AutoCloner

Multiple sequence alignment - TraesCS5A01G025800

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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	TraesCS5A01G025800	chr5A	100.000	2624	0	0	1	2624	20821571	20824194	0.000000e+00	4846
1	TraesCS5A01G025800	chr5D	93.826	1976	71	25	1	1951	32155980	32157929	0.000000e+00	2926
2	TraesCS5A01G025800	chr5D	88.333	720	48	16	1939	2624	432005952	432006669	0.000000e+00	832
3	TraesCS5A01G025800	chr5D	86.561	253	20	9	1940	2179	461905447	461905698	1.550000e-67	267
4	TraesCS5A01G025800	chr5D	85.771	253	23	5	1944	2185	118825609	118825859	3.350000e-64	255
5	TraesCS5A01G025800	chr5B	93.869	1941	72	21	1	1915	23891090	23893009	0.000000e+00	2881
6	TraesCS5A01G025800	chr1D	89.152	719	33	13	1949	2624	463250902	463250186	0.000000e+00	854
7	TraesCS5A01G025800	chr1D	85.878	262	21	9	1942	2189	9004352	9004093	5.570000e-67	265
8	TraesCS5A01G025800	chr6D	88.997	718	35	14	1949	2624	449815434	449814719	0.000000e+00	848
9	TraesCS5A01G025800	chr6D	83.426	718	69	22	1948	2624	309344090	309344798	2.870000e-174	621
10	TraesCS5A01G025800	chr6D	82.993	735	57	33	1931	2624	14163577	14164284	1.040000e-168	603
11	TraesCS5A01G025800	chr4D	88.982	717	36	10	1949	2624	35123713	35124427	0.000000e+00	846
12	TraesCS5A01G025800	chr4D	88.235	731	40	13	1936	2624	364025887	364026613	0.000000e+00	832
13	TraesCS5A01G025800	chr4D	81.918	365	24	15	1949	2272	319985803	319985440	1.200000e-68	270
14	TraesCS5A01G025800	chr1A	88.873	719	36	17	1948	2624	502503131	502502415	0.000000e+00	845
15	TraesCS5A01G025800	chr3D	88.456	719	37	14	1947	2624	606545768	606545055	0.000000e+00	826
16	TraesCS5A01G025800	chr3D	87.983	699	63	13	1942	2622	159430170	159430865	0.000000e+00	806
17	TraesCS5A01G025800	chr3D	87.649	251	19	4	1946	2185	597182186	597182435	5.530000e-72	281
18	TraesCS5A01G025800	chr3D	86.345	249	21	4	1948	2185	11327328	11327082	2.590000e-65	259
19	TraesCS5A01G025800	chr3D	85.944	249	22	5	1949	2185	402303011	402303258	1.210000e-63	254
20	TraesCS5A01G025800	chr7D	88.301	718	37	21	1948	2624	481608936	481609647	0.000000e+00	817
21	TraesCS5A01G025800	chr7D	80.192	520	57	22	1940	2418	628765247	628764733	5.380000e-92	348
22	TraesCS5A01G025800	chr7D	85.057	261	24	7	1939	2185	560574806	560575065	4.340000e-63	252
23	TraesCS5A01G025800	chr7A	95.111	450	21	1	2175	2624	428824423	428824871	0.000000e+00	708
24	TraesCS5A01G025800	chr2D	95.495	444	19	1	2181	2624	493076632	493077074	0.000000e+00	708
25	TraesCS5A01G025800	chrUn	89.157	249	16	3	1948	2185	45208432	45208184	1.530000e-77	300
26	TraesCS5A01G025800	chr2A	88.095	252	19	3	1938	2179	670467096	670467346	3.300000e-74	289
27	TraesCS5A01G025800	chr2A	85.932	263	22	7	1936	2185	136643345	136643085	1.550000e-67	267

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	TraesCS5A01G025800	chr5A	20821571	20824194	2623	False	4846	4846	100.000	1	2624	1	chr5A.!!$F1	2623
1	TraesCS5A01G025800	chr5D	32155980	32157929	1949	False	2926	2926	93.826	1	1951	1	chr5D.!!$F1	1950
2	TraesCS5A01G025800	chr5D	432005952	432006669	717	False	832	832	88.333	1939	2624	1	chr5D.!!$F3	685
3	TraesCS5A01G025800	chr5B	23891090	23893009	1919	False	2881	2881	93.869	1	1915	1	chr5B.!!$F1	1914
4	TraesCS5A01G025800	chr1D	463250186	463250902	716	True	854	854	89.152	1949	2624	1	chr1D.!!$R2	675
5	TraesCS5A01G025800	chr6D	449814719	449815434	715	True	848	848	88.997	1949	2624	1	chr6D.!!$R1	675
6	TraesCS5A01G025800	chr6D	309344090	309344798	708	False	621	621	83.426	1948	2624	1	chr6D.!!$F2	676
7	TraesCS5A01G025800	chr6D	14163577	14164284	707	False	603	603	82.993	1931	2624	1	chr6D.!!$F1	693
8	TraesCS5A01G025800	chr4D	35123713	35124427	714	False	846	846	88.982	1949	2624	1	chr4D.!!$F1	675
9	TraesCS5A01G025800	chr4D	364025887	364026613	726	False	832	832	88.235	1936	2624	1	chr4D.!!$F2	688
10	TraesCS5A01G025800	chr1A	502502415	502503131	716	True	845	845	88.873	1948	2624	1	chr1A.!!$R1	676
11	TraesCS5A01G025800	chr3D	606545055	606545768	713	True	826	826	88.456	1947	2624	1	chr3D.!!$R2	677
12	TraesCS5A01G025800	chr3D	159430170	159430865	695	False	806	806	87.983	1942	2622	1	chr3D.!!$F1	680
13	TraesCS5A01G025800	chr7D	481608936	481609647	711	False	817	817	88.301	1948	2624	1	chr7D.!!$F1	676
14	TraesCS5A01G025800	chr7D	628764733	628765247	514	True	348	348	80.192	1940	2418	1	chr7D.!!$R1	478

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
339	352	0.392461	ACCGACCAATCAACCATCCG	60.392	55.0	0.0	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2123	2169	0.324923	TACCAGGCCTGACATACGGT	60.325	55.0	34.91	22.9	0.0	4.83	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
271	272	2.280797	TGTCCTTCTGCACGCACC	60.281	61.111	0.00	0.00	0.00	5.01
272	273	3.414700	GTCCTTCTGCACGCACCG	61.415	66.667	0.00	0.00	0.00	4.94
273	274	4.680237	TCCTTCTGCACGCACCGG	62.680	66.667	0.00	0.00	0.00	5.28
312	325	2.190170	AAACACAACGCCGGCATCA	61.190	52.632	28.98	0.00	0.00	3.07
331	344	0.756294	ACTCACACACCGACCAATCA	59.244	50.000	0.00	0.00	0.00	2.57
334	347	0.591170	CACACACCGACCAATCAACC	59.409	55.000	0.00	0.00	0.00	3.77
336	349	1.202879	ACACACCGACCAATCAACCAT	60.203	47.619	0.00	0.00	0.00	3.55
339	352	0.392461	ACCGACCAATCAACCATCCG	60.392	55.000	0.00	0.00	0.00	4.18
342	355	1.714899	GACCAATCAACCATCCGGCG	61.715	60.000	0.00	0.00	34.57	6.46
433	446	3.434454	GAGGATCCTCCGTCGTCC	58.566	66.667	28.84	3.71	42.75	4.79
474	490	2.571212	CCCTCGCATTAAACTATGGCA	58.429	47.619	0.00	0.00	0.00	4.92
492	508	2.114670	AGCAATGGATGGCGAACCG	61.115	57.895	0.00	0.00	39.70	4.44
493	509	2.112198	GCAATGGATGGCGAACCGA	61.112	57.895	0.00	0.00	39.70	4.69
530	546	1.226688	CGCGCTCTCTCATTTCGGA	60.227	57.895	5.56	0.00	0.00	4.55
534	550	1.535015	CGCTCTCTCATTTCGGAGGAC	60.535	57.143	0.00	0.00	35.58	3.85
585	601	1.265905	GAATTTATAAGTGCCGCGGGG	59.734	52.381	29.38	15.40	0.00	5.73
837	861	1.866237	GCTCCGTGCGAACATTCAA	59.134	52.632	0.00	0.00	0.00	2.69
845	869	0.863119	GCGAACATTCAAGGCGATGC	60.863	55.000	0.00	0.00	0.00	3.91
927	951	2.947621	CGCGCGCGTATGTACACT	60.948	61.111	42.49	0.00	34.35	3.55
928	952	2.502123	CGCGCGCGTATGTACACTT	61.502	57.895	42.49	0.00	34.35	3.16
929	953	1.268946	GCGCGCGTATGTACACTTC	59.731	57.895	32.35	5.70	0.00	3.01
930	954	1.138047	GCGCGCGTATGTACACTTCT	61.138	55.000	32.35	0.00	0.00	2.85
931	955	1.857204	GCGCGCGTATGTACACTTCTA	60.857	52.381	32.35	0.00	0.00	2.10
932	956	1.771848	CGCGCGTATGTACACTTCTAC	59.228	52.381	24.19	0.00	0.00	2.59
933	957	2.114825	GCGCGTATGTACACTTCTACC	58.885	52.381	8.43	0.00	0.00	3.18
934	958	2.369600	CGCGTATGTACACTTCTACCG	58.630	52.381	0.00	0.00	0.00	4.02
970	994	1.443194	CGATCGGTTCACGTCCGTT	60.443	57.895	7.38	5.83	46.86	4.44
973	997	0.665369	ATCGGTTCACGTCCGTTGAC	60.665	55.000	13.17	0.00	46.86	3.18
996	1028	2.186125	GCTGGGGCGTAGGTGTAC	59.814	66.667	0.00	0.00	0.00	2.90
1467	1502	0.972983	TGAAGGCGGAGGAGGAAGAG	60.973	60.000	0.00	0.00	0.00	2.85
1468	1503	1.681486	GAAGGCGGAGGAGGAAGAGG	61.681	65.000	0.00	0.00	0.00	3.69
1469	1504	3.855853	GGCGGAGGAGGAAGAGGC	61.856	72.222	0.00	0.00	0.00	4.70
1711	1746	1.219393	CCTTCTTGGGCGGAGAGAC	59.781	63.158	0.00	0.00	0.00	3.36
1726	1761	3.394719	GAGAGACACCAAACTCCACTTC	58.605	50.000	0.00	0.00	34.13	3.01
1859	1899	6.588373	GGAAAAATTACATAAACACGGTGCAT	59.412	34.615	8.30	0.00	0.00	3.96
1871	1912	1.339247	ACGGTGCATCGTTCCCAAATA	60.339	47.619	21.54	0.00	40.85	1.40
1872	1913	1.740585	CGGTGCATCGTTCCCAAATAA	59.259	47.619	12.24	0.00	0.00	1.40
1960	2002	8.836268	ATACATAAATAAAGGACGCCGATAAA	57.164	30.769	0.00	0.00	0.00	1.40
1974	2016	1.790123	CGATAAATGCCACACGTGTGC	60.790	52.381	37.33	31.00	44.34	4.57
2024	2066	4.836175	TGTGTGGTGTATAAGAGGAACAGA	59.164	41.667	0.00	0.00	0.00	3.41
2030	2072	5.411781	GTGTATAAGAGGAACAGACCACAG	58.588	45.833	0.00	0.00	0.00	3.66
2033	2075	2.390225	AGAGGAACAGACCACAGACT	57.610	50.000	0.00	0.00	0.00	3.24
2123	2169	3.191669	CGTGTGGGCGAAATAGATAACA	58.808	45.455	0.00	0.00	0.00	2.41
2139	2195	0.036388	AACACCGTATGTCAGGCCTG	60.036	55.000	27.87	27.87	42.31	4.85
2201	2286	2.720590	CGTCCATGTTCGTTTAACTGCG	60.721	50.000	0.00	0.00	38.99	5.18
2272	2357	1.024271	TGGTTGCTCAACTGCAGTTC	58.976	50.000	28.97	18.25	44.27	3.01
2286	2371	4.711846	ACTGCAGTTCTCATGTATGGTCTA	59.288	41.667	15.25	0.00	0.00	2.59
2384	2475	5.735922	GCACTACAAGAAGGCATGACAAAAA	60.736	40.000	0.00	0.00	0.00	1.94
2524	2616	2.983229	TGCAAAAACACATGGCAACTT	58.017	38.095	0.00	0.00	37.61	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
105	106	3.573772	CTCGCACGAGCTCAACCCA	62.574	63.158	15.40	0.00	39.10	4.51
312	325	0.756294	TGATTGGTCGGTGTGTGAGT	59.244	50.000	0.00	0.00	0.00	3.41
331	344	1.006102	GATCGATCGCCGGATGGTT	60.006	57.895	11.09	0.00	39.14	3.67
342	355	1.200484	GGAGGTAAGGCTCGATCGATC	59.800	57.143	19.78	14.83	0.00	3.69
350	363	2.968574	TGAGATCATGGAGGTAAGGCTC	59.031	50.000	0.00	0.00	0.00	4.70
474	490	2.114670	CGGTTCGCCATCCATTGCT	61.115	57.895	0.00	0.00	37.00	3.91
510	526	2.160853	CGAAATGAGAGAGCGCGCA	61.161	57.895	35.10	12.17	0.00	6.09
521	537	1.879737	TTCGCCGTCCTCCGAAATGA	61.880	55.000	0.00	0.00	40.11	2.57
530	546	2.032071	CCTGGTTTTCGCCGTCCT	59.968	61.111	0.00	0.00	0.00	3.85
534	550	2.943653	GTGTCCTGGTTTTCGCCG	59.056	61.111	0.00	0.00	0.00	6.46
744	763	1.535202	AGATCGGAGATGGGAGGCC	60.535	63.158	0.00	0.00	45.12	5.19
845	869	1.373497	AAAGTCTCCGCTGCGACAG	60.373	57.895	25.45	18.14	32.68	3.51
916	940	5.227238	AGAACGGTAGAAGTGTACATACG	57.773	43.478	0.00	0.00	0.00	3.06
919	943	5.227238	CGTAGAACGGTAGAAGTGTACAT	57.773	43.478	0.00	0.00	38.08	2.29
1260	1295	2.507102	ACGGCGAGCTCAATCACG	60.507	61.111	16.62	12.08	0.00	4.35
1611	1646	1.702299	GAGCGATCACCACGTTTCG	59.298	57.895	0.00	0.00	34.83	3.46
1711	1746	7.254421	GCAAAATTAAAGAAGTGGAGTTTGGTG	60.254	37.037	0.00	0.00	0.00	4.17
1726	1761	6.463576	ACGCTACGTTAATCGCAAAATTAAAG	59.536	34.615	0.00	7.26	44.19	1.85
1859	1899	3.991773	CGAGAACACTTATTTGGGAACGA	59.008	43.478	0.00	0.00	0.00	3.85
1994	2036	7.681679	TCCTCTTATACACCACACAAAATGTA	58.318	34.615	0.00	0.00	40.64	2.29
2051	2094	2.200373	AAGAGGTGTGTGGGCATTAC	57.800	50.000	0.00	0.00	0.00	1.89
2123	2169	0.324923	TACCAGGCCTGACATACGGT	60.325	55.000	34.91	22.90	0.00	4.83
2169	2225	0.821517	ACATGGACGAGCGGTGAATA	59.178	50.000	0.00	0.00	0.00	1.75
2171	2227	0.669318	GAACATGGACGAGCGGTGAA	60.669	55.000	0.00	0.00	0.00	3.18
2201	2286	1.210155	GTTCAGCGACATGGCAACC	59.790	57.895	0.00	0.00	34.64	3.77
2272	2357	6.986250	TGCAGTAGATTAGACCATACATGAG	58.014	40.000	0.00	0.00	0.00	2.90
2286	2371	3.354948	TCATGGCAACTGCAGTAGATT	57.645	42.857	22.01	0.19	44.36	2.40
2356	2441	3.515502	TCATGCCTTCTTGTAGTGCTACT	59.484	43.478	10.28	0.00	37.00	2.57
2386	2477	8.897752	GCAACTCTCTCTTTTATCCAAACATAT	58.102	33.333	0.00	0.00	0.00	1.78
2393	2484	4.908601	TGGCAACTCTCTCTTTTATCCA	57.091	40.909	0.00	0.00	37.61	3.41
2463	2555	1.351430	GCGTGCACGTAAGCAGATGA	61.351	55.000	36.80	0.00	46.69	2.92
2524	2616	3.826157	CAGATGGCAACTCTTTTTACCCA	59.174	43.478	0.00	0.00	37.61	4.51
2563	2659	2.917933	GCAGGTATATGACAACTGCCA	58.082	47.619	3.02	0.00	46.47	4.92

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.