AutoCloner

Multiple sequence alignment - TraesCS5D01G098100

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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	TraesCS5D01G098100	chr5D	100.000	2555	0	0	1	2555	109533306	109535860	0.000000e+00	4719.0
1	TraesCS5D01G098100	chr5D	97.727	1892	27	3	1	1877	112839138	112841028	0.000000e+00	3241.0
2	TraesCS5D01G098100	chr5D	98.361	610	5	3	1947	2555	112842639	112843244	0.000000e+00	1066.0
3	TraesCS5D01G098100	chr5D	88.447	528	43	9	1060	1569	109578171	109577644	2.790000e-174	621.0
4	TraesCS5D01G098100	chr5D	98.864	88	1	0	2232	2319	431293736	431293823	9.460000e-35	158.0
5	TraesCS5D01G098100	chr5D	97.561	41	1	0	1928	1968	112841028	112841068	1.270000e-08	71.3
6	TraesCS5D01G098100	chr5A	88.956	996	73	16	1057	2029	118253457	118254438	0.000000e+00	1195.0
7	TraesCS5D01G098100	chr5A	93.056	144	9	1	2043	2186	118254607	118254749	2.580000e-50	209.0
8	TraesCS5D01G098100	chr5A	100.000	28	0	0	368	395	294865166	294865193	5.000000e-03	52.8
9	TraesCS5D01G098100	chr4A	89.925	536	38	11	1146	1673	699100518	699101045	0.000000e+00	676.0
10	TraesCS5D01G098100	chr7A	87.409	548	45	13	1146	1676	30383340	30382800	2.170000e-170	608.0
11	TraesCS5D01G098100	chr7A	88.565	446	40	3	1146	1583	30413736	30413294	4.840000e-147	531.0
12	TraesCS5D01G098100	chr7D	87.688	333	26	11	1353	1676	30062635	30062309	8.630000e-100	374.0
13	TraesCS5D01G098100	chr7D	97.802	91	2	0	2232	2322	519264633	519264543	9.460000e-35	158.0
14	TraesCS5D01G098100	chr7D	96.774	93	1	2	2235	2327	141292172	141292082	1.220000e-33	154.0
15	TraesCS5D01G098100	chr1D	98.876	89	1	0	2234	2322	337065274	337065186	2.630000e-35	159.0
16	TraesCS5D01G098100	chr3D	95.833	96	3	1	2233	2328	55092869	55092775	1.220000e-33	154.0
17	TraesCS5D01G098100	chr3D	93.204	103	7	0	2233	2335	475310592	475310490	4.400000e-33	152.0
18	TraesCS5D01G098100	chr3D	94.000	100	4	2	2235	2332	189004067	189003968	1.580000e-32	150.0
19	TraesCS5D01G098100	chr1B	91.964	112	6	3	2213	2322	328029445	328029555	1.220000e-33	154.0
20	TraesCS5D01G098100	chr6D	95.000	40	2	0	243	282	445458739	445458700	2.120000e-06	63.9
21	TraesCS5D01G098100	chr2D	100.000	30	0	0	1355	1384	584798262	584798291	3.550000e-04	56.5
22	TraesCS5D01G098100	chr2A	100.000	30	0	0	1355	1384	718934347	718934376	3.550000e-04	56.5

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	TraesCS5D01G098100	chr5D	109533306	109535860	2554	False	4719.000000	4719	100.000	1	2555	1	chr5D.!!$F1	2554
1	TraesCS5D01G098100	chr5D	112839138	112843244	4106	False	1459.433333	3241	97.883	1	2555	3	chr5D.!!$F3	2554
2	TraesCS5D01G098100	chr5D	109577644	109578171	527	True	621.000000	621	88.447	1060	1569	1	chr5D.!!$R1	509
3	TraesCS5D01G098100	chr5A	118253457	118254749	1292	False	702.000000	1195	91.006	1057	2186	2	chr5A.!!$F2	1129
4	TraesCS5D01G098100	chr4A	699100518	699101045	527	False	676.000000	676	89.925	1146	1673	1	chr4A.!!$F1	527
5	TraesCS5D01G098100	chr7A	30382800	30383340	540	True	608.000000	608	87.409	1146	1676	1	chr7A.!!$R1	530

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
360	375	1.08437	CATCTTCCGAACTGTCGCCC	61.084	60.0	0.0	0.0	46.28	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1918	2024	1.26148	ATCACGAAGCAGAGGACAGT	58.739	50.0	0.0	0.0	0.0	3.55	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
25	26	3.657350	GCCCCAACCCTAGGCACA	61.657	66.667	2.05	0.00	46.34	4.57
34	35	2.423446	CTAGGCACAGGATCCCGC	59.577	66.667	8.55	9.07	0.00	6.13
222	223	2.443952	ACCCGCCGAGATCCATGA	60.444	61.111	0.00	0.00	0.00	3.07
225	226	2.796193	CCGCCGAGATCCATGACCA	61.796	63.158	0.00	0.00	0.00	4.02
229	230	1.337384	CCGAGATCCATGACCACCCA	61.337	60.000	0.00	0.00	0.00	4.51
360	375	1.084370	CATCTTCCGAACTGTCGCCC	61.084	60.000	0.00	0.00	46.28	6.13
566	581	1.198408	CCGTACGTGAGCTGTTAGACA	59.802	52.381	15.21	0.00	0.00	3.41
581	596	6.274157	TGTTAGACAAGACATCTCTCTTCC	57.726	41.667	0.00	0.00	0.00	3.46
669	684	2.579410	TAAACCAAAGAGGAGGGTGC	57.421	50.000	0.00	0.00	41.22	5.01
681	696	1.226030	GAGGGTGCGTGTGTTGTACC	61.226	60.000	0.00	0.00	40.89	3.34
965	980	1.964608	CTCGCCAGAATCCTCCAGCA	61.965	60.000	0.00	0.00	0.00	4.41
1681	1736	1.086696	CTTTGTACTGATGCCCGTGG	58.913	55.000	0.00	0.00	0.00	4.94
1877	1983	4.142049	GCTGTAATCTCTAGCCTCTGTGTT	60.142	45.833	0.00	0.00	0.00	3.32
1878	1984	5.330455	TGTAATCTCTAGCCTCTGTGTTG	57.670	43.478	0.00	0.00	0.00	3.33
1879	1985	2.977772	ATCTCTAGCCTCTGTGTTGC	57.022	50.000	0.00	0.00	0.00	4.17
1880	1986	1.632589	TCTCTAGCCTCTGTGTTGCA	58.367	50.000	0.00	0.00	0.00	4.08
1881	1987	2.182827	TCTCTAGCCTCTGTGTTGCAT	58.817	47.619	0.00	0.00	0.00	3.96
1882	1988	2.093816	TCTCTAGCCTCTGTGTTGCATG	60.094	50.000	0.00	0.00	0.00	4.06
1883	1989	1.901833	TCTAGCCTCTGTGTTGCATGA	59.098	47.619	0.00	0.00	0.00	3.07
1884	1990	2.302733	TCTAGCCTCTGTGTTGCATGAA	59.697	45.455	0.00	0.00	0.00	2.57
1885	1991	2.211250	AGCCTCTGTGTTGCATGAAT	57.789	45.000	0.00	0.00	0.00	2.57
1886	1992	2.522185	AGCCTCTGTGTTGCATGAATT	58.478	42.857	0.00	0.00	0.00	2.17
1887	1993	2.895404	AGCCTCTGTGTTGCATGAATTT	59.105	40.909	0.00	0.00	0.00	1.82
1888	1994	3.322828	AGCCTCTGTGTTGCATGAATTTT	59.677	39.130	0.00	0.00	0.00	1.82
1889	1995	3.676646	GCCTCTGTGTTGCATGAATTTTC	59.323	43.478	0.00	0.00	0.00	2.29
1890	1996	4.240096	CCTCTGTGTTGCATGAATTTTCC	58.760	43.478	0.00	0.00	0.00	3.13
1891	1997	4.262121	CCTCTGTGTTGCATGAATTTTCCA	60.262	41.667	0.00	0.00	0.00	3.53
1892	1998	5.471556	TCTGTGTTGCATGAATTTTCCAT	57.528	34.783	0.00	0.00	0.00	3.41
1893	1999	5.231702	TCTGTGTTGCATGAATTTTCCATG	58.768	37.500	0.00	0.00	43.06	3.66
1894	2000	4.958509	TGTGTTGCATGAATTTTCCATGT	58.041	34.783	0.00	0.00	42.39	3.21
1895	2001	6.015603	TCTGTGTTGCATGAATTTTCCATGTA	60.016	34.615	0.00	1.07	42.39	2.29
1896	2002	6.699366	TGTGTTGCATGAATTTTCCATGTAT	58.301	32.000	0.00	0.00	42.39	2.29
1897	2003	6.812656	TGTGTTGCATGAATTTTCCATGTATC	59.187	34.615	0.00	3.75	42.39	2.24
1898	2004	7.037438	GTGTTGCATGAATTTTCCATGTATCT	58.963	34.615	0.00	0.00	42.39	1.98
1899	2005	7.009815	GTGTTGCATGAATTTTCCATGTATCTG	59.990	37.037	0.00	0.00	42.39	2.90
1900	2006	7.093858	TGTTGCATGAATTTTCCATGTATCTGA	60.094	33.333	0.00	0.00	42.39	3.27
1901	2007	7.591421	TGCATGAATTTTCCATGTATCTGAT	57.409	32.000	0.00	0.00	42.39	2.90
1902	2008	8.694581	TGCATGAATTTTCCATGTATCTGATA	57.305	30.769	0.00	0.00	42.39	2.15
1903	2009	8.570488	TGCATGAATTTTCCATGTATCTGATAC	58.430	33.333	18.64	18.64	42.39	2.24
1904	2010	8.025445	GCATGAATTTTCCATGTATCTGATACC	58.975	37.037	21.63	7.57	42.39	2.73
1905	2011	8.517878	CATGAATTTTCCATGTATCTGATACCC	58.482	37.037	21.63	2.40	37.28	3.69
1906	2012	7.815383	TGAATTTTCCATGTATCTGATACCCT	58.185	34.615	21.63	9.15	34.86	4.34
1907	2013	8.281531	TGAATTTTCCATGTATCTGATACCCTT	58.718	33.333	21.63	7.14	34.86	3.95
1908	2014	8.697507	AATTTTCCATGTATCTGATACCCTTC	57.302	34.615	21.63	1.07	34.86	3.46
1909	2015	7.451731	TTTTCCATGTATCTGATACCCTTCT	57.548	36.000	21.63	2.76	34.86	2.85
1910	2016	8.561536	TTTTCCATGTATCTGATACCCTTCTA	57.438	34.615	21.63	5.70	34.86	2.10
1911	2017	8.742125	TTTCCATGTATCTGATACCCTTCTAT	57.258	34.615	21.63	7.57	34.86	1.98
1912	2018	9.837681	TTTCCATGTATCTGATACCCTTCTATA	57.162	33.333	21.63	4.42	34.86	1.31
1913	2019	9.480861	TTCCATGTATCTGATACCCTTCTATAG	57.519	37.037	21.63	0.00	34.86	1.31
1914	2020	8.624670	TCCATGTATCTGATACCCTTCTATAGT	58.375	37.037	21.63	0.00	34.86	2.12
1915	2021	9.922477	CCATGTATCTGATACCCTTCTATAGTA	57.078	37.037	21.63	2.70	34.86	1.82
1922	2028	9.168553	TCTGATACCCTTCTATAGTAGTACTGT	57.831	37.037	13.29	8.94	0.00	3.55
1923	2029	9.439500	CTGATACCCTTCTATAGTAGTACTGTC	57.561	40.741	13.29	0.00	0.00	3.51
1924	2030	8.381636	TGATACCCTTCTATAGTAGTACTGTCC	58.618	40.741	13.29	0.00	0.00	4.02
1925	2031	6.845168	ACCCTTCTATAGTAGTACTGTCCT	57.155	41.667	13.29	1.24	0.00	3.85
1926	2032	6.840527	ACCCTTCTATAGTAGTACTGTCCTC	58.159	44.000	13.29	0.00	0.00	3.71
1927	2033	6.620682	ACCCTTCTATAGTAGTACTGTCCTCT	59.379	42.308	13.29	0.00	0.00	3.69
1957	2063	8.074370	TCGTGATAATCTACTGAAACTATTCCG	58.926	37.037	0.00	0.00	34.49	4.30
2210	4063	8.883731	ACACAATAGTTCTATAGTTGTTGATGC	58.116	33.333	13.52	0.00	31.19	3.91
2327	4180	3.522553	GACGGAGGGAGTAAATCTGTTG	58.477	50.000	0.00	0.00	32.76	3.33
2460	4314	3.334691	CTCACCGTGAACACCACATAAT	58.665	45.455	2.19	0.00	45.98	1.28
2461	4315	4.500127	CTCACCGTGAACACCACATAATA	58.500	43.478	2.19	0.00	45.98	0.98
2462	4316	4.895961	TCACCGTGAACACCACATAATAA	58.104	39.130	0.00	0.00	45.98	1.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
98	99	1.324005	GCTGGGCTCTAGTTCCGAGT	61.324	60.000	13.28	0.00	31.77	4.18
99	100	1.439644	GCTGGGCTCTAGTTCCGAG	59.560	63.158	9.45	9.45	0.00	4.63
100	101	2.415608	CGCTGGGCTCTAGTTCCGA	61.416	63.158	0.00	0.00	0.00	4.55
103	104	2.583593	CGCGCTGGGCTCTAGTTC	60.584	66.667	14.94	0.00	40.44	3.01
222	223	4.309950	GTCGTTCCGCTGGGTGGT	62.310	66.667	0.00	0.00	34.40	4.16
225	226	3.692406	GAGGTCGTTCCGCTGGGT	61.692	66.667	0.00	0.00	41.99	4.51
281	282	1.541588	GTGGGAGATTTTGTGGCTCAC	59.458	52.381	0.00	0.00	32.76	3.51
386	401	4.284550	ATGTTGCGGGTGGCTGGT	62.285	61.111	0.00	0.00	44.05	4.00
470	485	2.997315	TGGAGGAGCCGGAGTGTG	60.997	66.667	5.05	0.00	40.66	3.82
555	570	5.016173	AGAGAGATGTCTTGTCTAACAGCT	58.984	41.667	0.00	0.00	44.25	4.24
558	573	5.106118	CGGAAGAGAGATGTCTTGTCTAACA	60.106	44.000	0.00	0.00	36.89	2.41
566	581	0.457851	CCGCGGAAGAGAGATGTCTT	59.542	55.000	24.07	0.00	39.59	3.01
669	684	1.388768	CAGCATACGGTACAACACACG	59.611	52.381	0.00	0.00	0.00	4.49
681	696	1.085893	TGCCATGTCAACAGCATACG	58.914	50.000	0.00	0.00	0.00	3.06
965	980	5.630415	TGGATGGTTTATCGAAGGAAGAT	57.370	39.130	0.00	0.00	36.62	2.40
1039	1054	1.290009	CCTTTCTTTTGGCAGGGCG	59.710	57.895	0.00	0.00	0.00	6.13
1877	1983	7.591421	ATCAGATACATGGAAAATTCATGCA	57.409	32.000	0.00	0.00	44.09	3.96
1878	1984	8.025445	GGTATCAGATACATGGAAAATTCATGC	58.975	37.037	20.17	0.00	44.09	4.06
1879	1985	8.517878	GGGTATCAGATACATGGAAAATTCATG	58.482	37.037	20.17	4.51	45.31	3.07
1880	1986	8.451245	AGGGTATCAGATACATGGAAAATTCAT	58.549	33.333	20.17	0.00	37.48	2.57
1881	1987	7.815383	AGGGTATCAGATACATGGAAAATTCA	58.185	34.615	20.17	0.00	37.48	2.57
1882	1988	8.697507	AAGGGTATCAGATACATGGAAAATTC	57.302	34.615	20.17	1.28	37.48	2.17
1883	1989	8.506083	AGAAGGGTATCAGATACATGGAAAATT	58.494	33.333	20.17	4.79	37.48	1.82
1884	1990	8.050316	AGAAGGGTATCAGATACATGGAAAAT	57.950	34.615	20.17	0.19	37.48	1.82
1885	1991	7.451731	AGAAGGGTATCAGATACATGGAAAA	57.548	36.000	20.17	0.00	37.48	2.29
1886	1992	8.742125	ATAGAAGGGTATCAGATACATGGAAA	57.258	34.615	20.17	4.17	37.48	3.13
1887	1993	9.480861	CTATAGAAGGGTATCAGATACATGGAA	57.519	37.037	20.17	3.72	37.48	3.53
1888	1994	8.624670	ACTATAGAAGGGTATCAGATACATGGA	58.375	37.037	20.17	0.00	37.48	3.41
1889	1995	8.830915	ACTATAGAAGGGTATCAGATACATGG	57.169	38.462	20.17	9.59	37.48	3.66
1896	2002	9.168553	ACAGTACTACTATAGAAGGGTATCAGA	57.831	37.037	6.78	0.00	0.00	3.27
1897	2003	9.439500	GACAGTACTACTATAGAAGGGTATCAG	57.561	40.741	6.78	2.07	0.00	2.90
1898	2004	8.381636	GGACAGTACTACTATAGAAGGGTATCA	58.618	40.741	6.78	0.00	0.00	2.15
1899	2005	8.605065	AGGACAGTACTACTATAGAAGGGTATC	58.395	40.741	6.78	0.00	0.00	2.24
1900	2006	8.522921	AGGACAGTACTACTATAGAAGGGTAT	57.477	38.462	6.78	0.00	0.00	2.73
1901	2007	7.793709	AGAGGACAGTACTACTATAGAAGGGTA	59.206	40.741	6.78	1.45	0.00	3.69
1902	2008	6.620682	AGAGGACAGTACTACTATAGAAGGGT	59.379	42.308	6.78	2.35	0.00	4.34
1903	2009	6.938030	CAGAGGACAGTACTACTATAGAAGGG	59.062	46.154	6.78	0.00	0.00	3.95
1904	2010	6.428771	GCAGAGGACAGTACTACTATAGAAGG	59.571	46.154	6.78	0.00	0.00	3.46
1905	2011	7.221450	AGCAGAGGACAGTACTACTATAGAAG	58.779	42.308	6.78	0.00	0.00	2.85
1906	2012	7.139287	AGCAGAGGACAGTACTACTATAGAA	57.861	40.000	6.78	0.00	0.00	2.10
1907	2013	6.750660	AGCAGAGGACAGTACTACTATAGA	57.249	41.667	6.78	0.00	0.00	1.98
1908	2014	6.146510	CGAAGCAGAGGACAGTACTACTATAG	59.853	46.154	0.00	0.00	0.00	1.31
1909	2015	5.990386	CGAAGCAGAGGACAGTACTACTATA	59.010	44.000	0.00	0.00	0.00	1.31
1910	2016	4.817464	CGAAGCAGAGGACAGTACTACTAT	59.183	45.833	0.00	0.00	0.00	2.12
1911	2017	4.190001	CGAAGCAGAGGACAGTACTACTA	58.810	47.826	0.00	0.00	0.00	1.82
1912	2018	3.011119	CGAAGCAGAGGACAGTACTACT	58.989	50.000	0.00	0.00	0.00	2.57
1913	2019	2.748532	ACGAAGCAGAGGACAGTACTAC	59.251	50.000	0.00	0.00	0.00	2.73
1914	2020	2.747989	CACGAAGCAGAGGACAGTACTA	59.252	50.000	0.00	0.00	0.00	1.82
1915	2021	1.542030	CACGAAGCAGAGGACAGTACT	59.458	52.381	0.00	0.00	0.00	2.73
1916	2022	1.540267	TCACGAAGCAGAGGACAGTAC	59.460	52.381	0.00	0.00	0.00	2.73
1917	2023	1.905637	TCACGAAGCAGAGGACAGTA	58.094	50.000	0.00	0.00	0.00	2.74
1918	2024	1.261480	ATCACGAAGCAGAGGACAGT	58.739	50.000	0.00	0.00	0.00	3.55
1919	2025	3.510388	TTATCACGAAGCAGAGGACAG	57.490	47.619	0.00	0.00	0.00	3.51
1920	2026	3.701542	AGATTATCACGAAGCAGAGGACA	59.298	43.478	0.00	0.00	0.00	4.02
1921	2027	4.314740	AGATTATCACGAAGCAGAGGAC	57.685	45.455	0.00	0.00	0.00	3.85
1922	2028	5.009110	CAGTAGATTATCACGAAGCAGAGGA	59.991	44.000	0.00	0.00	0.00	3.71
1923	2029	5.009110	TCAGTAGATTATCACGAAGCAGAGG	59.991	44.000	0.00	0.00	0.00	3.69
1924	2030	6.066054	TCAGTAGATTATCACGAAGCAGAG	57.934	41.667	0.00	0.00	0.00	3.35
1925	2031	6.451064	TTCAGTAGATTATCACGAAGCAGA	57.549	37.500	0.00	0.00	0.00	4.26
1926	2032	6.754209	AGTTTCAGTAGATTATCACGAAGCAG	59.246	38.462	0.00	0.00	0.00	4.24
1927	2033	6.631016	AGTTTCAGTAGATTATCACGAAGCA	58.369	36.000	0.00	0.00	0.00	3.91
1957	2063	6.884836	GTCAAGGTGTCCCCAAATATATATCC	59.115	42.308	0.00	0.00	34.66	2.59
2210	4063	4.948864	ACGTATCGATAGCAAACAATCG	57.051	40.909	5.09	5.14	44.88	3.34
2327	4180	4.775236	ACCATTTCTCTCTCAATGCCTAC	58.225	43.478	0.00	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.