AutoCloner

Multiple sequence alignment - TraesCS3B01G458300

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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	TraesCS3B01G458300	chr3B	100.000	2731	0	0	1	2731	700798465	700801195	0.000000e+00	5044.0
1	TraesCS3B01G458300	chr3B	90.083	2279	181	21	1	2270	700809373	700811615	0.000000e+00	2915.0
2	TraesCS3B01G458300	chr3B	88.544	2191	205	25	1	2182	478551394	478549241	0.000000e+00	2614.0
3	TraesCS3B01G458300	chr3B	96.429	56	1	1	2270	2324	700824737	700824792	1.040000e-14	91.6
4	TraesCS3B01G458300	chr7D	90.142	2181	191	15	1	2177	432740982	432738822	0.000000e+00	2815.0
5	TraesCS3B01G458300	chr7D	86.806	576	62	7	1	572	182352890	182353455	4.960000e-177	630.0
6	TraesCS3B01G458300	chr3A	89.995	2179	167	17	1	2176	418766068	418763938	0.000000e+00	2769.0
7	TraesCS3B01G458300	chr4D	89.685	2191	190	20	2	2178	421049082	421046914	0.000000e+00	2761.0
8	TraesCS3B01G458300	chr4D	89.630	2189	173	22	1	2181	493971527	493969385	0.000000e+00	2736.0
9	TraesCS3B01G458300	chr4D	89.387	2186	202	18	1	2180	48684372	48682211	0.000000e+00	2724.0
10	TraesCS3B01G458300	chr6B	88.453	2191	199	25	1	2176	81980624	81982775	0.000000e+00	2595.0
11	TraesCS3B01G458300	chr6B	85.423	638	75	12	2	628	674355734	674355104	0.000000e+00	647.0
12	TraesCS3B01G458300	chr4A	89.165	2095	203	11	87	2178	327748724	327746651	0.000000e+00	2590.0
13	TraesCS3B01G458300	chr4A	87.546	2192	214	28	3	2177	60891167	60893316	0.000000e+00	2481.0
14	TraesCS3B01G458300	chr1A	90.081	1845	163	11	338	2176	327012029	327010199	0.000000e+00	2375.0
15	TraesCS3B01G458300	chr5B	90.685	1782	155	8	408	2185	375712287	375710513	0.000000e+00	2361.0
16	TraesCS3B01G458300	chr1B	89.173	1875	182	13	317	2185	192470244	192468385	0.000000e+00	2318.0
17	TraesCS3B01G458300	chr1D	90.087	1372	122	8	1	1370	338633146	338634505	0.000000e+00	1768.0
18	TraesCS3B01G458300	chr7B	94.175	103	6	0	2190	2292	389277117	389277219	1.010000e-34	158.0
19	TraesCS3B01G458300	chr6A	93.333	105	7	0	2188	2292	53494644	53494748	3.640000e-34	156.0

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	TraesCS3B01G458300	chr3B	700798465	700801195	2730	False	5044	5044	100.000	1	2731	1	chr3B.!!$F1	2730
1	TraesCS3B01G458300	chr3B	700809373	700811615	2242	False	2915	2915	90.083	1	2270	1	chr3B.!!$F2	2269
2	TraesCS3B01G458300	chr3B	478549241	478551394	2153	True	2614	2614	88.544	1	2182	1	chr3B.!!$R1	2181
3	TraesCS3B01G458300	chr7D	432738822	432740982	2160	True	2815	2815	90.142	1	2177	1	chr7D.!!$R1	2176
4	TraesCS3B01G458300	chr7D	182352890	182353455	565	False	630	630	86.806	1	572	1	chr7D.!!$F1	571
5	TraesCS3B01G458300	chr3A	418763938	418766068	2130	True	2769	2769	89.995	1	2176	1	chr3A.!!$R1	2175
6	TraesCS3B01G458300	chr4D	421046914	421049082	2168	True	2761	2761	89.685	2	2178	1	chr4D.!!$R2	2176
7	TraesCS3B01G458300	chr4D	493969385	493971527	2142	True	2736	2736	89.630	1	2181	1	chr4D.!!$R3	2180
8	TraesCS3B01G458300	chr4D	48682211	48684372	2161	True	2724	2724	89.387	1	2180	1	chr4D.!!$R1	2179
9	TraesCS3B01G458300	chr6B	81980624	81982775	2151	False	2595	2595	88.453	1	2176	1	chr6B.!!$F1	2175
10	TraesCS3B01G458300	chr6B	674355104	674355734	630	True	647	647	85.423	2	628	1	chr6B.!!$R1	626
11	TraesCS3B01G458300	chr4A	327746651	327748724	2073	True	2590	2590	89.165	87	2178	1	chr4A.!!$R1	2091
12	TraesCS3B01G458300	chr4A	60891167	60893316	2149	False	2481	2481	87.546	3	2177	1	chr4A.!!$F1	2174
13	TraesCS3B01G458300	chr1A	327010199	327012029	1830	True	2375	2375	90.081	338	2176	1	chr1A.!!$R1	1838
14	TraesCS3B01G458300	chr5B	375710513	375712287	1774	True	2361	2361	90.685	408	2185	1	chr5B.!!$R1	1777
15	TraesCS3B01G458300	chr1B	192468385	192470244	1859	True	2318	2318	89.173	317	2185	1	chr1B.!!$R1	1868
16	TraesCS3B01G458300	chr1D	338633146	338634505	1359	False	1768	1768	90.087	1	1370	1	chr1D.!!$F1	1369

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
555	661	0.678684	TCGATCTGCCAGGTACGACA	60.679	55.0	0.0	0.0	0.0	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2340	2493	0.179	CGCACTAGGGCCTCAAAGAT	59.821	55.0	10.74	0.0	0.0	2.4	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	64	2.431057	CCGACAGTTATTAGCCTCACCT	59.569	50.000	0.00	0.00	0.00	4.00
272	286	1.137086	AGATTCGATCCACGGTGAAGG	59.863	52.381	10.28	0.00	42.82	3.46
313	332	4.214971	GGTAGATAAGCATGGCAGTTCATG	59.785	45.833	0.00	0.00	45.26	3.07
336	415	6.495706	TGCTAGTTCATACGAGTTCATACTG	58.504	40.000	0.00	0.00	33.84	2.74
366	445	8.747471	CATGCAAGATCAGAATAGAGGTAGATA	58.253	37.037	0.00	0.00	0.00	1.98
385	464	2.544844	ACGGATGAAGTAGAAGGGGA	57.455	50.000	0.00	0.00	0.00	4.81
390	477	4.384208	CGGATGAAGTAGAAGGGGAATTGT	60.384	45.833	0.00	0.00	0.00	2.71
399	486	1.392407	AGGGGAATTGTGGGATTGGA	58.608	50.000	0.00	0.00	0.00	3.53
430	524	0.860618	GACACTAGCTAACCGCGACG	60.861	60.000	8.23	0.00	45.59	5.12
470	564	1.296392	CGGTGGATCAAGTGGCTGA	59.704	57.895	0.00	0.00	0.00	4.26
555	661	0.678684	TCGATCTGCCAGGTACGACA	60.679	55.000	0.00	0.00	0.00	4.35
977	1102	2.283894	CCCAAGGGAAGGGGTTGC	60.284	66.667	0.00	0.00	42.90	4.17
978	1103	2.525592	CCAAGGGAAGGGGTTGCA	59.474	61.111	0.00	0.00	0.00	4.08
1136	1266	4.083537	TGCCGTTTTAACTACATGCTCTTG	60.084	41.667	0.00	0.00	0.00	3.02
1150	1280	5.597182	ACATGCTCTTGAATAAGCCATGAAT	59.403	36.000	18.42	4.23	41.13	2.57
1177	1307	2.118313	TGTGCCTGACTCCATGAATG	57.882	50.000	0.00	0.00	0.00	2.67
1235	1365	2.743928	GCTCCCGGCTGTTGACAG	60.744	66.667	6.77	6.77	46.40	3.51
1258	1388	1.026718	GGGCAAGGAGTCGGTTCATG	61.027	60.000	0.00	0.00	0.00	3.07
1302	1432	2.920912	ACCGCCGAGGAAGAACCA	60.921	61.111	3.89	0.00	45.00	3.67
1411	1541	0.595095	CCCAAGTCACTTCTGCAAGC	59.405	55.000	0.00	0.00	32.09	4.01
1512	1643	2.624838	CAAGCTGAGGAACAACATTGGT	59.375	45.455	0.00	0.00	0.00	3.67
1514	1645	3.299503	AGCTGAGGAACAACATTGGTTT	58.700	40.909	0.00	0.00	34.21	3.27
1530	1661	1.353091	GTTTCTCCTGGAGGGTGACT	58.647	55.000	23.00	0.00	37.33	3.41
1556	1688	0.107508	CTGATGAACGGCAGGGTGAT	60.108	55.000	0.00	0.00	0.00	3.06
1572	1704	1.561542	GTGATCCTGGATCAGGGTTGT	59.438	52.381	33.86	0.00	46.20	3.32

Showing 1 to 25 of 301 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	64	3.663815	GAGAGGGAGCGGTGAGGGA	62.664	68.421	0.00	0.00	0.00	4.20
206	218	4.814234	AGTAGTGCATGACGAACAGAAAAA	59.186	37.500	0.00	0.00	0.00	1.94
277	291	5.721960	TGCTTATCTACCTCTATTCCCCATC	59.278	44.000	0.00	0.00	0.00	3.51
313	332	5.915758	CCAGTATGAACTCGTATGAACTAGC	59.084	44.000	0.00	0.00	39.69	3.42
325	404	4.937620	TCTTGCATGAACCAGTATGAACTC	59.062	41.667	0.00	0.00	39.69	3.01
336	415	5.469421	CCTCTATTCTGATCTTGCATGAACC	59.531	44.000	6.36	2.83	0.00	3.62
366	445	2.544844	TCCCCTTCTACTTCATCCGT	57.455	50.000	0.00	0.00	0.00	4.69
385	464	3.075283	TGTGTACCTCCAATCCCACAATT	59.925	43.478	0.00	0.00	30.55	2.32
390	477	2.039746	CTGTTGTGTACCTCCAATCCCA	59.960	50.000	0.00	0.00	0.00	4.37
399	486	3.231818	AGCTAGTGTCTGTTGTGTACCT	58.768	45.455	0.00	0.00	0.00	3.08
455	549	1.003580	GAAGGTCAGCCACTTGATCCA	59.996	52.381	0.00	0.00	37.19	3.41
458	552	2.575279	AGATGAAGGTCAGCCACTTGAT	59.425	45.455	0.00	0.00	32.25	2.57
470	564	3.866651	CGATGGACAAGAAGATGAAGGT	58.133	45.455	0.00	0.00	0.00	3.50
904	1029	2.222027	GCTAGTGACTGCACCAAGTTT	58.778	47.619	0.00	0.00	46.32	2.66
994	1120	1.617850	CCTCTCTATCGCCATGAGCTT	59.382	52.381	0.00	0.00	40.39	3.74
1008	1134	4.017037	TCACTATCAACCTTCCTCCTCTCT	60.017	45.833	0.00	0.00	0.00	3.10
1136	1266	7.380602	GCACAACATAGAATTCATGGCTTATTC	59.619	37.037	8.44	0.00	0.00	1.75
1150	1280	2.637382	TGGAGTCAGGCACAACATAGAA	59.363	45.455	0.00	0.00	0.00	2.10
1177	1307	0.102120	CTCTCCTCGATCTGCACACC	59.898	60.000	0.00	0.00	0.00	4.16
1227	1357	1.108727	CCTTGCCCTTGCTGTCAACA	61.109	55.000	0.00	0.00	38.71	3.33
1235	1365	2.747855	CCGACTCCTTGCCCTTGC	60.748	66.667	0.00	0.00	38.26	4.01
1258	1388	3.443045	CACCACCTCGGGCATTGC	61.443	66.667	0.00	0.00	40.22	3.56
1397	1527	1.736681	GGATGAGCTTGCAGAAGTGAC	59.263	52.381	0.00	0.00	0.00	3.67
1411	1541	0.252479	AGCTCTGGTGCAAGGATGAG	59.748	55.000	0.00	0.00	34.99	2.90
1450	1581	2.297701	GAAGTGCTTGGTGAAGTCCAA	58.702	47.619	0.00	0.00	44.03	3.53

Showing 1 to 25 of 303 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.