AutoCloner

Multiple sequence alignment - TraesCS2D01G559900

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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	TraesCS2D01G559900	chr2D	100.000	2264	0	0	1	2264	632766135	632768398	0.000000e+00	4181.0
1	TraesCS2D01G559900	chr2D	95.546	1549	63	4	1	1544	476789246	476790793	0.000000e+00	2473.0
2	TraesCS2D01G559900	chr2D	79.602	201	39	2	2031	2230	632768361	632768162	2.340000e-30	143.0
3	TraesCS2D01G559900	chr6B	93.490	2166	107	12	1	2159	281223417	281221279	0.000000e+00	3188.0
4	TraesCS2D01G559900	chr6B	96.040	303	12	0	1	303	149003036	149002734	5.620000e-136	494.0
5	TraesCS2D01G559900	chr6B	100.000	32	0	0	1909	1940	567116128	567116159	2.430000e-05	60.2
6	TraesCS2D01G559900	chr1D	92.208	2169	137	18	1	2157	14674871	14672723	0.000000e+00	3040.0
7	TraesCS2D01G559900	chr4A	91.348	2115	142	22	60	2156	564697244	564699335	0.000000e+00	2854.0
8	TraesCS2D01G559900	chr4A	93.421	76	4	1	2159	2234	564699278	564699204	6.610000e-21	111.0
9	TraesCS2D01G559900	chr5B	90.225	2179	173	26	1	2156	89726813	89728974	0.000000e+00	2808.0
10	TraesCS2D01G559900	chr5B	89.505	2163	185	28	1	2139	584816934	584814790	0.000000e+00	2699.0
11	TraesCS2D01G559900	chr5B	92.721	1786	117	8	1	1775	64293426	64295209	0.000000e+00	2566.0
12	TraesCS2D01G559900	chr5B	93.896	1245	41	10	709	1938	387878839	387880063	0.000000e+00	1845.0
13	TraesCS2D01G559900	chr5B	84.793	217	26	6	1943	2156	387880032	387880244	6.340000e-51	211.0
14	TraesCS2D01G559900	chr5B	94.175	103	6	0	2162	2264	387880308	387880410	8.370000e-35	158.0
15	TraesCS2D01G559900	chr5B	95.455	66	3	0	2162	2227	387880183	387880118	3.080000e-19	106.0
16	TraesCS2D01G559900	chr2A	91.061	1980	138	21	1	1960	48624241	48622281	0.000000e+00	2639.0
17	TraesCS2D01G559900	chr3A	89.363	1946	161	29	233	2156	497386153	497388074	0.000000e+00	2405.0
18	TraesCS2D01G559900	chr7D	87.124	1429	107	31	746	2156	460800557	460801926	0.000000e+00	1548.0
19	TraesCS2D01G559900	chr2B	96.501	343	12	0	1	343	15222346	15222004	3.260000e-158	568.0
20	TraesCS2D01G559900	chr5D	85.492	193	23	3	1947	2138	520880506	520880694	1.770000e-46	196.0
21	TraesCS2D01G559900	chr5D	92.500	80	3	3	2159	2237	520880655	520880578	6.610000e-21	111.0
22	TraesCS2D01G559900	chr4B	89.623	106	11	0	2159	2264	467347824	467347719	3.920000e-28	135.0
23	TraesCS2D01G559900	chr4D	94.203	69	4	0	2159	2227	495818513	495818445	3.080000e-19	106.0
24	TraesCS2D01G559900	chrUn	91.892	74	5	1	2162	2234	10401268	10401195	3.980000e-18	102.0
25	TraesCS2D01G559900	chrUn	91.892	74	5	1	2162	2234	349151541	349151468	3.980000e-18	102.0
26	TraesCS2D01G559900	chr3B	100.000	29	0	0	1910	1938	10032173	10032201	1.000000e-03	54.7

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	TraesCS2D01G559900	chr2D	632766135	632768398	2263	False	4181	4181	100.000000	1	2264	1	chr2D.!!$F2	2263
1	TraesCS2D01G559900	chr2D	476789246	476790793	1547	False	2473	2473	95.546000	1	1544	1	chr2D.!!$F1	1543
2	TraesCS2D01G559900	chr6B	281221279	281223417	2138	True	3188	3188	93.490000	1	2159	1	chr6B.!!$R2	2158
3	TraesCS2D01G559900	chr1D	14672723	14674871	2148	True	3040	3040	92.208000	1	2157	1	chr1D.!!$R1	2156
4	TraesCS2D01G559900	chr4A	564697244	564699335	2091	False	2854	2854	91.348000	60	2156	1	chr4A.!!$F1	2096
5	TraesCS2D01G559900	chr5B	89726813	89728974	2161	False	2808	2808	90.225000	1	2156	1	chr5B.!!$F2	2155
6	TraesCS2D01G559900	chr5B	584814790	584816934	2144	True	2699	2699	89.505000	1	2139	1	chr5B.!!$R2	2138
7	TraesCS2D01G559900	chr5B	64293426	64295209	1783	False	2566	2566	92.721000	1	1775	1	chr5B.!!$F1	1774
8	TraesCS2D01G559900	chr5B	387878839	387880410	1571	False	738	1845	90.954667	709	2264	3	chr5B.!!$F3	1555
9	TraesCS2D01G559900	chr2A	48622281	48624241	1960	True	2639	2639	91.061000	1	1960	1	chr2A.!!$R1	1959
10	TraesCS2D01G559900	chr3A	497386153	497388074	1921	False	2405	2405	89.363000	233	2156	1	chr3A.!!$F1	1923
11	TraesCS2D01G559900	chr7D	460800557	460801926	1369	False	1548	1548	87.124000	746	2156	1	chr7D.!!$F1	1410

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
700	704	0.470766	AGAACCAACACGGGCACTAA	59.529	50.0	0.0	0.0	40.22	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1953	2118	0.824109	CTACCGCCATTGTCTCTGGA	59.176	55.0	0.0	0.0	35.7	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
212	213	5.473066	TGATCTATCAAATCGATGAGCCA	57.527	39.130	0.00	0.00	35.39	4.75
323	324	3.018856	CAAGTATCATTGGCCTTGCTCA	58.981	45.455	3.32	0.00	0.00	4.26
405	406	4.322198	GGTTGCATGAGTTCACATTGGAAT	60.322	41.667	0.00	0.00	0.00	3.01
424	425	0.542333	TGAACAAGGTTGACGTGGGA	59.458	50.000	0.00	0.00	32.45	4.37
496	497	1.681166	GCCAGACATTGTGCCAGATCT	60.681	52.381	0.00	0.00	0.00	2.75
597	598	4.082245	CCGGAATGAAGCAATTTGGTAGTT	60.082	41.667	0.00	0.00	0.00	2.24
635	636	1.269448	CCGGAGAACAACAATTGTGGG	59.731	52.381	17.32	12.59	44.59	4.61
641	642	3.966665	AGAACAACAATTGTGGGGAATGT	59.033	39.130	17.32	11.19	44.59	2.71
700	704	0.470766	AGAACCAACACGGGCACTAA	59.529	50.000	0.00	0.00	40.22	2.24
772	776	1.307084	GGACTAGCCTTGGAGGGGT	60.307	63.158	0.00	0.00	40.47	4.95
795	800	1.684734	GCCGTGGAGGGAGGACTAA	60.685	63.158	0.00	0.00	41.48	2.24
872	879	1.095807	GGGAAGGCCTATTGACGTGC	61.096	60.000	5.16	0.00	0.00	5.34
1022	1034	1.477558	GGCTTCATCCGGTTCCATGAT	60.478	52.381	0.00	0.00	0.00	2.45
1041	1053	1.741770	GAGGCCACCGTGTGCTAAG	60.742	63.158	5.01	0.00	31.34	2.18
1154	1166	1.067295	TGCAAGGTGAAGGAGTCCAT	58.933	50.000	12.86	0.00	0.00	3.41
1222	1238	3.402110	CCCAACTATGCTTATGATCGCA	58.598	45.455	0.00	0.00	40.87	5.10
1346	1362	1.409064	CGCCTCCTCTATGCAAGTACA	59.591	52.381	0.00	0.00	0.00	2.90
1388	1404	3.960102	AGTGCCAAAAGATGTCCAAAAGA	59.040	39.130	0.00	0.00	0.00	2.52
1405	1421	7.276438	GTCCAAAAGAACCAATATGAAGATTGC	59.724	37.037	0.00	0.00	35.79	3.56
1431	1447	3.121030	CCAGCGGCTGTTCGAAGG	61.121	66.667	26.79	7.54	0.00	3.46
1466	1482	0.038159	CTTGGAGGAAGAGCGTCGTT	60.038	55.000	0.00	0.00	32.82	3.85
1485	1501	3.131223	CGTTAGAAAGAGAGGATGGAGCA	59.869	47.826	0.00	0.00	0.00	4.26
1606	1623	1.227853	GGCACGTGACAAGAAGGGT	60.228	57.895	22.23	0.00	0.00	4.34
1827	1858	4.614284	GTCAGCAATTTCTGTGATTTGTCG	59.386	41.667	4.99	0.00	35.63	4.35
1837	1868	5.000591	TCTGTGATTTGTCGGCAATTTCTA	58.999	37.500	1.89	0.00	34.18	2.10
1842	1873	6.974622	GTGATTTGTCGGCAATTTCTATGATT	59.025	34.615	1.89	0.00	34.18	2.57
1844	1875	7.488792	TGATTTGTCGGCAATTTCTATGATTTG	59.511	33.333	1.89	0.00	34.18	2.32
1847	1878	7.384439	TGTCGGCAATTTCTATGATTTGTTA	57.616	32.000	0.00	0.00	0.00	2.41
1848	1879	7.471721	TGTCGGCAATTTCTATGATTTGTTAG	58.528	34.615	0.00	0.00	0.00	2.34
1849	1880	6.414987	GTCGGCAATTTCTATGATTTGTTAGC	59.585	38.462	0.00	0.00	0.00	3.09
1850	1881	6.094742	TCGGCAATTTCTATGATTTGTTAGCA	59.905	34.615	0.00	0.00	0.00	3.49
1851	1882	6.751425	CGGCAATTTCTATGATTTGTTAGCAA	59.249	34.615	0.00	0.00	0.00	3.91
1853	1884	9.101655	GGCAATTTCTATGATTTGTTAGCAATT	57.898	29.630	0.00	0.00	34.18	2.32
1902	1951	4.080526	GGGGCAGAACAAAGGATTACTCTA	60.081	45.833	0.00	0.00	0.00	2.43
1953	2118	2.399580	GTAGGATGCTTGACCCTACCT	58.600	52.381	0.00	0.00	44.02	3.08
1975	2140	0.617820	AGAGACAATGGCGGTAGGGT	60.618	55.000	0.00	0.00	0.00	4.34
1987	2153	1.001269	GTAGGGTGGGGGCAAACTC	60.001	63.158	0.00	0.00	0.00	3.01
2159	2447	0.912486	AAGAAGCCTACCGCCAGATT	59.088	50.000	0.00	0.00	38.78	2.40
2160	2448	1.789523	AGAAGCCTACCGCCAGATTA	58.210	50.000	0.00	0.00	38.78	1.75
2207	2553	2.116238	GTAGGATCCTGCAACCTACCA	58.884	52.381	25.28	0.00	45.85	3.25
2227	2573	2.037367	AGAGGCTGTGGCGGTAGA	59.963	61.111	0.00	0.00	39.81	2.59
2229	2575	2.037367	AGGCTGTGGCGGTAGAGA	59.963	61.111	0.00	0.00	39.81	3.10
2232	2578	0.811616	GGCTGTGGCGGTAGAGATTG	60.812	60.000	0.00	0.00	39.81	2.67
2237	2583	2.499693	TGTGGCGGTAGAGATTGAATCA	59.500	45.455	8.03	0.00	0.00	2.57
2254	2600	2.649742	TCATCTCCTCCCCTCTGTTT	57.350	50.000	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
212	213	0.405585	CATCCCTTGTTGTCCCACCT	59.594	55.000	0.00	0.00	0.00	4.00
230	231	3.484953	ACTCCACCATAAGACCTACCA	57.515	47.619	0.00	0.00	0.00	3.25
323	324	1.069296	CGTGTTGCGGTCATCAAATGT	60.069	47.619	0.00	0.00	36.85	2.71
360	361	0.468226	ACCGTTGTGCCATCGGATAT	59.532	50.000	23.09	6.24	46.01	1.63
405	406	0.542333	TCCCACGTCAACCTTGTTCA	59.458	50.000	0.00	0.00	0.00	3.18
424	425	4.404185	AGGAAAGGATTAAACCAAGGCT	57.596	40.909	4.40	0.00	0.00	4.58
518	519	7.411372	CGAAATCTCTTCTTTCTTCTTCTTCCG	60.411	40.741	0.00	0.00	31.79	4.30
635	636	2.735134	GTGTCCTGTGTCGTTACATTCC	59.265	50.000	0.00	0.00	38.08	3.01
641	642	2.963548	TGTTGTGTCCTGTGTCGTTA	57.036	45.000	0.00	0.00	0.00	3.18
700	704	0.320421	CCTCCGTCCACGTGTTTGAT	60.320	55.000	15.65	0.00	37.74	2.57
872	879	1.019673	CAACCATCCGGATTGAGCAG	58.980	55.000	21.66	6.38	35.59	4.24
1022	1034	2.449031	CTTAGCACACGGTGGCCTCA	62.449	60.000	13.48	0.00	33.64	3.86
1041	1053	1.154150	GTGCGGCATGTCTTCTTGC	60.154	57.895	5.72	0.00	41.85	4.01
1154	1166	1.890489	TCCATGACTTCTTTCGGTCGA	59.110	47.619	0.00	0.00	35.45	4.20
1222	1238	0.604578	TAGGCGTTAGTTGGAAGCGT	59.395	50.000	0.00	0.00	0.00	5.07
1346	1362	5.512749	GCACTTCATGATCTATCCAGGTGAT	60.513	44.000	0.00	0.00	37.49	3.06
1388	1404	6.966534	CCTAAGGCAATCTTCATATTGGTT	57.033	37.500	0.00	0.00	37.34	3.67
1431	1447	3.222603	TCCAAGCCTCTTTGAAACCTTC	58.777	45.455	0.00	0.00	0.00	3.46
1466	1482	4.256983	TCTGCTCCATCCTCTCTTTCTA	57.743	45.455	0.00	0.00	0.00	2.10
1485	1501	2.219325	CTCCTCCTCGCGTTGCTTCT	62.219	60.000	5.77	0.00	0.00	2.85
1606	1623	2.104111	CTGAGTCATACGGGGCCATTTA	59.896	50.000	4.39	0.00	0.00	1.40
1644	1671	2.097036	TCGGTTACATGACGAGTCCAT	58.903	47.619	0.00	0.00	32.29	3.41
1827	1858	8.652810	ATTGCTAACAAATCATAGAAATTGCC	57.347	30.769	0.00	0.00	39.77	4.52
1837	1868	8.362639	AGTTCACAGAAATTGCTAACAAATCAT	58.637	29.630	1.31	0.00	39.77	2.45
1842	1873	6.449635	ACAGTTCACAGAAATTGCTAACAA	57.550	33.333	1.31	0.00	40.87	2.83
1844	1875	6.197096	CACAACAGTTCACAGAAATTGCTAAC	59.803	38.462	0.00	0.00	0.00	2.34
1847	1878	4.675510	CACAACAGTTCACAGAAATTGCT	58.324	39.130	0.00	0.00	0.00	3.91
1848	1879	3.243643	GCACAACAGTTCACAGAAATTGC	59.756	43.478	0.00	0.00	0.00	3.56
1849	1880	4.501559	CAGCACAACAGTTCACAGAAATTG	59.498	41.667	0.00	0.00	0.00	2.32
1850	1881	4.398988	TCAGCACAACAGTTCACAGAAATT	59.601	37.500	0.00	0.00	0.00	1.82
1851	1882	3.947196	TCAGCACAACAGTTCACAGAAAT	59.053	39.130	0.00	0.00	0.00	2.17
1853	1884	2.938451	CTCAGCACAACAGTTCACAGAA	59.062	45.455	0.00	0.00	0.00	3.02
1854	1885	2.168313	TCTCAGCACAACAGTTCACAGA	59.832	45.455	0.00	0.00	0.00	3.41
1855	1886	2.554142	TCTCAGCACAACAGTTCACAG	58.446	47.619	0.00	0.00	0.00	3.66
1856	1887	2.689553	TCTCAGCACAACAGTTCACA	57.310	45.000	0.00	0.00	0.00	3.58
1953	2118	0.824109	CTACCGCCATTGTCTCTGGA	59.176	55.000	0.00	0.00	35.70	3.86
1975	2140	1.059584	TCACAGAGAGTTTGCCCCCA	61.060	55.000	0.00	0.00	0.00	4.96
1987	2153	2.320367	CTCGTTTTCCTCGTCACAGAG	58.680	52.381	0.00	0.00	37.97	3.35
2027	2195	4.715130	AGGCTGTGGCGGTAGGGA	62.715	66.667	0.00	0.00	39.81	4.20
2102	2390	2.154007	GCTCGTTTTTCTCGTCACAGAG	59.846	50.000	0.00	0.00	39.52	3.35
2227	2573	3.909364	GAGGGGAGGAGATGATTCAATCT	59.091	47.826	0.00	0.00	39.66	2.40
2229	2575	3.651904	CAGAGGGGAGGAGATGATTCAAT	59.348	47.826	0.00	0.00	0.00	2.57
2232	2578	2.688477	ACAGAGGGGAGGAGATGATTC	58.312	52.381	0.00	0.00	0.00	2.52
2237	2583	1.283321	GCAAAACAGAGGGGAGGAGAT	59.717	52.381	0.00	0.00	0.00	2.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.