AutoCloner

Multiple sequence alignment - TraesCS4D01G212900

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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	TraesCS4D01G212900	chr4D	100.000	2519	0	0	1	2519	365851372	365853890	0.000000e+00	4652.0
1	TraesCS4D01G212900	chr4A	94.009	1903	73	14	1	1870	99019736	99017842	0.000000e+00	2844.0
2	TraesCS4D01G212900	chr4A	85.106	94	8	5	519	606	611196190	611196097	9.600000e-15	91.6
3	TraesCS4D01G212900	chr4B	95.152	1155	35	8	176	1324	450468064	450469203	0.000000e+00	1803.0
4	TraesCS4D01G212900	chr4B	98.043	562	11	0	1958	2519	450469830	450470391	0.000000e+00	977.0
5	TraesCS4D01G212900	chr4B	94.412	340	15	2	311	646	450476323	450476662	1.030000e-143	520.0
6	TraesCS4D01G212900	chr4B	96.959	296	7	2	1373	1667	450469529	450469823	1.740000e-136	496.0
7	TraesCS4D01G212900	chr4B	99.281	139	1	0	1	139	450467923	450468061	4.160000e-63	252.0
8	TraesCS4D01G212900	chr1D	75.776	838	170	22	1679	2505	314192915	314193730	2.350000e-105	392.0
9	TraesCS4D01G212900	chr5B	82.022	89	11	3	519	602	704482071	704482159	1.250000e-08	71.3

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	TraesCS4D01G212900	chr4D	365851372	365853890	2518	False	4652	4652	100.00000	1	2519	1	chr4D.!!$F1	2518
1	TraesCS4D01G212900	chr4A	99017842	99019736	1894	True	2844	2844	94.00900	1	1870	1	chr4A.!!$R1	1869
2	TraesCS4D01G212900	chr4B	450467923	450470391	2468	False	882	1803	97.35875	1	2519	4	chr4B.!!$F2	2518
3	TraesCS4D01G212900	chr1D	314192915	314193730	815	False	392	392	75.77600	1679	2505	1	chr1D.!!$F1	826

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
649	657	0.734889	CATCCAGGGCGTGACAAATC	59.265	55.0	9.09	0.0	0.0	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1887	2201	0.383949	TGGAAGCAGAAAAACGGTGC	59.616	50.0	0.0	0.0	37.48	5.01	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
157	158	4.440880	GCATACCTGCCATCAGAGATATC	58.559	47.826	0.00	0.00	42.95	1.63
190	191	1.038681	GGACGGAGGGGAGAGAAGAC	61.039	65.000	0.00	0.00	0.00	3.01
504	507	6.512741	CGTGGGTATGCTATTACCATTTTGAC	60.513	42.308	11.50	0.00	42.96	3.18
513	516	6.926272	GCTATTACCATTTTGACCAAAACACA	59.074	34.615	9.75	0.00	42.32	3.72
514	517	7.095816	GCTATTACCATTTTGACCAAAACACAC	60.096	37.037	9.75	0.00	42.32	3.82
603	611	4.518249	CCAATTCCTCTCAAACCCTAGTC	58.482	47.826	0.00	0.00	0.00	2.59
613	621	2.238898	CAAACCCTAGTCCTTACCCTGG	59.761	54.545	0.00	0.00	0.00	4.45
649	657	0.734889	CATCCAGGGCGTGACAAATC	59.265	55.000	9.09	0.00	0.00	2.17
697	705	4.829518	CGAGATCGCGCGGTGACA	62.830	66.667	31.69	10.88	33.49	3.58
698	706	2.506217	GAGATCGCGCGGTGACAA	60.506	61.111	31.69	9.99	0.00	3.18
767	780	4.941309	GTGGACGTTGGGGCGGTT	62.941	66.667	0.00	0.00	35.98	4.44
772	785	2.028337	CGTTGGGGCGGTTTTTGG	59.972	61.111	0.00	0.00	0.00	3.28
901	914	1.067916	GTTCACGTACGGGTGGTGT	59.932	57.895	18.57	0.00	38.46	4.16
1026	1039	0.517316	GTTCGAAGCAAAGCGTGGAT	59.483	50.000	0.00	0.00	0.00	3.41
1156	1189	3.370527	GGCTACCAACTTCAAGCAGGATA	60.371	47.826	2.82	0.00	36.68	2.59
1206	1239	0.321034	CAGCAGTAGCAGCACTTGGA	60.321	55.000	0.00	0.00	45.49	3.53
1287	1320	2.123589	TCAGTGGTTCCTCCTTCAACA	58.876	47.619	0.00	0.00	37.07	3.33
1390	1703	4.079970	TCCTCTCGCTGAAGAACTTAAGA	58.920	43.478	10.09	0.00	0.00	2.10
1391	1704	4.156922	TCCTCTCGCTGAAGAACTTAAGAG	59.843	45.833	10.09	0.36	0.00	2.85
1392	1705	4.420168	CTCTCGCTGAAGAACTTAAGAGG	58.580	47.826	10.09	0.00	0.00	3.69
1401	1714	9.040939	GCTGAAGAACTTAAGAGGAGATTATTC	57.959	37.037	10.09	5.68	0.00	1.75
1424	1737	4.273148	TGGAGCAAGAGAAAACTAGTCC	57.727	45.455	0.00	0.00	0.00	3.85
1495	1808	4.351054	CAGCTCCACCGGGGCTTT	62.351	66.667	4.17	0.00	38.25	3.51
1676	1990	4.656100	TCCTCAAATCCATGACCAAGAA	57.344	40.909	0.00	0.00	0.00	2.52
1872	2186	1.141053	CAGTATACCTGGGGCCAGTTC	59.859	57.143	4.39	0.00	42.15	3.01
1878	2192	3.177884	TGGGGCCAGTTCTGTGCT	61.178	61.111	4.39	0.00	0.00	4.40
1884	2198	1.615392	GGCCAGTTCTGTGCTGAAATT	59.385	47.619	0.00	0.00	36.12	1.82
1887	2201	3.611057	GCCAGTTCTGTGCTGAAATTCTG	60.611	47.826	0.00	0.00	36.12	3.02
1898	2212	3.182372	GCTGAAATTCTGCACCGTTTTTC	59.818	43.478	17.95	0.00	40.47	2.29
1899	2213	4.610945	CTGAAATTCTGCACCGTTTTTCT	58.389	39.130	0.00	0.00	0.00	2.52
1902	2216	1.388547	TTCTGCACCGTTTTTCTGCT	58.611	45.000	0.00	0.00	0.00	4.24
1911	2225	2.225727	CCGTTTTTCTGCTTCCAGTACC	59.774	50.000	0.00	0.00	40.09	3.34
1914	2228	4.935808	CGTTTTTCTGCTTCCAGTACCTAT	59.064	41.667	0.00	0.00	40.09	2.57
1918	2232	5.537300	TTCTGCTTCCAGTACCTATGATC	57.463	43.478	0.00	0.00	40.09	2.92
1920	2234	5.211973	TCTGCTTCCAGTACCTATGATCTT	58.788	41.667	0.00	0.00	40.09	2.40
1924	2238	5.605534	CTTCCAGTACCTATGATCTTGTGG	58.394	45.833	0.00	0.00	0.00	4.17
1925	2239	4.878968	TCCAGTACCTATGATCTTGTGGA	58.121	43.478	8.69	0.00	0.00	4.02
1926	2240	5.277250	TCCAGTACCTATGATCTTGTGGAA	58.723	41.667	8.69	0.00	0.00	3.53
1937	2251	5.957798	TGATCTTGTGGAAAGATTCAATGC	58.042	37.500	2.34	0.00	37.14	3.56
1941	2255	6.449698	TCTTGTGGAAAGATTCAATGCTTTC	58.550	36.000	0.00	0.00	45.68	2.62
2075	2389	4.022935	TGTGAATGGAATGAGAGCAACAAC	60.023	41.667	0.00	0.00	0.00	3.32
2234	2552	1.122227	AAACAGCCAGGTGCAATTGT	58.878	45.000	7.40	0.00	44.83	2.71
2239	2557	0.108520	GCCAGGTGCAATTGTGGATG	60.109	55.000	15.15	6.47	40.77	3.51
2328	2646	1.203001	GGGGACAGTTGGTTTCATGGA	60.203	52.381	0.00	0.00	0.00	3.41

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
157	158	4.851179	GTCCGCCCCTTTAGCCCG	62.851	72.222	0.00	0.00	0.00	6.13
190	191	1.030488	TGTCTCTTCCTACCTCGCCG	61.030	60.000	0.00	0.00	0.00	6.46
360	363	0.328258	CCGTTGGATCCTTTCCTGGT	59.672	55.000	14.23	0.00	45.68	4.00
504	507	7.435068	AGCTGTAAAGTATAGTGTGTTTTGG	57.565	36.000	0.00	0.00	0.00	3.28
513	516	9.570468	TGTAGCAGTATAGCTGTAAAGTATAGT	57.430	33.333	0.00	0.00	46.11	2.12
603	611	2.504585	GGGAAAGTAGACCAGGGTAAGG	59.495	54.545	0.00	0.00	0.00	2.69
613	621	3.202151	TGGATGGGATTGGGAAAGTAGAC	59.798	47.826	0.00	0.00	0.00	2.59
649	657	1.665916	CGCCTGGCTCATGATACCG	60.666	63.158	17.92	0.00	0.00	4.02
711	719	3.017581	CCAGGGTGGGAGAAGGGG	61.018	72.222	0.00	0.00	32.67	4.79
754	766	2.787567	CCAAAAACCGCCCCAACGT	61.788	57.895	0.00	0.00	0.00	3.99
787	800	3.215568	CAACGCCACCAAGCACCA	61.216	61.111	0.00	0.00	0.00	4.17
901	914	1.301087	CACGAACGCCACCCTACAA	60.301	57.895	0.00	0.00	0.00	2.41
1026	1039	0.532573	GTTCTGCCAGATCCGTCTCA	59.467	55.000	0.00	0.00	30.42	3.27
1156	1189	2.742053	CGGAAATCACCTTTGTCATCGT	59.258	45.455	0.00	0.00	0.00	3.73
1206	1239	2.303890	TGTGATCATTGTGAGCTGTCCT	59.696	45.455	0.00	0.00	33.24	3.85
1390	1703	5.605908	TCTCTTGCTCCATGAATAATCTCCT	59.394	40.000	0.00	0.00	0.00	3.69
1391	1704	5.862845	TCTCTTGCTCCATGAATAATCTCC	58.137	41.667	0.00	0.00	0.00	3.71
1392	1705	7.798596	TTTCTCTTGCTCCATGAATAATCTC	57.201	36.000	0.00	0.00	0.00	2.75
1401	1714	4.633565	GGACTAGTTTTCTCTTGCTCCATG	59.366	45.833	0.00	0.00	0.00	3.66
1424	1737	1.064803	TGCCTGTTAACAGTGCAAACG	59.935	47.619	31.93	19.31	42.68	3.60
1495	1808	3.410631	TCTTGAAATTGTAGCGGTCCA	57.589	42.857	0.00	0.00	0.00	4.02
1624	1938	3.419922	CGCATATCGCTTTCAAATGCTTC	59.580	43.478	0.00	0.00	40.56	3.86
1676	1990	2.021042	TGAGGGAATTCCATCCTAGGGT	60.021	50.000	30.74	0.00	45.61	4.34
1878	2192	4.358851	CAGAAAAACGGTGCAGAATTTCA	58.641	39.130	0.00	0.00	31.06	2.69
1884	2198	1.333619	GAAGCAGAAAAACGGTGCAGA	59.666	47.619	0.00	0.00	39.80	4.26
1887	2201	0.383949	TGGAAGCAGAAAAACGGTGC	59.616	50.000	0.00	0.00	37.48	5.01
1890	2204	2.225727	GGTACTGGAAGCAGAAAAACGG	59.774	50.000	0.00	0.00	37.60	4.44
1892	2206	5.938125	TCATAGGTACTGGAAGCAGAAAAAC	59.062	40.000	0.00	0.00	41.52	2.43
1898	2212	5.163364	ACAAGATCATAGGTACTGGAAGCAG	60.163	44.000	0.00	0.00	41.52	4.24
1899	2213	4.716784	ACAAGATCATAGGTACTGGAAGCA	59.283	41.667	0.00	0.00	41.52	3.91
1902	2216	5.277250	TCCACAAGATCATAGGTACTGGAA	58.723	41.667	0.00	0.00	41.52	3.53
1911	2225	7.861372	GCATTGAATCTTTCCACAAGATCATAG	59.139	37.037	0.00	0.00	36.07	2.23
1914	2228	5.713389	AGCATTGAATCTTTCCACAAGATCA	59.287	36.000	0.00	0.00	36.07	2.92
1918	2232	6.218019	TGAAAGCATTGAATCTTTCCACAAG	58.782	36.000	18.50	0.00	44.47	3.16
1920	2234	5.787953	TGAAAGCATTGAATCTTTCCACA	57.212	34.783	18.50	6.70	44.47	4.17
1937	2251	9.985318	CAATAGAGAGACTATTTTGCTTGAAAG	57.015	33.333	0.00	0.00	45.99	2.62
1941	2255	7.279536	TCAGCAATAGAGAGACTATTTTGCTTG	59.720	37.037	16.54	13.29	46.39	4.01
1942	2256	7.334090	TCAGCAATAGAGAGACTATTTTGCTT	58.666	34.615	16.54	5.24	46.39	3.91
1944	2258	7.545362	TTCAGCAATAGAGAGACTATTTTGC	57.455	36.000	11.38	11.38	45.99	3.68
1952	2266	9.787532	GATCTGTATATTCAGCAATAGAGAGAC	57.212	37.037	4.54	0.00	38.33	3.36
2075	2389	5.305585	TCAGTGGCCTTAACAGAAACTTAG	58.694	41.667	3.32	0.00	0.00	2.18
2234	2552	1.221840	GCTTCGGCTCCTTCATCCA	59.778	57.895	0.00	0.00	38.08	3.41
2239	2557	0.884704	TGTGTTGCTTCGGCTCCTTC	60.885	55.000	0.00	0.00	42.37	3.46
2328	2646	1.554617	GGGGCCTGTTTGCATTTATGT	59.445	47.619	0.84	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.