AutoCloner

Multiple sequence alignment - TraesCS2D01G552300

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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	TraesCS2D01G552300	chr2D	100.000	2588	0	0	1	2588	627627785	627630372	0.000000e+00	4780.0
1	TraesCS2D01G552300	chr2B	90.476	1722	87	40	582	2269	770056556	770054878	0.000000e+00	2200.0
2	TraesCS2D01G552300	chr2B	92.969	128	8	1	2462	2588	770054886	770054759	4.400000e-43	185.0
3	TraesCS2D01G552300	chr2A	90.539	1279	59	27	582	1842	758273695	758272461	0.000000e+00	1635.0
4	TraesCS2D01G552300	chr2A	89.214	751	56	10	1839	2574	758272358	758271618	0.000000e+00	915.0
5	TraesCS2D01G552300	chr2A	90.378	582	52	4	1	581	697391982	697392560	0.000000e+00	761.0
6	TraesCS2D01G552300	chr2A	93.711	159	9	1	2430	2588	758271619	758271462	1.200000e-58	237.0
7	TraesCS2D01G552300	chr1D	93.322	584	35	4	1	582	386914949	386915530	0.000000e+00	859.0
8	TraesCS2D01G552300	chr5D	93.139	583	37	3	1	581	546070582	546071163	0.000000e+00	852.0
9	TraesCS2D01G552300	chr5D	83.571	280	37	7	1266	1545	557006241	557005971	1.190000e-63	254.0
10	TraesCS2D01G552300	chr7D	92.624	583	37	6	1	581	88025141	88024563	0.000000e+00	833.0
11	TraesCS2D01G552300	chrUn	91.767	583	44	4	1	581	211003727	211003147	0.000000e+00	808.0
12	TraesCS2D01G552300	chr6D	91.610	584	44	4	1	582	107935908	107936488	0.000000e+00	802.0
13	TraesCS2D01G552300	chr1B	90.582	584	52	3	1	583	567690976	567690395	0.000000e+00	771.0
14	TraesCS2D01G552300	chr1B	92.188	64	3	2	2166	2227	418674252	418674315	3.550000e-14	89.8
15	TraesCS2D01G552300	chr1B	95.918	49	2	0	2180	2228	677585270	677585222	2.130000e-11	80.5
16	TraesCS2D01G552300	chr7A	90.411	584	48	8	1	581	269274585	269275163	0.000000e+00	761.0
17	TraesCS2D01G552300	chr7A	100.000	31	0	0	2178	2208	706847834	706847804	1.000000e-04	58.4
18	TraesCS2D01G552300	chr3A	90.223	583	54	3	1	581	364193567	364194148	0.000000e+00	758.0
19	TraesCS2D01G552300	chr5B	79.181	562	78	29	991	1542	709561214	709561746	1.140000e-93	353.0

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	TraesCS2D01G552300	chr2D	627627785	627630372	2587	False	4780.0	4780	100.000000	1	2588	1	chr2D.!!$F1	2587
1	TraesCS2D01G552300	chr2B	770054759	770056556	1797	True	1192.5	2200	91.722500	582	2588	2	chr2B.!!$R1	2006
2	TraesCS2D01G552300	chr2A	758271462	758273695	2233	True	929.0	1635	91.154667	582	2588	3	chr2A.!!$R1	2006
3	TraesCS2D01G552300	chr2A	697391982	697392560	578	False	761.0	761	90.378000	1	581	1	chr2A.!!$F1	580
4	TraesCS2D01G552300	chr1D	386914949	386915530	581	False	859.0	859	93.322000	1	582	1	chr1D.!!$F1	581
5	TraesCS2D01G552300	chr5D	546070582	546071163	581	False	852.0	852	93.139000	1	581	1	chr5D.!!$F1	580
6	TraesCS2D01G552300	chr7D	88024563	88025141	578	True	833.0	833	92.624000	1	581	1	chr7D.!!$R1	580
7	TraesCS2D01G552300	chrUn	211003147	211003727	580	True	808.0	808	91.767000	1	581	1	chrUn.!!$R1	580
8	TraesCS2D01G552300	chr6D	107935908	107936488	580	False	802.0	802	91.610000	1	582	1	chr6D.!!$F1	581
9	TraesCS2D01G552300	chr1B	567690395	567690976	581	True	771.0	771	90.582000	1	583	1	chr1B.!!$R1	582
10	TraesCS2D01G552300	chr7A	269274585	269275163	578	False	761.0	761	90.411000	1	581	1	chr7A.!!$F1	580
11	TraesCS2D01G552300	chr3A	364193567	364194148	581	False	758.0	758	90.223000	1	581	1	chr3A.!!$F1	580
12	TraesCS2D01G552300	chr5B	709561214	709561746	532	False	353.0	353	79.181000	991	1542	1	chr5B.!!$F1	551

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
715	722	0.174845	GACGGGTGGATCGAATCACA	59.825	55.0	18.74	1.6	35.74	3.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2458	2770	0.320421	ACGGTGTTTCCACATCTCCG	60.32	55.0	0.0	0.0	42.85	4.63	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
36	37	6.823689	GTGTAGGAACTGACCATCAACAATAT	59.176	38.462	0.00	0.00	41.52	1.28
125	126	7.647715	GTGCAGTGAATTTGTTTTGTATGTAGT	59.352	33.333	0.00	0.00	0.00	2.73
140	141	8.542497	TTGTATGTAGTACTAAAGTTGCCTTG	57.458	34.615	3.61	0.00	34.27	3.61
225	227	4.571984	CCAAAAAGAAAAGTTGCTTCCCTG	59.428	41.667	0.00	0.00	0.00	4.45
257	259	0.762082	TGCCTCCATTGCACCCAAAA	60.762	50.000	0.00	0.00	34.05	2.44
258	260	0.320683	GCCTCCATTGCACCCAAAAC	60.321	55.000	0.00	0.00	34.05	2.43
300	303	9.807649	TTTTGACGAAACCTACTTATATAGGAC	57.192	33.333	5.84	0.00	44.12	3.85
337	340	1.006571	TCGTGAGAAACCTGACGGC	60.007	57.895	4.79	0.00	40.74	5.68
339	342	2.027625	GTGAGAAACCTGACGGCGG	61.028	63.158	13.24	0.00	0.00	6.13
479	485	1.139853	GGGTGTGGCCAAACAATTTCA	59.860	47.619	27.43	6.34	39.65	2.69
591	597	2.726821	AGCCACGTCCATCAATCAAAT	58.273	42.857	0.00	0.00	0.00	2.32
597	603	5.817296	CCACGTCCATCAATCAAATAGAGAA	59.183	40.000	0.00	0.00	0.00	2.87
715	722	0.174845	GACGGGTGGATCGAATCACA	59.825	55.000	18.74	1.60	35.74	3.58
863	871	2.638363	ACTCCCTCCCTATTAATTCGCC	59.362	50.000	0.00	0.00	0.00	5.54
873	881	0.609681	TTAATTCGCCCCCACACCAC	60.610	55.000	0.00	0.00	0.00	4.16
901	909	2.337749	GATCGGACGCGGTCAGTCAT	62.338	60.000	12.47	0.00	40.20	3.06
902	910	2.337749	ATCGGACGCGGTCAGTCATC	62.338	60.000	12.47	0.00	40.20	2.92
905	913	0.669318	GGACGCGGTCAGTCATCAAA	60.669	55.000	12.47	0.00	40.20	2.69
929	937	4.656117	TTTCGCGCACGGAGCTGA	62.656	61.111	8.75	0.00	42.61	4.26
1181	1196	1.226603	GCGACAGCGTCCGTAAGAT	60.227	57.895	0.00	0.00	40.36	2.40
1183	1198	0.924363	CGACAGCGTCCGTAAGATCG	60.924	60.000	3.65	0.00	43.02	3.69
1185	1200	1.002684	GACAGCGTCCGTAAGATCGAT	60.003	52.381	0.00	0.00	43.02	3.59
1201	1216	3.140225	GATCCACTCGACCCGCTCC	62.140	68.421	0.00	0.00	0.00	4.70
1217	1232	0.181114	CTCCTTTGATCCATCCGCCA	59.819	55.000	0.00	0.00	0.00	5.69
1223	1238	0.827507	TGATCCATCCGCCAGATCGA	60.828	55.000	0.00	0.00	39.42	3.59
1236	1254	3.713288	CCAGATCGATACGCCTTTGTTA	58.287	45.455	0.00	0.00	0.00	2.41
1243	1279	3.607641	CGATACGCCTTTGTTAACACGTA	59.392	43.478	23.13	23.13	39.90	3.57
1248	1284	3.607310	CGCCTTTGTTAACACGTAATGCA	60.607	43.478	8.07	0.00	0.00	3.96
1740	1782	2.154462	ACTTGTTGATCGGCTTTCCAG	58.846	47.619	0.00	0.00	0.00	3.86
1902	2057	0.935196	AAGACTCGCCACGTGAAAAC	59.065	50.000	19.30	2.31	0.00	2.43
1914	2069	2.143122	CGTGAAAACCTGCTAGCAGAA	58.857	47.619	40.03	18.21	46.30	3.02
1929	2084	4.098055	AGCAGAATGAGTGTAGTGTACG	57.902	45.455	0.00	0.00	39.69	3.67
1930	2085	3.119459	AGCAGAATGAGTGTAGTGTACGG	60.119	47.826	0.00	0.00	39.69	4.02
1931	2086	3.367087	GCAGAATGAGTGTAGTGTACGGT	60.367	47.826	0.00	0.00	39.69	4.83
1932	2087	4.166523	CAGAATGAGTGTAGTGTACGGTG	58.833	47.826	0.00	0.00	39.69	4.94
1933	2088	3.825014	AGAATGAGTGTAGTGTACGGTGT	59.175	43.478	0.00	0.00	0.00	4.16
1934	2089	5.005740	AGAATGAGTGTAGTGTACGGTGTA	58.994	41.667	0.00	0.00	0.00	2.90
1935	2090	4.691860	ATGAGTGTAGTGTACGGTGTAC	57.308	45.455	0.22	0.22	0.00	2.90
1936	2091	2.813754	TGAGTGTAGTGTACGGTGTACC	59.186	50.000	4.78	0.00	0.00	3.34
1940	2095	2.224744	TGTAGTGTACGGTGTACCTGGA	60.225	50.000	0.00	0.00	0.00	3.86
1941	2096	1.999648	AGTGTACGGTGTACCTGGAA	58.000	50.000	0.00	0.00	0.00	3.53
1947	2102	1.700739	ACGGTGTACCTGGAATGGAAA	59.299	47.619	0.00	0.00	0.00	3.13
1953	2108	4.636206	GTGTACCTGGAATGGAAAGATGTC	59.364	45.833	0.00	0.00	0.00	3.06
1956	2111	3.331889	ACCTGGAATGGAAAGATGTCTGT	59.668	43.478	0.00	0.00	0.00	3.41
1958	2113	5.014123	ACCTGGAATGGAAAGATGTCTGTAA	59.986	40.000	0.00	0.00	0.00	2.41
1970	2125	9.587772	GAAAGATGTCTGTAATACTTTCTGCTA	57.412	33.333	0.00	0.00	39.60	3.49
2001	2156	3.631145	TTGCTAGTGCTTTTCTGCTTG	57.369	42.857	0.00	0.00	40.48	4.01
2046	2201	5.807011	CAGATCGTTGTACATTCAGTGATCA	59.193	40.000	0.00	0.00	34.88	2.92
2059	2214	3.118629	TCAGTGATCACCAATCTAGCACC	60.119	47.826	22.21	0.00	35.24	5.01
2114	2269	2.716217	CCTCAACCTTTGTCTGGGATC	58.284	52.381	0.00	0.00	0.00	3.36
2198	2366	5.071788	AGGAAAGAGTCAATTACACCACTGA	59.928	40.000	0.00	0.00	0.00	3.41
2217	2385	4.814234	ACTGATGCTAAAACTTGACGTGAA	59.186	37.500	0.00	0.00	0.00	3.18
2274	2442	3.482786	GCATCTAAGTTTGTTGTCTGCG	58.517	45.455	0.00	0.00	0.00	5.18
2276	2444	4.667668	GCATCTAAGTTTGTTGTCTGCGAG	60.668	45.833	0.00	0.00	0.00	5.03
2287	2455	1.032657	GTCTGCGAGACTGCTCCCTA	61.033	60.000	8.50	0.00	41.88	3.53
2302	2470	3.494398	GCTCCCTATGCCGATTTTGTCTA	60.494	47.826	0.00	0.00	0.00	2.59
2311	2479	3.188460	GCCGATTTTGTCTAGAAGCACAA	59.812	43.478	0.00	0.00	0.00	3.33
2313	2481	4.142816	CCGATTTTGTCTAGAAGCACAAGG	60.143	45.833	0.00	0.00	34.07	3.61
2359	2527	5.011090	TCTTGGTTAGTGATGAGGAATCG	57.989	43.478	0.00	0.00	38.22	3.34
2377	2547	3.380479	TCGTTGTTGGACCTCTAACAG	57.620	47.619	4.64	0.00	45.66	3.16
2379	2549	3.057734	CGTTGTTGGACCTCTAACAGAC	58.942	50.000	4.64	5.87	45.66	3.51
2437	2607	4.464069	ACTTGTAGAGAGACATCAAGGC	57.536	45.455	0.00	0.00	39.49	4.35
2438	2608	3.834813	ACTTGTAGAGAGACATCAAGGCA	59.165	43.478	0.00	0.00	39.49	4.75
2441	2611	5.426689	TGTAGAGAGACATCAAGGCAATT	57.573	39.130	0.00	0.00	0.00	2.32
2458	2770	3.398406	CAATTGTTGCCCTTGGTTTACC	58.602	45.455	0.00	0.00	0.00	2.85
2494	2806	3.249799	CACCGTAATGCAGTTGTCTTCAA	59.750	43.478	0.00	0.00	0.00	2.69
2555	2867	1.691196	TGCAGGAAGGAAACACTTGG	58.309	50.000	0.00	0.00	0.00	3.61

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
36	37	3.310501	CGTATCATGACTGCTCAATTGCA	59.689	43.478	0.00	0.00	41.05	4.08
73	74	8.109705	TGTGTGTATCTGTGAATTTTGCTAAT	57.890	30.769	0.00	0.00	0.00	1.73
140	141	9.824534	AAAAATGAGAAAAATCACACAAAACAC	57.175	25.926	0.00	0.00	30.46	3.32
300	303	4.148348	CACGACGAGTTCTTCAAAACTAGG	59.852	45.833	0.00	0.00	39.55	3.02
337	340	4.073169	TCGAAATTCAATTCCGTTTCCG	57.927	40.909	0.00	0.00	0.00	4.30
339	342	7.960738	TCAAGTATCGAAATTCAATTCCGTTTC	59.039	33.333	0.00	0.00	0.00	2.78
394	397	3.677596	CCACGTGCATTTATTTTGGGTTC	59.322	43.478	10.91	0.00	0.00	3.62
658	665	4.999939	GCCTTGGTTTGCGTGGCG	63.000	66.667	0.00	0.00	33.96	5.69
694	701	1.299926	GATTCGATCCACCCGTCGG	60.300	63.158	3.60	3.60	38.34	4.79
901	909	2.548295	GCGCGAAACTGGGGTTTGA	61.548	57.895	12.10	0.00	44.58	2.69
902	910	2.050442	GCGCGAAACTGGGGTTTG	60.050	61.111	12.10	0.00	44.58	2.93
969	978	4.364409	GGACGACAACAACGCGGC	62.364	66.667	12.47	0.00	0.00	6.53
1183	1198	2.413765	GAGCGGGTCGAGTGGATC	59.586	66.667	0.00	0.00	0.00	3.36
1185	1200	3.881019	AAGGAGCGGGTCGAGTGGA	62.881	63.158	0.53	0.00	0.00	4.02
1201	1216	2.149578	GATCTGGCGGATGGATCAAAG	58.850	52.381	14.83	0.00	36.73	2.77
1217	1232	4.565564	GTGTTAACAAAGGCGTATCGATCT	59.434	41.667	10.51	0.00	0.00	2.75
1223	1238	5.671825	GCATTACGTGTTAACAAAGGCGTAT	60.672	40.000	22.15	13.52	35.30	3.06
1236	1254	3.342719	TCCATCACATGCATTACGTGTT	58.657	40.909	13.54	4.88	46.67	3.32
1243	1279	2.359848	CGACCAATCCATCACATGCATT	59.640	45.455	0.00	0.00	0.00	3.56
1248	1284	4.963318	ATCTACGACCAATCCATCACAT	57.037	40.909	0.00	0.00	0.00	3.21
1740	1782	2.507407	TTTAGGGGAACATGGAGTGC	57.493	50.000	0.00	0.00	0.00	4.40
1743	1792	3.054065	AGAGCTTTTAGGGGAACATGGAG	60.054	47.826	0.00	0.00	0.00	3.86
1849	2004	3.869065	TCGTTCCCATGTTAGGATGAAC	58.131	45.455	0.00	0.00	32.10	3.18
1902	2057	2.687700	ACACTCATTCTGCTAGCAGG	57.312	50.000	37.60	25.65	43.75	4.85
1914	2069	3.441572	GGTACACCGTACACTACACTCAT	59.558	47.826	6.62	0.00	0.00	2.90
1929	2084	3.713826	TCTTTCCATTCCAGGTACACC	57.286	47.619	0.00	0.00	0.00	4.16
1930	2085	4.589908	ACATCTTTCCATTCCAGGTACAC	58.410	43.478	0.00	0.00	0.00	2.90
1931	2086	4.536090	AGACATCTTTCCATTCCAGGTACA	59.464	41.667	0.00	0.00	0.00	2.90
1932	2087	4.878397	CAGACATCTTTCCATTCCAGGTAC	59.122	45.833	0.00	0.00	0.00	3.34
1933	2088	4.536090	ACAGACATCTTTCCATTCCAGGTA	59.464	41.667	0.00	0.00	0.00	3.08
1934	2089	3.331889	ACAGACATCTTTCCATTCCAGGT	59.668	43.478	0.00	0.00	0.00	4.00
1935	2090	3.960571	ACAGACATCTTTCCATTCCAGG	58.039	45.455	0.00	0.00	0.00	4.45
1936	2091	7.989741	AGTATTACAGACATCTTTCCATTCCAG	59.010	37.037	0.00	0.00	0.00	3.86
1940	2095	9.965902	AGAAAGTATTACAGACATCTTTCCATT	57.034	29.630	10.46	0.00	40.51	3.16
1941	2096	9.388506	CAGAAAGTATTACAGACATCTTTCCAT	57.611	33.333	10.46	0.00	40.51	3.41
1953	2108	8.993121	CAACCCATATAGCAGAAAGTATTACAG	58.007	37.037	0.00	0.00	0.00	2.74
1958	2113	7.175641	GCAATCAACCCATATAGCAGAAAGTAT	59.824	37.037	0.00	0.00	0.00	2.12
1970	2125	4.443978	AGCACTAGCAATCAACCCATAT	57.556	40.909	0.00	0.00	45.49	1.78
2001	2156	7.985634	TCTGCTTGTTTTGTTTAATGACTTC	57.014	32.000	0.00	0.00	0.00	3.01
2046	2201	0.907704	TGGTCGGGTGCTAGATTGGT	60.908	55.000	0.00	0.00	0.00	3.67
2198	2366	7.167468	GTGATTTTTCACGTCAAGTTTTAGCAT	59.833	33.333	0.00	0.00	0.00	3.79
2274	2442	1.109920	TCGGCATAGGGAGCAGTCTC	61.110	60.000	0.00	0.00	38.62	3.36
2276	2444	0.394565	AATCGGCATAGGGAGCAGTC	59.605	55.000	0.00	0.00	0.00	3.51
2287	2455	3.375299	GTGCTTCTAGACAAAATCGGCAT	59.625	43.478	0.00	0.00	0.00	4.40
2302	2470	0.536006	GAGTGGTGCCTTGTGCTTCT	60.536	55.000	0.00	0.00	42.00	2.85
2321	2489	0.321122	AAGAGAAGAAGCGGCACTGG	60.321	55.000	1.45	0.00	0.00	4.00
2329	2497	5.482908	TCATCACTAACCAAGAGAAGAAGC	58.517	41.667	0.00	0.00	0.00	3.86
2359	2527	4.338379	AGTCTGTTAGAGGTCCAACAAC	57.662	45.455	0.00	0.00	34.43	3.32
2377	2547	4.149598	AGGTGTTTCCCATAAACCAAGTC	58.850	43.478	0.00	0.00	36.75	3.01
2379	2549	4.586841	TCAAGGTGTTTCCCATAAACCAAG	59.413	41.667	0.00	0.00	36.75	3.61
2437	2607	3.398406	GGTAAACCAAGGGCAACAATTG	58.602	45.455	3.24	3.24	34.89	2.32
2438	2608	2.036604	CGGTAAACCAAGGGCAACAATT	59.963	45.455	0.00	0.00	34.48	2.32
2441	2611	0.824182	CCGGTAAACCAAGGGCAACA	60.824	55.000	0.00	0.00	34.48	3.33
2458	2770	0.320421	ACGGTGTTTCCACATCTCCG	60.320	55.000	0.00	0.00	42.85	4.63
2483	2795	2.290960	GGTAGCCCCATTGAAGACAACT	60.291	50.000	0.00	0.00	38.90	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.