AutoCloner

Multiple sequence alignment - TraesCS6D01G325500

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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	TraesCS6D01G325500	chr6D	100.000	2144	0	0	1	2144	431399682	431397539	0.000000e+00	3960
1	TraesCS6D01G325500	chr2D	98.839	2067	12	2	1	2063	628285321	628283263	0.000000e+00	3674
2	TraesCS6D01G325500	chr2D	100.000	87	0	0	2058	2144	628289692	628289606	6.120000e-36	161
3	TraesCS6D01G325500	chr1D	98.403	2067	27	3	1	2063	254489353	254487289	0.000000e+00	3629
4	TraesCS6D01G325500	chr1D	95.884	2041	62	11	1	2036	244408269	244406246	0.000000e+00	3284
5	TraesCS6D01G325500	chr1D	95.686	2040	68	10	1	2036	244401818	244399795	0.000000e+00	3262
6	TraesCS6D01G325500	chr1D	94.860	2043	83	10	1	2036	244423806	244421779	0.000000e+00	3171
7	TraesCS6D01G325500	chr1D	98.851	87	1	0	2058	2144	254483268	254483354	2.850000e-34	156
8	TraesCS6D01G325500	chr3D	98.210	2067	29	4	1	2063	21897212	21895150	0.000000e+00	3605
9	TraesCS6D01G325500	chr3D	98.851	87	1	0	2058	2144	547383815	547383901	2.850000e-34	156
10	TraesCS6D01G325500	chr2A	97.589	2074	37	6	1	2063	276441421	276443492	0.000000e+00	3541
11	TraesCS6D01G325500	chr2A	100.000	86	0	0	2059	2144	724272136	724272221	2.200000e-35	159
12	TraesCS6D01G325500	chr3B	96.971	2080	37	8	1	2063	201506231	201504161	0.000000e+00	3469
13	TraesCS6D01G325500	chr3B	100.000	87	0	0	2058	2144	765995122	765995036	6.120000e-36	161
14	TraesCS6D01G325500	chr1A	97.781	1848	25	4	225	2063	554465601	554467441	0.000000e+00	3171
15	TraesCS6D01G325500	chr1A	100.000	87	0	0	2058	2144	554472307	554472221	6.120000e-36	161
16	TraesCS6D01G325500	chr2B	94.406	143	1	2	86	221	482854069	482853927	1.670000e-51	213
17	TraesCS6D01G325500	chr2B	100.000	101	0	0	21	121	655916504	655916404	1.010000e-43	187
18	TraesCS6D01G325500	chrUn	100.000	87	0	0	2058	2144	446839526	446839440	6.120000e-36	161
19	TraesCS6D01G325500	chr5D	100.000	87	0	0	2058	2144	483801485	483801399	6.120000e-36	161
20	TraesCS6D01G325500	chr3A	100.000	87	0	0	2058	2144	435414764	435414678	6.120000e-36	161

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	TraesCS6D01G325500	chr6D	431397539	431399682	2143	True	3960	3960	100.000	1	2144	1	chr6D.!!$R1	2143
1	TraesCS6D01G325500	chr2D	628283263	628285321	2058	True	3674	3674	98.839	1	2063	1	chr2D.!!$R1	2062
2	TraesCS6D01G325500	chr1D	254487289	254489353	2064	True	3629	3629	98.403	1	2063	1	chr1D.!!$R4	2062
3	TraesCS6D01G325500	chr1D	244406246	244408269	2023	True	3284	3284	95.884	1	2036	1	chr1D.!!$R2	2035
4	TraesCS6D01G325500	chr1D	244399795	244401818	2023	True	3262	3262	95.686	1	2036	1	chr1D.!!$R1	2035
5	TraesCS6D01G325500	chr1D	244421779	244423806	2027	True	3171	3171	94.860	1	2036	1	chr1D.!!$R3	2035
6	TraesCS6D01G325500	chr3D	21895150	21897212	2062	True	3605	3605	98.210	1	2063	1	chr3D.!!$R1	2062
7	TraesCS6D01G325500	chr2A	276441421	276443492	2071	False	3541	3541	97.589	1	2063	1	chr2A.!!$F1	2062
8	TraesCS6D01G325500	chr3B	201504161	201506231	2070	True	3469	3469	96.971	1	2063	1	chr3B.!!$R1	2062
9	TraesCS6D01G325500	chr1A	554465601	554467441	1840	False	3171	3171	97.781	225	2063	1	chr1A.!!$F1	1838

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
583	600	2.874849	TCCGTTAATAACCGACCGTTC	58.125	47.619	0.0	0.0	35.79	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2079	2111	0.179089	AGCCACTCGATTAGCTGCTG	60.179	55.0	13.43	0.0	34.89	4.41	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
549	566	3.424433	GCCAAACGAGTATTTCACGGAAG	60.424	47.826	0.00	0.00	34.65	3.46
583	600	2.874849	TCCGTTAATAACCGACCGTTC	58.125	47.619	0.00	0.00	35.79	3.95
1180	1199	9.959749	GACCAGATTGTAAACATGAAAAAGTAA	57.040	29.630	0.00	0.00	0.00	2.24
2063	2095	2.319844	AGAAGAACAAAAGGCCTTGGG	58.680	47.619	21.33	16.73	0.00	4.12
2064	2096	1.344438	GAAGAACAAAAGGCCTTGGGG	59.656	52.381	21.33	14.04	0.00	4.96
2065	2097	0.560688	AGAACAAAAGGCCTTGGGGA	59.439	50.000	21.33	0.00	33.58	4.81
2066	2098	1.062505	AGAACAAAAGGCCTTGGGGAA	60.063	47.619	21.33	0.00	33.58	3.97
2067	2099	1.765904	GAACAAAAGGCCTTGGGGAAA	59.234	47.619	21.33	0.00	33.58	3.13
2068	2100	2.116869	ACAAAAGGCCTTGGGGAAAT	57.883	45.000	21.33	0.00	33.58	2.17
2069	2101	1.699083	ACAAAAGGCCTTGGGGAAATG	59.301	47.619	21.33	11.75	33.58	2.32
2070	2102	0.692476	AAAAGGCCTTGGGGAAATGC	59.308	50.000	21.33	0.00	33.58	3.56
2071	2103	0.473501	AAAGGCCTTGGGGAAATGCA	60.474	50.000	21.33	0.00	31.52	3.96
2072	2104	1.194121	AAGGCCTTGGGGAAATGCAC	61.194	55.000	19.73	0.00	31.52	4.57
2073	2105	2.659063	GGCCTTGGGGAAATGCACC	61.659	63.158	0.00	0.00	42.04	5.01
2074	2106	1.610379	GCCTTGGGGAAATGCACCT	60.610	57.895	0.00	0.00	42.26	4.00
2075	2107	1.891722	GCCTTGGGGAAATGCACCTG	61.892	60.000	0.00	0.00	42.26	4.00
2076	2108	1.259840	CCTTGGGGAAATGCACCTGG	61.260	60.000	0.00	0.00	42.26	4.45
2077	2109	0.542702	CTTGGGGAAATGCACCTGGT	60.543	55.000	0.00	0.00	42.26	4.00
2078	2110	0.831288	TTGGGGAAATGCACCTGGTG	60.831	55.000	22.46	22.46	42.26	4.17
2087	2119	2.348620	CACCTGGTGCAGCAGCTA	59.651	61.111	34.98	6.94	42.74	3.32
2088	2120	1.302752	CACCTGGTGCAGCAGCTAA	60.303	57.895	34.98	6.54	42.74	3.09
2089	2121	0.679002	CACCTGGTGCAGCAGCTAAT	60.679	55.000	34.98	19.35	42.74	1.73
2090	2122	0.393537	ACCTGGTGCAGCAGCTAATC	60.394	55.000	34.98	0.00	42.74	1.75
2091	2123	1.434622	CCTGGTGCAGCAGCTAATCG	61.435	60.000	34.98	19.40	42.74	3.34
2092	2124	0.460811	CTGGTGCAGCAGCTAATCGA	60.461	55.000	30.93	3.07	42.74	3.59
2093	2125	0.460811	TGGTGCAGCAGCTAATCGAG	60.461	55.000	24.53	0.00	42.74	4.04
2094	2126	0.460987	GGTGCAGCAGCTAATCGAGT	60.461	55.000	17.64	0.00	42.74	4.18
2095	2127	0.649475	GTGCAGCAGCTAATCGAGTG	59.351	55.000	1.76	0.00	42.74	3.51
2096	2128	0.460811	TGCAGCAGCTAATCGAGTGG	60.461	55.000	1.76	0.00	42.74	4.00
2097	2129	1.770085	GCAGCAGCTAATCGAGTGGC	61.770	60.000	13.68	13.68	37.91	5.01
2098	2130	0.179089	CAGCAGCTAATCGAGTGGCT	60.179	55.000	18.39	18.39	37.22	4.75
2099	2131	0.539051	AGCAGCTAATCGAGTGGCTT	59.461	50.000	21.45	5.22	34.31	4.35
2100	2132	1.065854	AGCAGCTAATCGAGTGGCTTT	60.066	47.619	21.45	9.90	34.31	3.51
2101	2133	2.168521	AGCAGCTAATCGAGTGGCTTTA	59.831	45.455	21.45	0.00	34.31	1.85
2102	2134	2.541762	GCAGCTAATCGAGTGGCTTTAG	59.458	50.000	21.45	11.50	32.30	1.85
2103	2135	3.738281	GCAGCTAATCGAGTGGCTTTAGA	60.738	47.826	21.45	0.00	32.30	2.10
2104	2136	4.433615	CAGCTAATCGAGTGGCTTTAGAA	58.566	43.478	21.45	0.00	32.30	2.10
2105	2137	4.505922	CAGCTAATCGAGTGGCTTTAGAAG	59.494	45.833	21.45	5.31	32.30	2.85
2118	2150	4.670227	CTTTAGAAGCCTGTGTACAAGC	57.330	45.455	0.00	0.87	33.65	4.01
2119	2151	4.319177	CTTTAGAAGCCTGTGTACAAGCT	58.681	43.478	9.81	9.81	44.85	3.74
2120	2152	2.464157	AGAAGCCTGTGTACAAGCTC	57.536	50.000	14.61	9.58	42.36	4.09
2121	2153	1.071605	GAAGCCTGTGTACAAGCTCG	58.928	55.000	14.61	0.00	42.36	5.03
2122	2154	0.393077	AAGCCTGTGTACAAGCTCGT	59.607	50.000	14.61	0.00	42.36	4.18
2123	2155	1.254026	AGCCTGTGTACAAGCTCGTA	58.746	50.000	9.81	0.00	39.25	3.43
2124	2156	1.616865	AGCCTGTGTACAAGCTCGTAA	59.383	47.619	9.81	0.00	39.25	3.18
2125	2157	1.725164	GCCTGTGTACAAGCTCGTAAC	59.275	52.381	0.00	0.00	30.93	2.50
2126	2158	1.983605	CCTGTGTACAAGCTCGTAACG	59.016	52.381	0.00	0.00	0.00	3.18
2127	2159	2.351060	CCTGTGTACAAGCTCGTAACGA	60.351	50.000	0.00	0.00	0.00	3.85
2128	2160	3.302555	CTGTGTACAAGCTCGTAACGAA	58.697	45.455	0.00	0.00	34.74	3.85
2129	2161	3.302555	TGTGTACAAGCTCGTAACGAAG	58.697	45.455	0.00	0.00	34.74	3.79
2130	2162	2.660236	GTGTACAAGCTCGTAACGAAGG	59.340	50.000	0.00	0.00	34.74	3.46
2131	2163	2.257034	GTACAAGCTCGTAACGAAGGG	58.743	52.381	0.00	0.00	34.74	3.95
2132	2164	0.669625	ACAAGCTCGTAACGAAGGGC	60.670	55.000	0.00	0.00	34.74	5.19
2134	2166	3.551915	GCTCGTAACGAAGGGCGC	61.552	66.667	0.00	0.00	46.04	6.53
2135	2167	3.245315	CTCGTAACGAAGGGCGCG	61.245	66.667	0.00	0.00	46.04	6.86
2136	2168	3.672255	CTCGTAACGAAGGGCGCGA	62.672	63.158	12.10	0.00	46.04	5.87
2137	2169	2.581409	CGTAACGAAGGGCGCGAT	60.581	61.111	12.10	0.00	46.04	4.58
2138	2170	2.574222	CGTAACGAAGGGCGCGATC	61.574	63.158	12.10	0.00	46.04	3.69
2139	2171	1.226888	GTAACGAAGGGCGCGATCT	60.227	57.895	12.10	2.30	46.04	2.75
2140	2172	0.804933	GTAACGAAGGGCGCGATCTT	60.805	55.000	12.10	12.62	46.04	2.40
2141	2173	0.804544	TAACGAAGGGCGCGATCTTG	60.805	55.000	12.10	9.52	46.04	3.02
2142	2174	3.929948	CGAAGGGCGCGATCTTGC	61.930	66.667	12.10	5.88	0.00	4.01
2143	2175	2.512515	GAAGGGCGCGATCTTGCT	60.513	61.111	12.10	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
549	566	0.958876	AACGGAATTCCTTGTCGGCC	60.959	55.000	22.05	0.00	0.00	6.13
583	600	7.818493	TCATCGAGTTGTTCTAAAGAATCAG	57.182	36.000	0.00	0.00	36.33	2.90
1180	1199	1.112950	GTAAGGACCCGCTAAGCTCT	58.887	55.000	0.00	0.00	0.00	4.09
2070	2102	0.679002	ATTAGCTGCTGCACCAGGTG	60.679	55.000	21.18	16.16	42.90	4.00
2071	2103	0.393537	GATTAGCTGCTGCACCAGGT	60.394	55.000	17.24	17.24	44.84	4.00
2072	2104	1.434622	CGATTAGCTGCTGCACCAGG	61.435	60.000	18.42	0.19	42.74	4.45
2073	2105	0.460811	TCGATTAGCTGCTGCACCAG	60.461	55.000	18.42	4.55	42.74	4.00
2074	2106	0.460811	CTCGATTAGCTGCTGCACCA	60.461	55.000	18.42	1.07	42.74	4.17
2075	2107	0.460987	ACTCGATTAGCTGCTGCACC	60.461	55.000	18.42	0.00	42.74	5.01
2076	2108	0.649475	CACTCGATTAGCTGCTGCAC	59.351	55.000	18.42	2.22	42.74	4.57
2077	2109	0.460811	CCACTCGATTAGCTGCTGCA	60.461	55.000	18.42	0.88	42.74	4.41
2078	2110	1.770085	GCCACTCGATTAGCTGCTGC	61.770	60.000	13.43	7.62	40.05	5.25
2079	2111	0.179089	AGCCACTCGATTAGCTGCTG	60.179	55.000	13.43	0.00	34.89	4.41
2080	2112	0.539051	AAGCCACTCGATTAGCTGCT	59.461	50.000	7.57	7.57	37.05	4.24
2081	2113	1.373570	AAAGCCACTCGATTAGCTGC	58.626	50.000	0.00	0.00	35.30	5.25
2082	2114	4.046938	TCTAAAGCCACTCGATTAGCTG	57.953	45.455	0.00	0.00	35.30	4.24
2083	2115	4.688021	CTTCTAAAGCCACTCGATTAGCT	58.312	43.478	0.00	0.00	37.10	3.32
2097	2129	4.670227	GCTTGTACACAGGCTTCTAAAG	57.330	45.455	9.02	0.00	44.37	1.85
2106	2138	1.983605	CGTTACGAGCTTGTACACAGG	59.016	52.381	13.64	1.80	0.00	4.00
2107	2139	2.924903	TCGTTACGAGCTTGTACACAG	58.075	47.619	13.64	10.78	0.00	3.66
2108	2140	3.302555	CTTCGTTACGAGCTTGTACACA	58.697	45.455	13.64	0.00	37.14	3.72
2109	2141	2.660236	CCTTCGTTACGAGCTTGTACAC	59.340	50.000	13.64	13.06	37.14	2.90
2110	2142	2.352030	CCCTTCGTTACGAGCTTGTACA	60.352	50.000	13.64	2.97	37.14	2.90
2111	2143	2.257034	CCCTTCGTTACGAGCTTGTAC	58.743	52.381	13.64	8.19	37.14	2.90
2112	2144	1.403249	GCCCTTCGTTACGAGCTTGTA	60.403	52.381	9.92	9.92	37.14	2.41
2113	2145	0.669625	GCCCTTCGTTACGAGCTTGT	60.670	55.000	12.27	12.27	37.14	3.16
2114	2146	1.683790	CGCCCTTCGTTACGAGCTTG	61.684	60.000	7.69	0.00	37.14	4.01
2115	2147	1.445582	CGCCCTTCGTTACGAGCTT	60.446	57.895	7.69	0.00	37.14	3.74
2116	2148	2.181021	CGCCCTTCGTTACGAGCT	59.819	61.111	7.69	0.00	37.14	4.09
2117	2149	3.551915	GCGCCCTTCGTTACGAGC	61.552	66.667	7.69	7.47	41.07	5.03
2118	2150	2.931713	ATCGCGCCCTTCGTTACGAG	62.932	60.000	7.69	2.58	41.07	4.18
2119	2151	2.924922	GATCGCGCCCTTCGTTACGA	62.925	60.000	2.33	2.33	41.07	3.43
2120	2152	2.574222	GATCGCGCCCTTCGTTACG	61.574	63.158	0.00	0.00	41.07	3.18
2121	2153	0.804933	AAGATCGCGCCCTTCGTTAC	60.805	55.000	0.00	0.00	41.07	2.50
2122	2154	0.804544	CAAGATCGCGCCCTTCGTTA	60.805	55.000	0.00	0.00	41.07	3.18
2123	2155	2.100631	CAAGATCGCGCCCTTCGTT	61.101	57.895	0.00	0.00	41.07	3.85
2124	2156	2.509336	CAAGATCGCGCCCTTCGT	60.509	61.111	0.00	0.00	41.07	3.85
2125	2157	3.929948	GCAAGATCGCGCCCTTCG	61.930	66.667	0.00	3.73	42.12	3.79
2126	2158	2.512515	AGCAAGATCGCGCCCTTC	60.513	61.111	0.00	0.00	36.85	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.