AutoCloner

Multiple sequence alignment - TraesCS6A01G336200

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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	TraesCS6A01G336200	chr6A	100.000	2489	0	0	1	2489	569588208	569585720	0.000000e+00	4597
1	TraesCS6A01G336200	chr6A	74.515	361	52	22	26	350	12687675	12688031	1.210000e-23	121
2	TraesCS6A01G336200	chr5A	91.257	2505	185	20	1	2489	484592869	484595355	0.000000e+00	3382
3	TraesCS6A01G336200	chr2A	91.202	2512	180	23	1	2489	378393288	378390795	0.000000e+00	3376
4	TraesCS6A01G336200	chr1D	89.824	2506	196	23	3	2485	479088416	479085947	0.000000e+00	3160
5	TraesCS6A01G336200	chr1D	90.909	1254	83	17	1	1230	96103410	96102164	0.000000e+00	1655
6	TraesCS6A01G336200	chr2D	89.621	2505	201	30	7	2489	594644833	594642366	0.000000e+00	3131
7	TraesCS6A01G336200	chr2D	88.672	2516	233	34	3	2489	374125468	374127960	0.000000e+00	3020
8	TraesCS6A01G336200	chr2D	89.074	2407	209	36	107	2489	343541541	343543917	0.000000e+00	2939
9	TraesCS6A01G336200	chr7D	89.621	2505	197	33	9	2489	135379429	135381894	0.000000e+00	3127
10	TraesCS6A01G336200	chr5D	89.252	2512	208	29	1	2489	545975236	545972764	0.000000e+00	3086
11	TraesCS6A01G336200	chr5D	92.168	2094	143	16	403	2489	400782361	400780282	0.000000e+00	2939
12	TraesCS6A01G336200	chr3D	92.745	2095	135	15	403	2489	341359224	341361309	0.000000e+00	3011
13	TraesCS6A01G336200	chr3B	87.599	1387	127	30	198	1569	481648155	481646799	0.000000e+00	1567
14	TraesCS6A01G336200	chr4B	75.000	360	50	23	26	350	14706072	14706426	2.010000e-26	130
15	TraesCS6A01G336200	chr4B	74.367	316	46	21	26	311	417550606	417550296	4.380000e-18	102
16	TraesCS6A01G336200	chr1A	74.167	360	53	24	26	350	255477315	255476961	2.020000e-21	113
17	TraesCS6A01G336200	chr3A	83.036	112	15	4	24	133	745750159	745750268	5.670000e-17	99

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	TraesCS6A01G336200	chr6A	569585720	569588208	2488	True	4597	4597	100.000	1	2489	1	chr6A.!!$R1	2488
1	TraesCS6A01G336200	chr5A	484592869	484595355	2486	False	3382	3382	91.257	1	2489	1	chr5A.!!$F1	2488
2	TraesCS6A01G336200	chr2A	378390795	378393288	2493	True	3376	3376	91.202	1	2489	1	chr2A.!!$R1	2488
3	TraesCS6A01G336200	chr1D	479085947	479088416	2469	True	3160	3160	89.824	3	2485	1	chr1D.!!$R2	2482
4	TraesCS6A01G336200	chr1D	96102164	96103410	1246	True	1655	1655	90.909	1	1230	1	chr1D.!!$R1	1229
5	TraesCS6A01G336200	chr2D	594642366	594644833	2467	True	3131	3131	89.621	7	2489	1	chr2D.!!$R1	2482
6	TraesCS6A01G336200	chr2D	374125468	374127960	2492	False	3020	3020	88.672	3	2489	1	chr2D.!!$F2	2486
7	TraesCS6A01G336200	chr2D	343541541	343543917	2376	False	2939	2939	89.074	107	2489	1	chr2D.!!$F1	2382
8	TraesCS6A01G336200	chr7D	135379429	135381894	2465	False	3127	3127	89.621	9	2489	1	chr7D.!!$F1	2480
9	TraesCS6A01G336200	chr5D	545972764	545975236	2472	True	3086	3086	89.252	1	2489	1	chr5D.!!$R2	2488
10	TraesCS6A01G336200	chr5D	400780282	400782361	2079	True	2939	2939	92.168	403	2489	1	chr5D.!!$R1	2086
11	TraesCS6A01G336200	chr3D	341359224	341361309	2085	False	3011	3011	92.745	403	2489	1	chr3D.!!$F1	2086
12	TraesCS6A01G336200	chr3B	481646799	481648155	1356	True	1567	1567	87.599	198	1569	1	chr3B.!!$R1	1371

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
691	751	0.040067	CAGAAAACCTGCAAGCCGTC	60.04	55.0	0.0	0.0	35.89	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1519	1612	2.317973	CTCAGCTCCTCCATCATCAGA	58.682	52.381	0.0	0.0	0.0	3.27	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
25	26	7.093992	GCATTGTAGCCAAAAACCTAAACATA	58.906	34.615	0.00	0.00	33.44	2.29
35	36	8.303876	CCAAAAACCTAAACATACATTGTAGCT	58.696	33.333	2.53	0.00	37.68	3.32
83	84	0.625316	ACATGCATCCCAGCCAACTA	59.375	50.000	0.00	0.00	0.00	2.24
94	95	5.329399	TCCCAGCCAACTAAACATGTATTT	58.671	37.500	0.00	0.00	0.00	1.40
98	99	6.295011	CCAGCCAACTAAACATGTATTTTGGA	60.295	38.462	23.02	0.00	0.00	3.53
111	112	6.040209	TGTATTTTGGAAATTCAGCATGCT	57.960	33.333	16.30	16.30	34.76	3.79
122	125	4.800355	GCATGCTTGCTAGGCAAC	57.200	55.556	16.80	0.50	43.99	4.17
142	156	6.149474	GGCAACACTGAACATGTAGTATTCTT	59.851	38.462	0.00	0.00	0.00	2.52
196	238	5.714333	TGTGCAATAAAACATGTATCCTGGT	59.286	36.000	0.00	0.00	0.00	4.00
222	264	0.597568	AACATGCATGGTGTCCAACG	59.402	50.000	29.41	1.63	36.95	4.10
237	282	2.437651	TCCAACGGAATATGCATCCTGA	59.562	45.455	0.19	0.00	34.66	3.86
266	311	9.905713	AAATGAAACATCTATTCTAGCCAACTA	57.094	29.630	0.00	0.00	0.00	2.24
317	364	3.164268	TGCTGGCCAACTGAAAATATGT	58.836	40.909	7.01	0.00	0.00	2.29
346	394	7.040062	CCTGGTAACTGAGACATCTATTCTAGG	60.040	44.444	0.00	0.00	37.83	3.02
373	421	7.739498	AAACCAAAAATCTGTAGTACGACAT	57.261	32.000	9.36	0.00	0.00	3.06
385	433	5.747675	TGTAGTACGACATCGAAAACACAAA	59.252	36.000	8.54	0.00	43.02	2.83
630	689	7.123098	TCTCAATTGTGGCATCAAATTATGTCT	59.877	33.333	5.13	0.00	32.55	3.41
632	691	8.407832	TCAATTGTGGCATCAAATTATGTCTAG	58.592	33.333	5.13	0.00	32.55	2.43
667	726	3.361281	AATCTGAATCAGCTCCTTGCA	57.639	42.857	5.18	0.00	45.94	4.08
670	730	3.489355	TCTGAATCAGCTCCTTGCAAAA	58.511	40.909	5.18	0.00	45.94	2.44
685	745	3.668447	TGCAAAAACAGAAAACCTGCAA	58.332	36.364	0.00	0.00	46.81	4.08
686	746	3.683822	TGCAAAAACAGAAAACCTGCAAG	59.316	39.130	0.00	0.00	46.81	4.01
689	749	0.385390	AACAGAAAACCTGCAAGCCG	59.615	50.000	0.00	0.00	46.81	5.52
691	751	0.040067	CAGAAAACCTGCAAGCCGTC	60.040	55.000	0.00	0.00	35.89	4.79
692	752	0.179018	AGAAAACCTGCAAGCCGTCT	60.179	50.000	0.00	0.00	0.00	4.18
712	774	5.037385	GTCTCAACAAACAGAGGAAAAAGC	58.963	41.667	0.00	0.00	32.76	3.51
729	793	4.439253	AAAGCCAGGAAAACTCTGTAGT	57.561	40.909	0.00	0.00	37.65	2.73
876	957	6.830324	ACTAAGATTGTCATAATGGTGTGCAT	59.170	34.615	0.00	0.00	0.00	3.96
970	1056	8.109634	TCCTTCTTTTTATATATGCAGGGGATC	58.890	37.037	0.00	0.00	0.00	3.36
1267	1354	1.269448	CAAATGTTCCTGGTCCAACCG	59.731	52.381	0.00	0.00	42.58	4.44
1455	1548	3.695830	AAAATGAACACCTCTAGGCGA	57.304	42.857	0.00	0.00	39.32	5.54
1460	1553	2.631062	TGAACACCTCTAGGCGAAAAGA	59.369	45.455	0.00	0.00	39.32	2.52
1486	1579	9.995003	ATCACACAAATGTATTGGTAAAACAAT	57.005	25.926	0.00	0.00	43.13	2.71
1519	1612	4.556699	GCAACGAGTACAAGAAGCCAAAAT	60.557	41.667	0.00	0.00	0.00	1.82
1584	1677	8.217799	CCTATACCAGATCCAAAACCTATTGAA	58.782	37.037	0.00	0.00	31.84	2.69
1599	1692	7.921041	ACCTATTGAAAGTGATGAGGAGATA	57.079	36.000	0.00	0.00	0.00	1.98
1750	1843	0.100503	GCAGGTGACGCACTTTGTTT	59.899	50.000	9.31	0.00	34.40	2.83
1758	1851	1.748493	ACGCACTTTGTTTGTGACCAT	59.252	42.857	0.00	0.00	37.60	3.55
1773	1866	2.172505	TGACCATAATCATCCGCTGGTT	59.827	45.455	0.00	0.00	40.22	3.67
1806	1899	6.037786	TCGTTGTCCAAATACTTGAGATCT	57.962	37.500	0.00	0.00	34.14	2.75
1809	1902	6.536582	CGTTGTCCAAATACTTGAGATCTCAT	59.463	38.462	25.64	14.57	39.64	2.90
1825	1918	4.190370	TCTCATCAAGGCATCTCTCCTA	57.810	45.455	0.00	0.00	32.65	2.94
1844	1937	6.723298	TCCTAATGAAAAGGAGTTTTTGCA	57.277	33.333	0.00	0.00	39.06	4.08
1863	1956	5.550232	TGCACATCTTGTATAACTGCAAG	57.450	39.130	0.00	0.00	43.95	4.01
1918	2011	6.069381	ACAGAATTAAGTTTCCCTCTAGGCAT	60.069	38.462	0.00	0.00	34.51	4.40
1968	2061	5.278758	GGTGTGCAACTAAAATGCCTTAAGA	60.279	40.000	3.36	0.00	43.16	2.10
2026	2130	9.060347	CATAATGTTCCTGTGCAACTAGATTAT	57.940	33.333	0.00	0.00	38.04	1.28
2077	2181	6.369005	TGTGTGCAAAATGAAAGTGTTTTTG	58.631	32.000	0.00	0.00	41.19	2.44
2088	2193	5.760253	TGAAAGTGTTTTTGAAAAGGTGCAA	59.240	32.000	0.00	0.00	0.00	4.08
2259	2364	2.405559	TGGATCTGAGATGATGGTGCT	58.594	47.619	0.00	0.00	0.00	4.40
2485	2591	1.871039	GGCGTACCACGATTGCATATT	59.129	47.619	2.35	0.00	46.05	1.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
25	26	4.457603	TGCATTTTCCGTTAGCTACAATGT	59.542	37.500	0.00	0.00	0.00	2.71
35	36	4.728534	GCACACTTATGCATTTTCCGTTA	58.271	39.130	3.54	0.00	45.39	3.18
83	84	8.723311	CATGCTGAATTTCCAAAATACATGTTT	58.277	29.630	2.30	0.00	0.00	2.83
111	112	2.340210	TGTTCAGTGTTGCCTAGCAA	57.660	45.000	0.00	0.00	46.80	3.91
122	125	9.639601	TTCACTAAGAATACTACATGTTCAGTG	57.360	33.333	2.30	6.19	35.48	3.66
196	238	2.553602	GACACCATGCATGTTCAGTTGA	59.446	45.455	24.58	0.00	0.00	3.18
222	264	4.828939	TCATTTGGTCAGGATGCATATTCC	59.171	41.667	0.00	0.00	34.76	3.01
237	282	7.118723	TGGCTAGAATAGATGTTTCATTTGGT	58.881	34.615	0.00	0.00	42.77	3.67
266	311	4.269183	TCAGTTGGACAGTCAATGTGTTT	58.731	39.130	2.17	0.00	44.17	2.83
317	364	8.228206	AGAATAGATGTCTCAGTTACCAGGATA	58.772	37.037	0.00	0.00	0.00	2.59
346	394	6.358822	GTCGTACTACAGATTTTTGGTTTTGC	59.641	38.462	0.00	0.00	0.00	3.68
373	421	7.861372	TGTACAAAAGTTTCTTTGTGTTTTCGA	59.139	29.630	11.05	0.00	46.42	3.71
451	502	5.903010	TGTGGGACCAGAATATATGTGTAGT	59.097	40.000	0.00	0.00	0.00	2.73
453	504	5.071250	GGTGTGGGACCAGAATATATGTGTA	59.929	44.000	0.00	0.00	45.34	2.90
632	691	9.234384	CTGATTCAGATTTTTCTGCACATAATC	57.766	33.333	8.00	3.63	37.63	1.75
667	726	3.270027	GGCTTGCAGGTTTTCTGTTTTT	58.730	40.909	0.00	0.00	45.08	1.94
670	730	0.385390	CGGCTTGCAGGTTTTCTGTT	59.615	50.000	0.00	0.00	45.08	3.16
685	745	1.541233	CCTCTGTTTGTTGAGACGGCT	60.541	52.381	0.00	0.00	32.44	5.52
686	746	0.868406	CCTCTGTTTGTTGAGACGGC	59.132	55.000	0.00	0.00	32.44	5.68
689	749	5.037385	GCTTTTTCCTCTGTTTGTTGAGAC	58.963	41.667	0.00	0.00	32.44	3.36
691	751	4.142182	TGGCTTTTTCCTCTGTTTGTTGAG	60.142	41.667	0.00	0.00	0.00	3.02
692	752	3.766591	TGGCTTTTTCCTCTGTTTGTTGA	59.233	39.130	0.00	0.00	0.00	3.18
876	957	7.858498	ACCTAAAAGCTTAGTAAATAGCCAGA	58.142	34.615	0.00	0.00	38.14	3.86
1192	1279	3.062763	CTGACTGCAAAGACACCACTAG	58.937	50.000	0.00	0.00	0.00	2.57
1245	1332	2.698274	GGTTGGACCAGGAACATTTGTT	59.302	45.455	0.00	0.00	38.42	2.83
1297	1384	0.761187	TCTTCTCCTTGCACAGCACT	59.239	50.000	0.00	0.00	38.71	4.40
1460	1553	9.995003	ATTGTTTTACCAATACATTTGTGTGAT	57.005	25.926	0.00	0.00	33.37	3.06
1486	1579	3.459145	TGTACTCGTTGCAGCAAAACTA	58.541	40.909	10.11	0.00	0.00	2.24
1501	1594	6.372659	TCATCAGATTTTGGCTTCTTGTACTC	59.627	38.462	0.00	0.00	0.00	2.59
1519	1612	2.317973	CTCAGCTCCTCCATCATCAGA	58.682	52.381	0.00	0.00	0.00	3.27
1584	1677	7.201992	GGTTCATCTTCTATCTCCTCATCACTT	60.202	40.741	0.00	0.00	0.00	3.16
1599	1692	6.320672	CAGCAAATATTGGAGGTTCATCTTCT	59.679	38.462	0.00	0.00	0.00	2.85
1750	1843	2.485302	CCAGCGGATGATTATGGTCACA	60.485	50.000	0.00	0.00	0.00	3.58
1758	1851	5.554822	GTTTGTTAACCAGCGGATGATTA	57.445	39.130	2.48	0.00	0.00	1.75
1773	1866	5.838531	ATTTGGACAACGAAGGTTTGTTA	57.161	34.783	0.00	0.00	33.13	2.41
1806	1899	4.903649	TCATTAGGAGAGATGCCTTGATGA	59.096	41.667	0.00	0.00	35.92	2.92
1809	1902	5.698741	TTTCATTAGGAGAGATGCCTTGA	57.301	39.130	0.00	0.00	36.96	3.02
1825	1918	6.585416	AGATGTGCAAAAACTCCTTTTCATT	58.415	32.000	0.00	0.00	34.91	2.57
1844	1937	6.936900	AGTCAACTTGCAGTTATACAAGATGT	59.063	34.615	9.54	0.00	44.89	3.06
1863	1956	7.491696	GGATATAGAAACACACCTGTAGTCAAC	59.508	40.741	0.00	0.00	0.00	3.18
1968	2061	3.646637	AGTGAAGGTAACCTAGTTGCACT	59.353	43.478	0.00	0.00	31.13	4.40
1979	2072	4.124238	TGTAGTTGCACAGTGAAGGTAAC	58.876	43.478	4.15	2.28	0.00	2.50
2026	2130	8.033038	GGACATTATGTAGTTACACAGTGAAGA	58.967	37.037	7.81	0.00	39.30	2.87
2096	2201	4.337555	CAGAAGATAGTTGCAGGAAATGGG	59.662	45.833	0.00	0.00	0.00	4.00
2259	2364	2.554893	GTTATTGCCTTTGGTCCGAACA	59.445	45.455	0.00	0.00	0.00	3.18
2423	2529	4.728772	CTGAGCCATCCACCCAAAATATA	58.271	43.478	0.00	0.00	0.00	0.86

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.