AutoCloner

Multiple sequence alignment - TraesCS1D01G094500

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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	TraesCS1D01G094500	chr1D	100.000	1886	0	0	1	1886	80295343	80293458	0.000000e+00	3483
1	TraesCS1D01G094500	chr1D	100.000	253	0	0	2147	2399	80293197	80292945	3.610000e-128	468
2	TraesCS1D01G094500	chr2D	97.698	1303	27	3	586	1886	461088860	461090161	0.000000e+00	2237
3	TraesCS1D01G094500	chr2D	96.436	926	32	1	586	1511	76977888	76978812	0.000000e+00	1526
4	TraesCS1D01G094500	chr2D	90.755	768	44	21	1	758	461088241	461088991	0.000000e+00	1000
5	TraesCS1D01G094500	chrUn	96.626	1304	32	5	586	1886	30040432	30039138	0.000000e+00	2154
6	TraesCS1D01G094500	chrUn	95.458	1277	35	10	586	1850	32088228	32086963	0.000000e+00	2015
7	TraesCS1D01G094500	chrUn	90.382	759	45	21	12	758	30041044	30040302	0.000000e+00	972
8	TraesCS1D01G094500	chrUn	91.525	236	15	3	2148	2382	84447058	84446827	1.070000e-83	320
9	TraesCS1D01G094500	chr7A	94.806	1290	49	13	604	1886	77498338	77499616	0.000000e+00	1995
10	TraesCS1D01G094500	chr7A	94.569	1289	58	12	604	1886	559187486	559188768	0.000000e+00	1982
11	TraesCS1D01G094500	chr7A	87.030	771	66	23	2	758	77497656	77498406	0.000000e+00	839
12	TraesCS1D01G094500	chr7A	92.544	456	28	4	107	561	559186656	559187106	0.000000e+00	649
13	TraesCS1D01G094500	chr7A	92.032	251	15	4	2147	2392	559188828	559189078	4.910000e-92	348
14	TraesCS1D01G094500	chr7A	91.525	236	15	3	2148	2382	77499884	77500115	1.070000e-83	320
15	TraesCS1D01G094500	chr2A	94.651	1290	56	13	604	1886	757909986	757911269	0.000000e+00	1988
16	TraesCS1D01G094500	chr2A	95.488	1241	53	3	648	1886	45104090	45105329	0.000000e+00	1978
17	TraesCS1D01G094500	chr2A	93.761	593	34	3	1	591	45103363	45103954	0.000000e+00	887
18	TraesCS1D01G094500	chr2A	87.500	768	64	22	1	758	757909309	757910054	0.000000e+00	857
19	TraesCS1D01G094500	chr2A	93.925	214	11	1	2179	2392	757911761	757911972	2.970000e-84	322
20	TraesCS1D01G094500	chr3A	94.496	1290	59	12	604	1886	412385958	412384674	0.000000e+00	1978
21	TraesCS1D01G094500	chr3A	88.281	768	61	22	1	758	412386638	412385890	0.000000e+00	893
22	TraesCS1D01G094500	chr6D	93.683	1314	49	23	586	1886	450843900	450845192	0.000000e+00	1936
23	TraesCS1D01G094500	chr6D	92.428	766	34	18	1	758	450843281	450844030	0.000000e+00	1072
24	TraesCS1D01G094500	chr6D	89.987	759	48	20	12	758	100536132	100535390	0.000000e+00	955
25	TraesCS1D01G094500	chr6D	91.684	493	31	5	591	1080	445902413	445901928	0.000000e+00	675
26	TraesCS1D01G094500	chr6D	98.621	290	4	0	586	875	100535520	100535231	4.570000e-142	514
27	TraesCS1D01G094500	chr6D	89.130	276	7	8	2147	2399	450845480	450845755	2.970000e-84	322
28	TraesCS1D01G094500	chr5A	91.979	1309	87	8	591	1886	579247548	579248851	0.000000e+00	1820
29	TraesCS1D01G094500	chr7D	86.962	767	61	25	1	758	610751366	610752102	0.000000e+00	826
30	TraesCS1D01G094500	chr7D	91.949	236	13	4	2148	2382	610753343	610753573	2.300000e-85	326
31	TraesCS1D01G094500	chr5B	91.949	236	13	4	2148	2382	291494962	291494732	2.300000e-85	326
32	TraesCS1D01G094500	chr6B	90.717	237	15	5	2148	2382	645541569	645541800	2.320000e-80	309

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	TraesCS1D01G094500	chr1D	80292945	80295343	2398	True	1975.500000	3483	100.000000	1	2399	2	chr1D.!!$R1	2398
1	TraesCS1D01G094500	chr2D	461088241	461090161	1920	False	1618.500000	2237	94.226500	1	1886	2	chr2D.!!$F2	1885
2	TraesCS1D01G094500	chr2D	76977888	76978812	924	False	1526.000000	1526	96.436000	586	1511	1	chr2D.!!$F1	925
3	TraesCS1D01G094500	chrUn	32086963	32088228	1265	True	2015.000000	2015	95.458000	586	1850	1	chrUn.!!$R1	1264
4	TraesCS1D01G094500	chrUn	30039138	30041044	1906	True	1563.000000	2154	93.504000	12	1886	2	chrUn.!!$R3	1874
5	TraesCS1D01G094500	chr7A	77497656	77500115	2459	False	1051.333333	1995	91.120333	2	2382	3	chr7A.!!$F1	2380
6	TraesCS1D01G094500	chr7A	559186656	559189078	2422	False	993.000000	1982	93.048333	107	2392	3	chr7A.!!$F2	2285
7	TraesCS1D01G094500	chr2A	45103363	45105329	1966	False	1432.500000	1978	94.624500	1	1886	2	chr2A.!!$F1	1885
8	TraesCS1D01G094500	chr2A	757909309	757911972	2663	False	1055.666667	1988	92.025333	1	2392	3	chr2A.!!$F2	2391
9	TraesCS1D01G094500	chr3A	412384674	412386638	1964	True	1435.500000	1978	91.388500	1	1886	2	chr3A.!!$R1	1885
10	TraesCS1D01G094500	chr6D	450843281	450845755	2474	False	1110.000000	1936	91.747000	1	2399	3	chr6D.!!$F1	2398
11	TraesCS1D01G094500	chr6D	100535231	100536132	901	True	734.500000	955	94.304000	12	875	2	chr6D.!!$R2	863
12	TraesCS1D01G094500	chr5A	579247548	579248851	1303	False	1820.000000	1820	91.979000	591	1886	1	chr5A.!!$F1	1295
13	TraesCS1D01G094500	chr7D	610751366	610753573	2207	False	576.000000	826	89.455500	1	2382	2	chr7D.!!$F1	2381

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
441	448	0.460987	CCGGAAGCGAGCAGAAAGAT	60.461	55.0	0.0	0.0	0.0	2.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1816	2678	0.259065	ATGAGTCTAGGGTGCCTCGA	59.741	55.0	0.0	0.0	34.61	4.04	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
279	285	6.070366	AGGTGAGTTGGTAGAAATAGGGTTAC	60.070	42.308	0.00	0.00	0.00	2.50
441	448	0.460987	CCGGAAGCGAGCAGAAAGAT	60.461	55.000	0.00	0.00	0.00	2.40
1073	1580	2.564947	ACAGGACTGAGGACAATCTGAC	59.435	50.000	6.29	0.00	0.00	3.51
1162	1673	2.489722	GTTGGAGATGTTCAAGCCCTTC	59.510	50.000	0.00	0.00	0.00	3.46
1807	2669	4.225267	CACCCTAGACTCATTTAGGTGGTT	59.775	45.833	0.00	0.00	35.66	3.67
1808	2670	4.850386	ACCCTAGACTCATTTAGGTGGTTT	59.150	41.667	0.00	0.00	35.66	3.27
1809	2671	5.312443	ACCCTAGACTCATTTAGGTGGTTTT	59.688	40.000	0.00	0.00	35.66	2.43
1810	2672	6.183361	ACCCTAGACTCATTTAGGTGGTTTTT	60.183	38.462	0.00	0.00	35.66	1.94
1811	2673	6.374613	CCCTAGACTCATTTAGGTGGTTTTTC	59.625	42.308	0.00	0.00	35.66	2.29
1812	2674	5.941948	AGACTCATTTAGGTGGTTTTTCG	57.058	39.130	0.00	0.00	0.00	3.46
1813	2675	5.617252	AGACTCATTTAGGTGGTTTTTCGA	58.383	37.500	0.00	0.00	0.00	3.71
1814	2676	5.469084	AGACTCATTTAGGTGGTTTTTCGAC	59.531	40.000	0.00	0.00	0.00	4.20
1815	2677	4.212636	ACTCATTTAGGTGGTTTTTCGACG	59.787	41.667	0.00	0.00	0.00	5.12
1816	2678	4.128643	TCATTTAGGTGGTTTTTCGACGT	58.871	39.130	0.00	0.00	0.00	4.34
1817	2679	4.211794	TCATTTAGGTGGTTTTTCGACGTC	59.788	41.667	5.18	5.18	0.00	4.34
1818	2680	1.769733	TAGGTGGTTTTTCGACGTCG	58.230	50.000	31.30	31.30	41.45	5.12
1828	2690	3.129502	CGACGTCGAGGCACCCTA	61.130	66.667	33.35	0.00	43.02	3.53
1829	2691	2.799371	GACGTCGAGGCACCCTAG	59.201	66.667	4.75	0.00	31.76	3.02
1830	2692	1.748122	GACGTCGAGGCACCCTAGA	60.748	63.158	4.75	0.00	33.03	2.43
1833	2695	4.659986	TCGAGGCACCCTAGACTC	57.340	61.111	0.00	0.00	30.57	3.36
1834	2696	1.689412	TCGAGGCACCCTAGACTCA	59.311	57.895	0.00	0.00	30.57	3.41
1835	2697	0.259065	TCGAGGCACCCTAGACTCAT	59.741	55.000	0.00	0.00	30.57	2.90
1836	2698	1.115467	CGAGGCACCCTAGACTCATT	58.885	55.000	0.00	0.00	31.76	2.57
1837	2699	1.482593	CGAGGCACCCTAGACTCATTT	59.517	52.381	0.00	0.00	31.76	2.32
1838	2700	2.693591	CGAGGCACCCTAGACTCATTTA	59.306	50.000	0.00	0.00	31.76	1.40
1839	2701	3.243569	CGAGGCACCCTAGACTCATTTAG	60.244	52.174	0.00	0.00	31.76	1.85
1840	2702	3.041946	AGGCACCCTAGACTCATTTAGG	58.958	50.000	0.00	0.00	36.91	2.69
1841	2703	2.772515	GGCACCCTAGACTCATTTAGGT	59.227	50.000	0.00	0.00	35.66	3.08
1842	2704	3.200165	GGCACCCTAGACTCATTTAGGTT	59.800	47.826	0.00	0.00	35.66	3.50
1843	2705	4.192317	GCACCCTAGACTCATTTAGGTTG	58.808	47.826	0.00	0.00	35.66	3.77
1844	2706	4.323562	GCACCCTAGACTCATTTAGGTTGT	60.324	45.833	0.00	0.00	33.42	3.32
1845	2707	5.803470	GCACCCTAGACTCATTTAGGTTGTT	60.803	44.000	0.00	0.00	33.42	2.83
1846	2708	6.238648	CACCCTAGACTCATTTAGGTTGTTT	58.761	40.000	0.00	0.00	35.66	2.83
1847	2709	6.715264	CACCCTAGACTCATTTAGGTTGTTTT	59.285	38.462	0.00	0.00	35.66	2.43
1848	2710	7.230712	CACCCTAGACTCATTTAGGTTGTTTTT	59.769	37.037	0.00	0.00	35.66	1.94
1878	2740	2.369394	GGCACCCAAGACTCATTTAGG	58.631	52.381	0.00	0.00	0.00	2.69
1879	2741	2.290960	GGCACCCAAGACTCATTTAGGT	60.291	50.000	0.00	0.00	0.00	3.08
1880	2742	2.749621	GCACCCAAGACTCATTTAGGTG	59.250	50.000	0.00	0.00	44.85	4.00
1881	2743	3.347216	CACCCAAGACTCATTTAGGTGG	58.653	50.000	0.00	0.00	39.67	4.61
1882	2744	2.986728	ACCCAAGACTCATTTAGGTGGT	59.013	45.455	0.00	0.00	0.00	4.16
1883	2745	3.397955	ACCCAAGACTCATTTAGGTGGTT	59.602	43.478	0.00	0.00	0.00	3.67
1884	2746	4.141018	ACCCAAGACTCATTTAGGTGGTTT	60.141	41.667	0.00	0.00	0.00	3.27
1885	2747	4.832823	CCCAAGACTCATTTAGGTGGTTTT	59.167	41.667	0.00	0.00	0.00	2.43
2241	3924	6.183361	ACCCTAGACTCATTTAGGTGGTTTTT	60.183	38.462	0.00	0.00	35.66	1.94
2320	4559	6.989169	CCCTAGACTCATTTAGGTGATTCAAG	59.011	42.308	0.00	0.00	35.66	3.02
2329	4575	8.352201	TCATTTAGGTGATTCAAGTTCAACAAG	58.648	33.333	0.00	0.00	33.09	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
279	285	3.595173	GAAAATCCCCAAATCCAAACCG	58.405	45.455	0.00	0.00	0.00	4.44
441	448	1.269448	GATGCCCTCGAAAGCAACAAA	59.731	47.619	12.51	0.00	43.36	2.83
527	534	2.233271	GACCAATATGGATGCCCACAG	58.767	52.381	2.85	0.00	46.98	3.66
1073	1580	3.607422	TGTGAACAGCAAATGAGTTCG	57.393	42.857	11.76	0.00	43.36	3.95
1162	1673	2.633967	CCCTCCTCTCATTCTCATCCAG	59.366	54.545	0.00	0.00	0.00	3.86
1811	2673	3.109612	CTAGGGTGCCTCGACGTCG	62.110	68.421	31.30	31.30	41.45	5.12
1812	2674	1.748122	TCTAGGGTGCCTCGACGTC	60.748	63.158	5.18	5.18	34.61	4.34
1813	2675	2.045131	GTCTAGGGTGCCTCGACGT	61.045	63.158	0.00	0.00	36.78	4.34
1814	2676	1.716826	GAGTCTAGGGTGCCTCGACG	61.717	65.000	0.00	0.00	46.66	5.12
1815	2677	0.680280	TGAGTCTAGGGTGCCTCGAC	60.680	60.000	0.00	0.00	43.81	4.20
1816	2678	0.259065	ATGAGTCTAGGGTGCCTCGA	59.741	55.000	0.00	0.00	34.61	4.04
1817	2679	1.115467	AATGAGTCTAGGGTGCCTCG	58.885	55.000	0.00	0.00	34.61	4.63
1818	2680	3.070302	CCTAAATGAGTCTAGGGTGCCTC	59.930	52.174	0.00	0.00	34.61	4.70
1819	2681	3.041946	CCTAAATGAGTCTAGGGTGCCT	58.958	50.000	0.00	0.00	37.71	4.75
1820	2682	2.772515	ACCTAAATGAGTCTAGGGTGCC	59.227	50.000	8.40	0.00	39.29	5.01
1821	2683	4.192317	CAACCTAAATGAGTCTAGGGTGC	58.808	47.826	8.59	0.00	44.07	5.01
1823	2685	6.449830	AAACAACCTAAATGAGTCTAGGGT	57.550	37.500	8.40	0.00	39.29	4.34
1824	2686	7.761038	AAAAACAACCTAAATGAGTCTAGGG	57.239	36.000	8.40	0.00	39.29	3.53
1845	2707	1.104577	GGGTGCCCAGACGTCAAAAA	61.105	55.000	19.50	0.00	35.81	1.94
1846	2708	1.527380	GGGTGCCCAGACGTCAAAA	60.527	57.895	19.50	0.00	35.81	2.44
1847	2709	2.112297	GGGTGCCCAGACGTCAAA	59.888	61.111	19.50	0.00	35.81	2.69
1848	2710	3.164977	TGGGTGCCCAGACGTCAA	61.165	61.111	19.50	0.00	41.89	3.18
1856	2718	0.482446	AAATGAGTCTTGGGTGCCCA	59.518	50.000	5.73	5.73	45.63	5.36
1857	2719	2.369394	CTAAATGAGTCTTGGGTGCCC	58.631	52.381	0.00	0.00	0.00	5.36
1858	2720	2.290960	ACCTAAATGAGTCTTGGGTGCC	60.291	50.000	0.05	0.00	36.39	5.01
1859	2721	2.749621	CACCTAAATGAGTCTTGGGTGC	59.250	50.000	12.70	0.00	45.00	5.01
1861	2723	2.986728	ACCACCTAAATGAGTCTTGGGT	59.013	45.455	0.00	0.00	38.09	4.51
1862	2724	3.721087	ACCACCTAAATGAGTCTTGGG	57.279	47.619	0.00	0.00	0.00	4.12
2173	3456	2.771943	CCTAAATGAGTCTAGGGTGCCA	59.228	50.000	0.00	0.00	32.46	4.92
2247	3931	0.259065	TGAGTCTAGGGTGCCTCGAT	59.741	55.000	0.00	0.00	34.61	3.59
2320	4559	5.101628	TGTTGAACTTGATGCTTGTTGAAC	58.898	37.500	0.00	0.00	37.95	3.18
2329	4575	3.904571	TGATGCTTGTTGAACTTGATGC	58.095	40.909	0.00	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.