AutoCloner

Multiple sequence alignment - TraesCS6A01G287600

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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	TraesCS6A01G287600	chr6A	100.000	2798	0	0	1	2798	520052813	520050016	0.000000e+00	5168
1	TraesCS6A01G287600	chr6A	97.205	787	21	1	1	786	103681345	103682131	0.000000e+00	1330
2	TraesCS6A01G287600	chr6A	77.607	326	58	6	1086	1402	84060500	84060181	1.710000e-42	183
3	TraesCS6A01G287600	chr6B	94.656	1553	55	14	827	2367	564660887	564659351	0.000000e+00	2383
4	TraesCS6A01G287600	chr6B	87.648	421	21	10	2361	2779	564659323	564658932	7.060000e-126	460
5	TraesCS6A01G287600	chr6D	93.538	1563	56	12	786	2327	378264150	378262612	0.000000e+00	2285
6	TraesCS6A01G287600	chr6D	88.009	442	33	7	2362	2795	378262608	378262179	3.220000e-139	505
7	TraesCS6A01G287600	chr3A	97.967	787	15	1	1	786	571393834	571394620	0.000000e+00	1363
8	TraesCS6A01G287600	chr7A	97.212	789	20	2	1	787	39208469	39207681	0.000000e+00	1334
9	TraesCS6A01G287600	chr7A	88.706	788	87	2	1	786	690723861	690723074	0.000000e+00	961
10	TraesCS6A01G287600	chr2A	96.591	792	24	3	1	789	751533922	751533131	0.000000e+00	1310
11	TraesCS6A01G287600	chr2A	90.863	788	68	4	1	786	11221124	11220339	0.000000e+00	1053
12	TraesCS6A01G287600	chr1A	96.574	788	25	2	1	786	580087810	580088597	0.000000e+00	1304
13	TraesCS6A01G287600	chr4A	96.569	787	26	1	1	786	111101331	111102117	0.000000e+00	1303
14	TraesCS6A01G287600	chr5A	88.639	757	82	4	1	755	32913881	32914635	0.000000e+00	918

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	TraesCS6A01G287600	chr6A	520050016	520052813	2797	True	5168.0	5168	100.0000	1	2798	1	chr6A.!!$R2	2797
1	TraesCS6A01G287600	chr6A	103681345	103682131	786	False	1330.0	1330	97.2050	1	786	1	chr6A.!!$F1	785
2	TraesCS6A01G287600	chr6B	564658932	564660887	1955	True	1421.5	2383	91.1520	827	2779	2	chr6B.!!$R1	1952
3	TraesCS6A01G287600	chr6D	378262179	378264150	1971	True	1395.0	2285	90.7735	786	2795	2	chr6D.!!$R1	2009
4	TraesCS6A01G287600	chr3A	571393834	571394620	786	False	1363.0	1363	97.9670	1	786	1	chr3A.!!$F1	785
5	TraesCS6A01G287600	chr7A	39207681	39208469	788	True	1334.0	1334	97.2120	1	787	1	chr7A.!!$R1	786
6	TraesCS6A01G287600	chr7A	690723074	690723861	787	True	961.0	961	88.7060	1	786	1	chr7A.!!$R2	785
7	TraesCS6A01G287600	chr2A	751533131	751533922	791	True	1310.0	1310	96.5910	1	789	1	chr2A.!!$R2	788
8	TraesCS6A01G287600	chr2A	11220339	11221124	785	True	1053.0	1053	90.8630	1	786	1	chr2A.!!$R1	785
9	TraesCS6A01G287600	chr1A	580087810	580088597	787	False	1304.0	1304	96.5740	1	786	1	chr1A.!!$F1	785
10	TraesCS6A01G287600	chr4A	111101331	111102117	786	False	1303.0	1303	96.5690	1	786	1	chr4A.!!$F1	785
11	TraesCS6A01G287600	chr5A	32913881	32914635	754	False	918.0	918	88.6390	1	755	1	chr5A.!!$F1	754

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
523	526	2.417933	GCTGATTTGATCAAGACAGCGT	59.582	45.455	32.28	10.46	39.41	5.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2500	2569	0.539438	ATTCCGGGCTCAGTTGCAAA	60.539	50.0	0.0	0.0	34.04	3.68	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
338	341	2.674033	TGCGCTGCAAGGCTCAAT	60.674	55.556	9.73	0.00	34.76	2.57
523	526	2.417933	GCTGATTTGATCAAGACAGCGT	59.582	45.455	32.28	10.46	39.41	5.07
726	732	8.421784	TGATGTAAGACTTATTGGTATGACTCC	58.578	37.037	0.00	0.00	0.00	3.85
916	932	3.694566	GGTCGCCCTCTTTGATTAAACAT	59.305	43.478	0.00	0.00	0.00	2.71
989	1005	2.995450	GAGCCACACGTACGTTGCG	61.995	63.158	20.23	10.58	0.00	4.85
1012	1028	1.875963	GCAACAATGTCACTCCCCG	59.124	57.895	0.00	0.00	0.00	5.73
1055	1071	3.213402	CGTCCTCCTCCTCCTCGC	61.213	72.222	0.00	0.00	0.00	5.03
1143	1159	3.760035	TCCGAGTTCAGCCGCCTC	61.760	66.667	0.00	0.00	0.00	4.70
1161	1177	4.778415	CTCACGACGACGGGCCTG	62.778	72.222	11.02	11.02	43.22	4.85
1194	1210	2.476051	GAGCGCAACACCATCACG	59.524	61.111	11.47	0.00	0.00	4.35
1647	1663	3.952628	GAAAGGGACCGGGTCAGCG	62.953	68.421	27.32	0.00	33.68	5.18
1875	1891	2.823747	TCCTGCACGTGTCAGTATTACT	59.176	45.455	26.88	0.00	0.00	2.24
1876	1892	4.011698	TCCTGCACGTGTCAGTATTACTA	58.988	43.478	26.88	9.84	0.00	1.82
1877	1893	4.103357	CCTGCACGTGTCAGTATTACTAC	58.897	47.826	26.88	6.62	0.00	2.73
1975	1991	1.881602	CCAAGAGAGCTTTGCAGGC	59.118	57.895	5.73	5.73	30.14	4.85
2045	2061	5.181009	GTGGTGTTATAAACTGGTCTACCC	58.819	45.833	0.00	0.00	34.29	3.69
2087	2110	8.970293	GCTTTAGCTAGCTACAGTACTATTTTC	58.030	37.037	29.53	12.79	38.15	2.29
2093	2116	8.604890	GCTAGCTACAGTACTATTTTCTTTTGG	58.395	37.037	7.70	0.00	0.00	3.28
2138	2163	6.640907	TCATGTAGTAATTGCTGCATACGTAG	59.359	38.462	22.63	12.68	39.25	3.51
2139	2164	6.420903	CATGTAGTAATTGCTGCATACGTAGT	59.579	38.462	22.63	1.97	39.25	2.73
2159	2185	4.360563	AGTACATTAATCGGAGTTCTGCG	58.639	43.478	7.37	7.37	0.00	5.18
2160	2186	2.550978	ACATTAATCGGAGTTCTGCGG	58.449	47.619	13.08	0.00	0.00	5.69
2180	2206	2.418976	GGGCTACAAGTTCATTCGGTTC	59.581	50.000	0.00	0.00	0.00	3.62
2203	2231	9.968870	GTTCTATAAATCTGTCGTCTTATTCCT	57.031	33.333	0.00	0.00	0.00	3.36
2209	2237	8.649973	AAATCTGTCGTCTTATTCCTATTGTC	57.350	34.615	0.00	0.00	0.00	3.18
2210	2238	7.589958	ATCTGTCGTCTTATTCCTATTGTCT	57.410	36.000	0.00	0.00	0.00	3.41
2212	2240	8.515695	TCTGTCGTCTTATTCCTATTGTCTTA	57.484	34.615	0.00	0.00	0.00	2.10
2213	2241	9.132923	TCTGTCGTCTTATTCCTATTGTCTTAT	57.867	33.333	0.00	0.00	0.00	1.73
2324	2354	9.111613	TGTCGAAAATAACAACTTTTAGAGGAA	57.888	29.630	0.00	0.00	31.02	3.36
2330	2360	9.847224	AAATAACAACTTTTAGAGGAACAGAGA	57.153	29.630	0.00	0.00	0.00	3.10
2340	2370	3.006752	AGAGGAACAGAGAGAGCAACAAG	59.993	47.826	0.00	0.00	0.00	3.16
2359	2393	2.658422	CAGGTTGCCATGGCCAAC	59.342	61.111	33.44	30.78	41.09	3.77
2416	2481	4.201930	GCGCTAATACGATCTAGTATGCCT	60.202	45.833	0.00	0.00	37.39	4.75
2439	2504	5.626142	TGTAATGCACTAGGAGTTTCCAAA	58.374	37.500	0.00	0.00	39.61	3.28
2440	2505	6.065374	TGTAATGCACTAGGAGTTTCCAAAA	58.935	36.000	0.00	0.00	39.61	2.44
2441	2506	5.453567	AATGCACTAGGAGTTTCCAAAAC	57.546	39.130	0.00	0.00	39.61	2.43
2442	2507	3.892284	TGCACTAGGAGTTTCCAAAACA	58.108	40.909	5.46	0.00	39.61	2.83
2443	2508	4.274147	TGCACTAGGAGTTTCCAAAACAA	58.726	39.130	5.46	0.00	39.61	2.83
2444	2509	4.097286	TGCACTAGGAGTTTCCAAAACAAC	59.903	41.667	5.46	0.00	39.61	3.32
2445	2510	4.338400	GCACTAGGAGTTTCCAAAACAACT	59.662	41.667	5.46	5.20	39.61	3.16
2446	2511	5.529800	GCACTAGGAGTTTCCAAAACAACTA	59.470	40.000	5.46	5.94	39.61	2.24
2513	2582	1.008538	CGGTGTTTGCAACTGAGCC	60.009	57.895	0.00	0.00	0.00	4.70
2569	2638	2.434185	CGACAGCCTTTGCCGCTA	60.434	61.111	0.00	0.00	38.69	4.26
2663	2732	1.743958	CAAGAGTGGAGTACGATCCGT	59.256	52.381	0.00	0.00	42.77	4.69
2664	2733	1.666054	AGAGTGGAGTACGATCCGTC	58.334	55.000	0.00	0.00	42.77	4.79
2668	2737	1.033746	TGGAGTACGATCCGTCCCAC	61.034	60.000	0.00	0.00	42.77	4.61
2692	2761	2.202756	GTGATCGTCCCGAGCCAC	60.203	66.667	0.00	3.37	41.81	5.01
2790	2867	0.177373	GTGTCTAGGGTTTAGGCCGG	59.823	60.000	0.00	0.00	0.00	6.13
2795	2872	1.489230	CTAGGGTTTAGGCCGGTCATT	59.511	52.381	9.71	0.00	0.00	2.57
2796	2873	0.255033	AGGGTTTAGGCCGGTCATTC	59.745	55.000	9.71	0.00	0.00	2.67
2797	2874	0.255033	GGGTTTAGGCCGGTCATTCT	59.745	55.000	9.71	0.00	0.00	2.40

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
176	178	1.378646	TCCCCGCACAACACACAAA	60.379	52.632	0.00	0.00	0.00	2.83
338	341	0.249155	GGTCCACACGACTCGTTTCA	60.249	55.000	0.00	0.00	41.64	2.69
468	471	1.069765	CAACGGACTCCACTGCTGT	59.930	57.895	0.00	0.00	0.00	4.40
523	526	3.138304	ACACTTGCAGAATTCGCTGTTA	58.862	40.909	18.44	1.52	38.17	2.41
820	826	1.101049	AGTCTGTTTTGTGCCACCGG	61.101	55.000	0.00	0.00	0.00	5.28
916	932	0.320374	AGATGAAACAGGGCGACGAA	59.680	50.000	0.00	0.00	0.00	3.85
989	1005	1.461127	GGAGTGACATTGTTGCGAGTC	59.539	52.381	0.00	0.00	0.00	3.36
1161	1177	1.708027	CTCGTTGATTTCGTCCGCC	59.292	57.895	0.00	0.00	0.00	6.13
1282	1298	1.914634	TCGTAGTAGTCGACGAGGAC	58.085	55.000	10.46	7.33	44.06	3.85
1428	1444	2.811317	GCGTCCTGAGGCACGAAG	60.811	66.667	21.71	0.00	41.43	3.79
1875	1891	2.047061	GCACTCACCATATCCCCAGTA	58.953	52.381	0.00	0.00	0.00	2.74
1876	1892	0.839946	GCACTCACCATATCCCCAGT	59.160	55.000	0.00	0.00	0.00	4.00
1877	1893	1.135094	AGCACTCACCATATCCCCAG	58.865	55.000	0.00	0.00	0.00	4.45
1975	1991	4.161189	ACACTAGATGAATCAGGACACAGG	59.839	45.833	0.00	0.00	0.00	4.00
2087	2110	7.661847	AGAGTACACCAGAAGATTTACCAAAAG	59.338	37.037	0.00	0.00	0.00	2.27
2093	2116	7.324178	ACATGAGAGTACACCAGAAGATTTAC	58.676	38.462	0.00	0.00	0.00	2.01
2107	2132	6.042777	TGCAGCAATTACTACATGAGAGTAC	58.957	40.000	0.00	0.00	0.00	2.73
2138	2163	3.489785	CCGCAGAACTCCGATTAATGTAC	59.510	47.826	0.00	0.00	0.00	2.90
2139	2164	3.491964	CCCGCAGAACTCCGATTAATGTA	60.492	47.826	0.00	0.00	0.00	2.29
2140	2165	2.550978	CCGCAGAACTCCGATTAATGT	58.449	47.619	0.00	0.00	0.00	2.71
2155	2181	1.398390	GAATGAACTTGTAGCCCGCAG	59.602	52.381	0.00	0.00	0.00	5.18
2159	2185	2.109425	ACCGAATGAACTTGTAGCCC	57.891	50.000	0.00	0.00	0.00	5.19
2160	2186	3.335579	AGAACCGAATGAACTTGTAGCC	58.664	45.455	0.00	0.00	0.00	3.93
2236	2265	9.994432	AATTTTGTTTCGATCATTCTATGTCTC	57.006	29.630	0.00	0.00	0.00	3.36
2324	2354	0.761187	TGCCTTGTTGCTCTCTCTGT	59.239	50.000	0.00	0.00	0.00	3.41
2330	2360	2.724520	CAACCTGCCTTGTTGCTCT	58.275	52.632	0.00	0.00	36.95	4.09
2349	2379	1.066716	CACCTTGATTGTTGGCCATGG	60.067	52.381	6.09	7.63	0.00	3.66
2359	2393	6.072452	GGTAGGAAGAAAGAACACCTTGATTG	60.072	42.308	0.00	0.00	34.79	2.67
2416	2481	4.901197	TGGAAACTCCTAGTGCATTACA	57.099	40.909	0.00	0.00	37.46	2.41
2439	2504	7.414436	TCTTGTTTACGTACGTACTAGTTGTT	58.586	34.615	26.83	0.00	0.00	2.83
2440	2505	6.954944	TCTTGTTTACGTACGTACTAGTTGT	58.045	36.000	26.83	14.76	0.00	3.32
2441	2506	7.460637	GCATCTTGTTTACGTACGTACTAGTTG	60.461	40.741	26.83	25.05	0.00	3.16
2442	2507	6.524586	GCATCTTGTTTACGTACGTACTAGTT	59.475	38.462	26.83	16.40	0.00	2.24
2443	2508	6.024049	GCATCTTGTTTACGTACGTACTAGT	58.976	40.000	26.83	16.09	0.00	2.57
2444	2509	5.453587	GGCATCTTGTTTACGTACGTACTAG	59.546	44.000	26.83	22.76	0.00	2.57
2445	2510	5.123820	AGGCATCTTGTTTACGTACGTACTA	59.876	40.000	26.83	15.15	0.00	1.82
2446	2511	4.082571	AGGCATCTTGTTTACGTACGTACT	60.083	41.667	26.83	13.72	0.00	2.73
2475	2540	4.374702	GTGCGGTGCGTGCTCAAG	62.375	66.667	0.00	0.00	0.00	3.02
2500	2569	0.539438	ATTCCGGGCTCAGTTGCAAA	60.539	50.000	0.00	0.00	34.04	3.68
2513	2582	3.732471	GCTAGCTAAGCGATAGATTCCGG	60.732	52.174	7.70	0.00	44.35	5.14
2569	2638	3.325753	AAAGAGGGCGCAGAGGCT	61.326	61.111	10.83	0.00	45.89	4.58
2644	2713	2.015587	GACGGATCGTACTCCACTCTT	58.984	52.381	2.39	0.00	41.37	2.85
2663	2732	3.072468	GATCACGTCGGGGTGGGA	61.072	66.667	0.00	0.00	38.46	4.37
2664	2733	4.508128	CGATCACGTCGGGGTGGG	62.508	72.222	0.00	0.00	46.47	4.61
2692	2761	0.665068	TGCGTGTAAGCAGTACCACG	60.665	55.000	13.54	13.54	42.92	4.94
2731	2808	0.530650	GCTCGGATTTGCCAGATCGA	60.531	55.000	0.00	0.00	35.94	3.59
2770	2847	0.179119	CGGCCTAAACCCTAGACACG	60.179	60.000	0.00	0.00	0.00	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.