AutoCloner

Multiple sequence alignment - TraesCS4B01G276900

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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	TraesCS4B01G276900	chr4B	100.000	3797	0	0	1	3797	558577472	558581268	0.000000e+00	7012
1	TraesCS4B01G276900	chr4B	83.019	530	78	11	3261	3781	340553986	340553460	1.600000e-128	470
2	TraesCS4B01G276900	chr4D	97.625	3790	72	10	14	3797	446427392	446431169	0.000000e+00	6484
3	TraesCS4B01G276900	chr4D	89.544	373	28	6	3433	3797	85665190	85665559	2.670000e-126	462
4	TraesCS4B01G276900	chr4D	84.109	258	25	9	3060	3312	85600593	85600839	6.340000e-58	235
5	TraesCS4B01G276900	chr4D	86.029	136	18	1	3313	3448	85627507	85627641	1.100000e-30	145
6	TraesCS4B01G276900	chr4A	95.327	3809	137	16	1	3788	21066313	21062525	0.000000e+00	6010
7	TraesCS4B01G276900	chr4A	91.982	1322	80	12	1	1307	21074702	21073392	0.000000e+00	1831
8	TraesCS4B01G276900	chr4A	98.701	77	1	0	1294	1370	21069349	21069273	1.840000e-28	137

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	TraesCS4B01G276900	chr4B	558577472	558581268	3796	False	7012.0	7012	100.000	1	3797	1	chr4B.!!$F1	3796
1	TraesCS4B01G276900	chr4B	340553460	340553986	526	True	470.0	470	83.019	3261	3781	1	chr4B.!!$R1	520
2	TraesCS4B01G276900	chr4D	446427392	446431169	3777	False	6484.0	6484	97.625	14	3797	1	chr4D.!!$F4	3783
3	TraesCS4B01G276900	chr4A	21062525	21069349	6824	True	3073.5	6010	97.014	1	3788	2	chr4A.!!$R2	3787
4	TraesCS4B01G276900	chr4A	21073392	21074702	1310	True	1831.0	1831	91.982	1	1307	1	chr4A.!!$R1	1306

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
318	3356	1.599542	GCACCTTACTGATCGGCATTC	59.400	52.381	0.0	0.0	0.0	2.67	F
1269	4322	1.843851	TCTGGTGAACTTGTCCTTGGT	59.156	47.619	0.0	0.0	0.0	3.67	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2061	5114	0.892814	GGCTCAATCCAGGGCTATGC	60.893	60.000	0.0	0.0	0.0	3.14	R
2841	5895	1.816835	TCTACCACTGCTACCTGTTCG	59.183	52.381	0.0	0.0	0.0	3.95	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
243	3281	4.020218	CCCACTGATCTCCACAGTTTCTAA	60.020	45.833	0.00	0.00	44.69	2.10
318	3356	1.599542	GCACCTTACTGATCGGCATTC	59.400	52.381	0.00	0.00	0.00	2.67
324	3362	4.692625	CCTTACTGATCGGCATTCCTATTG	59.307	45.833	0.00	0.00	0.00	1.90
325	3363	5.511373	CCTTACTGATCGGCATTCCTATTGA	60.511	44.000	0.00	0.00	0.00	2.57
328	3366	6.114187	ACTGATCGGCATTCCTATTGATAA	57.886	37.500	0.00	0.00	0.00	1.75
787	3837	2.949142	TCGCTTTTACATCGTAGCACA	58.051	42.857	0.00	0.00	33.29	4.57
837	3887	3.277142	TGCATCAGATGTGCATCTCTT	57.723	42.857	12.18	0.56	46.76	2.85
891	3943	2.136229	GGGATTACCGGCGTAGGGT	61.136	63.158	6.01	0.00	41.62	4.34
943	3996	9.744468	TCTTGTTTTGCTTTCTCCTTTTTATAC	57.256	29.630	0.00	0.00	0.00	1.47
1269	4322	1.843851	TCTGGTGAACTTGTCCTTGGT	59.156	47.619	0.00	0.00	0.00	3.67
1416	4469	2.890371	GCATTTGCTGGGGCTGAG	59.110	61.111	0.00	0.00	39.59	3.35
1485	4538	8.212259	AGTTATTCTTCCTAGCATCCATGTAT	57.788	34.615	0.00	0.00	0.00	2.29
1635	4688	4.884164	GCAGCAGGATTTAGGACTATTGTT	59.116	41.667	0.00	0.00	0.00	2.83
1815	4868	3.006430	CACCCGGTTTGGCTAAGATTTTT	59.994	43.478	0.00	0.00	35.87	1.94
2238	5291	1.812571	GAAAATGGCAGTGTCGATGGT	59.187	47.619	0.00	0.00	0.00	3.55
2622	5675	3.383505	TGTCACCTATGGACAACTATCCG	59.616	47.826	0.00	0.00	41.96	4.18
2841	5895	3.426292	GGGCAGATCGTTTTTCTAGTTGC	60.426	47.826	0.00	0.00	0.00	4.17
3347	6403	0.035317	TCATGTCGCTTGCCTTGTCT	59.965	50.000	0.00	0.00	0.00	3.41
3406	6464	4.338682	CCGAGGCTTCAGTAACACTACTAT	59.661	45.833	0.00	0.00	36.14	2.12
3744	6808	3.510459	TCTCATTCTTCAGGACTGGTGA	58.490	45.455	0.00	0.00	0.00	4.02

Showing 1 to 20 of 20 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
250	3288	1.153168	GTGTGCCGGGTATGCATCT	60.153	57.895	0.19	0.00	41.46	2.90
252	3290	2.124320	GGTGTGCCGGGTATGCAT	60.124	61.111	2.18	3.79	41.46	3.96
264	3302	3.056962	CGGATCTAGATCTGGATGGTGTG	60.057	52.174	27.62	7.14	39.85	3.82
328	3366	9.150348	GGTTGCTGCATATTTTATTACTTTGTT	57.850	29.630	1.84	0.00	0.00	2.83
362	3400	6.313658	TCTGAATGTTTGGTATCAGAACATCG	59.686	38.462	13.42	8.18	43.79	3.84
787	3837	5.104402	TGGTCAGATTGTGTGGTGATATCAT	60.104	40.000	9.02	0.00	0.00	2.45
837	3887	1.677633	TCATCGTGACTGGGAGCGA	60.678	57.895	0.00	0.00	37.76	4.93
874	3924	1.068585	CACCCTACGCCGGTAATCC	59.931	63.158	1.90	0.00	30.42	3.01
943	3996	3.500982	CCACATGAACAAAATAGCCACG	58.499	45.455	0.00	0.00	0.00	4.94
1269	4322	1.002624	GCAAGATCCGTCACCCCAA	60.003	57.895	0.00	0.00	0.00	4.12
1416	4469	1.619827	CTGAGAGCATCATCCTCCTCC	59.380	57.143	0.00	0.00	37.28	4.30
1485	4538	3.724508	ACATGACGTGGAAATGCAAAA	57.275	38.095	0.00	0.00	0.00	2.44
1635	4688	2.040278	ACCAGCTTCAAATGGCAGTAGA	59.960	45.455	0.00	0.00	40.45	2.59
1815	4868	3.624777	GCTCAGATTCAAATCCTTCCCA	58.375	45.455	0.00	0.00	36.04	4.37
2061	5114	0.892814	GGCTCAATCCAGGGCTATGC	60.893	60.000	0.00	0.00	0.00	3.14
2238	5291	1.953686	GCCACTTGCTCCTTACACAAA	59.046	47.619	0.00	0.00	36.87	2.83
2622	5675	9.638239	TCAAAAGCTTGGAACACATTATTTATC	57.362	29.630	0.00	0.00	39.29	1.75
2841	5895	1.816835	TCTACCACTGCTACCTGTTCG	59.183	52.381	0.00	0.00	0.00	3.95
3535	6595	1.401552	CAACCACTCACCAATATGGCG	59.598	52.381	0.00	0.00	42.67	5.69
3553	6613	8.477984	GCATTTATTGCCTTTTGTCTTATCAA	57.522	30.769	0.00	0.00	46.15	2.57

Showing 1 to 20 of 20 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.