AutoCloner

Multiple sequence alignment - TraesCS3B01G374200

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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	TraesCS3B01G374200	chr3B	100.000	4100	0	0	1	4100	586865747	586861648	0.000000e+00	7572.0
1	TraesCS3B01G374200	chr3B	84.766	256	31	6	3522	3773	85328436	85328687	2.450000e-62	250.0
2	TraesCS3B01G374200	chr3B	74.709	344	45	26	558	874	728284077	728283749	9.310000e-22	115.0
3	TraesCS3B01G374200	chr3D	94.330	1499	56	8	1700	3172	447634380	447632885	0.000000e+00	2270.0
4	TraesCS3B01G374200	chr3D	86.767	801	31	29	313	1055	447635699	447634916	0.000000e+00	822.0
5	TraesCS3B01G374200	chr3D	91.234	559	20	5	1093	1651	447634908	447634379	0.000000e+00	734.0
6	TraesCS3B01G374200	chr3D	90.674	386	10	9	3165	3525	447632859	447632475	1.320000e-134	490.0
7	TraesCS3B01G374200	chr3D	84.861	251	31	3	3522	3772	56230981	56231224	3.170000e-61	246.0
8	TraesCS3B01G374200	chr3D	83.137	255	35	6	3526	3773	609468572	609468825	4.120000e-55	226.0
9	TraesCS3B01G374200	chr3D	80.970	268	20	9	3831	4098	447620841	447620605	2.520000e-42	183.0
10	TraesCS3B01G374200	chr3D	89.873	79	6	1	391	467	555534484	555534406	2.610000e-17	100.0
11	TraesCS3B01G374200	chr3D	87.500	80	6	3	391	467	206172733	206172811	5.640000e-14	89.8
12	TraesCS3B01G374200	chr5D	88.269	1560	113	39	1065	2574	191907534	191905995	0.000000e+00	1803.0
13	TraesCS3B01G374200	chr5D	90.838	513	30	8	2573	3082	191905963	191905465	0.000000e+00	671.0
14	TraesCS3B01G374200	chr5D	87.822	427	27	11	3124	3528	191905467	191905044	1.030000e-130	477.0
15	TraesCS3B01G374200	chr5D	84.047	257	33	7	3522	3773	499443957	499444210	1.470000e-59	241.0
16	TraesCS3B01G374200	chr5A	86.739	1561	112	36	1065	2574	229921773	229923289	0.000000e+00	1648.0
17	TraesCS3B01G374200	chr5A	89.082	980	44	32	2573	3528	229923321	229924261	0.000000e+00	1158.0
18	TraesCS3B01G374200	chr5A	98.529	68	1	0	242	309	14503831	14503764	2.000000e-23	121.0
19	TraesCS3B01G374200	chr5A	98.529	68	1	0	242	309	14509377	14509310	2.000000e-23	121.0
20	TraesCS3B01G374200	chr5A	98.529	68	1	0	242	309	14514971	14514904	2.000000e-23	121.0
21	TraesCS3B01G374200	chr5A	87.500	80	6	3	391	467	25130229	25130307	5.640000e-14	89.8
22	TraesCS3B01G374200	chr3A	90.738	1220	47	17	2365	3528	589374742	589373533	0.000000e+00	1567.0
23	TraesCS3B01G374200	chr3A	94.453	649	30	5	1700	2342	589376216	589375568	0.000000e+00	994.0
24	TraesCS3B01G374200	chr3A	95.251	379	14	4	1275	1651	589376591	589376215	7.590000e-167	597.0
25	TraesCS3B01G374200	chr3A	84.256	578	27	8	530	1055	589377287	589376722	4.730000e-139	505.0
26	TraesCS3B01G374200	chr3A	83.004	253	38	4	3524	3772	705229683	705229934	1.480000e-54	224.0
27	TraesCS3B01G374200	chr3A	96.296	108	3	1	1120	1227	589376712	589376606	4.210000e-40	176.0
28	TraesCS3B01G374200	chr5B	88.507	1192	80	26	1300	2470	196246055	196244900	0.000000e+00	1389.0
29	TraesCS3B01G374200	chr5B	89.511	982	52	22	2573	3528	196240441	196239485	0.000000e+00	1195.0
30	TraesCS3B01G374200	chr5B	90.099	202	13	5	1065	1264	196253058	196252862	5.260000e-64	255.0
31	TraesCS3B01G374200	chr5B	95.890	73	1	2	243	314	694223903	694223974	2.590000e-22	117.0
32	TraesCS3B01G374200	chr6D	84.444	360	32	10	527	874	51989455	51989802	2.360000e-87	333.0
33	TraesCS3B01G374200	chr6D	83.268	257	32	7	3522	3772	32611147	32611398	4.120000e-55	226.0
34	TraesCS3B01G374200	chr6D	82.156	269	41	5	3525	3788	456280725	456280459	1.480000e-54	224.0
35	TraesCS3B01G374200	chr6D	74.906	267	37	22	558	810	119199040	119199290	1.210000e-15	95.3
36	TraesCS3B01G374200	chr6D	87.500	80	6	3	391	467	378804328	378804250	5.640000e-14	89.8
37	TraesCS3B01G374200	chr6D	78.102	137	14	8	558	690	386197144	386197268	5.680000e-09	73.1
38	TraesCS3B01G374200	chr6B	83.473	357	43	10	529	874	118895622	118895973	6.610000e-83	318.0
39	TraesCS3B01G374200	chr6B	98.529	68	1	0	244	311	21014455	21014388	2.000000e-23	121.0
40	TraesCS3B01G374200	chr6B	97.222	72	1	1	243	314	679295995	679295925	2.000000e-23	121.0
41	TraesCS3B01G374200	chr2B	84.585	253	34	4	3522	3772	627653126	627653375	3.170000e-61	246.0
42	TraesCS3B01G374200	chr2B	83.004	253	38	4	3524	3773	788226216	788226466	1.480000e-54	224.0
43	TraesCS3B01G374200	chr6A	91.379	116	10	0	527	642	62925068	62925183	4.240000e-35	159.0
44	TraesCS3B01G374200	chr6A	91.379	116	10	0	527	642	62928711	62928826	4.240000e-35	159.0
45	TraesCS3B01G374200	chr6A	75.581	344	42	26	558	874	596778687	596778359	9.250000e-27	132.0
46	TraesCS3B01G374200	chr7B	98.551	69	1	0	243	311	166478489	166478421	5.570000e-24	122.0
47	TraesCS3B01G374200	chr1A	97.260	73	1	1	244	315	324861005	324861077	5.570000e-24	122.0
48	TraesCS3B01G374200	chr4B	75.000	344	44	26	558	874	497377724	497377396	2.000000e-23	121.0
49	TraesCS3B01G374200	chr1D	98.529	68	1	0	243	310	443784338	443784271	2.000000e-23	121.0
50	TraesCS3B01G374200	chr4D	74.812	266	39	17	558	810	481022454	481022704	1.210000e-15	95.3
51	TraesCS3B01G374200	chr4D	87.500	80	6	3	391	467	490887713	490887791	5.640000e-14	89.8
52	TraesCS3B01G374200	chrUn	87.500	80	6	3	391	467	345163480	345163558	5.640000e-14	89.8
53	TraesCS3B01G374200	chr7A	89.796	49	5	0	392	440	376783917	376783869	3.420000e-06	63.9
54	TraesCS3B01G374200	chr7D	87.234	47	6	0	4005	4051	449062207	449062253	2.000000e-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	TraesCS3B01G374200	chr3B	586861648	586865747	4099	True	7572.000000	7572	100.000000	1	4100	1	chr3B.!!$R1	4099
1	TraesCS3B01G374200	chr3D	447632475	447635699	3224	True	1079.000000	2270	90.751250	313	3525	4	chr3D.!!$R3	3212
2	TraesCS3B01G374200	chr5D	191905044	191907534	2490	True	983.666667	1803	88.976333	1065	3528	3	chr5D.!!$R1	2463
3	TraesCS3B01G374200	chr5A	229921773	229924261	2488	False	1403.000000	1648	87.910500	1065	3528	2	chr5A.!!$F2	2463
4	TraesCS3B01G374200	chr3A	589373533	589377287	3754	True	767.800000	1567	92.198800	530	3528	5	chr3A.!!$R1	2998
5	TraesCS3B01G374200	chr5B	196244900	196246055	1155	True	1389.000000	1389	88.507000	1300	2470	1	chr5B.!!$R2	1170
6	TraesCS3B01G374200	chr5B	196239485	196240441	956	True	1195.000000	1195	89.511000	2573	3528	1	chr5B.!!$R1	955

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
59	60	0.034059	ACGGGAGCACTCTCTTTGTG	59.966	55.0	39.31	3.33	F
1490	1588	0.032615	ACCTCGATCTTCTCCAGGCT	60.033	55.0	0.00	4.58	F
1547	1645	0.523072	CCTGTGCTCCGGTTTGATTG	59.477	55.0	0.00	2.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1896	1998	1.267806	CACACATCCCAGTCAAAGTGC	59.732	52.381	0.00	0.00	4.40	R
2999	4015	0.035458	ACAAGGGTTTCGAGGCAGAG	59.965	55.000	0.00	0.00	3.35	R
3508	4598	1.921982	CACCAATGGGAATGACACCA	58.078	50.000	3.55	41.76	4.17	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
19	20	2.286365	TGGTGATCAAACAAGGGACC	57.714	50.000	0.00	0.00	0.00	4.46
20	21	1.496857	TGGTGATCAAACAAGGGACCA	59.503	47.619	0.00	0.00	0.00	4.02
21	22	2.109834	TGGTGATCAAACAAGGGACCAT	59.890	45.455	0.00	0.00	0.00	3.55
22	23	2.755103	GGTGATCAAACAAGGGACCATC	59.245	50.000	0.00	0.00	0.00	3.51
23	24	3.562176	GGTGATCAAACAAGGGACCATCT	60.562	47.826	0.00	0.00	0.00	2.90
24	25	4.082125	GTGATCAAACAAGGGACCATCTT	58.918	43.478	0.00	0.00	0.00	2.40
25	26	4.156739	GTGATCAAACAAGGGACCATCTTC	59.843	45.833	0.00	0.00	0.00	2.87
26	27	3.154827	TCAAACAAGGGACCATCTTCC	57.845	47.619	0.00	0.00	34.52	3.46
27	28	2.716424	TCAAACAAGGGACCATCTTCCT	59.284	45.455	0.00	0.00	35.76	3.36
28	29	3.084786	CAAACAAGGGACCATCTTCCTC	58.915	50.000	0.00	0.00	35.76	3.71
29	30	2.350863	ACAAGGGACCATCTTCCTCT	57.649	50.000	0.00	0.00	35.76	3.69
30	31	2.637165	ACAAGGGACCATCTTCCTCTT	58.363	47.619	0.00	0.00	35.76	2.85
31	32	2.307098	ACAAGGGACCATCTTCCTCTTG	59.693	50.000	14.08	14.08	43.10	3.02
32	33	2.573462	CAAGGGACCATCTTCCTCTTGA	59.427	50.000	11.81	0.00	41.66	3.02
33	34	2.921221	AGGGACCATCTTCCTCTTGAA	58.079	47.619	0.00	0.00	35.76	2.69
44	45	2.846193	TCCTCTTGAAGAAACAACGGG	58.154	47.619	0.00	0.00	0.00	5.28
45	46	2.436542	TCCTCTTGAAGAAACAACGGGA	59.563	45.455	0.00	0.00	0.00	5.14
46	47	2.808543	CCTCTTGAAGAAACAACGGGAG	59.191	50.000	0.00	0.00	0.00	4.30
47	48	2.218603	TCTTGAAGAAACAACGGGAGC	58.781	47.619	0.00	0.00	0.00	4.70
48	49	1.946768	CTTGAAGAAACAACGGGAGCA	59.053	47.619	0.00	0.00	0.00	4.26
49	50	1.305201	TGAAGAAACAACGGGAGCAC	58.695	50.000	0.00	0.00	0.00	4.40
50	51	1.134220	TGAAGAAACAACGGGAGCACT	60.134	47.619	0.00	0.00	0.00	4.40
51	52	1.531578	GAAGAAACAACGGGAGCACTC	59.468	52.381	0.00	0.00	0.00	3.51
52	53	0.759346	AGAAACAACGGGAGCACTCT	59.241	50.000	0.00	0.00	0.00	3.24
53	54	1.149148	GAAACAACGGGAGCACTCTC	58.851	55.000	0.00	0.00	38.62	3.20

Showing 1 to 25 of 624 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	2.286365	TGGTCCCTTGTTTGATCACC	57.714	50.000	0.00	0.00	0.00	4.02
2	3	3.690460	AGATGGTCCCTTGTTTGATCAC	58.310	45.455	0.00	0.00	0.00	3.06
3	4	4.335416	GAAGATGGTCCCTTGTTTGATCA	58.665	43.478	0.00	0.00	0.00	2.92
4	5	3.696548	GGAAGATGGTCCCTTGTTTGATC	59.303	47.826	0.00	0.00	0.00	2.92
6	7	2.716424	AGGAAGATGGTCCCTTGTTTGA	59.284	45.455	0.00	0.00	38.59	2.69
7	8	3.084786	GAGGAAGATGGTCCCTTGTTTG	58.915	50.000	0.00	0.00	38.59	2.93
8	9	2.989571	AGAGGAAGATGGTCCCTTGTTT	59.010	45.455	0.00	0.00	38.59	2.83
9	10	2.637165	AGAGGAAGATGGTCCCTTGTT	58.363	47.619	0.00	0.00	38.59	2.83
10	11	2.307098	CAAGAGGAAGATGGTCCCTTGT	59.693	50.000	11.33	0.00	39.11	3.16
11	12	2.573462	TCAAGAGGAAGATGGTCCCTTG	59.427	50.000	12.52	12.52	41.98	3.61
12	13	2.921221	TCAAGAGGAAGATGGTCCCTT	58.079	47.619	0.00	0.00	38.59	3.95
13	14	2.649742	TCAAGAGGAAGATGGTCCCT	57.350	50.000	0.00	0.00	38.59	4.20
23	24	3.118186	TCCCGTTGTTTCTTCAAGAGGAA	60.118	43.478	0.00	0.00	31.22	3.36
24	25	2.436542	TCCCGTTGTTTCTTCAAGAGGA	59.563	45.455	0.00	0.00	32.07	3.71
25	26	2.808543	CTCCCGTTGTTTCTTCAAGAGG	59.191	50.000	0.00	0.00	0.00	3.69
26	27	2.224314	GCTCCCGTTGTTTCTTCAAGAG	59.776	50.000	0.00	0.00	0.00	2.85
27	28	2.218603	GCTCCCGTTGTTTCTTCAAGA	58.781	47.619	0.00	0.00	0.00	3.02
28	29	1.946768	TGCTCCCGTTGTTTCTTCAAG	59.053	47.619	0.00	0.00	0.00	3.02
29	30	1.673920	GTGCTCCCGTTGTTTCTTCAA	59.326	47.619	0.00	0.00	0.00	2.69
30	31	1.134220	AGTGCTCCCGTTGTTTCTTCA	60.134	47.619	0.00	0.00	0.00	3.02
31	32	1.531578	GAGTGCTCCCGTTGTTTCTTC	59.468	52.381	0.00	0.00	0.00	2.87
32	33	1.141053	AGAGTGCTCCCGTTGTTTCTT	59.859	47.619	0.00	0.00	0.00	2.52
33	34	0.759346	AGAGTGCTCCCGTTGTTTCT	59.241	50.000	0.00	0.00	0.00	2.52
34	35	1.149148	GAGAGTGCTCCCGTTGTTTC	58.851	55.000	0.00	0.00	35.01	2.78
35	36	0.759346	AGAGAGTGCTCCCGTTGTTT	59.241	50.000	0.00	0.00	42.30	2.83

Showing 1 to 25 of 592 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.