AutoCloner

Multiple sequence alignment - TraesCS7D01G166300

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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	TraesCS7D01G166300	chr7D	100.000	9395	0	0	1	9395	116891785	116882391	0.000000e+00	17350.0
1	TraesCS7D01G166300	chr7D	96.396	333	10	2	6987	7317	548476242	548476574	1.780000e-151	547.0
2	TraesCS7D01G166300	chr7D	96.657	329	8	3	6990	7316	562059990	562059663	2.310000e-150	544.0
3	TraesCS7D01G166300	chr7D	75.630	357	70	13	1	354	157098766	157099108	2.720000e-35	161.0
4	TraesCS7D01G166300	chr7D	89.011	91	7	2	6784	6874	116884911	116884824	9.970000e-20	110.0
5	TraesCS7D01G166300	chr7D	89.011	91	7	2	6875	6962	116885002	116884912	9.970000e-20	110.0
6	TraesCS7D01G166300	chr7D	93.023	43	3	0	9069	9111	249082621	249082579	7.880000e-06	63.9
7	TraesCS7D01G166300	chr7A	95.184	2305	71	19	2520	4796	120981936	120979644	0.000000e+00	3605.0
8	TraesCS7D01G166300	chr7A	96.344	1477	31	7	5132	6602	120972764	120971305	0.000000e+00	2407.0
9	TraesCS7D01G166300	chr7A	95.820	1244	41	8	7317	8559	120971160	120969927	0.000000e+00	1999.0
10	TraesCS7D01G166300	chr7A	92.369	996	58	10	1533	2521	120982948	120981964	0.000000e+00	1402.0
11	TraesCS7D01G166300	chr7A	89.668	784	39	15	790	1564	120983698	120982948	0.000000e+00	961.0
12	TraesCS7D01G166300	chr7A	94.415	376	15	3	8582	8954	120969935	120969563	2.940000e-159	573.0
13	TraesCS7D01G166300	chr7A	87.527	457	34	7	8951	9395	120822870	120822425	3.030000e-139	507.0
14	TraesCS7D01G166300	chr7A	98.069	259	5	0	4885	5143	120979640	120979382	1.440000e-122	451.0
15	TraesCS7D01G166300	chr7A	89.344	366	22	7	406	762	120984217	120983860	2.410000e-120	444.0
16	TraesCS7D01G166300	chr7A	79.669	423	68	10	1	406	252191932	252192353	1.190000e-73	289.0
17	TraesCS7D01G166300	chr7A	89.773	176	14	4	8231	8405	662136102	662135930	1.230000e-53	222.0
18	TraesCS7D01G166300	chr7A	93.007	143	6	3	6852	6990	120971306	120971164	1.240000e-48	206.0
19	TraesCS7D01G166300	chr7A	94.565	92	4	1	6784	6874	120971283	120971192	3.540000e-29	141.0
20	TraesCS7D01G166300	chr7B	88.477	2508	174	59	4390	6847	75892611	75890169	0.000000e+00	2924.0
21	TraesCS7D01G166300	chr7B	89.616	2138	129	45	7317	9395	75889848	75887745	0.000000e+00	2632.0
22	TraesCS7D01G166300	chr7B	89.062	1536	107	31	405	1920	75898487	75896993	0.000000e+00	1849.0
23	TraesCS7D01G166300	chr7B	90.370	1028	67	20	2036	3053	75896985	75895980	0.000000e+00	1321.0
24	TraesCS7D01G166300	chr7B	90.372	914	40	15	3041	3919	75894162	75893262	0.000000e+00	1157.0
25	TraesCS7D01G166300	chr7B	88.432	389	37	6	4003	4390	75893235	75892854	6.650000e-126	462.0
26	TraesCS7D01G166300	chr7B	90.698	301	18	8	405	703	75906266	75905974	8.840000e-105	392.0
27	TraesCS7D01G166300	chr7B	81.513	357	61	5	1	354	213470878	213471232	1.190000e-73	289.0
28	TraesCS7D01G166300	chr5D	96.988	332	8	2	6989	7318	35154845	35155176	2.960000e-154	556.0
29	TraesCS7D01G166300	chr5D	95.796	333	12	2	6987	7317	483523678	483524010	3.860000e-148	536.0
30	TraesCS7D01G166300	chr1D	96.687	332	7	4	6989	7317	131288934	131289264	4.960000e-152	549.0
31	TraesCS7D01G166300	chr1D	80.479	292	42	7	14	293	479319816	479319528	9.560000e-50	209.0
32	TraesCS7D01G166300	chr4A	96.375	331	10	2	6988	7316	7128775	7129105	2.310000e-150	544.0
33	TraesCS7D01G166300	chr4A	75.367	341	62	17	13	346	742372254	742371929	2.730000e-30	145.0
34	TraesCS7D01G166300	chr2A	95.575	339	13	2	6981	7317	27650730	27651068	8.300000e-150	542.0
35	TraesCS7D01G166300	chr2A	96.375	331	9	3	6990	7317	778156852	778157182	8.300000e-150	542.0
36	TraesCS7D01G166300	chr5A	96.061	330	11	2	6989	7316	30516839	30516510	3.860000e-148	536.0
37	TraesCS7D01G166300	chr5A	81.793	357	62	3	1	355	227113101	227112746	7.130000e-76	296.0
38	TraesCS7D01G166300	chr3D	79.905	423	63	14	1	406	566003439	566003856	3.320000e-74	291.0
39	TraesCS7D01G166300	chr3B	78.836	378	65	11	1	367	691482674	691483047	3.390000e-59	241.0
40	TraesCS7D01G166300	chr3B	80.000	220	37	6	128	343	787825537	787825321	1.260000e-33	156.0
41	TraesCS7D01G166300	chr3B	85.246	61	7	2	9069	9127	401278855	401278795	2.830000e-05	62.1
42	TraesCS7D01G166300	chr1B	81.126	302	45	8	1	292	684342791	684342492	2.040000e-56	231.0
43	TraesCS7D01G166300	chr1B	79.293	198	30	8	137	327	661982324	661982131	2.750000e-25	128.0
44	TraesCS7D01G166300	chr1B	93.333	45	3	0	9069	9113	17695231	17695275	6.090000e-07	67.6
45	TraesCS7D01G166300	chr2D	80.132	302	43	9	1	289	419360461	419360758	9.560000e-50	209.0
46	TraesCS7D01G166300	chr2D	95.556	45	2	0	9069	9113	12630830	12630874	1.310000e-08	73.1
47	TraesCS7D01G166300	chr4B	76.720	378	65	13	1	367	638158211	638157846	1.250000e-43	189.0
48	TraesCS7D01G166300	chr4D	82.710	214	34	3	13	224	439701588	439701376	4.480000e-43	187.0
49	TraesCS7D01G166300	chr4D	83.226	155	21	5	187	339	484745283	484745434	4.580000e-28	137.0
50	TraesCS7D01G166300	chr2B	84.173	139	22	0	217	355	689875255	689875393	1.650000e-27	135.0
51	TraesCS7D01G166300	chr6A	95.122	41	2	0	9071	9111	614482321	614482281	2.190000e-06	65.8
52	TraesCS7D01G166300	chr5B	92.857	42	3	0	9070	9111	598538735	598538776	2.830000e-05	62.1
53	TraesCS7D01G166300	chr5B	92.857	42	3	0	9070	9111	598565112	598565153	2.830000e-05	62.1
54	TraesCS7D01G166300	chr5B	92.857	42	3	0	9070	9111	598586121	598586162	2.830000e-05	62.1

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	TraesCS7D01G166300	chr7D	116882391	116891785	9394	True	17350.000000	17350	100.000000	1	9395	1	chr7D.!!$R1	9394
1	TraesCS7D01G166300	chr7A	120979382	120984217	4835	True	1372.600000	3605	92.926800	406	5143	5	chr7A.!!$R4	4737
2	TraesCS7D01G166300	chr7A	120969563	120972764	3201	True	1065.200000	2407	94.830200	5132	8954	5	chr7A.!!$R3	3822
3	TraesCS7D01G166300	chr7B	75887745	75898487	10742	True	1724.166667	2924	89.388167	405	9395	6	chr7B.!!$R2	8990

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
266	267	0.032130	GGCGCTTCATATCCGTCTCA	59.968	55.000	7.64	0.00	3.27	F
299	300	0.042581	TATGAGGGGTGCCAGTCAGA	59.957	55.000	0.00	0.00	3.27	F
1925	2124	0.104120	CAACCACCACGTGAGAGACA	59.896	55.000	19.30	35.23	3.41	F
2992	3225	0.541863	AGAAAGGACCCATAGCCACG	59.458	55.000	0.00	0.00	4.94	F
4019	6128	0.808125	TGTGTATGCCAACCGAATGC	59.192	50.000	0.00	0.00	3.56	F
4051	6160	2.635915	TGTGGGTAAACCTCATCGAGTT	59.364	45.455	0.00	37.80	3.01	F
4869	7232	2.561478	ACATCGGCTACCAGTTTTGT	57.439	45.000	0.00	0.00	2.83	F
4897	7260	2.030185	AGTAGCACACAAGTACTCCACG	60.030	50.000	0.00	0.00	4.94	F
6474	8885	2.224843	TGATCCAGTGCACCACAAGATT	60.225	45.455	14.63	36.74	2.40	F
7279	9961	0.037697	TGACGGTCGAGATGGTTTGG	60.038	55.000	3.34	0.00	3.28	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1842	2041	0.041312	ACGAGTGTTTTGATGCGTGC	60.041	50.000	0.00	0.00	0.00	5.34	R
2118	2321	3.669251	ACTGTGGCAGAAGAGAAGTAC	57.331	47.619	2.91	0.00	35.18	2.73	R
3478	5554	0.552848	AGAGAGAGAGAGAGGGGCAG	59.447	60.000	0.00	0.00	0.00	4.85	R
4824	7187	1.134965	GTAACTCGCACTCCAGCAGAT	60.135	52.381	0.00	0.00	0.00	2.90	R
4854	7217	1.944024	TGTTGACAAAACTGGTAGCCG	59.056	47.619	0.00	0.00	0.00	5.52	R
4882	7245	2.029623	AGTCACGTGGAGTACTTGTGT	58.970	47.619	17.00	2.94	31.03	3.72	R
6474	8885	1.774110	TGCTTTTTGGAAGGCAGTCA	58.226	45.000	0.00	0.00	42.16	3.41	R
6611	9027	4.218852	GCTGAAGGTGTGTAGTCTACTTCT	59.781	45.833	11.28	1.45	36.28	2.85	R
8010	10713	0.957888	GTCAGCCAAAGGAGTCCTGC	60.958	60.000	13.89	12.32	32.13	4.85	R
8620	11352	2.161855	TGACGTACATTACACCGACCT	58.838	47.619	0.00	0.00	0.00	3.85	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	End Stability
17	18	3.821995	ATGCGGACCGTTATTGCC	58.178	55.556	16.73	4.52
18	19	1.223487	ATGCGGACCGTTATTGCCT	59.777	52.632	16.73	4.75
19	20	0.814010	ATGCGGACCGTTATTGCCTC	60.814	55.000	16.73	4.70
20	21	2.178235	GCGGACCGTTATTGCCTCC	61.178	63.158	16.73	4.30
21	22	1.520666	CGGACCGTTATTGCCTCCT	59.479	57.895	5.48	3.69
22	23	0.529992	CGGACCGTTATTGCCTCCTC	60.530	60.000	5.48	3.71
23	24	0.179054	GGACCGTTATTGCCTCCTCC	60.179	60.000	0.00	4.30
24	25	0.539986	GACCGTTATTGCCTCCTCCA	59.460	55.000	0.00	3.86
25	26	0.988832	ACCGTTATTGCCTCCTCCAA	59.011	50.000	0.00	3.53
26	27	1.339727	ACCGTTATTGCCTCCTCCAAC	60.340	52.381	0.00	3.77
27	28	1.379527	CGTTATTGCCTCCTCCAACC	58.620	55.000	0.00	3.77
28	29	1.763968	GTTATTGCCTCCTCCAACCC	58.236	55.000	0.00	4.11
29	30	0.254747	TTATTGCCTCCTCCAACCCG	59.745	55.000	0.00	5.28
30	31	2.265467	TATTGCCTCCTCCAACCCGC	62.265	60.000	0.00	6.13
33	34	3.636231	CCTCCTCCAACCCGCACA	61.636	66.667	0.00	4.57
34	35	2.429930	CTCCTCCAACCCGCACAA	59.570	61.111	0.00	3.33
35	36	1.672356	CTCCTCCAACCCGCACAAG	60.672	63.158	0.00	3.16
36	37	2.111999	CTCCTCCAACCCGCACAAGA	62.112	60.000	0.00	3.02
37	38	1.002134	CCTCCAACCCGCACAAGAT	60.002	57.895	0.00	2.40
38	39	1.308069	CCTCCAACCCGCACAAGATG	61.308	60.000	0.00	2.90
39	40	0.321564	CTCCAACCCGCACAAGATGA	60.322	55.000	0.00	2.92
40	41	0.605319	TCCAACCCGCACAAGATGAC	60.605	55.000	0.00	3.06
41	42	0.888736	CCAACCCGCACAAGATGACA	60.889	55.000	0.00	3.58
42	43	0.238289	CAACCCGCACAAGATGACAC	59.762	55.000	0.00	3.67
43	44	0.108585	AACCCGCACAAGATGACACT	59.891	50.000	0.00	3.55

Showing 1 to 25 of 694 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	0.814010	GAGGCAATAACGGTCCGCAT	60.814	55.000	12.28	2.94	0.00	4.73
1	2	1.448893	GAGGCAATAACGGTCCGCA	60.449	57.895	12.28	0.00	0.00	5.69
2	3	2.178235	GGAGGCAATAACGGTCCGC	61.178	63.158	12.28	0.00	0.00	5.54
3	4	0.529992	GAGGAGGCAATAACGGTCCG	60.530	60.000	10.48	10.48	32.14	4.79
4	5	0.179054	GGAGGAGGCAATAACGGTCC	60.179	60.000	0.00	0.00	0.00	4.46
5	6	0.539986	TGGAGGAGGCAATAACGGTC	59.460	55.000	0.00	0.00	0.00	4.79
6	7	0.988832	TTGGAGGAGGCAATAACGGT	59.011	50.000	0.00	0.00	0.00	4.83
7	8	1.379527	GTTGGAGGAGGCAATAACGG	58.620	55.000	0.00	0.00	0.00	4.44
8	9	1.379527	GGTTGGAGGAGGCAATAACG	58.620	55.000	0.00	0.00	0.00	3.18
9	10	1.763968	GGGTTGGAGGAGGCAATAAC	58.236	55.000	0.00	0.00	0.00	1.89
10	11	0.254747	CGGGTTGGAGGAGGCAATAA	59.745	55.000	0.00	0.00	0.00	1.40
11	12	1.912220	CGGGTTGGAGGAGGCAATA	59.088	57.895	0.00	0.00	0.00	1.90
12	13	2.677228	CGGGTTGGAGGAGGCAAT	59.323	61.111	0.00	0.00	0.00	3.56
13	14	4.344865	GCGGGTTGGAGGAGGCAA	62.345	66.667	0.00	0.00	0.00	4.52
16	17	3.190738	TTGTGCGGGTTGGAGGAGG	62.191	63.158	0.00	0.00	0.00	4.30
17	18	1.672356	CTTGTGCGGGTTGGAGGAG	60.672	63.158	0.00	0.00	0.00	3.69
18	19	1.488705	ATCTTGTGCGGGTTGGAGGA	61.489	55.000	0.00	0.00	0.00	3.71
19	20	1.002134	ATCTTGTGCGGGTTGGAGG	60.002	57.895	0.00	0.00	0.00	4.30
20	21	0.321564	TCATCTTGTGCGGGTTGGAG	60.322	55.000	0.00	0.00	0.00	3.86
21	22	0.605319	GTCATCTTGTGCGGGTTGGA	60.605	55.000	0.00	0.00	0.00	3.53
22	23	0.888736	TGTCATCTTGTGCGGGTTGG	60.889	55.000	0.00	0.00	0.00	3.77
23	24	0.238289	GTGTCATCTTGTGCGGGTTG	59.762	55.000	0.00	0.00	0.00	3.77
24	25	0.108585	AGTGTCATCTTGTGCGGGTT	59.891	50.000	0.00	0.00	0.00	4.11
25	26	0.108585	AAGTGTCATCTTGTGCGGGT	59.891	50.000	0.00	0.00	0.00	5.28
26	27	0.798776	GAAGTGTCATCTTGTGCGGG	59.201	55.000	0.00	0.00	0.00	6.13

Showing 1 to 25 of 671 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.