AutoCloner

Multiple sequence alignment - TraesCS2D01G328700

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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	TraesCS2D01G328700	chr2D	100.000	4837	0	0	1	4837	421827324	421822488	0.000000e+00	8933.0
1	TraesCS2D01G328700	chr2D	87.983	233	25	3	4194	4425	627641137	627640907	6.170000e-69	272.0
2	TraesCS2D01G328700	chr2D	83.529	255	35	7	4174	4426	627640266	627640515	1.050000e-56	231.0
3	TraesCS2D01G328700	chr2D	90.769	65	2	2	4424	4484	567803187	567803251	3.100000e-12	84.2
4	TraesCS2D01G328700	chr2D	95.122	41	1	1	2151	2191	421825016	421825055	4.040000e-06	63.9
5	TraesCS2D01G328700	chr2D	95.122	41	1	1	2270	2309	421825134	421825174	4.040000e-06	63.9
6	TraesCS2D01G328700	chr2B	96.520	1868	58	6	2307	4170	494287172	494285308	0.000000e+00	3083.0
7	TraesCS2D01G328700	chr2B	89.903	2258	134	34	1	2209	494290322	494288110	0.000000e+00	2820.0
8	TraesCS2D01G328700	chr2B	85.472	413	44	9	4194	4597	32463477	32463882	2.690000e-112	416.0
9	TraesCS2D01G328700	chr2B	90.710	183	11	3	4424	4604	32650425	32650247	6.260000e-59	239.0
10	TraesCS2D01G328700	chr2B	95.161	62	3	0	4598	4659	32505248	32505309	1.110000e-16	99.0
11	TraesCS2D01G328700	chr2B	95.161	62	3	0	4598	4659	32649047	32648986	1.110000e-16	99.0
12	TraesCS2D01G328700	chr2B	94.286	35	1	1	2270	2303	494288128	494288162	9.000000e-03	52.8
13	TraesCS2D01G328700	chr2A	97.618	1637	34	4	2306	3938	568311803	568310168	0.000000e+00	2802.0
14	TraesCS2D01G328700	chr2A	96.683	1417	46	1	793	2209	568314195	568312780	0.000000e+00	2355.0
15	TraesCS2D01G328700	chr2A	84.547	673	71	24	145	794	568316868	568316206	1.900000e-178	636.0
16	TraesCS2D01G328700	chr2A	93.846	260	14	2	3915	4173	568309811	568309553	1.630000e-104	390.0
17	TraesCS2D01G328700	chr2A	92.683	41	2	1	2301	2340	768478219	768478259	1.880000e-04	58.4
18	TraesCS2D01G328700	chr2A	94.595	37	1	1	2270	2305	568312798	568312834	6.760000e-04	56.5
19	TraesCS2D01G328700	chr1B	91.903	247	20	0	4176	4422	516123932	516124178	3.580000e-91	346.0
20	TraesCS2D01G328700	chr7A	89.046	283	23	6	4559	4837	80919335	80919057	1.290000e-90	344.0
21	TraesCS2D01G328700	chr7A	89.691	97	8	1	4519	4613	80920737	80920641	6.570000e-24	122.0
22	TraesCS2D01G328700	chr6B	93.578	109	7	0	4613	4721	686808206	686808314	3.870000e-36	163.0
23	TraesCS2D01G328700	chr3D	85.455	165	12	9	4175	4337	379402054	379401900	1.390000e-35	161.0
24	TraesCS2D01G328700	chr4A	85.714	133	16	3	4180	4312	697823802	697823673	2.350000e-28	137.0
25	TraesCS2D01G328700	chr5B	86.555	119	12	4	4174	4292	419764392	419764506	1.410000e-25	128.0
26	TraesCS2D01G328700	chr1A	85.345	116	16	1	4705	4819	548234862	548234977	8.500000e-23	119.0
27	TraesCS2D01G328700	chr1A	90.769	65	2	2	4424	4484	585682591	585682527	3.100000e-12	84.2
28	TraesCS2D01G328700	chr1A	96.000	50	2	0	4493	4542	548233771	548233820	1.120000e-11	82.4
29	TraesCS2D01G328700	chr3A	81.579	114	9	7	4383	4484	525290336	525290223	3.100000e-12	84.2
30	TraesCS2D01G328700	chr3A	90.769	65	2	2	4424	4484	691394221	691394157	3.100000e-12	84.2
31	TraesCS2D01G328700	chr3A	86.885	61	8	0	4424	4484	743690214	743690274	8.690000e-08	69.4
32	TraesCS2D01G328700	chr7D	85.714	77	8	2	4710	4784	543095622	543095547	1.440000e-10	78.7
33	TraesCS2D01G328700	chr6A	86.154	65	5	1	4424	4484	236359068	236359132	3.120000e-07	67.6
34	TraesCS2D01G328700	chr4D	86.154	65	5	1	4424	4484	73983198	73983134	3.120000e-07	67.6
35	TraesCS2D01G328700	chr5D	100.000	30	0	0	2306	2335	550051602	550051573	6.760000e-04	56.5
36	TraesCS2D01G328700	chr1D	82.540	63	11	0	4249	4311	395194049	395193987	6.760000e-04	56.5

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	TraesCS2D01G328700	chr2D	421822488	421827324	4836	True	8933.00	8933	100.0000	1	4837	1	chr2D.!!$R1	4836
1	TraesCS2D01G328700	chr2B	494285308	494290322	5014	True	2951.50	3083	93.2115	1	4170	2	chr2B.!!$R2	4169
2	TraesCS2D01G328700	chr2A	568309553	568316868	7315	True	1545.75	2802	93.1735	145	4173	4	chr2A.!!$R1	4028
3	TraesCS2D01G328700	chr7A	80919057	80920737	1680	True	233.00	344	89.3685	4519	4837	2	chr7A.!!$R1	318

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
28	29	0.389391	CAGTCACACCACCTTCGAGT	59.611	55.0	0.00	0.00	0.00	4.18	F
1107	3187	0.995728	GCTTCGCTAACAGTGAGAGC	59.004	55.0	0.00	3.95	35.96	4.09	F
1911	3991	0.318762	AGGAGCTTGTCGAGGTGAAC	59.681	55.0	0.00	0.00	35.91	3.18	F
2251	4592	0.534203	TGCCACAGGTCGACTTTTCC	60.534	55.0	16.46	0.00	0.00	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1443	3523	1.381076	CTCCTGGGCCGGGTTTTTA	59.619	57.895	30.37	10.5	0.00	1.52	R
2235	4330	0.249741	ACGGGAAAAGTCGACCTGTG	60.250	55.000	13.01	0.0	41.09	3.66	R
3416	6406	4.359706	GCAGTTTACAAAGGAACCACAAG	58.640	43.478	0.00	0.0	0.00	3.16	R
4245	7619	0.470456	AGGCCGACGGGGTCATATAA	60.470	55.000	17.22	0.0	45.54	0.98	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	3.330192	TGGCAGTCACACCACCTT	58.670	55.556	0.00	0.00	0.00	3.50
25	26	1.961277	GGCAGTCACACCACCTTCG	60.961	63.158	0.00	0.00	0.00	3.79
28	29	0.389391	CAGTCACACCACCTTCGAGT	59.611	55.000	0.00	0.00	0.00	4.18
43	44	5.533903	ACCTTCGAGTGTCTTAGTAACAAGA	59.466	40.000	0.00	0.00	32.11	3.02
46	47	5.950883	TCGAGTGTCTTAGTAACAAGATGG	58.049	41.667	0.00	0.00	36.93	3.51
71	72	4.344390	CCACTTAAGGACCTAGGACATACC	59.656	50.000	17.98	10.27	39.35	2.73
74	75	5.043582	ACTTAAGGACCTAGGACATACCAGA	60.044	44.000	17.98	0.60	42.04	3.86
79	80	3.288964	ACCTAGGACATACCAGACTTCG	58.711	50.000	17.98	0.00	42.04	3.79
80	81	3.288964	CCTAGGACATACCAGACTTCGT	58.711	50.000	1.05	0.00	42.04	3.85
114	115	1.107114	TCTCGAAGCTTCTAGCCTGG	58.893	55.000	23.50	6.89	43.77	4.45
119	120	2.416893	CGAAGCTTCTAGCCTGGTTTTC	59.583	50.000	23.50	0.00	43.77	2.29
130	131	5.712152	AGCCTGGTTTTCTATTTTCTGTG	57.288	39.130	0.00	0.00	0.00	3.66
136	137	9.981114	CCTGGTTTTCTATTTTCTGTGTATTTT	57.019	29.630	0.00	0.00	0.00	1.82
231	233	7.553881	TTTTATGAACCATTTTCCGCAAAAA	57.446	28.000	0.00	0.00	40.98	1.94
277	280	5.283717	CGTGGATTTATTTCAAACAAGCGAG	59.716	40.000	0.00	0.00	0.00	5.03
284	287	8.581057	TTTATTTCAAACAAGCGAGCATTTTA	57.419	26.923	0.00	0.00	0.00	1.52
291	294	9.035607	TCAAACAAGCGAGCATTTTAAAATTTA	57.964	25.926	10.77	0.00	0.00	1.40
298	301	7.489113	AGCGAGCATTTTAAAATTTATGACCAG	59.511	33.333	10.77	0.00	0.00	4.00
367	370	7.739498	AACTCAGGAACGCTTCTTAAAATTA	57.261	32.000	0.00	0.00	0.00	1.40
407	410	9.950858	ATTCGTTATCATGTTTTAAAATTTGCG	57.049	25.926	3.52	4.74	0.00	4.85
409	412	9.347934	TCGTTATCATGTTTTAAAATTTGCGAT	57.652	25.926	3.52	5.49	0.00	4.58
410	413	9.605305	CGTTATCATGTTTTAAAATTTGCGATC	57.395	29.630	3.52	0.00	0.00	3.69
587	641	3.713826	TTTAAGGGGCAAGTGACTAGG	57.286	47.619	0.00	0.00	0.00	3.02
626	683	2.803956	GCCTAAAACGCACAGTCTACAA	59.196	45.455	0.00	0.00	0.00	2.41
636	693	2.476619	CACAGTCTACAAACTTCAGCGG	59.523	50.000	0.00	0.00	0.00	5.52

Showing 1 to 25 of 263 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	2.595238	ACTAAGACACTCGAAGGTGGT	58.405	47.619	9.35	0.00	41.09	4.16
22	23	6.387465	CCATCTTGTTACTAAGACACTCGAA	58.613	40.000	0.00	0.00	39.33	3.71
23	24	5.621555	GCCATCTTGTTACTAAGACACTCGA	60.622	44.000	0.00	0.00	39.33	4.04
25	26	4.870991	GGCCATCTTGTTACTAAGACACTC	59.129	45.833	0.00	0.00	39.33	3.51
28	29	3.585289	TGGGCCATCTTGTTACTAAGACA	59.415	43.478	0.00	0.00	39.33	3.41
46	47	1.485480	GTCCTAGGTCCTTAAGTGGGC	59.515	57.143	9.08	0.00	0.00	5.36
103	104	7.391833	ACAGAAAATAGAAAACCAGGCTAGAAG	59.608	37.037	0.00	0.00	0.00	2.85
107	108	6.303839	ACACAGAAAATAGAAAACCAGGCTA	58.696	36.000	0.00	0.00	0.00	3.93
108	109	5.140454	ACACAGAAAATAGAAAACCAGGCT	58.860	37.500	0.00	0.00	0.00	4.58
207	209	7.553881	TTTTTGCGGAAAATGGTTCATAAAA	57.446	28.000	15.83	0.00	32.44	1.52
231	233	6.200665	CACGGTTTTCACAAAATGTTCATGAT	59.799	34.615	0.00	0.00	32.22	2.45
339	342	3.194005	AGAAGCGTTCCTGAGTTTGAA	57.806	42.857	0.00	0.00	0.00	2.69
403	406	7.943413	TCAAAATTTTGAGAAATGATCGCAA	57.057	28.000	26.01	2.76	44.67	4.85
404	407	7.652909	AGTTCAAAATTTTGAGAAATGATCGCA	59.347	29.630	27.52	10.60	46.68	5.10
405	408	8.011067	AGTTCAAAATTTTGAGAAATGATCGC	57.989	30.769	27.52	12.35	46.68	4.58
409	412	9.889128	AGGAAAGTTCAAAATTTTGAGAAATGA	57.111	25.926	27.52	13.57	46.68	2.57
587	641	0.384353	GCCACGTTCGCTTCTGTTTC	60.384	55.000	0.00	0.00	0.00	2.78
626	683	2.014068	GCTCATTAGCCCGCTGAAGTT	61.014	52.381	0.00	0.00	43.40	2.66
726	786	0.178876	TGTGGATCCAGGGTTCCAGA	60.179	55.000	16.81	13.42	42.57	3.86
823	2903	2.420129	GGACCATAGCCGAACAGATTGT	60.420	50.000	0.00	0.00	0.00	2.71
888	2968	1.265454	TTCCTCCCGGAAGAAGAGGC	61.265	60.000	16.53	0.00	44.28	4.70
1107	3187	3.046087	CCGCCGCAGCATCCATAG	61.046	66.667	0.00	0.00	39.83	2.23
1234	3314	3.056328	GCTCTTGGGTTGGTCCGC	61.056	66.667	0.00	0.00	37.00	5.54
1443	3523	1.381076	CTCCTGGGCCGGGTTTTTA	59.619	57.895	30.37	10.50	0.00	1.52
1578	3658	2.793160	TACCGGTCTCGTGCTCGTCT	62.793	60.000	12.40	0.00	38.33	4.18

Showing 1 to 25 of 286 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.