AutoCloner

Multiple sequence alignment - TraesCS5A01G257400

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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	TraesCS5A01G257400	chr5A	100.000	2339	0	0	1	2339	472509197	472511535	0.000000e+00	4320
1	TraesCS5A01G257400	chr2A	96.994	1364	40	1	1	1363	77801821	77803184	0.000000e+00	2290
2	TraesCS5A01G257400	chr2A	96.772	1363	43	1	1	1363	382856645	382855284	0.000000e+00	2272
3	TraesCS5A01G257400	chr2B	96.112	1363	51	2	1	1363	325636807	325638167	0.000000e+00	2222
4	TraesCS5A01G257400	chr6D	95.308	1364	63	1	1	1363	462399748	462398385	0.000000e+00	2163
5	TraesCS5A01G257400	chr6D	94.872	1365	65	5	1	1363	452072047	452070686	0.000000e+00	2128
6	TraesCS5A01G257400	chr4B	95.172	1367	59	3	1	1361	364053867	364052502	0.000000e+00	2152
7	TraesCS5A01G257400	chr1D	95.158	1363	65	1	1	1362	176360148	176361510	0.000000e+00	2150
8	TraesCS5A01G257400	chr1D	94.380	1370	74	3	1	1369	356880594	356881961	0.000000e+00	2100
9	TraesCS5A01G257400	chr5B	93.979	1362	82	0	1	1362	684172823	684174184	0.000000e+00	2061
10	TraesCS5A01G257400	chr5B	92.318	781	38	11	1566	2336	439347968	439348736	0.000000e+00	1090
11	TraesCS5A01G257400	chr5B	92.737	179	11	2	1361	1539	439347724	439347900	8.290000e-65	257
12	TraesCS5A01G257400	chr5D	88.702	1009	51	27	1361	2339	370131046	370132021	0.000000e+00	1173

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	TraesCS5A01G257400	chr5A	472509197	472511535	2338	False	4320.0	4320	100.0000	1	2339	1	chr5A.!!$F1	2338
1	TraesCS5A01G257400	chr2A	77801821	77803184	1363	False	2290.0	2290	96.9940	1	1363	1	chr2A.!!$F1	1362
2	TraesCS5A01G257400	chr2A	382855284	382856645	1361	True	2272.0	2272	96.7720	1	1363	1	chr2A.!!$R1	1362
3	TraesCS5A01G257400	chr2B	325636807	325638167	1360	False	2222.0	2222	96.1120	1	1363	1	chr2B.!!$F1	1362
4	TraesCS5A01G257400	chr6D	462398385	462399748	1363	True	2163.0	2163	95.3080	1	1363	1	chr6D.!!$R2	1362
5	TraesCS5A01G257400	chr6D	452070686	452072047	1361	True	2128.0	2128	94.8720	1	1363	1	chr6D.!!$R1	1362
6	TraesCS5A01G257400	chr4B	364052502	364053867	1365	True	2152.0	2152	95.1720	1	1361	1	chr4B.!!$R1	1360
7	TraesCS5A01G257400	chr1D	176360148	176361510	1362	False	2150.0	2150	95.1580	1	1362	1	chr1D.!!$F1	1361
8	TraesCS5A01G257400	chr1D	356880594	356881961	1367	False	2100.0	2100	94.3800	1	1369	1	chr1D.!!$F2	1368
9	TraesCS5A01G257400	chr5B	684172823	684174184	1361	False	2061.0	2061	93.9790	1	1362	1	chr5B.!!$F1	1361
10	TraesCS5A01G257400	chr5B	439347724	439348736	1012	False	673.5	1090	92.5275	1361	2336	2	chr5B.!!$F2	975
11	TraesCS5A01G257400	chr5D	370131046	370132021	975	False	1173.0	1173	88.7020	1361	2339	1	chr5D.!!$F1	978

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
491	494	1.203174	ACCCATTTGCCCTACTTGCTT	60.203	47.619	0.0	0.0	0.0	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1794	1852	0.037326	CTGCTCCGGCTGTACAAAGA	60.037	55.0	0.0	0.0	39.59	2.52	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
182	184	1.617850	GTGGCCCATTGATGTTCAACA	59.382	47.619	0.00	0.00	39.45	3.33
203	205	7.886970	TCAACAGATTCTCTCAATTCCAATCTT	59.113	33.333	0.00	0.00	32.59	2.40
229	231	7.014422	TGCAACATGATATGCCAGATTTCATTA	59.986	33.333	16.27	0.00	41.87	1.90
266	268	5.106869	CGAAAAATGGTATGTTCTCGGTTCA	60.107	40.000	0.00	0.00	0.00	3.18
491	494	1.203174	ACCCATTTGCCCTACTTGCTT	60.203	47.619	0.00	0.00	0.00	3.91
694	697	4.082841	ACAATGTGCGTGAAATGATTGCTA	60.083	37.500	0.00	0.00	0.00	3.49
698	701	5.468592	TGTGCGTGAAATGATTGCTATTTT	58.531	33.333	0.00	0.00	0.00	1.82
766	769	3.144506	ACAACTCAGAATGCACTTCAGG	58.855	45.455	10.26	4.08	36.24	3.86
874	883	3.660669	TCCTCCTAGGGGTTTTGTGAAAT	59.339	43.478	8.16	0.00	35.59	2.17
880	889	7.070629	TCCTAGGGGTTTTGTGAAATTTAACT	58.929	34.615	9.46	0.00	0.00	2.24
1124	1133	1.473278	GAAGAACGGAGGACAGTCGAT	59.527	52.381	0.00	0.00	0.00	3.59
1184	1193	2.135139	TGCTTGTGACTTCGTTGCTAG	58.865	47.619	0.00	0.00	0.00	3.42
1254	1263	5.163854	GCTTGCGAGTTTAGCTAGATTTTCA	60.164	40.000	2.14	0.00	39.23	2.69
1457	1469	1.457346	CCAGGCTGCCTTTCTGTTAG	58.543	55.000	20.79	4.83	0.00	2.34
1495	1507	0.322008	GGCAAGCAGTAAGGCTGTCT	60.322	55.000	0.00	0.00	45.07	3.41
1563	1618	1.104577	GCGAGCTGGCTAGGTAGAGT	61.105	60.000	14.13	0.00	34.13	3.24
1564	1619	0.948678	CGAGCTGGCTAGGTAGAGTC	59.051	60.000	0.21	0.00	34.13	3.36
1713	1771	4.512944	GCATGCACGGTACTACTACTACTA	59.487	45.833	14.21	0.00	0.00	1.82
1714	1772	5.559799	GCATGCACGGTACTACTACTACTAC	60.560	48.000	14.21	0.00	0.00	2.73
1715	1773	5.344743	TGCACGGTACTACTACTACTACT	57.655	43.478	0.00	0.00	0.00	2.57
1727	1785	5.940595	ACTACTACTACTTGCGAACTCTTG	58.059	41.667	0.00	0.00	0.00	3.02
1759	1817	5.803020	AGCTATGTTTCGATTGTTTCCTC	57.197	39.130	0.00	0.00	0.00	3.71
1767	1825	3.399330	TCGATTGTTTCCTCGCTCTTTT	58.601	40.909	0.00	0.00	34.94	2.27
1771	1829	3.753294	TGTTTCCTCGCTCTTTTCTCT	57.247	42.857	0.00	0.00	0.00	3.10
1801	1859	9.191479	TGAACAAATTTCTAGGGTTTCTTTGTA	57.809	29.630	0.00	0.00	35.09	2.41
1887	1945	2.743928	GCCAGAGGACTGCCAACG	60.744	66.667	0.00	0.00	42.25	4.10
1911	1969	2.108976	GCTCCGGCGGATCATGAA	59.891	61.111	31.23	4.84	0.00	2.57
2038	2102	2.497273	GCCATGCAAGGGTGATTAGTTT	59.503	45.455	10.51	0.00	42.11	2.66
2045	2109	7.156876	TGCAAGGGTGATTAGTTTATGAAAG	57.843	36.000	0.00	0.00	0.00	2.62
2101	2168	4.947645	TGATCACCTGGCAAAAAGAAAAG	58.052	39.130	0.00	0.00	0.00	2.27
2102	2169	4.648762	TGATCACCTGGCAAAAAGAAAAGA	59.351	37.500	0.00	0.00	0.00	2.52
2111	2178	4.112634	GCAAAAAGAAAAGACCCAGTGTC	58.887	43.478	0.00	0.00	44.82	3.67
2121	2188	0.390124	ACCCAGTGTCGTCGCTTTAA	59.610	50.000	0.00	0.00	31.46	1.52
2140	2207	8.916654	CGCTTTAATATTCTGTATCCTGTAGTG	58.083	37.037	0.00	0.00	0.00	2.74
2141	2208	9.765795	GCTTTAATATTCTGTATCCTGTAGTGT	57.234	33.333	0.00	0.00	0.00	3.55
2147	2214	7.956328	ATTCTGTATCCTGTAGTGTAGTTCA	57.044	36.000	0.00	0.00	0.00	3.18
2166	2235	6.415573	AGTTCAGTCTAGTTCCAGTTTTTGT	58.584	36.000	0.00	0.00	0.00	2.83
2190	2259	3.193691	AGCGTGCAAGTTCTAGTCTACAT	59.806	43.478	0.59	0.00	0.00	2.29
2306	2377	3.173668	TCTTTGATAATACCGCTGCGT	57.826	42.857	21.59	11.45	0.00	5.24
2311	2382	5.585500	TTGATAATACCGCTGCGTTAATC	57.415	39.130	21.59	12.07	0.00	1.75
2327	2398	8.076714	TGCGTTAATCAGATCAGATAAATCAC	57.923	34.615	0.45	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	5.715439	AGTATCACAATTTGGGATCCAGA	57.285	39.130	17.22	0.00	35.05	3.86
83	85	5.366186	TCACCCACCTTAGTTAACAGTTGTA	59.634	40.000	8.61	0.00	0.00	2.41
182	184	6.662234	TTGCAAGATTGGAATTGAGAGAATCT	59.338	34.615	0.00	0.00	40.31	2.40
203	205	4.645588	TGAAATCTGGCATATCATGTTGCA	59.354	37.500	16.02	0.00	40.66	4.08
229	231	8.889717	CATACCATTTTTCGTATAACTCCAAGT	58.110	33.333	0.00	0.00	0.00	3.16
266	268	4.074970	CCACTCCACAAAATAAGCAGACT	58.925	43.478	0.00	0.00	0.00	3.24
491	494	5.003804	GCTTTGTATCTTCAGAACCCTCAA	58.996	41.667	0.00	0.00	0.00	3.02
694	697	6.045459	TCCCACCATAGATACCATGCTAAAAT	59.955	38.462	0.00	0.00	0.00	1.82
698	701	4.140575	TCCCACCATAGATACCATGCTA	57.859	45.455	0.00	0.00	0.00	3.49
766	769	2.033424	GCGCTAGAATCCCCATTGAAAC	59.967	50.000	0.00	0.00	0.00	2.78
874	883	6.031471	GGTCAAAAGAAGCGTCAAAGTTAAA	58.969	36.000	1.61	0.00	0.00	1.52
880	889	3.629855	TCATGGTCAAAAGAAGCGTCAAA	59.370	39.130	1.61	0.00	0.00	2.69
1015	1024	8.188139	CGCCAATGTTATACCAAATTTAAGAGT	58.812	33.333	0.00	0.00	0.00	3.24
1184	1193	3.987868	TCTGTTGCAGTGTTCGAATCTAC	59.012	43.478	0.00	1.48	32.61	2.59
1254	1263	6.729690	TTCTCAAACCATTCAGAAACCAAT	57.270	33.333	0.00	0.00	0.00	3.16
1371	1381	2.775032	TTCGGTTGCTACACGAGGGC	62.775	60.000	10.44	0.00	37.95	5.19
1447	1459	3.305398	AGGACGAGCACTAACAGAAAG	57.695	47.619	0.00	0.00	0.00	2.62
1457	1469	1.364626	CCATGAGCAAGGACGAGCAC	61.365	60.000	0.00	0.00	0.00	4.40
1495	1507	5.568482	GCATTCGGCATTGCGAATATATAA	58.432	37.500	20.36	2.39	43.97	0.98
1563	1618	2.124277	TCCATTTCTCTCGGTCTCGA	57.876	50.000	0.00	0.00	43.86	4.04
1564	1619	2.094700	TGTTCCATTTCTCTCGGTCTCG	60.095	50.000	0.00	0.00	37.82	4.04
1665	1720	2.599597	GCCATCTGCAGTGGGGAT	59.400	61.111	26.44	8.21	40.77	3.85
1713	1771	1.134220	TGTTCCCAAGAGTTCGCAAGT	60.134	47.619	0.00	0.00	39.48	3.16
1714	1772	1.532868	CTGTTCCCAAGAGTTCGCAAG	59.467	52.381	0.00	0.00	0.00	4.01
1715	1773	1.593196	CTGTTCCCAAGAGTTCGCAA	58.407	50.000	0.00	0.00	0.00	4.85
1727	1785	2.866762	CGAAACATAGCTAGCTGTTCCC	59.133	50.000	27.68	16.57	34.61	3.97
1759	1817	9.994432	AAATTTGTTCATATAGAGAAAAGAGCG	57.006	29.630	0.00	0.00	0.00	5.03
1788	1846	1.544759	CCGGCTGTACAAAGAAACCCT	60.545	52.381	0.00	0.00	0.00	4.34
1791	1849	1.197036	GCTCCGGCTGTACAAAGAAAC	59.803	52.381	0.00	0.00	35.22	2.78
1792	1850	1.202710	TGCTCCGGCTGTACAAAGAAA	60.203	47.619	0.00	0.00	39.59	2.52
1793	1851	0.394938	TGCTCCGGCTGTACAAAGAA	59.605	50.000	0.00	0.00	39.59	2.52
1794	1852	0.037326	CTGCTCCGGCTGTACAAAGA	60.037	55.000	0.00	0.00	39.59	2.52
1795	1853	0.320771	ACTGCTCCGGCTGTACAAAG	60.321	55.000	0.00	0.00	46.19	2.77
1796	1854	0.602638	CACTGCTCCGGCTGTACAAA	60.603	55.000	0.00	0.00	46.28	2.83
2038	2102	1.305219	GGCACGGCTGCACTTTCATA	61.305	55.000	0.50	0.00	46.28	2.15
2045	2109	3.542629	GAAACAGGCACGGCTGCAC	62.543	63.158	19.49	8.21	46.28	4.57
2060	2124	3.787785	TCAACAGCAACGTACTGAGAAA	58.212	40.909	21.55	5.06	38.55	2.52
2101	2168	0.038892	TAAAGCGACGACACTGGGTC	60.039	55.000	0.00	0.00	43.36	4.46
2102	2169	0.390124	TTAAAGCGACGACACTGGGT	59.610	50.000	0.00	0.00	0.00	4.51
2111	2178	6.641314	ACAGGATACAGAATATTAAAGCGACG	59.359	38.462	0.00	0.00	41.41	5.12
2121	2188	9.642343	TGAACTACACTACAGGATACAGAATAT	57.358	33.333	0.00	0.00	41.41	1.28
2140	2207	7.494952	ACAAAAACTGGAACTAGACTGAACTAC	59.505	37.037	0.00	0.00	0.00	2.73
2141	2208	7.562135	ACAAAAACTGGAACTAGACTGAACTA	58.438	34.615	0.00	0.00	0.00	2.24
2143	2210	6.315393	TGACAAAAACTGGAACTAGACTGAAC	59.685	38.462	0.00	0.00	0.00	3.18
2144	2211	6.411376	TGACAAAAACTGGAACTAGACTGAA	58.589	36.000	0.00	0.00	0.00	3.02
2145	2212	5.984725	TGACAAAAACTGGAACTAGACTGA	58.015	37.500	0.00	0.00	0.00	3.41
2146	2213	5.277538	GCTGACAAAAACTGGAACTAGACTG	60.278	44.000	0.00	0.00	0.00	3.51
2147	2214	4.816925	GCTGACAAAAACTGGAACTAGACT	59.183	41.667	0.00	0.00	0.00	3.24
2166	2235	1.613925	AGACTAGAACTTGCACGCTGA	59.386	47.619	0.00	0.00	0.00	4.26
2306	2377	8.421002	TGTCCGTGATTTATCTGATCTGATTAA	58.579	33.333	18.83	16.21	0.00	1.40
2311	2382	6.453943	AGATGTCCGTGATTTATCTGATCTG	58.546	40.000	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.