AutoCloner

Multiple sequence alignment - TraesCS7A01G227700

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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	TraesCS7A01G227700	chr7A	100.000	2817	0	0	1	2817	198192436	198189620	0.000000e+00	5203
1	TraesCS7A01G227700	chr7A	98.936	752	8	0	1	752	194562083	194562834	0.000000e+00	1345
2	TraesCS7A01G227700	chr7A	92.054	969	48	9	1868	2817	198026689	198025731	0.000000e+00	1336
3	TraesCS7A01G227700	chr7A	90.421	428	38	2	1	425	641403437	641403010	6.810000e-156	560
4	TraesCS7A01G227700	chr7B	92.812	1878	66	16	969	2817	329795597	329797434	0.000000e+00	2656
5	TraesCS7A01G227700	chr7B	93.333	165	11	0	752	916	329793990	329794154	7.790000e-61	244
6	TraesCS7A01G227700	chr7D	92.517	1871	76	26	969	2817	186828787	186830615	0.000000e+00	2621
7	TraesCS7A01G227700	chr7D	90.909	165	8	1	752	916	186825409	186825566	6.110000e-52	215
8	TraesCS7A01G227700	chr2A	98.558	763	9	2	1	763	579891377	579892137	0.000000e+00	1347
9	TraesCS7A01G227700	chr4B	98.404	752	12	0	1	752	50448560	50447809	0.000000e+00	1323
10	TraesCS7A01G227700	chr5A	97.900	762	16	0	1	762	163400133	163400894	0.000000e+00	1319
11	TraesCS7A01G227700	chr5A	91.714	350	27	2	421	768	326654707	326654358	4.220000e-133	484
12	TraesCS7A01G227700	chr5B	98.005	752	15	0	1	752	39517022	39516271	0.000000e+00	1306
13	TraesCS7A01G227700	chr5B	90.931	419	35	1	10	425	695846380	695845962	6.810000e-156	560
14	TraesCS7A01G227700	chr1D	91.589	428	33	1	1	425	467475753	467475326	3.130000e-164	588
15	TraesCS7A01G227700	chr1B	90.187	428	39	2	1	425	199667905	199667478	3.170000e-154	555
16	TraesCS7A01G227700	chr3D	93.675	332	21	0	421	752	380274512	380274181	5.420000e-137	497
17	TraesCS7A01G227700	chr3B	92.197	346	26	1	421	766	794005019	794004675	3.260000e-134	488
18	TraesCS7A01G227700	chr1A	92.174	345	26	1	421	764	576165376	576165720	1.170000e-133	486

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	TraesCS7A01G227700	chr7A	198189620	198192436	2816	True	5203	5203	100.0000	1	2817	1	chr7A.!!$R2	2816
1	TraesCS7A01G227700	chr7A	194562083	194562834	751	False	1345	1345	98.9360	1	752	1	chr7A.!!$F1	751
2	TraesCS7A01G227700	chr7A	198025731	198026689	958	True	1336	1336	92.0540	1868	2817	1	chr7A.!!$R1	949
3	TraesCS7A01G227700	chr7B	329793990	329797434	3444	False	1450	2656	93.0725	752	2817	2	chr7B.!!$F1	2065
4	TraesCS7A01G227700	chr7D	186825409	186830615	5206	False	1418	2621	91.7130	752	2817	2	chr7D.!!$F1	2065
5	TraesCS7A01G227700	chr2A	579891377	579892137	760	False	1347	1347	98.5580	1	763	1	chr2A.!!$F1	762
6	TraesCS7A01G227700	chr4B	50447809	50448560	751	True	1323	1323	98.4040	1	752	1	chr4B.!!$R1	751
7	TraesCS7A01G227700	chr5A	163400133	163400894	761	False	1319	1319	97.9000	1	762	1	chr5A.!!$F1	761
8	TraesCS7A01G227700	chr5B	39516271	39517022	751	True	1306	1306	98.0050	1	752	1	chr5B.!!$R1	751

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
885	886	1.384191	GATGAGCCCCCAAAGGTGT	59.616	57.895	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2572	5830	0.179189	CAACGGAAATTGCCTCGCTC	60.179	55.0	0.0	0.0	0.0	5.03	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
453	454	7.541162	AGTTAGTTTAGGTTTTTGTTGTGGAC	58.459	34.615	0.00	0.00	0.00	4.02
544	545	8.262601	TGATGGTATGGTCTCAATAGTACAAT	57.737	34.615	0.00	0.00	0.00	2.71
785	786	6.529220	AGCACAAACACTAGATTCTCTCTTT	58.471	36.000	0.00	0.00	35.28	2.52
786	787	6.995091	AGCACAAACACTAGATTCTCTCTTTT	59.005	34.615	0.00	0.00	35.28	2.27
837	838	8.429641	ACATCACGATAAGGTATTATTCCAAGT	58.570	33.333	0.00	0.00	31.57	3.16
838	839	8.926710	CATCACGATAAGGTATTATTCCAAGTC	58.073	37.037	0.00	0.00	31.57	3.01
841	842	7.599245	CACGATAAGGTATTATTCCAAGTCCTC	59.401	40.741	0.00	0.00	31.57	3.71
885	886	1.384191	GATGAGCCCCCAAAGGTGT	59.616	57.895	0.00	0.00	0.00	4.16
923	1852	6.009589	TGGCCACATTCTCTAATTCTCAAAA	58.990	36.000	0.00	0.00	0.00	2.44
984	4216	3.942739	GAACATTCGAACCGTTCAAACA	58.057	40.909	25.99	0.00	39.06	2.83
1034	4266	5.648960	CCTAAAAATAAGGCCACCGACTAAA	59.351	40.000	5.01	0.00	0.00	1.85
1035	4267	5.381174	AAAAATAAGGCCACCGACTAAAC	57.619	39.130	5.01	0.00	0.00	2.01
1036	4268	2.304751	ATAAGGCCACCGACTAAACG	57.695	50.000	5.01	0.00	0.00	3.60
1037	4269	0.390209	TAAGGCCACCGACTAAACGC	60.390	55.000	5.01	0.00	0.00	4.84
1056	4291	2.602217	CGCTGTGTTCAAAGTTAGCCAC	60.602	50.000	0.00	0.00	0.00	5.01
1076	4311	2.791567	CGAGACTCGTTCATCTCCAAG	58.208	52.381	16.83	0.00	38.53	3.61
1077	4312	2.420372	CGAGACTCGTTCATCTCCAAGA	59.580	50.000	16.83	0.00	38.53	3.02
1078	4313	3.729462	CGAGACTCGTTCATCTCCAAGAC	60.729	52.174	16.83	0.00	38.53	3.01
1079	4314	3.426615	AGACTCGTTCATCTCCAAGACT	58.573	45.455	0.00	0.00	0.00	3.24
1080	4315	3.442273	AGACTCGTTCATCTCCAAGACTC	59.558	47.826	0.00	0.00	0.00	3.36
1081	4316	2.494073	ACTCGTTCATCTCCAAGACTCC	59.506	50.000	0.00	0.00	0.00	3.85
1082	4317	2.493675	CTCGTTCATCTCCAAGACTCCA	59.506	50.000	0.00	0.00	0.00	3.86
1083	4318	2.897326	TCGTTCATCTCCAAGACTCCAA	59.103	45.455	0.00	0.00	0.00	3.53
1125	4360	1.081309	ACGTACATGCACGCACGTA	60.081	52.632	18.24	0.00	45.04	3.57
1126	4361	1.339134	CGTACATGCACGCACGTAC	59.661	57.895	16.23	16.23	40.75	3.67
1127	4362	1.339134	GTACATGCACGCACGTACG	59.661	57.895	15.01	15.01	36.21	3.67
1132	4367	0.795735	ATGCACGCACGTACGTAGAC	60.796	55.000	22.34	12.54	46.34	2.59
1135	4370	0.791983	CACGCACGTACGTAGACAGG	60.792	60.000	22.34	8.75	46.34	4.00
1185	4420	0.104672	TCTTCAACCTCTGACCCCCA	60.105	55.000	0.00	0.00	32.21	4.96
1210	4445	1.669437	GCTAGCCTGCTAATCCGGC	60.669	63.158	2.29	0.00	44.09	6.13
1220	4455	3.507411	TGCTAATCCGGCCTATAAGACT	58.493	45.455	0.00	0.00	0.00	3.24
1237	4472	3.643081	TCCCCCTCCATTCCCCCA	61.643	66.667	0.00	0.00	0.00	4.96
1302	4537	2.932187	GCTTTGCCAATAAGCCCTTGTG	60.932	50.000	0.00	0.00	41.62	3.33
1525	4760	1.135333	GCCTCCGTACTCTCCTTCTTG	59.865	57.143	0.00	0.00	0.00	3.02
1526	4761	2.448453	CCTCCGTACTCTCCTTCTTGT	58.552	52.381	0.00	0.00	0.00	3.16
1631	4866	8.233868	TCCTGTATTTCGTTAATTTGATGTGTG	58.766	33.333	0.00	0.00	0.00	3.82
1632	4867	8.020819	CCTGTATTTCGTTAATTTGATGTGTGT	58.979	33.333	0.00	0.00	0.00	3.72
1633	4868	8.942669	TGTATTTCGTTAATTTGATGTGTGTC	57.057	30.769	0.00	0.00	0.00	3.67
1634	4869	7.742525	TGTATTTCGTTAATTTGATGTGTGTCG	59.257	33.333	0.00	0.00	0.00	4.35
1659	4894	7.535940	CGGTTTTCGTTTTTGTGATACATGTAT	59.464	33.333	18.31	18.31	0.00	2.29
1741	4976	9.624697	TTCATTAATGGAAATTTTCACTCTTCG	57.375	29.630	15.36	0.00	0.00	3.79
1790	5025	7.253684	CCGTCGTGAATTGATCTCTAACTTTAC	60.254	40.741	0.00	0.00	0.00	2.01
1791	5026	7.485277	CGTCGTGAATTGATCTCTAACTTTACT	59.515	37.037	0.00	0.00	0.00	2.24
1792	5027	9.784680	GTCGTGAATTGATCTCTAACTTTACTA	57.215	33.333	0.00	0.00	0.00	1.82
1849	5084	4.546829	TGGTTGTTCTACTGTATCACCC	57.453	45.455	0.00	0.00	0.00	4.61
1944	5184	5.096443	ACAAGATCCTAGCAAAAGAGAGG	57.904	43.478	0.00	0.00	0.00	3.69
1966	5206	8.614814	AGAGGATGCTTTATTAATATAAGGCCA	58.385	33.333	5.01	0.00	44.40	5.36
1967	5207	9.413734	GAGGATGCTTTATTAATATAAGGCCAT	57.586	33.333	5.01	0.00	44.40	4.40
1968	5208	9.774071	AGGATGCTTTATTAATATAAGGCCATT	57.226	29.630	5.01	0.00	44.40	3.16
2041	5281	0.178767	TCCGTTGATGCATCCTCTGG	59.821	55.000	23.67	18.52	0.00	3.86
2202	5442	1.376609	AAATCGCATCGGTGGAAGGC	61.377	55.000	0.00	0.00	0.00	4.35
2304	5544	4.325204	GTGCATGCACAGTAACAATGAATG	59.675	41.667	39.12	0.00	45.53	2.67
2384	5642	2.966708	CGAAAGTTGAAGCATGAACACG	59.033	45.455	0.00	0.00	0.00	4.49
2468	5726	4.568152	TGGTTGCTAAACTTTCTTCTGC	57.432	40.909	0.00	0.00	36.48	4.26
2477	5735	2.843701	ACTTTCTTCTGCTGTGTGGAG	58.156	47.619	0.00	0.00	35.26	3.86
2497	5755	0.463116	GATGACGGCCGGGTACAATT	60.463	55.000	31.76	4.91	0.00	2.32
2549	5807	9.549509	TTAAATGACTCGTTAATGCATTACAAC	57.450	29.630	18.70	15.47	0.00	3.32
2556	5814	8.175069	ACTCGTTAATGCATTACAACTATTGTG	58.825	33.333	18.70	7.98	45.03	3.33
2576	5834	4.567959	TGTGTCATTCATCACAATAGAGCG	59.432	41.667	0.00	0.00	40.81	5.03
2692	5951	6.261158	GGATTGAGGTGACTAAAAATAGGCTC	59.739	42.308	0.00	0.00	44.43	4.70

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
397	398	3.127895	GCTCAGATCTCTCGTTGTAGTGT	59.872	47.826	0.00	0.00	0.00	3.55
453	454	4.752146	TCATACATGTGAGAAGCTGTGAG	58.248	43.478	9.11	0.00	0.00	3.51
785	786	6.033341	GGCATCAAAGCGACAACAAATATAA	58.967	36.000	0.00	0.00	34.64	0.98
786	787	5.124617	TGGCATCAAAGCGACAACAAATATA	59.875	36.000	0.00	0.00	34.64	0.86
837	838	0.680618	TAAAACCAACGGAGCGAGGA	59.319	50.000	0.00	0.00	32.30	3.71
838	839	0.794473	GTAAAACCAACGGAGCGAGG	59.206	55.000	0.00	0.00	0.00	4.63
930	1859	1.067295	TTGGAGAGAATGTGGCCACT	58.933	50.000	34.75	17.79	0.00	4.00
1005	4237	3.952323	GGTGGCCTTATTTTTAGGGAGAC	59.048	47.826	3.32	0.00	33.19	3.36
1034	4266	1.602377	GGCTAACTTTGAACACAGCGT	59.398	47.619	0.00	0.00	0.00	5.07
1035	4267	1.601903	TGGCTAACTTTGAACACAGCG	59.398	47.619	0.00	0.00	0.00	5.18
1036	4268	2.602217	CGTGGCTAACTTTGAACACAGC	60.602	50.000	0.00	0.00	0.00	4.40
1037	4269	2.869801	TCGTGGCTAACTTTGAACACAG	59.130	45.455	0.00	0.00	0.00	3.66
1056	4291	2.420372	TCTTGGAGATGAACGAGTCTCG	59.580	50.000	20.57	20.57	46.93	4.04
1076	4311	1.949257	CGGCAAGGTTGTTGGAGTC	59.051	57.895	0.00	0.00	0.00	3.36
1077	4312	2.193536	GCGGCAAGGTTGTTGGAGT	61.194	57.895	0.00	0.00	0.00	3.85
1078	4313	2.644992	GCGGCAAGGTTGTTGGAG	59.355	61.111	0.00	0.00	0.00	3.86
1079	4314	2.909965	GGCGGCAAGGTTGTTGGA	60.910	61.111	3.07	0.00	0.00	3.53
1080	4315	3.989787	GGGCGGCAAGGTTGTTGG	61.990	66.667	12.47	0.00	0.00	3.77
1081	4316	3.222855	TGGGCGGCAAGGTTGTTG	61.223	61.111	12.47	0.00	0.00	3.33
1082	4317	3.223589	GTGGGCGGCAAGGTTGTT	61.224	61.111	12.47	0.00	0.00	2.83
1083	4318	4.204028	AGTGGGCGGCAAGGTTGT	62.204	61.111	12.47	0.00	0.00	3.32
1125	4360	2.754658	CGAGGCCCCTGTCTACGT	60.755	66.667	0.00	0.00	0.00	3.57
1126	4361	2.439701	TCGAGGCCCCTGTCTACG	60.440	66.667	0.00	0.00	0.00	3.51
1127	4362	1.043673	ATGTCGAGGCCCCTGTCTAC	61.044	60.000	0.00	0.00	0.00	2.59
1132	4367	4.864334	GGCATGTCGAGGCCCCTG	62.864	72.222	10.76	0.00	43.69	4.45
1210	4445	3.569135	ATGGAGGGGGAGTCTTATAGG	57.431	52.381	0.00	0.00	0.00	2.57
1220	4455	2.538477	AATGGGGGAATGGAGGGGGA	62.538	60.000	0.00	0.00	0.00	4.81
1237	4472	0.323725	ATGCTTGCGTGGGGAAGAAT	60.324	50.000	0.00	0.00	43.63	2.40
1302	4537	2.482839	CGAAAGAGGGAGATGAGGAAGC	60.483	54.545	0.00	0.00	0.00	3.86
1547	4782	0.530744	TGCACGTATCTTCCTTCGCT	59.469	50.000	0.00	0.00	0.00	4.93
1631	4866	5.264712	TGTATCACAAAAACGAAAACCGAC	58.735	37.500	0.00	0.00	41.76	4.79
1632	4867	5.481200	TGTATCACAAAAACGAAAACCGA	57.519	34.783	0.00	0.00	41.76	4.69
1633	4868	5.683743	ACATGTATCACAAAAACGAAAACCG	59.316	36.000	0.00	0.00	45.44	4.44
1634	4869	8.736751	ATACATGTATCACAAAAACGAAAACC	57.263	30.769	12.75	0.00	0.00	3.27
1664	4899	9.137459	TCAAGTAATCCAGTTTCAAACCAAATA	57.863	29.630	0.00	0.00	0.00	1.40
1741	4976	6.089417	CGGTAAGAAAAGGCAATCAAATGAAC	59.911	38.462	0.00	0.00	0.00	3.18
1815	5050	8.783093	CAGTAGAACAACCAAAATCTCATACAA	58.217	33.333	0.00	0.00	0.00	2.41
1816	5051	7.936847	ACAGTAGAACAACCAAAATCTCATACA	59.063	33.333	0.00	0.00	0.00	2.29
1817	5052	8.324163	ACAGTAGAACAACCAAAATCTCATAC	57.676	34.615	0.00	0.00	0.00	2.39
1819	5054	9.167311	GATACAGTAGAACAACCAAAATCTCAT	57.833	33.333	0.00	0.00	0.00	2.90
1820	5055	8.154203	TGATACAGTAGAACAACCAAAATCTCA	58.846	33.333	0.00	0.00	0.00	3.27
1821	5056	8.443937	GTGATACAGTAGAACAACCAAAATCTC	58.556	37.037	0.00	0.00	0.00	2.75
1822	5057	7.390718	GGTGATACAGTAGAACAACCAAAATCT	59.609	37.037	0.00	0.00	0.00	2.40
1823	5058	7.361799	GGGTGATACAGTAGAACAACCAAAATC	60.362	40.741	11.92	0.00	38.12	2.17
1824	5059	6.433093	GGGTGATACAGTAGAACAACCAAAAT	59.567	38.462	11.92	0.00	38.12	1.82
1825	5060	5.766174	GGGTGATACAGTAGAACAACCAAAA	59.234	40.000	11.92	0.00	38.12	2.44
1826	5061	5.072600	AGGGTGATACAGTAGAACAACCAAA	59.927	40.000	16.55	0.00	40.34	3.28
1827	5062	4.595781	AGGGTGATACAGTAGAACAACCAA	59.404	41.667	16.55	0.00	40.34	3.67
1828	5063	4.164981	AGGGTGATACAGTAGAACAACCA	58.835	43.478	16.55	0.00	40.34	3.67
1918	5158	7.364232	CCTCTCTTTTGCTAGGATCTTGTAAGA	60.364	40.741	0.00	0.00	39.78	2.10
1999	5239	9.599866	CGGATGGCATGAAATATATCTTAGTAA	57.400	33.333	3.81	0.00	0.00	2.24
2024	5264	1.293924	GACCAGAGGATGCATCAACG	58.706	55.000	27.25	12.42	0.00	4.10
2041	5281	5.308014	TGGGTGATTCACATGCTATATGAC	58.692	41.667	18.09	0.00	35.86	3.06
2124	5364	2.627945	TGCAATCGCGTTAGGATCTTT	58.372	42.857	5.77	0.00	42.97	2.52
2202	5442	7.528307	CAAAAGATGTGATTGAGAAAGAGAGG	58.472	38.462	0.00	0.00	0.00	3.69
2384	5642	1.666189	GCCAATGCCGTAAGAGTTCTC	59.334	52.381	0.00	0.00	43.02	2.87
2468	5726	1.448540	GCCGTCATCCTCCACACAG	60.449	63.158	0.00	0.00	0.00	3.66
2477	5735	2.319890	ATTGTACCCGGCCGTCATCC	62.320	60.000	26.12	8.26	0.00	3.51
2527	5785	6.985188	AGTTGTAATGCATTAACGAGTCAT	57.015	33.333	20.46	0.00	0.00	3.06
2556	5814	4.447054	CCTCGCTCTATTGTGATGAATGAC	59.553	45.833	0.00	0.00	0.00	3.06
2572	5830	0.179189	CAACGGAAATTGCCTCGCTC	60.179	55.000	0.00	0.00	0.00	5.03
2576	5834	1.215382	GGCCAACGGAAATTGCCTC	59.785	57.895	0.00	0.00	0.00	4.70
2662	5921	1.112113	TAGTCACCTCAATCCTCGGC	58.888	55.000	0.00	0.00	0.00	5.54
2692	5951	3.796717	TCAATACTAAATCAGCTCGCACG	59.203	43.478	0.00	0.00	0.00	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.