AutoCloner

Multiple sequence alignment - TraesCS2D01G549700

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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	TraesCS2D01G549700	chr2D	100.000	2860	0	0	1	2860	625148120	625150979	0.000000e+00	5282.0
1	TraesCS2D01G549700	chr2D	86.653	1491	162	19	1	1463	635807963	635806482	0.000000e+00	1616.0
2	TraesCS2D01G549700	chr2D	83.183	1112	136	20	3	1084	636048302	636049392	0.000000e+00	970.0
3	TraesCS2D01G549700	chr2D	79.191	519	62	20	1473	1955	635901575	635901067	4.600000e-83	318.0
4	TraesCS2D01G549700	chr2D	88.060	268	30	2	1152	1418	635840941	635840675	1.650000e-82	316.0
5	TraesCS2D01G549700	chr2D	83.065	248	42	0	1506	1753	635806481	635806234	2.870000e-55	226.0
6	TraesCS2D01G549700	chr2D	82.353	187	31	2	1097	1282	636049450	636049635	8.200000e-36	161.0
7	TraesCS2D01G549700	chr2D	93.878	49	3	0	2259	2307	369542156	369542204	1.100000e-09	75.0
8	TraesCS2D01G549700	chr2B	95.263	2913	63	19	1	2860	767373276	767376166	0.000000e+00	4545.0
9	TraesCS2D01G549700	chr2B	86.002	893	97	13	475	1344	793920173	793919286	0.000000e+00	931.0
10	TraesCS2D01G549700	chr2B	86.536	817	87	9	1	810	793981182	793981982	0.000000e+00	878.0
11	TraesCS2D01G549700	chr2B	85.682	440	61	2	1	439	793920984	793920546	2.010000e-126	462.0
12	TraesCS2D01G549700	chr2B	84.586	266	12	12	2017	2259	793916437	793916178	1.320000e-58	237.0
13	TraesCS2D01G549700	chr2B	87.437	199	19	2	2445	2643	793915883	793915691	1.030000e-54	224.0
14	TraesCS2D01G549700	chr2B	78.788	264	42	7	863	1119	793981999	793982255	6.340000e-37	165.0
15	TraesCS2D01G549700	chrUn	83.700	1816	234	30	1	1769	124674177	124675977	0.000000e+00	1657.0
16	TraesCS2D01G549700	chrUn	82.582	488	76	7	1263	1744	124806281	124806765	3.410000e-114	422.0
17	TraesCS2D01G549700	chrUn	83.578	341	34	11	1477	1811	124712976	124713300	1.670000e-77	300.0
18	TraesCS2D01G549700	chr5D	72.540	437	90	23	1170	1583	552736478	552736907	6.480000e-22	115.0
19	TraesCS2D01G549700	chr5D	94.118	51	1	2	2249	2299	230412052	230412100	3.060000e-10	76.8
20	TraesCS2D01G549700	chr1B	69.340	1122	271	47	667	1744	169940	168848	6.520000e-17	99.0
21	TraesCS2D01G549700	chr5B	92.857	56	1	3	2250	2303	78959543	78959597	8.500000e-11	78.7
22	TraesCS2D01G549700	chr4D	89.062	64	5	2	2242	2304	34674711	34674649	8.500000e-11	78.7
23	TraesCS2D01G549700	chr3B	95.918	49	0	2	2250	2298	695558952	695558906	8.500000e-11	78.7
24	TraesCS2D01G549700	chr3B	91.228	57	2	3	2243	2297	39358921	39358866	1.100000e-09	75.0
25	TraesCS2D01G549700	chr1D	95.918	49	1	1	2251	2299	420554587	420554540	8.500000e-11	78.7
26	TraesCS2D01G549700	chr7B	92.453	53	3	1	2255	2307	245505329	245505278	1.100000e-09	75.0
27	TraesCS2D01G549700	chr1A	89.474	57	4	2	2242	2297	380965052	380965107	1.420000e-08	71.3

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	TraesCS2D01G549700	chr2D	625148120	625150979	2859	False	5282.0	5282	100.00000	1	2860	1	chr2D.!!$F2	2859
1	TraesCS2D01G549700	chr2D	635806234	635807963	1729	True	921.0	1616	84.85900	1	1753	2	chr2D.!!$R3	1752
2	TraesCS2D01G549700	chr2D	636048302	636049635	1333	False	565.5	970	82.76800	3	1282	2	chr2D.!!$F3	1279
3	TraesCS2D01G549700	chr2D	635901067	635901575	508	True	318.0	318	79.19100	1473	1955	1	chr2D.!!$R2	482
4	TraesCS2D01G549700	chr2B	767373276	767376166	2890	False	4545.0	4545	95.26300	1	2860	1	chr2B.!!$F1	2859
5	TraesCS2D01G549700	chr2B	793981182	793982255	1073	False	521.5	878	82.66200	1	1119	2	chr2B.!!$F2	1118
6	TraesCS2D01G549700	chr2B	793915691	793920984	5293	True	463.5	931	85.92675	1	2643	4	chr2B.!!$R1	2642
7	TraesCS2D01G549700	chrUn	124674177	124675977	1800	False	1657.0	1657	83.70000	1	1769	1	chrUn.!!$F1	1768

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
615	968	1.078143	CAGGGGCAGTAGCTGGAAC	60.078	63.158	0.0	0.0	41.7	3.62	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2280	4990	0.178926	TTGTACTCCCTCCGTCCCAA	60.179	55.0	0.0	0.0	0.0	4.12	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
478	816	2.514824	GGGGCGGATGCTGAAGAC	60.515	66.667	0.00	0.00	42.25	3.01
615	968	1.078143	CAGGGGCAGTAGCTGGAAC	60.078	63.158	0.00	0.00	41.70	3.62
778	1152	6.894735	TTTATAGTGTTGGAGGGGATACAA	57.105	37.500	0.00	0.00	39.74	2.41
822	1196	4.093011	AGAACATACTCAAGAGTCTGCCT	58.907	43.478	13.52	9.28	42.54	4.75
997	1386	4.625607	AGCAGTCTAAACCAGCTTTACT	57.374	40.909	0.00	0.00	34.64	2.24
1076	1471	4.273235	TCTTATCAACTTGCGGCATGTATG	59.727	41.667	20.04	18.26	0.00	2.39
1294	1737	0.110644	CAAGAAACGGCTCGCAGAAC	60.111	55.000	0.00	0.00	34.09	3.01
1295	1738	0.249911	AAGAAACGGCTCGCAGAACT	60.250	50.000	0.00	0.00	34.09	3.01
1296	1739	0.601558	AGAAACGGCTCGCAGAACTA	59.398	50.000	0.00	0.00	34.09	2.24
1297	1740	1.000506	AGAAACGGCTCGCAGAACTAA	59.999	47.619	0.00	0.00	34.09	2.24
1298	1741	1.126296	GAAACGGCTCGCAGAACTAAC	59.874	52.381	0.00	0.00	34.09	2.34
1299	1742	0.032952	AACGGCTCGCAGAACTAACA	59.967	50.000	0.00	0.00	34.09	2.41
1470	1919	2.564771	CTGCAACAACTTGGTCTCTCA	58.435	47.619	0.00	0.00	0.00	3.27
1998	2702	6.627087	TCATAATCTATTCCTGGGTGGATC	57.373	41.667	0.00	0.00	45.68	3.36
2050	4733	4.199310	GCCAGTCTGCAATATTGTAAGGA	58.801	43.478	16.61	4.55	0.00	3.36
2051	4734	4.640201	GCCAGTCTGCAATATTGTAAGGAA	59.360	41.667	16.61	0.00	0.00	3.36
2052	4735	5.125417	GCCAGTCTGCAATATTGTAAGGAAA	59.875	40.000	16.61	0.00	0.00	3.13
2053	4736	6.678900	GCCAGTCTGCAATATTGTAAGGAAAG	60.679	42.308	16.61	0.15	0.00	2.62
2054	4737	6.183360	CCAGTCTGCAATATTGTAAGGAAAGG	60.183	42.308	16.61	8.29	0.00	3.11
2062	4745	8.560374	GCAATATTGTAAGGAAAGGAGTACATC	58.440	37.037	16.61	0.00	0.00	3.06
2119	4810	4.024387	TGCACTTCCGTTTCTGTATTTCAC	60.024	41.667	0.00	0.00	0.00	3.18
2269	4979	9.826574	TCAAAGAAAACTTACTACTAAGCTTGA	57.173	29.630	9.86	0.00	33.72	3.02
2274	4984	8.590719	AAAACTTACTACTAAGCTTGAGACAC	57.409	34.615	9.86	0.00	33.72	3.67
2275	4985	7.527568	AACTTACTACTAAGCTTGAGACACT	57.472	36.000	9.86	0.00	33.72	3.55
2277	4987	8.632906	ACTTACTACTAAGCTTGAGACACTTA	57.367	34.615	9.86	0.00	33.72	2.24
2278	4988	9.245481	ACTTACTACTAAGCTTGAGACACTTAT	57.755	33.333	9.86	0.00	33.72	1.73
2283	4993	7.440523	ACTAAGCTTGAGACACTTATTTTGG	57.559	36.000	9.86	0.00	0.00	3.28
2286	4996	4.762251	AGCTTGAGACACTTATTTTGGGAC	59.238	41.667	0.00	0.00	0.00	4.46
2287	4997	4.378459	GCTTGAGACACTTATTTTGGGACG	60.378	45.833	0.00	0.00	0.00	4.79
2288	4998	3.670625	TGAGACACTTATTTTGGGACGG	58.329	45.455	0.00	0.00	0.00	4.79
2289	4999	3.325425	TGAGACACTTATTTTGGGACGGA	59.675	43.478	0.00	0.00	0.00	4.69
2518	5351	3.609853	TGTAGGTCATGTCATCTTTGCC	58.390	45.455	0.00	0.00	0.00	4.52
2651	5484	5.934625	AGTGAAGTAAGAAGTGCAATAGTGG	59.065	40.000	0.00	0.00	0.00	4.00
2688	5521	9.741647	GAAGATAAATTGATGGGACTGAAAATC	57.258	33.333	0.00	0.00	0.00	2.17
2738	5571	5.155278	TGGTGAAGTGATACGGTATTTGT	57.845	39.130	1.57	0.00	0.00	2.83
2764	5597	1.276421	CAAGGGTGAGATTCCGACAGT	59.724	52.381	0.00	0.00	0.00	3.55
2796	5629	4.035102	GGGGGCGCCAAAGAGAGT	62.035	66.667	30.85	0.00	0.00	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
215	216	2.028112	CACCCACTGTTCTAGCTGCTAA	60.028	50.000	11.02	0.00	0.00	3.09
478	816	6.935741	TCATTAAATATTCCCAGACCAACG	57.064	37.500	0.00	0.00	0.00	4.10
778	1152	7.009179	TCTTGATGACTATTTCCTCAACTGT	57.991	36.000	0.00	0.00	34.84	3.55
822	1196	3.899052	ATTGCTAGTACCCGCAGTTTA	57.101	42.857	6.75	0.00	37.46	2.01
997	1386	5.355071	CACCAAAATCTAGCAGTTGCATCTA	59.645	40.000	6.90	0.00	45.16	1.98
1076	1471	3.512516	GCAATCCAGGACCGCTGC	61.513	66.667	4.87	2.44	0.00	5.25
1288	1731	5.005779	CACCGAATGATAGTGTTAGTTCTGC	59.994	44.000	0.00	0.00	0.00	4.26
1294	1737	5.661458	ACTTCCACCGAATGATAGTGTTAG	58.339	41.667	0.00	0.00	0.00	2.34
1295	1738	5.670792	ACTTCCACCGAATGATAGTGTTA	57.329	39.130	0.00	0.00	0.00	2.41
1296	1739	4.553330	ACTTCCACCGAATGATAGTGTT	57.447	40.909	0.00	0.00	0.00	3.32
1297	1740	4.020573	TGAACTTCCACCGAATGATAGTGT	60.021	41.667	0.00	0.00	0.00	3.55
1298	1741	4.503910	TGAACTTCCACCGAATGATAGTG	58.496	43.478	0.00	0.00	0.00	2.74
1299	1742	4.466370	TCTGAACTTCCACCGAATGATAGT	59.534	41.667	0.00	0.00	0.00	2.12
1439	1888	1.002033	GTTGTTGCAGCTTCTCTGGTG	60.002	52.381	1.17	0.00	43.06	4.17
1470	1919	3.095163	CCTGGCTGGCTCCATCCT	61.095	66.667	9.87	0.00	35.22	3.24
1998	2702	5.363939	AGGTTTTCAGACTCACAAGAGAAG	58.636	41.667	0.00	0.00	44.98	2.85
2050	4733	7.416890	GCACTGACACTATAGATGTACTCCTTT	60.417	40.741	6.78	0.00	0.00	3.11
2051	4734	6.039941	GCACTGACACTATAGATGTACTCCTT	59.960	42.308	6.78	0.00	0.00	3.36
2052	4735	5.533154	GCACTGACACTATAGATGTACTCCT	59.467	44.000	6.78	0.00	0.00	3.69
2053	4736	5.299531	TGCACTGACACTATAGATGTACTCC	59.700	44.000	6.78	0.00	0.00	3.85
2054	4737	6.378710	TGCACTGACACTATAGATGTACTC	57.621	41.667	6.78	0.00	0.00	2.59
2062	4745	7.652727	ACACTGTATATGCACTGACACTATAG	58.347	38.462	7.29	0.00	0.00	1.31
2119	4810	8.128582	ACATGCACTGTTTAATCAATAATACGG	58.871	33.333	0.00	0.00	32.90	4.02
2262	4972	5.241728	GTCCCAAAATAAGTGTCTCAAGCTT	59.758	40.000	0.00	0.00	0.00	3.74
2263	4973	4.762251	GTCCCAAAATAAGTGTCTCAAGCT	59.238	41.667	0.00	0.00	0.00	3.74
2269	4979	3.307480	CCTCCGTCCCAAAATAAGTGTCT	60.307	47.826	0.00	0.00	0.00	3.41
2270	4980	3.007635	CCTCCGTCCCAAAATAAGTGTC	58.992	50.000	0.00	0.00	0.00	3.67
2274	4984	2.238898	ACTCCCTCCGTCCCAAAATAAG	59.761	50.000	0.00	0.00	0.00	1.73
2275	4985	2.271777	ACTCCCTCCGTCCCAAAATAA	58.728	47.619	0.00	0.00	0.00	1.40
2277	4987	1.558294	GTACTCCCTCCGTCCCAAAAT	59.442	52.381	0.00	0.00	0.00	1.82
2278	4988	0.978907	GTACTCCCTCCGTCCCAAAA	59.021	55.000	0.00	0.00	0.00	2.44
2280	4990	0.178926	TTGTACTCCCTCCGTCCCAA	60.179	55.000	0.00	0.00	0.00	4.12
2283	4993	1.777941	AGATTGTACTCCCTCCGTCC	58.222	55.000	0.00	0.00	0.00	4.79
2286	4996	2.101582	CCTCAAGATTGTACTCCCTCCG	59.898	54.545	0.00	0.00	0.00	4.63
2287	4997	2.436173	CCCTCAAGATTGTACTCCCTCC	59.564	54.545	0.00	0.00	0.00	4.30
2288	4998	2.158885	GCCCTCAAGATTGTACTCCCTC	60.159	54.545	0.00	0.00	0.00	4.30
2289	4999	1.840635	GCCCTCAAGATTGTACTCCCT	59.159	52.381	0.00	0.00	0.00	4.20
2651	5484	6.844696	TCAATTTATCTTCTGATGCCGTAC	57.155	37.500	0.00	0.00	34.32	3.67
2688	5521	7.831753	AGATTAGTGTTGTCCTGATATATCGG	58.168	38.462	13.82	13.82	0.00	4.18
2738	5571	4.758165	GTCGGAATCTCACCCTTGTTTTTA	59.242	41.667	0.00	0.00	0.00	1.52
2782	5615	1.578206	GAACCACTCTCTTTGGCGCC	61.578	60.000	22.73	22.73	37.69	6.53
2783	5616	0.884704	TGAACCACTCTCTTTGGCGC	60.885	55.000	0.00	0.00	37.69	6.53
2784	5617	1.734465	GATGAACCACTCTCTTTGGCG	59.266	52.381	0.00	0.00	37.69	5.69
2785	5618	1.734465	CGATGAACCACTCTCTTTGGC	59.266	52.381	0.00	0.00	37.69	4.52
2786	5619	2.738846	CACGATGAACCACTCTCTTTGG	59.261	50.000	0.00	0.00	40.32	3.28
2787	5620	3.185188	CACACGATGAACCACTCTCTTTG	59.815	47.826	0.00	0.00	0.00	2.77
2788	5621	3.393800	CACACGATGAACCACTCTCTTT	58.606	45.455	0.00	0.00	0.00	2.52
2789	5622	2.868044	GCACACGATGAACCACTCTCTT	60.868	50.000	0.00	0.00	0.00	2.85
2790	5623	1.337260	GCACACGATGAACCACTCTCT	60.337	52.381	0.00	0.00	0.00	3.10
2791	5624	1.071605	GCACACGATGAACCACTCTC	58.928	55.000	0.00	0.00	0.00	3.20
2792	5625	0.392706	TGCACACGATGAACCACTCT	59.607	50.000	0.00	0.00	0.00	3.24
2793	5626	1.195448	CTTGCACACGATGAACCACTC	59.805	52.381	0.00	0.00	0.00	3.51
2794	5627	1.229428	CTTGCACACGATGAACCACT	58.771	50.000	0.00	0.00	0.00	4.00
2795	5628	0.944386	ACTTGCACACGATGAACCAC	59.056	50.000	0.00	0.00	0.00	4.16
2796	5629	0.943673	CACTTGCACACGATGAACCA	59.056	50.000	0.00	0.00	0.00	3.67

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.