AutoCloner

Multiple sequence alignment - TraesCS1B01G222000

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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	TraesCS1B01G222000	chr1B	100.000	5225	0	0	1	5225	399332026	399337250	0.000000e+00	9649
1	TraesCS1B01G222000	chr1B	90.141	284	27	1	2028	2311	612222087	612222369	8.270000e-98	368
2	TraesCS1B01G222000	chr1D	96.046	4679	144	27	4	4658	297162037	297166698	0.000000e+00	7577
3	TraesCS1B01G222000	chr1D	87.319	276	33	1	4952	5225	297321060	297321335	1.090000e-81	315
4	TraesCS1B01G222000	chr1A	95.232	3943	118	16	626	4546	369694584	369698478	0.000000e+00	6176
5	TraesCS1B01G222000	chr1A	80.952	462	61	17	4	451	369693925	369694373	1.800000e-89	340
6	TraesCS1B01G222000	chr4A	89.490	314	32	1	1998	2311	521198675	521198987	3.790000e-106	396

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	TraesCS1B01G222000	chr1B	399332026	399337250	5224	False	9649	9649	100.000	1	5225	1	chr1B.!!$F1	5224
1	TraesCS1B01G222000	chr1D	297162037	297166698	4661	False	7577	7577	96.046	4	4658	1	chr1D.!!$F1	4654
2	TraesCS1B01G222000	chr1A	369693925	369698478	4553	False	3258	6176	88.092	4	4546	2	chr1A.!!$F1	4542

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
328	331	0.465097	GGAGGGACCGACGATCTACA	60.465	60.000	0.00	0.00	0.00	2.74	F
331	334	0.662085	GGGACCGACGATCTACAGAC	59.338	60.000	0.00	0.00	0.00	3.51	F
1247	1369	0.670854	GAGGTCAGACAAAGGGACGC	60.671	60.000	2.17	0.00	32.39	5.19	F
1306	1428	1.069765	GCGACCATGGATCCATCGT	59.930	57.895	28.10	26.02	33.90	3.73	F
2008	2130	1.302511	TCTTCCTTGTTGCCTCCGC	60.303	57.895	0.00	0.00	0.00	5.54	F
2844	2966	1.781429	CGTCTTATGAATCCAGTCGCG	59.219	52.381	0.00	0.00	0.00	5.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1479	1601	0.108424	ACTCAGCAGCGACAGATTCC	60.108	55.000	0.00	0.00	0.00	3.01	R
1893	2015	0.179078	CAGGAGCAGAGCTAGCCTTG	60.179	60.000	12.13	11.34	39.88	3.61	R
2269	2391	1.273759	TCTGCCATCTCTTGTGCTCT	58.726	50.000	0.00	0.00	0.00	4.09	R
2563	2685	2.746279	TCAGGAGGGTTTTTGCTCAA	57.254	45.000	0.00	0.00	0.00	3.02	R
3693	3815	1.213537	CTGCAAATCAAGCCCCACG	59.786	57.895	0.00	0.00	0.00	4.94	R
4740	4877	0.108585	AAGTCAACACAGGCACCGAT	59.891	50.000	0.00	0.00	0.00	4.18	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
26	27	2.610438	AACCAAGCCTCACCATTCAT	57.390	45.000	0.00	0.00	0.00	2.57
52	53	8.729756	TGACAAACTACATGAATTTATGTCCAG	58.270	33.333	18.18	13.67	41.31	3.86
66	67	9.467258	AATTTATGTCCAGAAAATATTGATGCG	57.533	29.630	0.00	0.00	0.00	4.73
71	72	3.374745	CAGAAAATATTGATGCGGCCAC	58.625	45.455	2.24	0.00	0.00	5.01
154	155	4.330894	CACAAACATCTATGATGCGTCACT	59.669	41.667	11.65	3.54	37.14	3.41
176	177	6.311445	CACTGATGAAGACTTTATTGTACGCT	59.689	38.462	0.00	0.00	0.00	5.07
180	181	5.716094	TGAAGACTTTATTGTACGCTGCTA	58.284	37.500	0.00	0.00	0.00	3.49
181	182	5.575606	TGAAGACTTTATTGTACGCTGCTAC	59.424	40.000	0.00	0.42	0.00	3.58
182	183	5.068234	AGACTTTATTGTACGCTGCTACA	57.932	39.130	0.00	3.13	0.00	2.74
191	192	2.813179	CGCTGCTACAATCACCGCC	61.813	63.158	0.00	0.00	0.00	6.13
296	297	2.425592	CTTGCACTCCCACACCGA	59.574	61.111	0.00	0.00	0.00	4.69
299	300	3.041940	GCACTCCCACACCGAACG	61.042	66.667	0.00	0.00	0.00	3.95
305	306	1.302192	CCCACACCGAACGACCAAT	60.302	57.895	0.00	0.00	0.00	3.16
319	322	0.546747	ACCAATGAAGGAGGGACCGA	60.547	55.000	0.00	0.00	44.74	4.69
328	331	0.465097	GGAGGGACCGACGATCTACA	60.465	60.000	0.00	0.00	0.00	2.74
331	334	0.662085	GGGACCGACGATCTACAGAC	59.338	60.000	0.00	0.00	0.00	3.51
349	352	2.683867	AGACGACGAAGGAGAGGTAATG	59.316	50.000	0.00	0.00	0.00	1.90
423	435	6.037610	GTCGATCAAGCTTATTTGAGTTGGAT	59.962	38.462	0.00	0.00	40.16	3.41
467	576	5.667466	TGAAAGTCAAGGGTTATATCGTCC	58.333	41.667	0.00	0.00	0.00	4.79
468	577	5.188163	TGAAAGTCAAGGGTTATATCGTCCA	59.812	40.000	0.00	0.00	0.00	4.02
760	880	1.938861	CAACACCCAAACTCGTCCG	59.061	57.895	0.00	0.00	0.00	4.79
761	881	1.227734	AACACCCAAACTCGTCCGG	60.228	57.895	0.00	0.00	0.00	5.14
815	936	1.529948	TCGACGAGGTTGGTGGACT	60.530	57.895	0.00	0.00	0.00	3.85
892	1013	4.765339	CCTTTTCCAAGTTTATTCCCGTCT	59.235	41.667	0.00	0.00	0.00	4.18
1247	1369	0.670854	GAGGTCAGACAAAGGGACGC	60.671	60.000	2.17	0.00	32.39	5.19

Showing 1 to 25 of 445 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.171003	GGTGAGGCTTGGTTTTGCTAT	58.829	47.619	0.00	0.00	0.00	2.97
1	2	1.133637	TGGTGAGGCTTGGTTTTGCTA	60.134	47.619	0.00	0.00	0.00	3.49
2	3	0.396974	TGGTGAGGCTTGGTTTTGCT	60.397	50.000	0.00	0.00	0.00	3.91
26	27	8.628630	TGGACATAAATTCATGTAGTTTGTCA	57.371	30.769	18.91	9.94	39.25	3.58
46	47	3.066621	GCCGCATCAATATTTTCTGGACA	59.933	43.478	0.00	0.00	0.00	4.02
52	53	3.066621	TCTGTGGCCGCATCAATATTTTC	59.933	43.478	21.54	0.00	0.00	2.29
66	67	3.068024	TCTCAATTGTGTTTTCTGTGGCC	59.932	43.478	5.13	0.00	0.00	5.36
71	72	7.650504	ACATTCACATCTCAATTGTGTTTTCTG	59.349	33.333	5.13	1.33	43.86	3.02
154	155	5.063438	GCAGCGTACAATAAAGTCTTCATCA	59.937	40.000	0.00	0.00	0.00	3.07
176	177	0.320858	TTTCGGCGGTGATTGTAGCA	60.321	50.000	7.21	0.00	0.00	3.49
180	181	0.322322	TACCTTTCGGCGGTGATTGT	59.678	50.000	7.21	0.00	35.98	2.71
181	182	1.663695	ATACCTTTCGGCGGTGATTG	58.336	50.000	7.21	0.00	35.98	2.67
182	183	3.547054	TTATACCTTTCGGCGGTGATT	57.453	42.857	7.21	0.00	35.98	2.57
264	265	0.033109	GCAAGGAGGCCCTGGTTTAT	60.033	55.000	0.00	0.00	43.48	1.40
296	297	1.003233	GTCCCTCCTTCATTGGTCGTT	59.997	52.381	0.00	0.00	0.00	3.85
299	300	0.107654	CGGTCCCTCCTTCATTGGTC	60.108	60.000	0.00	0.00	0.00	4.02
305	306	1.000019	ATCGTCGGTCCCTCCTTCA	60.000	57.895	0.00	0.00	0.00	3.02
319	322	1.664659	CCTTCGTCGTCTGTAGATCGT	59.335	52.381	0.00	0.00	0.00	3.73
328	331	2.486472	TTACCTCTCCTTCGTCGTCT	57.514	50.000	0.00	0.00	0.00	4.18
331	334	1.134367	TGCATTACCTCTCCTTCGTCG	59.866	52.381	0.00	0.00	0.00	5.12
349	352	1.168714	GTGGTGATCAGAGGGTTTGC	58.831	55.000	0.00	0.00	0.00	3.68
423	435	6.373005	TCAGAAGATTGATTTGGTACCAGA	57.627	37.500	15.65	11.70	0.00	3.86
760	880	0.880718	GCGTGGGAGATCGGAATTCC	60.881	60.000	15.01	15.01	0.00	3.01
761	881	0.880718	GGCGTGGGAGATCGGAATTC	60.881	60.000	0.00	0.00	0.00	2.17
923	1045	0.865111	CGGATCAAACAACAGCGACA	59.135	50.000	0.00	0.00	0.00	4.35

Showing 1 to 25 of 434 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.