AutoCloner

Multiple sequence alignment - TraesCS3A01G513000

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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	TraesCS3A01G513000	chr3A	100.000	3131	0	0	1	3131	732473276	732476406	0.000000e+00	5782
1	TraesCS3A01G513000	chr3D	95.723	2268	73	15	867	3131	603599581	603597335	0.000000e+00	3629
2	TraesCS3A01G513000	chr3B	92.712	1523	78	16	868	2377	810272098	810273600	0.000000e+00	2167
3	TraesCS3A01G513000	chr3B	92.170	613	31	3	2522	3131	810273799	810274397	0.000000e+00	850
4	TraesCS3A01G513000	chrUn	94.021	669	21	5	988	1656	267848685	267849334	0.000000e+00	996
5	TraesCS3A01G513000	chrUn	94.021	669	21	5	988	1656	267873048	267872399	0.000000e+00	996
6	TraesCS3A01G513000	chrUn	94.021	669	21	5	988	1656	276829417	276830066	0.000000e+00	996
7	TraesCS3A01G513000	chrUn	94.021	669	21	5	988	1656	282416954	282417603	0.000000e+00	996
8	TraesCS3A01G513000	chrUn	89.142	746	63	10	1646	2377	267849362	267850103	0.000000e+00	913
9	TraesCS3A01G513000	chrUn	85.683	901	89	30	1646	2527	267872371	267871492	0.000000e+00	913
10	TraesCS3A01G513000	chrUn	89.142	746	63	10	1646	2377	276830094	276830835	0.000000e+00	913
11	TraesCS3A01G513000	chrUn	89.142	746	63	10	1646	2377	282417631	282418372	0.000000e+00	913
12	TraesCS3A01G513000	chrUn	92.471	611	31	2	2522	3131	267850298	267850894	0.000000e+00	859
13	TraesCS3A01G513000	chrUn	92.471	611	31	2	2522	3131	267871435	267870839	0.000000e+00	859
14	TraesCS3A01G513000	chrUn	92.471	611	31	2	2522	3131	276831030	276831626	0.000000e+00	859
15	TraesCS3A01G513000	chrUn	92.471	611	31	2	2522	3131	282418567	282419163	0.000000e+00	859
16	TraesCS3A01G513000	chr5B	94.021	669	21	5	988	1656	595687535	595686886	0.000000e+00	996
17	TraesCS3A01G513000	chr5B	85.683	901	89	30	1646	2527	595686858	595685979	0.000000e+00	913
18	TraesCS3A01G513000	chr5B	92.471	611	31	2	2522	3131	595685922	595685326	0.000000e+00	859
19	TraesCS3A01G513000	chr5B	78.947	228	29	13	2151	2376	277802099	277802309	1.510000e-28	137
20	TraesCS3A01G513000	chr1D	81.046	612	95	15	2536	3131	480962261	480961655	4.730000e-128	468
21	TraesCS3A01G513000	chr1A	78.322	286	40	9	1868	2152	577501255	577500991	6.950000e-37	165
22	TraesCS3A01G513000	chr1A	94.118	68	2	2	1059	1124	577503251	577503184	5.520000e-18	102
23	TraesCS3A01G513000	chr5D	77.483	302	48	15	2835	3131	45142059	45142345	2.500000e-36	163
24	TraesCS3A01G513000	chr7B	78.947	228	29	13	2151	2376	188413831	188414041	1.510000e-28	137

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	TraesCS3A01G513000	chr3A	732473276	732476406	3130	False	5782.000000	5782	100.000	1	3131	1	chr3A.!!$F1	3130
1	TraesCS3A01G513000	chr3D	603597335	603599581	2246	True	3629.000000	3629	95.723	867	3131	1	chr3D.!!$R1	2264
2	TraesCS3A01G513000	chr3B	810272098	810274397	2299	False	1508.500000	2167	92.441	868	3131	2	chr3B.!!$F1	2263
3	TraesCS3A01G513000	chrUn	267848685	267850894	2209	False	922.666667	996	91.878	988	3131	3	chrUn.!!$F1	2143
4	TraesCS3A01G513000	chrUn	267870839	267873048	2209	True	922.666667	996	90.725	988	3131	3	chrUn.!!$R1	2143
5	TraesCS3A01G513000	chrUn	276829417	276831626	2209	False	922.666667	996	91.878	988	3131	3	chrUn.!!$F2	2143
6	TraesCS3A01G513000	chrUn	282416954	282419163	2209	False	922.666667	996	91.878	988	3131	3	chrUn.!!$F3	2143
7	TraesCS3A01G513000	chr5B	595685326	595687535	2209	True	922.666667	996	90.725	988	3131	3	chr5B.!!$R1	2143
8	TraesCS3A01G513000	chr1D	480961655	480962261	606	True	468.000000	468	81.046	2536	3131	1	chr1D.!!$R1	595

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
350	351	0.037605	CTGTGGTCCTACCCGTGTTC	60.038	60.0	0.0	0.0	37.5	3.18	F
943	952	0.041238	TCCCGAATCTCACTCCACCT	59.959	55.0	0.0	0.0	0.0	4.00	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1878	1948	3.402681	ACCCTGGTCATCAGCCGG	61.403	66.667	0.0	0.0	42.05	6.13	R
2767	2939	3.937814	CAGTAGTGCAATGTCTAACCCA	58.062	45.455	0.0	0.0	0.00	4.51	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
25	26	8.801715	ACAAAACGTTTACGAAGATAAGTAGA	57.198	30.769	15.03	0.00	43.02	2.59
26	27	9.248291	ACAAAACGTTTACGAAGATAAGTAGAA	57.752	29.630	15.03	0.00	43.02	2.10
30	31	9.468532	AACGTTTACGAAGATAAGTAGAAAAGT	57.531	29.630	9.53	0.00	43.02	2.66
31	32	9.122613	ACGTTTACGAAGATAAGTAGAAAAGTC	57.877	33.333	9.53	0.00	43.02	3.01
32	33	8.302750	CGTTTACGAAGATAAGTAGAAAAGTCG	58.697	37.037	0.00	0.00	43.02	4.18
33	34	9.334693	GTTTACGAAGATAAGTAGAAAAGTCGA	57.665	33.333	0.00	0.00	0.00	4.20
34	35	8.886816	TTACGAAGATAAGTAGAAAAGTCGAC	57.113	34.615	7.70	7.70	0.00	4.20
35	36	6.906659	ACGAAGATAAGTAGAAAAGTCGACA	58.093	36.000	19.50	0.00	32.20	4.35
36	37	7.536855	ACGAAGATAAGTAGAAAAGTCGACAT	58.463	34.615	19.50	1.86	32.20	3.06
37	38	8.027771	ACGAAGATAAGTAGAAAAGTCGACATT	58.972	33.333	19.50	9.64	32.20	2.71
38	39	8.861101	CGAAGATAAGTAGAAAAGTCGACATTT	58.139	33.333	17.87	17.87	32.20	2.32
42	43	9.903185	GATAAGTAGAAAAGTCGACATTTTAGC	57.097	33.333	18.72	11.81	32.20	3.09
43	44	7.964604	AAGTAGAAAAGTCGACATTTTAGCT	57.035	32.000	18.72	13.75	32.20	3.32
45	46	9.485206	AAGTAGAAAAGTCGACATTTTAGCTAA	57.515	29.630	18.72	0.86	32.20	3.09
46	47	9.654663	AGTAGAAAAGTCGACATTTTAGCTAAT	57.345	29.630	18.72	12.21	32.20	1.73
51	52	9.503427	AAAAGTCGACATTTTAGCTAATAATGC	57.497	29.630	25.20	20.03	33.61	3.56
52	53	7.190920	AGTCGACATTTTAGCTAATAATGCC	57.809	36.000	25.20	19.29	33.61	4.40
53	54	6.992715	AGTCGACATTTTAGCTAATAATGCCT	59.007	34.615	25.20	18.10	33.61	4.75
54	55	7.499232	AGTCGACATTTTAGCTAATAATGCCTT	59.501	33.333	25.20	15.22	33.61	4.35
55	56	7.798982	GTCGACATTTTAGCTAATAATGCCTTC	59.201	37.037	25.20	19.00	33.61	3.46
56	57	7.715249	TCGACATTTTAGCTAATAATGCCTTCT	59.285	33.333	25.20	14.77	33.61	2.85
57	58	8.988934	CGACATTTTAGCTAATAATGCCTTCTA	58.011	33.333	25.20	2.88	33.61	2.10
88	89	7.712204	TTTGGGGATCTTTAGTTAACATTCC	57.288	36.000	8.61	0.00	0.00	3.01
89	90	6.652205	TGGGGATCTTTAGTTAACATTCCT	57.348	37.500	8.61	0.00	0.00	3.36
90	91	7.758820	TGGGGATCTTTAGTTAACATTCCTA	57.241	36.000	8.61	0.00	0.00	2.94

Showing 1 to 25 of 538 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	8.801715	TCTACTTATCTTCGTAAACGTTTTGT	57.198	30.769	20.19	0.00	40.80	2.83
4	5	9.468532	ACTTTTCTACTTATCTTCGTAAACGTT	57.531	29.630	0.00	0.00	40.80	3.99
5	6	9.122613	GACTTTTCTACTTATCTTCGTAAACGT	57.877	33.333	2.02	0.00	40.80	3.99
6	7	8.302750	CGACTTTTCTACTTATCTTCGTAAACG	58.697	37.037	0.00	0.00	41.45	3.60
7	8	9.334693	TCGACTTTTCTACTTATCTTCGTAAAC	57.665	33.333	0.00	0.00	0.00	2.01
8	9	9.334693	GTCGACTTTTCTACTTATCTTCGTAAA	57.665	33.333	8.70	0.00	0.00	2.01
9	10	8.506437	TGTCGACTTTTCTACTTATCTTCGTAA	58.494	33.333	17.92	0.00	0.00	3.18
10	11	8.032952	TGTCGACTTTTCTACTTATCTTCGTA	57.967	34.615	17.92	0.00	0.00	3.43
11	12	6.906659	TGTCGACTTTTCTACTTATCTTCGT	58.093	36.000	17.92	0.00	0.00	3.85
12	13	7.972623	ATGTCGACTTTTCTACTTATCTTCG	57.027	36.000	17.92	0.00	0.00	3.79
16	17	9.903185	GCTAAAATGTCGACTTTTCTACTTATC	57.097	33.333	24.46	9.24	0.00	1.75
17	18	9.654663	AGCTAAAATGTCGACTTTTCTACTTAT	57.345	29.630	24.46	12.86	0.00	1.73
19	20	7.964604	AGCTAAAATGTCGACTTTTCTACTT	57.035	32.000	24.46	14.01	0.00	2.24
20	21	9.654663	ATTAGCTAAAATGTCGACTTTTCTACT	57.345	29.630	24.46	21.68	0.00	2.57
25	26	9.503427	GCATTATTAGCTAAAATGTCGACTTTT	57.497	29.630	25.40	20.26	33.96	2.27
26	27	8.129211	GGCATTATTAGCTAAAATGTCGACTTT	58.871	33.333	25.40	14.07	33.96	2.66
27	28	7.499232	AGGCATTATTAGCTAAAATGTCGACTT	59.501	33.333	25.40	7.74	39.58	3.01
28	29	6.992715	AGGCATTATTAGCTAAAATGTCGACT	59.007	34.615	25.40	19.62	39.58	4.18
29	30	7.190920	AGGCATTATTAGCTAAAATGTCGAC	57.809	36.000	25.40	9.11	39.58	4.20
30	31	7.715249	AGAAGGCATTATTAGCTAAAATGTCGA	59.285	33.333	25.40	2.76	39.58	4.20
31	32	7.865707	AGAAGGCATTATTAGCTAAAATGTCG	58.134	34.615	25.40	11.83	39.58	4.35
62	63	8.590204	GGAATGTTAACTAAAGATCCCCAAAAA	58.410	33.333	7.22	0.00	0.00	1.94
63	64	7.953493	AGGAATGTTAACTAAAGATCCCCAAAA	59.047	33.333	7.22	0.00	0.00	2.44
64	65	7.475299	AGGAATGTTAACTAAAGATCCCCAAA	58.525	34.615	7.22	0.00	0.00	3.28
65	66	7.039722	AGGAATGTTAACTAAAGATCCCCAA	57.960	36.000	7.22	0.00	0.00	4.12

Showing 1 to 25 of 555 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.