AutoCloner

Multiple sequence alignment - TraesCS3B01G333700

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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	TraesCS3B01G333700	chr3B	100.000	3783	0	0	1	3783	540206332	540210114	0.000000e+00	6986.0
1	TraesCS3B01G333700	chr3D	87.835	2351	111	61	1478	3783	414373751	414375971	0.000000e+00	2595.0
2	TraesCS3B01G333700	chr3D	93.617	1269	44	20	1	1253	414372346	414373593	0.000000e+00	1860.0
3	TraesCS3B01G333700	chr3D	94.595	148	6	2	1310	1456	414373618	414373764	1.060000e-55	228.0
4	TraesCS3B01G333700	chr3A	89.448	1611	77	37	1478	3049	536633709	536632153	0.000000e+00	1947.0
5	TraesCS3B01G333700	chr3A	90.999	1111	75	14	9	1110	536635229	536634135	0.000000e+00	1474.0
6	TraesCS3B01G333700	chr3A	90.563	604	14	16	3073	3671	536629950	536629385	0.000000e+00	760.0
7	TraesCS3B01G333700	chr3A	87.772	368	19	12	1112	1458	536634056	536633694	1.270000e-109	407.0
8	TraesCS3B01G333700	chr7A	96.774	31	1	0	2722	2752	434676755	434676725	7.000000e-03	52.8

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	TraesCS3B01G333700	chr3B	540206332	540210114	3782	False	6986	6986	100.000000	1	3783	1	chr3B.!!$F1	3782
1	TraesCS3B01G333700	chr3D	414372346	414375971	3625	False	1561	2595	92.015667	1	3783	3	chr3D.!!$F1	3782
2	TraesCS3B01G333700	chr3A	536629385	536635229	5844	True	1147	1947	89.695500	9	3671	4	chr3A.!!$R1	3662

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
636	642	0.311790	CAAGTTGGTGTGCTCGCATT	59.688	50.0	1.32	0.0	0.0	3.56	F
1932	2097	0.031994	CCGCACCTTCCCAACTTTTG	59.968	55.0	0.00	0.0	0.0	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2073	2244	0.249699	CGGGTATGCTGCCACGATTA	60.250	55.0	0.0	0.0	0.0	1.75	R
3245	5624	0.250793	ACGGGAGAAACACACACACA	59.749	50.0	0.0	0.0	0.0	3.72	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)

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	7.441836	ACTACATGTCAACTACAACTTGATGA	58.558	34.615	0.00	0.00	42.70	2.92
42	47	7.959175	ACTACAACTTGATGACAGGTAGTTTA	58.041	34.615	0.00	0.00	37.31	2.01
66	71	1.535028	CTGGACGCATGTTAAACTGCA	59.465	47.619	10.20	0.00	38.30	4.41
67	72	2.158559	TGGACGCATGTTAAACTGCAT	58.841	42.857	10.20	0.00	38.30	3.96
296	301	4.201960	GCCTCCTAGTAAAAATTGCTCAGC	60.202	45.833	0.00	0.00	0.00	4.26
403	409	3.469008	TGAGTTGACATTTGACGACCT	57.531	42.857	0.00	0.00	0.00	3.85
625	631	3.593442	TCAACAATCTCCCAAGTTGGT	57.407	42.857	20.54	0.00	41.14	3.67
629	635	1.270550	CAATCTCCCAAGTTGGTGTGC	59.729	52.381	20.54	0.00	35.17	4.57
632	638	1.227823	TCCCAAGTTGGTGTGCTCG	60.228	57.895	20.54	3.55	35.17	5.03
633	639	2.639286	CCAAGTTGGTGTGCTCGC	59.361	61.111	14.21	0.00	31.35	5.03
636	642	0.311790	CAAGTTGGTGTGCTCGCATT	59.688	50.000	1.32	0.00	0.00	3.56
637	643	1.535028	CAAGTTGGTGTGCTCGCATTA	59.465	47.619	1.32	0.00	0.00	1.90
638	644	2.113860	AGTTGGTGTGCTCGCATTAT	57.886	45.000	1.32	0.00	0.00	1.28
639	645	1.739466	AGTTGGTGTGCTCGCATTATG	59.261	47.619	1.32	0.00	0.00	1.90
641	647	2.675844	GTTGGTGTGCTCGCATTATGTA	59.324	45.455	1.32	0.00	0.00	2.29
644	650	4.893608	TGGTGTGCTCGCATTATGTATAT	58.106	39.130	1.32	0.00	0.00	0.86
673	679	5.405269	GGAATTGGTGTTGAAATGCAGTTAC	59.595	40.000	0.00	0.00	0.00	2.50
674	680	5.789643	ATTGGTGTTGAAATGCAGTTACT	57.210	34.783	0.00	0.00	0.00	2.24
679	685	7.199766	TGGTGTTGAAATGCAGTTACTAAAAG	58.800	34.615	0.00	0.00	0.00	2.27
681	687	7.704899	GGTGTTGAAATGCAGTTACTAAAAGTT	59.295	33.333	0.00	0.00	0.00	2.66
682	688	9.724839	GTGTTGAAATGCAGTTACTAAAAGTTA	57.275	29.630	0.00	0.00	0.00	2.24
694	700	8.610035	AGTTACTAAAAGTTAAGTGTTGACAGC	58.390	33.333	0.00	0.00	0.00	4.40
759	765	3.139077	GTGCCTTGTTGTAACTAGCTGT	58.861	45.455	0.00	0.00	31.71	4.40
812	818	1.585002	CGTGTGTTTGTTGGTGGCG	60.585	57.895	0.00	0.00	0.00	5.69
813	819	1.876263	GTGTGTTTGTTGGTGGCGC	60.876	57.895	0.00	0.00	0.00	6.53

Showing 1 to 25 of 198 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
42	47	3.938963	CAGTTTAACATGCGTCCAGGTAT	59.061	43.478	0.00	0.00	34.41	2.73
66	71	4.156455	ACCTGCAGAAACGATGGAATAT	57.844	40.909	17.39	0.00	0.00	1.28
67	72	3.627395	ACCTGCAGAAACGATGGAATA	57.373	42.857	17.39	0.00	0.00	1.75
218	223	8.157476	AGATTTCAGTTCTTGGTACTTGTGTAT	58.843	33.333	0.00	0.00	0.00	2.29
270	275	3.696548	AGCAATTTTTACTAGGAGGCTGC	59.303	43.478	0.00	0.00	0.00	5.25
296	301	1.278172	CCTTCGTATGCCGCGATCAG	61.278	60.000	8.23	0.00	38.21	2.90
364	369	1.067706	CATTTGGGTCTTGCGCATCAA	60.068	47.619	12.75	8.64	39.84	2.57
426	432	5.796350	AACAGCGTAAACCAACATCTATC	57.204	39.130	0.00	0.00	0.00	2.08
559	565	9.632638	AGCTATACATCAACCATTACATTTTCT	57.367	29.630	0.00	0.00	0.00	2.52
625	631	6.589907	CCACTTATATACATAATGCGAGCACA	59.410	38.462	0.00	0.00	0.00	4.57
637	643	9.693739	TTCAACACCAATTCCACTTATATACAT	57.306	29.630	0.00	0.00	0.00	2.29
638	644	9.521841	TTTCAACACCAATTCCACTTATATACA	57.478	29.630	0.00	0.00	0.00	2.29
641	647	7.981225	GCATTTCAACACCAATTCCACTTATAT	59.019	33.333	0.00	0.00	0.00	0.86
644	650	5.069648	TGCATTTCAACACCAATTCCACTTA	59.930	36.000	0.00	0.00	0.00	2.24
673	679	7.126398	GTCAGCTGTCAACACTTAACTTTTAG	58.874	38.462	14.67	0.00	0.00	1.85
674	680	6.037830	GGTCAGCTGTCAACACTTAACTTTTA	59.962	38.462	14.67	0.00	0.00	1.52
679	685	3.248602	CAGGTCAGCTGTCAACACTTAAC	59.751	47.826	14.67	0.00	0.00	2.01
681	687	2.434336	ACAGGTCAGCTGTCAACACTTA	59.566	45.455	14.67	0.00	0.00	2.24
682	688	1.210478	ACAGGTCAGCTGTCAACACTT	59.790	47.619	14.67	0.00	0.00	3.16
743	749	4.682778	AGTGGACAGCTAGTTACAACAA	57.317	40.909	0.00	0.00	0.00	2.83
759	765	1.300963	GGCTGCCAGATCAAGTGGA	59.699	57.895	15.17	0.00	37.23	4.02
812	818	4.778143	ATTGACAGGGACCGCGGC	62.778	66.667	28.58	18.35	0.00	6.53
813	819	2.046314	AATTGACAGGGACCGCGG	60.046	61.111	26.86	26.86	0.00	6.46
862	868	5.205759	GGAAATATCCATCCAAAAGCCAG	57.794	43.478	0.00	0.00	45.79	4.85
879	885	3.347216	CGTTGAGATTGGTGAGGGAAAT	58.653	45.455	0.00	0.00	0.00	2.17

Showing 1 to 25 of 167 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.