AutoCloner

Multiple sequence alignment - TraesCS5A01G065600

Loading Multiple Alignment...

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	TraesCS5A01G065600	chr5A	100.000	2390	0	0	1	2390	71456687	71459076	0.000000e+00	4414.0
1	TraesCS5A01G065600	chr5B	94.207	1847	72	16	1	1826	84664750	84666582	0.000000e+00	2785.0
2	TraesCS5A01G065600	chr5B	90.169	356	17	4	2044	2386	84666835	84667185	4.690000e-122	448.0
3	TraesCS5A01G065600	chr5B	92.818	181	8	2	1829	2009	84666659	84666834	8.480000e-65	257.0
4	TraesCS5A01G065600	chr5D	94.152	1556	49	7	94	1629	76003048	76004581	0.000000e+00	2331.0
5	TraesCS5A01G065600	chr5D	94.845	194	9	1	1947	2140	76023636	76023828	3.860000e-78	302.0
6	TraesCS5A01G065600	chr5D	93.532	201	7	3	1631	1826	76023164	76023363	6.460000e-76	294.0
7	TraesCS5A01G065600	chr5D	90.104	192	6	3	2209	2388	76024140	76024330	1.100000e-58	237.0
8	TraesCS5A01G065600	chr5D	75.333	450	64	31	957	1388	52457082	52457502	3.160000e-39	172.0
9	TraesCS5A01G065600	chr5D	93.043	115	7	1	1832	1946	76023443	76023556	1.470000e-37	167.0
10	TraesCS5A01G065600	chr5D	94.444	90	4	1	2135	2224	76023927	76024015	1.150000e-28	137.0
11	TraesCS5A01G065600	chr5D	90.323	62	5	1	1	62	76002988	76003048	1.970000e-11	80.5
12	TraesCS5A01G065600	chr6A	80.952	1155	149	34	296	1417	86400203	86399087	0.000000e+00	848.0
13	TraesCS5A01G065600	chr6D	79.665	1254	158	51	207	1417	68848944	68847745	0.000000e+00	813.0
14	TraesCS5A01G065600	chr6D	91.892	111	7	2	1474	1583	68720417	68720308	1.140000e-33	154.0
15	TraesCS5A01G065600	chr6D	87.288	118	14	1	432	549	68843208	68843092	1.490000e-27	134.0
16	TraesCS5A01G065600	chr6B	83.212	822	94	23	794	1583	143751335	143750526	0.000000e+00	713.0
17	TraesCS5A01G065600	chr2D	81.508	703	95	18	1067	1756	22107909	22107229	1.620000e-151	545.0
18	TraesCS5A01G065600	chr2A	78.998	419	60	15	1241	1636	23936925	23936512	6.550000e-66	261.0
19	TraesCS5A01G065600	chr7D	74.945	451	64	36	957	1388	534148480	534148900	6.840000e-36	161.0
20	TraesCS5A01G065600	chr7D	81.667	120	17	4	1271	1388	26854536	26854652	7.030000e-16	95.3

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	TraesCS5A01G065600	chr5A	71456687	71459076	2389	False	4414.000000	4414	100.0000	1	2390	1	chr5A.!!$F1	2389
1	TraesCS5A01G065600	chr5B	84664750	84667185	2435	False	1163.333333	2785	92.3980	1	2386	3	chr5B.!!$F1	2385
2	TraesCS5A01G065600	chr5D	76002988	76004581	1593	False	1205.750000	2331	92.2375	1	1629	2	chr5D.!!$F2	1628
3	TraesCS5A01G065600	chr5D	76023164	76024330	1166	False	227.400000	302	93.1936	1631	2388	5	chr5D.!!$F3	757
4	TraesCS5A01G065600	chr6A	86399087	86400203	1116	True	848.000000	848	80.9520	296	1417	1	chr6A.!!$R1	1121
5	TraesCS5A01G065600	chr6D	68847745	68848944	1199	True	813.000000	813	79.6650	207	1417	1	chr6D.!!$R3	1210
6	TraesCS5A01G065600	chr6B	143750526	143751335	809	True	713.000000	713	83.2120	794	1583	1	chr6B.!!$R1	789
7	TraesCS5A01G065600	chr2D	22107229	22107909	680	True	545.000000	545	81.5080	1067	1756	1	chr2D.!!$R1	689

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
203	210	1.376609	AATGGTCGAAAGGCGGATGC	61.377	55.000	0.0	0.0	41.33	3.91	F
1011	1072	1.379044	CCCAGGAATGGCAGTGTCC	60.379	63.158	0.0	0.0	0.00	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1088	1149	0.112412	GTCCTTCTTTCCCTTGGCCA	59.888	55.0	0.0	0.0	0.0	5.36	R
1911	2095	0.179032	TGGTTGTCACGGCTCACATT	60.179	50.0	0.0	0.0	0.0	2.71	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
65	67	8.347771	CCAAAGTTGTTCATCCTGTGATATATG	58.652	37.037	0.00	0.00	36.54	1.78
66	68	9.112725	CAAAGTTGTTCATCCTGTGATATATGA	57.887	33.333	0.00	0.00	36.54	2.15
159	164	3.329386	CATGTAGTGCCGCATATAGCTT	58.671	45.455	0.00	0.00	42.61	3.74
203	210	1.376609	AATGGTCGAAAGGCGGATGC	61.377	55.000	0.00	0.00	41.33	3.91
361	386	8.313292	ACAAATTTGCTAATCATATTGTGGTGT	58.687	29.630	18.12	0.00	0.00	4.16
685	721	9.897744	TGAAAGCAGAATTACAAGTCTTAAATG	57.102	29.630	0.00	0.00	29.75	2.32
815	874	6.129874	AGTCAGCATACTCCTTGTACATCTA	58.870	40.000	0.00	0.00	33.45	1.98
1011	1072	1.379044	CCCAGGAATGGCAGTGTCC	60.379	63.158	0.00	0.00	0.00	4.02
1030	1091	3.192844	GTCCTGGACACGAGTATTGAAGA	59.807	47.826	21.70	0.00	32.09	2.87
1054	1115	3.596214	GGAGTTATTCCAAGAGACGCAA	58.404	45.455	0.00	0.00	46.01	4.85
1106	1167	0.112412	GTGGCCAAGGGAAAGAAGGA	59.888	55.000	7.24	0.00	0.00	3.36
1142	1203	0.453390	GCTGATGCTAAACCTGTGCC	59.547	55.000	0.00	0.00	36.03	5.01
1165	1226	3.979495	CAGCAAAGAAATGAAGAGCACAC	59.021	43.478	0.00	0.00	0.00	3.82
1178	1239	3.912614	CACACGTGTGTTTGGGGT	58.087	55.556	35.03	1.83	42.83	4.95
1229	1290	5.350504	AATATCCAACCAGACTCTGAGTG	57.649	43.478	16.28	3.46	32.44	3.51
1262	1323	0.321475	TGGCACATGATCGACAAGCA	60.321	50.000	0.00	0.00	0.00	3.91
1265	1326	1.938577	GCACATGATCGACAAGCATCT	59.061	47.619	0.00	0.00	29.52	2.90
1466	1559	8.800370	TTGGTAATAATGTAGCATTGAAGTCA	57.200	30.769	4.78	0.00	31.88	3.41
1593	1698	0.028770	TCCTGCTTGTTTGCGTTTCG	59.971	50.000	0.00	0.00	35.36	3.46
1610	1715	4.143263	CGTTTCGCGGTAAGATGTAAGTTT	60.143	41.667	6.13	0.00	36.85	2.66
1629	1734	9.730420	GTAAGTTTCATGCTTTGAAGTAAAAGA	57.270	29.630	0.99	0.00	44.90	2.52
1733	1838	1.538876	CCCCTCCTTGTCCCAGTGA	60.539	63.158	0.00	0.00	0.00	3.41
1736	1841	1.355720	CCCTCCTTGTCCCAGTGAATT	59.644	52.381	0.00	0.00	0.00	2.17
1788	1898	6.166279	GTGAACTGACAGATCAATACTTCCA	58.834	40.000	16.14	0.00	33.30	3.53
1826	1936	6.624423	CAAGGATTTGTTATGCTTGCTAACT	58.376	36.000	6.16	0.00	39.81	2.24
1827	1937	6.840780	AGGATTTGTTATGCTTGCTAACTT	57.159	33.333	12.45	3.29	31.71	2.66
1845	2029	9.303116	TGCTAACTTAGATTTTTAACATTCCCA	57.697	29.630	0.00	0.00	0.00	4.37
1879	2063	2.622942	GGCAACAGATTTCAGTCAACCA	59.377	45.455	0.00	0.00	0.00	3.67
1882	2066	4.261741	GCAACAGATTTCAGTCAACCATGT	60.262	41.667	0.00	0.00	0.00	3.21
1911	2095	1.107114	ACATGTGAACGGTTTGCCAA	58.893	45.000	0.00	0.00	34.09	4.52
1946	2130	5.163248	TGACAACCAGTTGAGAATTACTCCA	60.163	40.000	17.06	0.00	44.34	3.86
1947	2131	5.063880	ACAACCAGTTGAGAATTACTCCAC	58.936	41.667	17.06	0.00	44.34	4.02
2019	2282	2.817258	CCGGCTTTTATCACAGGTTTCA	59.183	45.455	0.00	0.00	0.00	2.69
2025	2288	4.481930	TTTATCACAGGTTTCAGTTGCG	57.518	40.909	0.00	0.00	0.00	4.85
2027	2290	1.008538	CACAGGTTTCAGTTGCGCC	60.009	57.895	4.18	0.00	0.00	6.53
2082	2345	2.418976	GGCATCAAGTTTTACCGAGGTC	59.581	50.000	0.00	0.00	0.00	3.85
2125	2388	9.261180	CTACTCAAACTCTATCAGAACAACAAA	57.739	33.333	0.00	0.00	0.00	2.83
2219	2724	6.885735	AAATTTGAACACACAACTAGCAAC	57.114	33.333	0.00	0.00	0.00	4.17
2283	2788	4.635223	TCATGCATCAGACCTAATGCTAC	58.365	43.478	6.69	0.00	46.64	3.58
2326	2831	4.290155	GCGAGTATGCAACCCATAAATTG	58.710	43.478	0.00	0.00	38.11	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
81	86	2.171003	GCTGCACCTGATAAGGGTTTT	58.829	47.619	0.00	0.00	34.44	2.43
191	196	0.449388	CAGAACTGCATCCGCCTTTC	59.551	55.000	0.00	0.00	37.32	2.62
203	210	1.200020	GCCGACCCAAAATCAGAACTG	59.800	52.381	0.00	0.00	0.00	3.16
361	386	3.753815	TCACAAGATGTCAGGCAATGAA	58.246	40.909	0.00	0.00	40.43	2.57
641	676	6.642131	TGCTTTCAAGATGTTTACTGCAATTC	59.358	34.615	0.00	0.00	0.00	2.17
815	874	9.962783	GAACAGAAGGTCGTATAATTAGTACAT	57.037	33.333	0.00	0.00	0.00	2.29
937	998	6.480320	ACAACTAAGAAGTGTTAACTCTGCTG	59.520	38.462	17.06	9.44	34.77	4.41
1011	1072	4.169508	CACTCTTCAATACTCGTGTCCAG	58.830	47.826	0.00	0.00	0.00	3.86
1054	1115	3.490348	CTCTTGTCCCAACCAATTGAGT	58.510	45.455	7.12	0.00	38.15	3.41
1088	1149	0.112412	GTCCTTCTTTCCCTTGGCCA	59.888	55.000	0.00	0.00	0.00	5.36
1142	1203	3.005050	TGTGCTCTTCATTTCTTTGCTGG	59.995	43.478	0.00	0.00	0.00	4.85
1165	1226	2.422127	GGATATTCACCCCAAACACACG	59.578	50.000	0.00	0.00	0.00	4.49
1209	1270	2.497675	GCACTCAGAGTCTGGTTGGATA	59.502	50.000	19.99	0.00	31.51	2.59
1281	1342	1.066143	GTCTTGGCATCTTTCCTCCGA	60.066	52.381	0.00	0.00	0.00	4.55
1466	1559	3.772025	AGGCTACATTCTACTGTGAGCTT	59.228	43.478	0.00	0.00	31.84	3.74
1593	1698	4.332819	AGCATGAAACTTACATCTTACCGC	59.667	41.667	0.00	0.00	0.00	5.68
1610	1715	9.394767	TGCTATATCTTTTACTTCAAAGCATGA	57.605	29.630	0.00	0.00	34.26	3.07
1733	1838	5.640732	GCTTGTGAAATGTCGGTGATAATT	58.359	37.500	0.00	0.00	0.00	1.40
1736	1841	2.670905	CGCTTGTGAAATGTCGGTGATA	59.329	45.455	0.00	0.00	0.00	2.15
1788	1898	5.180271	CAAATCCTTGCTGGTTTAATGCAT	58.820	37.500	0.00	0.00	36.55	3.96
1836	2020	5.185828	GCCTCACTTTCTAATTGGGAATGTT	59.814	40.000	9.90	0.00	31.67	2.71
1845	2029	7.231317	TGAAATCTGTTGCCTCACTTTCTAATT	59.769	33.333	0.00	0.00	0.00	1.40
1879	2063	5.642063	CCGTTCACATGTTTAAGACCTACAT	59.358	40.000	0.00	0.00	32.98	2.29
1882	2066	5.217978	ACCGTTCACATGTTTAAGACCTA	57.782	39.130	0.00	0.00	0.00	3.08
1911	2095	0.179032	TGGTTGTCACGGCTCACATT	60.179	50.000	0.00	0.00	0.00	2.71
1946	2130	6.591834	GTGTCATCAGCATACTACAGAAAAGT	59.408	38.462	0.00	0.00	0.00	2.66
1947	2131	6.036517	GGTGTCATCAGCATACTACAGAAAAG	59.963	42.308	0.00	0.00	41.16	2.27
1948	2132	5.874810	GGTGTCATCAGCATACTACAGAAAA	59.125	40.000	0.00	0.00	41.16	2.29
2019	2282	0.958382	TGATAAAAGCCGGCGCAACT	60.958	50.000	23.20	7.24	37.52	3.16
2025	2288	1.173913	AACCTGTGATAAAAGCCGGC	58.826	50.000	21.89	21.89	0.00	6.13
2027	2290	3.915437	ACAAACCTGTGATAAAAGCCG	57.085	42.857	0.00	0.00	33.30	5.52
2082	2345	7.543947	TTGAGTAGAATGAACTGCATGTATG	57.456	36.000	0.00	0.00	37.28	2.39
2125	2388	5.948742	ACCTCGGTAGTACTTAGTAGAGT	57.051	43.478	0.00	0.00	0.00	3.24
2200	2567	2.223157	GCGTTGCTAGTTGTGTGTTCAA	60.223	45.455	0.00	0.00	0.00	2.69
2207	2574	2.686558	ACATTGCGTTGCTAGTTGTG	57.313	45.000	0.00	0.00	0.00	3.33
2219	2724	9.644993	TCGTTTGATCTATAAATTTACATTGCG	57.355	29.630	0.00	0.54	0.00	4.85
2283	2788	4.582459	GCGTGCTTATCTCTTTTAGCTTG	58.418	43.478	0.00	0.00	34.77	4.01
2326	2831	5.756195	TGCTTTGCATGTAACTATCATCC	57.244	39.130	0.00	0.00	31.71	3.51
2330	2835	6.308766	CCTTTGTTGCTTTGCATGTAACTATC	59.691	38.462	17.10	0.00	38.76	2.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.