AutoCloner

Multiple sequence alignment - TraesCS7B01G168400

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	TraesCS7B01G168400	chr7B	100.000	2264	0	0	1	2264	235458094	235455831	0.000000e+00	4181.0
1	TraesCS7B01G168400	chr7B	92.876	2302	116	25	1	2264	687040622	687042913	0.000000e+00	3299.0
2	TraesCS7B01G168400	chr5B	96.865	2265	68	3	1	2264	530940831	530938569	0.000000e+00	3786.0
3	TraesCS7B01G168400	chr5B	94.672	2177	71	10	1	2149	464634106	464636265	0.000000e+00	3336.0
4	TraesCS7B01G168400	chr3B	94.110	2292	93	10	1	2264	16124436	16122159	0.000000e+00	3446.0
5	TraesCS7B01G168400	chr3B	92.934	1486	65	16	814	2264	393329884	393331364	0.000000e+00	2126.0
6	TraesCS7B01G168400	chr3B	90.170	529	45	6	1738	2264	28618692	28619215	0.000000e+00	682.0
7	TraesCS7B01G168400	chr3B	87.136	412	38	8	1738	2149	112911553	112911949	9.530000e-124	453.0
8	TraesCS7B01G168400	chr3B	88.095	126	5	4	1706	1831	16201768	16201653	8.430000e-30	141.0
9	TraesCS7B01G168400	chr2B	93.848	2292	95	13	1	2264	563917140	563914867	0.000000e+00	3410.0
10	TraesCS7B01G168400	chr1B	92.268	2302	118	28	1	2264	38183391	38185670	0.000000e+00	3210.0
11	TraesCS7B01G168400	chr4B	97.429	1750	45	0	1	1750	402787203	402785454	0.000000e+00	2983.0
12	TraesCS7B01G168400	chr4A	97.171	1732	47	1	1	1732	712877478	712879207	0.000000e+00	2926.0
13	TraesCS7B01G168400	chr4A	91.403	1675	82	18	621	2264	698022900	698021257	0.000000e+00	2239.0
14	TraesCS7B01G168400	chr4A	94.778	517	27	0	1748	2264	712879259	712879775	0.000000e+00	806.0
15	TraesCS7B01G168400	chr4A	89.275	345	37	0	1920	2264	735294641	735294985	1.240000e-117	433.0
16	TraesCS7B01G168400	chr4A	94.714	227	12	0	2038	2264	712879431	712879657	9.950000e-94	353.0
17	TraesCS7B01G168400	chr4A	89.655	261	27	0	2004	2264	735294607	735294867	1.300000e-87	333.0
18	TraesCS7B01G168400	chr4A	92.174	230	18	0	1920	2149	712879549	712879778	2.170000e-85	326.0
19	TraesCS7B01G168400	chr4A	88.696	230	26	0	1920	2149	735294759	735294988	4.760000e-72	281.0
20	TraesCS7B01G168400	chr4A	87.209	86	7	2	1692	1777	514405870	514405789	6.660000e-16	95.3
21	TraesCS7B01G168400	chr7A	97.150	1719	48	1	1	1719	7487849	7486132	0.000000e+00	2902.0
22	TraesCS7B01G168400	chr6B	92.808	1752	76	19	557	2264	650646145	650644400	0.000000e+00	2492.0

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	TraesCS7B01G168400	chr7B	235455831	235458094	2263	True	4181.00	4181	100.00000	1	2264	1	chr7B.!!$R1	2263
1	TraesCS7B01G168400	chr7B	687040622	687042913	2291	False	3299.00	3299	92.87600	1	2264	1	chr7B.!!$F1	2263
2	TraesCS7B01G168400	chr5B	530938569	530940831	2262	True	3786.00	3786	96.86500	1	2264	1	chr5B.!!$R1	2263
3	TraesCS7B01G168400	chr5B	464634106	464636265	2159	False	3336.00	3336	94.67200	1	2149	1	chr5B.!!$F1	2148
4	TraesCS7B01G168400	chr3B	16122159	16124436	2277	True	3446.00	3446	94.11000	1	2264	1	chr3B.!!$R1	2263
5	TraesCS7B01G168400	chr3B	393329884	393331364	1480	False	2126.00	2126	92.93400	814	2264	1	chr3B.!!$F3	1450
6	TraesCS7B01G168400	chr3B	28618692	28619215	523	False	682.00	682	90.17000	1738	2264	1	chr3B.!!$F1	526
7	TraesCS7B01G168400	chr2B	563914867	563917140	2273	True	3410.00	3410	93.84800	1	2264	1	chr2B.!!$R1	2263
8	TraesCS7B01G168400	chr1B	38183391	38185670	2279	False	3210.00	3210	92.26800	1	2264	1	chr1B.!!$F1	2263
9	TraesCS7B01G168400	chr4B	402785454	402787203	1749	True	2983.00	2983	97.42900	1	1750	1	chr4B.!!$R1	1749
10	TraesCS7B01G168400	chr4A	698021257	698022900	1643	True	2239.00	2239	91.40300	621	2264	1	chr4A.!!$R2	1643
11	TraesCS7B01G168400	chr4A	712877478	712879778	2300	False	1102.75	2926	94.70925	1	2264	4	chr4A.!!$F1	2263
12	TraesCS7B01G168400	chr7A	7486132	7487849	1717	True	2902.00	2902	97.15000	1	1719	1	chr7A.!!$R1	1718
13	TraesCS7B01G168400	chr6B	650644400	650646145	1745	True	2492.00	2492	92.80800	557	2264	1	chr6B.!!$R1	1707

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
733	773	0.251653	TAGAGGTGGTGGTCGAGCTT	60.252	55.0	16.64	0.0	30.83	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1575	1652	0.247736	GTCCTCCTCTCGTGCATTGT	59.752	55.0	0.0	0.0	0.0	2.71	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
42	43	3.253188	GTGCTGCATTTGAGGTGAAACTA	59.747	43.478	5.27	0.00	36.74	2.24
154	155	3.193691	TGTTTGTGATGGAAAAACCGTGT	59.806	39.130	0.00	0.00	42.61	4.49
156	157	2.644676	TGTGATGGAAAAACCGTGTGA	58.355	42.857	0.00	0.00	42.61	3.58
458	459	5.126061	AGCGGACATGCAAGAATAAGAAAAT	59.874	36.000	0.00	0.00	37.31	1.82
733	773	0.251653	TAGAGGTGGTGGTCGAGCTT	60.252	55.000	16.64	0.00	30.83	3.74
784	824	1.800805	CACAAGTGCTAGAGGTGGTG	58.199	55.000	0.00	0.00	0.00	4.17
785	825	0.687354	ACAAGTGCTAGAGGTGGTGG	59.313	55.000	0.00	0.00	0.00	4.61
786	826	0.687354	CAAGTGCTAGAGGTGGTGGT	59.313	55.000	0.00	0.00	0.00	4.16
787	827	0.687354	AAGTGCTAGAGGTGGTGGTG	59.313	55.000	0.00	0.00	0.00	4.17
788	828	1.194781	AGTGCTAGAGGTGGTGGTGG	61.195	60.000	0.00	0.00	0.00	4.61
789	829	1.152118	TGCTAGAGGTGGTGGTGGT	60.152	57.895	0.00	0.00	0.00	4.16
790	830	1.192146	TGCTAGAGGTGGTGGTGGTC	61.192	60.000	0.00	0.00	0.00	4.02
791	831	1.890894	CTAGAGGTGGTGGTGGTCG	59.109	63.158	0.00	0.00	0.00	4.79
792	832	1.605058	CTAGAGGTGGTGGTGGTCGG	61.605	65.000	0.00	0.00	0.00	4.79
793	833	2.084089	TAGAGGTGGTGGTGGTCGGA	62.084	60.000	0.00	0.00	0.00	4.55
794	834	2.923035	AGGTGGTGGTGGTCGGAG	60.923	66.667	0.00	0.00	0.00	4.63
795	835	2.920912	GGTGGTGGTGGTCGGAGA	60.921	66.667	0.00	0.00	0.00	3.71
796	836	2.657237	GTGGTGGTGGTCGGAGAG	59.343	66.667	0.00	0.00	36.95	3.20
797	837	2.603473	TGGTGGTGGTCGGAGAGG	60.603	66.667	0.00	0.00	36.95	3.69
798	838	2.283676	GGTGGTGGTCGGAGAGGA	60.284	66.667	0.00	0.00	36.95	3.71
799	839	1.911766	GGTGGTGGTCGGAGAGGAA	60.912	63.158	0.00	0.00	36.95	3.36
800	840	1.592223	GTGGTGGTCGGAGAGGAAG	59.408	63.158	0.00	0.00	36.95	3.46
801	841	2.283529	TGGTGGTCGGAGAGGAAGC	61.284	63.158	0.00	0.00	36.95	3.86
802	842	2.283529	GGTGGTCGGAGAGGAAGCA	61.284	63.158	0.00	0.00	36.95	3.91
803	843	1.079750	GTGGTCGGAGAGGAAGCAC	60.080	63.158	0.00	0.00	36.95	4.40
804	844	1.533033	TGGTCGGAGAGGAAGCACA	60.533	57.895	0.00	0.00	36.95	4.57
805	845	1.118965	TGGTCGGAGAGGAAGCACAA	61.119	55.000	0.00	0.00	36.95	3.33
806	846	0.390472	GGTCGGAGAGGAAGCACAAG	60.390	60.000	0.00	0.00	36.95	3.16
807	847	0.318762	GTCGGAGAGGAAGCACAAGT	59.681	55.000	0.00	0.00	36.95	3.16
808	848	0.318441	TCGGAGAGGAAGCACAAGTG	59.682	55.000	0.00	0.00	0.00	3.16
1141	1217	1.067516	GGTGTGCTGATGTTTGCAAGT	59.932	47.619	0.00	0.00	41.10	3.16
1226	1302	3.780902	ACTATGCACATGATCGTCGAAA	58.219	40.909	0.00	0.00	0.00	3.46
1385	1462	5.365605	TGGATAGATCACGAGGTACCAAAAT	59.634	40.000	15.94	0.00	0.00	1.82
1487	1564	1.654954	GCGTCGTGAGAAGGAGGCTA	61.655	60.000	6.01	0.00	45.01	3.93
1575	1652	2.071778	AGAAAACTTGCAAGGGCTCA	57.928	45.000	29.18	0.00	41.91	4.26
1613	1690	0.318699	CGAGGCACGTGACAAGAAGA	60.319	55.000	26.11	0.00	37.22	2.87
1614	1691	1.865865	GAGGCACGTGACAAGAAGAA	58.134	50.000	26.11	0.00	0.00	2.52
1733	1866	4.640771	ACCTTGTGTGGTCATGAACTAT	57.359	40.909	12.94	0.00	34.86	2.12
1740	1937	7.609760	TGTGTGGTCATGAACTATTTATGTC	57.390	36.000	12.94	0.00	0.00	3.06
1983	2241	1.069765	CGCAGGTGACCAGACAAGT	59.930	57.895	3.63	0.00	0.00	3.16
2007	2266	2.029020	TCTGGTCTTTCTGATGGACACG	60.029	50.000	10.93	0.00	0.00	4.49
2048	2307	2.204136	TGCCTCCCACACCCAGAT	60.204	61.111	0.00	0.00	0.00	2.90
2051	2310	2.304056	CCTCCCACACCCAGATGCT	61.304	63.158	0.00	0.00	0.00	3.79
2082	2341	1.669115	GTCTGGCTCGCTTTGCTCA	60.669	57.895	0.00	0.00	0.00	4.26
2101	2360	1.069765	CGCAGGTGACCAGACAAGT	59.930	57.895	3.63	0.00	0.00	3.16
2149	2408	2.438434	CCAAGGTCCATGGCGTCC	60.438	66.667	6.96	9.51	0.00	4.79

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	2.843730	AGCACCACCATATTGTCTACCA	59.156	45.455	0.00	0.00	0.00	3.25
42	43	1.071471	CTGGCACCACCGAGTCTTT	59.929	57.895	0.00	0.00	43.94	2.52
154	155	3.009363	TCCAGATGGAACTCTTGCATTCA	59.991	43.478	0.00	0.00	42.07	2.57
156	157	3.726557	TCCAGATGGAACTCTTGCATT	57.273	42.857	0.00	0.00	42.07	3.56
733	773	1.073763	ACCACCTCTAGCATTTGTGCA	59.926	47.619	3.03	0.00	37.25	4.57
780	820	2.603473	CCTCTCCGACCACCACCA	60.603	66.667	0.00	0.00	0.00	4.17
781	821	1.889530	CTTCCTCTCCGACCACCACC	61.890	65.000	0.00	0.00	0.00	4.61
782	822	1.592223	CTTCCTCTCCGACCACCAC	59.408	63.158	0.00	0.00	0.00	4.16
783	823	2.283529	GCTTCCTCTCCGACCACCA	61.284	63.158	0.00	0.00	0.00	4.17
784	824	2.283529	TGCTTCCTCTCCGACCACC	61.284	63.158	0.00	0.00	0.00	4.61
785	825	1.079750	GTGCTTCCTCTCCGACCAC	60.080	63.158	0.00	0.00	0.00	4.16
786	826	1.118965	TTGTGCTTCCTCTCCGACCA	61.119	55.000	0.00	0.00	0.00	4.02
787	827	0.390472	CTTGTGCTTCCTCTCCGACC	60.390	60.000	0.00	0.00	0.00	4.79
788	828	0.318762	ACTTGTGCTTCCTCTCCGAC	59.681	55.000	0.00	0.00	0.00	4.79
789	829	0.318441	CACTTGTGCTTCCTCTCCGA	59.682	55.000	0.00	0.00	0.00	4.55
790	830	1.294659	GCACTTGTGCTTCCTCTCCG	61.295	60.000	17.36	0.00	0.00	4.63
791	831	0.036022	AGCACTTGTGCTTCCTCTCC	59.964	55.000	20.95	0.00	43.52	3.71
792	832	2.232452	TCTAGCACTTGTGCTTCCTCTC	59.768	50.000	29.37	0.00	43.52	3.20
793	833	2.233431	CTCTAGCACTTGTGCTTCCTCT	59.767	50.000	29.37	10.28	43.52	3.69
794	834	2.615869	CTCTAGCACTTGTGCTTCCTC	58.384	52.381	29.37	0.08	43.52	3.71
795	835	1.277557	CCTCTAGCACTTGTGCTTCCT	59.722	52.381	29.37	11.29	43.52	3.36
796	836	1.002544	ACCTCTAGCACTTGTGCTTCC	59.997	52.381	29.37	1.14	43.52	3.46
797	837	2.072298	CACCTCTAGCACTTGTGCTTC	58.928	52.381	29.37	1.49	43.52	3.86
798	838	1.271054	CCACCTCTAGCACTTGTGCTT	60.271	52.381	29.37	15.68	43.52	3.91
800	840	0.035458	ACCACCTCTAGCACTTGTGC	59.965	55.000	16.98	16.98	0.00	4.57
801	841	1.609061	CCACCACCTCTAGCACTTGTG	60.609	57.143	0.00	0.00	0.00	3.33
802	842	0.687354	CCACCACCTCTAGCACTTGT	59.313	55.000	0.00	0.00	0.00	3.16
803	843	0.687354	ACCACCACCTCTAGCACTTG	59.313	55.000	0.00	0.00	0.00	3.16
804	844	0.687354	CACCACCACCTCTAGCACTT	59.313	55.000	0.00	0.00	0.00	3.16
805	845	1.194781	CCACCACCACCTCTAGCACT	61.195	60.000	0.00	0.00	0.00	4.40
806	846	1.296715	CCACCACCACCTCTAGCAC	59.703	63.158	0.00	0.00	0.00	4.40
807	847	1.152118	ACCACCACCACCTCTAGCA	60.152	57.895	0.00	0.00	0.00	3.49
808	848	1.597461	GACCACCACCACCTCTAGC	59.403	63.158	0.00	0.00	0.00	3.42
809	849	0.898789	ACGACCACCACCACCTCTAG	60.899	60.000	0.00	0.00	0.00	2.43
810	850	0.405198	TACGACCACCACCACCTCTA	59.595	55.000	0.00	0.00	0.00	2.43
811	851	0.898789	CTACGACCACCACCACCTCT	60.899	60.000	0.00	0.00	0.00	3.69
812	852	0.896940	TCTACGACCACCACCACCTC	60.897	60.000	0.00	0.00	0.00	3.85
813	853	0.898789	CTCTACGACCACCACCACCT	60.899	60.000	0.00	0.00	0.00	4.00
814	854	1.590147	CTCTACGACCACCACCACC	59.410	63.158	0.00	0.00	0.00	4.61
815	855	0.896940	TCCTCTACGACCACCACCAC	60.897	60.000	0.00	0.00	0.00	4.16
962	1038	9.410556	GAACAATTGTTAGCACAAGACATAAAT	57.589	29.630	23.33	0.00	46.25	1.40
1141	1217	0.105964	CGGTCAGTGGACACCTTCAA	59.894	55.000	0.00	0.00	46.17	2.69
1226	1302	3.260475	TGTCATATGCGTTAGTTGGCT	57.740	42.857	0.00	0.00	0.00	4.75
1286	1363	9.990360	TTTGTTAGACATATGAGTGACAACTTA	57.010	29.630	10.38	0.00	36.52	2.24
1575	1652	0.247736	GTCCTCCTCTCGTGCATTGT	59.752	55.000	0.00	0.00	0.00	2.71
1613	1690	1.701292	AGTAGTACGGGGCCACTTTTT	59.299	47.619	1.96	0.00	0.00	1.94
1614	1691	1.277273	GAGTAGTACGGGGCCACTTTT	59.723	52.381	1.96	0.00	0.00	2.27
1703	1836	3.594603	ACCACACAAGGTCTCGAATAG	57.405	47.619	0.00	0.00	37.28	1.73
1740	1937	8.219769	GCACATAATCTCAAATAGTCTCGAATG	58.780	37.037	0.00	0.00	0.00	2.67
1983	2241	3.390967	TGTCCATCAGAAAGACCAGACAA	59.609	43.478	0.00	0.00	32.85	3.18
1992	2250	1.728971	GTCTGCGTGTCCATCAGAAAG	59.271	52.381	0.00	0.00	38.42	2.62
1994	2252	0.388520	CGTCTGCGTGTCCATCAGAA	60.389	55.000	0.00	0.00	38.42	3.02
2007	2266	4.021925	AGGGACCTTGGCGTCTGC	62.022	66.667	0.00	0.00	41.71	4.26
2048	2307	4.715130	ACGCCAGGGTCCCTAGCA	62.715	66.667	25.72	0.00	38.13	3.49
2051	2310	2.363795	CAGACGCCAGGGTCCCTA	60.364	66.667	11.12	0.00	37.66	3.53
2082	2341	1.069765	CTTGTCTGGTCACCTGCGT	59.930	57.895	0.00	0.00	0.00	5.24
2101	2360	2.046292	TCCATCAGACACACCAGACAA	58.954	47.619	0.00	0.00	0.00	3.18
2149	2408	2.893398	GTCTAGGTGTGGGAGGCG	59.107	66.667	0.00	0.00	0.00	5.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.