AutoCloner

Multiple sequence alignment - TraesCS1D01G051900

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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	TraesCS1D01G051900	chr1D	100.000	4545	0	0	1	4545	32547651	32543107	0.000000e+00	8394
1	TraesCS1D01G051900	chr1A	95.386	2861	110	14	924	3774	31779107	31781955	0.000000e+00	4532
2	TraesCS1D01G051900	chr1A	94.458	415	18	4	1	413	31778690	31779101	6.410000e-178	634
3	TraesCS1D01G051900	chr1B	93.069	3073	149	33	731	3774	50186582	50183545	0.000000e+00	4436
4	TraesCS1D01G051900	chr1B	87.293	543	62	4	4000	4538	658966128	658965589	8.360000e-172	614
5	TraesCS1D01G051900	chr1B	84.426	366	38	10	39	395	50186942	50186587	4.350000e-90	342
6	TraesCS1D01G051900	chr1B	85.437	103	10	3	3824	3921	50183522	50183420	8.040000e-18	102
7	TraesCS1D01G051900	chr7D	90.520	538	45	5	4010	4545	117875835	117876368	0.000000e+00	706
8	TraesCS1D01G051900	chr7D	89.350	554	51	6	3995	4545	532252817	532252269	0.000000e+00	689
9	TraesCS1D01G051900	chr7D	87.985	541	49	8	4010	4545	184986571	184986042	3.860000e-175	625
10	TraesCS1D01G051900	chr5D	89.599	548	50	5	4001	4545	477032797	477033340	0.000000e+00	689
11	TraesCS1D01G051900	chr5D	87.884	553	57	8	3998	4545	520846347	520846894	3.830000e-180	641
12	TraesCS1D01G051900	chr5D	86.631	561	56	13	3995	4545	445835201	445835752	1.810000e-168	603
13	TraesCS1D01G051900	chr6D	87.814	558	54	11	3998	4545	470263487	470264040	3.830000e-180	641
14	TraesCS1D01G051900	chr7B	87.138	552	55	10	4001	4545	113914679	113914137	3.010000e-171	612

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	TraesCS1D01G051900	chr1D	32543107	32547651	4544	True	8394.000000	8394	100.000	1	4545	1	chr1D.!!$R1	4544
1	TraesCS1D01G051900	chr1A	31778690	31781955	3265	False	2583.000000	4532	94.922	1	3774	2	chr1A.!!$F1	3773
2	TraesCS1D01G051900	chr1B	50183420	50186942	3522	True	1626.666667	4436	87.644	39	3921	3	chr1B.!!$R2	3882
3	TraesCS1D01G051900	chr1B	658965589	658966128	539	True	614.000000	614	87.293	4000	4538	1	chr1B.!!$R1	538
4	TraesCS1D01G051900	chr7D	117875835	117876368	533	False	706.000000	706	90.520	4010	4545	1	chr7D.!!$F1	535
5	TraesCS1D01G051900	chr7D	532252269	532252817	548	True	689.000000	689	89.350	3995	4545	1	chr7D.!!$R2	550
6	TraesCS1D01G051900	chr7D	184986042	184986571	529	True	625.000000	625	87.985	4010	4545	1	chr7D.!!$R1	535
7	TraesCS1D01G051900	chr5D	477032797	477033340	543	False	689.000000	689	89.599	4001	4545	1	chr5D.!!$F2	544
8	TraesCS1D01G051900	chr5D	520846347	520846894	547	False	641.000000	641	87.884	3998	4545	1	chr5D.!!$F3	547
9	TraesCS1D01G051900	chr5D	445835201	445835752	551	False	603.000000	603	86.631	3995	4545	1	chr5D.!!$F1	550
10	TraesCS1D01G051900	chr6D	470263487	470264040	553	False	641.000000	641	87.814	3998	4545	1	chr6D.!!$F1	547
11	TraesCS1D01G051900	chr7B	113914137	113914679	542	True	612.000000	612	87.138	4001	4545	1	chr7B.!!$R1	544

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
588	598	0.038159	GTTGTCCACGAGGTCTGAGG	60.038	60.0	0.00	0.00	35.89	3.86	F
599	609	0.543749	GGTCTGAGGGCTGCAGTTAT	59.456	55.0	16.64	0.46	34.98	1.89	F
2424	2456	1.135094	ACCTAGATGGCAGGGATGTG	58.865	55.0	0.00	0.00	40.22	3.21	F

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability	Orientation
2424	2456	0.883833	CAATAATGCGGCTCCCATCC	59.116	55.0	3.51	R
2793	2826	1.522668	TGCGATGAGGTGAACAAAGG	58.477	50.0	3.11	R
4489	4568	0.250295	TCCAACACCTTCCGAGCTTG	60.250	55.0	4.01	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
58	59	8.033626	GGTACTGGGTAGTTAGTGCATAATATC	58.966	40.741	0.00	38.36	1.63
89	96	6.615316	TGGTCAGATATATCAAAGGGAGTCAA	59.385	38.462	15.08	0.00	3.18
220	227	8.904099	AAAGTACATAATAGTGGTATTGGAGC	57.096	34.615	0.00	31.04	4.70
254	261	6.528423	TGTTTTTGTGGTGTGTTTTATTCTCG	59.472	34.615	0.00	0.00	4.04
396	406	5.113502	ACTTGCAACTTAAAGTCATGAGC	57.886	39.130	0.00	30.87	4.26
413	423	4.454728	TGAGCTTTGTCTTTTGCAACTT	57.545	36.364	0.00	0.00	2.66
414	424	4.175516	TGAGCTTTGTCTTTTGCAACTTG	58.824	39.130	0.00	0.00	3.16
415	425	4.082300	TGAGCTTTGTCTTTTGCAACTTGA	60.082	37.500	0.00	0.00	3.02
417	427	6.147864	AGCTTTGTCTTTTGCAACTTGATA	57.852	33.333	0.00	0.00	2.15
418	428	6.752168	AGCTTTGTCTTTTGCAACTTGATAT	58.248	32.000	0.00	0.00	1.63
419	429	7.212274	AGCTTTGTCTTTTGCAACTTGATATT	58.788	30.769	0.00	0.00	1.28
420	430	8.359642	AGCTTTGTCTTTTGCAACTTGATATTA	58.640	29.630	0.00	0.00	0.98
421	431	8.427774	GCTTTGTCTTTTGCAACTTGATATTAC	58.572	33.333	0.00	0.00	1.89
422	432	8.500837	TTTGTCTTTTGCAACTTGATATTACG	57.499	30.769	0.00	0.00	3.18
423	433	7.428282	TGTCTTTTGCAACTTGATATTACGA	57.572	32.000	0.00	0.00	3.43
424	434	7.518161	TGTCTTTTGCAACTTGATATTACGAG	58.482	34.615	0.00	0.00	4.18
425	435	6.961554	GTCTTTTGCAACTTGATATTACGAGG	59.038	38.462	0.00	0.00	4.63
426	436	6.653320	TCTTTTGCAACTTGATATTACGAGGT	59.347	34.615	0.00	0.00	3.85
427	437	6.811253	TTTGCAACTTGATATTACGAGGTT	57.189	33.333	0.00	0.00	3.50
428	438	6.811253	TTGCAACTTGATATTACGAGGTTT	57.189	33.333	0.00	0.00	3.27
429	439	7.908827	TTGCAACTTGATATTACGAGGTTTA	57.091	32.000	0.00	0.00	2.01
430	440	7.908827	TGCAACTTGATATTACGAGGTTTAA	57.091	32.000	0.00	0.00	1.52
431	441	8.500753	TGCAACTTGATATTACGAGGTTTAAT	57.499	30.769	0.00	0.00	1.40
432	442	8.394877	TGCAACTTGATATTACGAGGTTTAATG	58.605	33.333	0.00	0.00	1.90
433	443	8.609176	GCAACTTGATATTACGAGGTTTAATGA	58.391	33.333	0.00	0.00	2.57

Showing 1 to 25 of 400 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
58	59	8.651389	TCCCTTTGATATATCTGACCAGTTTAG	58.349	37.037	13.79	0.00	1.85
194	201	8.989980	GCTCCAATACCACTATTATGTACTTTC	58.010	37.037	0.00	0.00	2.62
220	227	4.732923	CACACCACAAAAACAGTTGATACG	59.267	41.667	0.00	32.59	3.06
307	316	6.721571	TTGACCGTTCATCTCATTTACTTC	57.278	37.500	0.00	0.00	3.01
396	406	8.629986	CGTAATATCAAGTTGCAAAAGACAAAG	58.370	33.333	0.00	0.00	2.77
413	423	9.675464	ACCTTTTCATTAAACCTCGTAATATCA	57.325	29.630	0.00	0.00	2.15
414	424	9.931210	CACCTTTTCATTAAACCTCGTAATATC	57.069	33.333	0.00	0.00	1.63
415	425	9.457436	ACACCTTTTCATTAAACCTCGTAATAT	57.543	29.630	0.00	0.00	1.28
417	427	7.229907	ACACACCTTTTCATTAAACCTCGTAAT	59.770	33.333	0.00	0.00	1.89
418	428	6.543100	ACACACCTTTTCATTAAACCTCGTAA	59.457	34.615	0.00	0.00	3.18
419	429	6.056884	ACACACCTTTTCATTAAACCTCGTA	58.943	36.000	0.00	0.00	3.43
420	430	4.885325	ACACACCTTTTCATTAAACCTCGT	59.115	37.500	0.00	0.00	4.18
421	431	5.432885	ACACACCTTTTCATTAAACCTCG	57.567	39.130	0.00	0.00	4.63
422	432	7.739498	TCTACACACCTTTTCATTAAACCTC	57.261	36.000	0.00	0.00	3.85
423	433	7.778382	AGTTCTACACACCTTTTCATTAAACCT	59.222	33.333	0.00	0.00	3.50
424	434	7.860872	CAGTTCTACACACCTTTTCATTAAACC	59.139	37.037	0.00	0.00	3.27
425	435	7.378728	GCAGTTCTACACACCTTTTCATTAAAC	59.621	37.037	0.00	0.00	2.01
426	436	7.284489	AGCAGTTCTACACACCTTTTCATTAAA	59.716	33.333	0.00	0.00	1.52
427	437	6.770785	AGCAGTTCTACACACCTTTTCATTAA	59.229	34.615	0.00	0.00	1.40
428	438	6.296026	AGCAGTTCTACACACCTTTTCATTA	58.704	36.000	0.00	0.00	1.90
429	439	5.133221	AGCAGTTCTACACACCTTTTCATT	58.867	37.500	0.00	0.00	2.57
430	440	4.718961	AGCAGTTCTACACACCTTTTCAT	58.281	39.130	0.00	0.00	2.57
431	441	4.150897	AGCAGTTCTACACACCTTTTCA	57.849	40.909	0.00	0.00	2.69
432	442	4.335594	ACAAGCAGTTCTACACACCTTTTC	59.664	41.667	0.00	0.00	2.29
433	443	4.270008	ACAAGCAGTTCTACACACCTTTT	58.730	39.130	0.00	0.00	2.27

Showing 1 to 25 of 360 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.