AutoCloner

Multiple sequence alignment - TraesCS3B01G382500

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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	TraesCS3B01G382500	chr3B	100.000	5404	0	0	1	5404	602359569	602364972	0.000000e+00	9980
1	TraesCS3B01G382500	chr3D	91.536	3887	174	72	1	3839	455874992	455878771	0.000000e+00	5212
2	TraesCS3B01G382500	chr3D	93.637	1493	46	10	3960	5404	455879056	455880547	0.000000e+00	2185
3	TraesCS3B01G382500	chr3A	89.351	2836	179	51	1	2768	598559043	598561823	0.000000e+00	3450
4	TraesCS3B01G382500	chr3A	90.972	1595	61	31	3862	5404	598563020	598564583	0.000000e+00	2071
5	TraesCS3B01G382500	chr3A	92.578	768	25	5	2770	3534	598561950	598562688	0.000000e+00	1074
6	TraesCS3B01G382500	chr3A	93.511	262	9	3	3580	3840	598562687	598562941	3.050000e-102	383

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	TraesCS3B01G382500	chr3B	602359569	602364972	5403	False	9980.0	9980	100.0000	1	5404	1	chr3B.!!$F1	5403
1	TraesCS3B01G382500	chr3D	455874992	455880547	5555	False	3698.5	5212	92.5865	1	5404	2	chr3D.!!$F1	5403
2	TraesCS3B01G382500	chr3A	598559043	598564583	5540	False	1744.5	3450	91.6030	1	5404	4	chr3A.!!$F1	5403

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	Hairpin	End Stability	Orientation
161	162	1.140589	CTTGAGCTCCGAGATGCGT	59.859	57.895	12.15	38.67	5.24	F
1514	1563	0.388520	CGCGTTGATCCTGTCAGTCA	60.389	55.000	0.00	38.29	3.41	F
1579	1628	0.533755	CGTGGAAGGGGATGATGCTC	60.534	60.000	0.00	0.00	4.26	F
1903	1971	0.767998	GGGGAAATCAGCTAGAGGGG	59.232	60.000	0.00	0.00	4.79	F
3761	3972	0.250513	AAGTTCTCCCAGCCTTAGCG	59.749	55.000	0.00	46.67	4.26	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1844	1910	0.486879	TGGCCCAAGGGAAATGAAGT	59.513	50.000	9.92	37.50	3.01	R
2844	3051	4.439974	CCAACAACAACACAGTGCAATAGT	60.440	41.667	0.00	0.00	2.12	R
3575	3786	0.036952	CCAACAGGCGACAGATCACT	60.037	55.000	0.00	0.00	3.41	R
3844	4055	0.317603	CTTTGCGCTGCTGCATATCC	60.318	55.000	16.29	45.78	2.59	R
4718	5115	0.792031	ATTCGCCGGACGTTTACAAC	59.208	50.000	5.05	44.19	3.32	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
47	48	2.037527	AGGGACTGGAGGTCGACC	59.962	66.667	27.67	27.67	45.35	4.79
161	162	1.140589	CTTGAGCTCCGAGATGCGT	59.859	57.895	12.15	0.00	38.67	5.24
164	165	2.824489	AGCTCCGAGATGCGTCGA	60.824	61.111	0.00	0.00	42.85	4.20
449	450	2.203788	AAGAGGGACGTGGAGGCA	60.204	61.111	0.00	0.00	0.00	4.75
659	692	4.164087	TGTGTCCACGGCGTTGGT	62.164	61.111	11.19	0.00	37.93	3.67
807	840	7.864379	CAGATTTTTCATCCTTCCATTTATCGG	59.136	37.037	0.00	0.00	0.00	4.18
1473	1522	2.428622	CCGGTTCCTCGGTTGGTT	59.571	61.111	0.00	0.00	44.60	3.67
1474	1523	1.670083	CCGGTTCCTCGGTTGGTTC	60.670	63.158	0.00	0.00	44.60	3.62
1511	1560	2.792290	CGCGCGTTGATCCTGTCAG	61.792	63.158	24.19	0.00	38.29	3.51
1512	1561	1.738099	GCGCGTTGATCCTGTCAGT	60.738	57.895	8.43	0.00	38.29	3.41
1513	1562	1.687494	GCGCGTTGATCCTGTCAGTC	61.687	60.000	8.43	0.00	38.29	3.51
1514	1563	0.388520	CGCGTTGATCCTGTCAGTCA	60.389	55.000	0.00	0.00	38.29	3.41
1520	1569	1.967779	TGATCCTGTCAGTCAAACGGA	59.032	47.619	0.00	0.00	31.80	4.69
1576	1625	2.105477	AGATTCGTGGAAGGGGATGATG	59.895	50.000	0.00	0.00	0.00	3.07
1579	1628	0.533755	CGTGGAAGGGGATGATGCTC	60.534	60.000	0.00	0.00	0.00	4.26
1581	1630	2.050144	GTGGAAGGGGATGATGCTCTA	58.950	52.381	0.00	0.00	0.00	2.43
1607	1656	2.031333	CAGCTGTGCTTGACCTTTTCTC	60.031	50.000	5.25	0.00	36.40	2.87
1637	1686	1.071071	ACCACGTCCGATCTTTTTGGA	59.929	47.619	0.00	0.00	35.32	3.53
1644	1693	4.024048	CGTCCGATCTTTTTGGATATTGGG	60.024	45.833	0.00	0.00	40.21	4.12
1690	1739	2.019984	CTTTACTCCCATTCAGCAGGC	58.980	52.381	0.00	0.00	0.00	4.85
1712	1761	4.678044	GCGCTGCATGTCTATTAGCCTATA	60.678	45.833	0.00	0.00	0.00	1.31
1725	1774	2.285827	GCCTATAGCTCTATGTGGCG	57.714	55.000	14.91	0.00	37.05	5.69
1743	1809	2.288666	GCGGTGCTAATGGAATGAGAA	58.711	47.619	0.00	0.00	0.00	2.87
1757	1823	8.924511	ATGGAATGAGAAAGACAGAAAAGTTA	57.075	30.769	0.00	0.00	0.00	2.24
1805	1871	9.748708	TGACTTTGTGGATATTTTTCTTTTGAG	57.251	29.630	0.00	0.00	0.00	3.02

Showing 1 to 25 of 118 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	1.862147	CGACAACGTCTACTCGCCG	60.862	63.158	0.00	0.00	34.56	6.46
164	165	3.382832	CTCTCCGAGGCCACCGTT	61.383	66.667	5.01	0.00	0.00	4.44
490	507	3.164269	CTCATCCCACCCCTCCCG	61.164	72.222	0.00	0.00	0.00	5.14
561	584	1.071385	CTCTCCCTGTCAACAACTGCT	59.929	52.381	0.00	0.00	0.00	4.24
659	692	1.538876	CCTCCCTGGACCTGGTTCA	60.539	63.158	15.72	7.76	38.35	3.18
968	1017	1.582937	ACGAGATGCGAACGCTACG	60.583	57.895	19.32	18.55	44.57	3.51
969	1018	0.522705	TCACGAGATGCGAACGCTAC	60.523	55.000	19.32	12.85	44.57	3.58
970	1019	0.248094	CTCACGAGATGCGAACGCTA	60.248	55.000	19.32	7.19	44.57	4.26
971	1020	1.515088	CTCACGAGATGCGAACGCT	60.515	57.895	19.32	5.89	44.57	5.07
1388	1437	3.698263	AAGTAGGAGCCGGGGGAGG	62.698	68.421	2.18	0.00	0.00	4.30
1465	1514	1.503818	CTCACCAACCGAACCAACCG	61.504	60.000	0.00	0.00	0.00	4.44
1470	1519	1.671379	GCCTCTCACCAACCGAACC	60.671	63.158	0.00	0.00	0.00	3.62
1471	1520	2.027625	CGCCTCTCACCAACCGAAC	61.028	63.158	0.00	0.00	0.00	3.95
1472	1521	2.342279	CGCCTCTCACCAACCGAA	59.658	61.111	0.00	0.00	0.00	4.30
1473	1522	4.373116	GCGCCTCTCACCAACCGA	62.373	66.667	0.00	0.00	0.00	4.69
1511	1560	0.942252	AAAAGCGACCTCCGTTTGAC	59.058	50.000	0.00	0.00	40.80	3.18
1512	1561	2.137523	GTAAAAGCGACCTCCGTTTGA	58.862	47.619	0.00	0.00	40.80	2.69
1513	1562	1.868498	TGTAAAAGCGACCTCCGTTTG	59.132	47.619	0.00	0.00	40.80	2.93
1514	1563	2.140717	CTGTAAAAGCGACCTCCGTTT	58.859	47.619	0.00	0.00	43.50	3.60
1520	1569	2.301870	TCCACATCTGTAAAAGCGACCT	59.698	45.455	0.00	0.00	0.00	3.85
1576	1625	3.012399	CACAGCTGCGCATAGAGC	58.988	61.111	12.24	11.55	40.87	4.09
1589	1638	3.567164	ACATGAGAAAAGGTCAAGCACAG	59.433	43.478	0.00	0.00	0.00	3.66
1607	1656	1.134936	TCGGACGTGGTTATGGACATG	60.135	52.381	0.00	0.00	0.00	3.21
1637	1686	3.600617	TCTTCCTTTTCCCCACCCAATAT	59.399	43.478	0.00	0.00	0.00	1.28
1644	1693	2.971901	TTCCTCTTCCTTTTCCCCAC	57.028	50.000	0.00	0.00	0.00	4.61

Showing 1 to 25 of 149 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.