AutoCloner

Multiple sequence alignment - TraesCS4A01G017600

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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	TraesCS4A01G017600	chr4A	100.000	3346	0	0	1	3346	11710788	11714133	0.000000e+00	6180
1	TraesCS4A01G017600	chr4D	92.170	1954	89	24	798	2711	455899050	455897121	0.000000e+00	2702
2	TraesCS4A01G017600	chr4D	94.876	605	28	3	2743	3346	455897118	455896516	0.000000e+00	942
3	TraesCS4A01G017600	chr4B	93.157	1739	94	17	981	2704	570091663	570089935	0.000000e+00	2529
4	TraesCS4A01G017600	chr4B	92.966	654	24	5	2712	3345	570089822	570089171	0.000000e+00	933
5	TraesCS4A01G017600	chr4B	93.077	130	8	1	90	218	550676168	550676297	4.410000e-44	189
6	TraesCS4A01G017600	chr4B	85.321	109	6	2	854	952	570091771	570091663	1.640000e-18	104
7	TraesCS4A01G017600	chr7D	94.521	219	11	1	1	219	66985508	66985291	1.490000e-88	337
8	TraesCS4A01G017600	chr2B	94.444	216	12	0	1	216	621187365	621187580	1.920000e-87	333
9	TraesCS4A01G017600	chr2B	84.475	219	14	8	1	219	254139934	254140132	7.320000e-47	198
10	TraesCS4A01G017600	chr2A	93.578	218	14	0	1	218	642937076	642936859	3.220000e-85	326
11	TraesCS4A01G017600	chr7B	93.151	219	15	0	1	219	725792797	725793015	4.160000e-84	322
12	TraesCS4A01G017600	chr6A	93.119	218	15	0	1	218	233816269	233816486	1.500000e-83	320
13	TraesCS4A01G017600	chr6A	90.244	123	12	0	1	123	77157859	77157981	9.610000e-36	161
14	TraesCS4A01G017600	chr1A	94.258	209	12	0	10	218	121877880	121877672	1.500000e-83	320
15	TraesCS4A01G017600	chr7A	93.839	211	11	2	10	218	228540658	228540448	1.940000e-82	316
16	TraesCS4A01G017600	chr3B	92.701	137	8	2	90	224	511029046	511028910	2.630000e-46	196

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	TraesCS4A01G017600	chr4A	11710788	11714133	3345	False	6180.000000	6180	100.000000	1	3346	1	chr4A.!!$F1	3345
1	TraesCS4A01G017600	chr4D	455896516	455899050	2534	True	1822.000000	2702	93.523000	798	3346	2	chr4D.!!$R1	2548
2	TraesCS4A01G017600	chr4B	570089171	570091771	2600	True	1188.666667	2529	90.481333	854	3345	3	chr4B.!!$R1	2491

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
383	384	0.039527	CGATCCGTGTGATCCGCATA	60.040	55.0	0.0	0.0	46.06	3.14	F
386	387	0.102300	TCCGTGTGATCCGCATAGTG	59.898	55.0	0.0	0.0	0.00	2.74	F
501	502	0.108520	TTACGGTGGTGGCGATTCTC	60.109	55.0	0.0	0.0	0.00	2.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1753	1798	0.815734	TGGCTACTGGCGACTACTTC	59.184	55.000	0.00	0.0	42.94	3.01	R
2256	2306	1.704641	TCCATATCACGTCCTGAGGG	58.295	55.000	0.00	0.0	30.20	4.30	R
2449	2499	7.498900	TCACTCAAAGTGTCAAATTACAGACAT	59.501	33.333	10.34	0.0	46.03	3.06	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
23	24	6.419980	GAGTACACGATCGGTATTATAGCT	57.580	41.667	20.98	10.18	0.00	3.32
24	25	6.814506	AGTACACGATCGGTATTATAGCTT	57.185	37.500	20.98	0.00	0.00	3.74
25	26	7.211966	AGTACACGATCGGTATTATAGCTTT	57.788	36.000	20.98	0.00	0.00	3.51
26	27	7.655490	AGTACACGATCGGTATTATAGCTTTT	58.345	34.615	20.98	0.00	0.00	2.27
27	28	8.139989	AGTACACGATCGGTATTATAGCTTTTT	58.860	33.333	20.98	0.00	0.00	1.94
49	50	8.939201	TTTTTATGCAAGTTTGTGAATTCTGA	57.061	26.923	7.05	0.00	0.00	3.27
50	51	8.939201	TTTTATGCAAGTTTGTGAATTCTGAA	57.061	26.923	7.05	0.00	0.00	3.02
51	52	8.578308	TTTATGCAAGTTTGTGAATTCTGAAG	57.422	30.769	7.05	0.00	0.00	3.02
52	53	5.581126	TGCAAGTTTGTGAATTCTGAAGT	57.419	34.783	7.05	0.00	0.00	3.01
53	54	6.691754	TGCAAGTTTGTGAATTCTGAAGTA	57.308	33.333	7.05	0.00	0.00	2.24
54	55	6.728200	TGCAAGTTTGTGAATTCTGAAGTAG	58.272	36.000	7.05	0.00	0.00	2.57
55	56	6.318648	TGCAAGTTTGTGAATTCTGAAGTAGT	59.681	34.615	7.05	0.00	0.00	2.73
56	57	6.634436	GCAAGTTTGTGAATTCTGAAGTAGTG	59.366	38.462	7.05	0.00	0.00	2.74
57	58	6.867662	AGTTTGTGAATTCTGAAGTAGTGG	57.132	37.500	7.05	0.00	0.00	4.00
58	59	6.591935	AGTTTGTGAATTCTGAAGTAGTGGA	58.408	36.000	7.05	0.00	0.00	4.02
59	60	7.227156	AGTTTGTGAATTCTGAAGTAGTGGAT	58.773	34.615	7.05	0.00	0.00	3.41
60	61	7.389053	AGTTTGTGAATTCTGAAGTAGTGGATC	59.611	37.037	7.05	0.00	0.00	3.36
61	62	5.734720	TGTGAATTCTGAAGTAGTGGATCC	58.265	41.667	4.20	4.20	0.00	3.36
62	63	5.485353	TGTGAATTCTGAAGTAGTGGATCCT	59.515	40.000	14.23	0.00	0.00	3.24
63	64	6.667848	TGTGAATTCTGAAGTAGTGGATCCTA	59.332	38.462	14.23	0.00	0.00	2.94
64	65	6.981559	GTGAATTCTGAAGTAGTGGATCCTAC	59.018	42.308	14.23	8.17	38.05	3.18
65	66	6.098409	TGAATTCTGAAGTAGTGGATCCTACC	59.902	42.308	14.23	0.71	38.46	3.18
66	67	4.603094	TCTGAAGTAGTGGATCCTACCA	57.397	45.455	14.23	2.19	38.46	3.25
67	68	5.144159	TCTGAAGTAGTGGATCCTACCAT	57.856	43.478	14.23	0.33	42.17	3.55
68	69	4.895889	TCTGAAGTAGTGGATCCTACCATG	59.104	45.833	14.23	0.13	42.17	3.66

Showing 1 to 25 of 541 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	6.419980	AGCTATAATACCGATCGTGTACTC	57.580	41.667	15.09	0.00	0.00	2.59
1	2	6.814506	AAGCTATAATACCGATCGTGTACT	57.185	37.500	15.09	8.45	0.00	2.73
2	3	7.864307	AAAAGCTATAATACCGATCGTGTAC	57.136	36.000	15.09	3.63	0.00	2.90
24	25	8.939201	TCAGAATTCACAAACTTGCATAAAAA	57.061	26.923	8.44	0.00	0.00	1.94
25	26	8.939201	TTCAGAATTCACAAACTTGCATAAAA	57.061	26.923	8.44	0.00	0.00	1.52
26	27	8.196771	ACTTCAGAATTCACAAACTTGCATAAA	58.803	29.630	8.44	0.00	0.00	1.40
27	28	7.715657	ACTTCAGAATTCACAAACTTGCATAA	58.284	30.769	8.44	0.00	0.00	1.90
28	29	7.275888	ACTTCAGAATTCACAAACTTGCATA	57.724	32.000	8.44	0.00	0.00	3.14
29	30	6.152932	ACTTCAGAATTCACAAACTTGCAT	57.847	33.333	8.44	0.00	0.00	3.96
30	31	5.581126	ACTTCAGAATTCACAAACTTGCA	57.419	34.783	8.44	0.00	0.00	4.08
31	32	6.634436	CACTACTTCAGAATTCACAAACTTGC	59.366	38.462	8.44	0.00	0.00	4.01
32	33	7.012327	TCCACTACTTCAGAATTCACAAACTTG	59.988	37.037	8.44	0.00	0.00	3.16
33	34	7.054124	TCCACTACTTCAGAATTCACAAACTT	58.946	34.615	8.44	0.00	0.00	2.66
34	35	6.591935	TCCACTACTTCAGAATTCACAAACT	58.408	36.000	8.44	0.00	0.00	2.66
35	36	6.861065	TCCACTACTTCAGAATTCACAAAC	57.139	37.500	8.44	0.00	0.00	2.93
36	37	6.655003	GGATCCACTACTTCAGAATTCACAAA	59.345	38.462	6.95	0.00	0.00	2.83
37	38	6.013379	AGGATCCACTACTTCAGAATTCACAA	60.013	38.462	15.82	0.00	0.00	3.33
38	39	5.485353	AGGATCCACTACTTCAGAATTCACA	59.515	40.000	15.82	0.00	0.00	3.58
39	40	5.983540	AGGATCCACTACTTCAGAATTCAC	58.016	41.667	15.82	0.00	0.00	3.18
40	41	6.098409	GGTAGGATCCACTACTTCAGAATTCA	59.902	42.308	15.82	0.00	42.29	2.57
41	42	6.098409	TGGTAGGATCCACTACTTCAGAATTC	59.902	42.308	15.82	0.00	42.29	2.17
42	43	5.964477	TGGTAGGATCCACTACTTCAGAATT	59.036	40.000	15.82	0.00	42.29	2.17
43	44	5.529289	TGGTAGGATCCACTACTTCAGAAT	58.471	41.667	15.82	0.00	42.29	2.40
44	45	4.942944	TGGTAGGATCCACTACTTCAGAA	58.057	43.478	15.82	0.00	42.29	3.02
45	46	4.603094	TGGTAGGATCCACTACTTCAGA	57.397	45.455	15.82	0.00	42.29	3.27

Showing 1 to 25 of 557 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.