AutoCloner

Multiple sequence alignment - TraesCS2D01G397000

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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	TraesCS2D01G397000	chr2D	100.000	2654	0	0	1	2654	508065027	508062374	0.000000e+00	4902.0
1	TraesCS2D01G397000	chr2D	85.714	63	7	2	2430	2491	508731685	508731746	6.130000e-07	65.8
2	TraesCS2D01G397000	chr2A	90.964	1162	67	23	811	1940	652571259	652570104	0.000000e+00	1530.0
3	TraesCS2D01G397000	chr2A	96.000	50	2	0	2412	2461	163569322	163569273	6.090000e-12	82.4
4	TraesCS2D01G397000	chr2B	85.422	1125	73	42	712	1785	597003228	597002144	0.000000e+00	1085.0
5	TraesCS2D01G397000	chr2B	88.142	253	28	2	2395	2646	776890828	776891079	1.540000e-77	300.0
6	TraesCS2D01G397000	chr2B	90.850	153	13	1	1825	1977	597002052	597001901	1.250000e-48	204.0
7	TraesCS2D01G397000	chr7A	90.272	257	25	0	2398	2654	156878458	156878202	1.180000e-88	337.0
8	TraesCS2D01G397000	chr7D	96.226	53	2	0	2409	2461	460642801	460642853	1.310000e-13	87.9
9	TraesCS2D01G397000	chr5B	94.340	53	3	0	2409	2461	415756291	415756343	6.090000e-12	82.4
10	TraesCS2D01G397000	chr5B	83.158	95	8	7	223	310	273889800	273889707	2.190000e-11	80.5
11	TraesCS2D01G397000	chr3D	97.778	45	1	0	2417	2461	350780055	350780099	7.880000e-11	78.7
12	TraesCS2D01G397000	chr3D	85.484	62	9	0	2430	2491	609803937	609803876	6.130000e-07	65.8
13	TraesCS2D01G397000	chr5D	85.507	69	8	2	219	285	406834139	406834207	1.320000e-08	71.3

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	TraesCS2D01G397000	chr2D	508062374	508065027	2653	True	4902.0	4902	100.000	1	2654	1	chr2D.!!$R1	2653
1	TraesCS2D01G397000	chr2A	652570104	652571259	1155	True	1530.0	1530	90.964	811	1940	1	chr2A.!!$R2	1129
2	TraesCS2D01G397000	chr2B	597001901	597003228	1327	True	644.5	1085	88.136	712	1977	2	chr2B.!!$R1	1265

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
627	628	0.033405	TTCGATTCTCTCCGGGGAGT	60.033	55.0	30.38	13.19	42.49	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2624	2757	0.039074	CGTCCGAGAGAGTGCAAAGT	60.039	55.0	0.0	0.0	0.0	2.66	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
20	21	3.291809	TGAAGTTCGCGAACATGTAGA	57.708	42.857	42.89	23.07	43.47	2.59
21	22	3.644823	TGAAGTTCGCGAACATGTAGAA	58.355	40.909	42.89	23.37	43.47	2.10
22	23	4.052608	TGAAGTTCGCGAACATGTAGAAA	58.947	39.130	42.89	22.03	43.47	2.52
23	24	4.508492	TGAAGTTCGCGAACATGTAGAAAA	59.492	37.500	42.89	20.67	43.47	2.29
24	25	5.006844	TGAAGTTCGCGAACATGTAGAAAAA	59.993	36.000	42.89	19.43	43.47	1.94
25	26	4.769215	AGTTCGCGAACATGTAGAAAAAC	58.231	39.130	42.89	20.40	43.47	2.43
26	27	4.510340	AGTTCGCGAACATGTAGAAAAACT	59.490	37.500	42.89	22.19	43.47	2.66
27	28	5.007332	AGTTCGCGAACATGTAGAAAAACTT	59.993	36.000	42.89	21.47	43.47	2.66
28	29	5.013861	TCGCGAACATGTAGAAAAACTTC	57.986	39.130	6.20	0.00	0.00	3.01
29	30	4.508492	TCGCGAACATGTAGAAAAACTTCA	59.492	37.500	6.20	0.00	0.00	3.02
30	31	4.607235	CGCGAACATGTAGAAAAACTTCAC	59.393	41.667	0.00	0.00	0.00	3.18
31	32	4.607235	GCGAACATGTAGAAAAACTTCACG	59.393	41.667	0.00	0.00	0.00	4.35
32	33	5.734311	CGAACATGTAGAAAAACTTCACGT	58.266	37.500	0.00	0.00	0.00	4.49
33	34	6.562640	GCGAACATGTAGAAAAACTTCACGTA	60.563	38.462	0.00	0.00	0.00	3.57
34	35	7.507304	CGAACATGTAGAAAAACTTCACGTAT	58.493	34.615	0.00	0.00	0.00	3.06
35	36	8.007716	CGAACATGTAGAAAAACTTCACGTATT	58.992	33.333	0.00	0.00	0.00	1.89
36	37	9.314501	GAACATGTAGAAAAACTTCACGTATTC	57.685	33.333	0.00	0.00	0.00	1.75
37	38	8.373048	ACATGTAGAAAAACTTCACGTATTCA	57.627	30.769	0.00	0.00	0.00	2.57
38	39	8.832521	ACATGTAGAAAAACTTCACGTATTCAA	58.167	29.630	0.00	0.00	0.00	2.69
39	40	9.658475	CATGTAGAAAAACTTCACGTATTCAAA	57.342	29.630	0.00	0.00	0.00	2.69
141	142	9.554724	TGAATATATCTTGAAAAACTCGCAAAC	57.445	29.630	0.00	0.00	0.00	2.93
142	143	9.774742	GAATATATCTTGAAAAACTCGCAAACT	57.225	29.630	0.00	0.00	0.00	2.66
143	144	9.774742	AATATATCTTGAAAAACTCGCAAACTC	57.225	29.630	0.00	0.00	0.00	3.01
144	145	4.287238	TCTTGAAAAACTCGCAAACTCC	57.713	40.909	0.00	0.00	0.00	3.85
145	146	3.692101	TCTTGAAAAACTCGCAAACTCCA	59.308	39.130	0.00	0.00	0.00	3.86

Showing 1 to 25 of 675 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	3.291809	TCTACATGTTCGCGAACTTCA	57.708	42.857	41.46	28.07	41.67	3.02
1	2	4.640805	TTTCTACATGTTCGCGAACTTC	57.359	40.909	41.46	23.81	41.67	3.01
2	3	5.007332	AGTTTTTCTACATGTTCGCGAACTT	59.993	36.000	41.46	35.17	41.67	2.66
3	4	4.510340	AGTTTTTCTACATGTTCGCGAACT	59.490	37.500	41.46	28.90	41.67	3.01
4	5	4.769215	AGTTTTTCTACATGTTCGCGAAC	58.231	39.130	38.12	38.12	41.50	3.95
5	6	5.006844	TGAAGTTTTTCTACATGTTCGCGAA	59.993	36.000	19.38	19.38	34.31	4.70
6	7	4.508492	TGAAGTTTTTCTACATGTTCGCGA	59.492	37.500	3.71	3.71	34.31	5.87
7	8	4.607235	GTGAAGTTTTTCTACATGTTCGCG	59.393	41.667	2.30	0.00	34.31	5.87
8	9	4.607235	CGTGAAGTTTTTCTACATGTTCGC	59.393	41.667	2.30	0.00	34.31	4.70
9	10	5.734311	ACGTGAAGTTTTTCTACATGTTCG	58.266	37.500	2.30	0.00	34.31	3.95
10	11	9.314501	GAATACGTGAAGTTTTTCTACATGTTC	57.685	33.333	2.30	0.00	34.31	3.18
11	12	8.832521	TGAATACGTGAAGTTTTTCTACATGTT	58.167	29.630	2.30	0.00	34.31	2.71
12	13	8.373048	TGAATACGTGAAGTTTTTCTACATGT	57.627	30.769	2.69	2.69	34.31	3.21
13	14	9.658475	TTTGAATACGTGAAGTTTTTCTACATG	57.342	29.630	0.00	0.00	34.31	3.21
115	116	9.554724	GTTTGCGAGTTTTTCAAGATATATTCA	57.445	29.630	0.00	0.00	0.00	2.57
116	117	9.774742	AGTTTGCGAGTTTTTCAAGATATATTC	57.225	29.630	0.00	0.00	0.00	1.75
117	118	9.774742	GAGTTTGCGAGTTTTTCAAGATATATT	57.225	29.630	0.00	0.00	0.00	1.28
118	119	8.398665	GGAGTTTGCGAGTTTTTCAAGATATAT	58.601	33.333	0.00	0.00	0.00	0.86
119	120	7.389330	TGGAGTTTGCGAGTTTTTCAAGATATA	59.611	33.333	0.00	0.00	0.00	0.86
120	121	6.206634	TGGAGTTTGCGAGTTTTTCAAGATAT	59.793	34.615	0.00	0.00	0.00	1.63
121	122	5.529430	TGGAGTTTGCGAGTTTTTCAAGATA	59.471	36.000	0.00	0.00	0.00	1.98
122	123	4.338118	TGGAGTTTGCGAGTTTTTCAAGAT	59.662	37.500	0.00	0.00	0.00	2.40
123	124	3.692101	TGGAGTTTGCGAGTTTTTCAAGA	59.308	39.130	0.00	0.00	0.00	3.02
124	125	4.027572	TGGAGTTTGCGAGTTTTTCAAG	57.972	40.909	0.00	0.00	0.00	3.02
125	126	4.442375	TTGGAGTTTGCGAGTTTTTCAA	57.558	36.364	0.00	0.00	0.00	2.69

Showing 1 to 25 of 674 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.