AutoCloner

Multiple sequence alignment - TraesCS1D01G001600

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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	TraesCS1D01G001600	chr1D	100.000	4403	0	0	1	4403	414385	418787	0.000000e+00	8131.0
1	TraesCS1D01G001600	chr1D	85.405	370	31	13	323	678	21844903	21845263	3.240000e-96	363.0
2	TraesCS1D01G001600	chr1D	90.511	137	10	3	3801	3935	481386483	481386618	1.260000e-40	178.0
3	TraesCS1D01G001600	chr7D	84.472	1230	169	8	2297	3510	399834009	399835232	0.000000e+00	1194.0
4	TraesCS1D01G001600	chr7D	91.556	675	55	2	1050	1723	399832945	399833618	0.000000e+00	929.0
5	TraesCS1D01G001600	chr7D	85.139	646	92	4	1080	1723	400185879	400185236	0.000000e+00	658.0
6	TraesCS1D01G001600	chr7D	86.994	346	34	7	340	678	8991691	8991350	3.210000e-101	379.0
7	TraesCS1D01G001600	chr7D	87.629	291	26	7	323	608	18920672	18920387	3.280000e-86	329.0
8	TraesCS1D01G001600	chr7A	84.372	1235	169	12	2297	3510	457684127	457685358	0.000000e+00	1190.0
9	TraesCS1D01G001600	chr7A	91.193	704	60	2	1050	1752	457683087	457683789	0.000000e+00	955.0
10	TraesCS1D01G001600	chr7A	81.159	621	111	6	1105	1722	203525581	203526198	1.100000e-135	494.0
11	TraesCS1D01G001600	chr7A	89.286	140	12	3	3801	3938	522496696	522496558	5.850000e-39	172.0
12	TraesCS1D01G001600	chr7A	97.222	36	1	0	2089	2124	528298873	528298838	1.320000e-05	62.1
13	TraesCS1D01G001600	chr7B	83.984	1230	175	8	2297	3510	409220901	409222124	0.000000e+00	1160.0
14	TraesCS1D01G001600	chr7B	90.588	680	54	4	1050	1729	409219860	409220529	0.000000e+00	893.0
15	TraesCS1D01G001600	chr7B	86.378	646	84	4	1080	1723	409750121	409749478	0.000000e+00	702.0
16	TraesCS1D01G001600	chr4D	84.475	657	97	5	1071	1723	503920962	503920307	1.030000e-180	643.0
17	TraesCS1D01G001600	chr4D	75.227	1102	233	26	2299	3372	491003141	491002052	1.840000e-133	486.0
18	TraesCS1D01G001600	chrUn	83.692	650	102	2	1076	1723	30086962	30087609	1.050000e-170	610.0
19	TraesCS1D01G001600	chr5A	76.377	1071	232	20	2299	3360	697068428	697069486	1.380000e-154	556.0
20	TraesCS1D01G001600	chr5A	76.377	1071	232	20	2299	3360	697200390	697201448	1.380000e-154	556.0
21	TraesCS1D01G001600	chr5A	76.421	1073	228	24	2299	3360	697282948	697284006	1.380000e-154	556.0
22	TraesCS1D01G001600	chr5A	83.705	583	93	1	1141	1723	706572683	706573263	2.310000e-152	549.0
23	TraesCS1D01G001600	chr5A	75.141	1066	239	20	2299	3360	697552563	697553606	1.110000e-130	477.0
24	TraesCS1D01G001600	chr5A	80.153	655	102	10	1072	1723	688614203	688613574	8.630000e-127	464.0
25	TraesCS1D01G001600	chr5A	78.291	585	123	4	2778	3360	697132988	697133570	1.500000e-99	374.0
26	TraesCS1D01G001600	chr5A	88.830	188	16	4	2089	2271	562386688	562386501	4.430000e-55	226.0
27	TraesCS1D01G001600	chr5A	96.364	55	2	0	623	677	505349224	505349170	1.690000e-14	91.6
28	TraesCS1D01G001600	chr4B	74.185	1073	257	18	2298	3360	649836201	649835139	3.150000e-116	429.0
29	TraesCS1D01G001600	chr3A	88.520	331	27	5	351	677	607224681	607224358	1.480000e-104	390.0
30	TraesCS1D01G001600	chr3A	94.872	39	2	0	3605	3643	732621753	732621715	1.320000e-05	62.1
31	TraesCS1D01G001600	chr4A	85.675	363	34	9	323	677	715877443	715877795	2.500000e-97	366.0
32	TraesCS1D01G001600	chr4A	85.337	341	29	9	350	678	622219443	622219112	2.540000e-87	333.0
33	TraesCS1D01G001600	chr4A	83.673	343	36	8	351	679	713367159	713367495	5.530000e-79	305.0
34	TraesCS1D01G001600	chr2B	89.789	284	20	8	323	600	779132002	779132282	5.420000e-94	355.0
35	TraesCS1D01G001600	chr2B	88.235	289	24	6	323	608	66552619	66552900	1.960000e-88	337.0
36	TraesCS1D01G001600	chr6D	84.469	367	33	11	323	677	461717117	461716763	1.520000e-89	340.0
37	TraesCS1D01G001600	chr6D	88.971	136	14	1	3801	3935	57999671	57999806	2.720000e-37	167.0
38	TraesCS1D01G001600	chr1B	84.127	378	30	14	323	680	656093053	656092686	5.450000e-89	339.0
39	TraesCS1D01G001600	chr1B	87.755	147	12	5	3800	3944	68290386	68290244	2.720000e-37	167.0
40	TraesCS1D01G001600	chr1A	85.088	342	37	8	351	690	591350242	591349913	1.960000e-88	337.0
41	TraesCS1D01G001600	chr3B	85.207	338	36	8	346	680	49874126	49873800	7.060000e-88	335.0
42	TraesCS1D01G001600	chr3B	94.872	39	2	0	3605	3643	810307993	810307955	1.320000e-05	62.1
43	TraesCS1D01G001600	chr5B	86.545	275	24	7	323	593	493285873	493285608	1.550000e-74	291.0
44	TraesCS1D01G001600	chr5B	89.630	135	11	3	3802	3933	570905874	570905740	7.570000e-38	169.0
45	TraesCS1D01G001600	chr5D	86.458	192	17	5	2089	2271	445106392	445106201	7.470000e-48	202.0
46	TraesCS1D01G001600	chr5D	78.736	174	23	5	2089	2262	461043803	461043962	2.170000e-18	104.0
47	TraesCS1D01G001600	chr5D	96.875	32	0	1	1953	1983	423246850	423246819	8.000000e-03	52.8
48	TraesCS1D01G001600	chr3D	85.354	198	22	4	2080	2271	418784969	418784773	9.660000e-47	198.0
49	TraesCS1D01G001600	chr6B	90.441	136	11	2	3801	3935	130075250	130075384	1.260000e-40	178.0
50	TraesCS1D01G001600	chr6A	89.362	141	13	2	3800	3938	112005147	112005007	4.530000e-40	176.0
51	TraesCS1D01G001600	chr6A	88.406	138	14	2	3800	3935	23496456	23496593	9.800000e-37	165.0
52	TraesCS1D01G001600	chr2D	88.194	144	13	4	3803	3944	37412737	37412596	7.570000e-38	169.0

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	TraesCS1D01G001600	chr1D	414385	418787	4402	False	8131.0	8131	100.0000	1	4403	1	chr1D.!!$F1	4402
1	TraesCS1D01G001600	chr7D	399832945	399835232	2287	False	1061.5	1194	88.0140	1050	3510	2	chr7D.!!$F1	2460
2	TraesCS1D01G001600	chr7D	400185236	400185879	643	True	658.0	658	85.1390	1080	1723	1	chr7D.!!$R3	643
3	TraesCS1D01G001600	chr7A	457683087	457685358	2271	False	1072.5	1190	87.7825	1050	3510	2	chr7A.!!$F2	2460
4	TraesCS1D01G001600	chr7A	203525581	203526198	617	False	494.0	494	81.1590	1105	1722	1	chr7A.!!$F1	617
5	TraesCS1D01G001600	chr7B	409219860	409222124	2264	False	1026.5	1160	87.2860	1050	3510	2	chr7B.!!$F1	2460
6	TraesCS1D01G001600	chr7B	409749478	409750121	643	True	702.0	702	86.3780	1080	1723	1	chr7B.!!$R1	643
7	TraesCS1D01G001600	chr4D	503920307	503920962	655	True	643.0	643	84.4750	1071	1723	1	chr4D.!!$R2	652
8	TraesCS1D01G001600	chr4D	491002052	491003141	1089	True	486.0	486	75.2270	2299	3372	1	chr4D.!!$R1	1073
9	TraesCS1D01G001600	chrUn	30086962	30087609	647	False	610.0	610	83.6920	1076	1723	1	chrUn.!!$F1	647
10	TraesCS1D01G001600	chr5A	697068428	697069486	1058	False	556.0	556	76.3770	2299	3360	1	chr5A.!!$F1	1061
11	TraesCS1D01G001600	chr5A	697200390	697201448	1058	False	556.0	556	76.3770	2299	3360	1	chr5A.!!$F3	1061
12	TraesCS1D01G001600	chr5A	697282948	697284006	1058	False	556.0	556	76.4210	2299	3360	1	chr5A.!!$F4	1061
13	TraesCS1D01G001600	chr5A	706572683	706573263	580	False	549.0	549	83.7050	1141	1723	1	chr5A.!!$F6	582
14	TraesCS1D01G001600	chr5A	697552563	697553606	1043	False	477.0	477	75.1410	2299	3360	1	chr5A.!!$F5	1061
15	TraesCS1D01G001600	chr5A	688613574	688614203	629	True	464.0	464	80.1530	1072	1723	1	chr5A.!!$R3	651
16	TraesCS1D01G001600	chr5A	697132988	697133570	582	False	374.0	374	78.2910	2778	3360	1	chr5A.!!$F2	582
17	TraesCS1D01G001600	chr4B	649835139	649836201	1062	True	429.0	429	74.1850	2298	3360	1	chr4B.!!$R1	1062

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	Hairpin	End Stability	Orientation
25	26	0.029567	CGTAAAAGCGTGCAACCCAA	59.970	50.0	0.00	4.12	F
1037	1038	0.034756	AGCGTTCCACAGCACATACA	59.965	50.0	35.48	2.29	F
1742	1752	0.033011	ATACCTGCTCCTCCGTGACT	60.033	55.0	0.00	3.41	F
1750	1760	0.179234	TCCTCCGTGACTTTGCACAA	59.821	50.0	38.69	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1723	1727	0.033011	AGTCACGGAGGAGCAGGTAT	60.033	55.0	0.00	0.00	0.00	2.73	R
2087	2238	0.315886	ACACGTGTGGCAGTTATCGA	59.684	50.0	22.71	0.00	34.19	3.59	R
3052	3203	0.179070	TCGTACTTGCACAGTGCCAA	60.179	50.0	23.06	15.07	44.23	4.52	R
3558	3747	0.183014	TGGTGCCCCTTCAAACGTTA	59.817	50.0	0.00	0.00	0.00	3.18	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	End Stability
19	20	1.860676	AGTTCTCGTAAAAGCGTGCA	58.139	45.000	4.57
20	21	2.206750	AGTTCTCGTAAAAGCGTGCAA	58.793	42.857	4.08
21	22	2.033151	AGTTCTCGTAAAAGCGTGCAAC	60.033	45.455	4.17
22	23	0.863144	TCTCGTAAAAGCGTGCAACC	59.137	50.000	3.77
23	24	0.110373	CTCGTAAAAGCGTGCAACCC	60.110	55.000	4.11
24	25	0.814410	TCGTAAAAGCGTGCAACCCA	60.814	50.000	4.51
25	26	0.029567	CGTAAAAGCGTGCAACCCAA	59.970	50.000	4.12
26	27	1.534175	CGTAAAAGCGTGCAACCCAAA	60.534	47.619	3.28
27	28	2.541556	GTAAAAGCGTGCAACCCAAAA	58.458	42.857	2.44
28	29	2.100605	AAAAGCGTGCAACCCAAAAA	57.899	40.000	1.94
29	30	1.364721	AAAGCGTGCAACCCAAAAAC	58.635	45.000	2.43
30	31	0.247736	AAGCGTGCAACCCAAAAACA	59.752	45.000	2.83
31	32	0.179113	AGCGTGCAACCCAAAAACAG	60.179	50.000	3.16
32	33	0.459411	GCGTGCAACCCAAAAACAGT	60.459	50.000	3.55
33	34	1.555477	CGTGCAACCCAAAAACAGTC	58.445	50.000	3.51
34	35	1.801025	CGTGCAACCCAAAAACAGTCC	60.801	52.381	3.85
35	36	1.205893	GTGCAACCCAAAAACAGTCCA	59.794	47.619	4.02
36	37	1.205893	TGCAACCCAAAAACAGTCCAC	59.794	47.619	4.02
37	38	1.205893	GCAACCCAAAAACAGTCCACA	59.794	47.619	4.17
38	39	2.887337	CAACCCAAAAACAGTCCACAC	58.113	47.619	3.82
39	40	2.223803	ACCCAAAAACAGTCCACACA	57.776	45.000	3.72
40	41	2.745968	ACCCAAAAACAGTCCACACAT	58.254	42.857	3.21
41	42	2.693074	ACCCAAAAACAGTCCACACATC	59.307	45.455	3.06
42	43	2.035832	CCCAAAAACAGTCCACACATCC	59.964	50.000	3.51
43	44	2.692557	CCAAAAACAGTCCACACATCCA	59.307	45.455	3.41

Showing 1 to 25 of 1,410 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	1.860676	TGCACGCTTTTACGAGAACT	58.139	45.000	0.00	36.70	3.01
1	2	2.295696	GTTGCACGCTTTTACGAGAAC	58.704	47.619	0.00	36.70	3.01
2	3	1.262151	GGTTGCACGCTTTTACGAGAA	59.738	47.619	0.00	36.70	2.87
3	4	0.863144	GGTTGCACGCTTTTACGAGA	59.137	50.000	0.00	36.70	4.04
4	5	0.110373	GGGTTGCACGCTTTTACGAG	60.110	55.000	0.00	36.70	4.18
5	6	0.814410	TGGGTTGCACGCTTTTACGA	60.814	50.000	0.00	36.70	3.43
6	7	0.029567	TTGGGTTGCACGCTTTTACG	59.970	50.000	0.00	39.50	3.18
7	8	2.211353	TTTGGGTTGCACGCTTTTAC	57.789	45.000	0.00	31.67	2.01
8	9	2.930682	GTTTTTGGGTTGCACGCTTTTA	59.069	40.909	0.00	31.67	1.52
9	10	1.735018	GTTTTTGGGTTGCACGCTTTT	59.265	42.857	0.00	31.67	2.27
10	11	1.338200	TGTTTTTGGGTTGCACGCTTT	60.338	42.857	0.00	31.67	3.51
11	12	0.247736	TGTTTTTGGGTTGCACGCTT	59.752	45.000	0.00	31.67	4.68
12	13	0.179113	CTGTTTTTGGGTTGCACGCT	60.179	50.000	0.00	31.67	5.07
13	14	0.459411	ACTGTTTTTGGGTTGCACGC	60.459	50.000	0.00	0.00	5.34
14	15	1.555477	GACTGTTTTTGGGTTGCACG	58.445	50.000	0.00	0.00	5.34
15	16	1.205893	TGGACTGTTTTTGGGTTGCAC	59.794	47.619	0.00	0.00	4.57
16	17	1.205893	GTGGACTGTTTTTGGGTTGCA	59.794	47.619	0.00	0.00	4.08
17	18	1.205893	TGTGGACTGTTTTTGGGTTGC	59.794	47.619	0.00	0.00	4.17
18	19	2.232452	TGTGTGGACTGTTTTTGGGTTG	59.768	45.455	0.00	0.00	3.77
19	20	2.530701	TGTGTGGACTGTTTTTGGGTT	58.469	42.857	0.00	0.00	4.11
20	21	2.223803	TGTGTGGACTGTTTTTGGGT	57.776	45.000	0.00	0.00	4.51
21	22	2.035832	GGATGTGTGGACTGTTTTTGGG	59.964	50.000	0.00	0.00	4.12
22	23	2.692557	TGGATGTGTGGACTGTTTTTGG	59.307	45.455	0.00	0.00	3.28
23	24	4.300803	CATGGATGTGTGGACTGTTTTTG	58.699	43.478	0.00	0.00	2.44
24	25	3.321682	CCATGGATGTGTGGACTGTTTTT	59.678	43.478	5.56	37.72	1.94

Showing 1 to 25 of 1,413 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.