AutoCloner

Multiple sequence alignment - TraesCS4A01G094200

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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	TraesCS4A01G094200	chr4A	100.000	2448	0	0	1	2448	102389031	102386584	0.000000e+00	4521.0
1	TraesCS4A01G094200	chr4A	92.308	91	7	0	2315	2405	312732186	312732096	1.980000e-26	130.0
2	TraesCS4A01G094200	chr5A	95.766	1795	70	4	1	1794	552595452	552597241	0.000000e+00	2889.0
3	TraesCS4A01G094200	chr5A	80.754	769	115	27	1022	1771	11951137	11951891	9.820000e-159	569.0
4	TraesCS4A01G094200	chr5A	83.636	275	39	3	787	1061	11950791	11951059	1.120000e-63	254.0
5	TraesCS4A01G094200	chr6A	93.753	1809	101	6	1	1800	467050755	467048950	0.000000e+00	2704.0
6	TraesCS4A01G094200	chr2A	93.514	1804	96	10	1	1794	753468818	753467026	0.000000e+00	2663.0
7	TraesCS4A01G094200	chr2A	81.115	789	119	23	1022	1794	4026213	4026987	2.690000e-169	604.0
8	TraesCS4A01G094200	chr2A	90.698	86	8	0	2144	2229	398507411	398507326	5.530000e-22	115.0
9	TraesCS4A01G094200	chr2A	88.542	96	10	1	2135	2229	398766351	398766256	5.530000e-22	115.0
10	TraesCS4A01G094200	chr1D	84.705	1118	135	28	691	1787	328835214	328834112	0.000000e+00	1085.0
11	TraesCS4A01G094200	chr1D	92.793	111	8	0	516	626	328835472	328835362	7.010000e-36	161.0
12	TraesCS4A01G094200	chr1A	92.447	609	22	14	1861	2448	539593888	539593283	0.000000e+00	848.0
13	TraesCS4A01G094200	chr1A	91.209	91	8	0	2315	2405	504399193	504399283	9.190000e-25	124.0
14	TraesCS4A01G094200	chr1A	92.593	81	6	0	2315	2395	525143325	525143245	1.540000e-22	117.0
15	TraesCS4A01G094200	chr7A	89.736	682	40	5	1794	2446	21854990	21855670	0.000000e+00	845.0
16	TraesCS4A01G094200	chr7A	90.205	633	40	4	1794	2405	21874087	21874718	0.000000e+00	806.0
17	TraesCS4A01G094200	chr7A	90.110	91	9	0	2315	2405	655417520	655417430	4.280000e-23	119.0
18	TraesCS4A01G094200	chr3B	90.354	622	25	10	1855	2448	104696598	104695984	0.000000e+00	784.0
19	TraesCS4A01G094200	chr3B	77.379	641	135	7	792	1428	441852146	441852780	2.970000e-99	372.0
20	TraesCS4A01G094200	chr4D	82.253	941	130	23	880	1794	326985568	326984639	0.000000e+00	778.0
21	TraesCS4A01G094200	chr2B	90.033	602	41	8	1794	2379	144073363	144072765	0.000000e+00	761.0
22	TraesCS4A01G094200	chr2B	83.607	61	10	0	1734	1794	447818006	447818066	9.450000e-05	58.4
23	TraesCS4A01G094200	chr6D	77.657	1016	176	27	799	1794	318564197	318563213	2.730000e-159	571.0
24	TraesCS4A01G094200	chr3D	86.486	111	15	0	516	626	552718329	552718219	3.310000e-24	122.0
25	TraesCS4A01G094200	chr5D	93.443	61	4	0	19	79	435472821	435472761	9.320000e-15	91.6
26	TraesCS4A01G094200	chr7D	84.722	72	5	4	1733	1800	565530274	565530205	1.570000e-07	67.6
27	TraesCS4A01G094200	chr6B	85.938	64	5	3	1733	1794	24729487	24729548	5.650000e-07	65.8
28	TraesCS4A01G094200	chr6B	86.441	59	7	1	1737	1794	625284554	625284496	2.030000e-06	63.9
29	TraesCS4A01G094200	chrUn	92.857	42	3	0	1757	1798	274279115	274279074	7.310000e-06	62.1

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	TraesCS4A01G094200	chr4A	102386584	102389031	2447	True	4521.0	4521	100.000	1	2448	1	chr4A.!!$R1	2447
1	TraesCS4A01G094200	chr5A	552595452	552597241	1789	False	2889.0	2889	95.766	1	1794	1	chr5A.!!$F1	1793
2	TraesCS4A01G094200	chr5A	11950791	11951891	1100	False	411.5	569	82.195	787	1771	2	chr5A.!!$F2	984
3	TraesCS4A01G094200	chr6A	467048950	467050755	1805	True	2704.0	2704	93.753	1	1800	1	chr6A.!!$R1	1799
4	TraesCS4A01G094200	chr2A	753467026	753468818	1792	True	2663.0	2663	93.514	1	1794	1	chr2A.!!$R3	1793
5	TraesCS4A01G094200	chr2A	4026213	4026987	774	False	604.0	604	81.115	1022	1794	1	chr2A.!!$F1	772
6	TraesCS4A01G094200	chr1D	328834112	328835472	1360	True	623.0	1085	88.749	516	1787	2	chr1D.!!$R1	1271
7	TraesCS4A01G094200	chr1A	539593283	539593888	605	True	848.0	848	92.447	1861	2448	1	chr1A.!!$R2	587
8	TraesCS4A01G094200	chr7A	21854990	21855670	680	False	845.0	845	89.736	1794	2446	1	chr7A.!!$F1	652
9	TraesCS4A01G094200	chr7A	21874087	21874718	631	False	806.0	806	90.205	1794	2405	1	chr7A.!!$F2	611
10	TraesCS4A01G094200	chr3B	104695984	104696598	614	True	784.0	784	90.354	1855	2448	1	chr3B.!!$R1	593
11	TraesCS4A01G094200	chr3B	441852146	441852780	634	False	372.0	372	77.379	792	1428	1	chr3B.!!$F1	636
12	TraesCS4A01G094200	chr4D	326984639	326985568	929	True	778.0	778	82.253	880	1794	1	chr4D.!!$R1	914
13	TraesCS4A01G094200	chr2B	144072765	144073363	598	True	761.0	761	90.033	1794	2379	1	chr2B.!!$R1	585
14	TraesCS4A01G094200	chr6D	318563213	318564197	984	True	571.0	571	77.657	799	1794	1	chr6D.!!$R1	995

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
500	507	2.691526	AGAGTACATAATCCGCGGTGAA	59.308	45.455	27.15	11.9	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2272	2551	0.035152	AATCATCAGTTGAGGCGGCA	60.035	50.0	13.08	0.0	37.89	5.69	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
29	30	7.765695	ACAGCCTCTTATTCTTTTCATTCAA	57.234	32.000	0.00	0.00	0.00	2.69
146	147	3.091545	AGCAACATGGATCCGATGTTTT	58.908	40.909	26.63	19.38	41.16	2.43
286	288	5.220739	GCCTAATTCAGACAACATAGCACAG	60.221	44.000	0.00	0.00	0.00	3.66
338	340	9.294030	GACAAAATATGTTTCAGATTCATCACC	57.706	33.333	0.00	0.00	44.12	4.02
488	492	6.377080	AGAGAATGACCATCCAGAGTACATA	58.623	40.000	0.00	0.00	0.00	2.29
489	493	6.841229	AGAGAATGACCATCCAGAGTACATAA	59.159	38.462	0.00	0.00	0.00	1.90
490	494	7.512058	AGAGAATGACCATCCAGAGTACATAAT	59.488	37.037	0.00	0.00	0.00	1.28
500	507	2.691526	AGAGTACATAATCCGCGGTGAA	59.308	45.455	27.15	11.90	0.00	3.18
744	835	5.528690	CAGAACTTTCACCTGTCTCATTTCA	59.471	40.000	0.00	0.00	0.00	2.69
899	994	5.945191	TCACCTACATTGAATTGATTGCAGA	59.055	36.000	0.00	0.00	0.00	4.26
1029	1125	2.507484	CACAAGGAGCCAGACATCAAA	58.493	47.619	0.00	0.00	0.00	2.69
1076	1294	2.404566	TTTGCTAAGCCAGGCCACGA	62.405	55.000	8.22	0.00	0.00	4.35
1226	1450	3.066380	CCGAACAATGACACACTCATGA	58.934	45.455	0.00	0.00	38.82	3.07
1251	1475	0.108186	CTTGCAGATGCCCGTCTACA	60.108	55.000	1.72	0.00	41.18	2.74
1351	1575	3.186909	CAACATTCGCGAAGGAGACATA	58.813	45.455	36.62	7.20	0.00	2.29
1551	1787	6.741109	TGAATATCCGAAAGCTATGTCGTTA	58.259	36.000	11.90	5.61	35.48	3.18
1716	1957	9.019656	ACATGCTAACCAGAACAAAAATGTATA	57.980	29.630	0.00	0.00	0.00	1.47
1745	1986	3.706373	CCCACTAGCTGGCACCGT	61.706	66.667	0.00	0.00	39.01	4.83
1764	2005	2.296365	CCAGCTGCCCCTCAAGAGA	61.296	63.158	8.66	0.00	0.00	3.10
1812	2053	5.183140	CCTAGTCCAAAACAATAAGGTGTGG	59.817	44.000	0.00	0.00	0.00	4.17
1826	2067	0.745845	GTGTGGATCATGAGCGCCTT	60.746	55.000	2.29	0.00	0.00	4.35
1845	2086	2.826979	TCTCGCAACATCTACGTCTC	57.173	50.000	0.00	0.00	0.00	3.36
1850	2091	2.541556	GCAACATCTACGTCTCCCTTC	58.458	52.381	0.00	0.00	0.00	3.46
1853	2094	4.498345	GCAACATCTACGTCTCCCTTCTAG	60.498	50.000	0.00	0.00	0.00	2.43
1891	2132	1.067212	GTCTCGCGATAACACCTCCAT	59.933	52.381	10.36	0.00	0.00	3.41
1940	2187	2.950309	CTCTACGAAGCTAACCTGCCTA	59.050	50.000	0.00	0.00	0.00	3.93
1960	2233	0.820871	GTTGCTCGTCCTCCAGATCT	59.179	55.000	0.00	0.00	0.00	2.75
2232	2511	2.436292	CCTCGACGGTCGGTCTCT	60.436	66.667	28.07	0.00	43.79	3.10
2272	2551	2.370445	CCCCTTCCCTCTCGTGCAT	61.370	63.158	0.00	0.00	0.00	3.96
2361	2640	4.319477	GCACTCGTGATTTAGCTTGTTTCA	60.319	41.667	0.39	0.00	0.00	2.69
2396	2675	0.940126	GGGCATCAGCATCTAACACG	59.060	55.000	0.00	0.00	44.61	4.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	94	0.818296	GAGCACCGTGTGTATCTCCT	59.182	55.000	0.00	0.00	35.75	3.69
95	96	1.630148	GTGAGCACCGTGTGTATCTC	58.370	55.000	0.00	0.00	35.75	2.75
123	124	1.210234	ACATCGGATCCATGTTGCTCA	59.790	47.619	18.56	0.00	29.75	4.26
338	340	0.179233	GAGTAAAACGGAAAGCGGCG	60.179	55.000	0.51	0.51	0.00	6.46
381	383	4.276926	ACTGGAAATTGTGAAGCAGAAGAC	59.723	41.667	0.00	0.00	0.00	3.01
386	388	2.029649	CCCACTGGAAATTGTGAAGCAG	60.030	50.000	0.00	0.00	36.38	4.24
446	448	8.316946	TCATTCTCTTCACTCTGTTCATTGTAT	58.683	33.333	0.00	0.00	0.00	2.29
447	449	7.600375	GTCATTCTCTTCACTCTGTTCATTGTA	59.400	37.037	0.00	0.00	0.00	2.41
488	492	1.922135	GCATGTGTTCACCGCGGATT	61.922	55.000	35.90	7.50	0.00	3.01
489	493	2.398554	GCATGTGTTCACCGCGGAT	61.399	57.895	35.90	13.97	0.00	4.18
490	494	3.047280	GCATGTGTTCACCGCGGA	61.047	61.111	35.90	7.50	0.00	5.54
500	507	4.012374	CCTGTGAGAAATAAGGCATGTGT	58.988	43.478	0.00	0.00	0.00	3.72
899	994	3.814504	ACTGGATCCCACAAGATGTTT	57.185	42.857	9.90	0.00	0.00	2.83
1029	1125	9.787532	GTTTTATTGATTGTGCACATGTAGTAT	57.212	29.630	22.39	9.99	0.00	2.12
1076	1294	7.719633	AGATAAGAGTGTTTTTGTGTACCATGT	59.280	33.333	0.00	0.00	0.00	3.21
1110	1332	7.920160	TTAGATGAATACAGATTGTTGTGCA	57.080	32.000	0.00	0.00	32.56	4.57
1111	1333	9.443283	GATTTAGATGAATACAGATTGTTGTGC	57.557	33.333	0.00	0.00	32.56	4.57
1189	1413	3.513912	TGTTCGGATCAATGTAGTCCAGT	59.486	43.478	0.00	0.00	32.23	4.00
1226	1450	0.463295	CGGGCATCTGCAAGTCTGAT	60.463	55.000	4.33	0.00	44.36	2.90
1251	1475	3.526385	GCATAATGCGACATTCGATGT	57.474	42.857	8.09	0.00	43.74	3.06
1351	1575	5.539955	AGTGACCCTAAAATGAAAAGCACAT	59.460	36.000	0.00	0.00	0.00	3.21
1470	1700	6.293407	CCATCGGTTAATCACGAGCATAATTT	60.293	38.462	0.00	0.00	42.89	1.82
1551	1787	9.924010	ACTGAGAATAGTAGAGTTTACATAGGT	57.076	33.333	0.00	0.00	0.00	3.08
1598	1839	5.121380	ACAGAAGAGTGCCATTATGGATT	57.879	39.130	16.46	0.00	40.96	3.01
1716	1957	2.308866	AGCTAGTGGGTGCACCTTTTAT	59.691	45.455	33.91	18.08	41.11	1.40
1718	1959	0.478507	AGCTAGTGGGTGCACCTTTT	59.521	50.000	33.91	21.00	41.11	2.27
1745	1986	2.203983	TCTTGAGGGGCAGCTGGA	60.204	61.111	17.12	0.00	0.00	3.86
1812	2053	2.515376	CGAGAAGGCGCTCATGATC	58.485	57.895	7.64	0.00	34.56	2.92
1826	2067	1.400846	GGAGACGTAGATGTTGCGAGA	59.599	52.381	0.00	0.00	38.36	4.04
1832	2073	4.641094	CACTAGAAGGGAGACGTAGATGTT	59.359	45.833	0.00	0.00	0.00	2.71
1845	2086	1.546961	ACCTCGACACACTAGAAGGG	58.453	55.000	0.00	0.00	0.00	3.95
1850	2091	3.240069	CGGTTTTACCTCGACACACTAG	58.760	50.000	0.00	0.00	35.66	2.57
1853	2094	1.788886	GACGGTTTTACCTCGACACAC	59.211	52.381	0.00	0.00	35.66	3.82
1901	2143	5.705905	CGTAGAGGAGGAAGGAAATTGTTTT	59.294	40.000	0.00	0.00	0.00	2.43
1918	2160	1.202428	GGCAGGTTAGCTTCGTAGAGG	60.202	57.143	0.00	0.00	38.43	3.69
1940	2187	0.820871	GATCTGGAGGACGAGCAACT	59.179	55.000	0.00	0.00	0.00	3.16
1960	2233	0.719015	AGGGGAATGTGGAGGAGAGA	59.281	55.000	0.00	0.00	0.00	3.10
2091	2366	2.676121	CCCATGCCAACGGAGCAA	60.676	61.111	0.31	0.00	44.83	3.91
2100	2375	2.282110	CCACGACAACCCATGCCA	60.282	61.111	0.00	0.00	0.00	4.92
2232	2511	0.906756	CAGGGAGAGGAGTGGAGCAA	60.907	60.000	0.00	0.00	0.00	3.91
2272	2551	0.035152	AATCATCAGTTGAGGCGGCA	60.035	50.000	13.08	0.00	37.89	5.69
2361	2640	1.291637	TGCCCAATTCATTCCATCCCT	59.708	47.619	0.00	0.00	0.00	4.20
2396	2675	4.194640	ACATAATCATCCTCTGTGTGTGC	58.805	43.478	0.00	0.00	0.00	4.57
2425	2713	5.818678	TGGTTTCTACTACATGGTTGACT	57.181	39.130	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.