AutoCloner

Multiple sequence alignment - TraesCS7D01G361900

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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	TraesCS7D01G361900	chr7D	100.000	2726	0	0	1	2726	464362365	464359640	0.000000e+00	5035.0
1	TraesCS7D01G361900	chr7D	79.331	1166	131	55	791	1887	464948052	464946928	0.000000e+00	717.0
2	TraesCS7D01G361900	chr7A	92.223	2546	95	29	1	2473	535271820	535274335	0.000000e+00	3509.0
3	TraesCS7D01G361900	chr7A	78.877	1193	137	64	767	1887	534766041	534767190	0.000000e+00	701.0
4	TraesCS7D01G361900	chr7A	87.109	256	10	7	2471	2726	535319102	535319334	4.470000e-68	268.0
5	TraesCS7D01G361900	chr7A	96.667	60	1	1	563	621	535272329	535272388	6.210000e-17	99.0
6	TraesCS7D01G361900	chr7B	94.173	1802	50	22	943	2726	489781330	489779566	0.000000e+00	2695.0
7	TraesCS7D01G361900	chr7B	93.075	852	48	7	1	849	489782601	489781758	0.000000e+00	1236.0
8	TraesCS7D01G361900	chr7B	84.514	762	89	16	944	1692	489552299	489551554	0.000000e+00	726.0
9	TraesCS7D01G361900	chr3B	87.991	458	25	14	2271	2725	49098296	49098726	5.210000e-142	514.0
10	TraesCS7D01G361900	chr2B	84.173	278	27	8	2449	2726	773937801	773938061	1.250000e-63	254.0
11	TraesCS7D01G361900	chr2B	95.238	42	2	0	2685	2726	110017187	110017228	1.750000e-07	67.6

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	TraesCS7D01G361900	chr7D	464359640	464362365	2725	True	5035.0	5035	100.000	1	2726	1	chr7D.!!$R1	2725
1	TraesCS7D01G361900	chr7D	464946928	464948052	1124	True	717.0	717	79.331	791	1887	1	chr7D.!!$R2	1096
2	TraesCS7D01G361900	chr7A	535271820	535274335	2515	False	1804.0	3509	94.445	1	2473	2	chr7A.!!$F3	2472
3	TraesCS7D01G361900	chr7A	534766041	534767190	1149	False	701.0	701	78.877	767	1887	1	chr7A.!!$F1	1120
4	TraesCS7D01G361900	chr7B	489779566	489782601	3035	True	1965.5	2695	93.624	1	2726	2	chr7B.!!$R2	2725
5	TraesCS7D01G361900	chr7B	489551554	489552299	745	True	726.0	726	84.514	944	1692	1	chr7B.!!$R1	748

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
374	384	0.325296	TGCCCTTCCATCCGTCTAGT	60.325	55.0	0.0	0.0	0.0	2.57	F
460	472	0.755686	GCGGAACCCTCTCTCATGAT	59.244	55.0	0.0	0.0	0.0	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1560	1953	0.114168	CCTGGATCTCCTCCTCCGAT	59.886	60.0	0.0	0.0	45.21	4.18	R
2034	2479	0.165944	CAAACCCGCACGAGATCAAC	59.834	55.0	0.0	0.0	0.00	3.18	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
49	50	4.932200	CGCAAATGATATAGTTCTCCCTCC	59.068	45.833	0.00	0.00	0.00	4.30
144	154	3.313274	ACTTTTACAACGCTCACAACG	57.687	42.857	0.00	0.00	0.00	4.10
206	216	5.536554	AGTATTTCTCACATTGAGTTGCG	57.463	39.130	3.19	0.00	44.58	4.85
210	220	2.832563	TCTCACATTGAGTTGCGACAA	58.167	42.857	6.90	0.00	44.58	3.18
267	277	6.849588	TGAGAACATGTATCCATCATTTCG	57.150	37.500	0.00	0.00	0.00	3.46
374	384	0.325296	TGCCCTTCCATCCGTCTAGT	60.325	55.000	0.00	0.00	0.00	2.57
430	440	1.538419	GGCGCGCTATCCTAAAGAACT	60.538	52.381	32.29	0.00	0.00	3.01
460	472	0.755686	GCGGAACCCTCTCTCATGAT	59.244	55.000	0.00	0.00	0.00	2.45
507	519	5.758296	GCTATATCGGTCCACAAAATTCTCA	59.242	40.000	0.00	0.00	0.00	3.27
656	668	3.713936	GATCGACATCCACGTGTGA	57.286	52.632	15.65	11.79	31.16	3.58
661	673	1.282248	GACATCCACGTGTGACACCG	61.282	60.000	15.65	7.99	31.16	4.94
892	921	2.665603	GGCTGTCCGCTTCTCCTT	59.334	61.111	0.00	0.00	39.13	3.36
897	926	1.446272	GTCCGCTTCTCCTTCCACG	60.446	63.158	0.00	0.00	0.00	4.94
921	965	1.295020	AATAACCAGCAGCCCCACTA	58.705	50.000	0.00	0.00	0.00	2.74
977	1331	0.756294	CAAAACCCAAACCCCACTCC	59.244	55.000	0.00	0.00	0.00	3.85
1104	1461	1.211969	CGTCGTCCTCACCATCGTT	59.788	57.895	0.00	0.00	0.00	3.85
1120	1477	2.040544	GTTGTCACCTCCATGGCCG	61.041	63.158	6.96	1.05	40.22	6.13
1763	2166	2.906458	CGGGAGCTCCTTGATGCT	59.094	61.111	31.36	0.00	42.82	3.79
1805	2223	3.436015	GCTAGTAGCCGAGTCGATGAATA	59.564	47.826	15.64	1.05	34.48	1.75
1806	2224	4.083431	GCTAGTAGCCGAGTCGATGAATAA	60.083	45.833	15.64	0.00	34.48	1.40
2013	2458	5.174943	CACAAAAACAGTTATTCTTTCCCGC	59.825	40.000	0.00	0.00	0.00	6.13
2034	2479	0.647410	CGGCTATTCTGTTCTGCACG	59.353	55.000	0.00	0.00	0.00	5.34
2168	2613	6.808829	TGTTTCAGTCATTTGCTCAGAAATT	58.191	32.000	0.00	0.00	0.00	1.82
2184	2629	2.596904	AATTCATTGCAGAGCATGGC	57.403	45.000	0.00	0.00	38.76	4.40
2194	2639	1.153086	GAGCATGGCTACAGGGGTG	60.153	63.158	0.00	0.00	39.88	4.61

Showing 1 to 25 of 49 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	8.877779	AGAACTATATCATTTGCGCATTATCTC	58.122	33.333	12.75	0.00	0.00	2.75
25	26	4.319177	AGGGAGAACTATATCATTTGCGC	58.681	43.478	0.00	0.00	0.00	6.09
112	122	6.537660	AGCGTTGTAAAAGTTACTTTCTCTGT	59.462	34.615	10.98	0.00	31.99	3.41
267	277	3.660865	AGATGAAAAGGACACGGTGTAC	58.339	45.455	15.79	15.79	0.00	2.90
327	337	8.514330	ACTTTTGTTGTGAGTTATTTCTACCA	57.486	30.769	0.00	0.00	0.00	3.25
374	384	4.075682	TCCGCCAAATGTTATTTCAGTGA	58.924	39.130	0.00	0.00	0.00	3.41
460	472	5.743467	CGTCATTAGTGCGGCATTTTAATA	58.257	37.500	5.72	0.00	0.00	0.98
523	535	9.634163	ACGTAAAAAGAGAAACAACTTTTGATT	57.366	25.926	0.00	0.00	42.80	2.57
533	545	3.803778	GGACGGACGTAAAAAGAGAAACA	59.196	43.478	0.00	0.00	0.00	2.83
546	558	4.295119	AAGCGCTTGGACGGACGT	62.295	61.111	24.40	0.00	0.00	4.34
661	673	4.265556	CGATTTCTACAACATCGACTGGAC	59.734	45.833	0.00	0.00	41.96	4.02
705	718	6.934056	TGCAAATATCTAAATGGTTGTTGCT	58.066	32.000	0.00	0.00	39.56	3.91
706	719	7.775397	ATGCAAATATCTAAATGGTTGTTGC	57.225	32.000	0.00	0.00	39.35	4.17
892	921	3.189702	GCTGCTGGTTATTTAAACGTGGA	59.810	43.478	0.00	0.00	0.00	4.02
897	926	2.829120	TGGGGCTGCTGGTTATTTAAAC	59.171	45.455	0.00	0.00	0.00	2.01
921	965	2.622447	CGGGGTTGGGGAAGGGAAT	61.622	63.158	0.00	0.00	0.00	3.01
941	1293	2.116556	GGCGTTTTGGGGGAGGAA	59.883	61.111	0.00	0.00	0.00	3.36
1104	1461	4.408821	GCGGCCATGGAGGTGACA	62.409	66.667	18.40	0.00	40.61	3.58
1309	1666	4.637489	CTCCATCTCGAGCGGCGG	62.637	72.222	9.78	5.26	41.33	6.13
1531	1918	3.249189	TTTCGCCACCAGGGAGCT	61.249	61.111	0.00	0.00	40.01	4.09
1534	1924	4.323477	CGGTTTCGCCACCAGGGA	62.323	66.667	4.00	0.00	40.01	4.20
1560	1953	0.114168	CCTGGATCTCCTCCTCCGAT	59.886	60.000	0.00	0.00	45.21	4.18
1750	2153	0.252479	CTGTGGAGCATCAAGGAGCT	59.748	55.000	0.00	0.00	45.25	4.09
1762	2165	1.078567	GGGAAGCAGCTCTGTGGAG	60.079	63.158	0.00	0.00	42.18	3.86
1763	2166	2.947532	CGGGAAGCAGCTCTGTGGA	61.948	63.158	0.00	0.00	0.00	4.02

Showing 1 to 25 of 61 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.