AutoCloner

Multiple sequence alignment - TraesCS5D01G017800

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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	TraesCS5D01G017800	chr5D	100.000	2357	0	0	1	2357	10472109	10469753	0.000000e+00	4353.0
1	TraesCS5D01G017800	chr5D	95.441	1338	54	4	631	1962	275171748	275170412	0.000000e+00	2126.0
2	TraesCS5D01G017800	chr1D	96.351	1343	41	5	631	1966	60171816	60170475	0.000000e+00	2202.0
3	TraesCS5D01G017800	chr1D	95.590	1338	48	4	631	1962	205134697	205133365	0.000000e+00	2134.0
4	TraesCS5D01G017800	chr1D	95.312	1344	53	5	631	1966	247505758	247504417	0.000000e+00	2124.0
5	TraesCS5D01G017800	chr1D	95.231	1342	54	6	631	1966	461539160	461540497	0.000000e+00	2115.0
6	TraesCS5D01G017800	chr1D	84.524	84	13	0	2144	2227	458288727	458288644	1.500000e-12	84.2
7	TraesCS5D01G017800	chr2D	96.071	1349	46	4	631	1972	73126872	73125524	0.000000e+00	2191.0
8	TraesCS5D01G017800	chr2D	95.607	1343	49	7	631	1966	621748803	621750142	0.000000e+00	2145.0
9	TraesCS5D01G017800	chr3D	95.740	1338	51	3	631	1962	584701392	584700055	0.000000e+00	2150.0
10	TraesCS5D01G017800	chr7D	95.590	1338	51	5	631	1962	497560907	497562242	0.000000e+00	2137.0
11	TraesCS5D01G017800	chr5A	93.972	647	21	1	1	629	8187946	8187300	0.000000e+00	963.0
12	TraesCS5D01G017800	chr5A	92.708	384	10	6	1988	2357	8187321	8186942	2.670000e-149	538.0
13	TraesCS5D01G017800	chr5B	83.707	669	68	13	1	629	10524776	10525443	5.610000e-166	593.0
14	TraesCS5D01G017800	chr5B	82.712	671	70	20	1	629	10432060	10431394	2.650000e-154	555.0
15	TraesCS5D01G017800	chr5B	86.196	326	32	8	1988	2305	10431415	10431095	8.070000e-90	340.0
16	TraesCS5D01G017800	chr7A	87.952	83	10	0	2145	2227	42801445	42801527	5.360000e-17	99.0
17	TraesCS5D01G017800	chr4B	90.566	53	4	1	1	52	9703137	9703085	4.200000e-08	69.4
18	TraesCS5D01G017800	chr6D	91.304	46	2	2	1	44	85798384	85798429	7.030000e-06	62.1
19	TraesCS5D01G017800	chr6A	91.304	46	2	2	1	44	103001027	103001072	7.030000e-06	62.1
20	TraesCS5D01G017800	chr3A	100.000	28	0	0	4	31	17227262	17227235	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	TraesCS5D01G017800	chr5D	10469753	10472109	2356	True	4353.0	4353	100.000	1	2357	1	chr5D.!!$R1	2356
1	TraesCS5D01G017800	chr5D	275170412	275171748	1336	True	2126.0	2126	95.441	631	1962	1	chr5D.!!$R2	1331
2	TraesCS5D01G017800	chr1D	60170475	60171816	1341	True	2202.0	2202	96.351	631	1966	1	chr1D.!!$R1	1335
3	TraesCS5D01G017800	chr1D	205133365	205134697	1332	True	2134.0	2134	95.590	631	1962	1	chr1D.!!$R2	1331
4	TraesCS5D01G017800	chr1D	247504417	247505758	1341	True	2124.0	2124	95.312	631	1966	1	chr1D.!!$R3	1335
5	TraesCS5D01G017800	chr1D	461539160	461540497	1337	False	2115.0	2115	95.231	631	1966	1	chr1D.!!$F1	1335
6	TraesCS5D01G017800	chr2D	73125524	73126872	1348	True	2191.0	2191	96.071	631	1972	1	chr2D.!!$R1	1341
7	TraesCS5D01G017800	chr2D	621748803	621750142	1339	False	2145.0	2145	95.607	631	1966	1	chr2D.!!$F1	1335
8	TraesCS5D01G017800	chr3D	584700055	584701392	1337	True	2150.0	2150	95.740	631	1962	1	chr3D.!!$R1	1331
9	TraesCS5D01G017800	chr7D	497560907	497562242	1335	False	2137.0	2137	95.590	631	1962	1	chr7D.!!$F1	1331
10	TraesCS5D01G017800	chr5A	8186942	8187946	1004	True	750.5	963	93.340	1	2357	2	chr5A.!!$R1	2356
11	TraesCS5D01G017800	chr5B	10524776	10525443	667	False	593.0	593	83.707	1	629	1	chr5B.!!$F1	628
12	TraesCS5D01G017800	chr5B	10431095	10432060	965	True	447.5	555	84.454	1	2305	2	chr5B.!!$R1	2304

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
625	667	0.249868	CTGCCTTCCAACACGACAGA	60.25	55.0	0.0	0.0	0.0	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1990	2041	0.249911	GCTCTGTCGTGTTGGGAAGT	60.25	55.0	0.0	0.0	0.0	3.01	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
81	83	0.319211	TGCCTTCCACTTACGACGTG	60.319	55.000	11.56	0.00	0.00	4.49
277	279	3.120304	GGTTGCTTCGTAGTGGTCATTTC	60.120	47.826	0.00	0.00	0.00	2.17
339	341	5.057149	ACTACAAGAAACAGAAATGTCGCT	58.943	37.500	0.00	0.00	0.00	4.93
479	502	6.270927	AGGATCCTGCAAGTATACATGTATGT	59.729	38.462	25.48	11.79	44.48	2.29
482	505	6.280643	TCCTGCAAGTATACATGTATGTCAC	58.719	40.000	25.48	16.65	41.97	3.67
616	658	2.436109	GTCCCTGCTGCCTTCCAA	59.564	61.111	0.00	0.00	0.00	3.53
617	659	1.973812	GTCCCTGCTGCCTTCCAAC	60.974	63.158	0.00	0.00	0.00	3.77
618	660	2.115910	CCCTGCTGCCTTCCAACA	59.884	61.111	0.00	0.00	0.00	3.33
619	661	2.270986	CCCTGCTGCCTTCCAACAC	61.271	63.158	0.00	0.00	0.00	3.32
620	662	2.620112	CCTGCTGCCTTCCAACACG	61.620	63.158	0.00	0.00	0.00	4.49
621	663	1.597854	CTGCTGCCTTCCAACACGA	60.598	57.895	0.00	0.00	0.00	4.35
622	664	1.845809	CTGCTGCCTTCCAACACGAC	61.846	60.000	0.00	0.00	0.00	4.34
623	665	1.891919	GCTGCCTTCCAACACGACA	60.892	57.895	0.00	0.00	0.00	4.35
624	666	1.845809	GCTGCCTTCCAACACGACAG	61.846	60.000	0.00	0.00	0.00	3.51
625	667	0.249868	CTGCCTTCCAACACGACAGA	60.250	55.000	0.00	0.00	0.00	3.41
626	668	0.249868	TGCCTTCCAACACGACAGAG	60.250	55.000	0.00	0.00	0.00	3.35
627	669	1.569479	GCCTTCCAACACGACAGAGC	61.569	60.000	0.00	0.00	0.00	4.09
628	670	0.951040	CCTTCCAACACGACAGAGCC	60.951	60.000	0.00	0.00	0.00	4.70
629	671	0.951040	CTTCCAACACGACAGAGCCC	60.951	60.000	0.00	0.00	0.00	5.19
656	698	5.222130	TTTTCTAGAAAAGGAGGATGCACCT	60.222	40.000	23.65	7.46	42.28	4.00
837	883	2.223688	CCAAACAGACATCGCACCAAAA	60.224	45.455	0.00	0.00	0.00	2.44
893	939	0.326238	ATACCGGGACTGGGTCACAT	60.326	55.000	6.32	0.00	35.39	3.21
981	1027	2.031012	CGCACAGACCTTGCCAGA	59.969	61.111	0.00	0.00	36.57	3.86
984	1030	1.302832	CACAGACCTTGCCAGACCC	60.303	63.158	0.00	0.00	0.00	4.46
1217	1263	1.841556	AGTTCCTCCCAAGACGGCA	60.842	57.895	0.00	0.00	0.00	5.69
1539	1586	5.776358	AGAACTCCTTGTAGATCTCCAGAT	58.224	41.667	0.00	0.00	37.51	2.90
1551	1598	1.770658	TCTCCAGATGCCGAATCCAAT	59.229	47.619	0.00	0.00	35.72	3.16
1586	1633	1.816537	CGACGATCATCACCACCCT	59.183	57.895	0.00	0.00	0.00	4.34
1620	1667	2.236395	GGAGTCCGAAGAAAGGATCCAA	59.764	50.000	15.82	0.00	40.30	3.53
1767	1814	4.402528	CCGGACCCCACATTCGCA	62.403	66.667	0.00	0.00	0.00	5.10
1770	1817	2.047655	GACCCCACATTCGCACGA	60.048	61.111	0.00	0.00	0.00	4.35
1771	1818	1.449601	GACCCCACATTCGCACGAT	60.450	57.895	0.00	0.00	0.00	3.73
1781	1828	3.186909	CATTCGCACGATGTTCCTCTAA	58.813	45.455	0.00	0.00	0.00	2.10
1967	2018	3.138798	GCGAGCGAGGGGTGAGTA	61.139	66.667	0.00	0.00	0.00	2.59
1968	2019	2.491022	GCGAGCGAGGGGTGAGTAT	61.491	63.158	0.00	0.00	0.00	2.12
1969	2020	1.655329	CGAGCGAGGGGTGAGTATC	59.345	63.158	0.00	0.00	0.00	2.24
1970	2021	0.820074	CGAGCGAGGGGTGAGTATCT	60.820	60.000	0.00	0.00	34.92	1.98
1971	2022	0.955905	GAGCGAGGGGTGAGTATCTC	59.044	60.000	0.00	0.00	34.92	2.75
1972	2023	0.259065	AGCGAGGGGTGAGTATCTCA	59.741	55.000	0.00	0.00	38.25	3.27
1973	2024	1.112113	GCGAGGGGTGAGTATCTCAA	58.888	55.000	0.88	0.00	42.46	3.02
1974	2025	1.480954	GCGAGGGGTGAGTATCTCAAA	59.519	52.381	0.88	0.00	42.46	2.69
1975	2026	2.482142	GCGAGGGGTGAGTATCTCAAAG	60.482	54.545	0.88	0.00	42.46	2.77
1976	2027	2.761208	CGAGGGGTGAGTATCTCAAAGT	59.239	50.000	0.88	0.00	42.46	2.66
1977	2028	3.429547	CGAGGGGTGAGTATCTCAAAGTG	60.430	52.174	0.88	0.00	42.46	3.16
1978	2029	3.515901	GAGGGGTGAGTATCTCAAAGTGT	59.484	47.826	0.88	0.00	42.46	3.55
1979	2030	3.261897	AGGGGTGAGTATCTCAAAGTGTG	59.738	47.826	0.88	0.00	42.46	3.82
1980	2031	3.008049	GGGGTGAGTATCTCAAAGTGTGT	59.992	47.826	0.88	0.00	42.46	3.72
1981	2032	4.222145	GGGGTGAGTATCTCAAAGTGTGTA	59.778	45.833	0.88	0.00	42.46	2.90
1982	2033	5.411781	GGGTGAGTATCTCAAAGTGTGTAG	58.588	45.833	0.88	0.00	42.46	2.74
1983	2034	5.047235	GGGTGAGTATCTCAAAGTGTGTAGT	60.047	44.000	0.88	0.00	42.46	2.73
1984	2035	6.456501	GGTGAGTATCTCAAAGTGTGTAGTT	58.543	40.000	0.88	0.00	42.46	2.24
1985	2036	6.366332	GGTGAGTATCTCAAAGTGTGTAGTTG	59.634	42.308	0.88	0.00	42.46	3.16
1986	2037	6.366332	GTGAGTATCTCAAAGTGTGTAGTTGG	59.634	42.308	0.88	0.00	42.46	3.77
1987	2038	6.041637	TGAGTATCTCAAAGTGTGTAGTTGGT	59.958	38.462	0.00	0.00	37.57	3.67
1988	2039	6.223852	AGTATCTCAAAGTGTGTAGTTGGTG	58.776	40.000	0.00	0.00	0.00	4.17
1989	2040	3.202906	TCTCAAAGTGTGTAGTTGGTGC	58.797	45.455	0.00	0.00	0.00	5.01
1990	2041	2.942376	CTCAAAGTGTGTAGTTGGTGCA	59.058	45.455	0.00	0.00	0.00	4.57
1991	2042	2.680841	TCAAAGTGTGTAGTTGGTGCAC	59.319	45.455	8.80	8.80	41.90	4.57
1992	2043	2.682856	CAAAGTGTGTAGTTGGTGCACT	59.317	45.455	17.98	0.00	42.05	4.40
1993	2044	2.710096	AGTGTGTAGTTGGTGCACTT	57.290	45.000	17.98	2.97	42.05	3.16
1994	2045	2.561569	AGTGTGTAGTTGGTGCACTTC	58.438	47.619	17.98	7.52	42.05	3.01
1995	2046	1.602377	GTGTGTAGTTGGTGCACTTCC	59.398	52.381	17.98	0.00	42.05	3.46
1996	2047	1.235724	GTGTAGTTGGTGCACTTCCC	58.764	55.000	17.98	0.00	38.66	3.97
1997	2048	0.840617	TGTAGTTGGTGCACTTCCCA	59.159	50.000	17.98	2.70	0.00	4.37
1998	2049	1.213182	TGTAGTTGGTGCACTTCCCAA	59.787	47.619	17.98	9.73	38.38	4.12
2100	2154	0.539986	AACCTCAACAGTCACCGTGT	59.460	50.000	0.00	0.00	0.00	4.49
2101	2155	0.179084	ACCTCAACAGTCACCGTGTG	60.179	55.000	0.00	0.00	34.45	3.82
2113	2167	3.395639	TCACCGTGTGACAAATTAGGAC	58.604	45.455	0.00	0.00	37.67	3.85
2208	2266	8.833231	AAATCCGTCAAGTAATCTACATATGG	57.167	34.615	7.80	0.00	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
81	83	1.831580	AGGAGGAACATGCTTTCTGC	58.168	50.000	0.00	0.00	43.25	4.26
266	268	7.911651	TCTTCTTATTCAGAGAAATGACCACT	58.088	34.615	0.00	0.00	33.10	4.00
277	279	7.308348	GGTCTCCTCGTATCTTCTTATTCAGAG	60.308	44.444	0.00	0.00	31.12	3.35
339	341	0.653636	GTGTCGCAGTTTTCGTGGAA	59.346	50.000	0.00	0.00	0.00	3.53
479	502	8.362464	AGTATTAACTAATGTGGTCTCTGTGA	57.638	34.615	0.00	0.00	32.84	3.58
482	505	7.782049	TGGAGTATTAACTAATGTGGTCTCTG	58.218	38.462	0.00	0.00	35.56	3.35
597	639	3.334054	GGAAGGCAGCAGGGACCT	61.334	66.667	0.00	0.00	34.45	3.85
616	658	3.800826	AAAAAGGGCTCTGTCGTGT	57.199	47.368	0.00	0.00	0.00	4.49
636	678	3.922171	AGGTGCATCCTCCTTTTCTAG	57.078	47.619	0.00	0.00	44.42	2.43
656	698	3.473647	CCAGATGCAGAGGCCGGA	61.474	66.667	5.05	0.00	40.13	5.14
837	883	3.807209	GCATCCGGCATTAGATGTTAGGT	60.807	47.826	0.00	0.00	41.60	3.08
1327	1374	1.657804	CTGTTACCCTTCCTGGAGGT	58.342	55.000	11.87	11.87	38.35	3.85
1375	1422	0.099791	AAACTTTGGTCGGCGTGTTG	59.900	50.000	6.85	0.00	0.00	3.33
1539	1586	3.005205	CGGATCATTGGATTCGGCA	57.995	52.632	0.00	0.00	46.63	5.69
1551	1598	4.451150	GCTGGCCACGTCGGATCA	62.451	66.667	0.00	4.86	36.56	2.92
1767	1814	2.483188	GCGGGATTTAGAGGAACATCGT	60.483	50.000	0.00	0.00	0.00	3.73
1770	1817	2.505819	ACAGCGGGATTTAGAGGAACAT	59.494	45.455	0.00	0.00	0.00	2.71
1771	1818	1.906574	ACAGCGGGATTTAGAGGAACA	59.093	47.619	0.00	0.00	0.00	3.18
1801	1848	0.905357	CCCATCCTCTTCGTCTTGGT	59.095	55.000	0.00	0.00	0.00	3.67
1962	2013	6.041637	ACCAACTACACACTTTGAGATACTCA	59.958	38.462	0.00	0.00	38.87	3.41
1966	2017	4.994852	GCACCAACTACACACTTTGAGATA	59.005	41.667	0.00	0.00	0.00	1.98
1967	2018	3.815401	GCACCAACTACACACTTTGAGAT	59.185	43.478	0.00	0.00	0.00	2.75
1968	2019	3.202906	GCACCAACTACACACTTTGAGA	58.797	45.455	0.00	0.00	0.00	3.27
1969	2020	2.942376	TGCACCAACTACACACTTTGAG	59.058	45.455	0.00	0.00	0.00	3.02
1970	2021	2.680841	GTGCACCAACTACACACTTTGA	59.319	45.455	5.22	0.00	34.43	2.69
1971	2022	2.682856	AGTGCACCAACTACACACTTTG	59.317	45.455	14.63	0.00	38.38	2.77
1972	2023	2.999331	AGTGCACCAACTACACACTTT	58.001	42.857	14.63	0.00	38.38	2.66
1973	2024	2.710096	AGTGCACCAACTACACACTT	57.290	45.000	14.63	0.00	38.38	3.16
1974	2025	2.561569	GAAGTGCACCAACTACACACT	58.438	47.619	14.63	0.00	43.14	3.55
1975	2026	1.602377	GGAAGTGCACCAACTACACAC	59.398	52.381	14.63	0.00	36.76	3.82
1976	2027	1.476110	GGGAAGTGCACCAACTACACA	60.476	52.381	14.63	0.00	36.76	3.72
1977	2028	1.235724	GGGAAGTGCACCAACTACAC	58.764	55.000	14.63	0.00	34.48	2.90
1978	2029	0.840617	TGGGAAGTGCACCAACTACA	59.159	50.000	14.63	2.73	32.89	2.74
1979	2030	1.975660	TTGGGAAGTGCACCAACTAC	58.024	50.000	14.63	0.00	41.56	2.73
1983	2034	1.380403	CGTGTTGGGAAGTGCACCAA	61.380	55.000	14.63	7.92	44.04	3.67
1984	2035	1.821759	CGTGTTGGGAAGTGCACCA	60.822	57.895	14.63	0.37	34.29	4.17
1985	2036	1.525077	TCGTGTTGGGAAGTGCACC	60.525	57.895	14.63	0.00	0.00	5.01
1986	2037	1.092921	TGTCGTGTTGGGAAGTGCAC	61.093	55.000	9.40	9.40	0.00	4.57
1987	2038	0.813610	CTGTCGTGTTGGGAAGTGCA	60.814	55.000	0.00	0.00	0.00	4.57
1988	2039	0.531974	TCTGTCGTGTTGGGAAGTGC	60.532	55.000	0.00	0.00	0.00	4.40
1989	2040	1.502231	CTCTGTCGTGTTGGGAAGTG	58.498	55.000	0.00	0.00	0.00	3.16
1990	2041	0.249911	GCTCTGTCGTGTTGGGAAGT	60.250	55.000	0.00	0.00	0.00	3.01
1991	2042	0.951040	GGCTCTGTCGTGTTGGGAAG	60.951	60.000	0.00	0.00	0.00	3.46
1992	2043	1.070786	GGCTCTGTCGTGTTGGGAA	59.929	57.895	0.00	0.00	0.00	3.97
1993	2044	1.837051	AGGCTCTGTCGTGTTGGGA	60.837	57.895	0.00	0.00	0.00	4.37
1994	2045	1.669115	CAGGCTCTGTCGTGTTGGG	60.669	63.158	0.00	0.00	0.00	4.12
1995	2046	2.320587	GCAGGCTCTGTCGTGTTGG	61.321	63.158	4.45	0.00	33.43	3.77
1996	2047	1.595109	TGCAGGCTCTGTCGTGTTG	60.595	57.895	4.45	0.00	33.43	3.33
1997	2048	1.595382	GTGCAGGCTCTGTCGTGTT	60.595	57.895	0.00	0.00	33.43	3.32
1998	2049	2.029666	GTGCAGGCTCTGTCGTGT	59.970	61.111	0.00	0.00	33.43	4.49
2100	2154	4.868171	GCTACATGTCGTCCTAATTTGTCA	59.132	41.667	0.00	0.00	0.00	3.58
2101	2155	4.026804	CGCTACATGTCGTCCTAATTTGTC	60.027	45.833	0.00	0.00	0.00	3.18
2113	2167	4.725280	CACAATTCAAATCGCTACATGTCG	59.275	41.667	0.00	0.00	0.00	4.35
2201	2259	8.072321	TGTACACCATTTTTATTGCCATATGT	57.928	30.769	1.24	0.00	0.00	2.29
2202	2260	8.939201	TTGTACACCATTTTTATTGCCATATG	57.061	30.769	0.00	0.00	0.00	1.78
2251	2315	9.277783	AGATATGTTCTGTTAGCAACAATATCC	57.722	33.333	17.01	8.40	41.61	2.59
2291	2355	8.572855	AGATTAATGAGAGAGAAAAGGTTTGG	57.427	34.615	0.00	0.00	0.00	3.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.