AutoCloner

Multiple sequence alignment - TraesCS6A01G394500

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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	TraesCS6A01G394500	chr6A	100.000	2264	0	0	1	2264	608000508	607998245	0.000000e+00	4181.0
1	TraesCS6A01G394500	chr6A	96.443	759	23	3	1	759	608038001	608037247	0.000000e+00	1249.0
2	TraesCS6A01G394500	chr6A	85.541	823	80	22	1226	2021	466145688	466146498	0.000000e+00	824.0
3	TraesCS6A01G394500	chr6B	93.630	1507	65	7	760	2264	703106737	703105260	0.000000e+00	2222.0
4	TraesCS6A01G394500	chr6B	93.497	1507	68	6	760	2264	703015070	703013592	0.000000e+00	2213.0
5	TraesCS6A01G394500	chr6B	93.431	1507	69	6	760	2264	703008218	703006740	0.000000e+00	2207.0
6	TraesCS6A01G394500	chr6B	93.377	1510	66	10	760	2264	703064120	703062640	0.000000e+00	2204.0
7	TraesCS6A01G394500	chr6B	93.232	1507	72	6	760	2264	703057227	703055749	0.000000e+00	2191.0
8	TraesCS6A01G394500	chr6B	93.599	1328	78	7	760	2084	702991691	702990368	0.000000e+00	1975.0
9	TraesCS6A01G394500	chr6B	94.610	1243	63	4	760	1999	702946731	702945490	0.000000e+00	1921.0
10	TraesCS6A01G394500	chr6B	95.588	340	12	2	1928	2264	702990442	702990103	1.980000e-150	542.0
11	TraesCS6A01G394500	chr6B	88.849	278	24	6	1990	2264	702945581	702945308	3.600000e-88	335.0
12	TraesCS6A01G394500	chr6B	91.803	61	5	0	760	820	238270889	238270949	4.010000e-13	86.1
13	TraesCS6A01G394500	chr3B	92.546	1194	74	6	765	1956	548879857	548881037	0.000000e+00	1698.0
14	TraesCS6A01G394500	chr3B	91.228	57	2	1	2031	2084	548881043	548881099	8.670000e-10	75.0
15	TraesCS6A01G394500	chr3D	91.881	1207	71	14	761	1956	116062285	116063475	0.000000e+00	1661.0
16	TraesCS6A01G394500	chr1D	90.974	1252	80	17	760	1981	198509345	198510593	0.000000e+00	1655.0
17	TraesCS6A01G394500	chr2B	90.955	1194	93	7	765	1956	292848174	292849354	0.000000e+00	1592.0
18	TraesCS6A01G394500	chr2B	90.879	1195	90	7	765	1956	71642713	71641535	0.000000e+00	1585.0
19	TraesCS6A01G394500	chr1B	93.582	1044	58	3	766	1808	449941660	449942695	0.000000e+00	1548.0
20	TraesCS6A01G394500	chr5D	93.019	1017	63	5	765	1779	358005917	358004907	0.000000e+00	1478.0
21	TraesCS6A01G394500	chr4A	95.407	762	28	3	1	762	318342210	318341456	0.000000e+00	1206.0
22	TraesCS6A01G394500	chr7A	89.947	756	67	8	1	753	429841600	429842349	0.000000e+00	966.0
23	TraesCS6A01G394500	chr7A	89.660	764	69	9	1	759	429849552	429850310	0.000000e+00	965.0
24	TraesCS6A01G394500	chr2A	89.761	752	64	9	14	759	573584093	573584837	0.000000e+00	950.0
25	TraesCS6A01G394500	chr2A	89.229	752	68	9	14	759	573602357	573603101	0.000000e+00	928.0
26	TraesCS6A01G394500	chr2A	89.252	735	68	8	29	759	573576047	573576774	0.000000e+00	909.0
27	TraesCS6A01G394500	chr2A	89.266	736	66	10	29	759	573594623	573595350	0.000000e+00	909.0
28	TraesCS6A01G394500	chr2A	85.235	149	12	7	2126	2264	748872042	748872190	6.520000e-31	145.0
29	TraesCS6A01G394500	chrUn	89.281	737	66	10	27	759	277094153	277093426	0.000000e+00	911.0

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	TraesCS6A01G394500	chr6A	607998245	608000508	2263	True	4181.0	4181	100.0000	1	2264	1	chr6A.!!$R1	2263
1	TraesCS6A01G394500	chr6A	608037247	608038001	754	True	1249.0	1249	96.4430	1	759	1	chr6A.!!$R2	758
2	TraesCS6A01G394500	chr6A	466145688	466146498	810	False	824.0	824	85.5410	1226	2021	1	chr6A.!!$F1	795
3	TraesCS6A01G394500	chr6B	703105260	703106737	1477	True	2222.0	2222	93.6300	760	2264	1	chr6B.!!$R5	1504
4	TraesCS6A01G394500	chr6B	703013592	703015070	1478	True	2213.0	2213	93.4970	760	2264	1	chr6B.!!$R2	1504
5	TraesCS6A01G394500	chr6B	703006740	703008218	1478	True	2207.0	2207	93.4310	760	2264	1	chr6B.!!$R1	1504
6	TraesCS6A01G394500	chr6B	703062640	703064120	1480	True	2204.0	2204	93.3770	760	2264	1	chr6B.!!$R4	1504
7	TraesCS6A01G394500	chr6B	703055749	703057227	1478	True	2191.0	2191	93.2320	760	2264	1	chr6B.!!$R3	1504
8	TraesCS6A01G394500	chr6B	702990103	702991691	1588	True	1258.5	1975	94.5935	760	2264	2	chr6B.!!$R7	1504
9	TraesCS6A01G394500	chr6B	702945308	702946731	1423	True	1128.0	1921	91.7295	760	2264	2	chr6B.!!$R6	1504
10	TraesCS6A01G394500	chr3B	548879857	548881099	1242	False	886.5	1698	91.8870	765	2084	2	chr3B.!!$F1	1319
11	TraesCS6A01G394500	chr3D	116062285	116063475	1190	False	1661.0	1661	91.8810	761	1956	1	chr3D.!!$F1	1195
12	TraesCS6A01G394500	chr1D	198509345	198510593	1248	False	1655.0	1655	90.9740	760	1981	1	chr1D.!!$F1	1221
13	TraesCS6A01G394500	chr2B	292848174	292849354	1180	False	1592.0	1592	90.9550	765	1956	1	chr2B.!!$F1	1191
14	TraesCS6A01G394500	chr2B	71641535	71642713	1178	True	1585.0	1585	90.8790	765	1956	1	chr2B.!!$R1	1191
15	TraesCS6A01G394500	chr1B	449941660	449942695	1035	False	1548.0	1548	93.5820	766	1808	1	chr1B.!!$F1	1042
16	TraesCS6A01G394500	chr5D	358004907	358005917	1010	True	1478.0	1478	93.0190	765	1779	1	chr5D.!!$R1	1014
17	TraesCS6A01G394500	chr4A	318341456	318342210	754	True	1206.0	1206	95.4070	1	762	1	chr4A.!!$R1	761
18	TraesCS6A01G394500	chr7A	429841600	429842349	749	False	966.0	966	89.9470	1	753	1	chr7A.!!$F1	752
19	TraesCS6A01G394500	chr7A	429849552	429850310	758	False	965.0	965	89.6600	1	759	1	chr7A.!!$F2	758
20	TraesCS6A01G394500	chr2A	573584093	573584837	744	False	950.0	950	89.7610	14	759	1	chr2A.!!$F2	745
21	TraesCS6A01G394500	chr2A	573602357	573603101	744	False	928.0	928	89.2290	14	759	1	chr2A.!!$F4	745
22	TraesCS6A01G394500	chr2A	573576047	573576774	727	False	909.0	909	89.2520	29	759	1	chr2A.!!$F1	730
23	TraesCS6A01G394500	chr2A	573594623	573595350	727	False	909.0	909	89.2660	29	759	1	chr2A.!!$F3	730
24	TraesCS6A01G394500	chrUn	277093426	277094153	727	True	911.0	911	89.2810	27	759	1	chrUn.!!$R1	732

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
438	448	0.587285	TAAACGTTGCGGCGTCAAAT	59.413	45.0	16.04	7.13	45.0	2.32	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1911	2003	0.117541	TAGGGTCCAGCAACCTACCA	59.882	55.0	3.36	0.0	39.42	3.25	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
356	365	1.922447	AGAAGAGAGAGAGAGAGGGCA	59.078	52.381	0.00	0.00	0.00	5.36
365	374	1.213182	AGAGAGAGGGCACGACATCTA	59.787	52.381	0.00	0.00	0.00	1.98
428	437	2.349275	TGCCGCTATAGTTAAACGTTGC	59.651	45.455	0.00	0.00	0.00	4.17
438	448	0.587285	TAAACGTTGCGGCGTCAAAT	59.413	45.000	16.04	7.13	45.00	2.32
520	530	2.837591	TCAACTCTCATCCCATTCCGAA	59.162	45.455	0.00	0.00	0.00	4.30
583	593	4.250431	GGCGCGTGCAAGTGTGTT	62.250	61.111	24.18	0.00	45.35	3.32
587	597	1.431440	GCGTGCAAGTGTGTTTGGA	59.569	52.632	0.59	0.00	0.00	3.53
708	719	1.338389	GCAAGCAAATGACCTGGCAAT	60.338	47.619	0.00	0.00	0.00	3.56
819	830	1.060163	TACTTAGAGGGGGCCATGGC	61.060	60.000	29.47	29.47	41.06	4.40
904	915	6.039270	TCCGGATGGTTGAAATAATGTGAATC	59.961	38.462	0.00	0.00	36.30	2.52
905	916	6.183360	CCGGATGGTTGAAATAATGTGAATCA	60.183	38.462	0.00	0.00	0.00	2.57
1015	1030	1.148273	GGCATGGCTTCATCCGGTA	59.852	57.895	12.86	0.00	0.00	4.02
1016	1031	0.465460	GGCATGGCTTCATCCGGTAA	60.465	55.000	12.86	0.00	0.00	2.85
1074	1089	1.503542	GCACAAGTGGGAGAATGCG	59.496	57.895	2.00	0.00	0.00	4.73
1095	1110	3.551846	GTCTTTGGACAAGGTGAAGGAA	58.448	45.455	0.00	0.00	41.75	3.36
1111	1127	7.288621	AGGTGAAGGAAAAAGATGTGAAGATTT	59.711	33.333	0.00	0.00	0.00	2.17
1143	1159	3.146066	GTGTGGAGATGTTTGCAAGGTA	58.854	45.455	0.00	0.00	0.00	3.08
1223	1239	4.380531	CCCAACTATGCTTATGATCGTGT	58.619	43.478	0.00	0.00	0.00	4.49
1389	1406	3.812167	GCCAGAAGATGTCCAAAAGGACT	60.812	47.826	15.01	1.95	39.41	3.85
1433	1450	0.033504	AGCGGCTGTTCGAAGAAAGA	59.966	50.000	0.00	0.00	45.90	2.52
1466	1484	1.176619	TGGAGGAAGAGCGTCGTCAA	61.177	55.000	8.03	0.00	34.74	3.18
1730	1752	1.154150	GCAAGAAGCCATGTGTCGC	60.154	57.895	0.00	0.00	37.23	5.19
1802	1870	7.917505	AGAACTAAAGTTTGTCAGCAATTTCTG	59.082	33.333	0.00	0.00	38.56	3.02
1803	1871	7.100458	ACTAAAGTTTGTCAGCAATTTCTGT	57.900	32.000	4.99	0.00	35.63	3.41
1804	1872	6.974622	ACTAAAGTTTGTCAGCAATTTCTGTG	59.025	34.615	4.99	0.00	35.63	3.66
1805	1873	5.581126	AAGTTTGTCAGCAATTTCTGTGA	57.419	34.783	4.99	0.00	35.63	3.58
1806	1874	5.779529	AGTTTGTCAGCAATTTCTGTGAT	57.220	34.783	4.99	0.00	35.63	3.06
1807	1875	6.152932	AGTTTGTCAGCAATTTCTGTGATT	57.847	33.333	4.99	0.00	35.63	2.57
1808	1876	6.576185	AGTTTGTCAGCAATTTCTGTGATTT	58.424	32.000	4.99	0.00	35.63	2.17
1809	1877	6.477688	AGTTTGTCAGCAATTTCTGTGATTTG	59.522	34.615	4.99	0.00	35.63	2.32
1810	1878	5.518848	TGTCAGCAATTTCTGTGATTTGT	57.481	34.783	4.99	0.00	35.63	2.83
1811	1879	5.522456	TGTCAGCAATTTCTGTGATTTGTC	58.478	37.500	4.99	0.00	35.63	3.18
1812	1880	5.067544	TGTCAGCAATTTCTGTGATTTGTCA	59.932	36.000	4.99	0.00	35.63	3.58
1813	1881	5.628193	GTCAGCAATTTCTGTGATTTGTCAG	59.372	40.000	4.99	0.00	35.63	3.51
1814	1882	4.384846	CAGCAATTTCTGTGATTTGTCAGC	59.615	41.667	0.00	0.00	0.00	4.26
1815	1883	4.038282	AGCAATTTCTGTGATTTGTCAGCA	59.962	37.500	0.00	0.00	0.00	4.41
1816	1884	4.746115	GCAATTTCTGTGATTTGTCAGCAA	59.254	37.500	0.00	0.00	0.00	3.91
1817	1885	5.407387	GCAATTTCTGTGATTTGTCAGCAAT	59.593	36.000	0.00	0.00	34.18	3.56
1818	1886	6.073440	GCAATTTCTGTGATTTGTCAGCAATT	60.073	34.615	0.00	0.00	37.75	2.32
1819	1887	7.519328	GCAATTTCTGTGATTTGTCAGCAATTT	60.519	33.333	0.00	0.00	36.17	1.82
1820	1888	7.647907	ATTTCTGTGATTTGTCAGCAATTTC	57.352	32.000	0.00	0.00	34.18	2.17
1821	1889	6.395426	TTCTGTGATTTGTCAGCAATTTCT	57.605	33.333	0.00	0.00	34.18	2.52
1910	2002	3.253838	TACCACCACACCCCCTGC	61.254	66.667	0.00	0.00	0.00	4.85
1911	2003	3.803311	TACCACCACACCCCCTGCT	62.803	63.158	0.00	0.00	0.00	4.24
1967	2059	0.331616	GGTAGGGGTGCCAATGTCTT	59.668	55.000	0.00	0.00	0.00	3.01
1999	2173	1.563924	ATAACTGTGTGGCGGTAGGA	58.436	50.000	0.00	0.00	35.19	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	6.515779	AGCCCCTAATCTAATCTCCATGATA	58.484	40.000	0.00	0.00	34.45	2.15
356	365	3.066900	CGGTCTCAGGAAATAGATGTCGT	59.933	47.826	0.00	0.00	0.00	4.34
428	437	1.011968	TCGGAGTTCATTTGACGCCG	61.012	55.000	12.19	12.19	35.14	6.46
438	448	2.378445	TTCATCGCATTCGGAGTTCA	57.622	45.000	0.00	0.00	36.13	3.18
520	530	5.986501	TTATAAGTGGCCGGAAAATGTTT	57.013	34.783	5.05	0.00	0.00	2.83
583	593	1.483004	TGTTGTCCGTTCTGAGTCCAA	59.517	47.619	0.00	0.00	0.00	3.53
587	597	1.341531	CCTCTGTTGTCCGTTCTGAGT	59.658	52.381	0.00	0.00	0.00	3.41
708	719	3.194755	TGTCTTCCAGTTATTCGCTGCTA	59.805	43.478	0.00	0.00	32.93	3.49
819	830	2.834549	ACATGTCCTAGAACCACCAGAG	59.165	50.000	0.00	0.00	0.00	3.35
1015	1030	1.097232	CACGGTGGCATCATCATGTT	58.903	50.000	0.00	0.00	31.86	2.71
1016	1031	0.035152	ACACGGTGGCATCATCATGT	60.035	50.000	13.48	0.00	31.86	3.21
1074	1089	3.208747	TCCTTCACCTTGTCCAAAGAC	57.791	47.619	0.00	0.00	43.83	3.01
1095	1110	5.047802	ACATGGCGAAATCTTCACATCTTTT	60.048	36.000	0.00	0.00	0.00	2.27
1111	1127	1.302431	CTCCACACCAACATGGCGA	60.302	57.895	0.00	0.00	42.67	5.54
1143	1159	0.178533	TTCGGTCGGTGGACAACTTT	59.821	50.000	0.00	0.00	45.28	2.66
1223	1239	2.235155	TCATAGGCGTTAGTTGGAAGCA	59.765	45.455	0.00	0.00	0.00	3.91
1389	1406	5.932303	GGCGCCTAAGACAATCTTCATATTA	59.068	40.000	22.15	0.00	37.89	0.98
1433	1450	3.703001	TCCTCCAAGCTTCTTCGAAAT	57.297	42.857	0.00	0.00	0.00	2.17
1466	1484	2.757894	TCCGCTCTATCCTCTCCTTT	57.242	50.000	0.00	0.00	0.00	3.11
1802	1870	4.682860	CCACAGAAATTGCTGACAAATCAC	59.317	41.667	20.85	0.00	39.77	3.06
1803	1871	4.341806	ACCACAGAAATTGCTGACAAATCA	59.658	37.500	20.85	0.00	39.77	2.57
1804	1872	4.682860	CACCACAGAAATTGCTGACAAATC	59.317	41.667	20.85	0.00	39.77	2.17
1805	1873	4.341806	TCACCACAGAAATTGCTGACAAAT	59.658	37.500	20.85	0.00	39.77	2.32
1806	1874	3.698539	TCACCACAGAAATTGCTGACAAA	59.301	39.130	20.85	0.00	39.77	2.83
1807	1875	3.286353	TCACCACAGAAATTGCTGACAA	58.714	40.909	20.85	0.00	40.87	3.18
1808	1876	2.929641	TCACCACAGAAATTGCTGACA	58.070	42.857	20.85	0.00	39.20	3.58
1809	1877	4.510038	AATCACCACAGAAATTGCTGAC	57.490	40.909	20.85	0.00	39.20	3.51
1810	1878	5.534207	AAAATCACCACAGAAATTGCTGA	57.466	34.783	20.85	0.00	39.20	4.26
1841	1931	1.271543	CCCCTCATCTCAGCACAACAA	60.272	52.381	0.00	0.00	0.00	2.83
1910	2002	1.201429	AGGGTCCAGCAACCTACCAG	61.201	60.000	3.36	0.00	39.42	4.00
1911	2003	0.117541	TAGGGTCCAGCAACCTACCA	59.882	55.000	3.36	0.00	39.42	3.25
1967	2059	5.008811	CCACACAGTTATTTTCCCGTAACAA	59.991	40.000	0.00	0.00	34.14	2.83
2102	2281	9.581099	AGTTTACGAAGTTGAAAAATGTTCAAT	57.419	25.926	1.50	0.00	37.78	2.57

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.