AutoCloner

Multiple sequence alignment - TraesCS6D01G280000

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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	TraesCS6D01G280000	chr6D	100.000	2381	0	0	1	2381	387881803	387884183	0.000000e+00	4397.0
1	TraesCS6D01G280000	chr6D	77.586	464	83	17	45	502	393927880	393927432	6.530000e-66	261.0
2	TraesCS6D01G280000	chr6D	81.089	349	32	20	956	1279	387780688	387781027	5.080000e-62	248.0
3	TraesCS6D01G280000	chr6B	92.367	773	34	10	728	1481	579094028	579094794	0.000000e+00	1077.0
4	TraesCS6D01G280000	chr6B	91.743	436	27	7	1948	2381	579355591	579356019	4.380000e-167	597.0
5	TraesCS6D01G280000	chr6B	85.560	464	27	11	1475	1909	579094899	579095351	1.300000e-122	449.0
6	TraesCS6D01G280000	chr6B	87.719	342	28	7	857	1189	578950441	578950777	1.030000e-103	387.0
7	TraesCS6D01G280000	chr6B	84.802	329	22	17	643	965	579102337	579102643	2.970000e-79	305.0
8	TraesCS6D01G280000	chr6B	91.667	156	13	0	2226	2381	579101694	579101849	1.430000e-52	217.0
9	TraesCS6D01G280000	chr6B	82.828	198	16	8	1678	1860	579353984	579354178	6.810000e-36	161.0
10	TraesCS6D01G280000	chr6A	90.141	710	33	7	643	1319	533253326	533254031	0.000000e+00	889.0
11	TraesCS6D01G280000	chr6A	94.626	428	15	2	1954	2381	533256492	533256911	0.000000e+00	656.0
12	TraesCS6D01G280000	chr6A	77.808	365	74	7	141	501	457451458	457451097	3.980000e-53	219.0
13	TraesCS6D01G280000	chr6A	88.953	172	11	3	1309	1480	533254450	533254613	3.100000e-49	206.0
14	TraesCS6D01G280000	chr6A	90.741	108	6	2	1475	1578	533254718	533254825	8.870000e-30	141.0
15	TraesCS6D01G280000	chr5D	83.600	500	65	11	3	498	372306505	372306991	1.000000e-123	453.0
16	TraesCS6D01G280000	chr5D	82.236	501	70	8	1	498	470050522	470050038	4.740000e-112	414.0
17	TraesCS6D01G280000	chr5D	79.430	491	87	9	15	498	9289509	9289026	3.790000e-88	335.0
18	TraesCS6D01G280000	chr4A	82.164	499	85	4	3	498	567224389	567224886	2.190000e-115	425.0
19	TraesCS6D01G280000	chr4D	81.783	516	79	8	3	505	324201196	324201709	3.660000e-113	418.0
20	TraesCS6D01G280000	chr4D	83.862	347	49	6	3	348	339455706	339456046	8.210000e-85	324.0
21	TraesCS6D01G280000	chr3B	78.728	503	97	8	3	500	508259755	508259258	6.350000e-86	327.0
22	TraesCS6D01G280000	chr5A	80.806	422	74	6	17	434	693653208	693653626	8.210000e-85	324.0
23	TraesCS6D01G280000	chr2D	81.433	307	45	7	21	317	372703213	372703517	8.500000e-60	241.0
24	TraesCS6D01G280000	chr2D	81.818	275	43	6	227	497	96688531	96688260	8.560000e-55	224.0
25	TraesCS6D01G280000	chr7D	82.310	277	45	4	227	500	83388659	83388384	1.100000e-58	237.0
26	TraesCS6D01G280000	chr5B	94.444	36	0	1	1329	1364	327153881	327153848	1.000000e-03	54.7
27	TraesCS6D01G280000	chr5B	94.444	36	1	1	1329	1363	327435060	327435025	1.000000e-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	TraesCS6D01G280000	chr6D	387881803	387884183	2380	False	4397	4397	100.00000	1	2381	1	chr6D.!!$F2	2380
1	TraesCS6D01G280000	chr6B	579094028	579095351	1323	False	763	1077	88.96350	728	1909	2	chr6B.!!$F2	1181
2	TraesCS6D01G280000	chr6B	579353984	579356019	2035	False	379	597	87.28550	1678	2381	2	chr6B.!!$F4	703
3	TraesCS6D01G280000	chr6B	579101694	579102643	949	False	261	305	88.23450	643	2381	2	chr6B.!!$F3	1738
4	TraesCS6D01G280000	chr6A	533253326	533256911	3585	False	473	889	91.11525	643	2381	4	chr6A.!!$F1	1738
5	TraesCS6D01G280000	chr4D	324201196	324201709	513	False	418	418	81.78300	3	505	1	chr4D.!!$F1	502

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
579	580	0.033642	CCATTTGTGTGTGCCATGCA	59.966	50.0	0.0	0.0	35.6	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2054	5088	0.102481	CAGAATGCTTGGCCTCATGC	59.898	55.0	3.32	3.62	42.34	4.06	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
93	94	2.117156	CCGCCATTGCCTTCTCCAG	61.117	63.158	0.00	0.00	0.00	3.86
94	95	2.768492	CGCCATTGCCTTCTCCAGC	61.768	63.158	0.00	0.00	0.00	4.85
115	116	2.998097	CACGGGATGACACCCCAT	59.002	61.111	5.48	0.00	46.62	4.00
120	121	1.202651	CGGGATGACACCCCATTAGAC	60.203	57.143	5.48	0.00	46.62	2.59
147	148	1.611491	GGACTGATCGGAGTCAGATCC	59.389	57.143	24.71	11.67	46.77	3.36
156	157	2.583593	GTCAGATCCGCTGTCCGC	60.584	66.667	0.00	0.00	45.14	5.54
163	164	4.529219	CCGCTGTCCGCCATGCTA	62.529	66.667	0.00	0.00	35.03	3.49
170	171	1.753078	TCCGCCATGCTAGAGACGT	60.753	57.895	0.00	0.00	0.00	4.34
172	173	1.299468	CGCCATGCTAGAGACGTCC	60.299	63.158	13.01	3.77	0.00	4.79
182	183	0.458025	AGAGACGTCCGAAAATCGCC	60.458	55.000	13.01	0.00	38.82	5.54
192	193	0.583917	GAAAATCGCCGGAGATGAGC	59.416	55.000	22.09	9.75	0.00	4.26
194	195	0.249657	AAATCGCCGGAGATGAGCTC	60.250	55.000	22.09	6.82	43.17	4.09
214	215	4.101448	GTGGCGGAGGGAGTGCAT	62.101	66.667	0.00	0.00	0.00	3.96
215	216	4.100084	TGGCGGAGGGAGTGCATG	62.100	66.667	0.00	0.00	0.00	4.06
219	220	2.669133	CGGAGGGAGTGCATGGGAA	61.669	63.158	0.00	0.00	0.00	3.97
220	221	1.691219	GGAGGGAGTGCATGGGAAA	59.309	57.895	0.00	0.00	0.00	3.13
226	227	1.457346	GAGTGCATGGGAAAGGAGTG	58.543	55.000	0.00	0.00	0.00	3.51
246	247	2.173782	TGTGAAGTGGCTAGGGTTTTGA	59.826	45.455	0.00	0.00	0.00	2.69
247	248	3.181434	TGTGAAGTGGCTAGGGTTTTGAT	60.181	43.478	0.00	0.00	0.00	2.57
251	252	0.254747	TGGCTAGGGTTTTGATCCGG	59.745	55.000	0.00	0.00	0.00	5.14
255	256	2.017049	CTAGGGTTTTGATCCGGCAAG	58.983	52.381	0.00	0.00	0.00	4.01
256	257	1.215382	GGGTTTTGATCCGGCAAGC	59.785	57.895	0.00	0.00	0.00	4.01
257	258	1.154035	GGTTTTGATCCGGCAAGCG	60.154	57.895	0.00	0.00	0.00	4.68
259	260	1.302913	TTTTGATCCGGCAAGCGGA	60.303	52.632	5.02	5.02	40.06	5.54
261	262	1.375853	TTTGATCCGGCAAGCGGATG	61.376	55.000	18.43	0.00	45.20	3.51

Showing 1 to 25 of 234 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	0.243907	CTGTCCGACACGACTCCATT	59.756	55.000	0.00	0.00	33.70	3.16
74	75	3.521796	GGAGAAGGCAATGGCGGC	61.522	66.667	0.00	0.00	42.47	6.53
115	116	2.879026	CGATCAGTCCGGATCTGTCTAA	59.121	50.000	24.21	12.16	41.21	2.10
152	153	1.725557	GACGTCTCTAGCATGGCGGA	61.726	60.000	8.70	0.00	0.00	5.54
156	157	0.738975	TTCGGACGTCTCTAGCATGG	59.261	55.000	16.46	0.00	0.00	3.66
162	163	1.202222	GGCGATTTTCGGACGTCTCTA	60.202	52.381	16.46	0.00	40.84	2.43
163	164	0.458025	GGCGATTTTCGGACGTCTCT	60.458	55.000	16.46	0.00	40.84	3.10
172	173	0.855349	CTCATCTCCGGCGATTTTCG	59.145	55.000	9.30	0.00	43.89	3.46
182	183	2.415010	CACCCGAGCTCATCTCCG	59.585	66.667	15.40	0.00	38.62	4.63
212	213	2.816087	CACTTCACACTCCTTTCCCATG	59.184	50.000	0.00	0.00	0.00	3.66
214	215	1.142870	CCACTTCACACTCCTTTCCCA	59.857	52.381	0.00	0.00	0.00	4.37
215	216	1.897560	CCACTTCACACTCCTTTCCC	58.102	55.000	0.00	0.00	0.00	3.97
219	220	1.625818	CCTAGCCACTTCACACTCCTT	59.374	52.381	0.00	0.00	0.00	3.36
220	221	1.270907	CCTAGCCACTTCACACTCCT	58.729	55.000	0.00	0.00	0.00	3.69
226	227	2.858745	TCAAAACCCTAGCCACTTCAC	58.141	47.619	0.00	0.00	0.00	3.18
256	257	4.091945	CCTCACATATATTTGCGTCATCCG	59.908	45.833	0.00	0.00	40.40	4.18
257	258	4.997395	ACCTCACATATATTTGCGTCATCC	59.003	41.667	0.00	0.00	0.00	3.51
259	260	4.686091	CGACCTCACATATATTTGCGTCAT	59.314	41.667	14.26	0.00	0.00	3.06
260	261	4.048504	CGACCTCACATATATTTGCGTCA	58.951	43.478	14.26	0.00	0.00	4.35
261	262	3.428870	CCGACCTCACATATATTTGCGTC	59.571	47.826	8.03	8.03	0.00	5.19
262	263	3.390135	CCGACCTCACATATATTTGCGT	58.610	45.455	0.00	0.00	0.00	5.24
331	332	3.054434	TCCAAATATGAGGCGGATATGGG	60.054	47.826	0.00	0.00	0.00	4.00
333	334	4.633126	CAGTCCAAATATGAGGCGGATATG	59.367	45.833	0.00	0.00	0.00	1.78
334	335	4.323792	CCAGTCCAAATATGAGGCGGATAT	60.324	45.833	0.00	0.00	0.00	1.63
335	336	3.007940	CCAGTCCAAATATGAGGCGGATA	59.992	47.826	0.00	0.00	0.00	2.59

Showing 1 to 25 of 226 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.