AutoCloner

Multiple sequence alignment - TraesCS4B01G361800

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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	TraesCS4B01G361800	chr4B	100.000	4559	0	0	1	4559	650934173	650938731	0.000000e+00	8419.0
1	TraesCS4B01G361800	chr4B	89.173	508	51	2	1180	1686	631974037	631973533	8.320000e-177	630.0
2	TraesCS4B01G361800	chr4B	97.222	144	4	0	1736	1879	436308121	436307978	1.270000e-60	244.0
3	TraesCS4B01G361800	chr4B	92.982	57	0	3	3750	3802	219608026	219608082	3.780000e-11	80.5
4	TraesCS4B01G361800	chr4D	94.184	1410	54	12	2366	3752	504316553	504317957	0.000000e+00	2124.0
5	TraesCS4B01G361800	chr4D	84.878	1726	147	50	76	1738	504314553	504316227	0.000000e+00	1637.0
6	TraesCS4B01G361800	chr4D	94.545	330	16	2	1877	2204	504316225	504316554	4.070000e-140	508.0
7	TraesCS4B01G361800	chr4D	94.972	179	7	2	2198	2375	75782047	75782224	3.470000e-71	279.0
8	TraesCS4B01G361800	chr4D	79.180	317	52	14	4124	4437	504318382	504318687	1.660000e-49	207.0
9	TraesCS4B01G361800	chr4D	88.430	121	11	2	4234	4351	504320612	504320732	4.750000e-30	143.0
10	TraesCS4B01G361800	chr5A	91.905	1396	69	23	2366	3747	688963897	688965262	0.000000e+00	1912.0
11	TraesCS4B01G361800	chr5A	83.631	1008	105	28	633	1607	688962565	688963545	0.000000e+00	893.0
12	TraesCS4B01G361800	chr5A	82.584	534	67	5	1	529	688961898	688962410	9.000000e-122	448.0
13	TraesCS4B01G361800	chr5A	90.455	220	21	0	1180	1399	32012843	32013062	1.600000e-74	291.0
14	TraesCS4B01G361800	chr5A	91.667	144	9	3	1738	1879	565680751	565680609	3.600000e-46	196.0
15	TraesCS4B01G361800	chr5A	82.741	197	22	10	4117	4308	688965721	688965910	1.010000e-36	165.0
16	TraesCS4B01G361800	chr5A	88.550	131	10	3	4233	4358	688967821	688967951	2.200000e-33	154.0
17	TraesCS4B01G361800	chr2D	89.587	509	45	5	1180	1686	632563526	632563024	1.380000e-179	640.0
18	TraesCS4B01G361800	chr1B	89.370	508	50	2	1180	1686	554152983	554153487	1.790000e-178	636.0
19	TraesCS4B01G361800	chr1B	88.976	508	52	2	1180	1686	625436165	625435661	3.870000e-175	625.0
20	TraesCS4B01G361800	chr1B	87.992	508	57	2	1180	1686	670625858	670625354	8.440000e-167	597.0
21	TraesCS4B01G361800	chr1B	87.841	403	48	1	1180	1581	298765091	298765493	5.340000e-129	472.0
22	TraesCS4B01G361800	chr1B	90.400	125	12	0	1180	1304	4617926	4617802	1.010000e-36	165.0
23	TraesCS4B01G361800	chr1B	83.453	139	13	5	1739	1877	461302827	461302699	2.230000e-23	121.0
24	TraesCS4B01G361800	chr1B	88.000	50	5	1	1831	1880	105688387	105688339	1.770000e-04	58.4
25	TraesCS4B01G361800	chr7B	88.976	508	52	2	1180	1686	704165055	704165559	3.870000e-175	625.0
26	TraesCS4B01G361800	chr7B	88.780	508	53	2	1180	1686	684172484	684172988	1.800000e-173	619.0
27	TraesCS4B01G361800	chr7B	94.318	176	9	1	2193	2368	92045849	92046023	7.520000e-68	268.0
28	TraesCS4B01G361800	chr7B	96.000	50	2	0	3742	3791	329379328	329379377	1.050000e-11	82.4
29	TraesCS4B01G361800	chr2B	88.780	508	53	2	1180	1686	695759599	695760103	1.800000e-173	619.0
30	TraesCS4B01G361800	chr5B	88.780	508	52	3	1180	1686	521346406	521346909	6.480000e-173	617.0
31	TraesCS4B01G361800	chr5B	88.583	508	54	2	1180	1686	567942880	567943384	8.380000e-172	614.0
32	TraesCS4B01G361800	chr5B	90.566	106	6	4	4235	4340	689887462	689887361	2.210000e-28	137.0
33	TraesCS4B01G361800	chr5B	94.444	54	1	2	3751	3804	262565664	262565715	1.050000e-11	82.4
34	TraesCS4B01G361800	chr5B	96.000	50	2	0	3742	3791	295798713	295798664	1.050000e-11	82.4
35	TraesCS4B01G361800	chr3B	80.762	551	66	28	3017	3540	811513822	811513285	1.190000e-105	394.0
36	TraesCS4B01G361800	chr3B	94.915	177	7	2	2202	2376	571752690	571752514	4.490000e-70	276.0
37	TraesCS4B01G361800	chr3B	94.828	174	9	0	2202	2375	120617078	120616905	5.810000e-69	272.0
38	TraesCS4B01G361800	chr3B	96.000	50	2	0	3742	3791	343958756	343958707	1.050000e-11	82.4
39	TraesCS4B01G361800	chr3B	89.062	64	6	1	3728	3791	558501209	558501147	1.360000e-10	78.7
40	TraesCS4B01G361800	chr3A	82.540	441	53	16	3017	3445	734281002	734280574	2.590000e-97	366.0
41	TraesCS4B01G361800	chr3A	87.324	142	16	2	1741	1881	80279101	80278961	1.310000e-35	161.0
42	TraesCS4B01G361800	chr3A	92.784	97	2	4	4232	4323	60628533	60628629	7.960000e-28	135.0
43	TraesCS4B01G361800	chr3A	89.796	49	5	0	1831	1879	71804181	71804229	3.810000e-06	63.9
44	TraesCS4B01G361800	chr6A	89.333	225	19	1	1180	1399	439516054	439516278	1.250000e-70	278.0
45	TraesCS4B01G361800	chr6A	93.750	96	3	2	4228	4323	611065999	611066091	1.710000e-29	141.0
46	TraesCS4B01G361800	chr6A	86.957	69	6	3	3725	3791	424099050	424099117	1.760000e-09	75.0
47	TraesCS4B01G361800	chr6B	95.882	170	7	0	2203	2372	211161479	211161648	4.490000e-70	276.0
48	TraesCS4B01G361800	chr6B	90.323	62	3	3	3745	3803	669617383	669617322	1.360000e-10	78.7
49	TraesCS4B01G361800	chr1D	95.376	173	8	0	2197	2369	238940210	238940382	4.490000e-70	276.0
50	TraesCS4B01G361800	chr1D	95.858	169	7	0	2203	2371	178466306	178466474	1.620000e-69	274.0
51	TraesCS4B01G361800	chr1D	92.553	188	11	3	2185	2370	201728659	201728845	2.700000e-67	267.0
52	TraesCS4B01G361800	chr1D	89.209	139	14	1	1739	1877	343892037	343891900	6.060000e-39	172.0
53	TraesCS4B01G361800	chr6D	95.858	169	7	0	2200	2368	392897142	392896974	1.620000e-69	274.0
54	TraesCS4B01G361800	chr4A	88.496	226	21	1	1180	1400	411855057	411854832	7.520000e-68	268.0
55	TraesCS4B01G361800	chr5D	90.210	143	13	1	1738	1879	447773098	447772956	7.790000e-43	185.0
56	TraesCS4B01G361800	chr5D	91.150	113	7	3	4228	4337	490026024	490026136	2.840000e-32	150.0
57	TraesCS4B01G361800	chr5D	91.089	101	7	2	4235	4334	546684259	546684160	7.960000e-28	135.0
58	TraesCS4B01G361800	chr5D	96.154	52	0	2	3744	3793	451485937	451485886	2.920000e-12	84.2
59	TraesCS4B01G361800	chr3D	92.000	125	10	0	1180	1304	216613671	216613547	4.690000e-40	176.0
60	TraesCS4B01G361800	chr3D	86.395	147	10	2	1738	1884	565688702	565688838	7.900000e-33	152.0
61	TraesCS4B01G361800	chr2A	76.923	143	17	5	1736	1877	769555335	769555462	2.940000e-07	67.6

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	TraesCS4B01G361800	chr4B	650934173	650938731	4558	False	8419.0	8419	100.0000	1	4559	1	chr4B.!!$F2	4558
1	TraesCS4B01G361800	chr4B	631973533	631974037	504	True	630.0	630	89.1730	1180	1686	1	chr4B.!!$R2	506
2	TraesCS4B01G361800	chr4D	504314553	504320732	6179	False	923.8	2124	88.2434	76	4437	5	chr4D.!!$F2	4361
3	TraesCS4B01G361800	chr5A	688961898	688967951	6053	False	714.4	1912	85.8822	1	4358	5	chr5A.!!$F2	4357
4	TraesCS4B01G361800	chr2D	632563024	632563526	502	True	640.0	640	89.5870	1180	1686	1	chr2D.!!$R1	506
5	TraesCS4B01G361800	chr1B	554152983	554153487	504	False	636.0	636	89.3700	1180	1686	1	chr1B.!!$F2	506
6	TraesCS4B01G361800	chr1B	625435661	625436165	504	True	625.0	625	88.9760	1180	1686	1	chr1B.!!$R4	506
7	TraesCS4B01G361800	chr1B	670625354	670625858	504	True	597.0	597	87.9920	1180	1686	1	chr1B.!!$R5	506
8	TraesCS4B01G361800	chr7B	704165055	704165559	504	False	625.0	625	88.9760	1180	1686	1	chr7B.!!$F4	506
9	TraesCS4B01G361800	chr7B	684172484	684172988	504	False	619.0	619	88.7800	1180	1686	1	chr7B.!!$F3	506
10	TraesCS4B01G361800	chr2B	695759599	695760103	504	False	619.0	619	88.7800	1180	1686	1	chr2B.!!$F1	506
11	TraesCS4B01G361800	chr5B	521346406	521346909	503	False	617.0	617	88.7800	1180	1686	1	chr5B.!!$F2	506
12	TraesCS4B01G361800	chr5B	567942880	567943384	504	False	614.0	614	88.5830	1180	1686	1	chr5B.!!$F3	506
13	TraesCS4B01G361800	chr3B	811513285	811513822	537	True	394.0	394	80.7620	3017	3540	1	chr3B.!!$R5	523

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
625	735	0.105593	TGAGGCATGATCTCGGCTTC	59.894	55.0	11.34	9.74	38.29	3.86	F
1027	1192	0.037605	CTAGGGTTTTCTCGCCGTGT	60.038	55.0	0.00	0.00	0.00	4.49	F
1777	2526	0.174845	CGGCTCCGTGGAATTACAGA	59.825	55.0	0.00	0.00	34.35	3.41	F
1830	2579	0.748005	TTTATCCCTGCAGCTTCGCC	60.748	55.0	8.66	0.00	0.00	5.54	F
1861	2610	1.021202	CTGAGTCTGGAGCGGAGTAG	58.979	60.0	0.00	0.00	0.00	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2390	3141	0.112995	TGGTTGAGGAAAGGCTGCAT	59.887	50.000	0.50	0.0	0.00	3.96	R
2617	3369	1.554617	ACCAAAAGCTGCACCAAAACT	59.445	42.857	1.02	0.0	0.00	2.66	R
3290	4075	0.663153	GGCGGAATGGATGTTAGTGC	59.337	55.000	0.00	0.0	0.00	4.40	R
3309	4094	2.806244	CAGTCTTTGGAACCTGTAACGG	59.194	50.000	0.00	0.0	0.00	4.44	R
3850	4655	1.068250	GAATCGAAGGAGCCCTCGG	59.932	63.158	7.60	0.0	30.89	4.63	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
26	27	1.444553	GTCAAGCCCGACTCGACAG	60.445	63.158	0.00	0.00	32.92	3.51
33	34	1.939838	GCCCGACTCGACAGAATTGTT	60.940	52.381	0.00	0.00	37.76	2.83
35	36	2.404215	CCGACTCGACAGAATTGTTGT	58.596	47.619	0.00	0.00	39.36	3.32
39	40	3.131396	ACTCGACAGAATTGTTGTCCAC	58.869	45.455	11.93	0.00	41.43	4.02
46	47	3.185188	CAGAATTGTTGTCCACTCACTCG	59.815	47.826	0.00	0.00	0.00	4.18
51	52	3.340034	TGTTGTCCACTCACTCGTTTTT	58.660	40.909	0.00	0.00	0.00	1.94
52	53	3.372822	TGTTGTCCACTCACTCGTTTTTC	59.627	43.478	0.00	0.00	0.00	2.29
58	59	3.377172	CCACTCACTCGTTTTTCAAAGGT	59.623	43.478	0.00	0.00	0.00	3.50
70	71	3.980646	TTCAAAGGTCCAATCAACACG	57.019	42.857	0.00	0.00	0.00	4.49
107	108	1.499438	TCGAGTCCCCATAGATCCACT	59.501	52.381	0.00	0.00	0.00	4.00
122	123	0.183731	CCACTGCCTCCCTAAATCCC	59.816	60.000	0.00	0.00	0.00	3.85
123	124	0.179045	CACTGCCTCCCTAAATCCCG	60.179	60.000	0.00	0.00	0.00	5.14
132	133	1.352352	CCCTAAATCCCGCCATCTGAT	59.648	52.381	0.00	0.00	0.00	2.90
148	149	5.701750	CCATCTGATCCACATCTCTCAAATC	59.298	44.000	0.00	0.00	0.00	2.17
154	155	2.092538	CCACATCTCTCAAATCAGGCCT	60.093	50.000	0.00	0.00	0.00	5.19
161	162	2.756760	TCTCAAATCAGGCCTCATTTGC	59.243	45.455	31.15	0.00	39.08	3.68
172	173	2.697751	GCCTCATTTGCTCCTCTCTCTA	59.302	50.000	0.00	0.00	0.00	2.43
174	175	3.960102	CCTCATTTGCTCCTCTCTCTAGT	59.040	47.826	0.00	0.00	0.00	2.57
181	182	3.118186	TGCTCCTCTCTCTAGTACCTCAC	60.118	52.174	0.00	0.00	0.00	3.51
191	192	6.722328	TCTCTAGTACCTCACTGAAATCTCA	58.278	40.000	0.00	0.00	38.24	3.27
193	194	7.338196	TCTCTAGTACCTCACTGAAATCTCAAG	59.662	40.741	0.00	0.00	38.24	3.02
205	206	5.129634	TGAAATCTCAAGTACAAAGCCACA	58.870	37.500	0.00	0.00	0.00	4.17
206	207	5.769662	TGAAATCTCAAGTACAAAGCCACAT	59.230	36.000	0.00	0.00	0.00	3.21
223	224	4.625324	GCCACATAAGTGTAGATTCACCCA	60.625	45.833	0.00	0.00	44.39	4.51
230	231	3.695060	AGTGTAGATTCACCCAGTAGTCG	59.305	47.826	0.00	0.00	38.91	4.18

Showing 1 to 25 of 409 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	2.435059	GAGTCGGGCTTGACAGGC	60.435	66.667	0.00	0.00	45.20	4.85
17	18	3.184581	GTGGACAACAATTCTGTCGAGTC	59.815	47.826	9.89	0.00	43.45	3.36
26	27	3.131396	ACGAGTGAGTGGACAACAATTC	58.869	45.455	0.00	0.00	0.00	2.17
33	34	3.254470	TGAAAAACGAGTGAGTGGACA	57.746	42.857	0.00	0.00	0.00	4.02
35	36	3.625764	CCTTTGAAAAACGAGTGAGTGGA	59.374	43.478	0.00	0.00	0.00	4.02
39	40	3.625764	TGGACCTTTGAAAAACGAGTGAG	59.374	43.478	0.00	0.00	0.00	3.51
46	47	5.005299	CGTGTTGATTGGACCTTTGAAAAAC	59.995	40.000	0.00	0.00	0.00	2.43
51	52	3.201353	TCGTGTTGATTGGACCTTTGA	57.799	42.857	0.00	0.00	0.00	2.69
52	53	3.980646	TTCGTGTTGATTGGACCTTTG	57.019	42.857	0.00	0.00	0.00	2.77
95	96	0.689623	GGGAGGCAGTGGATCTATGG	59.310	60.000	0.00	0.00	0.00	2.74
107	108	2.752807	GGCGGGATTTAGGGAGGCA	61.753	63.158	0.00	0.00	0.00	4.75
122	123	1.343789	AGAGATGTGGATCAGATGGCG	59.656	52.381	0.00	0.00	0.00	5.69
123	124	2.367894	TGAGAGATGTGGATCAGATGGC	59.632	50.000	0.00	0.00	0.00	4.40
132	133	2.092753	GGCCTGATTTGAGAGATGTGGA	60.093	50.000	0.00	0.00	0.00	4.02
148	149	0.255318	AGAGGAGCAAATGAGGCCTG	59.745	55.000	12.00	0.00	0.00	4.85
154	155	4.890581	GGTACTAGAGAGAGGAGCAAATGA	59.109	45.833	0.00	0.00	0.00	2.57
161	162	4.407621	TCAGTGAGGTACTAGAGAGAGGAG	59.592	50.000	0.00	0.00	41.55	3.69
172	173	6.493802	TGTACTTGAGATTTCAGTGAGGTACT	59.506	38.462	0.00	0.00	41.36	2.73
174	175	6.911250	TGTACTTGAGATTTCAGTGAGGTA	57.089	37.500	0.00	0.00	34.15	3.08
181	182	5.239306	TGTGGCTTTGTACTTGAGATTTCAG	59.761	40.000	0.00	0.00	34.15	3.02
205	206	6.039493	CGACTACTGGGTGAATCTACACTTAT	59.961	42.308	0.00	0.00	40.22	1.73
206	207	5.356190	CGACTACTGGGTGAATCTACACTTA	59.644	44.000	0.00	0.00	40.22	2.24
230	231	3.070018	CAGATTTGGGATACGATGGCTC	58.930	50.000	0.00	0.00	37.60	4.70
240	241	0.034186	TTCGGCAGCAGATTTGGGAT	60.034	50.000	0.00	0.00	0.00	3.85
275	276	5.221986	TGGATATTGACATGCTTCTATGGCT	60.222	40.000	0.00	0.00	36.99	4.75

Showing 1 to 25 of 376 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.