AutoCloner

Multiple sequence alignment - TraesCS2D01G380400

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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	TraesCS2D01G380400	chr2D	100.000	5965	0	0	1	5965	484851818	484857782	0.000000e+00	11016
1	TraesCS2D01G380400	chr2D	94.200	500	17	1	499	986	397963570	397964069	0.000000e+00	752
2	TraesCS2D01G380400	chr2D	94.000	500	15	7	498	986	6219498	6219993	0.000000e+00	743
3	TraesCS2D01G380400	chr2A	96.974	3404	63	14	2571	5965	628734418	628737790	0.000000e+00	5679
4	TraesCS2D01G380400	chr2A	97.482	1549	34	4	987	2532	628730513	628732059	0.000000e+00	2639
5	TraesCS2D01G380400	chr2A	92.368	511	27	3	1	500	628730010	628730519	0.000000e+00	717
6	TraesCS2D01G380400	chr2A	91.195	477	41	1	508	984	191972393	191971918	0.000000e+00	647
7	TraesCS2D01G380400	chr2B	92.843	1956	101	20	4014	5965	569498184	569500104	0.000000e+00	2800
8	TraesCS2D01G380400	chr2B	98.673	226	3	0	3798	4023	569497443	569497668	9.310000e-108	401
9	TraesCS2D01G380400	chr5D	96.192	499	8	3	499	986	11172007	11172505	0.000000e+00	806
10	TraesCS2D01G380400	chr5D	94.200	500	18	1	498	986	401034411	401034910	0.000000e+00	752
11	TraesCS2D01G380400	chr5D	94.355	496	17	1	502	986	529172861	529173356	0.000000e+00	750
12	TraesCS2D01G380400	chr6D	95.372	497	12	3	501	986	305074224	305074720	0.000000e+00	780
13	TraesCS2D01G380400	chr3D	94.779	498	15	1	500	986	533412852	533413349	0.000000e+00	765
14	TraesCS2D01G380400	chr3D	93.750	496	19	7	502	986	596278581	596279075	0.000000e+00	734
15	TraesCS2D01G380400	chr3D	91.734	496	29	7	502	986	612613101	612612607	0.000000e+00	678
16	TraesCS2D01G380400	chr7D	94.212	501	18	1	500	989	500789271	500788771	0.000000e+00	754
17	TraesCS2D01G380400	chr1D	93.988	499	18	1	500	986	75927935	75927437	0.000000e+00	745
18	TraesCS2D01G380400	chr3A	92.540	496	26	1	502	986	187438710	187438215	0.000000e+00	701
19	TraesCS2D01G380400	chr6B	94.667	75	3	1	500	574	13832028	13831955	1.360000e-21	115

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	TraesCS2D01G380400	chr2D	484851818	484857782	5964	False	11016.000000	11016	100.000	1	5965	1	chr2D.!!$F3	5964
1	TraesCS2D01G380400	chr2A	628730010	628737790	7780	False	3011.666667	5679	95.608	1	5965	3	chr2A.!!$F1	5964
2	TraesCS2D01G380400	chr2B	569497443	569500104	2661	False	1600.500000	2800	95.758	3798	5965	2	chr2B.!!$F1	2167
3	TraesCS2D01G380400	chr7D	500788771	500789271	500	True	754.000000	754	94.212	500	989	1	chr7D.!!$R1	489

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
205	206	0.846693	AGGGGCCATCATGTACCTTC	59.153	55.000	4.39	0.00	3.46	F
1004	1027	0.462759	GTGGCTGACCCTAGCATGAC	60.463	60.000	0.00	45.46	3.06	F
1840	1863	1.597937	GCTTTTGTCCAGAAGTGCGTG	60.598	52.381	0.33	0.00	5.34	F
2541	2567	0.036164	ATAAGCACGTCACCAGGCAA	59.964	50.000	0.00	0.00	4.52	F
2546	2572	0.036388	CACGTCACCAGGCAACCTAT	60.036	55.000	0.00	29.64	2.57	F
2548	2574	0.249120	CGTCACCAGGCAACCTATCA	59.751	55.000	0.00	29.64	2.15	F
3647	5993	0.932955	AGAGGGCTCCATCAGAGAGA	59.067	55.000	3.28	46.50	3.10	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1345	1368	1.160137	ATCTCAAGAACACGCTTGCC	58.840	50.000	0.00	0.00	43.78	4.52	R
2453	2479	1.452110	TGTTCATTGCCGGACTGATG	58.548	50.000	5.05	2.81	0.00	3.07	R
3647	5993	0.179009	TTCTTGCTGCTTGCCACTCT	60.179	50.000	0.00	0.00	42.00	3.24	R
4520	7391	2.373169	ACTCTTGCTTTCCACCTCATCA	59.627	45.455	0.00	0.00	0.00	3.07	R
4523	7394	2.806745	CGAACTCTTGCTTTCCACCTCA	60.807	50.000	0.00	0.00	0.00	3.86	R
4559	7430	2.361757	CCTCCTGCATCTCTGAGTACTG	59.638	54.545	0.00	2.90	0.00	2.74	R
5559	8439	0.178992	CTTCCTTGGGAGGTGTTGCA	60.179	55.000	0.00	0.00	43.97	4.08	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
90	91	6.552445	AGTAGCATCTTCTGTTGACCTAAT	57.448	37.500	0.00	0.00	0.00	1.73
106	107	9.413048	GTTGACCTAATGTATTGATACTCTAGC	57.587	37.037	3.11	0.00	34.41	3.42
124	125	7.200455	ACTCTAGCAACGTTTTAAAGCATTTT	58.800	30.769	0.00	0.00	40.09	1.82
153	154	8.889717	CGAAGGTTATACATAAACACCAGAAAT	58.110	33.333	0.17	0.00	32.42	2.17
205	206	0.846693	AGGGGCCATCATGTACCTTC	59.153	55.000	4.39	0.00	0.00	3.46
212	217	4.142381	GGCCATCATGTACCTTCAAAGAAC	60.142	45.833	0.00	0.00	0.00	3.01
241	246	3.334691	CTGTGCTCCGTTCTAATCCAAA	58.665	45.455	0.00	0.00	0.00	3.28
246	251	2.939103	CTCCGTTCTAATCCAAAGCCAG	59.061	50.000	0.00	0.00	0.00	4.85
274	279	4.020617	CCAGGAAGCTGCACGGGA	62.021	66.667	1.02	0.00	0.00	5.14
314	326	1.629043	CCCGTCATAGCTTAGCCCTA	58.371	55.000	0.00	0.00	0.00	3.53
392	404	6.015772	GTGGAAGTACAAGAGAGAGAAAGAGT	60.016	42.308	0.00	0.00	0.00	3.24
417	429	9.326413	GTGTTTTGTACTATATGTTCCATAGCT	57.674	33.333	0.00	0.00	30.45	3.32
418	430	9.542462	TGTTTTGTACTATATGTTCCATAGCTC	57.458	33.333	0.00	0.00	30.45	4.09
421	433	9.982651	TTTGTACTATATGTTCCATAGCTCTTC	57.017	33.333	0.00	0.00	30.45	2.87
430	442	5.707298	TGTTCCATAGCTCTTCTTTTCCTTG	59.293	40.000	0.00	0.00	0.00	3.61
454	466	4.412796	TGAACTATTGAGCTGGATCCTG	57.587	45.455	14.23	14.14	0.00	3.86
476	488	9.337714	TCCTGATATCCATATAATTCCTCACAA	57.662	33.333	0.00	0.00	0.00	3.33
579	602	8.433421	ACACAAGTTATAGCGTGCTATATTTT	57.567	30.769	19.27	14.20	40.09	1.82
654	677	4.985538	ACCTTAAGACACCATCGTAGAG	57.014	45.455	3.36	0.00	43.63	2.43
671	694	5.935206	TCGTAGAGAGACATAATCTAGCCAG	59.065	44.000	0.00	0.00	38.00	4.85
679	702	8.121833	AGAGACATAATCTAGCCAGATAGGAAT	58.878	37.037	0.00	0.00	40.81	3.01
751	774	4.672587	TTAACTCTGAACACTGAGCACT	57.327	40.909	0.00	0.00	34.47	4.40
793	816	6.703607	TGCAATAACCACAAAATAAACCTGTG	59.296	34.615	0.00	0.00	40.13	3.66
892	915	3.073022	CGCTAATTACGTGAATAGCGC	57.927	47.619	29.00	0.00	39.01	5.92
932	955	7.478520	TGCTAAAATATAGCGTTTCCTTCTC	57.521	36.000	3.31	0.00	43.13	2.87

Showing 1 to 25 of 106 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	0.588252	GATGGCATGTACACGCATCC	59.412	55.000	16.66	5.15	0.00	3.51
90	91	9.642327	TTAAAACGTTGCTAGAGTATCAATACA	57.358	29.630	0.00	0.00	37.82	2.29
124	125	8.095792	TCTGGTGTTTATGTATAACCTTCGAAA	58.904	33.333	0.00	0.00	0.00	3.46
144	145	5.452078	TGTAAGCTTCCAAATTTCTGGTG	57.548	39.130	0.00	0.00	37.74	4.17
146	147	4.619160	GCCTGTAAGCTTCCAAATTTCTGG	60.619	45.833	0.00	0.00	37.87	3.86
153	154	1.202927	AGCAGCCTGTAAGCTTCCAAA	60.203	47.619	0.00	0.00	42.61	3.28
205	206	1.826385	CACAGGGGCTAGGTTCTTTG	58.174	55.000	0.00	0.00	0.00	2.77
212	217	3.854669	CGGAGCACAGGGGCTAGG	61.855	72.222	0.00	0.00	45.99	3.02
241	246	3.928754	TCCTGGAATCTACATACTGGCT	58.071	45.455	0.00	0.00	0.00	4.75
246	251	4.061596	GCAGCTTCCTGGAATCTACATAC	58.938	47.826	12.13	0.00	39.54	2.39
274	279	5.063880	GGGGCATAATGTAGAAAAGATCGT	58.936	41.667	0.00	0.00	0.00	3.73
277	282	5.048846	ACGGGGCATAATGTAGAAAAGAT	57.951	39.130	0.00	0.00	0.00	2.40
314	326	7.466804	TCCAGTTTGGACACTTCCTATTTAAT	58.533	34.615	0.00	0.00	42.67	1.40
350	362	7.654022	ACTTCCACAAACTTCCTATTTTCAA	57.346	32.000	0.00	0.00	0.00	2.69
351	363	7.776030	TGTACTTCCACAAACTTCCTATTTTCA	59.224	33.333	0.00	0.00	0.00	2.69
367	379	6.015772	ACTCTTTCTCTCTCTTGTACTTCCAC	60.016	42.308	0.00	0.00	0.00	4.02
417	429	7.502226	TCAATAGTTCAAGCAAGGAAAAGAAGA	59.498	33.333	0.00	0.00	0.00	2.87
418	430	7.651808	TCAATAGTTCAAGCAAGGAAAAGAAG	58.348	34.615	0.00	0.00	0.00	2.85
421	433	5.860716	GCTCAATAGTTCAAGCAAGGAAAAG	59.139	40.000	0.00	0.00	34.86	2.27
430	442	3.563390	GGATCCAGCTCAATAGTTCAAGC	59.437	47.826	6.95	0.00	34.95	4.01
464	476	3.117093	TGGGGGTGTTTTGTGAGGAATTA	60.117	43.478	0.00	0.00	0.00	1.40
476	488	1.905894	GCCATGTAAATGGGGGTGTTT	59.094	47.619	14.08	0.00	41.94	2.83
654	677	7.710676	TTCCTATCTGGCTAGATTATGTCTC	57.289	40.000	18.48	0.00	40.79	3.36
734	757	2.992543	GCTAAGTGCTCAGTGTTCAGAG	59.007	50.000	0.00	0.00	38.95	3.35
751	774	5.995565	ATTGCACGGTAGATATAGGCTAA	57.004	39.130	0.00	0.00	0.00	3.09

Showing 1 to 25 of 118 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.