AutoCloner

Multiple sequence alignment - TraesCS5A01G484600

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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	TraesCS5A01G484600	chr5A	100.000	4096	0	0	1	4096	655989083	655993178	0.000000e+00	7564.0
1	TraesCS5A01G484600	chr5A	85.176	2017	249	27	1050	3045	655463794	655461807	0.000000e+00	2023.0
2	TraesCS5A01G484600	chr5A	76.570	589	128	8	2106	2686	597687192	597686606	8.550000e-82	315.0
3	TraesCS5A01G484600	chr5A	81.481	216	35	5	453	665	563329261	563329048	5.440000e-39	172.0
4	TraesCS5A01G484600	chr5D	94.836	3718	150	18	398	4096	528141385	528145079	0.000000e+00	5764.0
5	TraesCS5A01G484600	chr5D	85.075	2010	269	23	1050	3043	527907126	527905132	0.000000e+00	2021.0
6	TraesCS5A01G484600	chr5D	94.667	375	20	0	1	375	528140217	528140591	2.120000e-162	582.0
7	TraesCS5A01G484600	chr5B	96.324	1632	53	4	2465	4096	664948980	664950604	0.000000e+00	2675.0
8	TraesCS5A01G484600	chr5B	85.246	2013	260	25	1050	3043	664684964	664682970	0.000000e+00	2037.0
9	TraesCS5A01G484600	chr5B	91.142	937	53	14	131	1042	664948047	664948978	0.000000e+00	1243.0
10	TraesCS5A01G484600	chr5B	85.556	180	20	6	450	626	327602605	327602781	2.510000e-42	183.0
11	TraesCS5A01G484600	chr5B	91.071	112	10	0	1	112	664947951	664948062	7.090000e-33	152.0
12	TraesCS5A01G484600	chrUn	85.239	1233	154	21	1773	2989	263457706	263458926	0.000000e+00	1243.0
13	TraesCS5A01G484600	chrUn	96.795	156	5	0	3806	3961	147292144	147292299	1.130000e-65	261.0
14	TraesCS5A01G484600	chrUn	97.386	153	4	0	3809	3961	436598101	436597949	1.130000e-65	261.0
15	TraesCS5A01G484600	chrUn	96.154	156	6	0	3806	3961	147140686	147140841	5.250000e-64	255.0
16	TraesCS5A01G484600	chr2B	80.839	548	93	9	2148	2687	551638917	551639460	1.760000e-113	420.0
17	TraesCS5A01G484600	chr2B	76.636	107	21	4	1394	1498	551638199	551638303	5.720000e-04	56.5
18	TraesCS5A01G484600	chr2D	78.904	602	105	11	2106	2687	472471505	472472104	4.970000e-104	388.0
19	TraesCS5A01G484600	chr2A	78.347	605	106	13	2106	2687	613992508	613993110	6.470000e-98	368.0
20	TraesCS5A01G484600	chr7B	97.436	156	4	0	3806	3961	670987245	670987400	2.430000e-67	267.0
21	TraesCS5A01G484600	chr7B	97.436	156	4	0	3806	3961	671242744	671242899	2.430000e-67	267.0
22	TraesCS5A01G484600	chr6B	96.795	156	5	0	3806	3961	62220971	62221126	1.130000e-65	261.0
23	TraesCS5A01G484600	chr6B	96.154	156	6	0	3806	3961	647635591	647635746	5.250000e-64	255.0
24	TraesCS5A01G484600	chr1B	74.542	601	137	14	2093	2682	266110594	266111189	8.790000e-62	248.0
25	TraesCS5A01G484600	chr3A	81.860	215	32	6	454	665	475281059	475281269	1.510000e-39	174.0
26	TraesCS5A01G484600	chr4D	80.176	227	41	4	442	665	503360786	503361011	2.530000e-37	167.0
27	TraesCS5A01G484600	chr1A	83.815	173	26	2	486	657	551636652	551636823	3.280000e-36	163.0
28	TraesCS5A01G484600	chr7A	81.818	165	29	1	494	657	698768984	698769148	1.990000e-28	137.0
29	TraesCS5A01G484600	chr7A	81.818	165	29	1	494	657	698856010	698856174	1.990000e-28	137.0

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	TraesCS5A01G484600	chr5A	655989083	655993178	4095	False	7564.000000	7564	100.000000	1	4096	1	chr5A.!!$F1	4095
1	TraesCS5A01G484600	chr5A	655461807	655463794	1987	True	2023.000000	2023	85.176000	1050	3045	1	chr5A.!!$R3	1995
2	TraesCS5A01G484600	chr5A	597686606	597687192	586	True	315.000000	315	76.570000	2106	2686	1	chr5A.!!$R2	580
3	TraesCS5A01G484600	chr5D	528140217	528145079	4862	False	3173.000000	5764	94.751500	1	4096	2	chr5D.!!$F1	4095
4	TraesCS5A01G484600	chr5D	527905132	527907126	1994	True	2021.000000	2021	85.075000	1050	3043	1	chr5D.!!$R1	1993
5	TraesCS5A01G484600	chr5B	664682970	664684964	1994	True	2037.000000	2037	85.246000	1050	3043	1	chr5B.!!$R1	1993
6	TraesCS5A01G484600	chr5B	664947951	664950604	2653	False	1356.666667	2675	92.845667	1	4096	3	chr5B.!!$F2	4095
7	TraesCS5A01G484600	chrUn	263457706	263458926	1220	False	1243.000000	1243	85.239000	1773	2989	1	chrUn.!!$F3	1216
8	TraesCS5A01G484600	chr2B	551638199	551639460	1261	False	238.250000	420	78.737500	1394	2687	2	chr2B.!!$F1	1293
9	TraesCS5A01G484600	chr2D	472471505	472472104	599	False	388.000000	388	78.904000	2106	2687	1	chr2D.!!$F1	581
10	TraesCS5A01G484600	chr2A	613992508	613993110	602	False	368.000000	368	78.347000	2106	2687	1	chr2A.!!$F1	581
11	TraesCS5A01G484600	chr1B	266110594	266111189	595	False	248.000000	248	74.542000	2093	2682	1	chr1B.!!$F1	589

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
929	1728	0.455005	CTTCCCCGACGACTACTTCC	59.545	60.0	0.0	0.0	0.0	3.46	F
1868	2667	0.312416	CTCCCGTCGTCAGGATCATC	59.688	60.0	0.0	0.0	0.0	2.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1932	2734	0.109086	AGCAGGATCACGAGTTCACG	60.109	55.0	0.0	0.0	39.31	4.35	R
3576	4474	0.318762	GGCGCCAACCAATTTAACCA	59.681	50.0	24.8	0.0	0.00	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
75	76	0.955428	ATCGACATGCGGCAACTTGT	60.955	50.000	6.82	7.15	41.33	3.16
157	158	8.523915	TTGCATGTTATTTTCTGATAGTGGAT	57.476	30.769	0.00	0.00	0.00	3.41
164	165	8.462016	GTTATTTTCTGATAGTGGATGCAAAGT	58.538	33.333	0.00	0.00	0.00	2.66
180	181	5.792741	TGCAAAGTTTAAAATCATGGGAGG	58.207	37.500	0.00	0.00	0.00	4.30
188	190	8.096414	AGTTTAAAATCATGGGAGGAACAATTG	58.904	33.333	3.24	3.24	0.00	2.32
190	192	3.763557	ATCATGGGAGGAACAATTGGT	57.236	42.857	10.83	1.89	0.00	3.67
219	221	1.620819	CTCCCAACATCTATAGCGGCT	59.379	52.381	7.98	7.98	0.00	5.52
283	285	6.261158	CACGTGGTAGAGATGATTTCTAGAGA	59.739	42.308	7.95	0.00	33.74	3.10
312	314	5.869579	ACTGATTTTGGAGCTGTTTAGAGA	58.130	37.500	0.00	0.00	0.00	3.10
321	323	4.021894	GGAGCTGTTTAGAGAGACTTGTGA	60.022	45.833	0.00	0.00	0.00	3.58
445	1218	4.081752	CCCAATCCAATTTGAACCGAATGA	60.082	41.667	0.00	0.00	0.00	2.57
516	1293	8.105097	TCGAAAATCCAACATCACAAATTCTA	57.895	30.769	0.00	0.00	0.00	2.10
816	1614	1.202200	CGTTGGTTCTTTCGTTGCCAA	60.202	47.619	0.00	0.00	36.93	4.52
817	1615	2.732597	CGTTGGTTCTTTCGTTGCCAAA	60.733	45.455	0.00	0.00	40.37	3.28
929	1728	0.455005	CTTCCCCGACGACTACTTCC	59.545	60.000	0.00	0.00	0.00	3.46
935	1734	1.246056	CGACGACTACTTCCCCACCA	61.246	60.000	0.00	0.00	0.00	4.17
937	1736	2.381911	GACGACTACTTCCCCACCATA	58.618	52.381	0.00	0.00	0.00	2.74
975	1774	2.787249	CACGCTCAATTGCTCCCG	59.213	61.111	0.00	3.21	0.00	5.14
1005	1804	2.106332	GTCGTCGCCGGGATGATT	59.894	61.111	15.22	0.00	42.45	2.57
1042	1841	2.520741	CGCTCCTCCTCCTCCTCC	60.521	72.222	0.00	0.00	0.00	4.30
1043	1842	3.024217	GCTCCTCCTCCTCCTCCT	58.976	66.667	0.00	0.00	0.00	3.69
1044	1843	1.152546	GCTCCTCCTCCTCCTCCTC	60.153	68.421	0.00	0.00	0.00	3.71
1045	1844	1.541672	CTCCTCCTCCTCCTCCTCC	59.458	68.421	0.00	0.00	0.00	4.30
1046	1845	1.230650	TCCTCCTCCTCCTCCTCCA	60.231	63.158	0.00	0.00	0.00	3.86
1047	1846	1.232792	CCTCCTCCTCCTCCTCCAG	59.767	68.421	0.00	0.00	0.00	3.86
1048	1847	1.232792	CTCCTCCTCCTCCTCCAGG	59.767	68.421	0.00	0.00	45.15	4.45
1052	1851	2.235602	CTCCTCCTCCTCCAGGCTCA	62.236	65.000	0.00	0.00	43.08	4.26
1334	2133	2.809601	GCTCGCACCGTCGATTGT	60.810	61.111	0.00	0.00	37.87	2.71
1434	2233	2.835705	CGCCGTCGAGCTGGATACT	61.836	63.158	0.38	0.00	38.10	2.12
1446	2245	1.337384	TGGATACTGCCATGGACGCT	61.337	55.000	18.40	0.00	31.66	5.07
1508	2307	2.105128	CGGCCTCCGCTCTGTTAG	59.895	66.667	0.00	0.00	41.17	2.34
1542	2341	2.669229	TACTGGCACGACGACGGA	60.669	61.111	12.58	0.00	44.46	4.69
1806	2605	3.249189	TGGAGCTTTCGCCTGGGT	61.249	61.111	0.00	0.00	36.60	4.51
1839	2638	2.103373	CAGGACCTCGATCTCTCCAAA	58.897	52.381	0.00	0.00	0.00	3.28
1868	2667	0.312416	CTCCCGTCGTCAGGATCATC	59.688	60.000	0.00	0.00	0.00	2.92
1869	2668	1.008424	CCCGTCGTCAGGATCATCG	60.008	63.158	0.00	0.00	0.00	3.84
1931	2733	4.057428	GCTGCTCGTCCTGGTCGT	62.057	66.667	12.76	0.00	0.00	4.34
1932	2734	2.179517	CTGCTCGTCCTGGTCGTC	59.820	66.667	12.76	7.19	0.00	4.20
1933	2735	3.669036	CTGCTCGTCCTGGTCGTCG	62.669	68.421	12.76	7.04	0.00	5.12
1934	2736	3.735029	GCTCGTCCTGGTCGTCGT	61.735	66.667	12.76	0.00	0.00	4.34
1935	2737	2.176055	CTCGTCCTGGTCGTCGTG	59.824	66.667	12.76	3.03	0.00	4.35
1936	2738	2.281002	TCGTCCTGGTCGTCGTGA	60.281	61.111	12.76	0.00	0.00	4.35
1937	2739	1.848932	CTCGTCCTGGTCGTCGTGAA	61.849	60.000	12.76	0.00	0.00	3.18
1938	2740	1.728426	CGTCCTGGTCGTCGTGAAC	60.728	63.158	5.15	0.00	33.68	3.18
2033	2886	3.077695	AGGAAGAAGACTGGGAGGTAGAA	59.922	47.826	0.00	0.00	0.00	2.10
2057	2910	1.055040	GCCCTCACAGGATCAGCTAT	58.945	55.000	0.00	0.00	37.67	2.97
2060	2913	3.071602	GCCCTCACAGGATCAGCTATAAA	59.928	47.826	0.00	0.00	37.67	1.40
2129	2988	4.071875	TTCGGCCGCGTGTACCAT	62.072	61.111	23.51	0.00	0.00	3.55
2132	2991	4.770874	GGCCGCGTGTACCATGGT	62.771	66.667	23.55	23.55	0.00	3.55
2264	3129	1.228367	CAACCTGGTGCAGCTCCTT	60.228	57.895	18.08	2.20	0.00	3.36
2912	3810	2.124819	CAGATGCTGGAAGGCGCT	60.125	61.111	7.64	0.00	34.52	5.92
3005	3903	1.957562	CGGGTTCGTCAGAGTGTCT	59.042	57.895	0.00	0.00	0.00	3.41
3103	4001	4.640364	CTCCTCTTCAGCTGAAAGTTCTT	58.360	43.478	28.16	0.00	35.30	2.52
3105	4003	5.059833	TCCTCTTCAGCTGAAAGTTCTTTC	58.940	41.667	28.16	15.70	35.30	2.62
3114	4012	4.301628	CTGAAAGTTCTTTCCAATGTGGC	58.698	43.478	18.60	0.00	37.47	5.01
3129	4027	0.039165	GTGGCAGCTAGTTTGCAACC	60.039	55.000	18.75	0.00	43.28	3.77
3131	4029	1.210155	GCAGCTAGTTTGCAACCGG	59.790	57.895	14.12	0.00	41.17	5.28
3133	4031	1.971695	AGCTAGTTTGCAACCGGGC	60.972	57.895	6.32	0.00	34.99	6.13
3224	4122	3.079578	CAGCTGATTCAGAAAAGAGGCA	58.920	45.455	17.87	0.00	32.44	4.75
3309	4207	0.962356	ACAGGCAAAATCGGCAGGAG	60.962	55.000	0.00	0.00	0.00	3.69
3364	4262	3.661131	CGCTCCGATCCGATCCGT	61.661	66.667	2.69	0.00	0.00	4.69
3499	4397	1.425066	AGGATGACAAACAAGAGGGCA	59.575	47.619	0.00	0.00	0.00	5.36
3576	4474	6.769822	CCCTGTAGACATGAAGAAAGCAATAT	59.230	38.462	0.00	0.00	0.00	1.28
3732	4630	2.398554	GCAAGGGCGAGAATGCGAA	61.399	57.895	0.00	0.00	35.06	4.70
3844	4742	1.212935	AGCCAGCTTATCGGACCAAAT	59.787	47.619	0.00	0.00	0.00	2.32
3886	4784	5.350365	GCATGTTAATTTCTCGTACCACTCA	59.650	40.000	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
143	144	6.899393	AAACTTTGCATCCACTATCAGAAA	57.101	33.333	0.00	0.00	0.00	2.52
157	158	5.541868	TCCTCCCATGATTTTAAACTTTGCA	59.458	36.000	0.00	0.00	0.00	4.08
164	165	7.017056	ACCAATTGTTCCTCCCATGATTTTAAA	59.983	33.333	4.43	0.00	0.00	1.52
180	181	2.212900	GAGGCCGCCACCAATTGTTC	62.213	60.000	13.15	0.00	0.00	3.18
219	221	2.202690	CGATTGCCCGCTACGACA	60.203	61.111	0.00	0.00	0.00	4.35
248	250	2.215196	TCTACCACGTGAAAAGTTGCC	58.785	47.619	19.30	0.00	0.00	4.52
283	285	9.696917	CTAAACAGCTCCAAAATCAGTAAAAAT	57.303	29.630	0.00	0.00	0.00	1.82
312	314	3.181454	ACCACGAAATCCTTCACAAGTCT	60.181	43.478	0.00	0.00	0.00	3.24
321	323	1.244019	GCTGCCACCACGAAATCCTT	61.244	55.000	0.00	0.00	0.00	3.36
384	386	2.045829	TCCCGCAAAATAGCCGCA	60.046	55.556	0.00	0.00	0.00	5.69
665	1442	8.036585	TCCCTCCGTTCCATATAGATTAAAAA	57.963	34.615	0.00	0.00	0.00	1.94
670	1447	4.753186	ACTCCCTCCGTTCCATATAGATT	58.247	43.478	0.00	0.00	0.00	2.40
671	1448	4.405756	ACTCCCTCCGTTCCATATAGAT	57.594	45.455	0.00	0.00	0.00	1.98
673	1450	7.666388	CCTATATACTCCCTCCGTTCCATATAG	59.334	44.444	0.00	0.00	31.77	1.31
680	1477	4.920999	ACTCCTATATACTCCCTCCGTTC	58.079	47.826	0.00	0.00	0.00	3.95
929	1728	4.499633	GCGGTGGGGTATGGTGGG	62.500	72.222	0.00	0.00	0.00	4.61
998	1797	3.957535	CGGCCAGCGCAATCATCC	61.958	66.667	11.47	0.25	36.38	3.51
1022	1821	2.520741	GGAGGAGGAGGAGCGAGG	60.521	72.222	0.00	0.00	0.00	4.63
1027	1826	1.292941	TGGAGGAGGAGGAGGAGGAG	61.293	65.000	0.00	0.00	0.00	3.69
1069	1868	1.216941	CCGGCGTACACAAACTCGTT	61.217	55.000	6.01	0.00	0.00	3.85
1323	2122	0.320421	CAGGGACAACAATCGACGGT	60.320	55.000	0.00	0.00	0.00	4.83
1434	2233	1.375908	GAACTCAGCGTCCATGGCA	60.376	57.895	6.96	0.00	0.00	4.92
1446	2245	3.348205	TCGGCGTCGTCGAACTCA	61.348	61.111	21.06	0.00	36.50	3.41
1542	2341	1.000060	TCGAACTTCGTTCCACCGAAT	60.000	47.619	10.88	0.00	44.93	3.34
1593	2392	1.607801	CGATCCACACCTGCAGAGGA	61.608	60.000	17.39	16.51	42.93	3.71
1830	2629	1.258445	GCCTCGGGAGTTTGGAGAGA	61.258	60.000	0.00	0.00	0.00	3.10
1860	2659	1.355112	TGGATGATGGCGATGATCCT	58.645	50.000	23.61	0.00	41.66	3.24
1868	2667	0.933097	CGTTCTCTTGGATGATGGCG	59.067	55.000	0.00	0.00	0.00	5.69
1869	2668	2.315925	TCGTTCTCTTGGATGATGGC	57.684	50.000	0.00	0.00	0.00	4.40
1931	2733	0.109272	GCAGGATCACGAGTTCACGA	60.109	55.000	0.00	0.00	37.03	4.35
1932	2734	0.109086	AGCAGGATCACGAGTTCACG	60.109	55.000	0.00	0.00	39.31	4.35
1933	2735	1.634702	GAGCAGGATCACGAGTTCAC	58.365	55.000	0.00	0.00	0.00	3.18
1934	2736	0.532573	GGAGCAGGATCACGAGTTCA	59.467	55.000	0.00	0.00	0.00	3.18
1935	2737	0.820871	AGGAGCAGGATCACGAGTTC	59.179	55.000	0.00	0.00	0.00	3.01
1936	2738	0.534412	CAGGAGCAGGATCACGAGTT	59.466	55.000	0.00	0.00	0.00	3.01
1937	2739	1.326213	CCAGGAGCAGGATCACGAGT	61.326	60.000	0.00	0.00	0.00	4.18
1938	2740	1.440893	CCAGGAGCAGGATCACGAG	59.559	63.158	0.00	0.00	0.00	4.18
2033	2886	0.398522	TGATCCTGTGAGGGCCGTAT	60.399	55.000	0.00	0.00	35.59	3.06
2057	2910	4.255126	GCGTCGTGCAGGTCTTTA	57.745	55.556	6.26	0.00	45.45	1.85
2078	2931	0.672401	TGAGGTCGCGGAAACCATTC	60.672	55.000	16.76	7.77	39.39	2.67
2129	2988	3.311110	GACCTCGGGAGCACACCA	61.311	66.667	0.00	0.00	0.00	4.17
2189	3054	3.635268	GAACTCCTGCAGCCCCTGG	62.635	68.421	8.66	0.00	31.21	4.45
2871	3769	4.172512	CTGCCTCATGCTCGGCCT	62.173	66.667	15.05	0.00	45.71	5.19
2877	3775	2.353958	CACCACCTGCCTCATGCT	59.646	61.111	0.00	0.00	42.00	3.79
2930	3828	1.261938	TTCCAAGATCCTCCGGCGAA	61.262	55.000	9.30	0.00	0.00	4.70
2997	3895	0.597072	GTCGACGGGAAAGACACTCT	59.403	55.000	0.00	0.00	35.19	3.24
3005	3903	2.646719	CCTGACGTCGACGGGAAA	59.353	61.111	37.89	20.51	44.95	3.13
3103	4001	2.557924	CAAACTAGCTGCCACATTGGAA	59.442	45.455	0.00	0.00	40.96	3.53
3105	4003	1.403249	GCAAACTAGCTGCCACATTGG	60.403	52.381	0.00	0.00	41.55	3.16
3131	4029	3.877508	GTGTGTGTATCTATGGGAAAGCC	59.122	47.826	0.00	0.00	0.00	4.35
3133	4031	7.224753	GTGTATGTGTGTGTATCTATGGGAAAG	59.775	40.741	0.00	0.00	0.00	2.62
3248	4146	4.041740	TGCATCGATCTGTAGTTGTACC	57.958	45.455	0.00	0.00	0.00	3.34
3309	4207	0.460459	GCGTCTCCCTGTAAAGCTCC	60.460	60.000	0.00	0.00	0.00	4.70
3346	4244	3.661131	CGGATCGGATCGGAGCGT	61.661	66.667	17.77	0.00	0.00	5.07
3364	4262	1.984570	CTCTTCCCTGTCCGCTCCA	60.985	63.158	0.00	0.00	0.00	3.86
3576	4474	0.318762	GGCGCCAACCAATTTAACCA	59.681	50.000	24.80	0.00	0.00	3.67
3732	4630	2.874701	GGATCAAATGCGCTAGTGACAT	59.125	45.455	9.73	7.39	0.00	3.06
3844	4742	2.098614	TGCCTTGTGTTTCAGCTTTCA	58.901	42.857	0.00	0.00	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.