AutoCloner

Multiple sequence alignment - TraesCS5D01G425400

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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	TraesCS5D01G425400	chr5D	100.000	2237	0	0	1	2237	483824622	483826858	0.000000e+00	4132.0
1	TraesCS5D01G425400	chr5D	92.806	1390	62	12	694	2080	483985785	483987139	0.000000e+00	1978.0
2	TraesCS5D01G425400	chr5D	86.842	608	78	2	847	1452	483970687	483970080	0.000000e+00	678.0
3	TraesCS5D01G425400	chr5D	91.477	352	20	3	174	521	483985441	483985786	2.010000e-130	475.0
4	TraesCS5D01G425400	chr5D	95.808	167	7	0	1	167	483981419	483981585	1.020000e-68	270.0
5	TraesCS5D01G425400	chr5D	95.808	167	7	0	1	167	483985138	483985304	1.020000e-68	270.0
6	TraesCS5D01G425400	chr5D	91.515	165	10	1	2073	2237	483987164	483987324	8.040000e-55	224.0
7	TraesCS5D01G425400	chr5D	83.077	195	33	0	561	755	50979561	50979367	6.350000e-41	178.0
8	TraesCS5D01G425400	chr5D	90.526	95	4	2	1463	1557	483966458	483966369	1.090000e-23	121.0
9	TraesCS5D01G425400	chr5D	88.372	86	6	3	174	255	483981722	483981807	1.410000e-17	100.0
10	TraesCS5D01G425400	chr5A	93.581	1402	77	9	174	1564	605689788	605688389	0.000000e+00	2078.0
11	TraesCS5D01G425400	chr5A	93.574	996	51	5	581	1564	605366567	605365573	0.000000e+00	1472.0
12	TraesCS5D01G425400	chr5A	86.763	831	65	21	760	1549	605749551	605748725	0.000000e+00	883.0
13	TraesCS5D01G425400	chr5A	93.095	420	24	4	174	589	605367388	605366970	5.280000e-171	610.0
14	TraesCS5D01G425400	chr5A	88.453	433	42	4	1136	1564	605258620	605258192	1.180000e-142	516.0
15	TraesCS5D01G425400	chr5A	78.547	592	81	23	756	1335	605346370	605345813	4.570000e-92	348.0
16	TraesCS5D01G425400	chr5A	100.000	35	0	0	1366	1400	605258443	605258409	5.160000e-07	65.8
17	TraesCS5D01G425400	chr5B	89.474	817	63	10	756	1564	595162659	595161858	0.000000e+00	1011.0
18	TraesCS5D01G425400	chr5B	89.012	810	60	13	760	1557	595122430	595121638	0.000000e+00	976.0
19	TraesCS5D01G425400	chr6D	78.571	490	96	9	272	756	462848722	462849207	4.640000e-82	315.0
20	TraesCS5D01G425400	chr6A	83.278	299	47	3	458	755	211633499	211633795	2.830000e-69	272.0
21	TraesCS5D01G425400	chr1B	80.676	207	40	0	549	755	51230152	51229946	6.390000e-36	161.0
22	TraesCS5D01G425400	chr6B	73.427	286	64	11	472	750	56042566	56042846	1.830000e-16	97.1
23	TraesCS5D01G425400	chr4B	82.474	97	17	0	2140	2236	404842219	404842123	3.960000e-13	86.1
24	TraesCS5D01G425400	chr7A	81.944	72	11	2	1049	1119	121858706	121858636	2.400000e-05	60.2
25	TraesCS5D01G425400	chr7D	97.059	34	0	1	1049	1082	117472278	117472246	3.100000e-04	56.5

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	TraesCS5D01G425400	chr5D	483824622	483826858	2236	False	4132.000000	4132	100.0000	1	2237	1	chr5D.!!$F1	2236
1	TraesCS5D01G425400	chr5D	483981419	483987324	5905	False	552.833333	1978	92.6310	1	2237	6	chr5D.!!$F2	2236
2	TraesCS5D01G425400	chr5D	483966369	483970687	4318	True	399.500000	678	88.6840	847	1557	2	chr5D.!!$R2	710
3	TraesCS5D01G425400	chr5A	605688389	605689788	1399	True	2078.000000	2078	93.5810	174	1564	1	chr5A.!!$R2	1390
4	TraesCS5D01G425400	chr5A	605365573	605367388	1815	True	1041.000000	1472	93.3345	174	1564	2	chr5A.!!$R5	1390
5	TraesCS5D01G425400	chr5A	605748725	605749551	826	True	883.000000	883	86.7630	760	1549	1	chr5A.!!$R3	789
6	TraesCS5D01G425400	chr5A	605345813	605346370	557	True	348.000000	348	78.5470	756	1335	1	chr5A.!!$R1	579
7	TraesCS5D01G425400	chr5B	595161858	595162659	801	True	1011.000000	1011	89.4740	756	1564	1	chr5B.!!$R2	808
8	TraesCS5D01G425400	chr5B	595121638	595122430	792	True	976.000000	976	89.0120	760	1557	1	chr5B.!!$R1	797

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
434	4288	0.037697	TACTACCACACCAGCAAGCG	60.038	55.0	0.0	0.0	0.0	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1826	9785	0.179225	CTACACACGCCGTCAAATGC	60.179	55.0	0.0	0.0	0.0	3.56	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
64	65	6.001449	TGAATCCAGTCCCCAAATTAGTAG	57.999	41.667	0.00	0.00	0.00	2.57
99	3819	6.398234	TTTGGCTAACAGCTTTCACATAAA	57.602	33.333	0.00	0.00	41.99	1.40
124	3844	5.293569	GTGCGTGTCAGCTAATTATACCTTT	59.706	40.000	0.00	0.00	38.13	3.11
128	3848	6.238103	CGTGTCAGCTAATTATACCTTTGTGG	60.238	42.308	0.00	0.00	42.93	4.17
159	3879	0.807496	GCCTGTGGATCAACTTGCTC	59.193	55.000	1.02	0.00	0.00	4.26
162	3882	3.869912	GCCTGTGGATCAACTTGCTCTAA	60.870	47.826	1.02	0.00	0.00	2.10
167	3887	4.081420	GTGGATCAACTTGCTCTAAGGAGA	60.081	45.833	0.00	0.00	41.86	3.71
168	3888	4.081420	TGGATCAACTTGCTCTAAGGAGAC	60.081	45.833	0.00	0.00	41.86	3.36
169	3889	3.963428	TCAACTTGCTCTAAGGAGACC	57.037	47.619	0.00	0.00	41.86	3.85
170	3890	2.231478	TCAACTTGCTCTAAGGAGACCG	59.769	50.000	0.00	0.00	41.86	4.79
171	3891	1.187087	ACTTGCTCTAAGGAGACCGG	58.813	55.000	0.00	0.00	41.86	5.28
172	3892	1.187087	CTTGCTCTAAGGAGACCGGT	58.813	55.000	6.92	6.92	41.86	5.28
189	4039	3.750155	TGCGCCGTCGGTATGTCA	61.750	61.111	13.94	1.32	35.95	3.58
209	4063	6.524734	TGTCACTGTCATTCACTTTATGAGT	58.475	36.000	0.00	0.00	38.99	3.41
257	4111	5.238583	ACGACAGGAAAAGTTAGATCTTGG	58.761	41.667	0.00	0.00	0.00	3.61
356	4210	0.674895	GCAAGAACTCCATCACCGCT	60.675	55.000	0.00	0.00	0.00	5.52
434	4288	0.037697	TACTACCACACCAGCAAGCG	60.038	55.000	0.00	0.00	0.00	4.68
437	4291	2.725203	TACCACACCAGCAAGCGGTC	62.725	60.000	5.77	0.00	33.25	4.79
452	4306	1.380112	GGTCGAGGTAGGAGGCAGT	60.380	63.158	0.00	0.00	0.00	4.40
495	4349	4.450976	TGCATTTACTCCAGCGTAATGAT	58.549	39.130	0.00	0.00	0.00	2.45
541	4395	0.103026	CAGGAATCCGCTGACGATCA	59.897	55.000	0.00	0.00	43.93	2.92
565	4419	2.352960	GTGCCGGATCTGAAGTCAATTC	59.647	50.000	5.05	0.00	38.50	2.17
710	4975	2.158813	ACAAGAACATATTCGGCGGGAT	60.159	45.455	7.21	4.37	40.04	3.85
791	5056	6.451292	TCTCCTCTCCTAGTAATAACCGAT	57.549	41.667	0.00	0.00	0.00	4.18
995	5286	1.071228	GAAAGTTCCAGTACCACCCGT	59.929	52.381	0.00	0.00	0.00	5.28
1050	5342	3.512516	GGCAGCACGAAGGCATCC	61.513	66.667	0.00	0.00	35.83	3.51
1195	5488	1.357690	GTCGTCGTGGTGTCAGACA	59.642	57.895	0.00	0.00	34.80	3.41
1357	5664	1.202114	GCATGTTCCAATTCGAGGCAA	59.798	47.619	0.00	0.00	0.00	4.52
1418	5732	6.315393	GGTTTCATTACGTGGATGATACAGTT	59.685	38.462	24.27	0.00	37.27	3.16
1452	5766	7.936950	TCATATTTGTCTTCTCTAGCAATCG	57.063	36.000	0.00	0.00	0.00	3.34
1654	9613	5.012354	TGGAACTAGGTTGTTTCCGTTCTAT	59.988	40.000	0.00	0.00	32.43	1.98
1670	9629	5.041940	CGTTCTATGGTCAACCTAGCTAAC	58.958	45.833	0.10	0.00	36.82	2.34
1685	9644	2.221906	CTAACGTACTGGCGGCACCT	62.222	60.000	7.97	0.00	40.22	4.00
1720	9679	0.981943	ACCACCCCTTAACTCCTTCG	59.018	55.000	0.00	0.00	0.00	3.79
1774	9733	3.283684	CGGGCAAAACCTGTGCGA	61.284	61.111	0.00	0.00	43.18	5.10
1822	9781	1.228154	AGAAGGTGGTTGGCGGTTC	60.228	57.895	0.00	0.00	0.00	3.62
1824	9783	3.802852	AAGGTGGTTGGCGGTTCCC	62.803	63.158	0.00	0.00	0.00	3.97
1825	9784	4.589675	GGTGGTTGGCGGTTCCCA	62.590	66.667	0.00	0.00	0.00	4.37
1826	9785	2.983592	GTGGTTGGCGGTTCCCAG	60.984	66.667	0.00	0.00	36.00	4.45
1827	9786	4.966787	TGGTTGGCGGTTCCCAGC	62.967	66.667	0.00	0.00	36.00	4.85
1828	9787	4.966787	GGTTGGCGGTTCCCAGCA	62.967	66.667	0.00	0.00	37.78	4.41
1829	9788	2.676471	GTTGGCGGTTCCCAGCAT	60.676	61.111	0.00	0.00	36.27	3.79
1830	9789	2.117206	TTGGCGGTTCCCAGCATT	59.883	55.556	0.00	0.00	36.00	3.56
1831	9790	1.532794	TTGGCGGTTCCCAGCATTT	60.533	52.632	0.00	0.00	36.00	2.32
1832	9791	1.814772	TTGGCGGTTCCCAGCATTTG	61.815	55.000	0.00	0.00	36.00	2.32
1835	9794	1.501741	CGGTTCCCAGCATTTGACG	59.498	57.895	0.00	0.00	0.00	4.35
1839	9798	3.055719	CCCAGCATTTGACGGCGT	61.056	61.111	14.65	14.65	34.54	5.68
1911	9870	1.216710	GCGCAGAGTGCTCTACCTT	59.783	57.895	0.30	0.00	42.25	3.50
1924	9883	1.623811	TCTACCTTGGCCTGACAGTTC	59.376	52.381	3.32	0.00	0.00	3.01
1935	9894	2.551721	CCTGACAGTTCCAGCATTGTCT	60.552	50.000	0.93	0.00	40.36	3.41
1953	9912	1.668237	TCTGATCTCTCTCGAGTTGCG	59.332	52.381	13.13	2.25	38.45	4.85
1987	9946	1.883084	CATAGGGTCTTCGCGTGCC	60.883	63.158	5.77	4.19	0.00	5.01
1989	9948	1.895020	ATAGGGTCTTCGCGTGCCAA	61.895	55.000	5.77	0.00	0.00	4.52
2014	9973	2.102578	GGTGATATGGCTTTGGTGCTT	58.897	47.619	0.00	0.00	0.00	3.91
2028	9987	2.837591	TGGTGCTTCAGTTCAGGCTATA	59.162	45.455	0.00	0.00	0.00	1.31
2052	10011	1.079543	CCTGAGCCGACTTGACTGG	60.080	63.158	0.00	0.00	0.00	4.00
2081	10074	2.571216	CCGACGAGGTGTTGGTCCT	61.571	63.158	0.00	0.00	45.87	3.85
2126	10119	4.651045	ACTATGATGGCATACTCACTGTGA	59.349	41.667	10.50	10.50	35.94	3.58
2142	10135	1.947146	TGAAGTGCGACGACAACCG	60.947	57.895	0.00	0.00	45.44	4.44
2201	10194	3.835978	TGTTTGACTTCGGAAGGGAGATA	59.164	43.478	20.97	1.93	0.00	1.98
2223	10216	0.606604	AACTATGGACGACGGCTTGT	59.393	50.000	0.00	0.00	0.00	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
99	3819	4.099573	AGGTATAATTAGCTGACACGCACT	59.900	41.667	0.00	0.00	34.90	4.40
159	3879	2.202756	GCGCACCGGTCTCCTTAG	60.203	66.667	2.59	0.00	0.00	2.18
170	3890	4.807039	ACATACCGACGGCGCACC	62.807	66.667	15.39	0.00	35.83	5.01
171	3891	3.252484	GACATACCGACGGCGCAC	61.252	66.667	15.39	0.00	35.83	5.34
172	3892	3.750155	TGACATACCGACGGCGCA	61.750	61.111	15.39	0.00	35.83	6.09
209	4063	4.631377	GCTGTGTTCATGCTGTATAGAACA	59.369	41.667	14.53	14.53	45.57	3.18
219	4073	1.006220	TCGTCGCTGTGTTCATGCT	60.006	52.632	0.00	0.00	0.00	3.79
223	4077	1.299850	CCTGTCGTCGCTGTGTTCA	60.300	57.895	0.00	0.00	0.00	3.18
257	4111	4.349365	TGGATTTGGGTTTGGATTAGGTC	58.651	43.478	0.00	0.00	0.00	3.85
322	4176	1.455402	TTGCTGCAGCCTTCCACAA	60.455	52.632	34.64	18.08	41.18	3.33
434	4288	0.971447	AACTGCCTCCTACCTCGACC	60.971	60.000	0.00	0.00	0.00	4.79
437	4291	1.433879	CGAACTGCCTCCTACCTCG	59.566	63.158	0.00	0.00	0.00	4.63
452	4306	0.400815	ATATGGGTAGGTGGGGCGAA	60.401	55.000	0.00	0.00	0.00	4.70
495	4349	2.560981	TGGATCAGTTCTGCTTACGACA	59.439	45.455	0.00	0.00	0.00	4.35
541	4395	1.613630	ACTTCAGATCCGGCACCCT	60.614	57.895	0.00	0.00	0.00	4.34
545	4399	2.632377	GAATTGACTTCAGATCCGGCA	58.368	47.619	0.00	0.00	33.78	5.69
710	4975	1.751351	CACACAGGCTCTCGGAATCTA	59.249	52.381	0.00	0.00	0.00	1.98
995	5286	1.549950	GCTCAACCCTCCCCATTTTGA	60.550	52.381	0.00	0.00	0.00	2.69
1264	5564	7.602517	AATACGATACTACTGTACGTATCCC	57.397	40.000	16.47	0.00	41.91	3.85
1357	5664	4.296912	TGGATTTTATTCATGCACCCCAT	58.703	39.130	0.00	0.00	33.39	4.00
1452	5766	7.368480	TGCTACATGTATGATAATGCATGAC	57.632	36.000	23.70	14.22	44.08	3.06
1584	9543	1.344438	TGAGGGTGTCAGATGTCACAC	59.656	52.381	11.35	8.17	41.95	3.82
1654	9613	3.192001	CAGTACGTTAGCTAGGTTGACCA	59.808	47.826	0.00	0.00	38.89	4.02
1690	9649	1.382146	GGGGTGGTAGATCGGGTCA	60.382	63.158	0.00	0.00	0.00	4.02
1720	9679	2.771762	ATGAGGGGAGGAGCAGGC	60.772	66.667	0.00	0.00	0.00	4.85
1736	9695	3.461773	CTGGTCTCCGGTGGCGAT	61.462	66.667	0.00	0.00	0.00	4.58
1822	9781	3.055719	ACGCCGTCAAATGCTGGG	61.056	61.111	0.00	0.00	0.00	4.45
1824	9783	1.440850	CACACGCCGTCAAATGCTG	60.441	57.895	0.00	0.00	0.00	4.41
1825	9784	0.601576	TACACACGCCGTCAAATGCT	60.602	50.000	0.00	0.00	0.00	3.79
1826	9785	0.179225	CTACACACGCCGTCAAATGC	60.179	55.000	0.00	0.00	0.00	3.56
1827	9786	0.179225	GCTACACACGCCGTCAAATG	60.179	55.000	0.00	0.00	0.00	2.32
1828	9787	0.601576	TGCTACACACGCCGTCAAAT	60.602	50.000	0.00	0.00	0.00	2.32
1829	9788	1.218875	CTGCTACACACGCCGTCAAA	61.219	55.000	0.00	0.00	0.00	2.69
1830	9789	1.663388	CTGCTACACACGCCGTCAA	60.663	57.895	0.00	0.00	0.00	3.18
1831	9790	2.049526	CTGCTACACACGCCGTCA	60.050	61.111	0.00	0.00	0.00	4.35
1832	9791	2.049433	ACTGCTACACACGCCGTC	60.049	61.111	0.00	0.00	0.00	4.79
1835	9794	2.742372	CCCACTGCTACACACGCC	60.742	66.667	0.00	0.00	0.00	5.68
1839	9798	2.920384	TCCGCCCACTGCTACACA	60.920	61.111	0.00	0.00	38.05	3.72
1897	9856	0.252467	AGGCCAAGGTAGAGCACTCT	60.252	55.000	5.01	5.36	43.40	3.24
1899	9858	0.545309	TCAGGCCAAGGTAGAGCACT	60.545	55.000	5.01	0.00	0.00	4.40
1911	9870	1.782201	ATGCTGGAACTGTCAGGCCA	61.782	55.000	5.01	13.97	33.16	5.36
1924	9883	3.719924	GAGAGAGATCAGACAATGCTGG	58.280	50.000	0.00	0.00	36.55	4.85
1953	9912	4.067896	CCCTATGATGGTCAGCACAATAC	58.932	47.826	0.00	0.00	0.00	1.89
1987	9946	3.119388	CCAAAGCCATATCACCACTGTTG	60.119	47.826	0.00	0.00	0.00	3.33
1989	9948	2.041620	ACCAAAGCCATATCACCACTGT	59.958	45.455	0.00	0.00	0.00	3.55
2097	10090	2.304180	AGTATGCCATCATAGTCTGGGC	59.696	50.000	0.00	0.00	44.82	5.36
2098	10091	4.199432	GAGTATGCCATCATAGTCTGGG	57.801	50.000	11.06	0.00	45.59	4.45
2126	10119	0.806884	TTTCGGTTGTCGTCGCACTT	60.807	50.000	0.00	0.00	40.32	3.16
2142	10135	2.414806	GAACCCTCACGAAGACCTTTC	58.585	52.381	0.00	0.00	0.00	2.62
2169	10162	2.711542	GAAGTCAAACACCGGATCCAT	58.288	47.619	9.46	0.00	0.00	3.41
2171	10164	1.076332	CGAAGTCAAACACCGGATCC	58.924	55.000	9.46	0.00	0.00	3.36
2201	10194	0.606604	AGCCGTCGTCCATAGTTTGT	59.393	50.000	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.