AutoCloner

Multiple sequence alignment - TraesCS5A01G297500

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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	TraesCS5A01G297500	chr5A	100.000	2348	0	0	1	2348	505340186	505342533	0.000000e+00	4337
1	TraesCS5A01G297500	chr3D	89.660	2350	203	15	1	2347	422945055	422942743	0.000000e+00	2957
2	TraesCS5A01G297500	chr3D	89.305	2347	229	10	8	2347	126392434	126394765	0.000000e+00	2924
3	TraesCS5A01G297500	chr1D	89.422	2354	227	17	2	2347	217012044	217009705	0.000000e+00	2948
4	TraesCS5A01G297500	chr2B	88.813	2351	247	14	1	2343	243358837	243361179	0.000000e+00	2870
5	TraesCS5A01G297500	chr2B	88.351	2335	244	18	21	2347	424515192	424512878	0.000000e+00	2780
6	TraesCS5A01G297500	chr2B	85.311	177	18	7	1	170	722585101	722585276	2.400000e-40	176
7	TraesCS5A01G297500	chr5D	88.922	2338	231	15	16	2347	35280720	35278405	0.000000e+00	2857
8	TraesCS5A01G297500	chr5D	88.173	2359	244	26	3	2347	108339472	108341809	0.000000e+00	2778
9	TraesCS5A01G297500	chr7D	88.558	2351	257	11	3	2347	558450770	558453114	0.000000e+00	2841
10	TraesCS5A01G297500	chr2D	87.912	2366	247	32	1	2347	549979745	549982090	0.000000e+00	2748
11	TraesCS5A01G297500	chr3B	79.855	690	89	28	1	683	12155819	12156465	2.130000e-125	459

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	TraesCS5A01G297500	chr5A	505340186	505342533	2347	False	4337	4337	100.000	1	2348	1	chr5A.!!$F1	2347
1	TraesCS5A01G297500	chr3D	422942743	422945055	2312	True	2957	2957	89.660	1	2347	1	chr3D.!!$R1	2346
2	TraesCS5A01G297500	chr3D	126392434	126394765	2331	False	2924	2924	89.305	8	2347	1	chr3D.!!$F1	2339
3	TraesCS5A01G297500	chr1D	217009705	217012044	2339	True	2948	2948	89.422	2	2347	1	chr1D.!!$R1	2345
4	TraesCS5A01G297500	chr2B	243358837	243361179	2342	False	2870	2870	88.813	1	2343	1	chr2B.!!$F1	2342
5	TraesCS5A01G297500	chr2B	424512878	424515192	2314	True	2780	2780	88.351	21	2347	1	chr2B.!!$R1	2326
6	TraesCS5A01G297500	chr5D	35278405	35280720	2315	True	2857	2857	88.922	16	2347	1	chr5D.!!$R1	2331
7	TraesCS5A01G297500	chr5D	108339472	108341809	2337	False	2778	2778	88.173	3	2347	1	chr5D.!!$F1	2344
8	TraesCS5A01G297500	chr7D	558450770	558453114	2344	False	2841	2841	88.558	3	2347	1	chr7D.!!$F1	2344
9	TraesCS5A01G297500	chr2D	549979745	549982090	2345	False	2748	2748	87.912	1	2347	1	chr2D.!!$F1	2346
10	TraesCS5A01G297500	chr3B	12155819	12156465	646	False	459	459	79.855	1	683	1	chr3B.!!$F1	682

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
139	147	0.324552	CAGCCACCATCATTTCCCCA	60.325	55.0	0.0	0.0	0.0	4.96	F
1096	1130	0.179234	TGACGTGGAGCCTTTGTTCA	59.821	50.0	0.0	0.0	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1208	1242	0.036875	GGTCTTGGGGTCTTGTCCAG	59.963	60.000	0.0	0.0	34.17	3.86	R
2188	2234	1.002087	GTGGGACTTGAGTTCGACCAT	59.998	52.381	0.0	0.0	0.00	3.55	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
97	101	2.202878	GCGCACGCCTATTCCTCA	60.203	61.111	0.30	0.00	34.56	3.86
98	102	1.595382	GCGCACGCCTATTCCTCAT	60.595	57.895	0.30	0.00	34.56	2.90
139	147	0.324552	CAGCCACCATCATTTCCCCA	60.325	55.000	0.00	0.00	0.00	4.96
149	158	1.203237	CATTTCCCCACATTTCCCCC	58.797	55.000	0.00	0.00	0.00	5.40
197	222	2.359850	CACACCCACCATGGACGG	60.360	66.667	21.47	18.84	40.96	4.79
201	226	4.175337	CCCACCATGGACGGCGAT	62.175	66.667	21.47	0.00	40.96	4.58
258	284	1.215382	CTCGTTCGGCATGAGACCA	59.785	57.895	0.00	0.00	40.67	4.02
303	329	4.263572	CCCCGTGCAAGACCACCA	62.264	66.667	0.00	0.00	32.10	4.17
533	559	2.435938	GGCCTCGTCAATGCCGAA	60.436	61.111	0.00	0.00	35.08	4.30
536	562	1.970917	GCCTCGTCAATGCCGAAGTG	61.971	60.000	0.00	0.00	33.34	3.16
537	563	0.670546	CCTCGTCAATGCCGAAGTGT	60.671	55.000	0.00	0.00	33.34	3.55
538	564	0.716108	CTCGTCAATGCCGAAGTGTC	59.284	55.000	0.00	0.00	33.34	3.67
588	620	1.622607	CCCTCGAATGGTGCTACCCA	61.623	60.000	3.33	0.00	37.50	4.51
640	672	1.661480	CCGACTTCCACGTGTACCA	59.339	57.895	15.65	0.00	0.00	3.25
775	807	2.342279	CGGAGGCACGAGGAAACA	59.658	61.111	0.00	0.00	35.47	2.83
912	944	3.066190	CTGGCTACGACCCCGACA	61.066	66.667	0.00	0.00	39.50	4.35
998	1032	0.530288	TTCATGCGTGATCAGGTCGA	59.470	50.000	16.27	8.06	33.56	4.20
1077	1111	0.603569	AAGAGGACGAGTGCGACATT	59.396	50.000	0.00	0.00	41.64	2.71
1096	1130	0.179234	TGACGTGGAGCCTTTGTTCA	59.821	50.000	0.00	0.00	0.00	3.18
1206	1240	0.602638	TTTGCGAGTGTTGGCGAGAT	60.603	50.000	0.00	0.00	0.00	2.75
1208	1242	0.457853	TGCGAGTGTTGGCGAGATAC	60.458	55.000	0.00	0.00	0.00	2.24
1290	1324	1.098050	GGGAGTTTCATGAGCGCAAT	58.902	50.000	11.47	0.00	0.00	3.56
1345	1380	2.316108	GGTGGGTGTCCATTTTGAAGT	58.684	47.619	0.00	0.00	46.09	3.01
1409	1444	2.515979	TTGAGAGCGTCAAGGCCCA	61.516	57.895	0.00	0.00	40.45	5.36
1454	1489	1.625315	AGACATGGTGTGCTAGCAAGA	59.375	47.619	21.29	6.26	40.70	3.02
1489	1526	4.855388	GTGTCATCAAGTTTATGCTTGCAG	59.145	41.667	0.87	0.00	43.92	4.41
1545	1587	6.073167	TGCATGAAAACATTTGTAGGCATTTG	60.073	34.615	0.00	0.00	0.00	2.32
1633	1675	4.170256	GTCATCAAAGACGAGGAGAAGTC	58.830	47.826	0.00	0.00	37.63	3.01
1661	1703	0.546122	AATATGCCGCCCTCAAGTCA	59.454	50.000	0.00	0.00	0.00	3.41
1662	1704	0.767375	ATATGCCGCCCTCAAGTCAT	59.233	50.000	0.00	0.00	0.00	3.06
1752	1795	1.349026	CCAAGAAGGAGGACAAGCAGA	59.651	52.381	0.00	0.00	41.22	4.26
1754	1797	2.810852	CAAGAAGGAGGACAAGCAGAAC	59.189	50.000	0.00	0.00	0.00	3.01
1766	1809	2.089854	GCAGAACGCGACATCCAAT	58.910	52.632	15.93	0.00	0.00	3.16
1802	1845	2.170166	GTGGAGGGCATGATGAACAAA	58.830	47.619	0.00	0.00	0.00	2.83
1850	1893	4.303282	GGCGTTTCAAAAAGGAGCAAATA	58.697	39.130	0.00	0.00	0.00	1.40
1925	1968	2.025605	AGCCAAGATGCTTGAGATGGAA	60.026	45.455	8.64	0.00	38.85	3.53
1969	2012	4.814294	GATCGAGGCCGCCAACGT	62.814	66.667	21.99	13.21	37.70	3.99
2014	2057	2.278792	CGCGAGCATGATGACCGA	60.279	61.111	0.00	0.00	0.00	4.69
2093	2136	1.069204	GAGAAGATGCAGGCCGACATA	59.931	52.381	12.83	0.00	0.00	2.29
2211	2258	0.761323	TCGAACTCAAGTCCCACCCA	60.761	55.000	0.00	0.00	0.00	4.51
2229	2276	2.028294	CCCATTTTTGTGTGCTGGCATA	60.028	45.455	0.00	0.00	0.00	3.14
2276	2325	3.943381	CAGCATGAACTGTGTGGTGATAT	59.057	43.478	12.17	0.00	42.28	1.63
2332	2384	0.391661	GGTGCCGACATGAGACATGT	60.392	55.000	15.67	15.67	34.52	3.21
2336	2388	0.528466	CCGACATGAGACATGTCCGG	60.528	60.000	27.59	26.03	43.98	5.14
2347	2399	0.464193	CATGTCCGGTGGCATGATCA	60.464	55.000	22.44	0.00	43.60	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.134818	CGGAAATGGGTCGACATGAGA	60.135	52.381	18.91	0.00	0.00	3.27
13	14	0.107897	CCGGAAATGGGTCGACATGA	60.108	55.000	18.91	0.00	0.00	3.07
18	19	4.104183	GGGCCGGAAATGGGTCGA	62.104	66.667	5.05	0.00	0.00	4.20
84	85	1.472662	CCGGGATGAGGAATAGGCGT	61.473	60.000	0.00	0.00	0.00	5.68
139	147	0.116342	GGAGGGTTTGGGGGAAATGT	59.884	55.000	0.00	0.00	0.00	2.71
230	255	1.744368	CCGAACGAGACGAGGGAGA	60.744	63.158	0.00	0.00	0.00	3.71
239	264	1.248101	TGGTCTCATGCCGAACGAGA	61.248	55.000	0.00	0.00	33.46	4.04
303	329	2.741486	TTCTTTGGCTTAGGCGCGGT	62.741	55.000	8.83	0.00	39.81	5.68
311	337	2.504367	GTCAGCACCTTCTTTGGCTTA	58.496	47.619	0.00	0.00	33.60	3.09
345	371	0.891373	CTCTTGGCCGACTCTCTTGA	59.109	55.000	0.00	0.00	0.00	3.02
432	458	0.836606	TTGGTGACCTCTTGCTGTGA	59.163	50.000	2.11	0.00	0.00	3.58
556	588	3.207354	GAGGGAACGCGGATGAGA	58.793	61.111	12.47	0.00	0.00	3.27
720	752	2.590575	CGGTGTGGCGTTGAGGTT	60.591	61.111	0.00	0.00	0.00	3.50
765	797	4.595538	TGGCGCGTGTTTCCTCGT	62.596	61.111	8.43	0.00	0.00	4.18
894	926	3.834799	GTCGGGGTCGTAGCCAGG	61.835	72.222	5.64	0.00	37.54	4.45
912	944	2.251642	GCCGTCGGCTTTGTGTCTT	61.252	57.895	28.98	0.00	46.69	3.01
949	983	2.872388	CGGGATCATAGCCAGCGGT	61.872	63.158	0.00	0.00	0.00	5.68
977	1011	0.654683	GACCTGATCACGCATGAAGC	59.345	55.000	0.00	0.00	38.69	3.86
998	1032	0.824759	GAAGCCGTCTAGGTCCATGT	59.175	55.000	0.00	0.00	43.70	3.21
1008	1042	1.371558	GTCAAGTGGGAAGCCGTCT	59.628	57.895	0.00	0.00	0.00	4.18
1077	1111	0.179234	TGAACAAAGGCTCCACGTCA	59.821	50.000	0.00	0.00	0.00	4.35
1096	1130	2.048127	GTTGGCGAGCTCGTCCTT	60.048	61.111	35.43	0.00	44.42	3.36
1133	1167	2.949106	GCTTGCTCTTGCGCTTCA	59.051	55.556	9.73	0.00	43.34	3.02
1206	1240	1.975680	GTCTTGGGGTCTTGTCCAGTA	59.024	52.381	0.00	0.00	34.17	2.74
1208	1242	0.036875	GGTCTTGGGGTCTTGTCCAG	59.963	60.000	0.00	0.00	34.17	3.86
1234	1268	7.446001	TCCAAAAAGTTGAATGCTTTTGTTT	57.554	28.000	4.15	0.00	43.01	2.83
1290	1324	7.291566	TCACAATTTGGTAAGGAGGAAACTTA	58.708	34.615	0.78	0.00	44.43	2.24
1345	1380	1.667595	TGTTGGATCACCCTCCATCA	58.332	50.000	0.00	0.81	44.66	3.07
1443	1478	1.811679	GAGGGCGTCTTGCTAGCAC	60.812	63.158	19.17	5.19	45.43	4.40
1454	1489	1.202758	TGATGACACAAAAGAGGGCGT	60.203	47.619	0.00	0.00	0.00	5.68
1489	1526	5.659463	TGGCAAATAGTATGCAAATGAACC	58.341	37.500	0.00	0.00	45.60	3.62
1504	1541	5.532664	TCATGCAAGCATATTGGCAAATA	57.467	34.783	3.01	0.00	40.02	1.40
1545	1587	2.094338	CCTTGAATGCCTCCAAAGCTTC	60.094	50.000	0.00	0.00	0.00	3.86
1714	1757	1.671742	GAGTTGGTCTTCTCCCGCA	59.328	57.895	0.00	0.00	0.00	5.69
1720	1763	3.318313	TCCTTCTTGGAGTTGGTCTTCT	58.682	45.455	0.00	0.00	40.56	2.85
1752	1795	0.960364	AAGGCATTGGATGTCGCGTT	60.960	50.000	5.77	0.00	40.53	4.84
1754	1797	1.063006	CAAGGCATTGGATGTCGCG	59.937	57.895	2.43	0.00	40.53	5.87
1758	1801	1.027357	GCGATCAAGGCATTGGATGT	58.973	50.000	11.73	0.00	37.02	3.06
1802	1845	1.152271	TCCTCCTCCCTTGAGTCCTTT	59.848	52.381	0.00	0.00	36.86	3.11
1850	1893	1.281867	TGGATCTCCATGAAGGCGTTT	59.718	47.619	0.00	0.00	42.01	3.60
1925	1968	1.673665	CTTGGCTTGCTTCTCCGCT	60.674	57.895	0.00	0.00	0.00	5.52
1950	1993	2.125106	GTTGGCGGCCTCGATCTT	60.125	61.111	21.46	0.00	39.00	2.40
1969	2012	2.158813	ACTTCTTTCGCCTTGGTCTTGA	60.159	45.455	0.00	0.00	0.00	3.02
2014	2057	1.842562	CCACCTTCATGATCTCCACCT	59.157	52.381	0.00	0.00	0.00	4.00
2093	2136	1.030457	ACTCGTCGGTGAACTTGAGT	58.970	50.000	0.00	0.00	32.19	3.41
2152	2196	1.072173	TGGTCATGCTAGCACACAAGT	59.928	47.619	22.07	0.00	0.00	3.16
2188	2234	1.002087	GTGGGACTTGAGTTCGACCAT	59.998	52.381	0.00	0.00	0.00	3.55
2211	2258	4.247258	CACATATGCCAGCACACAAAAAT	58.753	39.130	1.58	0.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.