AutoCloner

Multiple sequence alignment - TraesCS1D01G070300

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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	TraesCS1D01G070300	chr1D	100.000	2507	0	0	1	2507	50969071	50971577	0.000000e+00	4630.0
1	TraesCS1D01G070300	chr1D	91.522	519	28	9	1997	2507	51561070	51561580	0.000000e+00	701.0
2	TraesCS1D01G070300	chr1D	96.117	206	6	2	1812	2015	51000187	50999982	4.000000e-88	335.0
3	TraesCS1D01G070300	chr1D	95.631	206	6	3	1812	2015	50967068	50966864	6.690000e-86	327.0
4	TraesCS1D01G070300	chr1A	96.686	1931	50	5	81	2011	299542092	299544008	0.000000e+00	3199.0
5	TraesCS1D01G070300	chr1A	97.243	1741	45	3	263	2003	97423109	97421372	0.000000e+00	2946.0
6	TraesCS1D01G070300	chr1A	95.059	506	17	3	2004	2507	50003512	50004011	0.000000e+00	789.0
7	TraesCS1D01G070300	chr1A	87.315	473	46	7	2040	2507	50709173	50709636	1.710000e-146	529.0
8	TraesCS1D01G070300	chr1A	98.454	194	3	0	1812	2005	299539683	299539490	2.390000e-90	342.0
9	TraesCS1D01G070300	chr1A	100.000	79	0	0	1	79	299541791	299541869	2.010000e-31	147.0
10	TraesCS1D01G070300	chr2A	96.623	1925	43	6	81	2004	102021830	102019927	0.000000e+00	3175.0
11	TraesCS1D01G070300	chr2A	97.423	194	4	1	1812	2005	102024226	102024418	1.860000e-86	329.0
12	TraesCS1D01G070300	chr2A	97.561	82	1	1	1	82	102022130	102022050	3.360000e-29	139.0
13	TraesCS1D01G070300	chr7A	93.715	891	43	8	1098	1988	533036606	533037483	0.000000e+00	1323.0
14	TraesCS1D01G070300	chr3B	95.796	452	15	3	1558	2007	448752602	448753051	0.000000e+00	726.0
15	TraesCS1D01G070300	chr4D	90.389	489	25	6	1518	2003	76028347	76028816	7.620000e-175	623.0
16	TraesCS1D01G070300	chr5B	93.617	47	3	0	136	182	260237153	260237107	1.240000e-08	71.3
17	TraesCS1D01G070300	chr2B	93.617	47	3	0	124	170	697521724	697521770	1.240000e-08	71.3
18	TraesCS1D01G070300	chr2B	84.375	64	10	0	117	180	801009263	801009200	2.080000e-06	63.9
19	TraesCS1D01G070300	chr7D	91.489	47	4	0	124	170	552506640	552506686	5.790000e-07	65.8
20	TraesCS1D01G070300	chr6D	86.207	58	7	1	117	174	452314409	452314353	7.490000e-06	62.1

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	TraesCS1D01G070300	chr1D	50969071	50971577	2506	False	4630	4630	100.000	1	2507	1	chr1D.!!$F1	2506
1	TraesCS1D01G070300	chr1D	51561070	51561580	510	False	701	701	91.522	1997	2507	1	chr1D.!!$F2	510
2	TraesCS1D01G070300	chr1A	97421372	97423109	1737	True	2946	2946	97.243	263	2003	1	chr1A.!!$R1	1740
3	TraesCS1D01G070300	chr1A	299541791	299544008	2217	False	1673	3199	98.343	1	2011	2	chr1A.!!$F3	2010
4	TraesCS1D01G070300	chr2A	102019927	102022130	2203	True	1657	3175	97.092	1	2004	2	chr2A.!!$R1	2003
5	TraesCS1D01G070300	chr7A	533036606	533037483	877	False	1323	1323	93.715	1098	1988	1	chr7A.!!$F1	890

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
948	1183	0.242017	GGTTGGCACAGTGATCAAGC	59.758	55.0	17.5	17.5	42.39	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2020	2255	0.447801	CGTGCTATGGTTGTGGCTTC	59.552	55.0	0.0	0.0	0.0	3.86	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
344	566	1.813178	GCTTGGTTCAGGTTAGGAAGC	59.187	52.381	0.00	0.00	41.75	3.86
433	667	9.996554	ATTATATCCTGTGATAACAATGTTCGA	57.003	29.630	0.22	0.00	37.04	3.71
434	668	9.825109	TTATATCCTGTGATAACAATGTTCGAA	57.175	29.630	0.22	0.00	37.04	3.71
435	669	8.731275	ATATCCTGTGATAACAATGTTCGAAA	57.269	30.769	0.22	0.00	37.04	3.46
436	670	6.236017	TCCTGTGATAACAATGTTCGAAAC	57.764	37.500	0.22	0.00	0.00	2.78
437	671	5.760743	TCCTGTGATAACAATGTTCGAAACA	59.239	36.000	0.22	0.73	46.94	2.83
438	672	6.261158	TCCTGTGATAACAATGTTCGAAACAA	59.739	34.615	0.22	0.00	45.86	2.83
439	673	7.040755	TCCTGTGATAACAATGTTCGAAACAAT	60.041	33.333	0.22	0.00	45.86	2.71
789	1024	8.524870	AAAAACTTATGCTTATTGTCTGCAAG	57.475	30.769	0.00	0.00	40.24	4.01
948	1183	0.242017	GGTTGGCACAGTGATCAAGC	59.758	55.000	17.50	17.50	42.39	4.01
1420	1655	4.137543	CAGCAAAGTTACCAAAGAGAGGT	58.862	43.478	0.00	0.00	43.14	3.85
1741	1976	2.432972	GGCACCAAAATGCTGCCG	60.433	61.111	1.23	0.00	45.38	5.69
1912	2147	3.189910	GGGGTAATTCGTCTGGTTTTGAC	59.810	47.826	0.00	0.00	0.00	3.18
1934	2169	3.073274	GTTGGAGGGTGCAACTTAGAT	57.927	47.619	0.00	0.00	43.96	1.98
2020	2255	6.688637	TCTCTCTTAATCAATTGTGGCATG	57.311	37.500	5.13	0.00	0.00	4.06
2024	2259	5.653507	TCTTAATCAATTGTGGCATGAAGC	58.346	37.500	5.13	0.00	44.65	3.86
2038	2276	1.533625	TGAAGCCACAACCATAGCAC	58.466	50.000	0.00	0.00	0.00	4.40
2042	2280	1.006832	GCCACAACCATAGCACGTAG	58.993	55.000	0.00	0.00	0.00	3.51
2043	2281	1.404986	GCCACAACCATAGCACGTAGA	60.405	52.381	0.00	0.00	0.00	2.59
2047	2285	4.394920	CCACAACCATAGCACGTAGAAAAT	59.605	41.667	0.00	0.00	0.00	1.82
2050	2288	6.533723	CACAACCATAGCACGTAGAAAATCTA	59.466	38.462	0.00	0.00	0.00	1.98
2075	2313	7.790027	AGACTCTGTTTAGTGAGATGCATATT	58.210	34.615	0.00	0.00	34.65	1.28
2078	2316	7.130917	CTCTGTTTAGTGAGATGCATATTTGC	58.869	38.462	0.00	0.61	39.66	3.68
2114	2352	5.423015	ACACAGGAAGTTATGTCATGCTAG	58.577	41.667	0.00	0.00	29.97	3.42
2116	2354	4.163078	ACAGGAAGTTATGTCATGCTAGCT	59.837	41.667	17.23	0.00	29.97	3.32
2117	2355	5.363868	ACAGGAAGTTATGTCATGCTAGCTA	59.636	40.000	17.23	2.58	29.97	3.32
2118	2356	5.694006	CAGGAAGTTATGTCATGCTAGCTAC	59.306	44.000	17.23	11.84	0.00	3.58
2119	2357	4.991687	GGAAGTTATGTCATGCTAGCTACC	59.008	45.833	17.23	1.89	0.00	3.18
2120	2358	4.608948	AGTTATGTCATGCTAGCTACCC	57.391	45.455	17.23	2.27	0.00	3.69
2121	2359	3.005897	AGTTATGTCATGCTAGCTACCCG	59.994	47.826	17.23	0.00	0.00	5.28
2122	2360	0.681733	ATGTCATGCTAGCTACCCGG	59.318	55.000	17.23	0.00	0.00	5.73
2130	2368	1.413077	GCTAGCTACCCGGAAGTGAAT	59.587	52.381	7.70	0.00	0.00	2.57
2138	2376	3.089284	ACCCGGAAGTGAATTTTCCATC	58.911	45.455	0.73	0.00	43.46	3.51
2175	2416	5.890985	CACACATATATGGGAAAAAGGGTGA	59.109	40.000	21.89	0.00	34.60	4.02
2218	2459	5.012148	AGACCTGCACAGTTTCATTAGTAGT	59.988	40.000	0.00	0.00	0.00	2.73
2289	2530	7.446106	AACTATGATTGTTATAGTCCCCACA	57.554	36.000	0.00	0.00	39.71	4.17
2290	2531	7.067496	ACTATGATTGTTATAGTCCCCACAG	57.933	40.000	0.00	0.00	36.84	3.66
2356	2597	4.180817	CCAAAAACGAGGAAGCACTTTTT	58.819	39.130	0.00	0.00	0.00	1.94
2409	2650	5.106078	GGTACTGTGTTCAGAACAACCAAAA	60.106	40.000	22.39	6.80	44.16	2.44
2471	2712	5.514500	ACTTTCTAGGGCATAAACTTCCA	57.486	39.130	0.00	0.00	0.00	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	80	8.674263	AACAACATTCAATATTCCTTTTTGCA	57.326	26.923	0.00	0.00	0.00	4.08
344	566	4.214980	GTTGTCCACAGAATCACAACAG	57.785	45.455	8.54	0.00	45.27	3.16
428	662	3.552604	TGCTGCCTAATTGTTTCGAAC	57.447	42.857	0.00	0.00	0.00	3.95
429	663	4.576216	TTTGCTGCCTAATTGTTTCGAA	57.424	36.364	0.00	0.00	0.00	3.71
430	664	4.782019	ATTTGCTGCCTAATTGTTTCGA	57.218	36.364	0.00	0.00	0.00	3.71
431	665	6.751425	TCATAATTTGCTGCCTAATTGTTTCG	59.249	34.615	15.73	3.45	30.84	3.46
432	666	8.652810	ATCATAATTTGCTGCCTAATTGTTTC	57.347	30.769	15.73	0.00	30.84	2.78
433	667	8.259411	TGATCATAATTTGCTGCCTAATTGTTT	58.741	29.630	15.73	4.25	30.84	2.83
434	668	7.784037	TGATCATAATTTGCTGCCTAATTGTT	58.216	30.769	15.73	5.16	30.84	2.83
435	669	7.350744	TGATCATAATTTGCTGCCTAATTGT	57.649	32.000	15.73	9.29	30.84	2.71
436	670	6.866770	CCTGATCATAATTTGCTGCCTAATTG	59.133	38.462	15.73	5.50	30.84	2.32
437	671	6.779049	TCCTGATCATAATTTGCTGCCTAATT	59.221	34.615	12.45	12.45	32.53	1.40
438	672	6.309357	TCCTGATCATAATTTGCTGCCTAAT	58.691	36.000	0.00	0.00	0.00	1.73
439	673	5.693961	TCCTGATCATAATTTGCTGCCTAA	58.306	37.500	0.00	0.00	0.00	2.69
630	864	5.955959	ACCTACAACTACATGTCCTGTCATA	59.044	40.000	0.00	0.00	39.39	2.15
965	1200	5.704888	CAAGTTGTTTTGTTGTGTCCACTA	58.295	37.500	0.00	0.00	0.00	2.74
1204	1439	5.064707	GTGAAGTGCTTTGTTGTGAACTCTA	59.935	40.000	0.00	0.00	0.00	2.43
1434	1669	2.983898	AGTCCCCTTGCCTTTGTTACTA	59.016	45.455	0.00	0.00	0.00	1.82
1741	1976	6.705863	ATCCTAATCTGCTGGTCAAAATTC	57.294	37.500	0.00	0.00	0.00	2.17
2020	2255	0.447801	CGTGCTATGGTTGTGGCTTC	59.552	55.000	0.00	0.00	0.00	3.86
2024	2259	2.665649	TCTACGTGCTATGGTTGTGG	57.334	50.000	0.00	0.00	0.00	4.17
2038	2276	9.279904	CACTAAACAGAGTCTAGATTTTCTACG	57.720	37.037	0.00	0.00	0.00	3.51
2043	2281	9.868277	CATCTCACTAAACAGAGTCTAGATTTT	57.132	33.333	0.00	0.00	31.38	1.82
2047	2285	5.946377	TGCATCTCACTAAACAGAGTCTAGA	59.054	40.000	0.00	0.00	0.00	2.43
2050	2288	5.674052	ATGCATCTCACTAAACAGAGTCT	57.326	39.130	0.00	0.00	0.00	3.24
2075	2313	3.884693	CCTGTGTCCAATATAGCATGCAA	59.115	43.478	21.98	5.05	0.00	4.08
2078	2316	5.371526	ACTTCCTGTGTCCAATATAGCATG	58.628	41.667	0.00	0.00	0.00	4.06
2087	2325	4.698201	TGACATAACTTCCTGTGTCCAA	57.302	40.909	0.00	0.00	40.07	3.53
2114	2352	2.422479	GGAAAATTCACTTCCGGGTAGC	59.578	50.000	0.00	0.00	33.40	3.58
2116	2354	3.791953	TGGAAAATTCACTTCCGGGTA	57.208	42.857	0.00	0.00	44.61	3.69
2117	2355	2.668144	TGGAAAATTCACTTCCGGGT	57.332	45.000	0.00	0.00	44.61	5.28
2118	2356	3.088532	TGATGGAAAATTCACTTCCGGG	58.911	45.455	0.00	0.00	44.61	5.73
2119	2357	4.989279	ATGATGGAAAATTCACTTCCGG	57.011	40.909	0.00	0.00	44.61	5.14
2120	2358	7.483307	ACATTATGATGGAAAATTCACTTCCG	58.517	34.615	0.00	0.00	44.61	4.30
2121	2359	9.657419	AAACATTATGATGGAAAATTCACTTCC	57.343	29.630	0.00	1.07	42.41	3.46
2130	2368	8.206867	TGTGTGGAAAAACATTATGATGGAAAA	58.793	29.630	0.00	0.00	37.60	2.29
2138	2376	9.695526	CCCATATATGTGTGGAAAAACATTATG	57.304	33.333	11.73	0.00	38.81	1.90
2198	2439	8.721478	ACATTTACTACTAATGAAACTGTGCAG	58.279	33.333	0.00	0.00	36.67	4.41
2315	2556	9.227777	GTTTTTGGTACCTTTCTACATATGACT	57.772	33.333	14.36	0.00	0.00	3.41
2367	2608	9.449719	CACAGTACCAGAATAAAACTCCTTTAT	57.550	33.333	0.00	0.00	41.16	1.40
2369	2610	7.287810	ACACAGTACCAGAATAAAACTCCTTT	58.712	34.615	0.00	0.00	0.00	3.11
2384	2625	3.055021	TGGTTGTTCTGAACACAGTACCA	60.055	43.478	28.19	28.19	41.97	3.25
2409	2650	6.312141	AGGTTGGCTAATTATTTGGCAAAT	57.688	33.333	26.86	26.86	45.29	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.