AutoCloner

Multiple sequence alignment - TraesCS3D01G292800

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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	TraesCS3D01G292800	chr3D	100.000	2576	0	0	1	2576	402776192	402773617	0.000000e+00	4758
1	TraesCS3D01G292800	chr3D	85.211	568	58	10	2027	2576	572482095	572482654	6.220000e-156	560
2	TraesCS3D01G292800	chr3A	92.663	1990	75	30	9	1967	523728753	523726804	0.000000e+00	2800
3	TraesCS3D01G292800	chr3A	85.810	599	63	15	1996	2576	729398227	729397633	1.310000e-172	616
4	TraesCS3D01G292800	chr3A	79.365	252	27	16	1965	2198	80492829	80492585	1.230000e-33	154
5	TraesCS3D01G292800	chr3B	94.126	1413	49	20	1	1404	528494224	528492837	0.000000e+00	2119
6	TraesCS3D01G292800	chr3B	90.927	518	26	11	1465	1967	528492687	528492176	0.000000e+00	676
7	TraesCS3D01G292800	chr4D	87.781	622	62	8	1969	2576	79949804	79949183	0.000000e+00	715
8	TraesCS3D01G292800	chr5A	86.786	613	73	7	1969	2576	338920431	338921040	0.000000e+00	676
9	TraesCS3D01G292800	chr6D	86.688	616	67	10	1969	2576	291391125	291391733	0.000000e+00	669
10	TraesCS3D01G292800	chr1D	86.169	629	64	13	1965	2576	458348232	458348854	0.000000e+00	658
11	TraesCS3D01G292800	chr2D	86.560	625	49	19	1969	2576	20057777	20058383	0.000000e+00	656
12	TraesCS3D01G292800	chr2D	85.466	633	66	10	1969	2576	460839974	460840605	1.010000e-178	636
13	TraesCS3D01G292800	chr5D	84.864	588	65	11	2009	2576	10651119	10651702	2.880000e-159	571
14	TraesCS3D01G292800	chr2A	83.713	614	75	14	1980	2574	440766230	440766837	8.050000e-155	556
15	TraesCS3D01G292800	chr2A	78.007	291	35	20	1965	2233	612752645	612752928	3.430000e-34	156
16	TraesCS3D01G292800	chr7B	75.762	656	92	38	1965	2574	665209297	665209931	4.230000e-68	268
17	TraesCS3D01G292800	chr2B	77.778	279	39	18	1969	2233	730643192	730643461	1.600000e-32	150
18	TraesCS3D01G292800	chr7A	78.049	246	35	15	1969	2198	95232161	95232403	1.240000e-28	137

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	TraesCS3D01G292800	chr3D	402773617	402776192	2575	True	4758.0	4758	100.0000	1	2576	1	chr3D.!!$R1	2575
1	TraesCS3D01G292800	chr3D	572482095	572482654	559	False	560.0	560	85.2110	2027	2576	1	chr3D.!!$F1	549
2	TraesCS3D01G292800	chr3A	523726804	523728753	1949	True	2800.0	2800	92.6630	9	1967	1	chr3A.!!$R2	1958
3	TraesCS3D01G292800	chr3A	729397633	729398227	594	True	616.0	616	85.8100	1996	2576	1	chr3A.!!$R3	580
4	TraesCS3D01G292800	chr3B	528492176	528494224	2048	True	1397.5	2119	92.5265	1	1967	2	chr3B.!!$R1	1966
5	TraesCS3D01G292800	chr4D	79949183	79949804	621	True	715.0	715	87.7810	1969	2576	1	chr4D.!!$R1	607
6	TraesCS3D01G292800	chr5A	338920431	338921040	609	False	676.0	676	86.7860	1969	2576	1	chr5A.!!$F1	607
7	TraesCS3D01G292800	chr6D	291391125	291391733	608	False	669.0	669	86.6880	1969	2576	1	chr6D.!!$F1	607
8	TraesCS3D01G292800	chr1D	458348232	458348854	622	False	658.0	658	86.1690	1965	2576	1	chr1D.!!$F1	611
9	TraesCS3D01G292800	chr2D	20057777	20058383	606	False	656.0	656	86.5600	1969	2576	1	chr2D.!!$F1	607
10	TraesCS3D01G292800	chr2D	460839974	460840605	631	False	636.0	636	85.4660	1969	2576	1	chr2D.!!$F2	607
11	TraesCS3D01G292800	chr5D	10651119	10651702	583	False	571.0	571	84.8640	2009	2576	1	chr5D.!!$F1	567
12	TraesCS3D01G292800	chr2A	440766230	440766837	607	False	556.0	556	83.7130	1980	2574	1	chr2A.!!$F1	594
13	TraesCS3D01G292800	chr7B	665209297	665209931	634	False	268.0	268	75.7620	1965	2574	1	chr7B.!!$F1	609

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
451	452	0.526524	GCCACACGTCAGCTAGCTAG	60.527	60.0	18.86	16.84	0.0	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1789	1916	0.037326	ATGTGCGTCGACAAGTCCAT	60.037	50.0	17.16	6.84	0.0	3.41	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
81	82	6.092122	TGACCATTGATTTCAGACGTTATCAC	59.908	38.462	0.00	0.00	0.00	3.06
148	149	6.658831	CCAAATTCGGTACAGTAGCATATTG	58.341	40.000	10.37	8.50	34.08	1.90
262	263	6.418101	AGTAGCCACAAATGTATGAAGACAT	58.582	36.000	0.00	0.00	41.92	3.06
337	338	6.631962	TCAAAAGATTATGTTCATGCATGCA	58.368	32.000	25.04	25.04	0.00	3.96
338	339	7.269316	TCAAAAGATTATGTTCATGCATGCAT	58.731	30.769	27.46	27.46	37.08	3.96
339	340	7.766738	TCAAAAGATTATGTTCATGCATGCATT	59.233	29.630	30.32	17.91	33.90	3.56
340	341	7.477144	AAAGATTATGTTCATGCATGCATTG	57.523	32.000	30.32	23.29	33.90	2.82
418	419	4.098960	AGGAGCATGCATTATTCCAGTTTG	59.901	41.667	21.98	0.00	0.00	2.93
451	452	0.526524	GCCACACGTCAGCTAGCTAG	60.527	60.000	18.86	16.84	0.00	3.42
589	593	2.689471	TGCATGTGGAGTGGATTATTGC	59.311	45.455	0.00	0.00	0.00	3.56
637	641	1.747355	GTCGACCGGAACATAGGAGAA	59.253	52.381	9.46	0.00	0.00	2.87
808	814	4.142687	GGTTCATCCAACATTACTCCAACG	60.143	45.833	0.00	0.00	36.61	4.10
877	883	3.760035	CGCGGTGGCTCCACTACT	61.760	66.667	17.57	0.00	45.52	2.57
927	933	3.051479	CGGGCCCACGTTGTAACC	61.051	66.667	24.92	0.00	0.00	2.85
951	960	2.095008	CGGTATGGTCCATCTCATCGAG	60.095	54.545	7.92	0.00	0.00	4.04
954	963	2.364972	TGGTCCATCTCATCGAGCTA	57.635	50.000	0.00	0.00	0.00	3.32
955	964	2.234143	TGGTCCATCTCATCGAGCTAG	58.766	52.381	0.00	0.00	0.00	3.42
956	965	1.067915	GGTCCATCTCATCGAGCTAGC	60.068	57.143	6.62	6.62	0.00	3.42
957	966	1.885887	GTCCATCTCATCGAGCTAGCT	59.114	52.381	19.45	19.45	0.00	3.32
1073	1084	0.391130	ACCGAGCACCTACGTACGTA	60.391	55.000	25.41	25.41	0.00	3.57
1074	1085	0.026803	CCGAGCACCTACGTACGTAC	59.973	60.000	23.60	15.90	0.00	3.67
1095	1106	0.248094	TGTAAGCATCTCGTCTCGCG	60.248	55.000	0.00	0.00	43.01	5.87
1163	1174	2.031516	GCTGTCGTGCTCTGCATGT	61.032	57.895	10.91	0.00	44.84	3.21
1174	1185	2.417933	GCTCTGCATGTTCTTGATCGTT	59.582	45.455	0.00	0.00	0.00	3.85
1232	1243	2.359107	TGCCGGACGTCGTCTACT	60.359	61.111	23.69	0.00	37.11	2.57
1244	1255	3.826754	TCTACTCTGCTGCGGCCG	61.827	66.667	24.05	24.05	37.74	6.13
1245	1256	4.880537	CTACTCTGCTGCGGCCGG	62.881	72.222	29.38	12.76	37.74	6.13
1446	1460	2.938539	GATTCTCGTGGAGCGTCGGG	62.939	65.000	0.00	0.00	42.13	5.14
1639	1755	7.285401	TCTGTGTAGCAATGATCTACTGTATCA	59.715	37.037	0.00	0.00	37.78	2.15
1641	1757	6.364706	GTGTAGCAATGATCTACTGTATCAGC	59.635	42.308	0.00	0.00	36.82	4.26
1702	1820	6.713450	ACGTGGTGTTGGGATAATATTATTCC	59.287	38.462	21.86	21.86	38.97	3.01
1763	1890	1.605232	GGAATCATGCATGCACGATGA	59.395	47.619	28.12	24.48	33.31	2.92
1789	1916	2.170397	TCTGCATGCGGATCTCCTTTTA	59.830	45.455	25.40	0.00	0.00	1.52
1795	1922	2.771943	TGCGGATCTCCTTTTATGGACT	59.228	45.455	0.00	0.00	31.94	3.85
1796	1923	3.199946	TGCGGATCTCCTTTTATGGACTT	59.800	43.478	0.00	0.00	31.94	3.01
1890	2024	1.614903	ACCGACTGTAATCACGAACCA	59.385	47.619	0.00	0.00	0.00	3.67
1925	2059	1.134995	GGCGTGTCATCTGACTCATCA	60.135	52.381	11.35	0.00	44.99	3.07
1946	2083	2.551270	TGGTAGGCTCAGAAAGACCAT	58.449	47.619	0.00	0.00	30.70	3.55
1953	2090	4.081198	AGGCTCAGAAAGACCATTGAGTAG	60.081	45.833	2.75	0.00	39.33	2.57
1967	2105	7.777095	ACCATTGAGTAGTGAGAGATACTTTC	58.223	38.462	0.00	0.00	32.43	2.62
2041	2181	4.792521	TTTATTGGGTTGGACCGAAATG	57.207	40.909	0.00	0.00	39.41	2.32
2043	2183	0.478942	TTGGGTTGGACCGAAATGGA	59.521	50.000	0.00	0.00	39.83	3.41
2047	2187	0.608035	GTTGGACCGAAATGGAGGCA	60.608	55.000	0.00	0.00	42.00	4.75
2229	2410	1.134818	CCATTGATTCCTCACGGACGA	60.135	52.381	0.00	0.00	39.60	4.20
2354	2581	1.185315	GTGCTCTGCCTCTCTCTCTT	58.815	55.000	0.00	0.00	0.00	2.85
2497	2743	2.032620	GGGAGGCGTATCTTCTCTTCA	58.967	52.381	0.00	0.00	0.00	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
148	149	6.149129	ACTCTTCAAGTTTTCCAAATGGAC	57.851	37.500	0.54	0.00	38.48	4.02
262	263	6.427441	TGTGGGTAGCATATATTTTCAACCA	58.573	36.000	0.00	0.00	0.00	3.67
337	338	4.175516	CAGCGTTTTGGAATACATGCAAT	58.824	39.130	0.00	0.00	39.28	3.56
338	339	3.573598	CAGCGTTTTGGAATACATGCAA	58.426	40.909	0.00	0.00	37.61	4.08
339	340	2.094803	CCAGCGTTTTGGAATACATGCA	60.095	45.455	0.00	0.00	40.87	3.96
340	341	2.529151	CCAGCGTTTTGGAATACATGC	58.471	47.619	0.00	0.00	40.87	4.06
341	342	2.735126	GCCCAGCGTTTTGGAATACATG	60.735	50.000	4.60	0.00	40.87	3.21
418	419	2.033141	TGGCCTGTCTGCTTCTGC	59.967	61.111	3.32	0.00	40.20	4.26
432	433	0.526524	CTAGCTAGCTGACGTGTGGC	60.527	60.000	27.68	0.00	0.00	5.01
522	523	3.826754	CACCGCCGCTCTCAGCTA	61.827	66.667	0.00	0.00	39.60	3.32
589	593	3.065371	CCTCTTGCTTACTTAATTGCCCG	59.935	47.826	0.00	0.00	0.00	6.13
637	641	0.322816	ACGCCATGAGCCAATGTTCT	60.323	50.000	0.00	0.00	38.78	3.01
665	669	2.279502	TATGCTCCGTGTCCGTGCTC	62.280	60.000	0.00	0.00	34.29	4.26
774	780	0.179000	GGATGAACCTGGCGTGATCT	59.821	55.000	0.00	0.00	35.41	2.75
868	874	4.202367	GGATAATTGGTGGGAGTAGTGGAG	60.202	50.000	0.00	0.00	0.00	3.86
874	880	2.120312	TGCGGATAATTGGTGGGAGTA	58.880	47.619	0.00	0.00	0.00	2.59
875	881	0.916086	TGCGGATAATTGGTGGGAGT	59.084	50.000	0.00	0.00	0.00	3.85
876	882	1.676006	GTTGCGGATAATTGGTGGGAG	59.324	52.381	0.00	0.00	0.00	4.30
877	883	1.004862	TGTTGCGGATAATTGGTGGGA	59.995	47.619	0.00	0.00	0.00	4.37
927	933	1.006102	GAGATGGACCATACCGGCG	60.006	63.158	7.05	0.00	39.03	6.46
951	960	6.457799	GCTCTCTATTTATAGGACGAGCTAGC	60.458	46.154	6.62	6.62	39.53	3.42
954	963	4.393680	CGCTCTCTATTTATAGGACGAGCT	59.606	45.833	20.72	0.00	39.93	4.09
955	964	4.437659	CCGCTCTCTATTTATAGGACGAGC	60.438	50.000	17.17	17.17	39.41	5.03
956	965	4.437659	GCCGCTCTCTATTTATAGGACGAG	60.438	50.000	0.00	3.31	0.00	4.18
957	966	3.439476	GCCGCTCTCTATTTATAGGACGA	59.561	47.826	0.00	0.00	0.00	4.20
1073	1084	1.202043	CGAGACGAGATGCTTACACGT	60.202	52.381	0.00	0.00	37.29	4.49
1074	1085	1.457738	CGAGACGAGATGCTTACACG	58.542	55.000	0.00	0.00	0.00	4.49
1075	1086	1.192793	GCGAGACGAGATGCTTACAC	58.807	55.000	0.00	0.00	0.00	2.90
1076	1087	3.624305	GCGAGACGAGATGCTTACA	57.376	52.632	0.00	0.00	0.00	2.41
1095	1106	3.853475	TGGAGCTAGCTAACGTTAAACC	58.147	45.455	19.38	11.71	0.00	3.27
1163	1174	0.804544	CCCGCGCTAACGATCAAGAA	60.805	55.000	5.56	0.00	43.93	2.52
1446	1460	3.812053	AGGTACTACGTCGTATGATCCAC	59.188	47.826	5.39	0.00	36.02	4.02
1510	1621	8.546597	AACCAAATGCAAACCATACTTATTTC	57.453	30.769	0.00	0.00	32.67	2.17
1521	1632	7.758076	GGACTATACTTAAACCAAATGCAAACC	59.242	37.037	0.00	0.00	0.00	3.27
1559	1670	5.830991	TGAGCTTGTTTATTACAACTGGGTT	59.169	36.000	0.00	0.00	41.73	4.11
1584	1698	1.308047	ATCTGCGTGTTTCAACAGCA	58.692	45.000	12.95	12.95	40.05	4.41
1639	1755	1.270907	AGGACAATCCAGTCTTCGCT	58.729	50.000	0.00	0.00	39.61	4.93
1641	1757	5.390991	GCTTAAAAGGACAATCCAGTCTTCG	60.391	44.000	0.00	0.00	39.61	3.79
1702	1820	1.061131	ACGATCGACACCGTACGTAAG	59.939	52.381	24.34	0.00	42.31	2.34
1763	1890	1.945394	GAGATCCGCATGCAGATGTTT	59.055	47.619	20.94	6.51	31.50	2.83
1789	1916	0.037326	ATGTGCGTCGACAAGTCCAT	60.037	50.000	17.16	6.84	0.00	3.41
1795	1922	4.937696	ATGAAATAATGTGCGTCGACAA	57.062	36.364	17.16	0.00	0.00	3.18
1796	1923	4.937696	AATGAAATAATGTGCGTCGACA	57.062	36.364	17.16	0.00	0.00	4.35
1829	1963	5.106078	TGGAAAGTTGCACGTACTTCTTTTT	60.106	36.000	2.84	0.00	34.88	1.94
1830	1964	4.396790	TGGAAAGTTGCACGTACTTCTTTT	59.603	37.500	2.84	0.00	34.88	2.27
1831	1965	3.942748	TGGAAAGTTGCACGTACTTCTTT	59.057	39.130	2.84	5.76	34.88	2.52
1834	1968	2.870411	ACTGGAAAGTTGCACGTACTTC	59.130	45.455	2.84	0.00	34.88	3.01
1899	2033	2.125912	AGATGACACGCCGCTGAC	60.126	61.111	0.00	0.00	0.00	3.51
1925	2059	2.551270	TGGTCTTTCTGAGCCTACCAT	58.449	47.619	0.00	0.00	42.12	3.55
1953	2090	5.005875	GGCGCTAAAAGAAAGTATCTCTCAC	59.994	44.000	7.64	0.00	37.42	3.51
2022	2162	2.309162	TCCATTTCGGTCCAACCCAATA	59.691	45.455	0.00	0.00	33.75	1.90
2093	2255	2.606065	GCGGTTAGTTCACGCCAAAATT	60.606	45.455	0.00	0.00	46.92	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.