AutoCloner

Multiple sequence alignment - TraesCS1B01G163100

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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	TraesCS1B01G163100	chr1B	100.000	1472	0	0	1	1472	283876249	283874778	0.000000e+00	2719.0
1	TraesCS1B01G163100	chr1B	92.799	1472	106	0	1	1472	1806602	1808073	0.000000e+00	2132.0
2	TraesCS1B01G163100	chr1B	92.292	1466	109	2	1	1466	3693727	3695188	0.000000e+00	2078.0
3	TraesCS1B01G163100	chr1B	100.000	606	0	0	1734	2339	283874516	283873911	0.000000e+00	1120.0
4	TraesCS1B01G163100	chr1B	86.355	535	60	9	1807	2339	639498030	639497507	2.610000e-159	571.0
5	TraesCS1B01G163100	chr6B	94.840	1473	73	3	1	1472	507581838	507580368	0.000000e+00	2296.0
6	TraesCS1B01G163100	chr6B	84.288	541	43	18	1799	2339	634707094	634706596	7.510000e-135	490.0
7	TraesCS1B01G163100	chr7B	93.690	1458	92	0	1	1458	460570444	460571901	0.000000e+00	2183.0
8	TraesCS1B01G163100	chr7B	89.742	1316	134	1	157	1472	535245294	535243980	0.000000e+00	1681.0
9	TraesCS1B01G163100	chr3B	90.557	1472	134	3	1	1472	470376702	470378168	0.000000e+00	1943.0
10	TraesCS1B01G163100	chr3B	85.606	1452	205	4	22	1472	125892123	125893571	0.000000e+00	1520.0
11	TraesCS1B01G163100	chr4B	86.965	1473	187	5	3	1472	422027796	422029266	0.000000e+00	1652.0
12	TraesCS1B01G163100	chr7D	85.898	1475	198	9	3	1472	7795918	7797387	0.000000e+00	1563.0
13	TraesCS1B01G163100	chr7D	83.824	136	18	3	2207	2339	608761855	608761989	2.440000e-25	126.0
14	TraesCS1B01G163100	chr5B	88.828	546	44	7	1796	2339	553261905	553262435	0.000000e+00	654.0
15	TraesCS1B01G163100	chr5B	87.985	541	55	6	1798	2336	288299996	288300528	4.240000e-177	630.0
16	TraesCS1B01G163100	chr1A	87.934	547	44	8	1796	2339	361633469	361633996	1.970000e-175	625.0
17	TraesCS1B01G163100	chr1A	92.000	75	2	4	1735	1806	569248192	569248119	4.110000e-18	102.0
18	TraesCS1B01G163100	chr7A	80.545	550	64	24	1796	2339	63897177	63897689	1.310000e-102	383.0
19	TraesCS1B01G163100	chr5D	86.408	103	8	4	2139	2236	402761621	402761520	8.840000e-20	108.0
20	TraesCS1B01G163100	chr4A	90.909	77	1	5	1734	1806	624842094	624842168	5.320000e-17	99.0
21	TraesCS1B01G163100	chrUn	91.667	72	3	3	1734	1803	371796319	371796249	1.910000e-16	97.1
22	TraesCS1B01G163100	chr2A	91.667	72	3	3	1734	1803	24652358	24652288	1.910000e-16	97.1
23	TraesCS1B01G163100	chr2A	91.667	72	3	3	1734	1803	24680425	24680355	1.910000e-16	97.1
24	TraesCS1B01G163100	chr2A	91.667	72	3	3	1734	1803	24682091	24682021	1.910000e-16	97.1
25	TraesCS1B01G163100	chr2A	91.667	72	3	3	1734	1803	24707602	24707532	1.910000e-16	97.1
26	TraesCS1B01G163100	chr2A	91.667	72	3	3	1734	1803	25656486	25656556	1.910000e-16	97.1
27	TraesCS1B01G163100	chr6D	85.556	90	5	6	1734	1819	62122849	62122934	1.150000e-13	87.9

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	TraesCS1B01G163100	chr1B	283873911	283876249	2338	True	1919.5	2719	100.000	1	2339	2	chr1B.!!$R2	2338
1	TraesCS1B01G163100	chr1B	1806602	1808073	1471	False	2132.0	2132	92.799	1	1472	1	chr1B.!!$F1	1471
2	TraesCS1B01G163100	chr1B	3693727	3695188	1461	False	2078.0	2078	92.292	1	1466	1	chr1B.!!$F2	1465
3	TraesCS1B01G163100	chr1B	639497507	639498030	523	True	571.0	571	86.355	1807	2339	1	chr1B.!!$R1	532
4	TraesCS1B01G163100	chr6B	507580368	507581838	1470	True	2296.0	2296	94.840	1	1472	1	chr6B.!!$R1	1471
5	TraesCS1B01G163100	chr7B	460570444	460571901	1457	False	2183.0	2183	93.690	1	1458	1	chr7B.!!$F1	1457
6	TraesCS1B01G163100	chr7B	535243980	535245294	1314	True	1681.0	1681	89.742	157	1472	1	chr7B.!!$R1	1315
7	TraesCS1B01G163100	chr3B	470376702	470378168	1466	False	1943.0	1943	90.557	1	1472	1	chr3B.!!$F2	1471
8	TraesCS1B01G163100	chr3B	125892123	125893571	1448	False	1520.0	1520	85.606	22	1472	1	chr3B.!!$F1	1450
9	TraesCS1B01G163100	chr4B	422027796	422029266	1470	False	1652.0	1652	86.965	3	1472	1	chr4B.!!$F1	1469
10	TraesCS1B01G163100	chr7D	7795918	7797387	1469	False	1563.0	1563	85.898	3	1472	1	chr7D.!!$F1	1469
11	TraesCS1B01G163100	chr5B	553261905	553262435	530	False	654.0	654	88.828	1796	2339	1	chr5B.!!$F2	543
12	TraesCS1B01G163100	chr5B	288299996	288300528	532	False	630.0	630	87.985	1798	2336	1	chr5B.!!$F1	538
13	TraesCS1B01G163100	chr1A	361633469	361633996	527	False	625.0	625	87.934	1796	2339	1	chr1A.!!$F1	543
14	TraesCS1B01G163100	chr7A	63897177	63897689	512	False	383.0	383	80.545	1796	2339	1	chr7A.!!$F1	543

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
109	112	0.394352	CCCCACTAAATTGCCGCTCT	60.394	55.0	0.00	0.00	0.00	4.09	F
1007	1014	0.591170	ACGAAGGCCAACATGTTTCG	59.409	50.0	21.86	21.86	44.33	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1147	1154	1.614996	ATCGTGGGATGTTGTTGCAA	58.385	45.0	0.00	0.0	0.0	4.08	R
2280	2298	2.985957	TTTCTTTTGCTTGGCTTGCT	57.014	40.0	4.23	0.0	0.0	3.91	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
109	112	0.394352	CCCCACTAAATTGCCGCTCT	60.394	55.000	0.00	0.00	0.00	4.09
138	141	2.096496	CGACCCAATCATTGACAGCTTC	59.904	50.000	0.00	0.00	0.00	3.86
221	224	1.551452	ACTGCAGTCCTAGACTCACC	58.449	55.000	15.25	0.00	41.37	4.02
276	279	6.115446	TCCTAAGTCCATCATAGCAAAACTG	58.885	40.000	0.00	0.00	0.00	3.16
345	348	1.502190	GGCAAGCTGTTTAGTCGCC	59.498	57.895	0.00	0.00	0.00	5.54
382	385	4.738243	GCAAACCGAAAAATACTGGTGGTT	60.738	41.667	0.00	0.00	39.76	3.67
420	423	1.195674	GAAGTTCAGAACCGCTGCTTC	59.804	52.381	9.85	2.66	44.52	3.86
521	524	6.588719	TGGCATCTTAGTAAAAACTGCAAT	57.411	33.333	0.00	0.00	0.00	3.56
736	740	5.010213	TGGCAAAAAGGCTTATTAACGAACT	59.990	36.000	0.00	0.00	44.55	3.01
739	743	6.419710	GCAAAAAGGCTTATTAACGAACTTGT	59.580	34.615	0.00	0.00	0.00	3.16
768	772	2.625314	TCTATCTAATGCTGCTGCTCGT	59.375	45.455	17.00	4.51	40.48	4.18
783	787	0.881796	CTCGTGAGCTGGACTGTGTA	59.118	55.000	0.00	0.00	0.00	2.90
822	826	4.736126	TTTTCAGCAGGTAGATCGATCA	57.264	40.909	26.47	10.44	0.00	2.92
880	884	1.630148	CAAGAACGCTTACTCCTCCG	58.370	55.000	0.00	0.00	31.81	4.63
889	893	2.165845	GCTTACTCCTCCGTTCTTGCTA	59.834	50.000	0.00	0.00	0.00	3.49
926	933	0.608130	CACCATGACTTCGTCTGGGA	59.392	55.000	0.00	0.00	36.17	4.37
942	949	0.623723	GGGACTCCAAGGTGCCAATA	59.376	55.000	0.00	0.00	45.25	1.90
1007	1014	0.591170	ACGAAGGCCAACATGTTTCG	59.409	50.000	21.86	21.86	44.33	3.46
1147	1154	0.840722	ACCAACCTCCCTGGACGATT	60.841	55.000	0.00	0.00	39.71	3.34
1208	1215	2.496817	GCCTTCGGTCGCTCTGAT	59.503	61.111	0.00	0.00	0.00	2.90
1277	1284	1.208052	CGAGGATCACACCCACAGAAT	59.792	52.381	0.00	0.00	33.17	2.40
1336	1343	5.128008	TGGGTCTTTCGGTTCAAAAAGAAAT	59.872	36.000	0.00	0.00	41.70	2.17
1395	1402	6.551227	TCCTCTCTGCTGCTATTCATTAACTA	59.449	38.462	0.00	0.00	0.00	2.24
1782	1792	9.174166	ACAAAGTTGTACTAAATCAAAGACACT	57.826	29.630	0.00	0.00	40.16	3.55
1794	1804	7.611213	AATCAAAGACACTTATTTAGGACGG	57.389	36.000	0.00	0.00	0.00	4.79
1938	1948	9.691362	AACAACAATAACAATCCATAGTTCAAC	57.309	29.630	0.00	0.00	0.00	3.18
1971	1981	4.957759	ACACTGCCGAAATTATGTAACC	57.042	40.909	0.00	0.00	0.00	2.85
2114	2124	7.626452	GCTTTACTGTATTAGAAAAGGTGGCTG	60.626	40.741	0.00	0.00	0.00	4.85
2115	2125	5.242795	ACTGTATTAGAAAAGGTGGCTGT	57.757	39.130	0.00	0.00	0.00	4.40
2118	2128	6.206829	ACTGTATTAGAAAAGGTGGCTGTTTC	59.793	38.462	0.00	0.00	0.00	2.78
2135	2145	6.863645	GGCTGTTTCTCAAGTAAAGGAAATTC	59.136	38.462	0.00	0.00	31.74	2.17
2136	2146	6.578919	GCTGTTTCTCAAGTAAAGGAAATTCG	59.421	38.462	0.00	0.00	31.74	3.34
2137	2147	6.966021	TGTTTCTCAAGTAAAGGAAATTCGG	58.034	36.000	0.00	0.00	31.74	4.30
2280	2298	9.616156	TTAGACTTTTCAAGTACATTGTTACCA	57.384	29.630	0.00	0.00	43.03	3.25
2288	2306	1.993956	ACATTGTTACCAGCAAGCCA	58.006	45.000	0.00	0.00	0.00	4.75
2293	2311	0.673437	GTTACCAGCAAGCCAAGCAA	59.327	50.000	0.00	0.00	0.00	3.91

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
109	112	0.911769	ATGATTGGGTCGAAGGCTGA	59.088	50.000	0.00	0.00	0.00	4.26
221	224	9.612620	GAAAAACTGACATAAAATAGACTGTGG	57.387	33.333	0.00	0.00	0.00	4.17
276	279	3.202706	GCCCTTCGAATGGCGTCC	61.203	66.667	25.56	4.14	41.80	4.79
345	348	2.028643	CGGTTTGCAAACGTTTTTCCAG	59.971	45.455	30.40	11.53	39.77	3.86
382	385	8.330466	TGAACTTCGAGATTTTTAATGCCTAA	57.670	30.769	0.00	0.00	0.00	2.69
474	477	9.709304	CCAAGAGGATATTGTTGGTGGTACCAT	62.709	44.444	19.72	2.05	42.72	3.55
521	524	0.475632	TTTCCAGAGGAAGGAGGGCA	60.476	55.000	0.00	0.00	43.06	5.36
736	740	4.161565	AGCATTAGATAGACGGTTCCACAA	59.838	41.667	0.00	0.00	0.00	3.33
739	743	3.492656	GCAGCATTAGATAGACGGTTCCA	60.493	47.826	0.00	0.00	0.00	3.53
768	772	1.704641	ACAGTACACAGTCCAGCTCA	58.295	50.000	0.00	0.00	0.00	4.26
783	787	1.696063	AATCCTGCAACAGCAACAGT	58.304	45.000	0.00	0.00	37.91	3.55
822	826	0.688087	GGGAGAGGGACCGTTCATCT	60.688	60.000	0.00	0.00	0.00	2.90
880	884	4.759782	TCAGCATAGTCCTTAGCAAGAAC	58.240	43.478	0.00	0.00	0.00	3.01
889	893	2.171448	GGTGTGGATCAGCATAGTCCTT	59.829	50.000	0.00	0.00	43.22	3.36
926	933	3.826729	GACTTTTATTGGCACCTTGGAGT	59.173	43.478	0.00	0.00	0.00	3.85
942	949	3.077359	CCAGGCGAAGATCTTGACTTTT	58.923	45.455	14.00	0.00	0.00	2.27
1007	1014	2.750948	CTGATTGGGCAATATGCTTGC	58.249	47.619	2.00	0.68	44.28	4.01
1147	1154	1.614996	ATCGTGGGATGTTGTTGCAA	58.385	45.000	0.00	0.00	0.00	4.08
1208	1215	1.901159	CCCAAATCTTCCATGCAACCA	59.099	47.619	0.00	0.00	0.00	3.67
1277	1284	7.892778	TCTGCTACAATGTTACGAATTGTAA	57.107	32.000	9.53	0.00	45.25	2.41
1336	1343	7.280876	CCATTGCTTAGCAGAAGTATTGTCTTA	59.719	37.037	7.08	0.00	40.61	2.10
1395	1402	7.121759	AGCATTAGTTCAGATTACAACAGCAAT	59.878	33.333	0.00	0.00	0.00	3.56
1756	1766	9.174166	AGTGTCTTTGATTTAGTACAACTTTGT	57.826	29.630	0.00	0.00	44.86	2.83
1768	1778	9.158233	CCGTCCTAAATAAGTGTCTTTGATTTA	57.842	33.333	0.00	0.00	0.00	1.40
1769	1779	7.881232	TCCGTCCTAAATAAGTGTCTTTGATTT	59.119	33.333	0.00	0.00	0.00	2.17
1770	1780	7.391620	TCCGTCCTAAATAAGTGTCTTTGATT	58.608	34.615	0.00	0.00	0.00	2.57
1771	1781	6.942976	TCCGTCCTAAATAAGTGTCTTTGAT	58.057	36.000	0.00	0.00	0.00	2.57
1772	1782	6.349243	TCCGTCCTAAATAAGTGTCTTTGA	57.651	37.500	0.00	0.00	0.00	2.69
1773	1783	6.649557	ACTTCCGTCCTAAATAAGTGTCTTTG	59.350	38.462	0.00	0.00	0.00	2.77
1774	1784	6.766429	ACTTCCGTCCTAAATAAGTGTCTTT	58.234	36.000	0.00	0.00	0.00	2.52
1775	1785	6.356186	ACTTCCGTCCTAAATAAGTGTCTT	57.644	37.500	0.00	0.00	0.00	3.01
1776	1786	5.997384	ACTTCCGTCCTAAATAAGTGTCT	57.003	39.130	0.00	0.00	0.00	3.41
1777	1787	6.861144	ACTACTTCCGTCCTAAATAAGTGTC	58.139	40.000	0.00	0.00	32.85	3.67
1778	1788	6.847421	ACTACTTCCGTCCTAAATAAGTGT	57.153	37.500	0.00	0.00	32.85	3.55
1779	1789	8.218338	TCTACTACTTCCGTCCTAAATAAGTG	57.782	38.462	0.00	0.00	32.85	3.16
1780	1790	8.993404	ATCTACTACTTCCGTCCTAAATAAGT	57.007	34.615	0.00	0.00	34.86	2.24
1783	1793	9.512588	CCTTATCTACTACTTCCGTCCTAAATA	57.487	37.037	0.00	0.00	0.00	1.40
1784	1794	8.003629	ACCTTATCTACTACTTCCGTCCTAAAT	58.996	37.037	0.00	0.00	0.00	1.40
1785	1795	7.349598	ACCTTATCTACTACTTCCGTCCTAAA	58.650	38.462	0.00	0.00	0.00	1.85
1786	1796	6.904626	ACCTTATCTACTACTTCCGTCCTAA	58.095	40.000	0.00	0.00	0.00	2.69
1787	1797	6.506538	ACCTTATCTACTACTTCCGTCCTA	57.493	41.667	0.00	0.00	0.00	2.94
1788	1798	5.385628	ACCTTATCTACTACTTCCGTCCT	57.614	43.478	0.00	0.00	0.00	3.85
1789	1799	7.573968	TTTACCTTATCTACTACTTCCGTCC	57.426	40.000	0.00	0.00	0.00	4.79
1816	1826	7.675619	TGGAGCTATCTGAATGACCTTGATATA	59.324	37.037	0.00	0.00	0.00	0.86
1876	1886	5.904984	ATGCACTATTGTCCCACCTTATA	57.095	39.130	0.00	0.00	0.00	0.98
1956	1966	9.349145	CTTTTAGTTTGGGTTACATAATTTCGG	57.651	33.333	0.00	0.00	0.00	4.30
1967	1977	7.352738	TGGGTACTTTCTTTTAGTTTGGGTTA	58.647	34.615	0.00	0.00	0.00	2.85
1971	1981	7.067737	TCAGTTGGGTACTTTCTTTTAGTTTGG	59.932	37.037	0.00	0.00	33.85	3.28
2033	2043	6.931840	GTGAAGAGATCAGAAACAAGGTTACT	59.068	38.462	0.00	0.00	39.19	2.24
2083	2093	9.614792	ACCTTTTCTAATACAGTAAAGCTATGG	57.385	33.333	0.00	0.00	39.23	2.74
2098	2108	5.385198	TGAGAAACAGCCACCTTTTCTAAT	58.615	37.500	0.00	0.00	39.22	1.73
2114	2124	6.967135	ACCGAATTTCCTTTACTTGAGAAAC	58.033	36.000	0.00	0.00	31.51	2.78
2115	2125	7.283580	TGAACCGAATTTCCTTTACTTGAGAAA	59.716	33.333	0.00	0.00	33.13	2.52
2118	2128	6.554334	TGAACCGAATTTCCTTTACTTGAG	57.446	37.500	0.00	0.00	0.00	3.02
2135	2145	7.969387	ATTATCAACGATTTTTGATGAACCG	57.031	32.000	8.74	0.00	44.33	4.44
2226	2239	5.736207	GCAACCTTTCACTTAAAGACCTTGG	60.736	44.000	0.00	0.00	46.44	3.61
2227	2240	5.163561	TGCAACCTTTCACTTAAAGACCTTG	60.164	40.000	0.00	0.53	46.44	3.61
2232	2245	6.959639	AATCTGCAACCTTTCACTTAAAGA	57.040	33.333	0.00	0.00	46.44	2.52
2237	2250	5.625150	AGTCTAATCTGCAACCTTTCACTT	58.375	37.500	0.00	0.00	0.00	3.16
2280	2298	2.985957	TTTCTTTTGCTTGGCTTGCT	57.014	40.000	4.23	0.00	0.00	3.91

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.