AutoCloner

Multiple sequence alignment - TraesCS3B01G325300

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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	TraesCS3B01G325300	chr3B	100.000	2198	0	0	1	2198	526178615	526180812	0.000000e+00	4060.0
1	TraesCS3B01G325300	chr3D	95.493	1176	34	12	385	1550	400499363	400500529	0.000000e+00	1860.0
2	TraesCS3B01G325300	chr3D	89.443	682	46	13	1539	2198	400500553	400501230	0.000000e+00	837.0
3	TraesCS3B01G325300	chr3A	93.866	538	20	7	754	1279	519390811	519391347	0.000000e+00	798.0
4	TraesCS3B01G325300	chr3A	93.659	205	11	2	1247	1449	519391347	519391551	2.740000e-79	305.0
5	TraesCS3B01G325300	chr3A	95.385	130	6	0	1539	1668	519391651	519391780	7.950000e-50	207.0
6	TraesCS3B01G325300	chr3A	96.154	52	2	0	1480	1531	519391551	519391602	3.890000e-13	86.1
7	TraesCS3B01G325300	chr3A	80.000	95	16	3	352	445	547356696	547356788	1.410000e-07	67.6

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	TraesCS3B01G325300	chr3B	526178615	526180812	2197	False	4060.000	4060	100.000	1	2198	1	chr3B.!!$F1	2197
1	TraesCS3B01G325300	chr3D	400499363	400501230	1867	False	1348.500	1860	92.468	385	2198	2	chr3D.!!$F1	1813
2	TraesCS3B01G325300	chr3A	519390811	519391780	969	False	349.025	798	94.766	754	1668	4	chr3A.!!$F2	914

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
35	36	0.035056	AGCCGTCCAGGATCAAAAGG	60.035	55.0	0.0	0.0	45.0	3.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1554	1647	1.065854	CGAGGAGCTTCCATTTGGAGT	60.066	52.381	0.0	0.0	46.36	3.85	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
21	22	3.819564	TGTCTCAAATGCTATAGCCGT	57.180	42.857	21.84	8.04	41.18	5.68
22	23	3.717707	TGTCTCAAATGCTATAGCCGTC	58.282	45.455	21.84	4.90	41.18	4.79
23	24	3.060602	GTCTCAAATGCTATAGCCGTCC	58.939	50.000	21.84	0.00	41.18	4.79
24	25	2.698274	TCTCAAATGCTATAGCCGTCCA	59.302	45.455	21.84	3.07	41.18	4.02
25	26	3.062763	CTCAAATGCTATAGCCGTCCAG	58.937	50.000	21.84	8.69	41.18	3.86
26	27	2.146342	CAAATGCTATAGCCGTCCAGG	58.854	52.381	21.84	1.81	44.97	4.45
27	28	1.717032	AATGCTATAGCCGTCCAGGA	58.283	50.000	21.84	0.74	45.00	3.86
28	29	1.944177	ATGCTATAGCCGTCCAGGAT	58.056	50.000	21.84	3.27	45.00	3.24
29	30	1.257743	TGCTATAGCCGTCCAGGATC	58.742	55.000	21.84	0.00	45.00	3.36
30	31	1.257743	GCTATAGCCGTCCAGGATCA	58.742	55.000	14.13	0.00	45.00	2.92
31	32	1.618837	GCTATAGCCGTCCAGGATCAA	59.381	52.381	14.13	0.00	45.00	2.57
32	33	2.037251	GCTATAGCCGTCCAGGATCAAA	59.963	50.000	14.13	0.00	45.00	2.69
33	34	3.494398	GCTATAGCCGTCCAGGATCAAAA	60.494	47.826	14.13	0.00	45.00	2.44
34	35	2.691409	TAGCCGTCCAGGATCAAAAG	57.309	50.000	0.00	0.00	45.00	2.27
35	36	0.035056	AGCCGTCCAGGATCAAAAGG	60.035	55.000	0.00	0.00	45.00	3.11
36	37	0.035439	GCCGTCCAGGATCAAAAGGA	60.035	55.000	0.00	0.00	45.00	3.36
37	38	1.739067	CCGTCCAGGATCAAAAGGAC	58.261	55.000	12.47	12.47	45.46	3.85
38	39	1.679032	CCGTCCAGGATCAAAAGGACC	60.679	57.143	15.21	0.00	46.02	4.46
39	40	1.739067	GTCCAGGATCAAAAGGACCG	58.261	55.000	11.77	0.00	43.67	4.79
40	41	1.003233	GTCCAGGATCAAAAGGACCGT	59.997	52.381	11.77	0.00	43.67	4.83
41	42	1.003118	TCCAGGATCAAAAGGACCGTG	59.997	52.381	0.00	0.00	0.00	4.94
42	43	1.003118	CCAGGATCAAAAGGACCGTGA	59.997	52.381	0.00	0.00	0.00	4.35
43	44	2.350522	CAGGATCAAAAGGACCGTGAG	58.649	52.381	0.00	0.00	0.00	3.51
44	45	1.087501	GGATCAAAAGGACCGTGAGC	58.912	55.000	0.00	3.37	0.00	4.26
45	46	1.087501	GATCAAAAGGACCGTGAGCC	58.912	55.000	1.05	0.00	0.00	4.70

Showing 1 to 25 of 337 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	4.119862	GACGGCTATAGCATTTGAGACAA	58.880	43.478	25.53	0.00	44.36	3.18
1	2	3.492656	GGACGGCTATAGCATTTGAGACA	60.493	47.826	25.53	0.00	44.36	3.41
2	3	3.060602	GGACGGCTATAGCATTTGAGAC	58.939	50.000	25.53	5.27	44.36	3.36
3	4	2.698274	TGGACGGCTATAGCATTTGAGA	59.302	45.455	25.53	0.93	44.36	3.27
4	5	3.062763	CTGGACGGCTATAGCATTTGAG	58.937	50.000	25.53	11.60	44.36	3.02
5	6	2.224281	CCTGGACGGCTATAGCATTTGA	60.224	50.000	25.53	6.01	44.36	2.69
6	7	2.146342	CCTGGACGGCTATAGCATTTG	58.854	52.381	25.53	14.12	44.36	2.32
7	8	2.047061	TCCTGGACGGCTATAGCATTT	58.953	47.619	25.53	9.23	44.36	2.32
8	9	1.717032	TCCTGGACGGCTATAGCATT	58.283	50.000	25.53	11.82	44.36	3.56
9	10	1.827969	GATCCTGGACGGCTATAGCAT	59.172	52.381	25.53	13.41	44.36	3.79
10	11	1.257743	GATCCTGGACGGCTATAGCA	58.742	55.000	25.53	4.32	44.36	3.49
11	12	1.257743	TGATCCTGGACGGCTATAGC	58.742	55.000	16.78	16.78	41.14	2.97
12	13	4.310769	CTTTTGATCCTGGACGGCTATAG	58.689	47.826	0.00	0.00	0.00	1.31
13	14	3.071023	CCTTTTGATCCTGGACGGCTATA	59.929	47.826	0.00	0.00	0.00	1.31
14	15	2.158755	CCTTTTGATCCTGGACGGCTAT	60.159	50.000	0.00	0.00	0.00	2.97
15	16	1.209504	CCTTTTGATCCTGGACGGCTA	59.790	52.381	0.00	0.00	0.00	3.93
16	17	0.035056	CCTTTTGATCCTGGACGGCT	60.035	55.000	0.00	0.00	0.00	5.52
17	18	0.035439	TCCTTTTGATCCTGGACGGC	60.035	55.000	0.00	0.00	0.00	5.68
18	19	1.739067	GTCCTTTTGATCCTGGACGG	58.261	55.000	0.00	0.00	39.39	4.79
20	21	1.003233	ACGGTCCTTTTGATCCTGGAC	59.997	52.381	0.00	12.31	45.86	4.02
21	22	1.003118	CACGGTCCTTTTGATCCTGGA	59.997	52.381	0.00	0.00	0.00	3.86
22	23	1.003118	TCACGGTCCTTTTGATCCTGG	59.997	52.381	0.00	0.00	0.00	4.45
23	24	2.350522	CTCACGGTCCTTTTGATCCTG	58.649	52.381	0.00	0.00	0.00	3.86
24	25	1.339151	GCTCACGGTCCTTTTGATCCT	60.339	52.381	0.00	0.00	0.00	3.24
25	26	1.087501	GCTCACGGTCCTTTTGATCC	58.912	55.000	0.00	0.00	0.00	3.36

Showing 1 to 25 of 344 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.