCGCCAGAAGTT	57.871	45.000	1.58	0.00	2.66
22	23	3.275617	AACATATGCCGCCAGAAGTTA	57.724	42.857	1.58	0.00	2.24
23	24	3.275617	ACATATGCCGCCAGAAGTTAA	57.724	42.857	1.58	0.00	2.01
24	25	3.820557	ACATATGCCGCCAGAAGTTAAT	58.179	40.909	1.58	0.00	1.40
25	26	4.968259	ACATATGCCGCCAGAAGTTAATA	58.032	39.130	1.58	0.00	0.98
26	27	5.560724	ACATATGCCGCCAGAAGTTAATAT	58.439	37.500	1.58	0.00	1.28
27	28	5.412594	ACATATGCCGCCAGAAGTTAATATG	59.587	40.000	1.58	34.45	1.78
28	29	2.571212	TGCCGCCAGAAGTTAATATGG	58.429	47.619	0.00	35.84	2.74
29	30	1.880027	GCCGCCAGAAGTTAATATGGG	59.120	52.381	0.00	33.23	4.00
30	31	2.486548	GCCGCCAGAAGTTAATATGGGA	60.487	50.000	0.00	33.23	4.37
31	32	3.815809	CCGCCAGAAGTTAATATGGGAA	58.184	45.455	0.00	33.23	3.97
32	33	4.204012	CCGCCAGAAGTTAATATGGGAAA	58.796	43.478	0.00	33.23	3.13
33	34	4.827284	CCGCCAGAAGTTAATATGGGAAAT	59.173	41.667	0.00	33.23	2.17
34	35	6.001460	CCGCCAGAAGTTAATATGGGAAATA	58.999	40.000	0.00	33.23	1.40
35	36	6.488683	CCGCCAGAAGTTAATATGGGAAATAA	59.511	38.462	0.00	33.23	1.40
36	37	7.360361	CGCCAGAAGTTAATATGGGAAATAAC	58.640	38.462	0.00	33.23	1.89
37	38	7.012894	CGCCAGAAGTTAATATGGGAAATAACA	59.987	37.037	0.00	33.23	2.41
38	39	8.352942	GCCAGAAGTTAATATGGGAAATAACAG	58.647	37.037	0.00	33.23	3.16
39	40	9.627123	CCAGAAGTTAATATGGGAAATAACAGA	57.373	33.333	0.00	32.10	3.41
51	52	7.771183	TGGGAAATAACAGAATATTGTTGAGC	58.229	34.615	0.00	41.18	4.26
52	53	7.395772	TGGGAAATAACAGAATATTGTTGAGCA	59.604	33.333	0.00	41.18	4.26
53	54	7.917505	GGGAAATAACAGAATATTGTTGAGCAG	59.082	37.037	0.00	41.18	4.24
54	55	7.917505	GGAAATAACAGAATATTGTTGAGCAGG	59.082	37.037	0.00	41.18	4.85
55	56	6.949352	ATAACAGAATATTGTTGAGCAGGG	57.051	37.500	0.00	41.18	4.45

Showing 1 to 25 of 341 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	3.492102	ACTTCTGGCGGCATATGTTAT	57.508	42.857	13.85	0.00	0.00	1.89
1	2	3.275617	AACTTCTGGCGGCATATGTTA	57.724	42.857	21.19	0.00	0.00	2.41
2	3	2.128771	AACTTCTGGCGGCATATGTT	57.871	45.000	13.85	16.74	0.00	2.71
3	4	3.275617	TTAACTTCTGGCGGCATATGT	57.724	42.857	13.85	11.21	0.00	2.29
4	5	5.163723	CCATATTAACTTCTGGCGGCATATG	60.164	44.000	13.85	14.31	0.00	1.78
5	6	4.943705	CCATATTAACTTCTGGCGGCATAT	59.056	41.667	13.85	1.44	0.00	1.78
6	7	4.323417	CCATATTAACTTCTGGCGGCATA	58.677	43.478	13.85	1.26	0.00	3.14
7	8	3.149196	CCATATTAACTTCTGGCGGCAT	58.851	45.455	13.85	0.00	0.00	4.40
8	9	2.571212	CCATATTAACTTCTGGCGGCA	58.429	47.619	12.58	12.58	0.00	5.69
9	10	1.880027	CCCATATTAACTTCTGGCGGC	59.120	52.381	0.00	0.00	0.00	6.53
10	11	3.485463	TCCCATATTAACTTCTGGCGG	57.515	47.619	0.00	0.00	0.00	6.13
11	12	7.012894	TGTTATTTCCCATATTAACTTCTGGCG	59.987	37.037	0.00	0.00	0.00	5.69
12	13	8.232913	TGTTATTTCCCATATTAACTTCTGGC	57.767	34.615	0.00	0.00	0.00	4.85
13	14	9.627123	TCTGTTATTTCCCATATTAACTTCTGG	57.373	33.333	0.00	0.00	0.00	3.86
25	26	8.416329	GCTCAACAATATTCTGTTATTTCCCAT	58.584	33.333	0.00	0.00	37.43	4.00
26	27	7.395772	TGCTCAACAATATTCTGTTATTTCCCA	59.604	33.333	0.00	0.00	37.43	4.37
27	28	7.771183	TGCTCAACAATATTCTGTTATTTCCC	58.229	34.615	0.00	0.00	37.43	3.97
28	29	7.917505	CCTGCTCAACAATATTCTGTTATTTCC	59.082	37.037	0.00	0.00	37.43	3.13
29	30	7.917505	CCCTGCTCAACAATATTCTGTTATTTC	59.082	37.037	0.00	0.00	37.43	2.17
30	31	7.615365	TCCCTGCTCAACAATATTCTGTTATTT	59.385	33.333	0.00	0.00	37.43	1.40
31	32	7.118723	TCCCTGCTCAACAATATTCTGTTATT	58.881	34.615	0.00	0.00	37.43	1.40
32	33	6.662755	TCCCTGCTCAACAATATTCTGTTAT	58.337	36.000	0.00	0.00	37.43	1.89
33	34	6.061022	TCCCTGCTCAACAATATTCTGTTA	57.939	37.500	0.00	0.00	37.43	2.41
34	35	4.922206	TCCCTGCTCAACAATATTCTGTT	58.078	39.130	0.00	0.00	40.17	3.16
35	36	4.574674	TCCCTGCTCAACAATATTCTGT	57.425	40.909	0.00	0.00	0.00	3.41

Showing 1 to 25 of 362 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.