AutoCloner

Multiple sequence alignment - TraesCS2B01G257900

Loading Multiple Alignment...

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	TraesCS2B01G257900	chr2B	100.000	2243	0	0	1	2243	311333678	311335920	0.000000e+00	4143.0
1	TraesCS2B01G257900	chr2B	89.697	165	14	3	599	761	220962432	220962595	8.120000e-50	207.0
2	TraesCS2B01G257900	chr2B	100.000	41	0	0	802	842	220962970	220963010	2.390000e-10	76.8
3	TraesCS2B01G257900	chr7B	92.862	1513	102	4	735	2243	253264612	253263102	0.000000e+00	2191.0
4	TraesCS2B01G257900	chr7B	93.019	616	39	3	1	614	354695434	354694821	0.000000e+00	896.0
5	TraesCS2B01G257900	chr7B	88.721	727	53	14	838	1536	663107679	663108404	0.000000e+00	861.0
6	TraesCS2B01G257900	chr7B	86.364	198	21	4	1602	1795	263791538	263791343	6.280000e-51	211.0
7	TraesCS2B01G257900	chr4B	92.563	1479	103	4	769	2243	141079996	141081471	0.000000e+00	2115.0
8	TraesCS2B01G257900	chr4B	93.042	618	39	3	1	616	161395611	161396226	0.000000e+00	900.0
9	TraesCS2B01G257900	chr4B	88.066	729	68	13	3	722	298705904	298705186	0.000000e+00	846.0
10	TraesCS2B01G257900	chr4B	92.758	359	20	4	1891	2243	621660522	621660880	4.270000e-142	514.0
11	TraesCS2B01G257900	chr7D	91.712	929	70	5	743	1668	354527320	354528244	0.000000e+00	1282.0
12	TraesCS2B01G257900	chr7D	90.948	928	78	4	744	1668	195395540	195396464	0.000000e+00	1243.0
13	TraesCS2B01G257900	chr7D	90.944	773	56	2	769	1541	346185041	346184283	0.000000e+00	1027.0
14	TraesCS2B01G257900	chr7D	88.547	716	54	17	841	1536	588678986	588678279	0.000000e+00	843.0
15	TraesCS2B01G257900	chr7D	92.593	540	32	4	1710	2243	195396466	195397003	0.000000e+00	769.0
16	TraesCS2B01G257900	chr7D	92.015	551	36	4	1700	2243	346184185	346183636	0.000000e+00	767.0
17	TraesCS2B01G257900	chr7D	90.942	552	37	8	1700	2243	354528244	354528790	0.000000e+00	730.0
18	TraesCS2B01G257900	chr6B	94.728	607	29	2	1	605	51088087	51088692	0.000000e+00	941.0
19	TraesCS2B01G257900	chr6B	94.069	607	30	5	1	605	217771812	217771210	0.000000e+00	917.0
20	TraesCS2B01G257900	chr1B	93.193	617	40	2	1	616	484050596	484051211	0.000000e+00	905.0
21	TraesCS2B01G257900	chr1B	93.593	359	17	5	1891	2243	30060643	30061001	4.240000e-147	531.0
22	TraesCS2B01G257900	chr1B	86.378	323	39	2	1541	1858	280435876	280436198	4.580000e-92	348.0
23	TraesCS2B01G257900	chr4A	93.042	618	39	3	1	616	700409024	700408409	0.000000e+00	900.0
24	TraesCS2B01G257900	chr2A	91.796	646	45	6	1	642	451945124	451944483	0.000000e+00	893.0
25	TraesCS2B01G257900	chr2A	91.026	156	12	2	607	761	235806333	235806487	2.260000e-50	209.0
26	TraesCS2B01G257900	chr3B	92.903	620	33	10	1	616	598451544	598450932	0.000000e+00	891.0
27	TraesCS2B01G257900	chr3B	92.479	359	21	4	1891	2243	658959599	658959957	1.990000e-140	508.0
28	TraesCS2B01G257900	chr3B	91.944	360	21	5	1891	2243	383919956	383920314	4.300000e-137	497.0
29	TraesCS2B01G257900	chr3B	95.122	41	2	0	802	842	556457111	556457151	5.170000e-07	65.8
30	TraesCS2B01G257900	chr7A	85.097	718	67	19	851	1536	680406665	680407374	0.000000e+00	697.0
31	TraesCS2B01G257900	chr7A	86.293	321	39	3	1543	1860	238546879	238547197	5.930000e-91	344.0
32	TraesCS2B01G257900	chr5B	86.704	361	36	8	1544	1894	308024175	308023817	7.510000e-105	390.0
33	TraesCS2B01G257900	chr5B	92.683	41	3	0	802	842	380598298	380598338	2.410000e-05	60.2
34	TraesCS2B01G257900	chr4D	92.825	223	12	2	1700	1919	35645001	35644780	9.990000e-84	320.0
35	TraesCS2B01G257900	chr4D	94.702	151	8	0	605	755	310939806	310939656	3.720000e-58	235.0
36	TraesCS2B01G257900	chr4D	94.118	153	8	1	603	755	384432246	384432397	4.820000e-57	231.0
37	TraesCS2B01G257900	chr4D	93.836	146	9	0	610	755	153518863	153518718	1.040000e-53	220.0
38	TraesCS2B01G257900	chr1A	94.040	151	7	2	605	755	273196596	273196448	6.230000e-56	228.0
39	TraesCS2B01G257900	chr2D	93.878	147	9	0	609	755	295070438	295070292	2.900000e-54	222.0
40	TraesCS2B01G257900	chr3D	92.763	152	10	1	605	755	368369480	368369329	3.750000e-53	219.0
41	TraesCS2B01G257900	chr6A	80.259	309	40	13	1543	1839	416958135	416957836	1.740000e-51	213.0

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	TraesCS2B01G257900	chr2B	311333678	311335920	2242	False	4143	4143	100.0000	1	2243	1	chr2B.!!$F1	2242
1	TraesCS2B01G257900	chr7B	253263102	253264612	1510	True	2191	2191	92.8620	735	2243	1	chr7B.!!$R1	1508
2	TraesCS2B01G257900	chr7B	354694821	354695434	613	True	896	896	93.0190	1	614	1	chr7B.!!$R3	613
3	TraesCS2B01G257900	chr7B	663107679	663108404	725	False	861	861	88.7210	838	1536	1	chr7B.!!$F1	698
4	TraesCS2B01G257900	chr4B	141079996	141081471	1475	False	2115	2115	92.5630	769	2243	1	chr4B.!!$F1	1474
5	TraesCS2B01G257900	chr4B	161395611	161396226	615	False	900	900	93.0420	1	616	1	chr4B.!!$F2	615
6	TraesCS2B01G257900	chr4B	298705186	298705904	718	True	846	846	88.0660	3	722	1	chr4B.!!$R1	719
7	TraesCS2B01G257900	chr7D	195395540	195397003	1463	False	1006	1243	91.7705	744	2243	2	chr7D.!!$F1	1499
8	TraesCS2B01G257900	chr7D	354527320	354528790	1470	False	1006	1282	91.3270	743	2243	2	chr7D.!!$F2	1500
9	TraesCS2B01G257900	chr7D	346183636	346185041	1405	True	897	1027	91.4795	769	2243	2	chr7D.!!$R2	1474
10	TraesCS2B01G257900	chr7D	588678279	588678986	707	True	843	843	88.5470	841	1536	1	chr7D.!!$R1	695
11	TraesCS2B01G257900	chr6B	51088087	51088692	605	False	941	941	94.7280	1	605	1	chr6B.!!$F1	604
12	TraesCS2B01G257900	chr6B	217771210	217771812	602	True	917	917	94.0690	1	605	1	chr6B.!!$R1	604
13	TraesCS2B01G257900	chr1B	484050596	484051211	615	False	905	905	93.1930	1	616	1	chr1B.!!$F3	615
14	TraesCS2B01G257900	chr4A	700408409	700409024	615	True	900	900	93.0420	1	616	1	chr4A.!!$R1	615
15	TraesCS2B01G257900	chr2A	451944483	451945124	641	True	893	893	91.7960	1	642	1	chr2A.!!$R1	641
16	TraesCS2B01G257900	chr3B	598450932	598451544	612	True	891	891	92.9030	1	616	1	chr3B.!!$R1	615
17	TraesCS2B01G257900	chr7A	680406665	680407374	709	False	697	697	85.0970	851	1536	1	chr7A.!!$F2	685

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
285	288	0.038892	AAAAATGCTCGCTGCCACTG	60.039	50.0	0.0	0.0	42.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1662	1742	0.032678	ACTGCCAGACTGAAGACACG	59.967	55.0	3.32	0.0	0.0	4.49	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
35	36	0.675083	TGTCCGTAGCTTTCCAACGA	59.325	50.000	7.53	0.00	38.89	3.85
37	38	2.289195	TGTCCGTAGCTTTCCAACGATT	60.289	45.455	7.53	0.00	38.89	3.34
38	39	2.093783	GTCCGTAGCTTTCCAACGATTG	59.906	50.000	7.53	0.00	38.89	2.67
39	40	1.202031	CCGTAGCTTTCCAACGATTGC	60.202	52.381	7.53	0.00	38.89	3.56
40	41	1.463056	CGTAGCTTTCCAACGATTGCA	59.537	47.619	0.00	0.00	38.89	4.08
202	204	4.825546	ATATGAAAAAGATGCGCCTCAG	57.174	40.909	15.26	0.00	0.00	3.35
285	288	0.038892	AAAAATGCTCGCTGCCACTG	60.039	50.000	0.00	0.00	42.00	3.66
354	357	5.155509	TCTCGAAAAGTGTTCAACATGTG	57.844	39.130	0.00	0.00	0.00	3.21
375	378	4.947388	GTGGAAGTTGCACCTAATCCATAA	59.053	41.667	16.06	0.00	39.02	1.90
636	643	4.857130	AGGGTGGGACTATTTAGAAACC	57.143	45.455	0.00	0.00	0.00	3.27
637	644	3.526430	AGGGTGGGACTATTTAGAAACCC	59.474	47.826	0.00	0.00	45.32	4.11
660	667	5.012251	CCCCCTCTAGAGTTCCTAAATAAGC	59.988	48.000	18.42	0.00	0.00	3.09
680	687	2.243994	GCTTATTTAGGAACCACCCCCT	59.756	50.000	0.00	0.00	40.05	4.79
681	688	3.687551	GCTTATTTAGGAACCACCCCCTC	60.688	52.174	0.00	0.00	40.05	4.30
684	691	1.103811	TTAGGAACCACCCCCTCCTA	58.896	55.000	0.00	0.00	40.20	2.94
700	709	4.202577	CCCTCCTAACCTGTTTCTTTTCCT	60.203	45.833	0.00	0.00	0.00	3.36
717	726	0.108424	CCTGAAGGAAGTGAGCGAGG	60.108	60.000	0.00	0.00	37.39	4.63
722	731	2.202676	GAAGTGAGCGAGGGAGCG	60.203	66.667	0.00	0.00	43.00	5.03
723	732	2.676822	AAGTGAGCGAGGGAGCGA	60.677	61.111	0.00	0.00	43.00	4.93
724	733	2.606155	GAAGTGAGCGAGGGAGCGAG	62.606	65.000	0.00	0.00	43.00	5.03
725	734	4.863925	GTGAGCGAGGGAGCGAGC	62.864	72.222	0.00	0.00	43.00	5.03
749	758	2.572284	GTAGCGACGCAAGGGAGT	59.428	61.111	23.70	1.14	46.39	3.85
881	890	3.415212	CCGCATATCCATCCATCTTGTT	58.585	45.455	0.00	0.00	0.00	2.83
892	913	2.040278	TCCATCTTGTTGGCTTGTAGCT	59.960	45.455	0.00	0.00	41.99	3.32
911	940	2.419297	GCTAGCCAAGAAAGCAGAGCTA	60.419	50.000	2.29	0.00	38.25	3.32
924	953	4.113617	AGCTACGCTCCTGACCAA	57.886	55.556	0.00	0.00	30.62	3.67
932	966	0.178990	GCTCCTGACCAACACCCTTT	60.179	55.000	0.00	0.00	0.00	3.11
985	1031	1.364171	GACATGGAGGGATCGTCGG	59.636	63.158	0.00	0.00	0.00	4.79
1089	1135	2.032071	CAAAAGGCGTCGGGGAGT	59.968	61.111	0.00	0.00	0.00	3.85
1169	1215	4.834453	CCTGCCGCTCTGCCTCAG	62.834	72.222	0.00	0.00	0.00	3.35
1243	1289	0.537188	CGCCATTGTCCAGGACTAGT	59.463	55.000	20.82	0.00	33.15	2.57
1294	1345	5.736616	ACTATTTCATTCTCCTACCCCCTTT	59.263	40.000	0.00	0.00	0.00	3.11
1299	1350	4.853276	TCATTCTCCTACCCCCTTTGTTTA	59.147	41.667	0.00	0.00	0.00	2.01
1305	1356	6.046286	TCTCCTACCCCCTTTGTTTAATTCTT	59.954	38.462	0.00	0.00	0.00	2.52
1319	1370	9.912634	TTGTTTAATTCTTTGGAGATTGATCAC	57.087	29.630	0.00	0.00	0.00	3.06
1359	1410	5.348986	GTTAGATGCCAGATCGAACAACTA	58.651	41.667	0.00	0.00	34.96	2.24
1404	1455	3.284449	GTTGCTTTCCGTGCCCGT	61.284	61.111	0.00	0.00	0.00	5.28
1493	1562	2.826128	TCGTGAGTTTCAGTCTGGCTAT	59.174	45.455	0.00	0.00	0.00	2.97
1581	1661	4.113354	CTCCTAGCAATTAACTCGGTGTC	58.887	47.826	0.00	0.00	0.00	3.67
1707	1819	2.710377	TGATGTTAACTGCCGCAATCT	58.290	42.857	7.22	0.00	0.00	2.40
1708	1820	3.081061	TGATGTTAACTGCCGCAATCTT	58.919	40.909	7.22	0.00	0.00	2.40
1718	1830	1.299541	CCGCAATCTTCGGCAGTTAT	58.700	50.000	0.00	0.00	40.46	1.89
1734	1846	4.443034	GCAGTTATCTATTTCAGTCCCGGT	60.443	45.833	0.00	0.00	0.00	5.28
1762	1877	6.512415	GCCTGATCTAGTCGAAAAATGAATGG	60.512	42.308	0.00	0.00	0.00	3.16
1812	1930	4.899502	AGTTAGCTTGCTCAACATAGTGT	58.100	39.130	0.00	0.00	0.00	3.55
1841	1959	3.678056	ATTCTGCTCGAACAGTTACCA	57.322	42.857	15.10	0.00	38.84	3.25
1985	2104	6.048509	AGTGGATTCACAAACACAAAAATCC	58.951	36.000	6.96	5.23	45.91	3.01
2017	2136	1.765904	TGTGTGTGGAAGTTAGCAGGA	59.234	47.619	0.00	0.00	0.00	3.86
2220	2345	9.461312	AGGAAGTTAACATCATAATTTACAGCA	57.539	29.630	12.51	0.00	0.00	4.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	68	3.769536	ACTGTTTTTGCTCCAGTTTTCG	58.230	40.909	0.00	0.00	36.03	3.46
202	204	1.269166	CGCCGTTGGATAGATATCGC	58.731	55.000	0.00	0.00	33.52	4.58
285	288	4.820744	ATGGTGCGGCCCATGACC	62.821	66.667	18.34	10.17	43.65	4.02
354	357	5.193679	AGTTATGGATTAGGTGCAACTTCC	58.806	41.667	10.94	13.21	36.74	3.46
375	378	5.063817	GGCGTGTAATATACCGTTGAAAAGT	59.936	40.000	0.00	0.00	0.00	2.66
636	643	5.012251	GCTTATTTAGGAACTCTAGAGGGGG	59.988	48.000	23.50	0.00	41.75	5.40
637	644	5.841783	AGCTTATTTAGGAACTCTAGAGGGG	59.158	44.000	23.50	0.00	41.75	4.79
660	667	3.117625	GGAGGGGGTGGTTCCTAAATAAG	60.118	52.174	0.00	0.00	36.25	1.73
666	673	1.103811	TTAGGAGGGGGTGGTTCCTA	58.896	55.000	0.00	0.00	41.46	2.94
669	676	0.549413	AGGTTAGGAGGGGGTGGTTC	60.549	60.000	0.00	0.00	0.00	3.62
680	687	5.640158	TCAGGAAAAGAAACAGGTTAGGA	57.360	39.130	0.00	0.00	0.00	2.94
681	688	5.241728	CCTTCAGGAAAAGAAACAGGTTAGG	59.758	44.000	0.00	0.00	37.39	2.69
684	691	4.867086	TCCTTCAGGAAAAGAAACAGGTT	58.133	39.130	0.00	0.00	42.18	3.50
700	709	0.541998	TCCCTCGCTCACTTCCTTCA	60.542	55.000	0.00	0.00	0.00	3.02
730	739	4.124351	TCCCTTGCGTCGCTACCG	62.124	66.667	19.50	3.77	0.00	4.02
731	740	2.202756	CTCCCTTGCGTCGCTACC	60.203	66.667	19.50	0.00	0.00	3.18
732	741	1.805945	CACTCCCTTGCGTCGCTAC	60.806	63.158	19.50	0.00	0.00	3.58
733	742	1.934220	CTCACTCCCTTGCGTCGCTA	61.934	60.000	19.50	10.26	0.00	4.26
734	743	3.288308	CTCACTCCCTTGCGTCGCT	62.288	63.158	19.50	0.00	0.00	4.93
735	744	2.811317	CTCACTCCCTTGCGTCGC	60.811	66.667	11.10	11.10	0.00	5.19
736	745	2.811317	GCTCACTCCCTTGCGTCG	60.811	66.667	0.00	0.00	0.00	5.12
737	746	2.811317	CGCTCACTCCCTTGCGTC	60.811	66.667	0.00	0.00	42.93	5.19
738	747	4.379243	CCGCTCACTCCCTTGCGT	62.379	66.667	0.00	0.00	45.90	5.24
892	913	2.417379	CGTAGCTCTGCTTTCTTGGCTA	60.417	50.000	0.00	0.00	40.44	3.93
911	940	2.426023	GGTGTTGGTCAGGAGCGT	59.574	61.111	0.00	0.00	0.00	5.07
924	953	1.665442	GCCGCAAATCAAAGGGTGT	59.335	52.632	0.00	0.00	0.00	4.16
950	986	1.160145	TCGACCCCTTCTTCCCCTT	59.840	57.895	0.00	0.00	0.00	3.95
1047	1093	1.554822	CCCACCACCTTCTCCTCCTTA	60.555	57.143	0.00	0.00	0.00	2.69
1122	1168	1.528309	CCACTTGGCCTCCACGTTT	60.528	57.895	3.32	0.00	33.65	3.60
1123	1169	2.113139	CCACTTGGCCTCCACGTT	59.887	61.111	3.32	0.00	33.65	3.99
1169	1215	2.556287	CGAACCTGCGCTTGTTCC	59.444	61.111	26.00	14.71	38.05	3.62
1286	1337	5.220521	TCCAAAGAATTAAACAAAGGGGGT	58.779	37.500	0.00	0.00	0.00	4.95
1294	1345	9.076781	TGTGATCAATCTCCAAAGAATTAAACA	57.923	29.630	0.00	0.00	34.49	2.83
1299	1350	7.668886	AGTTCTGTGATCAATCTCCAAAGAATT	59.331	33.333	0.00	0.00	34.49	2.17
1305	1356	5.488262	TCAGTTCTGTGATCAATCTCCAA	57.512	39.130	0.00	0.00	0.00	3.53
1319	1370	6.958193	GCATCTAACGAAAATCTTCAGTTCTG	59.042	38.462	0.00	0.00	33.45	3.02
1359	1410	2.544694	GGACGCACATCAATCGATCTCT	60.545	50.000	0.00	0.00	0.00	3.10
1404	1455	8.654094	TCAAGCAGATATCCAAATCAAGATCTA	58.346	33.333	0.00	0.00	0.00	1.98
1493	1562	5.594725	CCATCAGCTGTAGTAAGGAGAACTA	59.405	44.000	14.67	0.00	0.00	2.24
1581	1661	2.987547	CTGGGGCTGTGGCAGTTG	60.988	66.667	0.00	0.00	40.87	3.16
1600	1680	2.504175	TCGGGCCTGAAATAGCTAACTT	59.496	45.455	13.31	0.00	0.00	2.66
1662	1742	0.032678	ACTGCCAGACTGAAGACACG	59.967	55.000	3.32	0.00	0.00	4.49
1707	1819	5.357257	GGACTGAAATAGATAACTGCCGAA	58.643	41.667	0.00	0.00	0.00	4.30
1708	1820	4.202223	GGGACTGAAATAGATAACTGCCGA	60.202	45.833	0.00	0.00	0.00	5.54
1718	1830	2.037144	GCCTACCGGGACTGAAATAGA	58.963	52.381	6.32	0.00	37.23	1.98
1734	1846	5.362717	TCATTTTTCGACTAGATCAGGCCTA	59.637	40.000	3.98	0.00	0.00	3.93
1771	1889	2.236395	ACTACCGGAGCTGCAAATACTT	59.764	45.455	9.46	0.00	0.00	2.24
1812	1930	5.822278	CTGTTCGAGCAGAATAGCTAACTA	58.178	41.667	23.33	0.00	46.75	2.24
1841	1959	1.899814	TCCCGAACTGCAACAGTAGAT	59.100	47.619	0.00	0.00	44.62	1.98
1850	1968	1.207089	CCTATCACTTCCCGAACTGCA	59.793	52.381	0.00	0.00	0.00	4.41
1985	2104	4.808414	TCCACACACAAAGATAGAGAGG	57.192	45.455	0.00	0.00	0.00	3.69
2017	2136	3.876309	TTTCCTAACTGTTGGCCTCTT	57.124	42.857	3.32	0.00	0.00	2.85
2082	2202	5.675684	AACCCTGTGAAAATTGAAACACT	57.324	34.783	0.00	0.00	34.81	3.55
2094	2214	6.098124	ACTGATGAATTTTCAAACCCTGTGAA	59.902	34.615	0.00	0.00	41.13	3.18
2192	2317	9.722056	CTGTAAATTATGATGTTAACTTCCTGC	57.278	33.333	16.44	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.