AutoCloner

Multiple sequence alignment - TraesCS7D01G456800

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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	TraesCS7D01G456800	chr7D	100.000	2421	0	0	1	2421	575440511	575442931	0.000000e+00	4471.0
1	TraesCS7D01G456800	chr7D	84.746	1003	94	37	691	1659	574764578	574763601	0.000000e+00	950.0
2	TraesCS7D01G456800	chr7D	87.763	760	53	24	904	1641	575408162	575408903	0.000000e+00	852.0
3	TraesCS7D01G456800	chr7D	82.644	991	86	44	691	1643	574774558	574773616	0.000000e+00	798.0
4	TraesCS7D01G456800	chr7B	94.863	1421	46	16	1	1415	636982841	636984240	0.000000e+00	2194.0
5	TraesCS7D01G456800	chr7B	89.735	906	65	19	1410	2305	636984350	636985237	0.000000e+00	1133.0
6	TraesCS7D01G456800	chr7B	83.417	995	96	37	708	1659	634580200	634579232	0.000000e+00	859.0
7	TraesCS7D01G456800	chr7B	84.430	912	80	25	747	1642	636940033	636940898	0.000000e+00	841.0
8	TraesCS7D01G456800	chr7B	90.769	195	13	5	691	884	634647762	634647572	3.090000e-64	255.0
9	TraesCS7D01G456800	chr7B	83.099	284	39	4	42	320	636938741	636939020	1.440000e-62	250.0
10	TraesCS7D01G456800	chr7A	93.885	1292	46	14	944	2217	665427555	665428831	0.000000e+00	1917.0
11	TraesCS7D01G456800	chr7A	84.399	923	77	40	747	1643	664999447	665000328	0.000000e+00	845.0
12	TraesCS7D01G456800	chr7A	82.914	954	86	43	738	1659	664415345	664414437	0.000000e+00	787.0
13	TraesCS7D01G456800	chr7A	83.582	871	76	38	815	1653	664372217	664371382	0.000000e+00	754.0
14	TraesCS7D01G456800	chr7A	90.389	437	31	8	1	428	665426302	665426736	4.520000e-157	564.0
15	TraesCS7D01G456800	chr7A	92.023	351	15	8	474	823	665426738	665427076	4.680000e-132	481.0
16	TraesCS7D01G456800	chr7A	87.611	339	36	5	1658	1994	75066132	75066466	2.920000e-104	388.0
17	TraesCS7D01G456800	chr7A	80.224	268	43	6	67	329	664418070	664417808	2.460000e-45	193.0
18	TraesCS7D01G456800	chr7A	90.278	72	7	0	762	833	664374387	664374316	7.130000e-16	95.3
19	TraesCS7D01G456800	chrUn	85.588	340	41	3	1659	1991	324024235	324024573	1.380000e-92	350.0
20	TraesCS7D01G456800	chr1B	83.420	386	49	9	1655	2038	631962644	631963016	6.410000e-91	344.0
21	TraesCS7D01G456800	chr1B	83.193	357	47	8	1691	2040	24539085	24538735	5.020000e-82	315.0
22	TraesCS7D01G456800	chr3B	85.759	323	41	5	1672	1992	542753925	542753606	1.070000e-88	337.0
23	TraesCS7D01G456800	chr3B	85.496	131	18	1	1663	1793	22471862	22471733	4.200000e-28	135.0
24	TraesCS7D01G456800	chr2D	85.761	309	37	5	1687	1991	76750793	76750488	1.080000e-83	320.0
25	TraesCS7D01G456800	chr6B	85.577	312	33	7	1734	2044	703398994	703399294	1.400000e-82	316.0
26	TraesCS7D01G456800	chr3D	98.830	171	2	0	192	362	594534898	594534728	3.020000e-79	305.0

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	TraesCS7D01G456800	chr7D	575440511	575442931	2420	False	4471.000000	4471	100.0000	1	2421	1	chr7D.!!$F2	2420
1	TraesCS7D01G456800	chr7D	574763601	574764578	977	True	950.000000	950	84.7460	691	1659	1	chr7D.!!$R1	968
2	TraesCS7D01G456800	chr7D	575408162	575408903	741	False	852.000000	852	87.7630	904	1641	1	chr7D.!!$F1	737
3	TraesCS7D01G456800	chr7D	574773616	574774558	942	True	798.000000	798	82.6440	691	1643	1	chr7D.!!$R2	952
4	TraesCS7D01G456800	chr7B	636982841	636985237	2396	False	1663.500000	2194	92.2990	1	2305	2	chr7B.!!$F2	2304
5	TraesCS7D01G456800	chr7B	634579232	634580200	968	True	859.000000	859	83.4170	708	1659	1	chr7B.!!$R1	951
6	TraesCS7D01G456800	chr7B	636938741	636940898	2157	False	545.500000	841	83.7645	42	1642	2	chr7B.!!$F1	1600
7	TraesCS7D01G456800	chr7A	665426302	665428831	2529	False	987.333333	1917	92.0990	1	2217	3	chr7A.!!$F3	2216
8	TraesCS7D01G456800	chr7A	664999447	665000328	881	False	845.000000	845	84.3990	747	1643	1	chr7A.!!$F2	896
9	TraesCS7D01G456800	chr7A	664414437	664418070	3633	True	490.000000	787	81.5690	67	1659	2	chr7A.!!$R2	1592
10	TraesCS7D01G456800	chr7A	664371382	664374387	3005	True	424.650000	754	86.9300	762	1653	2	chr7A.!!$R1	891

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
668	2792	0.249911	AATCTAGCGGCCGGTTCATC	60.25	55.0	37.09	13.23	0.0	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1799	6585	1.407437	GCTCCTCGGATGTCATTTGGT	60.407	52.381	0.0	0.0	0.0	3.67	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
103	107	2.169769	GTCAAATCCTATCCCACCACGA	59.830	50.000	0.00	0.00	0.00	4.35
169	175	4.287326	ACCTCCCACCTAGAAAAAGAAGAG	59.713	45.833	0.00	0.00	0.00	2.85
341	1898	7.314393	TCAAGTTTGGTTAACTGGTACAAAAC	58.686	34.615	5.42	0.00	46.34	2.43
446	2069	4.158786	CCTACATGTCAGAGGATGGAGAT	58.841	47.826	0.00	0.00	32.89	2.75
668	2792	0.249911	AATCTAGCGGCCGGTTCATC	60.250	55.000	37.09	13.23	0.00	2.92
889	5445	2.176798	TCCATTCCTCTCTCTCCCTCTC	59.823	54.545	0.00	0.00	0.00	3.20
916	5491	1.750332	CGCCACATCTCTCTCTCTCCT	60.750	57.143	0.00	0.00	0.00	3.69
933	5519	1.352156	CCTTCTAACCACACGCTCGC	61.352	60.000	0.00	0.00	0.00	5.03
1175	5791	2.551270	GTGAGCGACGGCAACAAG	59.449	61.111	0.00	0.00	43.41	3.16
1694	6480	2.282110	CCACGGACATTGCACCCA	60.282	61.111	0.00	0.00	0.00	4.51
1710	6496	1.518572	CCACGCTACACCCACGATC	60.519	63.158	0.00	0.00	0.00	3.69
1723	6509	2.093783	CCCACGATCGAAAACTTAGCAC	59.906	50.000	24.34	0.00	0.00	4.40
1733	6519	9.607285	GATCGAAAACTTAGCACAAAGAAATAA	57.393	29.630	0.00	0.00	0.00	1.40
1799	6585	3.871485	AGGTGCTTGCAAAATTTTGTGA	58.129	36.364	27.13	16.90	40.24	3.58
1808	6594	6.116680	TGCAAAATTTTGTGACCAAATGAC	57.883	33.333	27.13	10.26	40.14	3.06
1823	6609	2.611225	ATGACATCCGAGGAGCTTTC	57.389	50.000	0.00	0.00	0.00	2.62
1841	6627	7.060600	AGCTTTCTACAAAAACAAAGTTTGC	57.939	32.000	15.59	0.00	39.16	3.68
1842	6628	6.873605	AGCTTTCTACAAAAACAAAGTTTGCT	59.126	30.769	15.59	0.00	39.16	3.91
1883	6670	0.398318	GTGGGTGGAGAGCAAGAGTT	59.602	55.000	0.00	0.00	0.00	3.01
1927	6714	4.073169	TCATTCGTTGTTATTTGGCGAC	57.927	40.909	0.00	0.00	0.00	5.19
1944	6731	2.542824	GCGACCAAACTTTGCAAGCTAA	60.543	45.455	0.00	0.00	0.00	3.09
2058	6860	3.142174	GCAGCCACTACTTTCTCTGTTT	58.858	45.455	0.00	0.00	0.00	2.83
2096	6898	8.749354	ACATGTTTCCTTTCTAATATTGGTTCC	58.251	33.333	0.00	0.00	0.00	3.62
2097	6899	8.971073	CATGTTTCCTTTCTAATATTGGTTCCT	58.029	33.333	0.00	0.00	0.00	3.36
2262	7064	5.514500	TTAAGCCTCTGGACCTTACAATT	57.486	39.130	0.00	0.00	0.00	2.32
2265	7067	3.844211	AGCCTCTGGACCTTACAATTACA	59.156	43.478	0.00	0.00	0.00	2.41
2266	7068	3.939592	GCCTCTGGACCTTACAATTACAC	59.060	47.826	0.00	0.00	0.00	2.90
2267	7069	4.514401	CCTCTGGACCTTACAATTACACC	58.486	47.826	0.00	0.00	0.00	4.16
2268	7070	4.514401	CTCTGGACCTTACAATTACACCC	58.486	47.826	0.00	0.00	0.00	4.61
2269	7071	4.172807	TCTGGACCTTACAATTACACCCT	58.827	43.478	0.00	0.00	0.00	4.34
2270	7072	5.343715	TCTGGACCTTACAATTACACCCTA	58.656	41.667	0.00	0.00	0.00	3.53
2271	7073	5.188359	TCTGGACCTTACAATTACACCCTAC	59.812	44.000	0.00	0.00	0.00	3.18
2272	7074	4.845225	TGGACCTTACAATTACACCCTACA	59.155	41.667	0.00	0.00	0.00	2.74
2273	7075	5.046159	TGGACCTTACAATTACACCCTACAG	60.046	44.000	0.00	0.00	0.00	2.74
2274	7076	5.188359	GGACCTTACAATTACACCCTACAGA	59.812	44.000	0.00	0.00	0.00	3.41
2275	7077	6.296030	GGACCTTACAATTACACCCTACAGAA	60.296	42.308	0.00	0.00	0.00	3.02
2305	7107	8.553459	AATACAACTACAGAATTCAGGTTGAG	57.447	34.615	24.97	14.40	37.86	3.02
2306	7108	6.174720	ACAACTACAGAATTCAGGTTGAGA	57.825	37.500	24.97	5.57	37.86	3.27
2307	7109	6.591935	ACAACTACAGAATTCAGGTTGAGAA	58.408	36.000	24.97	5.31	37.86	2.87
2308	7110	6.483640	ACAACTACAGAATTCAGGTTGAGAAC	59.516	38.462	24.97	0.00	37.86	3.01
2317	7119	3.821306	GGTTGAGAACCCAGGTGTT	57.179	52.632	0.00	0.00	46.12	3.32
2318	7120	2.067365	GGTTGAGAACCCAGGTGTTT	57.933	50.000	0.00	0.00	46.12	2.83
2319	7121	2.384828	GGTTGAGAACCCAGGTGTTTT	58.615	47.619	0.00	0.00	46.12	2.43
2320	7122	2.764010	GGTTGAGAACCCAGGTGTTTTT	59.236	45.455	0.00	0.00	46.12	1.94
2321	7123	3.181479	GGTTGAGAACCCAGGTGTTTTTC	60.181	47.826	0.00	0.00	46.12	2.29
2322	7124	2.661718	TGAGAACCCAGGTGTTTTTCC	58.338	47.619	0.00	0.00	0.00	3.13
2323	7125	2.243736	TGAGAACCCAGGTGTTTTTCCT	59.756	45.455	0.00	0.00	35.45	3.36
2329	7131	1.593196	CAGGTGTTTTTCCTGCGAGA	58.407	50.000	0.00	0.00	44.46	4.04
2330	7132	1.946768	CAGGTGTTTTTCCTGCGAGAA	59.053	47.619	0.00	0.00	44.46	2.87
2331	7133	2.357637	CAGGTGTTTTTCCTGCGAGAAA	59.642	45.455	0.00	0.00	44.46	2.52
2332	7134	3.020984	AGGTGTTTTTCCTGCGAGAAAA	58.979	40.909	9.04	9.04	42.48	2.29
2399	7201	4.794278	TTTCCGTAGATGCAGAGTTACA	57.206	40.909	0.00	0.00	0.00	2.41
2400	7202	4.371855	TTCCGTAGATGCAGAGTTACAG	57.628	45.455	0.00	0.00	0.00	2.74
2401	7203	3.353557	TCCGTAGATGCAGAGTTACAGT	58.646	45.455	0.00	0.00	0.00	3.55
2402	7204	3.762288	TCCGTAGATGCAGAGTTACAGTT	59.238	43.478	0.00	0.00	0.00	3.16
2403	7205	4.945543	TCCGTAGATGCAGAGTTACAGTTA	59.054	41.667	0.00	0.00	0.00	2.24
2404	7206	5.066117	TCCGTAGATGCAGAGTTACAGTTAG	59.934	44.000	0.00	0.00	0.00	2.34
2405	7207	4.735822	CGTAGATGCAGAGTTACAGTTAGC	59.264	45.833	0.00	0.00	0.00	3.09
2406	7208	5.449314	CGTAGATGCAGAGTTACAGTTAGCT	60.449	44.000	0.00	0.00	0.00	3.32
2408	7210	3.319137	TGCAGAGTTACAGTTAGCTGG	57.681	47.619	11.56	0.00	46.62	4.85
2409	7211	2.003301	GCAGAGTTACAGTTAGCTGGC	58.997	52.381	11.56	0.00	46.62	4.85
2410	7212	2.612972	GCAGAGTTACAGTTAGCTGGCA	60.613	50.000	11.56	0.00	46.62	4.92
2411	7213	3.664107	CAGAGTTACAGTTAGCTGGCAA	58.336	45.455	11.56	1.97	46.62	4.52
2412	7214	4.065088	CAGAGTTACAGTTAGCTGGCAAA	58.935	43.478	11.56	0.00	46.62	3.68
2413	7215	4.515191	CAGAGTTACAGTTAGCTGGCAAAA	59.485	41.667	11.56	0.00	46.62	2.44
2414	7216	4.757149	AGAGTTACAGTTAGCTGGCAAAAG	59.243	41.667	11.56	0.00	46.62	2.27
2415	7217	3.253432	AGTTACAGTTAGCTGGCAAAAGC	59.747	43.478	11.56	0.00	46.62	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	3.945285	AGCGGAACTTCTCAACTTTTTCA	59.055	39.130	0.00	0.00	0.00	2.69
103	107	7.918536	TTAACATGCATGCAAAATGGTATTT	57.081	28.000	26.68	10.93	0.00	1.40
169	175	1.873698	TTGTGTTCTGCCCTACGAAC	58.126	50.000	0.00	0.00	39.85	3.95
341	1898	6.210078	TGTGCATGCATGATGTAATTACATG	58.790	36.000	30.88	20.79	46.20	3.21
351	1911	4.718940	ATATGGATGTGCATGCATGATG	57.281	40.909	30.64	6.09	46.94	3.07
518	2286	9.445878	CATGTATATATGTTCCTTCATTGAGCT	57.554	33.333	1.46	0.00	0.00	4.09
537	2511	8.110860	TGCTTCTTCGAGATGTATCATGTATA	57.889	34.615	0.00	0.00	0.00	1.47
889	5445	0.671251	GAGAGATGTGGCGGGTAGAG	59.329	60.000	0.00	0.00	0.00	2.43
916	5491	1.731613	CGCGAGCGTGTGGTTAGAA	60.732	57.895	0.00	0.00	34.35	2.10
933	5519	4.441792	TGGTTGATTGGATCATGAGTACG	58.558	43.478	0.09	0.00	39.39	3.67
1081	5686	4.568359	TGACGAACGTAGGAGATACAGTAC	59.432	45.833	0.00	0.00	33.65	2.73
1082	5687	4.758688	TGACGAACGTAGGAGATACAGTA	58.241	43.478	0.00	0.00	33.65	2.74
1083	5688	3.603532	TGACGAACGTAGGAGATACAGT	58.396	45.455	0.00	0.00	33.65	3.55
1084	5689	3.546417	GCTGACGAACGTAGGAGATACAG	60.546	52.174	0.00	2.44	33.65	2.74
1085	5690	2.353889	GCTGACGAACGTAGGAGATACA	59.646	50.000	0.00	0.00	33.65	2.29
1694	6480	1.588824	TTCGATCGTGGGTGTAGCGT	61.589	55.000	15.94	0.00	0.00	5.07
1753	6539	5.695851	AACATTTGCTCATAATCGGATCC	57.304	39.130	0.00	0.00	0.00	3.36
1799	6585	1.407437	GCTCCTCGGATGTCATTTGGT	60.407	52.381	0.00	0.00	0.00	3.67
1808	6594	3.526931	TTGTAGAAAGCTCCTCGGATG	57.473	47.619	0.00	0.00	0.00	3.51
1823	6609	7.810766	TTGAGAGCAAACTTTGTTTTTGTAG	57.189	32.000	3.48	0.00	36.50	2.74
1841	6627	9.708222	CCACGTTTCAGATTTTATATTTGAGAG	57.292	33.333	0.00	0.00	0.00	3.20
1842	6628	8.673711	CCCACGTTTCAGATTTTATATTTGAGA	58.326	33.333	0.00	0.00	0.00	3.27
1903	6690	4.023963	TCGCCAAATAACAACGAATGAACA	60.024	37.500	0.00	0.00	0.00	3.18
2112	6914	7.041916	GCCACTCTCATTCTCATTTGATAAGAG	60.042	40.741	0.00	0.00	0.00	2.85
2232	7034	4.540502	AGGTCCAGAGGCTTAAAATAACCT	59.459	41.667	0.00	0.00	34.43	3.50
2233	7035	4.856509	AGGTCCAGAGGCTTAAAATAACC	58.143	43.478	0.00	0.00	0.00	2.85
2234	7036	6.882678	TGTAAGGTCCAGAGGCTTAAAATAAC	59.117	38.462	0.00	0.00	0.00	1.89
2237	7039	5.514500	TGTAAGGTCCAGAGGCTTAAAAT	57.486	39.130	0.00	0.00	0.00	1.82
2249	7051	4.845225	TGTAGGGTGTAATTGTAAGGTCCA	59.155	41.667	0.00	0.00	0.00	4.02
2311	7113	2.341846	TTCTCGCAGGAAAAACACCT	57.658	45.000	0.00	0.00	38.40	4.00
2312	7114	3.430333	TTTTCTCGCAGGAAAAACACC	57.570	42.857	10.20	0.00	40.70	4.16
2376	7178	5.543714	TGTAACTCTGCATCTACGGAAAAA	58.456	37.500	0.00	0.00	0.00	1.94
2377	7179	5.142061	TGTAACTCTGCATCTACGGAAAA	57.858	39.130	0.00	0.00	0.00	2.29
2378	7180	4.219944	ACTGTAACTCTGCATCTACGGAAA	59.780	41.667	9.28	0.00	0.00	3.13
2379	7181	3.762288	ACTGTAACTCTGCATCTACGGAA	59.238	43.478	9.28	0.00	0.00	4.30
2380	7182	3.353557	ACTGTAACTCTGCATCTACGGA	58.646	45.455	9.28	0.00	0.00	4.69
2381	7183	3.784701	ACTGTAACTCTGCATCTACGG	57.215	47.619	0.00	0.00	0.00	4.02
2382	7184	4.735822	GCTAACTGTAACTCTGCATCTACG	59.264	45.833	0.00	0.00	0.00	3.51
2383	7185	5.746245	CAGCTAACTGTAACTCTGCATCTAC	59.254	44.000	0.00	0.00	39.22	2.59
2384	7186	5.163509	CCAGCTAACTGTAACTCTGCATCTA	60.164	44.000	0.00	0.00	42.81	1.98
2385	7187	4.382470	CCAGCTAACTGTAACTCTGCATCT	60.382	45.833	0.00	0.00	42.81	2.90
2386	7188	3.868077	CCAGCTAACTGTAACTCTGCATC	59.132	47.826	0.00	0.00	42.81	3.91
2387	7189	3.866651	CCAGCTAACTGTAACTCTGCAT	58.133	45.455	0.00	0.00	42.81	3.96
2388	7190	2.612972	GCCAGCTAACTGTAACTCTGCA	60.613	50.000	0.00	0.00	42.81	4.41
2389	7191	2.003301	GCCAGCTAACTGTAACTCTGC	58.997	52.381	0.00	0.00	42.81	4.26
2390	7192	3.319137	TGCCAGCTAACTGTAACTCTG	57.681	47.619	0.00	0.00	42.81	3.35
2391	7193	4.351874	TTTGCCAGCTAACTGTAACTCT	57.648	40.909	0.00	0.00	42.81	3.24
2392	7194	4.613850	GCTTTTGCCAGCTAACTGTAACTC	60.614	45.833	0.00	0.00	42.81	3.01
2393	7195	3.253432	GCTTTTGCCAGCTAACTGTAACT	59.747	43.478	0.00	0.00	42.81	2.24
2394	7196	3.565516	GCTTTTGCCAGCTAACTGTAAC	58.434	45.455	0.00	0.00	42.81	2.50
2395	7197	3.915437	GCTTTTGCCAGCTAACTGTAA	57.085	42.857	0.00	0.00	42.81	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.