AutoCloner

Multiple sequence alignment - TraesCS2A01G403000

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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	TraesCS2A01G403000	chr2A	100.000	3444	0	0	1	3444	657131768	657128325	0.000000e+00	6360.0
1	TraesCS2A01G403000	chr4A	95.917	2180	63	10	713	2871	125469859	125467685	0.000000e+00	3509.0
2	TraesCS2A01G403000	chr4A	93.697	587	35	1	1	585	125470509	125469923	0.000000e+00	878.0
3	TraesCS2A01G403000	chr4A	93.966	232	6	3	2915	3138	125467695	125467464	9.150000e-91	344.0
4	TraesCS2A01G403000	chr4A	91.080	213	12	1	3220	3432	125467465	125467260	7.280000e-72	281.0
5	TraesCS2A01G403000	chr4D	98.409	1949	26	1	769	2717	341388834	341390777	0.000000e+00	3422.0
6	TraesCS2A01G403000	chr4D	96.056	786	28	2	1	784	341387648	341388432	0.000000e+00	1277.0
7	TraesCS2A01G403000	chr4D	99.057	530	5	0	2915	3444	341392904	341393433	0.000000e+00	952.0
8	TraesCS2A01G403000	chr4D	98.830	171	1	1	2701	2871	341392745	341392914	1.550000e-78	303.0
9	TraesCS2A01G403000	chr4D	96.429	168	5	1	614	781	341388430	341388596	3.390000e-70	276.0
10	TraesCS2A01G403000	chr4B	95.317	1986	52	11	727	2688	423036946	423038914	0.000000e+00	3114.0
11	TraesCS2A01G403000	chr4B	93.071	534	36	1	1	534	423017664	423018196	0.000000e+00	780.0
12	TraesCS2A01G403000	chr4B	93.371	528	16	7	2915	3442	423039031	423039539	0.000000e+00	763.0
13	TraesCS2A01G403000	chr4B	90.698	172	5	4	525	692	423035624	423035788	5.790000e-53	219.0
14	TraesCS2A01G403000	chr4B	96.269	134	4	1	2738	2871	423038909	423039041	5.790000e-53	219.0
15	TraesCS2A01G403000	chr5D	84.848	99	12	3	977	1073	410562478	410562575	2.830000e-16	97.1

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	TraesCS2A01G403000	chr2A	657128325	657131768	3443	True	6360.00	6360	100.00000	1	3444	1	chr2A.!!$R1	3443
1	TraesCS2A01G403000	chr4A	125467260	125470509	3249	True	1253.00	3509	93.66500	1	3432	4	chr4A.!!$R1	3431
2	TraesCS2A01G403000	chr4D	341387648	341393433	5785	False	1246.00	3422	97.75620	1	3444	5	chr4D.!!$F1	3443
3	TraesCS2A01G403000	chr4B	423035624	423039539	3915	False	1078.75	3114	93.91375	525	3442	4	chr4B.!!$F2	2917
4	TraesCS2A01G403000	chr4B	423017664	423018196	532	False	780.00	780	93.07100	1	534	1	chr4B.!!$F1	533

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
725	1879	2.290641	AGTTGGATGTGCTTTCGTGTTC	59.709	45.455	0.00	0.0	0.00	3.18	F
1933	3361	3.578716	AGCTAAAGCGCTATCCTTATGGA	59.421	43.478	12.05	0.0	46.26	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	3692	1.305381	AAGGCCGACTACTGCTCCT	60.305	57.895	0.0	0.0	0.0	3.69	R
2886	6317	0.398696	ATTTGCGGGTGGTGTCAGTA	59.601	50.000	0.0	0.0	0.0	2.74	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
27	28	7.100458	ACACTTTGCTGATTTAACTTGTCTT	57.900	32.000	0.00	0.00	0.00	3.01
105	106	8.892723	TGCAAGACATATTTCGAAAGATATTGT	58.107	29.630	23.59	18.06	41.60	2.71
177	178	9.717942	CTTCTTTGTGGGATAGAGATAATAAGG	57.282	37.037	0.00	0.00	0.00	2.69
239	240	6.541641	GGAGCTTATGGGCTATGATAAATGAG	59.458	42.308	0.00	0.00	43.20	2.90
404	405	2.312390	GGAGAGCTCCTAAGGATCGTT	58.688	52.381	10.93	5.87	46.16	3.85
411	412	3.522553	CTCCTAAGGATCGTTTGGTGAC	58.477	50.000	22.26	0.00	0.00	3.67
557	560	6.882610	AGTTGTGCTTGTGAATCTTATCAA	57.117	33.333	0.00	0.00	0.00	2.57
725	1879	2.290641	AGTTGGATGTGCTTTCGTGTTC	59.709	45.455	0.00	0.00	0.00	3.18
1803	3231	8.695456	GTTGAAACCATAGGGATTATTCACATT	58.305	33.333	0.00	0.00	38.05	2.71
1804	3232	9.928618	TTGAAACCATAGGGATTATTCACATTA	57.071	29.630	0.00	0.00	38.05	1.90
1933	3361	3.578716	AGCTAAAGCGCTATCCTTATGGA	59.421	43.478	12.05	0.00	46.26	3.41
2245	3692	2.865079	TGGGTTCATTAGGTTTTCGCA	58.135	42.857	0.00	0.00	0.00	5.10
2566	4013	7.043059	GCTCTTACATGAAGTATAAGCTGTCAC	60.043	40.741	0.00	0.00	37.51	3.67
2589	4036	5.105228	ACCATCCATTAAAATGTGCTTCAGG	60.105	40.000	2.25	0.00	34.60	3.86
2860	6291	2.288640	GCGCCTAAGTATCCCGTACAAT	60.289	50.000	0.00	0.00	35.67	2.71
2861	6292	3.057315	GCGCCTAAGTATCCCGTACAATA	60.057	47.826	0.00	0.00	35.67	1.90
2862	6293	4.479619	CGCCTAAGTATCCCGTACAATAC	58.520	47.826	0.00	0.00	35.67	1.89
2863	6294	4.217118	CGCCTAAGTATCCCGTACAATACT	59.783	45.833	6.70	6.70	39.74	2.12
2864	6295	5.467705	GCCTAAGTATCCCGTACAATACTG	58.532	45.833	11.31	3.83	38.41	2.74
2865	6296	5.010415	GCCTAAGTATCCCGTACAATACTGT	59.990	44.000	11.31	0.00	38.41	3.55
2866	6297	6.207417	GCCTAAGTATCCCGTACAATACTGTA	59.793	42.308	11.31	0.00	38.41	2.74
2880	6311	7.476540	ACAATACTGTACTGATCCTGTACAA	57.523	36.000	21.32	13.00	44.01	2.41
2881	6312	8.079211	ACAATACTGTACTGATCCTGTACAAT	57.921	34.615	21.32	17.01	44.01	2.71
2882	6313	9.197306	ACAATACTGTACTGATCCTGTACAATA	57.803	33.333	21.32	18.14	44.01	1.90
2883	6314	9.464714	CAATACTGTACTGATCCTGTACAATAC	57.535	37.037	21.32	5.18	44.01	1.89
2884	6315	8.998277	ATACTGTACTGATCCTGTACAATACT	57.002	34.615	21.32	11.70	44.01	2.12
2885	6316	7.101652	ACTGTACTGATCCTGTACAATACTG	57.898	40.000	21.32	14.94	44.01	2.74
2886	6317	6.663953	ACTGTACTGATCCTGTACAATACTGT	59.336	38.462	21.32	15.37	44.01	3.55
2887	6318	7.832685	ACTGTACTGATCCTGTACAATACTGTA	59.167	37.037	21.32	0.00	44.01	2.74
2898	6329	4.267349	ACAATACTGTACTGACACCACC	57.733	45.455	2.96	0.00	32.54	4.61
2899	6330	3.007614	ACAATACTGTACTGACACCACCC	59.992	47.826	2.96	0.00	32.54	4.61
2900	6331	1.250328	TACTGTACTGACACCACCCG	58.750	55.000	6.77	0.00	0.00	5.28
2901	6332	1.374252	CTGTACTGACACCACCCGC	60.374	63.158	0.00	0.00	0.00	6.13
2902	6333	2.094757	CTGTACTGACACCACCCGCA	62.095	60.000	0.00	0.00	0.00	5.69
2903	6334	1.070105	GTACTGACACCACCCGCAA	59.930	57.895	0.00	0.00	0.00	4.85
2904	6335	0.533308	GTACTGACACCACCCGCAAA	60.533	55.000	0.00	0.00	0.00	3.68
2905	6336	0.398696	TACTGACACCACCCGCAAAT	59.601	50.000	0.00	0.00	0.00	2.32
2906	6337	0.467290	ACTGACACCACCCGCAAATT	60.467	50.000	0.00	0.00	0.00	1.82
2907	6338	0.673437	CTGACACCACCCGCAAATTT	59.327	50.000	0.00	0.00	0.00	1.82
2908	6339	1.068434	CTGACACCACCCGCAAATTTT	59.932	47.619	0.00	0.00	0.00	1.82
2909	6340	1.482593	TGACACCACCCGCAAATTTTT	59.517	42.857	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	9.696917	AAAAGCTTCAACAATATCTTTCGAAAT	57.303	25.926	11.70	0.00	0.00	2.17
105	106	8.682936	AGAGAGATAAAAGTGAAAAGCTTCAA	57.317	30.769	0.00	0.00	43.18	2.69
239	240	4.562394	CACACAACTCCATGAAAACACAAC	59.438	41.667	0.00	0.00	0.00	3.32
282	283	4.408276	AGGAGCACACTTACTCTACTCAA	58.592	43.478	0.00	0.00	33.29	3.02
404	405	4.006989	CCCACATTATTCTTCGTCACCAA	58.993	43.478	0.00	0.00	0.00	3.67
411	412	2.355756	CCTGCACCCACATTATTCTTCG	59.644	50.000	0.00	0.00	0.00	3.79
509	510	7.846644	AACAACATGAGCAAAGAAAATTCAA	57.153	28.000	0.00	0.00	0.00	2.69
517	518	5.733091	GCACAACTAACAACATGAGCAAAGA	60.733	40.000	0.00	0.00	31.07	2.52
557	560	4.698575	GCTATAGCCAAAGTAGTTGAGCT	58.301	43.478	14.13	11.04	42.65	4.09
725	1879	7.254455	CGCATGGAGAAAACTTACACCTATAAG	60.254	40.741	0.00	0.00	38.03	1.73
1101	2515	4.069232	CACGCGAGGAAGAGGCCA	62.069	66.667	15.93	0.00	0.00	5.36
1803	3231	5.871465	TGCAAACAGATACGCAAATTCTA	57.129	34.783	0.00	0.00	0.00	2.10
1804	3232	4.764679	TGCAAACAGATACGCAAATTCT	57.235	36.364	0.00	0.00	0.00	2.40
1898	3326	4.432892	GCGCTTTAGCTGTAATTTTTGTGC	60.433	41.667	0.00	0.00	39.32	4.57
2245	3692	1.305381	AAGGCCGACTACTGCTCCT	60.305	57.895	0.00	0.00	0.00	3.69
2566	4013	5.105228	ACCTGAAGCACATTTTAATGGATGG	60.105	40.000	7.33	2.77	40.70	3.51
2817	6248	1.439353	GCCTAAGCAGCGCATAAGCA	61.439	55.000	11.47	0.00	38.97	3.91
2876	6307	4.221262	GGGTGGTGTCAGTACAGTATTGTA	59.779	45.833	3.20	0.00	38.76	2.41
2877	6308	3.007614	GGGTGGTGTCAGTACAGTATTGT	59.992	47.826	3.20	0.00	41.39	2.71
2878	6309	3.596214	GGGTGGTGTCAGTACAGTATTG	58.404	50.000	0.00	0.00	35.91	1.90
2879	6310	2.232941	CGGGTGGTGTCAGTACAGTATT	59.767	50.000	0.00	0.00	35.91	1.89
2880	6311	1.822990	CGGGTGGTGTCAGTACAGTAT	59.177	52.381	0.00	0.00	35.91	2.12
2881	6312	1.250328	CGGGTGGTGTCAGTACAGTA	58.750	55.000	0.00	0.00	35.91	2.74
2882	6313	2.046938	CGGGTGGTGTCAGTACAGT	58.953	57.895	0.00	0.00	35.91	3.55
2883	6314	1.374252	GCGGGTGGTGTCAGTACAG	60.374	63.158	0.00	0.00	35.91	2.74
2884	6315	1.687297	TTGCGGGTGGTGTCAGTACA	61.687	55.000	0.00	0.00	0.00	2.90
2885	6316	0.533308	TTTGCGGGTGGTGTCAGTAC	60.533	55.000	0.00	0.00	0.00	2.73
2886	6317	0.398696	ATTTGCGGGTGGTGTCAGTA	59.601	50.000	0.00	0.00	0.00	2.74
2887	6318	0.467290	AATTTGCGGGTGGTGTCAGT	60.467	50.000	0.00	0.00	0.00	3.41
2888	6319	0.673437	AAATTTGCGGGTGGTGTCAG	59.327	50.000	0.00	0.00	0.00	3.51
2889	6320	1.115467	AAAATTTGCGGGTGGTGTCA	58.885	45.000	0.00	0.00	0.00	3.58
2890	6321	2.232756	AAAAATTTGCGGGTGGTGTC	57.767	45.000	0.00	0.00	0.00	3.67
2910	6341	5.927689	CCGTATGGTGTCAGTACAGTAAAAA	59.072	40.000	0.00	0.00	35.91	1.94
2911	6342	5.243507	TCCGTATGGTGTCAGTACAGTAAAA	59.756	40.000	0.00	0.00	35.91	1.52
2912	6343	4.766373	TCCGTATGGTGTCAGTACAGTAAA	59.234	41.667	0.00	0.00	35.91	2.01
2913	6344	4.156556	GTCCGTATGGTGTCAGTACAGTAA	59.843	45.833	0.00	0.00	35.91	2.24
3067	6506	7.720957	TGTTCAATGATTATATCCCACTCCAAG	59.279	37.037	0.00	0.00	0.00	3.61
3257	6696	2.355481	GCTGCTGTTGTTGGCTGC	60.355	61.111	0.00	0.00	43.58	5.25

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.