AutoCloner

Multiple sequence alignment - TraesCS2D01G182700

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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	TraesCS2D01G182700	chr2D	100.000	4304	0	0	1	4304	127005159	127000856	0.000000e+00	7949.0
1	TraesCS2D01G182700	chr2D	90.141	1491	133	11	2817	4304	126999119	127000598	0.000000e+00	1927.0
2	TraesCS2D01G182700	chr2A	93.794	2433	102	25	1788	4188	133705998	133703583	0.000000e+00	3611.0
3	TraesCS2D01G182700	chr2A	96.636	1754	42	9	1	1738	133707758	133706006	0.000000e+00	2896.0
4	TraesCS2D01G182700	chr2A	85.921	831	85	12	3302	4121	133702774	133703583	0.000000e+00	857.0
5	TraesCS2D01G182700	chr2A	89.528	487	51	0	2817	3303	133702184	133702670	6.110000e-173	617.0
6	TraesCS2D01G182700	chr2B	93.608	2159	98	21	6	2137	180620267	180618122	0.000000e+00	3186.0
7	TraesCS2D01G182700	chr2B	93.028	1592	87	9	2734	4304	180617256	180615668	0.000000e+00	2303.0
8	TraesCS2D01G182700	chr2B	97.522	565	13	1	2152	2716	61125056	61125619	0.000000e+00	965.0
9	TraesCS2D01G182700	chr2B	96.957	493	10	1	2136	2628	180617961	180617474	0.000000e+00	822.0
10	TraesCS2D01G182700	chr2B	89.106	615	64	3	3026	3640	180613993	180614604	0.000000e+00	761.0
11	TraesCS2D01G182700	chr2B	88.518	479	44	4	3650	4127	180614704	180615172	1.740000e-158	569.0
12	TraesCS2D01G182700	chr2B	95.210	167	8	0	2275	2441	61922338	61922504	9.180000e-67	265.0
13	TraesCS2D01G182700	chr2B	98.969	97	1	0	2633	2729	180617412	180617316	1.590000e-39	174.0
14	TraesCS2D01G182700	chr2B	86.538	104	12	2	3873	3975	8282938	8283040	3.520000e-21	113.0
15	TraesCS2D01G182700	chr5A	84.772	637	78	18	850	1477	110674686	110674060	4.730000e-174	621.0
16	TraesCS2D01G182700	chr5A	81.503	346	53	11	3965	4304	11113630	11113970	1.520000e-69	274.0
17	TraesCS2D01G182700	chr5D	84.202	633	83	16	854	1477	107789945	107789321	2.210000e-167	599.0
18	TraesCS2D01G182700	chr5D	87.000	100	11	2	3877	3975	332500272	332500174	1.270000e-20	111.0
19	TraesCS2D01G182700	chr5B	82.965	634	89	17	854	1477	117909077	117908453	4.860000e-154	555.0
20	TraesCS2D01G182700	chr5B	81.214	346	54	11	3965	4304	13459737	13460077	7.090000e-68	268.0
21	TraesCS2D01G182700	chr1A	83.369	469	65	11	850	1312	44978626	44979087	5.150000e-114	422.0
22	TraesCS2D01G182700	chr1A	86.000	100	12	2	3877	3975	73129864	73129962	5.890000e-19	106.0
23	TraesCS2D01G182700	chr6D	82.991	341	50	8	3968	4302	309715976	309716314	6.990000e-78	302.0
24	TraesCS2D01G182700	chr6D	90.840	131	12	0	1347	1477	438550617	438550487	4.420000e-40	176.0
25	TraesCS2D01G182700	chr6D	88.889	99	10	1	3877	3975	323001493	323001590	2.100000e-23	121.0
26	TraesCS2D01G182700	chr6B	82.175	331	48	11	3968	4291	477618079	477618405	1.520000e-69	274.0
27	TraesCS2D01G182700	chr6B	88.000	75	8	1	1123	1197	197771523	197771450	2.130000e-13	87.9
28	TraesCS2D01G182700	chr1B	95.210	167	8	0	2275	2441	96875202	96875368	9.180000e-67	265.0
29	TraesCS2D01G182700	chr3A	80.523	344	60	7	3965	4304	120343709	120344049	1.540000e-64	257.0
30	TraesCS2D01G182700	chr7B	94.012	167	10	0	2275	2441	76935691	76935857	1.990000e-63	254.0
31	TraesCS2D01G182700	chrUn	90.000	100	8	2	3877	3975	96558717	96558619	1.260000e-25	128.0

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	TraesCS2D01G182700	chr2D	127000856	127005159	4303	True	7949.00	7949	100.0000	1	4304	1	chr2D.!!$R1	4303
1	TraesCS2D01G182700	chr2D	126999119	127000598	1479	False	1927.00	1927	90.1410	2817	4304	1	chr2D.!!$F1	1487
2	TraesCS2D01G182700	chr2A	133703583	133707758	4175	True	3253.50	3611	95.2150	1	4188	2	chr2A.!!$R1	4187
3	TraesCS2D01G182700	chr2A	133702184	133703583	1399	False	737.00	857	87.7245	2817	4121	2	chr2A.!!$F1	1304
4	TraesCS2D01G182700	chr2B	180615668	180620267	4599	True	1621.25	3186	95.6405	6	4304	4	chr2B.!!$R1	4298
5	TraesCS2D01G182700	chr2B	61125056	61125619	563	False	965.00	965	97.5220	2152	2716	1	chr2B.!!$F2	564
6	TraesCS2D01G182700	chr2B	180613993	180615172	1179	False	665.00	761	88.8120	3026	4127	2	chr2B.!!$F4	1101
7	TraesCS2D01G182700	chr5A	110674060	110674686	626	True	621.00	621	84.7720	850	1477	1	chr5A.!!$R1	627
8	TraesCS2D01G182700	chr5D	107789321	107789945	624	True	599.00	599	84.2020	854	1477	1	chr5D.!!$R1	623
9	TraesCS2D01G182700	chr5B	117908453	117909077	624	True	555.00	555	82.9650	854	1477	1	chr5B.!!$R1	623

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
910	912	2.826128	ACGAGTTGGATCACTTCTGCTA	59.174	45.455	0.0	0.0	0.0	3.49	F
1706	1734	1.777272	AGGGAAAAGAGCTGAAGTGGT	59.223	47.619	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1776	1806	2.099405	ACAGTGGACAAAAACAGTGGG	58.901	47.619	0.0	0.0	41.24	4.61	R
3307	3741	1.933247	ATCTACGCTTTGCTCTCAGC	58.067	50.000	0.0	0.0	42.82	4.26	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
347	349	2.996621	CAGTTTCCTCGATTGTCACTCC	59.003	50.000	0.00	0.00	0.00	3.85
558	560	4.829872	TCCCAGTTAATAAGGAAAGCGA	57.170	40.909	0.00	0.00	0.00	4.93
910	912	2.826128	ACGAGTTGGATCACTTCTGCTA	59.174	45.455	0.00	0.00	0.00	3.49
917	919	3.295973	GGATCACTTCTGCTAGACCTCT	58.704	50.000	0.00	0.00	0.00	3.69
938	944	9.920946	ACCTCTTTGTTGATAATATATTGGTGT	57.079	29.630	8.28	0.00	0.00	4.16
1039	1046	2.223665	GCCTCATATGAGCCAAAACTGC	60.224	50.000	24.81	16.51	40.75	4.40
1078	1086	7.012799	GGATTTTTGGGAGTTCAGATGAGATAC	59.987	40.741	0.00	0.00	0.00	2.24
1080	1088	5.604758	TTGGGAGTTCAGATGAGATACTG	57.395	43.478	0.00	0.00	35.72	2.74
1464	1478	5.390991	GGACTTTAGGAGAAATTTCGCAGTG	60.391	44.000	21.24	9.99	0.00	3.66
1515	1529	6.688813	GGATATTTGTTGCTCGAGTTTCATTC	59.311	38.462	15.13	0.00	0.00	2.67
1522	1536	6.871492	TGTTGCTCGAGTTTCATTCTACATTA	59.129	34.615	15.13	0.00	0.00	1.90
1529	1543	9.031360	TCGAGTTTCATTCTACATTATGCTTAC	57.969	33.333	0.00	0.00	0.00	2.34
1570	1584	5.565455	TGCATGAGGTCCATCATACATAA	57.435	39.130	0.00	0.00	37.84	1.90
1604	1618	8.893219	TTCAGTATATCAAGTCAAATAGCCAG	57.107	34.615	0.00	0.00	0.00	4.85
1648	1676	8.229253	GGTTTTCCTTTTCCTTTTCTGTACTA	57.771	34.615	0.00	0.00	36.94	1.82
1649	1677	8.857098	GGTTTTCCTTTTCCTTTTCTGTACTAT	58.143	33.333	0.00	0.00	36.94	2.12
1706	1734	1.777272	AGGGAAAAGAGCTGAAGTGGT	59.223	47.619	0.00	0.00	0.00	4.16
1707	1735	2.979678	AGGGAAAAGAGCTGAAGTGGTA	59.020	45.455	0.00	0.00	0.00	3.25
1708	1736	3.589288	AGGGAAAAGAGCTGAAGTGGTAT	59.411	43.478	0.00	0.00	0.00	2.73
1716	1746	6.319141	AGAGCTGAAGTGGTATTTTGAAAC	57.681	37.500	0.00	0.00	0.00	2.78
1748	1778	7.710044	CACTGTAGATATCTCAAATCAAGTGCT	59.290	37.037	8.95	0.00	31.15	4.40
1754	1784	9.381033	AGATATCTCAAATCAAGTGCTATATGC	57.619	33.333	0.00	0.00	43.25	3.14
1776	1806	5.009911	TGCAATGGAGTATCATTATTGGTGC	59.990	40.000	0.00	0.00	35.78	5.01
1785	1815	3.505386	TCATTATTGGTGCCCACTGTTT	58.495	40.909	0.00	0.00	30.78	2.83
1786	1816	3.900601	TCATTATTGGTGCCCACTGTTTT	59.099	39.130	0.00	0.00	30.78	2.43
1799	1829	4.158764	CCCACTGTTTTTGTCCACTGTTAA	59.841	41.667	0.00	0.00	0.00	2.01
1816	1846	6.148480	CACTGTTAATAGATTATCCTGCCTGC	59.852	42.308	6.19	0.00	0.00	4.85
1828	1858	0.899720	CTGCCTGCCAATCCAATTGT	59.100	50.000	4.43	0.00	38.59	2.71
1831	1861	2.902486	TGCCTGCCAATCCAATTGTTTA	59.098	40.909	4.43	0.00	38.59	2.01
1841	1871	7.523709	GCCAATCCAATTGTTTATACGATGGAT	60.524	37.037	4.43	9.82	37.50	3.41
1847	1877	8.668353	CCAATTGTTTATACGATGGATCTATGG	58.332	37.037	4.43	0.00	0.00	2.74
1852	1882	6.850752	TTATACGATGGATCTATGGCTTCA	57.149	37.500	0.00	0.00	0.00	3.02
1878	1908	3.750639	TTATTGTTCGCCGAATGTTCC	57.249	42.857	1.55	0.00	0.00	3.62
1896	1926	2.972625	TCCGAGTATTTGGTGCTTGAG	58.027	47.619	0.00	0.00	0.00	3.02
1912	1945	1.388547	TGAGTGTCCAACTTGTTGGC	58.611	50.000	23.47	18.82	40.07	4.52
1918	1951	2.569404	TGTCCAACTTGTTGGCCTTTTT	59.431	40.909	23.47	0.00	41.81	1.94
1919	1952	2.935849	GTCCAACTTGTTGGCCTTTTTG	59.064	45.455	23.47	0.00	41.81	2.44
1946	1979	9.651718	GAGTTAATTTCAGTAGTCAAAAGTGTG	57.348	33.333	0.00	0.00	0.00	3.82
1947	1980	9.174166	AGTTAATTTCAGTAGTCAAAAGTGTGT	57.826	29.630	0.00	0.00	0.00	3.72
1948	1981	9.783256	GTTAATTTCAGTAGTCAAAAGTGTGTT	57.217	29.630	0.00	0.00	0.00	3.32
1951	1984	5.229921	TCAGTAGTCAAAAGTGTGTTTGC	57.770	39.130	0.00	0.00	38.20	3.68
1952	1985	4.697828	TCAGTAGTCAAAAGTGTGTTTGCA	59.302	37.500	0.00	0.00	38.20	4.08
1953	1986	5.182190	TCAGTAGTCAAAAGTGTGTTTGCAA	59.818	36.000	0.00	0.00	38.20	4.08
1957	1994	6.799926	AGTCAAAAGTGTGTTTGCAAAAAT	57.200	29.167	14.67	0.00	38.20	1.82
1960	1997	8.778358	AGTCAAAAGTGTGTTTGCAAAAATAAA	58.222	25.926	14.67	0.00	38.20	1.40
1993	2030	1.606885	CCAACCGATGGGCTGCAATT	61.607	55.000	0.50	0.00	46.27	2.32
2001	2038	5.357878	ACCGATGGGCTGCAATTATATATTG	59.642	40.000	0.50	0.00	36.48	1.90
2491	2693	0.752054	CTCTCAGGGTCATCTCCAGC	59.248	60.000	0.00	0.00	0.00	4.85
3144	3471	3.737172	GCGGTGCATTCAGCCGTT	61.737	61.111	13.47	0.00	46.41	4.44
3266	3593	2.163390	CATCACTCGAGGCGCTGTG	61.163	63.158	18.41	5.60	34.48	3.66
3307	3741	3.608241	GCAGCATCGTGAGTACTAGCTAG	60.608	52.174	19.44	19.44	0.00	3.42
3435	3869	2.422832	GTCCTCTTCGTGTTAGTCCGAT	59.577	50.000	0.00	0.00	32.44	4.18
3456	3890	1.525941	GATGGTTCGTTCCGGGAAAA	58.474	50.000	11.82	0.00	0.00	2.29
3808	4336	4.616802	CGACGTAATTTTGCTGAATTGCTT	59.383	37.500	0.00	1.70	31.85	3.91
3871	4404	1.286501	CAAGCATGTGCATTGCCATC	58.713	50.000	17.87	4.45	45.16	3.51
3907	4449	2.862541	TGCCACTTTGCATACTTGTCT	58.137	42.857	0.00	0.00	36.04	3.41
4025	4568	1.549243	TAGCCGCCACTTGTCCATCA	61.549	55.000	0.00	0.00	0.00	3.07
4072	4628	1.196012	GGAACTCTCCCTCGGAACAT	58.804	55.000	0.00	0.00	35.42	2.71
4109	4678	5.767168	GTCCTAATATGGCAGAAGAGCAAAT	59.233	40.000	0.00	0.00	35.83	2.32
4201	4770	4.820894	ACAAGTTCATCCTACCACTACC	57.179	45.455	0.00	0.00	0.00	3.18
4203	4772	4.595781	ACAAGTTCATCCTACCACTACCAA	59.404	41.667	0.00	0.00	0.00	3.67
4208	4777	1.272807	TCCTACCACTACCAAGGTGC	58.727	55.000	1.07	0.00	38.87	5.01
4233	4802	6.183360	CCATCCTACCATCAAATCCAAAAGAC	60.183	42.308	0.00	0.00	0.00	3.01
4249	4818	6.381994	TCCAAAAGACGGTGTTATCCTACTAT	59.618	38.462	0.00	0.00	0.00	2.12

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
347	349	3.131400	GGGCTACCTTCTAGAACACAGAG	59.869	52.174	0.00	0.00	0.00	3.35
449	451	8.335532	AGCAGTGCTATTTTGTCACTTTTATA	57.664	30.769	18.11	0.00	38.85	0.98
558	560	5.175388	AGTGCATATCACCATCATAGCAT	57.825	39.130	0.00	0.00	46.81	3.79
817	819	2.529780	TTCAGCAAGGCACCAAAATG	57.470	45.000	0.00	0.00	0.00	2.32
845	847	6.639632	AGAAAACTGCAACATAGTGACATT	57.360	33.333	0.00	0.00	0.00	2.71
1039	1046	6.991938	TCCCAAAAATCCTTATTTCACTGTG	58.008	36.000	0.17	0.17	34.12	3.66
1078	1086	7.280876	GGAGATATACTCAGCTAGATCTGTCAG	59.719	44.444	5.18	0.00	46.54	3.51
1080	1088	6.542370	GGGAGATATACTCAGCTAGATCTGTC	59.458	46.154	5.18	0.00	46.54	3.51
1464	1478	8.930760	CAGAAACTAATATATGCTCTAGGTTGC	58.069	37.037	0.00	0.00	0.00	4.17
1503	1517	9.031360	GTAAGCATAATGTAGAATGAAACTCGA	57.969	33.333	0.00	0.00	0.00	4.04
1504	1518	7.998767	CGTAAGCATAATGTAGAATGAAACTCG	59.001	37.037	0.00	0.00	0.00	4.18
1529	1543	8.707938	TCATGCAAGGTATAAATATCATCTCG	57.292	34.615	0.00	0.00	0.00	4.04
1604	1618	2.290323	ACCTGAATGACCCAACTGCTAC	60.290	50.000	0.00	0.00	0.00	3.58
1649	1677	9.742144	ACACAAATTGTAACCTAACACCATATA	57.258	29.630	0.00	0.00	36.32	0.86
1751	1781	6.294899	GCACCAATAATGATACTCCATTGCAT	60.295	38.462	0.00	0.00	37.34	3.96
1754	1784	6.017400	GGCACCAATAATGATACTCCATTG	57.983	41.667	0.00	0.00	37.34	2.82
1776	1806	2.099405	ACAGTGGACAAAAACAGTGGG	58.901	47.619	0.00	0.00	41.24	4.61
1785	1815	9.613428	CAGGATAATCTATTAACAGTGGACAAA	57.387	33.333	0.00	0.00	0.00	2.83
1786	1816	7.715249	GCAGGATAATCTATTAACAGTGGACAA	59.285	37.037	0.00	0.00	0.00	3.18
1799	1829	4.324874	GGATTGGCAGGCAGGATAATCTAT	60.325	45.833	0.00	0.00	0.00	1.98
1816	1846	7.270757	TCCATCGTATAAACAATTGGATTGG	57.729	36.000	10.83	5.19	44.42	3.16
1828	1858	7.239763	TGAAGCCATAGATCCATCGTATAAA	57.760	36.000	0.00	0.00	0.00	1.40
1831	1861	5.946942	ATGAAGCCATAGATCCATCGTAT	57.053	39.130	0.00	0.00	0.00	3.06
1841	1871	9.639601	CGAACAATAATAGTATGAAGCCATAGA	57.360	33.333	0.00	0.00	36.04	1.98
1844	1874	6.149474	GGCGAACAATAATAGTATGAAGCCAT	59.851	38.462	9.16	0.00	38.30	4.40
1847	1877	5.404366	TCGGCGAACAATAATAGTATGAAGC	59.596	40.000	7.35	0.00	0.00	3.86
1852	1882	7.095355	GGAACATTCGGCGAACAATAATAGTAT	60.095	37.037	26.22	0.72	0.00	2.12
1878	1908	3.067106	ACACTCAAGCACCAAATACTCG	58.933	45.455	0.00	0.00	0.00	4.18
1912	1945	8.846211	TGACTACTGAAATTAACTCCAAAAAGG	58.154	33.333	0.00	0.00	39.47	3.11
1918	1951	8.836413	CACTTTTGACTACTGAAATTAACTCCA	58.164	33.333	0.00	0.00	0.00	3.86
1919	1952	8.837389	ACACTTTTGACTACTGAAATTAACTCC	58.163	33.333	0.00	0.00	0.00	3.85
1953	1986	9.239551	GGTTGGTCCTTACTACTGATTTATTTT	57.760	33.333	0.00	0.00	0.00	1.82
1957	1994	5.716228	TCGGTTGGTCCTTACTACTGATTTA	59.284	40.000	0.00	0.00	0.00	1.40
1960	1997	3.705051	TCGGTTGGTCCTTACTACTGAT	58.295	45.455	0.00	0.00	0.00	2.90
2044	2083	6.940298	CCAACTCTAAACCTGGTCATTCTTTA	59.060	38.462	0.00	0.00	0.00	1.85
2051	2090	4.781775	TTTCCAACTCTAAACCTGGTCA	57.218	40.909	0.00	0.00	0.00	4.02
2241	2443	4.569943	TGCAGAATCTACAGAAAGGTGAC	58.430	43.478	0.00	0.00	0.00	3.67
2491	2693	4.950050	AGCTCTTAGTCCGACAATAATGG	58.050	43.478	0.40	0.00	0.00	3.16
3144	3471	2.049156	CCGTCGCTGCTGTCAGAA	60.049	61.111	3.32	0.00	42.95	3.02
3186	3513	2.423446	GGCTGGACCATCCTAGCG	59.577	66.667	7.14	0.00	39.75	4.26
3266	3593	2.962253	GCTGGTAGGCATCGTCGC	60.962	66.667	0.00	0.00	0.00	5.19
3307	3741	1.933247	ATCTACGCTTTGCTCTCAGC	58.067	50.000	0.00	0.00	42.82	4.26
3548	3985	3.826157	CTGGCCACAATTCAGGTCTTAAA	59.174	43.478	0.00	0.00	0.00	1.52
3808	4336	6.745794	ATGAAATTTCAGAACCTTTTGGGA	57.254	33.333	24.17	0.00	41.78	4.37
3907	4449	1.351076	TCTCAACCAGGCTGACATGA	58.649	50.000	17.94	15.17	0.00	3.07
3951	4493	2.548493	GCAGGCAACCAATCAACATGTT	60.548	45.455	4.92	4.92	37.17	2.71
4025	4568	6.351796	GGGTTTACATTTTATGGGAAGCATGT	60.352	38.462	0.00	0.00	32.22	3.21
4072	4628	6.687901	GCCATATTAGGACAAGTGGTATGTGA	60.688	42.308	0.00	0.00	0.00	3.58
4109	4678	3.510753	TCCATTGCTTGCTGCTTGAATTA	59.489	39.130	0.00	0.00	43.37	1.40
4201	4770	1.212688	TGATGGTAGGATGGCACCTTG	59.787	52.381	12.73	0.00	41.00	3.61
4203	4772	1.595311	TTGATGGTAGGATGGCACCT	58.405	50.000	12.25	12.25	43.32	4.00
4208	4777	5.893255	TCTTTTGGATTTGATGGTAGGATGG	59.107	40.000	0.00	0.00	0.00	3.51
4233	4802	5.618056	TTAGCGATAGTAGGATAACACCG	57.382	43.478	0.00	0.00	39.35	4.94
4249	4818	0.874175	CGCCGATGACCAATTAGCGA	60.874	55.000	0.00	0.00	40.57	4.93

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.