AutoCloner

Multiple sequence alignment - TraesCS6A01G109800

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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	TraesCS6A01G109800	chr6A	100.000	2680	0	0	1	2680	79127048	79124369	0.000000e+00	4950.0
1	TraesCS6A01G109800	chr2D	95.685	2688	101	11	1	2680	306151149	306153829	0.000000e+00	4307.0
2	TraesCS6A01G109800	chr2D	95.510	2472	98	8	215	2680	637310224	637307760	0.000000e+00	3938.0
3	TraesCS6A01G109800	chr2D	95.469	2472	97	11	215	2680	17982853	17985315	0.000000e+00	3930.0
4	TraesCS6A01G109800	chr2A	94.792	2688	129	9	1	2680	444301181	444303865	0.000000e+00	4178.0
5	TraesCS6A01G109800	chrUn	95.916	2473	86	10	215	2680	257942593	257945057	0.000000e+00	3993.0
6	TraesCS6A01G109800	chrUn	95.714	2473	86	11	215	2680	233526787	233524328	0.000000e+00	3962.0
7	TraesCS6A01G109800	chr4D	95.512	2473	96	10	215	2680	123687443	123689907	0.000000e+00	3938.0
8	TraesCS6A01G109800	chr6D	95.148	2473	107	8	215	2680	283185893	283188359	0.000000e+00	3890.0
9	TraesCS6A01G109800	chr7D	94.984	2472	109	10	215	2680	307087978	307090440	0.000000e+00	3864.0
10	TraesCS6A01G109800	chr7D	90.847	437	31	6	1	435	307193095	307193524	6.430000e-161	577.0
11	TraesCS6A01G109800	chr7D	90.115	435	37	4	1	435	306583564	306583992	6.480000e-156	560.0
12	TraesCS6A01G109800	chr2B	93.919	296	12	4	1	295	357341396	357341686	2.450000e-120	442.0
13	TraesCS6A01G109800	chr2B	92.857	294	17	2	2	295	357715623	357715912	8.870000e-115	424.0
14	TraesCS6A01G109800	chr2B	96.429	56	2	0	1	56	357538342	357538397	2.840000e-15	93.5

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	TraesCS6A01G109800	chr6A	79124369	79127048	2679	True	4950	4950	100.000	1	2680	1	chr6A.!!$R1	2679
1	TraesCS6A01G109800	chr2D	306151149	306153829	2680	False	4307	4307	95.685	1	2680	1	chr2D.!!$F2	2679
2	TraesCS6A01G109800	chr2D	637307760	637310224	2464	True	3938	3938	95.510	215	2680	1	chr2D.!!$R1	2465
3	TraesCS6A01G109800	chr2D	17982853	17985315	2462	False	3930	3930	95.469	215	2680	1	chr2D.!!$F1	2465
4	TraesCS6A01G109800	chr2A	444301181	444303865	2684	False	4178	4178	94.792	1	2680	1	chr2A.!!$F1	2679
5	TraesCS6A01G109800	chrUn	257942593	257945057	2464	False	3993	3993	95.916	215	2680	1	chrUn.!!$F1	2465
6	TraesCS6A01G109800	chrUn	233524328	233526787	2459	True	3962	3962	95.714	215	2680	1	chrUn.!!$R1	2465
7	TraesCS6A01G109800	chr4D	123687443	123689907	2464	False	3938	3938	95.512	215	2680	1	chr4D.!!$F1	2465
8	TraesCS6A01G109800	chr6D	283185893	283188359	2466	False	3890	3890	95.148	215	2680	1	chr6D.!!$F1	2465
9	TraesCS6A01G109800	chr7D	307087978	307090440	2462	False	3864	3864	94.984	215	2680	1	chr7D.!!$F2	2465

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
759	762	0.616395	TGGGCGTGGATTCTACCTCA	60.616	55.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2112	2125	1.202687	GGGCGATCCATCTTGATGACA	60.203	52.381	11.76	0.0	35.0	3.58	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
98	99	4.695606	AGGTGAGGTGGGACTTAAGAATA	58.304	43.478	10.09	0.00	0.00	1.75
99	100	5.289510	AGGTGAGGTGGGACTTAAGAATAT	58.710	41.667	10.09	0.00	0.00	1.28
136	137	4.083581	TCTTCAAAGCAAGAATTAGCGC	57.916	40.909	0.00	0.00	35.48	5.92
151	152	2.113860	AGCGCATAGAAAGGAAGCAA	57.886	45.000	11.47	0.00	0.00	3.91
167	168	4.502087	GGAAGCAACATTTCCTTTCAGCTT	60.502	41.667	0.00	0.00	43.03	3.74
268	269	9.409253	AGTAGTAGAGGGATAGGTACTTATTCT	57.591	37.037	3.49	3.71	41.75	2.40
356	357	7.038154	TCTCAATCCAAAACTGATTCGTTTT	57.962	32.000	11.14	11.14	45.20	2.43
378	379	1.030488	TGGAAAAACCAACGCCGACA	61.030	50.000	0.00	0.00	46.75	4.35
444	445	4.662278	TGAAAAAGATGGAGTTACCTGGG	58.338	43.478	0.00	0.00	39.86	4.45
512	513	8.504005	TCTCTCACGTCCATTCTTTTATTTTTC	58.496	33.333	0.00	0.00	0.00	2.29
590	593	2.644798	AGGCACCTACCTTGAAAGACAT	59.355	45.455	0.00	0.00	36.28	3.06
621	624	7.448420	TCCTTTTCAAAATGTATGGAATTGCA	58.552	30.769	0.79	0.79	0.00	4.08
683	686	5.573380	ATGGTAGAATCATACATGTGGCT	57.427	39.130	9.11	0.00	0.00	4.75
754	757	1.906574	AGTTTCTGGGCGTGGATTCTA	59.093	47.619	0.00	0.00	0.00	2.10
759	762	0.616395	TGGGCGTGGATTCTACCTCA	60.616	55.000	0.00	0.00	0.00	3.86
776	779	7.463431	TCTACCTCAGATCTAAGGGATACTTC	58.537	42.308	16.78	0.00	40.64	3.01
903	906	2.099921	TCTAAGTGCTCCGAATCAGCTC	59.900	50.000	0.00	0.00	37.79	4.09
914	917	4.023193	TCCGAATCAGCTCTTTTTGGAAAC	60.023	41.667	6.39	0.00	31.40	2.78
1152	1156	4.969484	ACGAACAAATAGGTGGTCTTTCT	58.031	39.130	0.00	0.00	32.72	2.52
1187	1191	4.099419	ACAAAAGTTTTTCCCTCGCATCTT	59.901	37.500	0.00	0.00	0.00	2.40
1341	1348	6.662865	TTCAAAGACATGGGCTTCATTTTA	57.337	33.333	0.00	0.00	32.92	1.52
1468	1476	8.349245	CGTTTATTTGCTAATATGATGGTTGGA	58.651	33.333	1.38	0.00	0.00	3.53
1511	1519	2.375174	AGTGGGTTTGCTTGGACTATGA	59.625	45.455	0.00	0.00	0.00	2.15
1586	1594	8.696043	TTATAGTTCTAGCATTAACCGGTCTA	57.304	34.615	8.04	3.33	0.00	2.59
1634	1642	7.043961	AGCTCATGTTTCTACGATCTCAATA	57.956	36.000	0.00	0.00	0.00	1.90
1676	1684	7.649533	TGCTACAAATCTCCATCAAAATGAT	57.350	32.000	0.00	0.00	37.65	2.45
1678	1686	7.977293	TGCTACAAATCTCCATCAAAATGATTG	59.023	33.333	0.00	0.00	34.28	2.67
1988	2001	7.121168	GGGAACATCAAGATGAATGAGTTAACA	59.879	37.037	16.39	0.00	41.20	2.41
2137	2150	2.115427	TCAAGATGGATCGCCCTTACA	58.885	47.619	0.00	0.00	35.38	2.41
2169	2182	6.096423	ACGAACTCATACTAATGCAAGGACTA	59.904	38.462	0.00	0.00	32.76	2.59
2185	2198	2.742053	GGACTACTCGCAAGCAAATTCA	59.258	45.455	0.00	0.00	37.18	2.57
2192	2205	3.577667	TCGCAAGCAAATTCAGAAATGG	58.422	40.909	0.00	0.00	37.18	3.16
2220	2233	2.289547	GCTACCGAAAGAACAAGCAACA	59.710	45.455	0.00	0.00	0.00	3.33
2223	2236	2.354821	ACCGAAAGAACAAGCAACAGAC	59.645	45.455	0.00	0.00	0.00	3.51
2275	2288	3.186613	CGTTTTCTTGCTCCTTGGTACTC	59.813	47.826	0.00	0.00	0.00	2.59
2334	2347	2.804697	TCGTTCGATGTCTTGAACCA	57.195	45.000	0.00	0.00	41.12	3.67
2421	2434	2.016393	CTCACTTCGCCCGCCTATCA	62.016	60.000	0.00	0.00	0.00	2.15
2496	2509	5.008712	CACTATCGCTCATGACTGGTAGTAA	59.991	44.000	12.70	0.00	0.00	2.24
2534	2547	0.872388	CGGCCTTTGTTAAGCTTCGT	59.128	50.000	0.00	0.00	0.00	3.85
2640	2653	1.809619	GCCAACGCACGCTAGATGA	60.810	57.895	0.00	0.00	34.03	2.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
98	99	5.752036	TGAAGAGATGTTCCAGACAAGAT	57.248	39.130	0.00	0.00	42.62	2.40
99	100	5.551305	TTGAAGAGATGTTCCAGACAAGA	57.449	39.130	0.00	0.00	42.62	3.02
151	152	9.665719	TTTTTAAAAGAAGCTGAAAGGAAATGT	57.334	25.926	0.14	0.00	0.00	2.71
167	168	2.446285	TCCCCGGGGACTTTTTAAAAGA	59.554	45.455	39.67	11.95	39.76	2.52
268	269	1.227527	CAATGATACCGCTGCCCGA	60.228	57.895	0.00	0.00	40.02	5.14
378	379	6.013032	TGAAAGGAAAGGAGACTGATCTTGAT	60.013	38.462	0.00	0.00	42.68	2.57
512	513	1.483415	CCAAGGCAGGATGGGAAAATG	59.517	52.381	0.00	0.00	35.86	2.32
590	593	5.480073	CCATACATTTTGAAAAGGAGGTCCA	59.520	40.000	9.45	0.00	38.89	4.02
621	624	2.556622	CAAAGCCTGTGTATTTTCGGGT	59.443	45.455	0.00	0.00	33.07	5.28
754	757	5.103043	TGGAAGTATCCCTTAGATCTGAGGT	60.103	44.000	27.00	15.24	45.95	3.85
759	762	9.851267	AAATCTATGGAAGTATCCCTTAGATCT	57.149	33.333	14.14	0.00	45.95	2.75
776	779	6.677913	CGCCCCTTAAAATGTAAATCTATGG	58.322	40.000	0.00	0.00	0.00	2.74
792	795	1.743995	GAAGCTTTCGCGCCCCTTA	60.744	57.895	0.00	0.00	42.32	2.69
869	872	2.756691	TTAGAGCGCTACCCGGCA	60.757	61.111	11.50	0.00	37.44	5.69
883	886	2.100584	AGAGCTGATTCGGAGCACTTAG	59.899	50.000	0.00	0.00	39.05	2.18
914	917	1.838715	TGGCAAATTGATCCAATGGGG	59.161	47.619	0.00	0.00	34.04	4.96
994	997	3.048501	CGACAGTGAGCAGCATATACAG	58.951	50.000	0.00	0.00	0.00	2.74
1187	1191	9.505995	GAAATAACGAAAAAGTAAAAGTGACCA	57.494	29.630	0.00	0.00	0.00	4.02
1314	1320	4.151121	TGAAGCCCATGTCTTTGAAATCA	58.849	39.130	0.00	0.00	0.00	2.57
1391	1399	9.153479	ACAATAAGAGATTAGCTCAAGGAGTAT	57.847	33.333	0.00	0.00	46.45	2.12
1531	1539	6.407752	GGGACCAAGATTTCCTACGAAATAGA	60.408	42.308	0.00	0.00	46.48	1.98
1586	1594	8.091449	GCTTGTGATATAGCTACACCTAATTCT	58.909	37.037	9.71	0.00	34.57	2.40
1855	1867	4.701651	TCGGTAAGTGATCTAGCTCCTA	57.298	45.455	0.00	0.00	0.00	2.94
1872	1884	3.189287	GCAATTCTGACTTGTTCATCGGT	59.811	43.478	9.14	0.00	32.17	4.69
1929	1942	3.793797	TCGATAACGAAGCTGAATGGA	57.206	42.857	0.00	0.00	45.74	3.41
1988	2001	7.336679	TGTTCAATTTGGTCGATCTGATACATT	59.663	33.333	0.00	0.00	0.00	2.71
1990	2003	6.169800	TGTTCAATTTGGTCGATCTGATACA	58.830	36.000	0.00	0.00	0.00	2.29
2104	2117	6.016527	CGATCCATCTTGATGACAAATTCCAT	60.017	38.462	11.76	0.00	35.49	3.41
2112	2125	1.202687	GGGCGATCCATCTTGATGACA	60.203	52.381	11.76	0.00	35.00	3.58
2137	2150	4.771590	TTAGTATGAGTTCGTTGACCGT	57.228	40.909	0.00	0.00	37.94	4.83
2169	2182	3.988379	TTTCTGAATTTGCTTGCGAGT	57.012	38.095	2.14	0.00	0.00	4.18
2185	2198	2.838202	TCGGTAGCCTTCTTCCATTTCT	59.162	45.455	0.00	0.00	30.86	2.52
2192	2205	3.660865	TGTTCTTTCGGTAGCCTTCTTC	58.339	45.455	0.00	0.00	0.00	2.87
2220	2233	1.608717	AAGGGATGAGCGCGAAGTCT	61.609	55.000	12.10	0.00	34.07	3.24
2223	2236	2.817423	GCAAGGGATGAGCGCGAAG	61.817	63.158	12.10	0.00	34.07	3.79
2421	2434	1.286260	GACGAAGCCGAGCCGATAT	59.714	57.895	0.00	0.00	39.50	1.63
2462	2475	2.168313	TGAGCGATAGTGAAGCCATCAA	59.832	45.455	0.00	0.00	40.50	2.57
2496	2509	5.775701	AGGCCGAATACTACATAGAGACAAT	59.224	40.000	0.00	0.00	0.00	2.71
2513	2526	1.533731	CGAAGCTTAACAAAGGCCGAA	59.466	47.619	0.00	0.00	0.00	4.30
2547	2560	1.884926	GAGGCATTCGGGAAGCGAG	60.885	63.158	0.00	0.00	0.00	5.03

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.