AutoCloner

Multiple sequence alignment - TraesCS2D01G442300

Loading Multiple Alignment...

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	TraesCS2D01G442300	chr2D	100.000	2501	0	0	1	2501	552608706	552606206	0.000000e+00	4619
1	TraesCS2D01G442300	chr2A	94.742	1008	36	5	778	1770	693243883	693242878	0.000000e+00	1552
2	TraesCS2D01G442300	chr2A	87.260	730	48	18	1773	2498	693242633	693241945	0.000000e+00	791
3	TraesCS2D01G442300	chr2B	97.365	835	19	2	779	1612	658211008	658210176	0.000000e+00	1417
4	TraesCS2D01G442300	chr2B	83.427	531	63	17	1646	2153	658210175	658209647	1.050000e-128	470
5	TraesCS2D01G442300	chr6D	96.974	694	21	0	1	694	470315417	470316110	0.000000e+00	1166
6	TraesCS2D01G442300	chr6D	85.876	708	95	5	2	706	27472285	27471580	0.000000e+00	749
7	TraesCS2D01G442300	chr6D	91.365	498	43	0	995	1492	349915386	349914889	0.000000e+00	682
8	TraesCS2D01G442300	chr1D	90.649	663	61	1	1	663	457532881	457532220	0.000000e+00	880
9	TraesCS2D01G442300	chr1D	85.614	709	95	7	1	705	341271518	341272223	0.000000e+00	737
10	TraesCS2D01G442300	chr5A	87.019	701	85	5	1	699	205005550	205004854	0.000000e+00	785
11	TraesCS2D01G442300	chr5D	86.370	697	92	3	1	695	136873846	136873151	0.000000e+00	758
12	TraesCS2D01G442300	chr5D	86.522	690	82	10	5	689	436797157	436796474	0.000000e+00	749
13	TraesCS2D01G442300	chr3A	86.533	698	82	11	1	693	715797992	715797302	0.000000e+00	758
14	TraesCS2D01G442300	chr3A	86.351	696	87	8	1	693	675885273	675884583	0.000000e+00	752
15	TraesCS2D01G442300	chr6A	91.968	498	40	0	995	1492	494477961	494478458	0.000000e+00	699
16	TraesCS2D01G442300	chr6B	91.566	498	42	0	995	1492	530572822	530573319	0.000000e+00	688

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	TraesCS2D01G442300	chr2D	552606206	552608706	2500	True	4619.0	4619	100.000	1	2501	1	chr2D.!!$R1	2500
1	TraesCS2D01G442300	chr2A	693241945	693243883	1938	True	1171.5	1552	91.001	778	2498	2	chr2A.!!$R1	1720
2	TraesCS2D01G442300	chr2B	658209647	658211008	1361	True	943.5	1417	90.396	779	2153	2	chr2B.!!$R1	1374
3	TraesCS2D01G442300	chr6D	470315417	470316110	693	False	1166.0	1166	96.974	1	694	1	chr6D.!!$F1	693
4	TraesCS2D01G442300	chr6D	27471580	27472285	705	True	749.0	749	85.876	2	706	1	chr6D.!!$R1	704
5	TraesCS2D01G442300	chr1D	457532220	457532881	661	True	880.0	880	90.649	1	663	1	chr1D.!!$R1	662
6	TraesCS2D01G442300	chr1D	341271518	341272223	705	False	737.0	737	85.614	1	705	1	chr1D.!!$F1	704
7	TraesCS2D01G442300	chr5A	205004854	205005550	696	True	785.0	785	87.019	1	699	1	chr5A.!!$R1	698
8	TraesCS2D01G442300	chr5D	136873151	136873846	695	True	758.0	758	86.370	1	695	1	chr5D.!!$R1	694
9	TraesCS2D01G442300	chr5D	436796474	436797157	683	True	749.0	749	86.522	5	689	1	chr5D.!!$R2	684
10	TraesCS2D01G442300	chr3A	715797302	715797992	690	True	758.0	758	86.533	1	693	1	chr3A.!!$R2	692
11	TraesCS2D01G442300	chr3A	675884583	675885273	690	True	752.0	752	86.351	1	693	1	chr3A.!!$R1	692

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
846	858	0.112995	AAAATGGGCCTCACAGCAGA	59.887	50.0	4.53	0.0	0.0	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1747	1773	1.021202	TGAAACAAACAGGTCCGCAG	58.979	50.0	0.0	0.0	0.0	5.18	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
88	90	5.570439	GCAGGTAGCTAAGCATCAAGGATAT	60.570	44.000	0.00	0.00	41.15	1.63
204	207	7.998383	TGGGATAATGCTAGCAAAATTCTAGAA	59.002	33.333	23.54	7.82	36.50	2.10
243	246	3.189287	AGCTGCTTTGTATGTTGCACTAC	59.811	43.478	0.00	0.00	0.00	2.73
523	530	8.932434	ACTTTTTAAACCCCAAATAAATGCAT	57.068	26.923	0.00	0.00	0.00	3.96
699	708	2.775384	TCCCTAGCCACGTCCATTATTT	59.225	45.455	0.00	0.00	0.00	1.40
700	709	3.968649	TCCCTAGCCACGTCCATTATTTA	59.031	43.478	0.00	0.00	0.00	1.40
703	712	5.768164	CCCTAGCCACGTCCATTATTTATTT	59.232	40.000	0.00	0.00	0.00	1.40
704	713	6.938030	CCCTAGCCACGTCCATTATTTATTTA	59.062	38.462	0.00	0.00	0.00	1.40
705	714	7.610305	CCCTAGCCACGTCCATTATTTATTTAT	59.390	37.037	0.00	0.00	0.00	1.40
706	715	9.010029	CCTAGCCACGTCCATTATTTATTTATT	57.990	33.333	0.00	0.00	0.00	1.40
745	754	8.903570	TTTGTATACATTTTTGAGCGGTAATG	57.096	30.769	6.36	6.34	34.87	1.90
746	755	7.618502	TGTATACATTTTTGAGCGGTAATGT	57.381	32.000	15.45	15.45	42.20	2.71
747	756	8.046294	TGTATACATTTTTGAGCGGTAATGTT	57.954	30.769	16.12	8.80	40.55	2.71
748	757	8.516234	TGTATACATTTTTGAGCGGTAATGTTT	58.484	29.630	16.12	11.95	40.55	2.83
749	758	9.349145	GTATACATTTTTGAGCGGTAATGTTTT	57.651	29.630	16.12	9.01	40.55	2.43
750	759	8.825667	ATACATTTTTGAGCGGTAATGTTTTT	57.174	26.923	16.12	3.13	40.55	1.94
840	852	1.270550	CTGACACAAAATGGGCCTCAC	59.729	52.381	4.53	0.00	0.00	3.51
846	858	0.112995	AAAATGGGCCTCACAGCAGA	59.887	50.000	4.53	0.00	0.00	4.26
865	877	0.485099	ACCACATAAAGCCCAACCCA	59.515	50.000	0.00	0.00	0.00	4.51
874	886	3.473113	AAGCCCAACCCAAATGATACT	57.527	42.857	0.00	0.00	0.00	2.12
905	917	6.619801	CACAAGGAAGGTGCTATATAAACC	57.380	41.667	6.25	6.25	0.00	3.27
942	954	1.608154	GAACCCTACTGCCCTTCCC	59.392	63.158	0.00	0.00	0.00	3.97
963	975	2.985116	GCCTCTCCCAAACCCTCCC	61.985	68.421	0.00	0.00	0.00	4.30
1622	1646	6.932400	CGGTAAAATATGATGTAGCCCTTGTA	59.068	38.462	0.00	0.00	0.00	2.41
1623	1647	7.606456	CGGTAAAATATGATGTAGCCCTTGTAT	59.394	37.037	0.00	0.00	0.00	2.29

Showing 1 to 25 of 70 entries

Previous1 2 3Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
139	141	9.237187	TGGTTGCTCAATTACTTATTGTTGATA	57.763	29.630	0.00	0.00	43.41	2.15
204	207	4.763793	AGCAGCTTCATCACACTATTTGTT	59.236	37.500	0.00	0.00	35.67	2.83
208	211	4.763793	ACAAAGCAGCTTCATCACACTATT	59.236	37.500	8.48	0.00	0.00	1.73
243	246	5.375417	TCACACAAAACATAAGGCATCTG	57.625	39.130	0.00	0.00	0.00	2.90
320	324	6.306643	AGAGCTATAAGGAAGCAACTTCTT	57.693	37.500	7.24	0.00	42.62	2.52
322	326	8.581578	ACTATAGAGCTATAAGGAAGCAACTTC	58.418	37.037	6.78	0.00	42.62	3.01
523	530	2.311841	TCAGTCTAGATCCTGTCCCACA	59.688	50.000	9.50	0.00	0.00	4.17
719	728	9.515020	CATTACCGCTCAAAAATGTATACAAAT	57.485	29.630	10.14	0.00	0.00	2.32
720	729	8.516234	ACATTACCGCTCAAAAATGTATACAAA	58.484	29.630	10.14	0.00	39.96	2.83
721	730	8.046294	ACATTACCGCTCAAAAATGTATACAA	57.954	30.769	10.14	0.00	39.96	2.41
722	731	7.618502	ACATTACCGCTCAAAAATGTATACA	57.381	32.000	8.27	8.27	39.96	2.29
723	732	8.905103	AAACATTACCGCTCAAAAATGTATAC	57.095	30.769	0.00	0.00	40.66	1.47
724	733	9.915629	AAAAACATTACCGCTCAAAAATGTATA	57.084	25.926	0.00	0.00	40.66	1.47
725	734	8.825667	AAAAACATTACCGCTCAAAAATGTAT	57.174	26.923	0.00	0.00	40.66	2.29
840	852	1.098050	GGGCTTTATGTGGTCTGCTG	58.902	55.000	0.00	0.00	0.00	4.41
846	858	0.485099	TGGGTTGGGCTTTATGTGGT	59.515	50.000	0.00	0.00	0.00	4.16
905	917	2.006772	GGCACGAAGAGTTATGCGG	58.993	57.895	0.00	0.00	39.02	5.69
942	954	0.322906	GAGGGTTTGGGAGAGGCTTG	60.323	60.000	0.00	0.00	0.00	4.01
1622	1646	1.757118	CTACCCACATCGTCTGGACAT	59.243	52.381	1.63	0.00	0.00	3.06
1623	1647	1.182667	CTACCCACATCGTCTGGACA	58.817	55.000	1.63	0.00	0.00	4.02
1624	1648	0.460311	CCTACCCACATCGTCTGGAC	59.540	60.000	0.00	0.00	0.00	4.02
1648	1672	2.292828	AATTGCTTGTAGTGGGCTGT	57.707	45.000	0.00	0.00	0.00	4.40
1651	1675	1.204704	GGGAAATTGCTTGTAGTGGGC	59.795	52.381	0.00	0.00	0.00	5.36
1654	1678	3.573967	ACAAGGGGAAATTGCTTGTAGTG	59.426	43.478	0.00	0.00	36.62	2.74
1655	1679	3.844640	ACAAGGGGAAATTGCTTGTAGT	58.155	40.909	0.00	0.00	36.62	2.73

Showing 1 to 25 of 86 entries

Previous1 2 3 4Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.