AutoCloner

Multiple sequence alignment - TraesCS2B01G160300

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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	TraesCS2B01G160300	chr2B	100.000	2866	0	0	1	2866	133808080	133805215	0.000000e+00	5293.0
1	TraesCS2B01G160300	chr2B	95.690	2738	109	2	34	2763	133704122	133701386	0.000000e+00	4394.0
2	TraesCS2B01G160300	chr2B	78.078	1852	334	44	34	1869	134349590	134347795	0.000000e+00	1105.0
3	TraesCS2B01G160300	chr2B	81.220	1262	199	22	34	1285	134365640	134364407	0.000000e+00	983.0
4	TraesCS2B01G160300	chr2D	93.584	2790	119	10	1	2763	81942779	81940023	0.000000e+00	4106.0
5	TraesCS2B01G160300	chr2D	78.298	1880	342	39	34	1899	82266517	82264690	0.000000e+00	1151.0
6	TraesCS2B01G160300	chr2A	94.264	2127	99	13	702	2823	82131400	82129292	0.000000e+00	3230.0
7	TraesCS2B01G160300	chr2A	85.302	2463	286	35	37	2476	82200964	82198555	0.000000e+00	2473.0
8	TraesCS2B01G160300	chr2A	78.367	1849	335	38	34	1869	82537982	82536186	0.000000e+00	1138.0
9	TraesCS2B01G160300	chr2A	78.237	1838	335	38	34	1858	82358001	82356216	0.000000e+00	1118.0
10	TraesCS2B01G160300	chr2A	78.761	339	33	20	2236	2542	82064184	82063853	1.050000e-44	191.0
11	TraesCS2B01G160300	chr2A	97.101	69	2	0	34	102	82131469	82131401	1.800000e-22	117.0
12	TraesCS2B01G160300	chr2A	100.000	42	0	0	2781	2822	73540656	73540697	8.510000e-11	78.7
13	TraesCS2B01G160300	chr2A	97.778	45	1	0	2780	2824	745094748	745094704	8.510000e-11	78.7
14	TraesCS2B01G160300	chr3A	100.000	45	0	0	2781	2825	79455063	79455019	1.830000e-12	84.2
15	TraesCS2B01G160300	chr3D	100.000	44	0	0	2781	2824	67728918	67728875	6.580000e-12	82.4
16	TraesCS2B01G160300	chr3D	97.778	45	0	1	2782	2826	602205251	602205208	3.060000e-10	76.8
17	TraesCS2B01G160300	chr6D	97.778	45	1	0	2780	2824	39676410	39676454	8.510000e-11	78.7
18	TraesCS2B01G160300	chrUn	97.727	44	1	0	2781	2824	267647702	267647659	3.060000e-10	76.8
19	TraesCS2B01G160300	chr6A	90.909	55	3	2	2771	2824	540610169	540610222	3.960000e-09	73.1

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	TraesCS2B01G160300	chr2B	133805215	133808080	2865	True	5293.0	5293	100.0000	1	2866	1	chr2B.!!$R2	2865
1	TraesCS2B01G160300	chr2B	133701386	133704122	2736	True	4394.0	4394	95.6900	34	2763	1	chr2B.!!$R1	2729
2	TraesCS2B01G160300	chr2B	134347795	134349590	1795	True	1105.0	1105	78.0780	34	1869	1	chr2B.!!$R3	1835
3	TraesCS2B01G160300	chr2B	134364407	134365640	1233	True	983.0	983	81.2200	34	1285	1	chr2B.!!$R4	1251
4	TraesCS2B01G160300	chr2D	81940023	81942779	2756	True	4106.0	4106	93.5840	1	2763	1	chr2D.!!$R1	2762
5	TraesCS2B01G160300	chr2D	82264690	82266517	1827	True	1151.0	1151	78.2980	34	1899	1	chr2D.!!$R2	1865
6	TraesCS2B01G160300	chr2A	82198555	82200964	2409	True	2473.0	2473	85.3020	37	2476	1	chr2A.!!$R2	2439
7	TraesCS2B01G160300	chr2A	82129292	82131469	2177	True	1673.5	3230	95.6825	34	2823	2	chr2A.!!$R6	2789
8	TraesCS2B01G160300	chr2A	82536186	82537982	1796	True	1138.0	1138	78.3670	34	1869	1	chr2A.!!$R4	1835
9	TraesCS2B01G160300	chr2A	82356216	82358001	1785	True	1118.0	1118	78.2370	34	1858	1	chr2A.!!$R3	1824

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
654	692	0.804989	GCAACGCAGCTAACCTCATT	59.195	50.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	2098	4.141482	ACCTTGTGTCTCTAAAGCCAAGAA	60.141	41.667	0.0	0.0	32.96	2.52	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
102	116	2.039879	ACTCACCACTTCCACCAATACC	59.960	50.000	0.00	0.00	0.00	2.73
105	119	1.002773	ACCACTTCCACCAATACCGTC	59.997	52.381	0.00	0.00	0.00	4.79
173	187	4.502016	ACCATCAGATTATATGCTGCGAG	58.498	43.478	0.00	0.00	32.27	5.03
181	195	1.337384	ATATGCTGCGAGGGTCACCA	61.337	55.000	0.00	0.00	40.13	4.17
205	219	3.927555	CTTGCAAAGGACCTCCGTA	57.072	52.632	0.00	0.00	41.27	4.02
267	281	5.424895	ACTTCTTGATGCTGATAGAAGACCT	59.575	40.000	19.09	2.53	43.92	3.85
273	287	6.586344	TGATGCTGATAGAAGACCTAAAAGG	58.414	40.000	0.00	0.00	42.49	3.11
327	341	5.347907	GCAAGAAGAAAGGCAAGATCAATTG	59.652	40.000	0.00	0.00	0.00	2.32
346	381	6.201615	TCAATTGCTGAATACAGAAGATAGCG	59.798	38.462	0.00	0.00	46.03	4.26
399	434	1.985684	GCTGTTAACCAATCGCAAAGC	59.014	47.619	2.48	0.00	0.00	3.51
449	484	2.096819	TGCTCGAAGAAACACAAACACC	59.903	45.455	0.00	0.00	34.09	4.16
468	503	1.687563	CCTCGACCCAACAACCTTTT	58.312	50.000	0.00	0.00	0.00	2.27
530	565	7.270579	GCAGTGGATTAAAGAATTACGTTCAAC	59.729	37.037	0.00	0.00	39.39	3.18
591	626	3.884693	CTGCACTGGCCATGTCAATAATA	59.115	43.478	5.51	0.00	40.13	0.98
639	677	3.715628	AACTGTGTGGAAATCAGCAAC	57.284	42.857	0.00	0.00	33.12	4.17
654	692	0.804989	GCAACGCAGCTAACCTCATT	59.195	50.000	0.00	0.00	0.00	2.57
732	770	5.122239	CGAGGCAGAACAAAAGATCATGTTA	59.878	40.000	10.38	0.00	39.73	2.41
741	779	8.955061	AACAAAAGATCATGTTAAAGTCATCG	57.045	30.769	9.09	0.00	37.96	3.84
750	788	4.385825	TGTTAAAGTCATCGCTGAAGGTT	58.614	39.130	0.00	0.00	31.85	3.50
835	873	3.655777	ACACCCCTTCCTATTGAGAAACA	59.344	43.478	0.00	0.00	0.00	2.83
839	877	5.222337	ACCCCTTCCTATTGAGAAACATTGT	60.222	40.000	0.00	0.00	0.00	2.71
973	1011	1.911357	TGATCATCACCAGGCTGAAGT	59.089	47.619	17.94	2.87	0.00	3.01
1227	1265	4.988744	CTCAGAGAGCCGGACCTA	57.011	61.111	5.05	0.00	0.00	3.08
1530	1583	9.406828	GTTCACTAATTTGTAAAACCATTCCTC	57.593	33.333	0.00	0.00	0.00	3.71
1768	1821	0.031314	ACACTGTCACACGCTGAGAG	59.969	55.000	6.36	6.36	44.38	3.20
1996	2051	3.575256	ACAGTACAATAAGGGACACGTGA	59.425	43.478	25.01	0.00	0.00	4.35
2041	2096	3.632145	GCAGGTGTGAGGAGAAAAAGAAA	59.368	43.478	0.00	0.00	0.00	2.52
2043	2098	5.221322	GCAGGTGTGAGGAGAAAAAGAAAAT	60.221	40.000	0.00	0.00	0.00	1.82
2779	2858	7.398332	GGTAAGCCTATAGCCCTATACTAAACA	59.602	40.741	0.00	0.00	45.47	2.83
2781	2860	8.450780	AAGCCTATAGCCCTATACTAAACAAT	57.549	34.615	0.00	0.00	45.47	2.71
2784	2863	8.101419	GCCTATAGCCCTATACTAAACAATTGT	58.899	37.037	4.92	4.92	34.35	2.71
2794	2873	4.828829	ACTAAACAATTGTACTCCCTCCG	58.171	43.478	12.39	0.00	0.00	4.63
2799	2878	0.042131	ATTGTACTCCCTCCGTCCCA	59.958	55.000	0.00	0.00	0.00	4.37
2823	2902	8.292448	CCATAATATAAGATCGTTTTGCAAGCT	58.708	33.333	0.00	0.00	0.00	3.74
2824	2903	9.669353	CATAATATAAGATCGTTTTGCAAGCTT	57.331	29.630	0.00	0.00	0.00	3.74
2825	2904	7.975866	AATATAAGATCGTTTTGCAAGCTTG	57.024	32.000	22.44	22.44	0.00	4.01
2839	2918	4.291540	CAAGCTTGCAACTAACAACAGA	57.708	40.909	14.65	0.00	0.00	3.41
2840	2919	4.671377	CAAGCTTGCAACTAACAACAGAA	58.329	39.130	14.65	0.00	0.00	3.02
2841	2920	5.284079	CAAGCTTGCAACTAACAACAGAAT	58.716	37.500	14.65	0.00	0.00	2.40
2842	2921	5.113502	AGCTTGCAACTAACAACAGAATC	57.886	39.130	0.00	0.00	0.00	2.52
2843	2922	4.022849	AGCTTGCAACTAACAACAGAATCC	60.023	41.667	0.00	0.00	0.00	3.01
2844	2923	4.466828	CTTGCAACTAACAACAGAATCCG	58.533	43.478	0.00	0.00	0.00	4.18
2845	2924	2.225491	TGCAACTAACAACAGAATCCGC	59.775	45.455	0.00	0.00	0.00	5.54
2846	2925	2.225491	GCAACTAACAACAGAATCCGCA	59.775	45.455	0.00	0.00	0.00	5.69
2847	2926	3.810373	CAACTAACAACAGAATCCGCAC	58.190	45.455	0.00	0.00	0.00	5.34
2848	2927	3.120321	ACTAACAACAGAATCCGCACA	57.880	42.857	0.00	0.00	0.00	4.57
2849	2928	3.067106	ACTAACAACAGAATCCGCACAG	58.933	45.455	0.00	0.00	0.00	3.66
2850	2929	0.593128	AACAACAGAATCCGCACAGC	59.407	50.000	0.00	0.00	0.00	4.40
2851	2930	0.534877	ACAACAGAATCCGCACAGCA	60.535	50.000	0.00	0.00	0.00	4.41
2852	2931	0.592637	CAACAGAATCCGCACAGCAA	59.407	50.000	0.00	0.00	0.00	3.91
2853	2932	1.001487	CAACAGAATCCGCACAGCAAA	60.001	47.619	0.00	0.00	0.00	3.68
2854	2933	0.593128	ACAGAATCCGCACAGCAAAC	59.407	50.000	0.00	0.00	0.00	2.93
2855	2934	0.592637	CAGAATCCGCACAGCAAACA	59.407	50.000	0.00	0.00	0.00	2.83
2856	2935	1.200716	CAGAATCCGCACAGCAAACAT	59.799	47.619	0.00	0.00	0.00	2.71
2857	2936	1.888512	AGAATCCGCACAGCAAACATT	59.111	42.857	0.00	0.00	0.00	2.71
2858	2937	1.987770	GAATCCGCACAGCAAACATTG	59.012	47.619	0.00	0.00	0.00	2.82
2859	2938	0.961019	ATCCGCACAGCAAACATTGT	59.039	45.000	0.00	0.00	0.00	2.71
2860	2939	1.598882	TCCGCACAGCAAACATTGTA	58.401	45.000	0.00	0.00	0.00	2.41
2861	2940	1.950216	TCCGCACAGCAAACATTGTAA	59.050	42.857	0.00	0.00	0.00	2.41
2862	2941	2.359214	TCCGCACAGCAAACATTGTAAA	59.641	40.909	0.00	0.00	0.00	2.01
2863	2942	3.119291	CCGCACAGCAAACATTGTAAAA	58.881	40.909	0.00	0.00	0.00	1.52
2864	2943	3.740321	CCGCACAGCAAACATTGTAAAAT	59.260	39.130	0.00	0.00	0.00	1.82
2865	2944	4.143347	CCGCACAGCAAACATTGTAAAATC	60.143	41.667	0.00	0.00	0.00	2.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
55	69	2.113986	GAGCTGTGCCCTGGTTGT	59.886	61.111	0.00	0.00	0.00	3.32
102	116	2.509052	TCCTGATTATTCTGGCGACG	57.491	50.000	5.84	0.00	40.00	5.12
105	119	3.251729	CCAACATCCTGATTATTCTGGCG	59.748	47.826	5.84	3.20	40.00	5.69
153	167	3.869832	CCCTCGCAGCATATAATCTGATG	59.130	47.826	8.32	0.00	33.27	3.07
173	187	0.465460	TGCAAGTTCAGTGGTGACCC	60.465	55.000	0.00	0.00	30.10	4.46
181	195	2.576615	GAGGTCCTTTGCAAGTTCAGT	58.423	47.619	0.00	0.00	0.00	3.41
205	219	5.677567	CATTGTACCGGGGAAAGTAACTAT	58.322	41.667	6.32	0.00	0.00	2.12
261	275	4.357097	AGTGGATTTCCCCTTTTAGGTCTT	59.643	41.667	0.00	0.00	31.93	3.01
327	341	4.022762	TCCTCGCTATCTTCTGTATTCAGC	60.023	45.833	0.00	0.00	41.10	4.26
346	381	4.764172	ACTGTATGATGTTCTTGCTCCTC	58.236	43.478	0.00	0.00	0.00	3.71
399	434	2.222027	GTGTCTTGAAGTGGGTCTTGG	58.778	52.381	0.00	0.00	36.40	3.61
449	484	1.336755	CAAAAGGTTGTTGGGTCGAGG	59.663	52.381	0.00	0.00	0.00	4.63
468	503	5.001237	TGTAAGAGTTCTGTTTGTCGACA	57.999	39.130	15.76	15.76	0.00	4.35
544	579	1.464734	AGATCATGGTCTGTCGACGT	58.535	50.000	7.96	0.00	41.16	4.34
591	626	1.490490	TCACACCCAGCAAGACTTTCT	59.510	47.619	0.00	0.00	0.00	2.52
639	677	0.179111	TCGGAATGAGGTTAGCTGCG	60.179	55.000	0.00	0.00	0.00	5.18
654	692	5.068591	TCTCGTGAATCCTATGATTTTCGGA	59.931	40.000	13.61	0.00	41.30	4.55
732	770	3.070018	CAGAACCTTCAGCGATGACTTT	58.930	45.455	1.08	0.00	0.00	2.66
741	779	2.225255	GAGTCTTTGCAGAACCTTCAGC	59.775	50.000	0.00	0.00	39.77	4.26
750	788	0.469494	TGCCTGTGAGTCTTTGCAGA	59.531	50.000	0.00	0.00	0.00	4.26
835	873	9.342308	TCTGTTGTCTTTCAAGATTTCTACAAT	57.658	29.630	0.00	0.00	37.39	2.71
839	877	7.498900	TGCTTCTGTTGTCTTTCAAGATTTCTA	59.501	33.333	0.00	0.00	37.39	2.10
973	1011	8.960591	GGGATTTTCTTCATTGAGAAATGTCTA	58.039	33.333	10.20	0.48	43.15	2.59
1227	1265	5.244851	TCGCAAGATATGAGATAGCTCCTTT	59.755	40.000	5.36	0.00	45.01	3.11
1285	1323	4.660789	TTCGTTAGCCACCTCTAATACC	57.339	45.455	0.00	0.00	31.92	2.73
1530	1583	6.651225	CCTTCTAGTTCTTGGGTAAAGTCTTG	59.349	42.308	0.00	0.00	37.18	3.02
2041	2096	5.474876	CCTTGTGTCTCTAAAGCCAAGAATT	59.525	40.000	0.00	0.00	32.96	2.17
2043	2098	4.141482	ACCTTGTGTCTCTAAAGCCAAGAA	60.141	41.667	0.00	0.00	32.96	2.52
2743	2822	1.117150	TAGGCTTACCATCCGTGACC	58.883	55.000	0.00	0.00	39.06	4.02
2779	2858	1.201424	GGGACGGAGGGAGTACAATT	58.799	55.000	0.00	0.00	0.00	2.32
2781	2860	0.042131	ATGGGACGGAGGGAGTACAA	59.958	55.000	0.00	0.00	0.00	2.41
2784	2863	4.687262	ATATTATGGGACGGAGGGAGTA	57.313	45.455	0.00	0.00	0.00	2.59
2794	2873	8.094798	TGCAAAACGATCTTATATTATGGGAC	57.905	34.615	0.00	0.00	0.00	4.46
2799	2878	9.669353	CAAGCTTGCAAAACGATCTTATATTAT	57.331	29.630	14.65	0.00	0.00	1.28
2823	2902	3.304391	GCGGATTCTGTTGTTAGTTGCAA	60.304	43.478	0.00	0.00	0.00	4.08
2824	2903	2.225491	GCGGATTCTGTTGTTAGTTGCA	59.775	45.455	0.00	0.00	0.00	4.08
2825	2904	2.225491	TGCGGATTCTGTTGTTAGTTGC	59.775	45.455	0.00	0.00	0.00	4.17
2826	2905	3.249799	TGTGCGGATTCTGTTGTTAGTTG	59.750	43.478	0.00	0.00	0.00	3.16
2827	2906	3.472652	TGTGCGGATTCTGTTGTTAGTT	58.527	40.909	0.00	0.00	0.00	2.24
2828	2907	3.067106	CTGTGCGGATTCTGTTGTTAGT	58.933	45.455	0.00	0.00	0.00	2.24
2829	2908	2.159653	GCTGTGCGGATTCTGTTGTTAG	60.160	50.000	0.00	0.00	0.00	2.34
2830	2909	1.804151	GCTGTGCGGATTCTGTTGTTA	59.196	47.619	0.00	0.00	0.00	2.41
2831	2910	0.593128	GCTGTGCGGATTCTGTTGTT	59.407	50.000	0.00	0.00	0.00	2.83
2832	2911	0.534877	TGCTGTGCGGATTCTGTTGT	60.535	50.000	0.00	0.00	0.00	3.32
2833	2912	0.592637	TTGCTGTGCGGATTCTGTTG	59.407	50.000	0.00	0.00	0.00	3.33
2834	2913	1.001378	GTTTGCTGTGCGGATTCTGTT	60.001	47.619	0.00	0.00	0.00	3.16
2835	2914	0.593128	GTTTGCTGTGCGGATTCTGT	59.407	50.000	0.00	0.00	0.00	3.41
2836	2915	0.592637	TGTTTGCTGTGCGGATTCTG	59.407	50.000	0.00	0.00	0.00	3.02
2837	2916	1.538047	ATGTTTGCTGTGCGGATTCT	58.462	45.000	0.00	0.00	0.00	2.40
2838	2917	1.987770	CAATGTTTGCTGTGCGGATTC	59.012	47.619	0.00	0.00	0.00	2.52
2839	2918	1.340889	ACAATGTTTGCTGTGCGGATT	59.659	42.857	0.00	0.00	0.00	3.01
2840	2919	0.961019	ACAATGTTTGCTGTGCGGAT	59.039	45.000	0.00	0.00	0.00	4.18
2841	2920	1.598882	TACAATGTTTGCTGTGCGGA	58.401	45.000	0.00	0.00	0.00	5.54
2842	2921	2.414058	TTACAATGTTTGCTGTGCGG	57.586	45.000	0.00	0.00	0.00	5.69
2843	2922	4.933514	GATTTTACAATGTTTGCTGTGCG	58.066	39.130	0.00	0.00	0.00	5.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.