AutoCloner

Multiple sequence alignment - TraesCS6B01G037100

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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	TraesCS6B01G037100	chr6B	100.000	2981	0	0	1	2981	21457708	21460688	0.000000e+00	5505.0
1	TraesCS6B01G037100	chr6B	94.334	2171	89	6	1	2164	15116660	15114517	0.000000e+00	3297.0
2	TraesCS6B01G037100	chr6B	79.111	1283	215	40	937	2191	14323460	14324717	0.000000e+00	835.0
3	TraesCS6B01G037100	chr6D	86.380	2188	231	34	817	2981	8245322	8247465	0.000000e+00	2327.0
4	TraesCS6B01G037100	chr6D	91.679	1382	74	10	820	2190	8147353	8146002	0.000000e+00	1877.0
5	TraesCS6B01G037100	chr6D	90.196	1224	93	18	975	2190	8249768	8250972	0.000000e+00	1570.0
6	TraesCS6B01G037100	chr6D	77.896	1217	236	29	969	2174	8552823	8551629	0.000000e+00	726.0
7	TraesCS6B01G037100	chr6D	77.753	881	169	22	1419	2286	8402245	8401379	1.580000e-142	516.0
8	TraesCS6B01G037100	chr6D	92.012	338	18	5	447	782	8244912	8245242	1.620000e-127	466.0
9	TraesCS6B01G037100	chr6A	91.552	1231	96	8	964	2190	8624545	8623319	0.000000e+00	1690.0
10	TraesCS6B01G037100	chr6A	89.593	1230	115	9	964	2190	8712215	8713434	0.000000e+00	1550.0
11	TraesCS6B01G037100	chr6A	90.134	598	44	7	1	591	8711314	8711903	0.000000e+00	763.0
12	TraesCS6B01G037100	chr6A	81.596	614	66	31	2398	2981	8258475	8257879	5.820000e-127	464.0
13	TraesCS6B01G037100	chr6A	85.776	232	21	8	524	754	8625045	8624825	4.970000e-58	235.0
14	TraesCS6B01G037100	chr7A	78.715	1043	197	22	1139	2170	162577976	162579004	0.000000e+00	673.0
15	TraesCS6B01G037100	chr5D	78.066	1158	183	48	1874	2981	24880863	24879727	0.000000e+00	665.0
16	TraesCS6B01G037100	chr5D	92.683	41	1	1	25	63	226456395	226456435	1.150000e-04	58.4
17	TraesCS6B01G037100	chr1B	83.333	60	10	0	16	75	307005532	307005591	4.150000e-04	56.5
18	TraesCS6B01G037100	chr1B	100.000	29	0	0	42	70	15377569	15377541	1.000000e-03	54.7

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	TraesCS6B01G037100	chr6B	21457708	21460688	2980	False	5505.000000	5505	100.000000	1	2981	1	chr6B.!!$F2	2980
1	TraesCS6B01G037100	chr6B	15114517	15116660	2143	True	3297.000000	3297	94.334000	1	2164	1	chr6B.!!$R1	2163
2	TraesCS6B01G037100	chr6B	14323460	14324717	1257	False	835.000000	835	79.111000	937	2191	1	chr6B.!!$F1	1254
3	TraesCS6B01G037100	chr6D	8146002	8147353	1351	True	1877.000000	1877	91.679000	820	2190	1	chr6D.!!$R1	1370
4	TraesCS6B01G037100	chr6D	8244912	8250972	6060	False	1454.333333	2327	89.529333	447	2981	3	chr6D.!!$F1	2534
5	TraesCS6B01G037100	chr6D	8551629	8552823	1194	True	726.000000	726	77.896000	969	2174	1	chr6D.!!$R3	1205
6	TraesCS6B01G037100	chr6D	8401379	8402245	866	True	516.000000	516	77.753000	1419	2286	1	chr6D.!!$R2	867
7	TraesCS6B01G037100	chr6A	8711314	8713434	2120	False	1156.500000	1550	89.863500	1	2190	2	chr6A.!!$F1	2189
8	TraesCS6B01G037100	chr6A	8623319	8625045	1726	True	962.500000	1690	88.664000	524	2190	2	chr6A.!!$R2	1666
9	TraesCS6B01G037100	chr6A	8257879	8258475	596	True	464.000000	464	81.596000	2398	2981	1	chr6A.!!$R1	583
10	TraesCS6B01G037100	chr7A	162577976	162579004	1028	False	673.000000	673	78.715000	1139	2170	1	chr7A.!!$F1	1031
11	TraesCS6B01G037100	chr5D	24879727	24880863	1136	True	665.000000	665	78.066000	1874	2981	1	chr5D.!!$R1	1107

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
173	179	1.343142	ACTGGTGTGTCGTATGCAAGA	59.657	47.619	0.00	0.0	0.00	3.02	F
372	379	1.369839	TTTGTCGCGGTTGCAGAACA	61.370	50.000	6.13	0.0	42.97	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1519	6064	1.393603	CTCTCGAGGTCAGCACCATA	58.606	55.0	13.56	0.00	46.68	2.74	R
2198	6744	0.248296	TGAAAACTTCGTTGCGCCAC	60.248	50.0	4.18	2.21	0.00	5.01	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
173	179	1.343142	ACTGGTGTGTCGTATGCAAGA	59.657	47.619	0.00	0.00	0.00	3.02
221	227	2.553079	TCACACTTTGGTTGCGTTTC	57.447	45.000	0.00	0.00	0.00	2.78
260	266	3.922240	GCCGGCTAATATTATTTCGTCGA	59.078	43.478	22.15	0.00	0.00	4.20
290	297	2.283676	ACGGACGATGACTGGGGT	60.284	61.111	0.00	0.00	0.00	4.95
372	379	1.369839	TTTGTCGCGGTTGCAGAACA	61.370	50.000	6.13	0.00	42.97	3.18
455	462	1.540363	GGTTGCAGAAAGACGAGTCCA	60.540	52.381	0.00	0.00	0.00	4.02
473	480	5.497474	AGTCCAAACTTTACACAAGTGACT	58.503	37.500	7.28	0.00	30.78	3.41
511	519	3.246226	CACTATAAGATGACACAAGCGGC	59.754	47.826	0.00	0.00	0.00	6.53
671	680	6.307318	CGCCGGACACATAATAGTAAGTAATC	59.693	42.308	5.05	0.00	0.00	1.75
1519	6064	1.078426	AAACGCGGCTTCTGGCTAT	60.078	52.632	12.47	0.00	41.46	2.97
1539	6084	1.954362	ATGGTGCTGACCTCGAGAGC	61.954	60.000	15.71	15.69	43.58	4.09
1561	6106	2.745884	TCAAGCCCAATGTCGCGG	60.746	61.111	6.13	0.00	0.00	6.46
1680	6225	4.157817	GCATGCGCCAAAGTTCTG	57.842	55.556	4.18	0.00	0.00	3.02
2177	6723	1.247567	CATGAACCAAGAACGGGCTT	58.752	50.000	0.00	0.00	0.00	4.35
2191	6737	4.882842	ACGGGCTTTGAAAATTGGTAAT	57.117	36.364	0.00	0.00	0.00	1.89
2198	6744	7.131565	GGCTTTGAAAATTGGTAATTTGTGTG	58.868	34.615	0.75	0.00	40.05	3.82
2208	6754	0.869454	AATTTGTGTGTGGCGCAACG	60.869	50.000	11.00	0.00	45.99	4.10
2252	6798	2.817844	GCTGGTAATTCCTGTTTCGGTT	59.182	45.455	0.00	0.00	37.45	4.44
2260	6806	7.493320	GGTAATTCCTGTTTCGGTTTTCTTTTT	59.507	33.333	0.00	0.00	0.00	1.94
2283	6829	6.428083	TCCTAACTGGATGTTTGTTGTCTA	57.572	37.500	0.00	0.00	40.56	2.59
2288	6834	7.907214	AACTGGATGTTTGTTGTCTACTATC	57.093	36.000	0.00	0.00	34.84	2.08
2289	6835	7.004555	ACTGGATGTTTGTTGTCTACTATCA	57.995	36.000	0.00	0.00	0.00	2.15
2294	6840	8.946085	GGATGTTTGTTGTCTACTATCAATTCA	58.054	33.333	0.00	0.00	0.00	2.57
2303	6849	6.157820	TGTCTACTATCAATTCATGAACCCCA	59.842	38.462	11.07	0.00	42.54	4.96
2320	6866	3.012518	CCCCAATGAGTTCATGTCTCAC	58.987	50.000	19.43	3.18	43.32	3.51
2322	6868	3.688185	CCCAATGAGTTCATGTCTCACTG	59.312	47.826	19.43	18.60	43.32	3.66
2329	6875	3.766591	AGTTCATGTCTCACTGGGTAGAG	59.233	47.826	0.00	0.00	0.00	2.43
2330	6876	3.739401	TCATGTCTCACTGGGTAGAGA	57.261	47.619	0.00	0.00	38.49	3.10
2340	6886	4.081420	TCACTGGGTAGAGAAGAAAGCATC	60.081	45.833	0.00	0.00	0.00	3.91
2343	6889	2.159028	GGGTAGAGAAGAAAGCATCGCT	60.159	50.000	0.00	0.00	42.56	4.93
2344	6890	2.863137	GGTAGAGAAGAAAGCATCGCTG	59.137	50.000	0.00	0.00	39.62	5.18
2346	6892	0.376502	GAGAAGAAAGCATCGCTGGC	59.623	55.000	0.00	0.00	39.62	4.85
2350	6896	2.042686	AGAAAGCATCGCTGGCAATA	57.957	45.000	0.00	0.00	39.62	1.90
2362	6908	3.432592	CGCTGGCAATATCTGAAGATGAG	59.567	47.826	2.99	0.00	36.05	2.90
2364	6910	5.247084	GCTGGCAATATCTGAAGATGAGAT	58.753	41.667	2.99	0.00	36.05	2.75
2371	6917	7.668492	CAATATCTGAAGATGAGATGTCCAGA	58.332	38.462	2.99	0.00	36.05	3.86
2375	6921	6.346896	TCTGAAGATGAGATGTCCAGAAATG	58.653	40.000	0.00	0.00	0.00	2.32
2381	6927	8.674263	AGATGAGATGTCCAGAAATGTATTTC	57.326	34.615	8.87	8.87	44.91	2.17
2409	6955	5.798132	TCTGACTTGTGCTTAAGATCATGT	58.202	37.500	6.67	11.60	0.00	3.21
2421	6967	8.264347	TGCTTAAGATCATGTAAACTGGATGTA	58.736	33.333	6.67	0.00	0.00	2.29
2427	6974	6.121776	TCATGTAAACTGGATGTAGGTTGT	57.878	37.500	0.00	0.00	0.00	3.32
2477	7028	5.010415	CCAGAGAACCAGAAAGCAAAAGAAT	59.990	40.000	0.00	0.00	0.00	2.40
2478	7029	6.207417	CCAGAGAACCAGAAAGCAAAAGAATA	59.793	38.462	0.00	0.00	0.00	1.75
2485	7036	4.925646	CAGAAAGCAAAAGAATAACCCTGC	59.074	41.667	0.00	0.00	0.00	4.85
2486	7037	4.835056	AGAAAGCAAAAGAATAACCCTGCT	59.165	37.500	0.00	0.00	41.72	4.24
2529	7080	7.649370	AATAGTATGATCTGCTTTCATGTCG	57.351	36.000	0.00	0.00	35.50	4.35
2530	7081	5.268118	AGTATGATCTGCTTTCATGTCGA	57.732	39.130	0.00	0.00	35.50	4.20
2536	7087	6.088173	TGATCTGCTTTCATGTCGAATTTTG	58.912	36.000	0.00	0.00	32.32	2.44
2544	7104	7.201350	GCTTTCATGTCGAATTTTGTATGTTCC	60.201	37.037	0.00	0.00	32.32	3.62
2583	7144	9.645059	TTGTCTTTTTGTTCAATTGTATGTCAA	57.355	25.926	5.13	3.04	40.53	3.18
2631	7209	9.882996	TTCAGATTATGCTTAGAAATATTTGCG	57.117	29.630	5.17	0.00	0.00	4.85
2638	7216	8.755696	ATGCTTAGAAATATTTGCGTTTTGAA	57.244	26.923	5.17	0.00	0.00	2.69
2764	7364	9.862371	GTATCATTGGGTAGTATATCTGAACAG	57.138	37.037	0.00	0.00	0.00	3.16
2771	7371	9.429109	TGGGTAGTATATCTGAACAGTTGATTA	57.571	33.333	0.00	0.00	0.00	1.75
2799	7401	2.028748	ACTCAAATGGCCATTGCAGTTC	60.029	45.455	31.28	0.00	40.13	3.01
2803	7405	0.040058	ATGGCCATTGCAGTTCTCCA	59.960	50.000	14.09	0.00	40.13	3.86
2813	7415	1.674962	GCAGTTCTCCATGCAATCCTC	59.325	52.381	0.00	0.00	42.11	3.71
2816	7418	4.746089	GCAGTTCTCCATGCAATCCTCTAT	60.746	45.833	0.00	0.00	42.11	1.98
2862	7464	1.820519	TCTGTTTTGCCATGGATCTGC	59.179	47.619	18.40	0.00	0.00	4.26
2878	7481	5.221601	TGGATCTGCTATGGAGAGTTTCATC	60.222	44.000	0.00	0.00	0.00	2.92
2912	7515	8.655935	ACTCATAAAGTTTCCCTTTGAATGAT	57.344	30.769	0.00	0.00	43.27	2.45
2937	7540	6.183347	AGTTGTGGATCCTTATCTCTTTTGG	58.817	40.000	14.23	0.00	32.29	3.28
2938	7541	5.116084	TGTGGATCCTTATCTCTTTTGGG	57.884	43.478	14.23	0.00	32.29	4.12
2940	7543	4.079730	GTGGATCCTTATCTCTTTTGGGGT	60.080	45.833	14.23	0.00	32.29	4.95
2945	7553	6.152638	TCCTTATCTCTTTTGGGGTTGAAT	57.847	37.500	0.00	0.00	0.00	2.57
2948	7556	2.956132	TCTCTTTTGGGGTTGAATGCA	58.044	42.857	0.00	0.00	0.00	3.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
173	179	2.315176	TGCATTGTTGGGTTAGCAACT	58.685	42.857	0.00	0.00	32.08	3.16
184	190	4.796830	GTGTGAAGCAGATATGCATTGTTG	59.203	41.667	15.82	1.92	37.25	3.33
260	266	1.221840	GTCCGTCCACCAGCATCAT	59.778	57.895	0.00	0.00	0.00	2.45
290	297	2.173356	GGATGGGATTGTCTCACCATGA	59.827	50.000	0.00	0.00	43.40	3.07
372	379	2.355115	GGGGTTGGATGGTCGCTT	59.645	61.111	0.00	0.00	0.00	4.68
455	462	9.046296	CAATCTCTAGTCACTTGTGTAAAGTTT	57.954	33.333	0.46	0.00	0.00	2.66
511	519	6.090898	CGGAAGAGTAGTGTCCATTACTTTTG	59.909	42.308	9.47	0.00	34.57	2.44
671	680	7.381766	TGATCACAAAACATGGAGATACTTG	57.618	36.000	0.00	0.00	30.83	3.16
1519	6064	1.393603	CTCTCGAGGTCAGCACCATA	58.606	55.000	13.56	0.00	46.68	2.74
1539	6084	1.875963	GACATTGGGCTTGACCACG	59.124	57.895	0.00	0.00	41.03	4.94
1696	6241	1.396996	CGCTTTTCGTAACATCCCAGG	59.603	52.381	0.00	0.00	0.00	4.45
2177	6723	6.037610	GCCACACACAAATTACCAATTTTCAA	59.962	34.615	0.00	0.00	38.97	2.69
2191	6737	1.923227	TTCGTTGCGCCACACACAAA	61.923	50.000	12.54	0.00	0.00	2.83
2198	6744	0.248296	TGAAAACTTCGTTGCGCCAC	60.248	50.000	4.18	2.21	0.00	5.01
2220	6766	8.142485	ACAGGAATTACCAGCTTACTAAACTA	57.858	34.615	0.00	0.00	42.04	2.24
2221	6767	7.017319	ACAGGAATTACCAGCTTACTAAACT	57.983	36.000	0.00	0.00	42.04	2.66
2224	6770	6.592607	CGAAACAGGAATTACCAGCTTACTAA	59.407	38.462	0.00	0.00	42.04	2.24
2229	6775	3.081804	CCGAAACAGGAATTACCAGCTT	58.918	45.455	0.00	0.00	42.04	3.74
2283	6829	6.434302	TCATTGGGGTTCATGAATTGATAGT	58.566	36.000	12.12	0.00	33.34	2.12
2288	6834	5.047164	TGAACTCATTGGGGTTCATGAATTG	60.047	40.000	12.12	3.74	44.28	2.32
2289	6835	5.085920	TGAACTCATTGGGGTTCATGAATT	58.914	37.500	12.12	0.00	44.28	2.17
2303	6849	3.328931	ACCCAGTGAGACATGAACTCATT	59.671	43.478	22.18	17.76	44.41	2.57
2320	6866	3.452474	CGATGCTTTCTTCTCTACCCAG	58.548	50.000	0.00	0.00	0.00	4.45
2322	6868	2.159028	AGCGATGCTTTCTTCTCTACCC	60.159	50.000	0.00	0.00	33.89	3.69
2329	6875	0.523072	TTGCCAGCGATGCTTTCTTC	59.477	50.000	0.00	0.00	36.40	2.87
2330	6876	1.180029	ATTGCCAGCGATGCTTTCTT	58.820	45.000	0.00	0.00	36.40	2.52
2340	6886	3.396560	TCATCTTCAGATATTGCCAGCG	58.603	45.455	0.00	0.00	32.63	5.18
2343	6889	6.183810	ACATCTCATCTTCAGATATTGCCA	57.816	37.500	0.00	0.00	32.63	4.92
2344	6890	5.642919	GGACATCTCATCTTCAGATATTGCC	59.357	44.000	0.00	0.00	32.63	4.52
2346	6892	7.668492	TCTGGACATCTCATCTTCAGATATTG	58.332	38.462	0.00	0.00	32.63	1.90
2350	6896	6.556974	TTTCTGGACATCTCATCTTCAGAT	57.443	37.500	0.00	0.00	34.56	2.90
2371	6917	8.078596	GCACAAGTCAGAAAGAGAAATACATTT	58.921	33.333	0.00	0.00	0.00	2.32
2375	6921	6.793492	AGCACAAGTCAGAAAGAGAAATAC	57.207	37.500	0.00	0.00	0.00	1.89
2381	6927	6.648310	TGATCTTAAGCACAAGTCAGAAAGAG	59.352	38.462	0.00	0.00	0.00	2.85
2382	6928	6.524734	TGATCTTAAGCACAAGTCAGAAAGA	58.475	36.000	0.00	0.00	0.00	2.52
2383	6929	6.791887	TGATCTTAAGCACAAGTCAGAAAG	57.208	37.500	0.00	0.00	0.00	2.62
2387	6933	7.601073	TTACATGATCTTAAGCACAAGTCAG	57.399	36.000	0.00	2.39	0.00	3.51
2395	6941	7.112122	ACATCCAGTTTACATGATCTTAAGCA	58.888	34.615	0.00	0.00	0.00	3.91
2421	6967	8.962679	TGTTTCAACAGAAAATTAGTACAACCT	58.037	29.630	0.00	0.00	33.40	3.50
2427	6974	8.626526	GGTCCTTGTTTCAACAGAAAATTAGTA	58.373	33.333	0.00	0.00	40.50	1.82
2506	7057	6.986250	TCGACATGAAAGCAGATCATACTAT	58.014	36.000	0.00	0.00	35.80	2.12
2558	7118	9.814899	ATTGACATACAATTGAACAAAAAGACA	57.185	25.926	13.59	0.00	45.60	3.41
2607	7176	9.669353	AACGCAAATATTTCTAAGCATAATCTG	57.331	29.630	0.00	0.00	0.00	2.90
2697	7286	4.353737	CAAAACATACATGATTCCCAGCG	58.646	43.478	0.00	0.00	0.00	5.18
2744	7344	7.727578	TCAACTGTTCAGATATACTACCCAA	57.272	36.000	6.83	0.00	0.00	4.12
2760	7360	5.670792	TGAGTACGGGATAATCAACTGTT	57.329	39.130	0.00	0.00	35.00	3.16
2764	7364	5.277828	GCCATTTGAGTACGGGATAATCAAC	60.278	44.000	0.00	0.00	45.13	3.18
2771	7371	0.916086	TGGCCATTTGAGTACGGGAT	59.084	50.000	0.00	0.00	0.00	3.85
2775	7375	1.472082	TGCAATGGCCATTTGAGTACG	59.528	47.619	28.68	15.97	40.13	3.67
2799	7401	5.662208	AGATAGGATAGAGGATTGCATGGAG	59.338	44.000	0.00	0.00	0.00	3.86
2803	7405	6.503217	TGGAAAGATAGGATAGAGGATTGCAT	59.497	38.462	0.00	0.00	0.00	3.96
2808	7410	8.748179	TTTCATGGAAAGATAGGATAGAGGAT	57.252	34.615	0.00	0.00	0.00	3.24
2862	7464	8.663911	GTTCTTTTCAGATGAAACTCTCCATAG	58.336	37.037	7.49	1.20	43.01	2.23
2896	7499	6.208599	TCCACAACTATCATTCAAAGGGAAAC	59.791	38.462	0.00	0.00	39.39	2.78
2912	7515	7.338710	CCAAAAGAGATAAGGATCCACAACTA	58.661	38.462	15.82	0.00	31.81	2.24
2914	7517	5.358160	CCCAAAAGAGATAAGGATCCACAAC	59.642	44.000	15.82	2.71	31.81	3.32
2940	7543	6.071784	AGTGATCAGCTTATTGTTGCATTCAA	60.072	34.615	0.00	7.18	0.00	2.69
2945	7553	4.074259	ACAGTGATCAGCTTATTGTTGCA	58.926	39.130	0.00	0.00	0.00	4.08
2948	7556	4.940046	CCTCACAGTGATCAGCTTATTGTT	59.060	41.667	2.97	0.00	0.00	2.83
2955	7563	2.093606	CACATCCTCACAGTGATCAGCT	60.094	50.000	2.97	0.00	35.33	4.24
2957	7565	2.235650	ACCACATCCTCACAGTGATCAG	59.764	50.000	2.97	0.00	35.33	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.