AutoCloner

Multiple sequence alignment - TraesCS2A01G350600

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	TraesCS2A01G350600	chr2A	100.000	2404	0	0	1	2404	590727198	590724795	0.000000e+00	4440.0
1	TraesCS2A01G350600	chr2A	94.366	1136	50	9	762	1894	590720303	590719179	0.000000e+00	1731.0
2	TraesCS2A01G350600	chr2A	90.856	853	43	16	764	1616	590690741	590689924	0.000000e+00	1110.0
3	TraesCS2A01G350600	chr2A	94.716	511	25	2	1895	2404	590695740	590695231	0.000000e+00	793.0
4	TraesCS2A01G350600	chr2D	92.153	2192	119	25	1	2177	446641955	446639802	0.000000e+00	3046.0
5	TraesCS2A01G350600	chr2D	96.209	211	7	1	2195	2404	446624154	446623944	6.360000e-91	344.0
6	TraesCS2A01G350600	chr2D	80.795	151	20	8	539	685	643444563	643444708	2.530000e-20	110.0
7	TraesCS2A01G350600	chr2B	90.816	980	62	16	744	1709	526525141	526524176	0.000000e+00	1286.0
8	TraesCS2A01G350600	chr2B	92.414	435	23	3	1	430	526592916	526592487	1.580000e-171	612.0
9	TraesCS2A01G350600	chr2B	88.363	507	45	7	969	1469	526397658	526397160	4.420000e-167	597.0
10	TraesCS2A01G350600	chr2B	94.833	329	15	2	424	751	526583744	526583417	1.650000e-141	512.0
11	TraesCS2A01G350600	chr2B	89.130	184	13	4	1464	1642	526396998	526396817	3.110000e-54	222.0
12	TraesCS2A01G350600	chr2B	91.852	135	11	0	1742	1876	526524176	526524042	3.150000e-44	189.0
13	TraesCS2A01G350600	chr2B	81.373	102	14	4	568	664	799380544	799380645	7.130000e-11	78.7
14	TraesCS2A01G350600	chr4A	82.840	169	26	2	1694	1860	737178697	737178530	5.350000e-32	148.0
15	TraesCS2A01G350600	chr5D	82.249	169	29	1	1691	1859	42067800	42067967	6.930000e-31	145.0
16	TraesCS2A01G350600	chr5D	80.488	164	30	1	1697	1860	328440024	328439863	9.020000e-25	124.0
17	TraesCS2A01G350600	chr5D	79.245	159	29	3	556	712	36547880	36547724	9.090000e-20	108.0
18	TraesCS2A01G350600	chr5B	81.548	168	28	3	1694	1860	36612052	36611887	4.170000e-28	135.0
19	TraesCS2A01G350600	chr5A	80.357	168	32	1	1694	1861	342342381	342342215	2.510000e-25	126.0
20	TraesCS2A01G350600	chr5A	75.877	228	43	11	513	731	414412982	414413206	3.270000e-19	106.0
21	TraesCS2A01G350600	chr4D	80.240	167	31	2	1697	1863	112100396	112100560	9.020000e-25	124.0
22	TraesCS2A01G350600	chr6A	80.488	164	26	4	553	712	115037600	115037761	1.170000e-23	121.0
23	TraesCS2A01G350600	chr3D	78.981	157	28	3	208	362	593077705	593077858	4.230000e-18	102.0
24	TraesCS2A01G350600	chr3D	79.365	126	21	4	142	264	584179130	584179253	1.530000e-12	84.2
25	TraesCS2A01G350600	chr6B	92.683	41	3	0	1630	1670	675547648	675547608	2.580000e-05	60.2
26	TraesCS2A01G350600	chr3B	100.000	28	0	0	1630	1657	52424133	52424106	4.000000e-03	52.8

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	TraesCS2A01G350600	chr2A	590724795	590727198	2403	True	4440.0	4440	100.0000	1	2404	1	chr2A.!!$R4	2403
1	TraesCS2A01G350600	chr2A	590719179	590720303	1124	True	1731.0	1731	94.3660	762	1894	1	chr2A.!!$R3	1132
2	TraesCS2A01G350600	chr2A	590689924	590690741	817	True	1110.0	1110	90.8560	764	1616	1	chr2A.!!$R1	852
3	TraesCS2A01G350600	chr2A	590695231	590695740	509	True	793.0	793	94.7160	1895	2404	1	chr2A.!!$R2	509
4	TraesCS2A01G350600	chr2D	446639802	446641955	2153	True	3046.0	3046	92.1530	1	2177	1	chr2D.!!$R2	2176
5	TraesCS2A01G350600	chr2B	526524042	526525141	1099	True	737.5	1286	91.3340	744	1876	2	chr2B.!!$R4	1132
6	TraesCS2A01G350600	chr2B	526396817	526397658	841	True	409.5	597	88.7465	969	1642	2	chr2B.!!$R3	673

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
931	940	0.24636	TCATCATCACGTCCAAGCGT	59.754	50.0	0.0	0.0	46.88	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2018	2214	0.179081	CTCTCCCCGGTCCGATTTTC	60.179	60.0	14.39	0.0	0.0	2.29	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
66	67	2.435805	GGGAGAATATCTGGTGCACTGA	59.564	50.000	17.98	15.40	0.00	3.41
68	69	4.445448	GGGAGAATATCTGGTGCACTGATT	60.445	45.833	23.28	13.64	38.52	2.57
137	138	5.828747	AGCATATTCAGACAATGTTGATGC	58.171	37.500	0.00	11.20	37.86	3.91
150	151	8.780846	ACAATGTTGATGCATGTTCATAAAAT	57.219	26.923	2.46	0.00	0.00	1.82
252	254	4.974645	AGATTTAGCCCATTATCGGACA	57.025	40.909	0.00	0.00	0.00	4.02
253	255	5.304686	AGATTTAGCCCATTATCGGACAA	57.695	39.130	0.00	0.00	0.00	3.18
283	285	7.441157	TCAAATTTGTCAGTTGTATTCTCGAGT	59.559	33.333	17.47	0.00	0.00	4.18
404	406	1.036707	TGACATCCGGTGCATCGATA	58.963	50.000	23.56	9.10	0.00	2.92
406	408	0.319900	ACATCCGGTGCATCGATAGC	60.320	55.000	23.56	5.21	0.00	2.97
429	431	2.045326	TCACAAGGGTGGGGTACTAGAT	59.955	50.000	0.00	0.00	45.32	1.98
444	446	6.095160	GGGTACTAGATACATTCCCACGATAG	59.905	46.154	0.00	0.00	37.60	2.08
477	479	2.589492	CGGTTCATCGGCTGATCGC	61.589	63.158	4.63	0.00	32.72	4.58
483	485	2.845550	ATCGGCTGATCGCTACGCA	61.846	57.895	0.90	0.00	39.13	5.24
526	529	7.387673	CCTTTGCTTTACAGGAATTTTAAAGGG	59.612	37.037	0.00	0.00	37.72	3.95
562	565	8.436778	AGAAAATTTTATTAGTGCCCTTTGGTT	58.563	29.630	2.75	0.00	0.00	3.67
563	566	8.988546	AAAATTTTATTAGTGCCCTTTGGTTT	57.011	26.923	0.37	0.00	0.00	3.27
577	580	8.010105	TGCCCTTTGGTTTATATAGAAATGGAT	58.990	33.333	0.00	0.00	0.00	3.41
617	620	7.815383	AGGATAAGAACCAATCCATCACATTA	58.185	34.615	4.31	0.00	43.55	1.90
625	628	7.161773	ACCAATCCATCACATTACAAAAGAG	57.838	36.000	0.00	0.00	0.00	2.85
670	673	7.337938	TGAAAAGATTCCTATGCTACACATCA	58.662	34.615	0.00	0.00	36.10	3.07
676	679	7.776969	AGATTCCTATGCTACACATCAAATTGT	59.223	33.333	0.00	0.00	40.38	2.71
689	692	8.906867	ACACATCAAATTGTATATCTTTCCCTG	58.093	33.333	0.00	0.00	0.00	4.45
735	738	6.996180	TTTACCTCCTATCCTATGAACCAG	57.004	41.667	0.00	0.00	0.00	4.00
741	748	6.995091	CCTCCTATCCTATGAACCAGAAAAAG	59.005	42.308	0.00	0.00	0.00	2.27
758	765	7.012799	CCAGAAAAAGGCCTTTGATAGATAGAC	59.987	40.741	31.02	9.55	32.36	2.59
879	888	1.783711	CTGAGATAAGATGCGCGTCAC	59.216	52.381	30.02	17.56	0.00	3.67
923	932	3.717400	AGCGTAATCTCATCATCACGT	57.283	42.857	0.00	0.00	0.00	4.49
925	934	2.726760	GCGTAATCTCATCATCACGTCC	59.273	50.000	0.00	0.00	0.00	4.79
926	935	3.795488	GCGTAATCTCATCATCACGTCCA	60.795	47.826	0.00	0.00	0.00	4.02
927	936	4.359706	CGTAATCTCATCATCACGTCCAA	58.640	43.478	0.00	0.00	0.00	3.53
928	937	4.442403	CGTAATCTCATCATCACGTCCAAG	59.558	45.833	0.00	0.00	0.00	3.61
930	939	0.926155	CTCATCATCACGTCCAAGCG	59.074	55.000	0.00	0.00	37.94	4.68
931	940	0.246360	TCATCATCACGTCCAAGCGT	59.754	50.000	0.00	0.00	46.88	5.07
932	941	1.474879	TCATCATCACGTCCAAGCGTA	59.525	47.619	0.00	0.00	43.83	4.42
933	942	2.094442	TCATCATCACGTCCAAGCGTAA	60.094	45.455	0.00	0.00	43.83	3.18
934	943	2.665649	TCATCACGTCCAAGCGTAAT	57.334	45.000	0.00	0.00	43.83	1.89
935	944	2.967362	TCATCACGTCCAAGCGTAATT	58.033	42.857	0.00	0.00	43.83	1.40
1333	1349	2.828549	CAACCGCACCCCATAGGC	60.829	66.667	0.00	0.00	40.58	3.93
1380	1398	3.497103	CAGGCCTGGAATGTGATGATA	57.503	47.619	26.14	0.00	0.00	2.15
1387	1405	4.554292	CTGGAATGTGATGATAGTCCGAG	58.446	47.826	0.00	0.00	33.95	4.63
1625	1815	5.982890	AATTGCACTTGGTATTTGCTACT	57.017	34.783	0.00	0.00	37.16	2.57
1713	1909	3.077556	CTCCAGTAGGGCAGCGGT	61.078	66.667	0.00	0.00	36.21	5.68
1721	1917	2.046009	TAGGGCAGCGGTGACAACAA	62.046	55.000	23.96	0.53	30.34	2.83
1732	1928	0.458716	TGACAACAACGCGTCAGTGA	60.459	50.000	14.44	0.00	37.23	3.41
2018	2214	1.482177	CCAGATCTGAGAGGTAGGGGG	60.482	61.905	24.62	0.00	0.00	5.40
2059	2255	5.096521	AGAGATCATGTGCTATGGGGAATA	58.903	41.667	0.00	0.00	0.00	1.75
2091	2287	4.903045	ATAAGACGGTTGGAGGAAGAAA	57.097	40.909	0.00	0.00	0.00	2.52
2168	2364	2.736721	TGATCGCCGAAACTGAAAAGAG	59.263	45.455	0.00	0.00	0.00	2.85
2242	2439	5.186198	GCCTACAACATCAACATAGAAGGT	58.814	41.667	0.00	0.00	0.00	3.50
2268	2465	6.037172	TCCGACTTAAAAGCATCTTCAATAGC	59.963	38.462	0.00	0.00	0.00	2.97
2286	2483	2.369394	AGCTGCCCTACAATAAAGCAC	58.631	47.619	0.00	0.00	33.08	4.40
2294	2491	5.402398	CCCTACAATAAAGCACTGAAAAGC	58.598	41.667	0.00	0.00	0.00	3.51
2390	2587	6.378280	CCCTGAAATTGATGCCCTAATATACC	59.622	42.308	0.00	0.00	0.00	2.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	67	7.672983	AATGTTCTACACGAGTTTGATGAAT	57.327	32.000	0.00	0.00	0.00	2.57
68	69	7.490962	AAAATGTTCTACACGAGTTTGATGA	57.509	32.000	0.00	0.00	0.00	2.92
118	119	6.762702	ACATGCATCAACATTGTCTGAATA	57.237	33.333	0.00	0.00	0.00	1.75
126	127	9.697250	GAATTTTATGAACATGCATCAACATTG	57.303	29.630	0.00	0.00	0.00	2.82
209	211	8.668510	ATCTAAAGTCCAACTTGTGCTATATG	57.331	34.615	0.00	0.00	38.66	1.78
237	239	3.214328	GACATTTGTCCGATAATGGGCT	58.786	45.455	0.00	0.00	39.07	5.19
253	255	9.683069	GAGAATACAACTGACAAATTTGACATT	57.317	29.630	24.64	15.34	32.85	2.71
404	406	0.844661	TACCCCACCCTTGTGATGCT	60.845	55.000	0.00	0.00	45.76	3.79
406	408	0.991920	AGTACCCCACCCTTGTGATG	59.008	55.000	0.00	0.00	45.76	3.07
429	431	1.611977	CTCGGCTATCGTGGGAATGTA	59.388	52.381	0.00	0.00	40.32	2.29
538	541	8.988546	AAACCAAAGGGCACTAATAAAATTTT	57.011	26.923	8.75	8.75	37.90	1.82
546	549	9.930158	TTTCTATATAAACCAAAGGGCACTAAT	57.070	29.630	0.00	0.00	37.90	1.73
549	552	7.287696	CCATTTCTATATAAACCAAAGGGCACT	59.712	37.037	0.00	0.00	37.90	4.40
551	554	7.358263	TCCATTTCTATATAAACCAAAGGGCA	58.642	34.615	0.00	0.00	37.90	5.36
585	588	8.742125	ATGGATTGGTTCTTATCCTACATAGA	57.258	34.615	0.00	0.00	40.80	1.98
642	645	8.579850	TGTGTAGCATAGGAATCTTTTCATTT	57.420	30.769	0.00	0.00	33.23	2.32
664	667	8.906867	ACAGGGAAAGATATACAATTTGATGTG	58.093	33.333	2.79	0.00	34.75	3.21
714	717	5.942977	TCTGGTTCATAGGATAGGAGGTA	57.057	43.478	0.00	0.00	30.70	3.08
724	727	3.701664	AGGCCTTTTTCTGGTTCATAGG	58.298	45.455	0.00	0.00	0.00	2.57
735	738	7.865706	TGTCTATCTATCAAAGGCCTTTTTC	57.134	36.000	28.42	9.25	0.00	2.29
758	765	2.224281	TGCTGACCGGGCTATCTAAATG	60.224	50.000	9.82	0.00	0.00	2.32
800	809	2.870372	GGCCAACAGTGATGACGC	59.130	61.111	0.00	0.00	0.00	5.19
860	869	1.536072	GGTGACGCGCATCTTATCTCA	60.536	52.381	5.73	0.00	0.00	3.27
879	888	3.484557	GGACGTTACACATACGCAAATGG	60.485	47.826	0.00	0.00	42.49	3.16
887	896	2.331194	ACGCTTGGACGTTACACATAC	58.669	47.619	0.00	0.00	45.75	2.39
923	932	7.639113	AAGGAAATATGAAATTACGCTTGGA	57.361	32.000	0.00	0.00	0.00	3.53
925	934	9.573133	AGAAAAGGAAATATGAAATTACGCTTG	57.427	29.630	0.00	0.00	0.00	4.01
926	935	9.573133	CAGAAAAGGAAATATGAAATTACGCTT	57.427	29.630	0.00	0.00	0.00	4.68
927	936	7.702348	GCAGAAAAGGAAATATGAAATTACGCT	59.298	33.333	0.00	0.00	0.00	5.07
928	937	7.702348	AGCAGAAAAGGAAATATGAAATTACGC	59.298	33.333	0.00	0.00	0.00	4.42
932	941	9.956720	CGATAGCAGAAAAGGAAATATGAAATT	57.043	29.630	0.00	0.00	0.00	1.82
933	942	9.342308	TCGATAGCAGAAAAGGAAATATGAAAT	57.658	29.630	0.00	0.00	0.00	2.17
934	943	8.731275	TCGATAGCAGAAAAGGAAATATGAAA	57.269	30.769	0.00	0.00	0.00	2.69
935	944	8.612619	GTTCGATAGCAGAAAAGGAAATATGAA	58.387	33.333	0.00	0.00	0.00	2.57
1380	1398	8.808092	AGCTTTATTCTATTATAAGCTCGGACT	58.192	33.333	0.00	0.00	0.00	3.85
1418	1436	5.871834	TGCTTTACTTAGCTCCCAGTAAAA	58.128	37.500	19.02	8.96	42.29	1.52
1419	1437	5.492855	TGCTTTACTTAGCTCCCAGTAAA	57.507	39.130	18.11	18.11	41.22	2.01
1625	1815	2.038033	AGACGTTTTTGTAGGCTAGGCA	59.962	45.455	19.70	1.52	0.00	4.75
1688	1884	0.828343	GCCCTACTGGAGCCGACTAT	60.828	60.000	0.00	0.00	35.39	2.12
1713	1909	0.458716	TCACTGACGCGTTGTTGTCA	60.459	50.000	15.53	4.25	42.49	3.58
1732	1928	2.227388	CACTACCGGTGTTAGAACGAGT	59.773	50.000	19.93	6.15	40.79	4.18
1799	1995	2.616842	CACCGAAAGTACAAAGCACCTT	59.383	45.455	0.00	0.00	0.00	3.50
1983	2179	4.406972	CAGATCTGGTGAGGTCCTTATCAA	59.593	45.833	15.38	0.00	28.07	2.57
2018	2214	0.179081	CTCTCCCCGGTCCGATTTTC	60.179	60.000	14.39	0.00	0.00	2.29
2059	2255	4.022329	CCAACCGTCTTATTTTCTGGCTTT	60.022	41.667	0.00	0.00	0.00	3.51
2108	2304	4.019174	AGCCATTGGATCGAAAATGAACT	58.981	39.130	6.95	11.63	36.13	3.01
2113	2309	4.678840	GCTTTGAGCCATTGGATCGAAAAT	60.679	41.667	21.09	0.00	40.43	1.82
2117	2313	1.065199	AGCTTTGAGCCATTGGATCGA	60.065	47.619	15.77	11.53	43.77	3.59
2242	2439	6.817765	ATTGAAGATGCTTTTAAGTCGGAA	57.182	33.333	0.00	0.00	0.00	4.30
2268	2465	3.609853	TCAGTGCTTTATTGTAGGGCAG	58.390	45.455	0.00	0.00	33.47	4.85
2294	2491	4.156739	GTGCCCTAAATTTCTCTCCAACTG	59.843	45.833	0.00	0.00	0.00	3.16
2345	2542	3.703052	GGGCAGATGTTGGAGATGAAAAT	59.297	43.478	0.00	0.00	0.00	1.82
2350	2547	1.211212	TCAGGGCAGATGTTGGAGATG	59.789	52.381	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.