AutoCloner

Multiple sequence alignment - TraesCS2B01G347200

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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	TraesCS2B01G347200	chr2B	100.000	2869	0	0	1	2869	493986679	493989547	0.000000e+00	5299.0
1	TraesCS2B01G347200	chr2B	82.949	217	11	3	1	191	494260936	494261152	3.800000e-39	172.0
2	TraesCS2B01G347200	chr2B	88.235	51	5	1	2274	2323	91895089	91895139	3.090000e-05	60.2
3	TraesCS2B01G347200	chr2B	97.059	34	1	0	2321	2354	475643890	475643923	1.110000e-04	58.4
4	TraesCS2B01G347200	chr2A	90.823	2430	113	34	522	2869	567734722	567737123	0.000000e+00	3151.0
5	TraesCS2B01G347200	chr2A	95.222	293	9	3	1346	1638	546771202	546770915	2.600000e-125	459.0
6	TraesCS2B01G347200	chr2A	91.544	272	9	4	1	259	546771548	546771278	2.100000e-96	363.0
7	TraesCS2B01G347200	chr2A	91.597	238	15	1	2215	2447	546742975	546742738	9.910000e-85	324.0
8	TraesCS2B01G347200	chr2A	94.079	152	9	0	2704	2855	546742739	546742588	6.180000e-57	231.0
9	TraesCS2B01G347200	chr2A	90.909	99	7	2	1860	1957	546743098	546743001	6.450000e-27	132.0
10	TraesCS2B01G347200	chr2A	96.053	76	2	1	184	259	567734357	567734431	3.880000e-24	122.0
11	TraesCS2B01G347200	chr2A	85.965	114	5	4	367	472	567734506	567734616	8.400000e-21	111.0
12	TraesCS2B01G347200	chr2D	90.602	1511	74	22	486	1982	421479915	421481371	0.000000e+00	1941.0
13	TraesCS2B01G347200	chr2D	96.166	313	12	0	2557	2869	421481985	421482297	1.970000e-141	512.0
14	TraesCS2B01G347200	chr2D	86.158	419	33	3	2052	2445	421481512	421481930	2.040000e-116	429.0
15	TraesCS2B01G347200	chr2D	79.885	522	22	21	1	467	421477216	421477709	3.590000e-79	305.0
16	TraesCS2B01G347200	chr2D	82.949	217	11	4	1	191	421792508	421792724	3.800000e-39	172.0
17	TraesCS2B01G347200	chr2D	97.059	68	2	0	2470	2537	421481925	421481992	6.500000e-22	115.0
18	TraesCS2B01G347200	chr2D	88.608	79	7	2	1981	2057	421481418	421481496	8.460000e-16	95.3
19	TraesCS2B01G347200	chr3B	98.874	888	10	0	1837	2724	9687473	9688360	0.000000e+00	1585.0
20	TraesCS2B01G347200	chr4B	94.366	71	4	0	24	94	404513457	404513527	3.020000e-20	110.0
21	TraesCS2B01G347200	chr7A	94.595	37	2	0	2296	2332	297901367	297901403	1.110000e-04	58.4

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	TraesCS2B01G347200	chr2B	493986679	493989547	2868	False	5299.000000	5299	100.000000	1	2869	1	chr2B.!!$F3	2868
1	TraesCS2B01G347200	chr2A	567734357	567737123	2766	False	1128.000000	3151	90.947000	184	2869	3	chr2A.!!$F1	2685
2	TraesCS2B01G347200	chr2A	546770915	546771548	633	True	411.000000	459	93.383000	1	1638	2	chr2A.!!$R2	1637
3	TraesCS2B01G347200	chr2A	546742588	546743098	510	True	229.000000	324	92.195000	1860	2855	3	chr2A.!!$R1	995
4	TraesCS2B01G347200	chr2D	421477216	421482297	5081	False	566.216667	1941	89.746333	1	2869	6	chr2D.!!$F2	2868
5	TraesCS2B01G347200	chr3B	9687473	9688360	887	False	1585.000000	1585	98.874000	1837	2724	1	chr3B.!!$F1	887

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
337	409	0.521867	CAACATCGACATGCAAGCGG	60.522	55.0	0.0	0.0	32.57	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2182	4626	1.000274	GCGTTTGTTTGCCATCCTCTT	60.0	47.619	0.0	0.0	0.0	2.85	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
40	46	2.601666	TGAGGTGAGCTGAGCGGT	60.602	61.111	0.00	0.00	0.00	5.68
142	170	6.484364	TGCTCCATCACTATCTCAACATAA	57.516	37.500	0.00	0.00	0.00	1.90
147	175	6.841229	TCCATCACTATCTCAACATAACCTCT	59.159	38.462	0.00	0.00	0.00	3.69
180	208	1.640593	TTCTGTTCTGGTGGGTGCCA	61.641	55.000	0.00	0.00	36.97	4.92
285	345	6.888632	ACTTATTGAAGATGCTGGTTCAGATT	59.111	34.615	0.00	0.00	36.45	2.40
304	364	6.650807	TCAGATTTGTTTCAGTGTGATACCTC	59.349	38.462	0.00	0.00	29.04	3.85
329	401	1.831106	TGGACTAGCCAACATCGACAT	59.169	47.619	3.71	0.00	45.87	3.06
337	409	0.521867	CAACATCGACATGCAAGCGG	60.522	55.000	0.00	0.00	32.57	5.52
355	427	2.555199	CGGCAATTCCTTCTCGAAGAT	58.445	47.619	8.19	0.00	40.79	2.40
406	479	2.304092	CTTGGGGATGATGTGGTGATG	58.696	52.381	0.00	0.00	0.00	3.07
430	510	1.281925	CCTAGGTGGTGGATGGCCTT	61.282	60.000	3.32	0.00	34.31	4.35
472	571	6.954616	TTGCAAGCTGATTTGTTCAATATG	57.045	33.333	0.00	0.00	32.78	1.78
476	575	5.002464	AGCTGATTTGTTCAATATGTGGC	57.998	39.130	0.00	0.00	32.78	5.01
491	590	3.512033	TGTGGCTGTGGTGTTTAAAAC	57.488	42.857	0.00	0.00	0.00	2.43
561	2869	8.192110	TGTTTCCACAAATTTTAGTGTTACTCC	58.808	33.333	7.61	0.00	33.99	3.85
562	2870	7.883391	TTCCACAAATTTTAGTGTTACTCCA	57.117	32.000	7.61	0.00	33.99	3.86
563	2871	8.472007	TTCCACAAATTTTAGTGTTACTCCAT	57.528	30.769	7.61	0.00	33.99	3.41
564	2872	9.575868	TTCCACAAATTTTAGTGTTACTCCATA	57.424	29.630	7.61	0.00	33.99	2.74
565	2873	9.005777	TCCACAAATTTTAGTGTTACTCCATAC	57.994	33.333	7.61	0.00	33.99	2.39
603	2911	4.894114	GGGCTAACTAATCACCTACTCTCA	59.106	45.833	0.00	0.00	0.00	3.27
754	3064	3.822735	TGCCCACTTTTTCAGATCAAGAG	59.177	43.478	0.00	0.00	0.00	2.85
771	3081	1.132817	AGAGTTCCACCCCTGTACAGT	60.133	52.381	21.18	0.98	0.00	3.55
772	3082	1.697982	GAGTTCCACCCCTGTACAGTT	59.302	52.381	21.18	2.70	0.00	3.16
839	3151	7.351952	CCCCATGAATATACATTGATCCTCAT	58.648	38.462	0.00	0.00	0.00	2.90
892	3204	3.496870	GGTAGATGGATCTTGCCGGAAAT	60.497	47.826	5.05	0.00	38.32	2.17
902	3214	3.826157	TCTTGCCGGAAATTCTTCAATGT	59.174	39.130	5.05	0.00	32.75	2.71
1042	3360	2.093288	TGATCAAGTAGCTGGCAAGAGG	60.093	50.000	0.00	0.00	0.00	3.69
1048	3366	1.807142	GTAGCTGGCAAGAGGTTTGAC	59.193	52.381	0.00	0.00	0.00	3.18
1052	3370	1.896660	GGCAAGAGGTTTGACCGCA	60.897	57.895	3.75	0.00	44.90	5.69
1053	3371	1.576421	GCAAGAGGTTTGACCGCAG	59.424	57.895	3.75	0.00	44.90	5.18
1055	3373	1.876416	GCAAGAGGTTTGACCGCAGTA	60.876	52.381	3.75	0.00	44.90	2.74
1307	3629	3.182182	CACATGTCCAGACGAGTATGTG	58.818	50.000	12.02	12.02	39.22	3.21
1644	3966	2.235898	CCTCCTCAAGAACTAGCAGCTT	59.764	50.000	0.00	0.00	0.00	3.74
1661	3988	1.696832	CTTTTAGCTGCCTCGTCGCC	61.697	60.000	0.00	0.00	0.00	5.54
1662	3989	2.443260	TTTTAGCTGCCTCGTCGCCA	62.443	55.000	0.00	0.00	0.00	5.69
1663	3990	2.835701	TTTAGCTGCCTCGTCGCCAG	62.836	60.000	0.00	0.00	0.00	4.85
1704	4031	4.456253	CGTCTGTCCGTCCGTCCG	62.456	72.222	0.00	0.00	0.00	4.79
1741	4068	0.874607	ACTGTCGTCGTTGCCTGTTC	60.875	55.000	0.00	0.00	0.00	3.18
2025	4425	3.454375	GGAAGAGACAACAACGAGTTCA	58.546	45.455	0.00	0.00	38.74	3.18
2086	4529	6.242396	ACATATTAAGCAGTACCAACCACAA	58.758	36.000	0.00	0.00	0.00	3.33
2182	4626	5.079643	ACTAACTGGTAAACGTTCCCTAGA	58.920	41.667	15.56	0.00	0.00	2.43
2292	4755	4.321899	GCACCTCTGAAAAATTACCATGCA	60.322	41.667	0.00	0.00	0.00	3.96
2748	5221	6.530534	TCTGAGTTTATAAAGAGCAAGTACGC	59.469	38.462	0.00	0.00	0.00	4.42
2764	5237	2.689785	CGCTTTCGAGGCCAATGCA	61.690	57.895	5.01	0.00	37.22	3.96
2808	5281	6.814146	TGGTAAGGACAACATTTTGAAACAAC	59.186	34.615	0.00	0.00	36.48	3.32
2847	5320	8.110860	TGAATTTTGAGAGGGATTTTAGTGTC	57.889	34.615	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.654317	CTCAGCTCACCTCAGAATGC	58.346	55.000	0.00	0.00	34.76	3.56
27	33	1.226831	GCTCTACCGCTCAGCTCAC	60.227	63.158	0.00	0.00	0.00	3.51
40	46	2.714991	CGAGGCAGGCACAGCTCTA	61.715	63.158	0.00	0.00	41.93	2.43
142	170	1.696063	ATTGCACACAAAGCAGAGGT	58.304	45.000	0.00	0.00	43.75	3.85
147	175	3.130869	AGAACAGAATTGCACACAAAGCA	59.869	39.130	0.00	0.00	39.77	3.91
180	208	1.379843	CCGCCAGCCCAAAGGTATT	60.380	57.895	0.00	0.00	34.57	1.89
224	260	5.815740	TGATTAAGCCGGAAAGTTAGATCAC	59.184	40.000	5.05	0.00	0.00	3.06
285	345	4.641396	CCAGAGGTATCACACTGAAACAA	58.359	43.478	0.00	0.00	32.90	2.83
337	409	4.154918	ACAACATCTTCGAGAAGGAATTGC	59.845	41.667	12.32	0.00	38.88	3.56
339	411	5.799213	AGACAACATCTTCGAGAAGGAATT	58.201	37.500	12.32	2.72	38.88	2.17
341	413	4.873746	AGACAACATCTTCGAGAAGGAA	57.126	40.909	12.32	0.00	38.88	3.36
342	414	4.280929	TCAAGACAACATCTTCGAGAAGGA	59.719	41.667	12.32	1.20	44.99	3.36
343	415	4.560128	TCAAGACAACATCTTCGAGAAGG	58.440	43.478	12.32	1.06	44.99	3.46
344	416	5.694006	ACTTCAAGACAACATCTTCGAGAAG	59.306	40.000	6.51	6.51	44.99	2.85
345	417	5.463392	CACTTCAAGACAACATCTTCGAGAA	59.537	40.000	0.00	0.00	44.99	2.87
355	427	3.942748	GGGTACAACACTTCAAGACAACA	59.057	43.478	0.00	0.00	0.00	3.33
406	479	2.544768	ATCCACCACCTAGGGATGC	58.455	57.895	14.81	0.00	43.89	3.91
472	571	3.512033	TGTTTTAAACACCACAGCCAC	57.488	42.857	6.41	0.00	36.25	5.01
476	575	9.352784	CCATATGTATTGTTTTAAACACCACAG	57.647	33.333	20.66	12.13	41.97	3.66
491	590	0.881118	GCCCACGGCCATATGTATTG	59.119	55.000	2.24	0.00	44.06	1.90
561	2869	3.202906	CCCCCTGAACACGTTATGTATG	58.797	50.000	0.00	0.00	42.31	2.39
562	2870	2.420967	GCCCCCTGAACACGTTATGTAT	60.421	50.000	0.00	0.00	42.31	2.29
563	2871	1.065998	GCCCCCTGAACACGTTATGTA	60.066	52.381	0.00	0.00	42.31	2.29
564	2872	0.322187	GCCCCCTGAACACGTTATGT	60.322	55.000	0.00	0.00	46.42	2.29
565	2873	0.035439	AGCCCCCTGAACACGTTATG	60.035	55.000	0.00	0.00	0.00	1.90
603	2911	0.978146	AAGGTGATAGGAGCAGCGGT	60.978	55.000	0.00	0.00	38.68	5.68
754	3064	2.105993	AGAAACTGTACAGGGGTGGAAC	59.894	50.000	26.12	8.84	0.00	3.62
771	3081	1.872952	CAACCGTCTGCATGTGAGAAA	59.127	47.619	0.00	0.00	0.00	2.52
772	3082	1.202639	ACAACCGTCTGCATGTGAGAA	60.203	47.619	0.00	0.00	0.00	2.87
839	3151	1.374560	CCAATTTATGGCGTCGGTGA	58.625	50.000	0.00	0.00	43.80	4.02
892	3204	0.667453	TTGCGCTGCACATTGAAGAA	59.333	45.000	9.73	0.00	38.71	2.52
1042	3360	1.589803	AGGTTGTACTGCGGTCAAAC	58.410	50.000	0.00	9.52	0.00	2.93
1048	3366	0.447801	GATGCAAGGTTGTACTGCGG	59.552	55.000	0.00	0.00	0.00	5.69
1052	3370	0.035439	CCGGGATGCAAGGTTGTACT	60.035	55.000	0.00	0.00	0.00	2.73
1053	3371	0.322187	ACCGGGATGCAAGGTTGTAC	60.322	55.000	6.32	0.00	33.96	2.90
1055	3373	1.303317	GACCGGGATGCAAGGTTGT	60.303	57.895	6.32	0.00	38.57	3.32
1273	3595	1.393539	GACATGTGGATCGTTTCACGG	59.606	52.381	1.15	0.00	42.81	4.94
1307	3629	7.117454	CGTTACATATGCACTTACAAGCTTAC	58.883	38.462	0.00	0.00	0.00	2.34
1348	3670	2.119484	ATCGGAACCCCTGAACGCAA	62.119	55.000	0.00	0.00	0.00	4.85
1644	3966	2.125673	GGCGACGAGGCAGCTAAA	60.126	61.111	0.00	0.00	45.92	1.85
1682	4009	3.450115	GGACGGACAGACGGAGGG	61.450	72.222	0.00	0.00	38.39	4.30
1688	4015	3.319926	GACGGACGGACGGACAGAC	62.320	68.421	6.00	0.00	38.39	3.51
1704	4031	1.407979	AGTATTCATGGACGGACGGAC	59.592	52.381	0.00	0.00	0.00	4.79
1708	4035	2.159282	ACGACAGTATTCATGGACGGAC	60.159	50.000	0.00	0.00	0.00	4.79
1712	4039	3.146618	ACGACGACAGTATTCATGGAC	57.853	47.619	0.00	0.00	0.00	4.02
2025	4425	1.679032	GGTGGGTTTTCTCATAGCGCT	60.679	52.381	17.26	17.26	30.68	5.92
2182	4626	1.000274	GCGTTTGTTTGCCATCCTCTT	60.000	47.619	0.00	0.00	0.00	2.85
2292	4755	4.630644	TGCTGGAAGTTTCTTCAGAGAT	57.369	40.909	10.88	0.00	35.30	2.75
2748	5221	2.660189	AAATGCATTGGCCTCGAAAG	57.340	45.000	13.82	0.00	40.13	2.62

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.