AutoCloner

Multiple sequence alignment - TraesCS4B01G058500

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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	TraesCS4B01G058500	chr4B	100.000	5721	0	0	1	5721	49735145	49740865	0.000000e+00	10565.0
1	TraesCS4B01G058500	chr4B	87.273	165	15	3	5129	5293	483582139	483581981	3.520000e-42	183.0
2	TraesCS4B01G058500	chr4A	93.035	2283	109	23	309	2557	567692364	567690098	0.000000e+00	3290.0
3	TraesCS4B01G058500	chr4A	93.696	698	30	5	3325	4010	567688557	567687862	0.000000e+00	1033.0
4	TraesCS4B01G058500	chr4A	94.788	614	25	3	2557	3169	567690068	567689461	0.000000e+00	950.0
5	TraesCS4B01G058500	chr4A	94.523	493	19	5	4628	5119	567687011	567686526	0.000000e+00	754.0
6	TraesCS4B01G058500	chr4A	91.286	482	24	7	4152	4630	567687613	567687147	4.830000e-180	641.0
7	TraesCS4B01G058500	chr4A	85.115	477	18	17	5263	5721	567686062	567685621	6.810000e-119	438.0
8	TraesCS4B01G058500	chr4A	90.698	129	8	2	4040	4164	567687861	567687733	9.860000e-38	169.0
9	TraesCS4B01G058500	chr4A	83.582	134	8	7	3213	3332	567689453	567689320	4.680000e-21	113.0
10	TraesCS4B01G058500	chr4A	87.097	93	12	0	123	215	567692474	567692382	7.840000e-19	106.0
11	TraesCS4B01G058500	chr4D	89.707	1535	81	37	427	1935	34660045	34661528	0.000000e+00	1888.0
12	TraesCS4B01G058500	chr4D	93.359	1280	43	15	2150	3412	34661896	34663150	0.000000e+00	1855.0
13	TraesCS4B01G058500	chr4D	93.911	969	47	5	4149	5116	34664105	34665062	0.000000e+00	1452.0
14	TraesCS4B01G058500	chr4D	93.734	766	25	10	3396	4144	34663204	34663963	0.000000e+00	1127.0
15	TraesCS4B01G058500	chr4D	90.719	334	16	8	5390	5721	34665670	34665990	1.140000e-116	431.0
16	TraesCS4B01G058500	chr4D	98.165	109	2	0	2005	2113	34661787	34661895	2.100000e-44	191.0
17	TraesCS4B01G058500	chr4D	95.050	101	5	0	1933	2033	34661686	34661786	5.930000e-35	159.0
18	TraesCS4B01G058500	chr5B	89.375	160	9	6	5128	5285	299602222	299602375	1.630000e-45	195.0
19	TraesCS4B01G058500	chr7B	88.199	161	13	4	5128	5288	78552429	78552583	2.720000e-43	187.0
20	TraesCS4B01G058500	chr2A	88.199	161	13	4	5128	5287	141506317	141506472	2.720000e-43	187.0
21	TraesCS4B01G058500	chr2A	100.000	29	0	0	328	356	14805867	14805839	3.000000e-03	54.7
22	TraesCS4B01G058500	chr1B	87.500	168	14	5	5121	5288	632020920	632021080	2.720000e-43	187.0
23	TraesCS4B01G058500	chr1B	100.000	28	0	0	329	356	120967798	120967825	1.000000e-02	52.8
24	TraesCS4B01G058500	chr3B	85.955	178	19	5	5115	5289	404830303	404830477	9.790000e-43	185.0
25	TraesCS4B01G058500	chr3D	87.730	163	13	6	5130	5289	315480578	315480420	3.520000e-42	183.0
26	TraesCS4B01G058500	chr1D	88.199	161	10	7	5127	5285	7349702	7349855	3.520000e-42	183.0
27	TraesCS4B01G058500	chr1D	92.105	38	3	0	316	353	476706552	476706589	3.000000e-03	54.7
28	TraesCS4B01G058500	chr2D	87.349	166	12	7	5123	5285	617101220	617101061	1.270000e-41	182.0
29	TraesCS4B01G058500	chr1A	88.525	61	6	1	1258	1318	4556425	4556484	7.950000e-09	73.1
30	TraesCS4B01G058500	chr5D	95.000	40	2	0	315	354	319252832	319252793	4.790000e-06	63.9
31	TraesCS4B01G058500	chr5A	86.792	53	7	0	249	301	69097195	69097143	6.190000e-05	60.2
32	TraesCS4B01G058500	chr6B	92.500	40	3	0	316	355	637125239	637125200	2.230000e-04	58.4
33	TraesCS4B01G058500	chr6D	100.000	29	0	0	327	355	16509865	16509837	3.000000e-03	54.7
34	TraesCS4B01G058500	chr6D	100.000	29	0	0	327	355	422327570	422327598	3.000000e-03	54.7
35	TraesCS4B01G058500	chr6D	100.000	29	0	0	327	355	422936377	422936349	3.000000e-03	54.7

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	TraesCS4B01G058500	chr4B	49735145	49740865	5720	False	10565.000000	10565	100.000000	1	5721	1	chr4B.!!$F1	5720
1	TraesCS4B01G058500	chr4A	567685621	567692474	6853	True	832.666667	3290	90.424444	123	5721	9	chr4A.!!$R1	5598
2	TraesCS4B01G058500	chr4D	34660045	34665990	5945	False	1014.714286	1888	93.520714	427	5721	7	chr4D.!!$F1	5294

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	Hairpin	End Stability	Orientation
645	649	0.094730	CGAAAGAATCCAACGGACGC	59.905	55.000	32.98	5.19	F
1347	1385	0.032952	TCTGTTACGGAAAGCAGCGT	59.967	50.000	0.00	5.07	F
2134	2362	0.593128	CCACAGGAAGAAAACTGCCG	59.407	55.000	38.25	5.69	F
2139	2367	0.668535	GGAAGAAAACTGCCGTGCTT	59.331	50.000	0.00	3.91	F
3857	4972	1.134521	TGTCCCACCTAACATGATCGC	60.135	52.381	0.00	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1499	1537	0.917259	GCAGTGCTCGTGTAATCTCG	59.083	55.000	8.18	0.0	0.00	4.04	R
3278	3552	1.261619	GCCAGAACATATAGCACACGC	59.738	52.381	0.00	0.0	38.99	5.34	R
3965	5092	0.114168	TCCCATGGAAACCCCTTGTG	59.886	55.000	15.22	0.0	38.15	3.33	R
4096	5224	1.419762	TGCTTCACCCAGAGTAGCAAA	59.580	47.619	0.00	0.0	37.21	3.68	R
5383	7165	0.390866	AGTGCATCAGCTGAACCTCG	60.391	55.000	22.50	8.2	42.74	4.63	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	7.760131	CAACAATTGTGAAGTCTGAACATTT	57.240	32.000	12.82	0.00	0.00	2.32
25	26	7.614908	CAACAATTGTGAAGTCTGAACATTTG	58.385	34.615	12.82	14.94	39.39	2.32
26	27	6.866480	ACAATTGTGAAGTCTGAACATTTGT	58.134	32.000	11.07	15.76	40.66	2.83
27	28	7.322664	ACAATTGTGAAGTCTGAACATTTGTT	58.677	30.769	11.07	0.00	41.76	2.83
28	29	7.276218	ACAATTGTGAAGTCTGAACATTTGTTG	59.724	33.333	11.07	9.66	41.76	3.33
29	30	6.507958	TTGTGAAGTCTGAACATTTGTTGA	57.492	33.333	0.00	0.00	38.56	3.18
30	31	5.879237	TGTGAAGTCTGAACATTTGTTGAC	58.121	37.500	0.00	3.58	38.56	3.18
31	32	5.647658	TGTGAAGTCTGAACATTTGTTGACT	59.352	36.000	9.44	9.44	40.66	3.41
32	33	6.150976	TGTGAAGTCTGAACATTTGTTGACTT	59.849	34.615	20.35	20.35	45.63	3.01
35	36	6.369059	AGTCTGAACATTTGTTGACTTCTG	57.631	37.500	9.44	0.00	37.76	3.02
36	37	6.115446	AGTCTGAACATTTGTTGACTTCTGA	58.885	36.000	9.44	0.00	37.76	3.27
37	38	6.599244	AGTCTGAACATTTGTTGACTTCTGAA	59.401	34.615	9.44	0.00	37.76	3.02
38	39	7.121168	AGTCTGAACATTTGTTGACTTCTGAAA	59.879	33.333	9.44	0.00	37.76	2.69
39	40	7.917505	GTCTGAACATTTGTTGACTTCTGAAAT	59.082	33.333	0.00	0.00	38.56	2.17
40	41	9.119418	TCTGAACATTTGTTGACTTCTGAAATA	57.881	29.630	0.00	0.00	38.56	1.40
41	42	9.903682	CTGAACATTTGTTGACTTCTGAAATAT	57.096	29.630	0.00	0.00	38.56	1.28
49	50	9.739276	TTGTTGACTTCTGAAATATATTCAGGT	57.261	29.630	15.86	8.52	44.43	4.00
50	51	9.166173	TGTTGACTTCTGAAATATATTCAGGTG	57.834	33.333	15.86	11.80	44.43	4.00
51	52	8.616076	GTTGACTTCTGAAATATATTCAGGTGG	58.384	37.037	15.86	9.89	44.43	4.61
52	53	7.282585	TGACTTCTGAAATATATTCAGGTGGG	58.717	38.462	15.86	8.04	44.43	4.61
53	54	7.127186	TGACTTCTGAAATATATTCAGGTGGGA	59.873	37.037	15.86	0.00	44.43	4.37
54	55	7.283329	ACTTCTGAAATATATTCAGGTGGGAC	58.717	38.462	15.86	0.00	44.43	4.46
55	56	6.187727	TCTGAAATATATTCAGGTGGGACC	57.812	41.667	15.86	0.00	44.43	4.46
56	57	5.073144	TCTGAAATATATTCAGGTGGGACCC	59.927	44.000	15.86	2.45	44.43	4.46
57	58	4.105697	TGAAATATATTCAGGTGGGACCCC	59.894	45.833	8.45	2.69	39.75	4.95

Showing 1 to 25 of 243 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	7.276218	ACAAATGTTCAGACTTCACAATTGTTG	59.724	33.333	8.77	3.76	40.15	3.33
1	2	7.322664	ACAAATGTTCAGACTTCACAATTGTT	58.677	30.769	8.77	0.00	40.15	2.83
2	3	6.866480	ACAAATGTTCAGACTTCACAATTGT	58.134	32.000	4.92	4.92	38.92	2.71
3	4	7.488792	TCAACAAATGTTCAGACTTCACAATTG	59.511	33.333	3.24	3.24	37.35	2.32
4	5	7.489113	GTCAACAAATGTTCAGACTTCACAATT	59.511	33.333	8.64	0.00	35.83	2.32
5	6	6.974622	GTCAACAAATGTTCAGACTTCACAAT	59.025	34.615	8.64	0.00	35.83	2.71
6	7	6.150976	AGTCAACAAATGTTCAGACTTCACAA	59.849	34.615	11.42	0.00	37.76	3.33
7	8	5.647658	AGTCAACAAATGTTCAGACTTCACA	59.352	36.000	11.42	0.00	37.76	3.58
8	9	6.124088	AGTCAACAAATGTTCAGACTTCAC	57.876	37.500	11.42	0.00	37.76	3.18
9	10	6.757897	AAGTCAACAAATGTTCAGACTTCA	57.242	33.333	18.72	0.00	42.52	3.02
11	12	6.599244	TCAGAAGTCAACAAATGTTCAGACTT	59.401	34.615	22.01	22.01	45.63	3.01
12	13	6.115446	TCAGAAGTCAACAAATGTTCAGACT	58.885	36.000	11.42	11.42	40.66	3.24
13	14	6.363577	TCAGAAGTCAACAAATGTTCAGAC	57.636	37.500	8.09	8.09	35.83	3.51
14	15	7.389803	TTTCAGAAGTCAACAAATGTTCAGA	57.610	32.000	0.00	0.00	35.83	3.27
15	16	9.903682	ATATTTCAGAAGTCAACAAATGTTCAG	57.096	29.630	0.00	0.00	35.83	3.02
23	24	9.739276	ACCTGAATATATTTCAGAAGTCAACAA	57.261	29.630	20.22	0.00	46.57	2.83
24	25	9.166173	CACCTGAATATATTTCAGAAGTCAACA	57.834	33.333	20.22	2.37	46.57	3.33
25	26	8.616076	CCACCTGAATATATTTCAGAAGTCAAC	58.384	37.037	20.22	0.00	46.57	3.18
26	27	7.775093	CCCACCTGAATATATTTCAGAAGTCAA	59.225	37.037	20.22	0.00	46.57	3.18
27	28	7.127186	TCCCACCTGAATATATTTCAGAAGTCA	59.873	37.037	20.22	3.87	46.57	3.41
28	29	7.442666	GTCCCACCTGAATATATTTCAGAAGTC	59.557	40.741	20.22	0.07	46.57	3.01
29	30	7.283329	GTCCCACCTGAATATATTTCAGAAGT	58.717	38.462	20.22	12.40	46.57	3.01
30	31	6.712547	GGTCCCACCTGAATATATTTCAGAAG	59.287	42.308	20.22	14.47	46.57	2.85
31	32	6.410388	GGGTCCCACCTGAATATATTTCAGAA	60.410	42.308	20.22	0.00	46.57	3.02
32	33	5.073144	GGGTCCCACCTGAATATATTTCAGA	59.927	44.000	20.22	6.11	46.57	3.27

Showing 1 to 25 of 271 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.