AutoCloner

Multiple sequence alignment - TraesCS5A01G289800

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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	TraesCS5A01G289800	chr5A	100.000	2767	0	0	1	2767	496335883	496333117	0.000000e+00	5110.0
1	TraesCS5A01G289800	chr5A	97.655	1450	33	1	66	1514	666132471	666133920	0.000000e+00	2488.0
2	TraesCS5A01G289800	chr5A	97.802	910	19	1	58	966	664889331	664888422	0.000000e+00	1568.0
3	TraesCS5A01G289800	chr5A	94.502	582	13	10	2204	2767	664887895	664887315	0.000000e+00	880.0
4	TraesCS5A01G289800	chr5A	93.997	583	15	11	2204	2767	666133970	666134551	0.000000e+00	865.0
5	TraesCS5A01G289800	chr5A	96.701	485	15	1	1031	1514	664888429	664887945	0.000000e+00	806.0
6	TraesCS5A01G289800	chr3A	97.501	2721	48	12	66	2767	80083615	80080896	0.000000e+00	4630.0
7	TraesCS5A01G289800	chr3A	96.721	61	2	0	1	61	18891519	18891459	4.880000e-18	102.0
8	TraesCS5A01G289800	chr3A	96.721	61	2	0	1	61	133849939	133849999	4.880000e-18	102.0
9	TraesCS5A01G289800	chr3A	96.721	61	2	0	1	61	219929013	219928953	4.880000e-18	102.0
10	TraesCS5A01G289800	chr3A	96.721	61	2	0	1	61	672609516	672609576	4.880000e-18	102.0
11	TraesCS5A01G289800	chr1D	93.542	2648	77	34	180	2766	404282251	404284865	0.000000e+00	3856.0
12	TraesCS5A01G289800	chr1D	98.990	99	1	0	80	178	404281988	404282086	7.870000e-41	178.0
13	TraesCS5A01G289800	chr7A	95.885	1458	46	6	58	1510	653015652	653014204	0.000000e+00	2348.0
14	TraesCS5A01G289800	chr7A	91.156	848	17	14	1956	2767	653011536	653010711	0.000000e+00	1098.0
15	TraesCS5A01G289800	chr7A	97.425	466	11	1	1503	1968	653013828	653013364	0.000000e+00	793.0
16	TraesCS5A01G289800	chr7A	83.425	181	19	9	2007	2180	458689505	458689329	1.030000e-34	158.0
17	TraesCS5A01G289800	chr7A	87.770	139	8	6	2262	2399	119582623	119582493	1.330000e-33	154.0
18	TraesCS5A01G289800	chr7A	88.372	129	14	1	2056	2183	119582966	119582838	1.330000e-33	154.0
19	TraesCS5A01G289800	chr7A	87.770	139	8	6	2262	2399	145766773	145766643	1.330000e-33	154.0
20	TraesCS5A01G289800	chr7A	96.721	61	2	0	1	61	326814901	326814841	4.880000e-18	102.0
21	TraesCS5A01G289800	chrUn	97.317	410	11	0	1037	1446	477751036	477751445	0.000000e+00	697.0
22	TraesCS5A01G289800	chr4A	81.979	283	48	3	58	337	148888065	148888347	1.280000e-58	237.0
23	TraesCS5A01G289800	chr4A	94.118	68	2	2	1	66	31867260	31867193	4.880000e-18	102.0
24	TraesCS5A01G289800	chr5B	80.769	260	45	5	66	322	231110317	231110060	6.040000e-47	198.0
25	TraesCS5A01G289800	chr3D	83.415	205	27	4	1812	2010	270460054	270460257	1.690000e-42	183.0
26	TraesCS5A01G289800	chr3D	90.476	126	10	2	2056	2180	270460267	270460391	6.130000e-37	165.0
27	TraesCS5A01G289800	chr3D	87.591	137	8	6	2262	2397	270460605	270460733	1.720000e-32	150.0
28	TraesCS5A01G289800	chr7D	82.000	200	33	3	58	255	111043327	111043129	1.700000e-37	167.0
29	TraesCS5A01G289800	chr2A	96.721	61	2	0	1	61	381668464	381668404	4.880000e-18	102.0
30	TraesCS5A01G289800	chr2A	96.667	60	2	0	2	61	560159143	560159202	1.750000e-17	100.0
31	TraesCS5A01G289800	chr2A	95.082	61	3	0	1	61	417469590	417469530	2.270000e-16	97.1

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	TraesCS5A01G289800	chr5A	496333117	496335883	2766	True	5110.000000	5110	100.000	1	2767	1	chr5A.!!$R1	2766
1	TraesCS5A01G289800	chr5A	666132471	666134551	2080	False	1676.500000	2488	95.826	66	2767	2	chr5A.!!$F1	2701
2	TraesCS5A01G289800	chr5A	664887315	664889331	2016	True	1084.666667	1568	96.335	58	2767	3	chr5A.!!$R2	2709
3	TraesCS5A01G289800	chr3A	80080896	80083615	2719	True	4630.000000	4630	97.501	66	2767	1	chr3A.!!$R2	2701
4	TraesCS5A01G289800	chr1D	404281988	404284865	2877	False	2017.000000	3856	96.266	80	2766	2	chr1D.!!$F1	2686
5	TraesCS5A01G289800	chr7A	653010711	653015652	4941	True	1413.000000	2348	94.822	58	2767	3	chr7A.!!$R5	2709

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
816	989	1.33416	TCAGTCGGAAACCAGTGCTA	58.666	50.0	0.0	0.0	0.0	3.49	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2189	4642	0.333652	TCCGTGATCCCACCAGAGTA	59.666	55.0	0.0	0.0	40.12	2.59	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
327	492	3.305314	GGCCACGAGTATGGACCA	58.695	61.111	0.00	0.00	42.70	4.02
367	532	8.452534	ACACTATACGTTTTGTTGTTTTCTTGA	58.547	29.630	0.00	0.00	0.00	3.02
375	540	7.506474	GTTTTGTTGTTTTCTTGACGTTGAAT	58.494	30.769	0.00	0.00	0.00	2.57
498	670	5.595885	GCTAGAGTCAGAAGTCATGCATTA	58.404	41.667	0.00	0.00	0.00	1.90
766	939	1.874872	GCCTGTTACAGCCGTGTTTTA	59.125	47.619	6.88	0.00	38.19	1.52
816	989	1.334160	TCAGTCGGAAACCAGTGCTA	58.666	50.000	0.00	0.00	0.00	3.49
1099	1283	3.550820	TGAAACTTGAAAGGCTACTGCA	58.449	40.909	0.00	0.00	41.91	4.41
1177	1367	3.515562	AGAATGAGTTCTGGACTGGTCT	58.484	45.455	0.00	0.00	42.97	3.85
1231	1421	2.025767	TTTGTGCATGCGGCCTGTTT	62.026	50.000	14.09	0.00	43.89	2.83
1405	1605	6.070653	TGGGAGTATAACCTGTTGAATTACGT	60.071	38.462	0.00	0.00	0.00	3.57
1495	1695	4.256110	CATCTCATGGTGTGTTCTTGCTA	58.744	43.478	0.00	0.00	0.00	3.49
1942	2533	4.273811	CGAGAGCAGCTGCAAAGA	57.726	55.556	38.24	0.00	45.16	2.52
1969	4400	3.229293	TCATCCCATGTTGAAGCAAACA	58.771	40.909	2.64	2.64	43.82	2.83
2058	4489	0.820871	AAAACTGAACCTGCCGCAAA	59.179	45.000	0.00	0.00	0.00	3.68
2093	4526	1.741706	GTTCCGTCCACGAGATACTCA	59.258	52.381	0.00	0.00	43.02	3.41
2188	4641	9.237187	TGAGATGAGAGGCTAGTTGTTATATAG	57.763	37.037	0.00	0.00	0.00	1.31
2189	4642	9.238368	GAGATGAGAGGCTAGTTGTTATATAGT	57.762	37.037	0.00	0.00	0.00	2.12
2243	4696	7.708752	AGAGTCAAGATTCGCTAAAGAAATAGG	59.291	37.037	0.00	0.00	33.43	2.57
2244	4697	7.556844	AGTCAAGATTCGCTAAAGAAATAGGA	58.443	34.615	0.00	0.00	33.43	2.94
2245	4698	7.708752	AGTCAAGATTCGCTAAAGAAATAGGAG	59.291	37.037	0.00	0.00	33.43	3.69
2246	4699	7.492994	GTCAAGATTCGCTAAAGAAATAGGAGT	59.507	37.037	0.00	0.00	33.43	3.85
2247	4700	8.692710	TCAAGATTCGCTAAAGAAATAGGAGTA	58.307	33.333	0.00	0.00	33.43	2.59
2248	4701	8.973378	CAAGATTCGCTAAAGAAATAGGAGTAG	58.027	37.037	0.00	0.00	33.43	2.57
2452	4929	8.788813	CAAAGCACATTTCAATATAGAACGTTC	58.211	33.333	20.71	20.71	0.00	3.95
2495	4972	0.392998	AGCACGGCCTACAAATGGAG	60.393	55.000	0.00	0.00	0.00	3.86
2496	4973	0.676782	GCACGGCCTACAAATGGAGT	60.677	55.000	0.00	0.00	0.00	3.85
2497	4974	1.406341	GCACGGCCTACAAATGGAGTA	60.406	52.381	0.00	0.00	0.00	2.59
2498	4975	2.937873	GCACGGCCTACAAATGGAGTAA	60.938	50.000	0.00	0.00	0.00	2.24
2499	4976	3.340034	CACGGCCTACAAATGGAGTAAA	58.660	45.455	0.00	0.00	0.00	2.01
2500	4977	3.754323	CACGGCCTACAAATGGAGTAAAA	59.246	43.478	0.00	0.00	0.00	1.52
2501	4978	4.398044	CACGGCCTACAAATGGAGTAAAAT	59.602	41.667	0.00	0.00	0.00	1.82
2502	4979	4.638865	ACGGCCTACAAATGGAGTAAAATC	59.361	41.667	0.00	0.00	0.00	2.17
2503	4980	4.638421	CGGCCTACAAATGGAGTAAAATCA	59.362	41.667	0.00	0.00	0.00	2.57
2504	4981	5.299279	CGGCCTACAAATGGAGTAAAATCAT	59.701	40.000	0.00	0.00	0.00	2.45
2505	4982	6.183360	CGGCCTACAAATGGAGTAAAATCATT	60.183	38.462	0.00	0.00	33.12	2.57
2506	4983	7.555965	GGCCTACAAATGGAGTAAAATCATTT	58.444	34.615	0.00	0.00	40.44	2.32
2507	4984	8.040727	GGCCTACAAATGGAGTAAAATCATTTT	58.959	33.333	0.02	0.02	38.55	1.82
2508	4985	9.435688	GCCTACAAATGGAGTAAAATCATTTTT	57.564	29.630	0.00	0.00	38.55	1.94
2512	4989	9.541143	ACAAATGGAGTAAAATCATTTTTCGTT	57.459	25.926	0.00	0.00	38.55	3.85
2557	5052	6.486657	ACTGCTATTTTCTGTTTAGTTGCTCA	59.513	34.615	0.00	0.00	0.00	4.26

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
367	532	2.577606	TGGATGGAACCATTCAACGT	57.422	45.000	11.91	0.00	38.84	3.99
375	540	2.780414	AGATCTGGATGGATGGAACCA	58.220	47.619	0.00	0.00	44.41	3.67
498	670	7.339212	TGAAAGCATACTTAGCATTGGTAATGT	59.661	33.333	8.64	10.82	36.81	2.71
565	737	1.767681	ACCTCTCATCAATGCCTCTCC	59.232	52.381	0.00	0.00	0.00	3.71
766	939	0.442310	CGACGCACAAATCCGTGATT	59.558	50.000	0.00	0.00	39.34	2.57
816	989	5.166398	CGTTTACCTAAGTTGATCCTCGTT	58.834	41.667	0.00	0.00	0.00	3.85
1126	1316	4.959596	ACGCTTCTTTCTCGTGATAGTA	57.040	40.909	5.13	0.00	34.92	1.82
1405	1605	1.295792	GTCACGGTTTGCTTCTGTCA	58.704	50.000	0.00	0.00	0.00	3.58
1483	1683	5.480422	TCACTAAGAGGATAGCAAGAACACA	59.520	40.000	0.00	0.00	0.00	3.72
1516	2107	6.670027	AGATGCCTTTTCTTTAGACTAGGAGA	59.330	38.462	9.43	0.00	30.43	3.71
1839	2430	2.223479	GGCGCTGAAACAAGAGAACAAA	60.223	45.455	7.64	0.00	0.00	2.83
1942	2533	3.259123	GCTTCAACATGGGATGAACCTTT	59.741	43.478	0.00	0.00	38.98	3.11
1969	4400	8.635765	TCAGTTATAGCTTCAGGTTCAATTTT	57.364	30.769	0.00	0.00	0.00	1.82
2188	4641	0.460311	CCGTGATCCCACCAGAGTAC	59.540	60.000	0.00	0.00	40.12	2.73
2189	4642	0.333652	TCCGTGATCCCACCAGAGTA	59.666	55.000	0.00	0.00	40.12	2.59
2190	4643	1.078528	TCCGTGATCCCACCAGAGT	59.921	57.895	0.00	0.00	40.12	3.24
2243	4696	7.255208	GGGATACAGTGCTAGTACTTTCTACTC	60.255	44.444	11.16	3.13	39.74	2.59
2244	4697	6.546772	GGGATACAGTGCTAGTACTTTCTACT	59.453	42.308	11.16	0.00	39.74	2.57
2245	4698	6.320672	TGGGATACAGTGCTAGTACTTTCTAC	59.679	42.308	11.16	0.00	39.74	2.59
2246	4699	6.429151	TGGGATACAGTGCTAGTACTTTCTA	58.571	40.000	11.16	1.95	39.74	2.10
2247	4700	5.269991	TGGGATACAGTGCTAGTACTTTCT	58.730	41.667	11.16	0.00	39.74	2.52
2248	4701	5.452077	CCTGGGATACAGTGCTAGTACTTTC	60.452	48.000	11.16	8.45	46.06	2.62
2452	4929	6.978674	TGTGTAATATAGTCAGAAGGGGAG	57.021	41.667	0.00	0.00	0.00	4.30
2498	4975	9.691362	ACTAGCATTTACAACGAAAAATGATTT	57.309	25.926	10.98	0.00	42.90	2.17
2499	4976	9.128107	CACTAGCATTTACAACGAAAAATGATT	57.872	29.630	10.98	2.58	42.90	2.57
2500	4977	7.754924	CCACTAGCATTTACAACGAAAAATGAT	59.245	33.333	10.98	7.64	42.90	2.45
2501	4978	7.081349	CCACTAGCATTTACAACGAAAAATGA	58.919	34.615	10.98	0.00	42.90	2.57
2502	4979	6.861055	ACCACTAGCATTTACAACGAAAAATG	59.139	34.615	0.00	0.90	43.05	2.32
2503	4980	6.977213	ACCACTAGCATTTACAACGAAAAAT	58.023	32.000	0.00	0.00	0.00	1.82
2504	4981	6.380095	ACCACTAGCATTTACAACGAAAAA	57.620	33.333	0.00	0.00	0.00	1.94
2505	4982	7.493743	TTACCACTAGCATTTACAACGAAAA	57.506	32.000	0.00	0.00	0.00	2.29
2506	4983	7.388224	TCATTACCACTAGCATTTACAACGAAA	59.612	33.333	0.00	0.00	0.00	3.46
2507	4984	6.874664	TCATTACCACTAGCATTTACAACGAA	59.125	34.615	0.00	0.00	0.00	3.85
2508	4985	6.311935	GTCATTACCACTAGCATTTACAACGA	59.688	38.462	0.00	0.00	0.00	3.85
2509	4986	6.312918	AGTCATTACCACTAGCATTTACAACG	59.687	38.462	0.00	0.00	0.00	4.10
2510	4987	7.464358	CAGTCATTACCACTAGCATTTACAAC	58.536	38.462	0.00	0.00	0.00	3.32
2511	4988	6.093495	GCAGTCATTACCACTAGCATTTACAA	59.907	38.462	0.00	0.00	0.00	2.41
2512	4989	5.584649	GCAGTCATTACCACTAGCATTTACA	59.415	40.000	0.00	0.00	0.00	2.41
2557	5052	5.687166	ATCATTTTTCAGATGGCACCATT	57.313	34.783	3.16	0.00	36.70	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.