AutoCloner

Multiple sequence alignment - TraesCS1B01G016200

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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	TraesCS1B01G016200	chr1B	100.000	4497	0	0	1	4497	7902813	7898317	0.000000e+00	8305
1	TraesCS1B01G016200	chr1B	97.244	4499	120	4	1	4497	567735587	567731091	0.000000e+00	7618
2	TraesCS1B01G016200	chr1B	97.088	4499	124	7	1	4497	676864401	676859908	0.000000e+00	7576
3	TraesCS1B01G016200	chr6B	97.399	4498	112	5	1	4497	572516290	572511797	0.000000e+00	7653
4	TraesCS1B01G016200	chr4A	97.065	4498	128	4	2	4497	673171281	673166786	0.000000e+00	7572
5	TraesCS1B01G016200	chr2B	96.821	4498	137	5	1	4497	785300765	785296273	0.000000e+00	7509
6	TraesCS1B01G016200	chr2B	96.333	4499	124	11	1	4497	662568065	662572524	0.000000e+00	7356
7	TraesCS1B01G016200	chr5B	96.777	4499	136	5	1	4497	18261522	18257031	0.000000e+00	7496
8	TraesCS1B01G016200	chr5B	96.503	2002	55	3	2497	4497	568809872	568811859	0.000000e+00	3295
9	TraesCS1B01G016200	chr3B	96.577	4499	143	7	1	4497	667633189	667637678	0.000000e+00	7444
10	TraesCS1B01G016200	chr3B	91.617	167	12	2	3964	4129	13141464	13141629	3.500000e-56	230
11	TraesCS1B01G016200	chr7B	96.087	4498	149	6	1	4497	629987599	629992070	0.000000e+00	7306
12	TraesCS1B01G016200	chr2A	94.520	3960	213	4	1	3958	773697694	773693737	0.000000e+00	6107

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	TraesCS1B01G016200	chr1B	7898317	7902813	4496	True	8305	8305	100.000	1	4497	1	chr1B.!!$R1	4496
1	TraesCS1B01G016200	chr1B	567731091	567735587	4496	True	7618	7618	97.244	1	4497	1	chr1B.!!$R2	4496
2	TraesCS1B01G016200	chr1B	676859908	676864401	4493	True	7576	7576	97.088	1	4497	1	chr1B.!!$R3	4496
3	TraesCS1B01G016200	chr6B	572511797	572516290	4493	True	7653	7653	97.399	1	4497	1	chr6B.!!$R1	4496
4	TraesCS1B01G016200	chr4A	673166786	673171281	4495	True	7572	7572	97.065	2	4497	1	chr4A.!!$R1	4495
5	TraesCS1B01G016200	chr2B	785296273	785300765	4492	True	7509	7509	96.821	1	4497	1	chr2B.!!$R1	4496
6	TraesCS1B01G016200	chr2B	662568065	662572524	4459	False	7356	7356	96.333	1	4497	1	chr2B.!!$F1	4496
7	TraesCS1B01G016200	chr5B	18257031	18261522	4491	True	7496	7496	96.777	1	4497	1	chr5B.!!$R1	4496
8	TraesCS1B01G016200	chr5B	568809872	568811859	1987	False	3295	3295	96.503	2497	4497	1	chr5B.!!$F1	2000
9	TraesCS1B01G016200	chr3B	667633189	667637678	4489	False	7444	7444	96.577	1	4497	1	chr3B.!!$F2	4496
10	TraesCS1B01G016200	chr7B	629987599	629992070	4471	False	7306	7306	96.087	1	4497	1	chr7B.!!$F1	4496
11	TraesCS1B01G016200	chr2A	773693737	773697694	3957	True	6107	6107	94.520	1	3958	1	chr2A.!!$R1	3957

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	Hairpin	End Stability	Orientation
86	87	1.000274	TCACATCGATCCTGCATACCG	60.000	52.381	0.00	4.02	F
329	330	1.224592	CCAAGCCGCCATTACCTCT	59.775	57.895	0.00	3.69	F
1769	1776	1.072648	CCTAAACGGAAAGGTGGTGGA	59.927	52.381	33.16	4.02	F
2314	2322	2.513897	CCCGAACCCCGCAGAATC	60.514	66.667	36.84	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1683	1690	1.344942	GCACGTCTGTACTCTTGGCG	61.345	60.000	0.00	0.00	5.69	R
2299	2307	0.391130	TCAAGATTCTGCGGGGTTCG	60.391	55.000	0.00	42.76	3.95	R
2791	2800	0.527565	ACAGCGCCATTCAACCATTC	59.472	50.000	2.29	0.00	2.67	R
3595	3606	2.105128	GCGATCTCCGTCCCAGTG	59.895	66.667	0.00	41.15	3.66	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
84	85	3.005261	AGACTCACATCGATCCTGCATAC	59.995	47.826	0.00	0.00	0.00	2.39
86	87	1.000274	TCACATCGATCCTGCATACCG	60.000	52.381	0.00	0.00	0.00	4.02
101	102	3.639538	CATACCGTCCAAATAGAGTCCG	58.360	50.000	0.00	0.00	0.00	4.79
329	330	1.224592	CCAAGCCGCCATTACCTCT	59.775	57.895	0.00	0.00	0.00	3.69
398	399	4.124351	GATCCGACGGTCGCACCA	62.124	66.667	24.26	8.40	38.47	4.17
849	850	6.712998	TGTTGAGAATTCCTTCCGTGAAAATA	59.287	34.615	0.65	0.00	31.27	1.40
958	960	7.443879	TCAGTGTGCTTAATGAAGATGTTTACA	59.556	33.333	0.00	0.00	34.25	2.41
1080	1084	4.870021	AAGAACAGGCCTAATCCTCATT	57.130	40.909	3.98	0.00	33.25	2.57
1192	1196	2.158971	GCACCACAATCCACCAAGTTTT	60.159	45.455	0.00	0.00	0.00	2.43
1357	1361	4.141482	ACTTGGCTCTTCTTCAGGTACAAA	60.141	41.667	0.00	0.00	0.00	2.83
1411	1417	5.408880	TTTATGTGACCTATGTGTCCGAA	57.591	39.130	0.00	0.00	34.25	4.30
1428	1435	7.874016	TGTGTCCGAATAGTTGTGTTTACTATT	59.126	33.333	7.72	7.72	46.28	1.73
1497	1504	4.692625	ACATTTGATCCTTTGTCTCGTGAG	59.307	41.667	0.00	0.00	0.00	3.51
1510	1517	3.693085	GTCTCGTGAGTACCCACTAATGA	59.307	47.826	5.94	0.00	34.21	2.57
1683	1690	6.034044	TGTTGTACAACTTGAAAATTGCGTTC	59.966	34.615	32.58	7.05	41.67	3.95
1769	1776	1.072648	CCTAAACGGAAAGGTGGTGGA	59.927	52.381	0.00	0.00	33.16	4.02
1971	1978	9.906660	TTTCATTTGTGTTTGTAGATGGTAATC	57.093	29.630	0.00	0.00	0.00	1.75
2035	2042	9.699410	ATAAGAGGGACAACAATGATGAATTTA	57.301	29.630	0.00	0.00	0.00	1.40
2299	2307	3.889520	AAGAGTTTCCGTCTATGTCCC	57.110	47.619	0.00	0.00	0.00	4.46
2314	2322	2.513897	CCCGAACCCCGCAGAATC	60.514	66.667	0.00	0.00	36.84	2.52
2609	2618	6.930164	TGCATTGTTTTAGATCTGTTTGCATT	59.070	30.769	5.18	0.00	32.01	3.56
2791	2800	4.161333	GCTTCACGATGTCCTGAATTTTG	58.839	43.478	0.00	0.00	0.00	2.44
2858	2867	9.778741	AATACTCTCATTTGAACTTCACAAGTA	57.221	29.630	0.00	0.00	41.91	2.24
2912	2921	9.410556	GATAATCAATGCATATTGTAAACACCC	57.589	33.333	0.00	0.00	43.33	4.61
2928	2937	1.407258	CACCCACAACACCGTGATTTT	59.593	47.619	5.28	0.00	39.34	1.82
2986	2995	2.881266	TATGTTGGGTAGGGCTAGGT	57.119	50.000	0.00	0.00	0.00	3.08
3077	3086	8.311395	AGAGTAATGGATGAGTATTTCAGACA	57.689	34.615	0.00	0.00	39.68	3.41
3595	3606	6.257630	ACTTTTTGTGATGTGGTGCATAAAAC	59.742	34.615	0.00	0.00	38.06	2.43
3667	3678	1.346395	AGTCAAGGCCACGTATTGTCA	59.654	47.619	5.01	0.00	0.00	3.58
3758	3770	4.625607	AGGAGTAGGTATTAGCATTGGC	57.374	45.455	0.00	0.00	41.61	4.52
3857	3869	6.094881	GGGATAGATTTCGACAATTTTCCACA	59.905	38.462	0.00	0.00	0.00	4.17
3884	3896	8.810652	TTTATTTATTGCTTTTGTGAGACACC	57.189	30.769	0.00	0.00	32.73	4.16
3966	3980	3.897325	TCTGCGATATTACGGACATGTC	58.103	45.455	17.91	17.91	0.00	3.06
4017	4031	1.106351	TGTGCCGTGCCACATCTTTT	61.106	50.000	0.00	0.00	40.55	2.27
4061	4075	2.107552	ACTAAGGTTAGGCTTGCCACAA	59.892	45.455	14.54	4.63	35.08	3.33
4169	4211	8.330247	TGTAGAAATTTGCCCCTAAATGTAGTA	58.670	33.333	0.00	0.00	31.05	1.82

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
16	17	5.836898	AGGTTCACATGGATCATGCATATTT	59.163	36.000	0.00	0.00	44.80	1.40
84	85	1.533338	CGTCGGACTCTATTTGGACGG	60.533	57.143	6.57	0.00	42.35	4.79
86	87	3.119566	AGTTCGTCGGACTCTATTTGGAC	60.120	47.826	0.00	0.00	0.00	4.02
101	102	2.543848	TGCACAAACATCTCAGTTCGTC	59.456	45.455	0.00	0.00	0.00	4.20
274	275	2.098871	CGTACGGCGTCATCGACA	59.901	61.111	19.21	0.00	46.73	4.35
329	330	3.081409	GCTAGGCGGTCTTGGGGA	61.081	66.667	0.00	0.00	0.00	4.81
398	399	3.819877	GAGTTTGGACGGCCACGGT	62.820	63.158	11.33	0.00	45.94	4.83
499	500	2.275380	GGGTGCCGGTGAATTTGCT	61.275	57.895	1.90	0.00	0.00	3.91
893	895	9.997482	TTGGTCAAATAATAAATCGCTTTCTAC	57.003	29.630	0.00	0.00	0.00	2.59
913	915	2.027653	TGATGCCGTCTGTATTTGGTCA	60.028	45.455	0.00	0.00	0.00	4.02
958	960	3.066621	TCGTTACGTAGCCCGAATATGTT	59.933	43.478	4.24	0.00	40.70	2.71
1398	1404	4.755411	ACACAACTATTCGGACACATAGG	58.245	43.478	1.50	0.00	0.00	2.57
1497	1504	4.820173	GGCCAGTTAATCATTAGTGGGTAC	59.180	45.833	0.00	0.00	0.00	3.34
1510	1517	2.871096	TCCGTTTCTGGCCAGTTAAT	57.129	45.000	31.58	0.00	0.00	1.40
1572	1579	5.007682	ACTTATTGACTTACATTGCCGGTT	58.992	37.500	1.90	0.00	0.00	4.44
1683	1690	1.344942	GCACGTCTGTACTCTTGGCG	61.345	60.000	0.00	0.00	0.00	5.69
1769	1776	2.784347	GTGCTTGGCTTTCTACTCCTT	58.216	47.619	0.00	0.00	0.00	3.36
1936	1943	6.096036	ACAAACACAAATGAAACACGATCAA	58.904	32.000	0.00	0.00	0.00	2.57
1971	1978	2.353579	ACCTTCCGTGTTCAACTTTTCG	59.646	45.455	0.00	0.00	0.00	3.46
2035	2042	6.969043	TCCCAACTCCTTGATGTACATTAAT	58.031	36.000	12.91	0.00	0.00	1.40
2045	2052	2.850833	TCTCCATCCCAACTCCTTGAT	58.149	47.619	0.00	0.00	0.00	2.57
2299	2307	0.391130	TCAAGATTCTGCGGGGTTCG	60.391	55.000	0.00	0.00	42.76	3.95
2314	2322	8.373981	ACCCATAGACTCATCAGAAATATCAAG	58.626	37.037	0.00	0.00	0.00	3.02
2791	2800	0.527565	ACAGCGCCATTCAACCATTC	59.472	50.000	2.29	0.00	0.00	2.67
2912	2921	4.035017	GTCAGAAAAATCACGGTGTTGTG	58.965	43.478	8.17	4.24	41.28	3.33
2928	2937	5.107259	CGTTGTTGATATGAAACGGTCAGAA	60.107	40.000	0.00	0.00	40.43	3.02
3595	3606	2.105128	GCGATCTCCGTCCCAGTG	59.895	66.667	0.00	0.00	41.15	3.66
3637	3648	3.941483	CGTGGCCTTGACTCATTAATCTT	59.059	43.478	3.32	0.00	0.00	2.40
3758	3770	3.369157	CCTTCTACGGGACTAAAACCCTG	60.369	52.174	0.00	0.00	44.72	4.45
3966	3980	3.118629	TGGCTAGCTAAGTCATGAACCAG	60.119	47.826	15.72	0.00	33.94	4.00
4039	4053	2.907696	TGTGGCAAGCCTAACCTTAGTA	59.092	45.455	12.96	0.00	36.94	1.82
4061	4075	5.888982	TCTACAGAAAAACCTCTTCCAGT	57.111	39.130	0.00	0.00	0.00	4.00
4169	4211	2.478894	CGCGAGTAGGAACAACAACAAT	59.521	45.455	0.00	0.00	0.00	2.71
4350	4392	3.826754	CTAGCTGGAGTGCGCGGA	61.827	66.667	8.83	0.00	38.13	5.54

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.