AutoCloner

Multiple sequence alignment - TraesCS2D01G210800

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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	TraesCS2D01G210800	chr2D	100.000	2414	0	0	1	2414	167550646	167548233	0.000000e+00	4458
1	TraesCS2D01G210800	chr2D	94.831	2341	89	10	1	2336	260388079	260385766	0.000000e+00	3624
2	TraesCS2D01G210800	chr2D	94.145	2340	114	15	1	2331	450557233	450554908	0.000000e+00	3541
3	TraesCS2D01G210800	chr2D	98.734	79	1	0	2336	2414	113895344	113895266	9.000000e-30	141
4	TraesCS2D01G210800	chr2D	98.734	79	1	0	2336	2414	272606772	272606850	9.000000e-30	141
5	TraesCS2D01G210800	chr2D	98.734	79	1	0	2336	2414	301504019	301503941	9.000000e-30	141
6	TraesCS2D01G210800	chr3D	94.423	2349	118	10	1	2342	541034899	541032557	0.000000e+00	3600
7	TraesCS2D01G210800	chr3D	93.454	2322	118	13	28	2337	415199833	415197534	0.000000e+00	3415
8	TraesCS2D01G210800	chr3D	93.171	2343	127	14	1	2335	397849386	397851703	0.000000e+00	3410
9	TraesCS2D01G210800	chr3D	91.977	1720	111	11	632	2335	355324848	355326556	0.000000e+00	2386
10	TraesCS2D01G210800	chr7D	94.027	2344	120	16	1	2335	188532562	188534894	0.000000e+00	3535
11	TraesCS2D01G210800	chr5D	94.025	2343	104	10	1	2336	249656387	249654074	0.000000e+00	3518
12	TraesCS2D01G210800	chr5D	98.734	79	1	0	2336	2414	327347588	327347666	9.000000e-30	141
13	TraesCS2D01G210800	chr4D	94.057	2322	114	15	27	2337	476807252	476809560	0.000000e+00	3502
14	TraesCS2D01G210800	chr1D	93.641	2343	131	12	1	2331	349280150	349277814	0.000000e+00	3485
15	TraesCS2D01G210800	chr6B	89.862	1736	123	28	632	2331	239554140	239555858	0.000000e+00	2182
16	TraesCS2D01G210800	chr5B	89.931	1450	120	11	902	2334	569256377	569254937	0.000000e+00	1845
17	TraesCS2D01G210800	chr3A	88.307	1069	81	16	1296	2347	477692015	477690974	0.000000e+00	1242
18	TraesCS2D01G210800	chr3A	98.734	79	1	0	2336	2414	87847714	87847636	9.000000e-30	141
19	TraesCS2D01G210800	chr7A	98.734	79	1	0	2336	2414	288635910	288635832	9.000000e-30	141
20	TraesCS2D01G210800	chr7A	98.734	79	1	0	2336	2414	517641033	517640955	9.000000e-30	141
21	TraesCS2D01G210800	chr5A	98.734	79	1	0	2336	2414	624968534	624968456	9.000000e-30	141
22	TraesCS2D01G210800	chr3B	98.734	79	1	0	2336	2414	592292985	592292907	9.000000e-30	141

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	TraesCS2D01G210800	chr2D	167548233	167550646	2413	True	4458	4458	100.000	1	2414	1	chr2D.!!$R2	2413
1	TraesCS2D01G210800	chr2D	260385766	260388079	2313	True	3624	3624	94.831	1	2336	1	chr2D.!!$R3	2335
2	TraesCS2D01G210800	chr2D	450554908	450557233	2325	True	3541	3541	94.145	1	2331	1	chr2D.!!$R5	2330
3	TraesCS2D01G210800	chr3D	541032557	541034899	2342	True	3600	3600	94.423	1	2342	1	chr3D.!!$R2	2341
4	TraesCS2D01G210800	chr3D	415197534	415199833	2299	True	3415	3415	93.454	28	2337	1	chr3D.!!$R1	2309
5	TraesCS2D01G210800	chr3D	397849386	397851703	2317	False	3410	3410	93.171	1	2335	1	chr3D.!!$F2	2334
6	TraesCS2D01G210800	chr3D	355324848	355326556	1708	False	2386	2386	91.977	632	2335	1	chr3D.!!$F1	1703
7	TraesCS2D01G210800	chr7D	188532562	188534894	2332	False	3535	3535	94.027	1	2335	1	chr7D.!!$F1	2334
8	TraesCS2D01G210800	chr5D	249654074	249656387	2313	True	3518	3518	94.025	1	2336	1	chr5D.!!$R1	2335
9	TraesCS2D01G210800	chr4D	476807252	476809560	2308	False	3502	3502	94.057	27	2337	1	chr4D.!!$F1	2310
10	TraesCS2D01G210800	chr1D	349277814	349280150	2336	True	3485	3485	93.641	1	2331	1	chr1D.!!$R1	2330
11	TraesCS2D01G210800	chr6B	239554140	239555858	1718	False	2182	2182	89.862	632	2331	1	chr6B.!!$F1	1699
12	TraesCS2D01G210800	chr5B	569254937	569256377	1440	True	1845	1845	89.931	902	2334	1	chr5B.!!$R1	1432
13	TraesCS2D01G210800	chr3A	477690974	477692015	1041	True	1242	1242	88.307	1296	2347	1	chr3A.!!$R2	1051

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
807	821	0.60613	TCCCACGCGTGTACACTCTA	60.606	55.0	34.81	10.21	0.0	2.43	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2387	2481	0.104855	TATGTCCATGGCTCACGCTC	59.895	55.0	6.96	0.0	36.09	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
133	138	9.341078	ACCAAGTTTAGTATTTTTCCTCGTTAA	57.659	29.630	0.00	0.00	0.00	2.01
177	187	6.796705	ACGTCGAAGGTTTCATATTTTTCT	57.203	33.333	0.00	0.00	0.00	2.52
282	292	1.880941	CCTAACCCTAGCTCCCAACT	58.119	55.000	0.00	0.00	0.00	3.16
341	352	4.739793	CCCTCAGATCTGGTCTTCTAGAT	58.260	47.826	22.42	0.00	43.02	1.98
434	445	1.758514	GGGGCGATCAGTGAGAGGA	60.759	63.158	0.00	0.00	0.00	3.71
482	495	1.599606	CCCACCACTGACTCCTCGAG	61.600	65.000	5.13	5.13	35.52	4.04
706	720	9.185192	CCACAAACTATTCAAAAATTGTCTCTC	57.815	33.333	0.00	0.00	30.97	3.20
772	786	8.078596	TGCAATTAGCTTCTTTTTCTTCTTCTC	58.921	33.333	0.00	0.00	45.94	2.87
806	820	1.457823	TTCCCACGCGTGTACACTCT	61.458	55.000	34.81	3.57	0.00	3.24
807	821	0.606130	TCCCACGCGTGTACACTCTA	60.606	55.000	34.81	10.21	0.00	2.43
821	837	1.068753	CTCTAGATGCTGCGGTGGG	59.931	63.158	0.00	0.00	0.00	4.61
824	840	0.811616	CTAGATGCTGCGGTGGGTTC	60.812	60.000	0.00	0.00	0.00	3.62
911	927	0.777446	TTTAAGCCACCCTCTGCCTT	59.223	50.000	0.00	0.00	0.00	4.35
923	939	2.045045	TGCCTTTGCCATCCCTCG	60.045	61.111	0.00	0.00	36.33	4.63
1114	1144	1.479389	GGGCAATATCAAGGTGGAGGG	60.479	57.143	0.00	0.00	0.00	4.30
1326	1356	2.235016	GCTTTCACCACCCACAACATA	58.765	47.619	0.00	0.00	0.00	2.29
1356	1386	1.149101	ACACCAACATCTTCCCCACT	58.851	50.000	0.00	0.00	0.00	4.00
1450	1480	2.750350	CAAGGTGGAGAAGGCGGT	59.250	61.111	0.00	0.00	0.00	5.68
1545	1598	4.745351	ACTATGTGAGAGATGCTATGGGA	58.255	43.478	0.00	0.00	0.00	4.37
1659	1713	3.433598	GCTTGTTGGCCCTATCTACATGA	60.434	47.826	0.00	0.00	0.00	3.07
2003	2094	1.890979	GCATCAGCGCATGTAGGCT	60.891	57.895	11.47	0.00	40.90	4.58
2004	2095	1.442526	GCATCAGCGCATGTAGGCTT	61.443	55.000	11.47	0.00	37.41	4.35
2005	2096	0.306840	CATCAGCGCATGTAGGCTTG	59.693	55.000	11.47	0.00	37.41	4.01
2006	2097	0.816825	ATCAGCGCATGTAGGCTTGG	60.817	55.000	11.47	0.00	37.41	3.61
2007	2098	1.746615	CAGCGCATGTAGGCTTGGT	60.747	57.895	11.47	0.00	37.41	3.67
2008	2099	1.450312	AGCGCATGTAGGCTTGGTC	60.450	57.895	11.47	0.00	35.61	4.02
2009	2100	2.813179	GCGCATGTAGGCTTGGTCG	61.813	63.158	0.30	0.00	0.00	4.79
2010	2101	2.173669	CGCATGTAGGCTTGGTCGG	61.174	63.158	0.00	0.00	0.00	4.79
2011	2102	2.472909	GCATGTAGGCTTGGTCGGC	61.473	63.158	0.00	0.00	0.00	5.54
2012	2103	2.173669	CATGTAGGCTTGGTCGGCG	61.174	63.158	0.00	0.00	34.19	6.46
2013	2104	4.752879	TGTAGGCTTGGTCGGCGC	62.753	66.667	0.00	0.00	34.19	6.53
2014	2105	4.752879	GTAGGCTTGGTCGGCGCA	62.753	66.667	10.83	0.00	34.19	6.09
2015	2106	3.781307	TAGGCTTGGTCGGCGCAT	61.781	61.111	10.83	0.00	34.19	4.73
2070	2161	1.017177	GCTTGTTGGGTGCATGCATG	61.017	55.000	25.64	22.70	37.10	4.06
2093	2184	4.717629	CTTCTGTCGTGGCGGCGA	62.718	66.667	12.98	0.00	38.68	5.54
2157	2249	2.151202	CCAACGGTCAAACAGCTACAT	58.849	47.619	0.00	0.00	0.00	2.29
2253	2347	2.675423	GGGTTTCGGGCAAGGGAC	60.675	66.667	0.00	0.00	0.00	4.46
2284	2378	3.877508	ACTGAGCAAAAGTTAAGAGCGTT	59.122	39.130	0.00	0.00	0.00	4.84
2337	2431	4.381932	GGGCACAGATGTAAAAATCCCTTG	60.382	45.833	0.00	0.00	0.00	3.61
2343	2437	8.090214	CACAGATGTAAAAATCCCTTGTTTCAT	58.910	33.333	0.00	0.00	0.00	2.57
2353	2447	9.492973	AAAATCCCTTGTTTCATACTTTTGATG	57.507	29.630	0.00	0.00	0.00	3.07
2354	2448	7.781324	ATCCCTTGTTTCATACTTTTGATGT	57.219	32.000	0.00	0.00	0.00	3.06
2355	2449	7.595819	TCCCTTGTTTCATACTTTTGATGTT	57.404	32.000	0.00	0.00	0.00	2.71
2356	2450	7.657336	TCCCTTGTTTCATACTTTTGATGTTC	58.343	34.615	0.00	0.00	0.00	3.18
2357	2451	7.505585	TCCCTTGTTTCATACTTTTGATGTTCT	59.494	33.333	0.00	0.00	0.00	3.01
2358	2452	7.809806	CCCTTGTTTCATACTTTTGATGTTCTC	59.190	37.037	0.00	0.00	0.00	2.87
2359	2453	8.352201	CCTTGTTTCATACTTTTGATGTTCTCA	58.648	33.333	0.00	0.00	0.00	3.27
2360	2454	9.734620	CTTGTTTCATACTTTTGATGTTCTCAA	57.265	29.630	0.00	0.00	42.15	3.02
2379	2473	9.194716	GTTCTCAAACTTTTTAAATTTTCACGC	57.805	29.630	0.00	0.00	32.36	5.34
2380	2474	8.467402	TCTCAAACTTTTTAAATTTTCACGCA	57.533	26.923	0.00	0.00	0.00	5.24
2381	2475	8.926710	TCTCAAACTTTTTAAATTTTCACGCAA	58.073	25.926	0.00	0.00	0.00	4.85
2382	2476	9.701355	CTCAAACTTTTTAAATTTTCACGCAAT	57.299	25.926	0.00	0.00	0.00	3.56
2390	2484	7.504922	TTAAATTTTCACGCAATACATGAGC	57.495	32.000	0.00	0.00	31.06	4.26
2409	2503	2.022764	CGTGAGCCATGGACATAACA	57.977	50.000	18.40	2.44	0.00	2.41
2410	2504	1.665679	CGTGAGCCATGGACATAACAC	59.334	52.381	18.40	13.35	0.00	3.32
2411	2505	2.677902	CGTGAGCCATGGACATAACACT	60.678	50.000	18.40	0.00	0.00	3.55
2412	2506	3.430236	CGTGAGCCATGGACATAACACTA	60.430	47.826	18.40	0.00	0.00	2.74
2413	2507	4.708177	GTGAGCCATGGACATAACACTAT	58.292	43.478	18.40	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
282	292	0.387929	GGTATGATCGGACGGCTGAA	59.612	55.000	2.50	0.00	32.06	3.02
316	326	2.246067	AGAAGACCAGATCTGAGGGCTA	59.754	50.000	24.62	0.00	44.38	3.93
341	352	1.214305	AGCCAGCCCACCTAATTCCA	61.214	55.000	0.00	0.00	0.00	3.53
373	384	2.281139	TTGTGATCCAACGGCGCA	60.281	55.556	10.83	0.00	0.00	6.09
425	436	4.551215	ACCAATAGGATCTCCTCTCACT	57.449	45.455	1.00	0.00	44.77	3.41
427	438	4.406972	CACAACCAATAGGATCTCCTCTCA	59.593	45.833	1.00	0.00	44.77	3.27
434	445	2.158900	CCGAGCACAACCAATAGGATCT	60.159	50.000	0.00	0.00	38.69	2.75
636	650	9.593565	AATAAATTTGGCCCTTAAAAATTTGGA	57.406	25.926	23.66	12.05	41.30	3.53
772	786	3.708890	GTGGGAAACGGTGGTTTAAAAG	58.291	45.455	0.00	0.00	46.04	2.27
806	820	1.220749	GAACCCACCGCAGCATCTA	59.779	57.895	0.00	0.00	0.00	1.98
807	821	2.045926	GAACCCACCGCAGCATCT	60.046	61.111	0.00	0.00	0.00	2.90
911	927	0.982852	AGATGGACGAGGGATGGCAA	60.983	55.000	0.00	0.00	0.00	4.52
923	939	1.969923	CAGAGAGGATGGGAGATGGAC	59.030	57.143	0.00	0.00	0.00	4.02
1114	1144	2.954611	GGTGAAGTTCCTTGCGGC	59.045	61.111	0.00	0.00	0.00	6.53
1134	1164	1.446272	GCCGGACACGAGGAAGAAG	60.446	63.158	5.05	0.00	44.60	2.85
1326	1356	3.260884	AGATGTTGGTGTACTCCGTGAAT	59.739	43.478	9.33	1.06	0.00	2.57
1545	1598	5.543790	AGAACTTGATAAAAGGGCCAACAAT	59.456	36.000	6.18	0.00	0.00	2.71
1659	1713	8.401490	AGCTCTCTAAGAAAACAATCAACATT	57.599	30.769	0.00	0.00	0.00	2.71
1959	2031	0.812811	CCATGATGCACTGACCGAGG	60.813	60.000	0.00	0.00	0.00	4.63
1998	2089	3.781307	ATGCGCCGACCAAGCCTA	61.781	61.111	4.18	0.00	0.00	3.93
2003	2094	2.745884	CCTTCATGCGCCGACCAA	60.746	61.111	4.18	0.00	0.00	3.67
2006	2097	3.567797	GAGCCTTCATGCGCCGAC	61.568	66.667	4.18	0.00	36.02	4.79
2010	2101	3.567797	GACCGAGCCTTCATGCGC	61.568	66.667	0.00	0.00	36.02	6.09
2011	2102	3.257561	CGACCGAGCCTTCATGCG	61.258	66.667	0.00	0.00	36.02	4.73
2012	2103	2.892425	CCGACCGAGCCTTCATGC	60.892	66.667	0.00	0.00	0.00	4.06
2013	2104	2.892425	GCCGACCGAGCCTTCATG	60.892	66.667	0.00	0.00	0.00	3.07
2014	2105	4.514577	CGCCGACCGAGCCTTCAT	62.515	66.667	0.00	0.00	40.02	2.57
2039	2130	1.532316	AACAAGCCTGCCTGCATGT	60.532	52.632	0.00	0.23	44.28	3.21
2070	2161	2.743928	CCACGACAGAAGCCTGCC	60.744	66.667	0.00	0.00	44.16	4.85
2093	2184	1.861542	TTGCATTAAACGCCTGCGCT	61.862	50.000	9.73	0.00	44.19	5.92
2253	2347	2.695147	ACTTTTGCTCAGTTTTCCCCAG	59.305	45.455	0.00	0.00	0.00	4.45
2284	2378	2.783379	AGCTCTACTCATCCATCCCA	57.217	50.000	0.00	0.00	0.00	4.37
2353	2447	9.194716	GCGTGAAAATTTAAAAAGTTTGAGAAC	57.805	29.630	5.68	0.08	36.46	3.01
2354	2448	8.926710	TGCGTGAAAATTTAAAAAGTTTGAGAA	58.073	25.926	5.68	0.00	36.46	2.87
2355	2449	8.467402	TGCGTGAAAATTTAAAAAGTTTGAGA	57.533	26.923	5.68	0.00	36.46	3.27
2356	2450	9.701355	ATTGCGTGAAAATTTAAAAAGTTTGAG	57.299	25.926	5.68	0.00	36.46	3.02
2364	2458	8.431593	GCTCATGTATTGCGTGAAAATTTAAAA	58.568	29.630	0.00	0.00	42.05	1.52
2365	2459	7.201308	CGCTCATGTATTGCGTGAAAATTTAAA	60.201	33.333	13.59	0.00	42.05	1.52
2366	2460	6.250315	CGCTCATGTATTGCGTGAAAATTTAA	59.750	34.615	13.59	0.00	42.05	1.52
2367	2461	5.736824	CGCTCATGTATTGCGTGAAAATTTA	59.263	36.000	13.59	0.00	42.05	1.40
2368	2462	4.558470	CGCTCATGTATTGCGTGAAAATTT	59.442	37.500	13.59	0.00	42.05	1.82
2369	2463	4.097714	CGCTCATGTATTGCGTGAAAATT	58.902	39.130	13.59	0.00	42.05	1.82
2370	2464	3.683989	CGCTCATGTATTGCGTGAAAAT	58.316	40.909	13.59	0.00	42.05	1.82
2371	2465	3.116063	CGCTCATGTATTGCGTGAAAA	57.884	42.857	13.59	0.00	42.05	2.29
2372	2466	2.804421	CGCTCATGTATTGCGTGAAA	57.196	45.000	13.59	0.00	42.05	2.69
2378	2472	0.305922	GGCTCACGCTCATGTATTGC	59.694	55.000	0.00	0.00	36.09	3.56
2379	2473	1.655484	TGGCTCACGCTCATGTATTG	58.345	50.000	0.00	0.00	36.09	1.90
2380	2474	2.216046	CATGGCTCACGCTCATGTATT	58.784	47.619	0.00	0.00	38.69	1.89
2381	2475	1.541889	CCATGGCTCACGCTCATGTAT	60.542	52.381	0.00	0.00	40.31	2.29
2382	2476	0.179076	CCATGGCTCACGCTCATGTA	60.179	55.000	0.00	0.00	40.31	2.29
2383	2477	1.450848	CCATGGCTCACGCTCATGT	60.451	57.895	0.00	0.00	40.31	3.21
2384	2478	1.153309	TCCATGGCTCACGCTCATG	60.153	57.895	6.96	0.00	40.96	3.07
2385	2479	1.153289	GTCCATGGCTCACGCTCAT	60.153	57.895	6.96	0.00	36.09	2.90
2386	2480	1.902765	ATGTCCATGGCTCACGCTCA	61.903	55.000	6.96	0.00	36.09	4.26
2387	2481	0.104855	TATGTCCATGGCTCACGCTC	59.895	55.000	6.96	0.00	36.09	5.03
2388	2482	0.541392	TTATGTCCATGGCTCACGCT	59.459	50.000	6.96	0.00	36.09	5.07
2389	2483	0.657840	GTTATGTCCATGGCTCACGC	59.342	55.000	6.96	0.00	0.00	5.34
2390	2484	1.665679	GTGTTATGTCCATGGCTCACG	59.334	52.381	6.96	0.00	0.00	4.35
2391	2485	2.991250	AGTGTTATGTCCATGGCTCAC	58.009	47.619	6.96	9.32	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.