AutoCloner

Multiple sequence alignment - TraesCS3B01G230900

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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	TraesCS3B01G230900	chr3B	100.000	5580	0	0	1	5580	348492081	348486502	0.000000e+00	10305.0
1	TraesCS3B01G230900	chr3B	87.006	177	21	2	5327	5501	648741459	648741283	1.230000e-46	198.0
2	TraesCS3B01G230900	chr3B	84.118	170	20	6	5331	5495	292163576	292163409	2.080000e-34	158.0
3	TraesCS3B01G230900	chr3A	96.525	3712	90	11	1858	5562	307916722	307913043	0.000000e+00	6104.0
4	TraesCS3B01G230900	chr3A	94.658	1142	22	10	612	1735	307917840	307916720	0.000000e+00	1735.0
5	TraesCS3B01G230900	chr3A	84.150	612	80	16	1	599	293928326	293928933	1.350000e-160	577.0
6	TraesCS3B01G230900	chr3A	83.987	612	84	12	1	599	293810896	293810286	4.850000e-160	575.0
7	TraesCS3B01G230900	chr3A	87.500	144	16	2	5354	5495	11684400	11684257	1.240000e-36	165.0
8	TraesCS3B01G230900	chr3A	86.806	144	17	2	5354	5495	686550031	686549888	5.790000e-35	159.0
9	TraesCS3B01G230900	chr3D	97.938	1843	26	3	1858	3699	248812062	248810231	0.000000e+00	3182.0
10	TraesCS3B01G230900	chr3D	96.486	1878	54	5	3694	5562	248807970	248806096	0.000000e+00	3092.0
11	TraesCS3B01G230900	chr3D	94.133	1142	26	14	612	1735	248813178	248812060	0.000000e+00	1700.0
12	TraesCS3B01G230900	chr3D	80.453	353	52	15	5142	5490	315762444	315762105	2.580000e-63	254.0
13	TraesCS3B01G230900	chr7B	96.235	664	23	2	4918	5580	357528900	357528238	0.000000e+00	1086.0
14	TraesCS3B01G230900	chr7B	96.875	128	4	0	1733	1860	332242761	332242888	1.220000e-51	215.0
15	TraesCS3B01G230900	chr1A	84.804	612	79	11	1	599	244608563	244609173	2.220000e-168	603.0
16	TraesCS3B01G230900	chr1D	84.565	609	82	10	1	599	166902048	166902654	1.340000e-165	593.0
17	TraesCS3B01G230900	chr1D	84.452	611	81	12	1	599	208808854	208809462	1.730000e-164	590.0
18	TraesCS3B01G230900	chr1D	87.500	56	3	4	1916	1968	416034134	416034188	1.680000e-05	62.1
19	TraesCS3B01G230900	chr5D	84.565	609	80	12	1	597	157126545	157127151	4.810000e-165	592.0
20	TraesCS3B01G230900	chr5D	96.094	128	5	0	1733	1860	179325941	179325814	5.660000e-50	209.0
21	TraesCS3B01G230900	chr5D	75.904	166	33	5	5328	5490	527578776	527578937	1.670000e-10	78.7
22	TraesCS3B01G230900	chr5D	75.904	166	33	5	5328	5490	527608381	527608542	1.670000e-10	78.7
23	TraesCS3B01G230900	chr6A	84.314	612	81	13	1	599	272892406	272893015	8.060000e-163	584.0
24	TraesCS3B01G230900	chr6A	86.806	144	17	2	5354	5495	29294189	29294046	5.790000e-35	159.0
25	TraesCS3B01G230900	chr2D	84.288	611	83	11	1	599	278268067	278267458	8.060000e-163	584.0
26	TraesCS3B01G230900	chr7D	84.211	608	79	14	1	597	342377459	342376858	4.850000e-160	575.0
27	TraesCS3B01G230900	chr7D	84.722	144	19	3	5357	5498	406898134	406897992	2.100000e-29	141.0
28	TraesCS3B01G230900	chr4A	85.092	436	44	14	5055	5482	700562456	700562878	5.170000e-115	425.0
29	TraesCS3B01G230900	chr4A	83.293	413	55	9	5085	5490	700731579	700731984	8.830000e-98	368.0
30	TraesCS3B01G230900	chr4A	94.928	138	7	0	1732	1869	477881884	477881747	3.390000e-52	217.0
31	TraesCS3B01G230900	chr4A	94.815	135	7	0	1726	1860	530174013	530173879	1.570000e-50	211.0
32	TraesCS3B01G230900	chr4A	90.728	151	13	1	1710	1860	95379658	95379509	3.410000e-47	200.0
33	TraesCS3B01G230900	chr4A	87.379	103	12	1	1046	1148	309074236	309074135	3.530000e-22	117.0
34	TraesCS3B01G230900	chr4B	83.014	365	42	14	5142	5498	251669088	251669440	4.200000e-81	313.0
35	TraesCS3B01G230900	chr4B	96.154	130	5	0	1734	1863	55926031	55925902	4.380000e-51	213.0
36	TraesCS3B01G230900	chr4B	84.615	91	7	1	1065	1148	259782513	259782603	3.580000e-12	84.2
37	TraesCS3B01G230900	chr4B	97.561	41	1	0	1935	1975	457413388	457413348	2.790000e-08	71.3
38	TraesCS3B01G230900	chr4B	90.385	52	5	0	1097	1148	330774471	330774420	1.000000e-07	69.4
39	TraesCS3B01G230900	chr5B	82.597	362	43	14	5142	5495	208440721	208440372	9.080000e-78	302.0
40	TraesCS3B01G230900	chr1B	86.341	205	25	3	908	1111	672333080	672333282	2.620000e-53	220.0
41	TraesCS3B01G230900	chr1B	90.426	94	9	0	5402	5495	654250414	654250507	2.110000e-24	124.0
42	TraesCS3B01G230900	chr5A	92.667	150	8	2	1712	1860	156158010	156158157	4.380000e-51	213.0
43	TraesCS3B01G230900	chr6B	92.958	142	8	2	1724	1864	214087134	214087274	7.330000e-49	206.0
44	TraesCS3B01G230900	chr6B	92.361	144	9	2	1718	1860	341467158	341467300	2.640000e-48	204.0
45	TraesCS3B01G230900	chr6B	97.674	43	1	0	1935	1977	156067355	156067397	2.160000e-09	75.0
46	TraesCS3B01G230900	chr6B	90.385	52	2	3	1936	1986	123500545	123500496	1.300000e-06	65.8
47	TraesCS3B01G230900	chr6D	92.157	51	3	1	1933	1983	410110865	410110914	2.790000e-08	71.3
48	TraesCS3B01G230900	chr6D	90.566	53	3	1	1927	1977	51141485	51141537	1.000000e-07	69.4
49	TraesCS3B01G230900	chr4D	97.561	41	1	0	1935	1975	372361557	372361517	2.790000e-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	TraesCS3B01G230900	chr3B	348486502	348492081	5579	True	10305.0	10305	100.000000	1	5580	1	chr3B.!!$R2	5579
1	TraesCS3B01G230900	chr3A	307913043	307917840	4797	True	3919.5	6104	95.591500	612	5562	2	chr3A.!!$R4	4950
2	TraesCS3B01G230900	chr3A	293928326	293928933	607	False	577.0	577	84.150000	1	599	1	chr3A.!!$F1	598
3	TraesCS3B01G230900	chr3A	293810286	293810896	610	True	575.0	575	83.987000	1	599	1	chr3A.!!$R2	598
4	TraesCS3B01G230900	chr3D	248806096	248813178	7082	True	2658.0	3182	96.185667	612	5562	3	chr3D.!!$R2	4950
5	TraesCS3B01G230900	chr7B	357528238	357528900	662	True	1086.0	1086	96.235000	4918	5580	1	chr7B.!!$R1	662
6	TraesCS3B01G230900	chr1A	244608563	244609173	610	False	603.0	603	84.804000	1	599	1	chr1A.!!$F1	598
7	TraesCS3B01G230900	chr1D	166902048	166902654	606	False	593.0	593	84.565000	1	599	1	chr1D.!!$F1	598
8	TraesCS3B01G230900	chr1D	208808854	208809462	608	False	590.0	590	84.452000	1	599	1	chr1D.!!$F2	598
9	TraesCS3B01G230900	chr5D	157126545	157127151	606	False	592.0	592	84.565000	1	597	1	chr5D.!!$F1	596
10	TraesCS3B01G230900	chr6A	272892406	272893015	609	False	584.0	584	84.314000	1	599	1	chr6A.!!$F1	598
11	TraesCS3B01G230900	chr2D	278267458	278268067	609	True	584.0	584	84.288000	1	599	1	chr2D.!!$R1	598
12	TraesCS3B01G230900	chr7D	342376858	342377459	601	True	575.0	575	84.211000	1	597	1	chr7D.!!$R1	596

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	Hairpin	End Stability	Orientation
950	985	1.078918	TCACCGGCAGCAGATCAAG	60.079	57.895	0.00	0.00	3.02	F
1748	1783	0.032130	CATGTACTCCATCCGTCCGG	59.968	60.000	0.00	0.00	5.14	F
2341	2376	1.398390	CCCTTTCTCGCAATCTTTCGG	59.602	52.381	0.00	0.00	4.30	F
2845	2880	1.899814	TGCACAAGGATTCTACCTCGT	59.100	47.619	0.00	39.62	4.18	F
3782	6085	2.615912	GCAGCCTGCTTAGAACTATTGG	59.384	50.000	10.04	40.96	3.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1845	1880	0.604578	TGTTTTACTCCCTCCGTCCG	59.395	55.000	0.00	0.00	0.00	4.79	R
2930	2965	2.513317	TCCAAATGCCTATGACATCCCA	59.487	45.455	0.00	0.00	0.00	4.37	R
4112	6417	0.538977	AGCACACAAGGCATTGCTCT	60.539	50.000	11.69	0.18	41.53	4.09	R
4139	6444	2.180017	GCAGCACAAGGAATGCCG	59.820	61.111	0.00	0.00	44.53	5.69	R
5031	7343	4.016444	TGGCTTGTTTCACCTCATTATCC	58.984	43.478	0.00	0.00	0.00	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	1.687563	TCTGTGACGTCTTGGTCTGA	58.312	50.000	17.92	8.47	37.81	3.27
43	44	4.330347	TCTGATCGTTGAACACAAACGAAA	59.670	37.500	14.41	6.43	34.13	3.46
105	112	5.058490	CCAAAGTCTAAACGACACCCTAAA	58.942	41.667	0.00	0.00	45.32	1.85
106	113	5.528320	CCAAAGTCTAAACGACACCCTAAAA	59.472	40.000	0.00	0.00	45.32	1.52
148	157	1.146152	TGGGGAATTTCGTGACCCTTT	59.854	47.619	9.14	0.00	42.00	3.11
150	159	2.510613	GGGAATTTCGTGACCCTTTGA	58.489	47.619	0.00	0.00	39.28	2.69
201	211	3.143728	GTTTCCCCACACATACGAACTT	58.856	45.455	0.00	0.00	0.00	2.66
202	212	2.754946	TCCCCACACATACGAACTTC	57.245	50.000	0.00	0.00	0.00	3.01
242	252	9.020731	ACTAAAGTATTTCGAAATTTCATGGGT	57.979	29.630	27.10	15.11	40.09	4.51
246	256	6.884295	AGTATTTCGAAATTTCATGGGTCTGA	59.116	34.615	27.10	3.03	0.00	3.27
249	259	3.081061	CGAAATTTCATGGGTCTGACCA	58.919	45.455	26.94	14.17	46.24	4.02
256	266	6.528537	TTTCATGGGTCTGACCAAATAATG	57.471	37.500	26.94	19.47	45.13	1.90
287	297	3.193691	CGACACCTATTATAGCCTCTGGG	59.806	52.174	0.00	0.00	0.00	4.45
311	321	6.426937	GGCGAAATTTATGGAGTAGCATCTTA	59.573	38.462	0.00	0.00	0.00	2.10
395	407	4.410883	TGAAACTCTGTTCTTGTTCCCCTA	59.589	41.667	0.00	0.00	0.00	3.53
396	408	5.104277	TGAAACTCTGTTCTTGTTCCCCTAA	60.104	40.000	0.00	0.00	0.00	2.69
412	424	3.470709	CCCTAACGCATGTCATCATCTT	58.529	45.455	0.00	0.00	31.15	2.40
477	491	6.089249	AGACCCTTCATTTGTAAGCAAAAG	57.911	37.500	0.00	0.00	46.23	2.27
480	494	6.280643	ACCCTTCATTTGTAAGCAAAAGAAC	58.719	36.000	6.63	0.00	46.23	3.01
505	519	6.741109	TGTATCCAATTTAAGCAGCATCATG	58.259	36.000	0.00	0.00	0.00	3.07
511	526	5.752892	ATTTAAGCAGCATCATGTCTCAG	57.247	39.130	0.00	0.00	0.00	3.35
515	530	2.026542	AGCAGCATCATGTCTCAGGAAA	60.027	45.455	0.00	0.00	0.00	3.13
525	540	7.364522	TCATGTCTCAGGAAAATTAGAAACG	57.635	36.000	0.00	0.00	0.00	3.60
526	541	6.934645	TCATGTCTCAGGAAAATTAGAAACGT	59.065	34.615	0.00	0.00	0.00	3.99
528	543	8.717821	CATGTCTCAGGAAAATTAGAAACGTTA	58.282	33.333	0.00	0.00	0.00	3.18

Showing 1 to 25 of 127 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	8.661257	TCATATATTTCGTTTGTGTTCAACGAT	58.339	29.630	8.57	0.00	37.16	3.73
64	65	9.143155	AGACTTTGGGTTTGTTTAGATTAACAT	57.857	29.630	0.00	0.00	37.81	2.71
69	70	8.132995	CGTTTAGACTTTGGGTTTGTTTAGATT	58.867	33.333	0.00	0.00	0.00	2.40
70	71	7.499895	TCGTTTAGACTTTGGGTTTGTTTAGAT	59.500	33.333	0.00	0.00	0.00	1.98
72	73	6.908820	GTCGTTTAGACTTTGGGTTTGTTTAG	59.091	38.462	0.00	0.00	46.13	1.85
119	126	5.359860	GTCACGAAATTCCCCATTATTCCTT	59.640	40.000	0.00	0.00	0.00	3.36
127	135	0.999712	AGGGTCACGAAATTCCCCAT	59.000	50.000	7.60	0.00	40.70	4.00
128	136	0.774908	AAGGGTCACGAAATTCCCCA	59.225	50.000	7.60	0.00	40.70	4.96
148	157	1.064825	GGTTTCAGACCCCTCCTTCA	58.935	55.000	0.00	0.00	43.06	3.02
235	245	5.439721	CTCATTATTTGGTCAGACCCATGA	58.560	41.667	17.59	14.02	37.50	3.07
242	252	5.245531	GTGTCACCTCATTATTTGGTCAGA	58.754	41.667	0.00	0.00	30.72	3.27
246	256	4.000988	GTCGTGTCACCTCATTATTTGGT	58.999	43.478	0.00	0.00	33.87	3.67
287	297	5.931441	AGATGCTACTCCATAAATTTCGC	57.069	39.130	0.00	0.00	0.00	4.70
299	309	9.856488	TTGGACGAAATATATAAGATGCTACTC	57.144	33.333	0.00	0.00	0.00	2.59
311	321	5.182001	GCATGAAGGCTTGGACGAAATATAT	59.818	40.000	3.46	0.00	0.00	0.86
359	369	7.500227	AGAACAGAGTTTCAAGTGATGATTCAA	59.500	33.333	0.00	0.00	38.03	2.69
361	371	7.432350	AGAACAGAGTTTCAAGTGATGATTC	57.568	36.000	0.00	0.00	38.03	2.52
395	407	4.547406	CATGAAGATGATGACATGCGTT	57.453	40.909	0.00	0.00	36.82	4.84
412	424	5.970317	ACATTGAACAAGATCAAGCATGA	57.030	34.783	0.00	0.00	42.21	3.07
456	470	6.478512	TTCTTTTGCTTACAAATGAAGGGT	57.521	33.333	12.91	0.00	46.57	4.34
494	508	1.201424	TCCTGAGACATGATGCTGCT	58.799	50.000	0.00	0.00	0.00	4.24
505	519	8.080083	TGTAACGTTTCTAATTTTCCTGAGAC	57.920	34.615	5.91	0.00	0.00	3.36
539	556	8.560374	GCAGGTCAATTAAATTATCAGGTACTC	58.440	37.037	0.00	0.00	34.60	2.59
562	579	5.511088	ACGAATTACTAAAACTCACGCAG	57.489	39.130	0.00	0.00	0.00	5.18
573	590	9.603298	CGCTACATATACTGAACGAATTACTAA	57.397	33.333	0.00	0.00	0.00	2.24

Showing 1 to 25 of 140 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.