AutoCloner

Multiple sequence alignment - TraesCS5A01G364600

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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	TraesCS5A01G364600	chr5A	100.000	2927	0	0	1	2927	564870657	564873583	0.000000e+00	5406
1	TraesCS5A01G364600	chr5A	98.444	2828	36	5	1	2822	579994666	579991841	0.000000e+00	4972
2	TraesCS5A01G364600	chr5A	94.497	1799	87	9	1026	2822	669688148	669689936	0.000000e+00	2763
3	TraesCS5A01G364600	chr5A	93.780	1045	40	12	1	1029	669686929	669687964	0.000000e+00	1546
4	TraesCS5A01G364600	chr5A	97.143	105	3	0	2823	2927	470210667	470210563	8.340000e-41	178
5	TraesCS5A01G364600	chr5A	97.115	104	3	0	2824	2927	310514659	310514762	3.000000e-40	176
6	TraesCS5A01G364600	chr2A	98.300	2824	43	4	1	2823	724965697	724962878	0.000000e+00	4944
7	TraesCS5A01G364600	chr2A	97.143	105	3	0	2823	2927	110902483	110902587	8.340000e-41	178
8	TraesCS5A01G364600	chr7A	97.453	1845	42	5	978	2822	36253243	36251404	0.000000e+00	3142
9	TraesCS5A01G364600	chr7A	98.361	976	15	1	4	978	36254276	36253301	0.000000e+00	1712
10	TraesCS5A01G364600	chr7A	98.095	105	2	0	2823	2927	627396770	627396874	1.790000e-42	183
11	TraesCS5A01G364600	chr3D	95.753	1813	67	7	1026	2834	555156088	555154282	0.000000e+00	2913
12	TraesCS5A01G364600	chr3D	95.870	460	19	0	519	978	555156833	555156374	0.000000e+00	745
13	TraesCS5A01G364600	chr3D	95.856	362	12	3	164	523	555175546	555175186	1.510000e-162	582
14	TraesCS5A01G364600	chr2D	94.278	1800	91	8	1026	2823	2170407	2172196	0.000000e+00	2743
15	TraesCS5A01G364600	chr2D	95.789	475	15	2	560	1029	2169749	2170223	0.000000e+00	761
16	TraesCS5A01G364600	chr7B	93.885	1799	89	12	1026	2822	289877423	289879202	0.000000e+00	2693
17	TraesCS5A01G364600	chr7B	94.160	976	54	3	1	975	289876231	289877204	0.000000e+00	1483
18	TraesCS5A01G364600	chr1B	91.519	1745	132	11	1087	2822	669571284	669569547	0.000000e+00	2388
19	TraesCS5A01G364600	chr1B	91.850	638	43	2	342	979	669572240	669571612	0.000000e+00	881
20	TraesCS5A01G364600	chr1B	89.785	372	32	6	1	369	669572661	669572293	3.410000e-129	472
21	TraesCS5A01G364600	chr4B	89.337	1810	157	19	1026	2823	120260446	120258661	0.000000e+00	2241
22	TraesCS5A01G364600	chr4B	87.977	707	64	11	1	696	653920780	653921476	0.000000e+00	815
23	TraesCS5A01G364600	chr4B	88.144	582	56	8	459	1028	592246303	592246883	0.000000e+00	680
24	TraesCS5A01G364600	chr2B	86.700	1827	181	26	1026	2820	758233762	758231966	0.000000e+00	1971
25	TraesCS5A01G364600	chr6B	90.574	732	56	6	1	729	316319984	316320705	0.000000e+00	957
26	TraesCS5A01G364600	chr3A	90.855	503	43	2	485	987	198182314	198182813	0.000000e+00	671
27	TraesCS5A01G364600	chr7D	88.017	242	23	5	6	243	26328942	26329181	6.180000e-72	281
28	TraesCS5A01G364600	chr4A	96.491	114	3	1	2814	2927	110703987	110703875	1.380000e-43	187
29	TraesCS5A01G364600	chr4A	97.143	105	3	0	2823	2927	554681975	554681871	8.340000e-41	178
30	TraesCS5A01G364600	chr6A	96.190	105	4	0	2823	2927	215284207	215284311	3.880000e-39	172
31	TraesCS5A01G364600	chr1A	96.190	105	4	0	2823	2927	155921390	155921494	3.880000e-39	172
32	TraesCS5A01G364600	chr1A	96.190	105	4	0	2823	2927	293117995	293118099	3.880000e-39	172

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	TraesCS5A01G364600	chr5A	564870657	564873583	2926	False	5406.0	5406	100.000000	1	2927	1	chr5A.!!$F2	2926
1	TraesCS5A01G364600	chr5A	579991841	579994666	2825	True	4972.0	4972	98.444000	1	2822	1	chr5A.!!$R2	2821
2	TraesCS5A01G364600	chr5A	669686929	669689936	3007	False	2154.5	2763	94.138500	1	2822	2	chr5A.!!$F3	2821
3	TraesCS5A01G364600	chr2A	724962878	724965697	2819	True	4944.0	4944	98.300000	1	2823	1	chr2A.!!$R1	2822
4	TraesCS5A01G364600	chr7A	36251404	36254276	2872	True	2427.0	3142	97.907000	4	2822	2	chr7A.!!$R1	2818
5	TraesCS5A01G364600	chr3D	555154282	555156833	2551	True	1829.0	2913	95.811500	519	2834	2	chr3D.!!$R2	2315
6	TraesCS5A01G364600	chr2D	2169749	2172196	2447	False	1752.0	2743	95.033500	560	2823	2	chr2D.!!$F1	2263
7	TraesCS5A01G364600	chr7B	289876231	289879202	2971	False	2088.0	2693	94.022500	1	2822	2	chr7B.!!$F1	2821
8	TraesCS5A01G364600	chr1B	669569547	669572661	3114	True	1247.0	2388	91.051333	1	2822	3	chr1B.!!$R1	2821
9	TraesCS5A01G364600	chr4B	120258661	120260446	1785	True	2241.0	2241	89.337000	1026	2823	1	chr4B.!!$R1	1797
10	TraesCS5A01G364600	chr4B	653920780	653921476	696	False	815.0	815	87.977000	1	696	1	chr4B.!!$F2	695
11	TraesCS5A01G364600	chr4B	592246303	592246883	580	False	680.0	680	88.144000	459	1028	1	chr4B.!!$F1	569
12	TraesCS5A01G364600	chr2B	758231966	758233762	1796	True	1971.0	1971	86.700000	1026	2820	1	chr2B.!!$R1	1794
13	TraesCS5A01G364600	chr6B	316319984	316320705	721	False	957.0	957	90.574000	1	729	1	chr6B.!!$F1	728

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
624	724	4.59085	TGTCCTGAATCCATATGTCGAG	57.409	45.455	1.24	0.0	0.00	4.04	F
1012	1219	3.20129	GTGAAGGACATGCTGACCATAG	58.799	50.000	0.00	0.0	34.63	2.23	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1760	2469	1.915141	AGCCTCACCAATTGTCTTGG	58.085	50.0	4.43	2.5	44.91	3.61	R
2880	3623	0.107268	AACCGGAAAAGTACGCCTGT	59.893	50.0	9.46	0.0	0.00	4.00	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
624	724	4.590850	TGTCCTGAATCCATATGTCGAG	57.409	45.455	1.24	0.00	0.00	4.04
906	1016	7.854534	TCATTTATCTGCTACGAATTCATGTG	58.145	34.615	6.22	0.00	0.00	3.21
1012	1219	3.201290	GTGAAGGACATGCTGACCATAG	58.799	50.000	0.00	0.00	34.63	2.23
1170	1868	4.352298	GGTGAGGGAAATGAGGGATCTTAT	59.648	45.833	0.00	0.00	0.00	1.73
1472	2176	6.859508	GTCGGGTCCAGTTTATTTAGTTTTTG	59.140	38.462	0.00	0.00	0.00	2.44
1760	2469	3.353557	GAGTTGGTAAGGGATTGGGTTC	58.646	50.000	0.00	0.00	0.00	3.62
2550	3292	2.937519	TGTTACCACCAATGTTCTGCA	58.062	42.857	0.00	0.00	0.00	4.41
2824	3567	4.605183	AGCTCTGTCCTCTTGTAGTGTAT	58.395	43.478	0.00	0.00	0.00	2.29
2827	3570	5.677598	GCTCTGTCCTCTTGTAGTGTATGTC	60.678	48.000	0.00	0.00	0.00	3.06
2828	3571	5.321927	TCTGTCCTCTTGTAGTGTATGTCA	58.678	41.667	0.00	0.00	0.00	3.58
2829	3572	5.183331	TCTGTCCTCTTGTAGTGTATGTCAC	59.817	44.000	0.00	0.00	46.46	3.67
2841	3584	5.376854	GTGTATGTCACATTTGCTTCCTT	57.623	39.130	0.00	0.00	45.51	3.36
2842	3585	5.393962	GTGTATGTCACATTTGCTTCCTTC	58.606	41.667	0.00	0.00	45.51	3.46
2843	3586	5.182001	GTGTATGTCACATTTGCTTCCTTCT	59.818	40.000	0.00	0.00	45.51	2.85
2844	3587	5.769662	TGTATGTCACATTTGCTTCCTTCTT	59.230	36.000	0.00	0.00	30.04	2.52
2845	3588	4.836125	TGTCACATTTGCTTCCTTCTTC	57.164	40.909	0.00	0.00	0.00	2.87
2846	3589	3.569701	TGTCACATTTGCTTCCTTCTTCC	59.430	43.478	0.00	0.00	0.00	3.46
2847	3590	3.823304	GTCACATTTGCTTCCTTCTTCCT	59.177	43.478	0.00	0.00	0.00	3.36
2848	3591	3.822735	TCACATTTGCTTCCTTCTTCCTG	59.177	43.478	0.00	0.00	0.00	3.86
2849	3592	3.822735	CACATTTGCTTCCTTCTTCCTGA	59.177	43.478	0.00	0.00	0.00	3.86
2850	3593	4.279169	CACATTTGCTTCCTTCTTCCTGAA	59.721	41.667	0.00	0.00	0.00	3.02
2851	3594	4.895297	ACATTTGCTTCCTTCTTCCTGAAA	59.105	37.500	0.00	0.00	33.79	2.69
2852	3595	5.010415	ACATTTGCTTCCTTCTTCCTGAAAG	59.990	40.000	0.00	0.00	33.79	2.62
2863	3606	2.348998	CTGAAAGGACCCGCTGCT	59.651	61.111	0.00	0.00	0.00	4.24
2864	3607	1.743252	CTGAAAGGACCCGCTGCTC	60.743	63.158	0.00	0.00	0.00	4.26
2865	3608	2.347490	GAAAGGACCCGCTGCTCA	59.653	61.111	0.00	0.00	0.00	4.26
2866	3609	1.302511	GAAAGGACCCGCTGCTCAA	60.303	57.895	0.00	0.00	0.00	3.02
2867	3610	0.678048	GAAAGGACCCGCTGCTCAAT	60.678	55.000	0.00	0.00	0.00	2.57
2868	3611	0.962356	AAAGGACCCGCTGCTCAATG	60.962	55.000	0.00	0.00	0.00	2.82
2869	3612	2.825836	GGACCCGCTGCTCAATGG	60.826	66.667	0.00	0.00	0.00	3.16
2870	3613	2.045926	GACCCGCTGCTCAATGGT	60.046	61.111	0.00	0.00	0.00	3.55
2871	3614	2.360350	ACCCGCTGCTCAATGGTG	60.360	61.111	0.00	0.00	0.00	4.17
2872	3615	3.136123	CCCGCTGCTCAATGGTGG	61.136	66.667	0.00	0.00	0.00	4.61
2873	3616	3.136123	CCGCTGCTCAATGGTGGG	61.136	66.667	0.00	0.00	0.00	4.61
2874	3617	2.046023	CGCTGCTCAATGGTGGGA	60.046	61.111	0.00	0.00	0.00	4.37
2875	3618	2.401766	CGCTGCTCAATGGTGGGAC	61.402	63.158	0.00	0.00	0.00	4.46
2876	3619	1.303561	GCTGCTCAATGGTGGGACA	60.304	57.895	0.00	0.00	0.00	4.02
2877	3620	1.310933	GCTGCTCAATGGTGGGACAG	61.311	60.000	0.00	0.00	41.80	3.51
2895	3638	1.873863	GCCACAGGCGTACTTTTCC	59.126	57.895	0.00	0.00	39.62	3.13
2896	3639	1.908066	GCCACAGGCGTACTTTTCCG	61.908	60.000	0.00	0.00	39.62	4.30
2897	3640	1.296056	CCACAGGCGTACTTTTCCGG	61.296	60.000	0.00	0.00	0.00	5.14
2898	3641	0.601841	CACAGGCGTACTTTTCCGGT	60.602	55.000	0.00	0.00	0.00	5.28
2899	3642	0.107268	ACAGGCGTACTTTTCCGGTT	59.893	50.000	0.00	0.00	0.00	4.44
2900	3643	0.515564	CAGGCGTACTTTTCCGGTTG	59.484	55.000	0.00	0.00	0.00	3.77
2901	3644	0.604511	AGGCGTACTTTTCCGGTTGG	60.605	55.000	0.00	0.00	0.00	3.77
2902	3645	0.603439	GGCGTACTTTTCCGGTTGGA	60.603	55.000	0.00	0.00	44.61	3.53
2918	3661	1.838112	TGGAACAATCATCACCTGGC	58.162	50.000	0.00	0.00	31.92	4.85
2919	3662	1.106285	GGAACAATCATCACCTGGCC	58.894	55.000	0.00	0.00	0.00	5.36
2920	3663	1.616725	GGAACAATCATCACCTGGCCA	60.617	52.381	4.71	4.71	0.00	5.36
2921	3664	1.747355	GAACAATCATCACCTGGCCAG	59.253	52.381	26.87	26.87	0.00	4.85
2922	3665	0.994247	ACAATCATCACCTGGCCAGA	59.006	50.000	34.91	15.58	0.00	3.86
2923	3666	1.340405	ACAATCATCACCTGGCCAGAC	60.340	52.381	34.91	0.00	0.00	3.51
2924	3667	1.064906	CAATCATCACCTGGCCAGACT	60.065	52.381	34.91	15.78	0.00	3.24
2925	3668	1.293062	ATCATCACCTGGCCAGACTT	58.707	50.000	34.91	14.94	0.00	3.01
2926	3669	0.615331	TCATCACCTGGCCAGACTTC	59.385	55.000	34.91	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
624	724	5.105310	ACACCCACACTCAGATATAACACTC	60.105	44.000	0.00	0.00	0.00	3.51
995	1202	1.765314	GGTCTATGGTCAGCATGTCCT	59.235	52.381	0.00	0.00	44.96	3.85
1012	1219	3.265791	CAAGGTCTTCATAGTGCAGGTC	58.734	50.000	0.00	0.00	0.00	3.85
1760	2469	1.915141	AGCCTCACCAATTGTCTTGG	58.085	50.000	4.43	2.50	44.91	3.61
2824	3567	3.569701	GGAAGAAGGAAGCAAATGTGACA	59.430	43.478	0.00	0.00	0.00	3.58
2827	3570	3.822735	TCAGGAAGAAGGAAGCAAATGTG	59.177	43.478	0.00	0.00	0.00	3.21
2828	3571	4.104383	TCAGGAAGAAGGAAGCAAATGT	57.896	40.909	0.00	0.00	0.00	2.71
2829	3572	5.458041	TTTCAGGAAGAAGGAAGCAAATG	57.542	39.130	0.00	0.00	37.57	2.32
2830	3573	4.525874	CCTTTCAGGAAGAAGGAAGCAAAT	59.474	41.667	0.00	0.00	37.67	2.32
2833	3576	2.711009	TCCTTTCAGGAAGAAGGAAGCA	59.289	45.455	2.51	0.00	42.51	3.91
2834	3577	3.425162	TCCTTTCAGGAAGAAGGAAGC	57.575	47.619	2.51	0.00	42.51	3.86
2844	3587	3.068881	CAGCGGGTCCTTTCAGGA	58.931	61.111	0.00	0.00	43.43	3.86
2845	3588	2.747855	GCAGCGGGTCCTTTCAGG	60.748	66.667	0.00	0.00	36.46	3.86
2846	3589	1.743252	GAGCAGCGGGTCCTTTCAG	60.743	63.158	4.57	0.00	35.49	3.02
2847	3590	2.050836	TTGAGCAGCGGGTCCTTTCA	62.051	55.000	13.49	0.00	40.83	2.69
2848	3591	0.678048	ATTGAGCAGCGGGTCCTTTC	60.678	55.000	13.49	0.00	40.83	2.62
2849	3592	0.962356	CATTGAGCAGCGGGTCCTTT	60.962	55.000	13.49	0.00	40.83	3.11
2850	3593	1.377725	CATTGAGCAGCGGGTCCTT	60.378	57.895	13.49	0.00	40.83	3.36
2851	3594	2.270205	CATTGAGCAGCGGGTCCT	59.730	61.111	13.49	0.00	40.83	3.85
2852	3595	2.825836	CCATTGAGCAGCGGGTCC	60.826	66.667	13.49	0.00	40.83	4.46
2853	3596	2.045926	ACCATTGAGCAGCGGGTC	60.046	61.111	9.23	9.23	41.89	4.46
2854	3597	2.360350	CACCATTGAGCAGCGGGT	60.360	61.111	0.00	0.00	0.00	5.28
2855	3598	3.136123	CCACCATTGAGCAGCGGG	61.136	66.667	0.00	0.00	0.00	6.13
2856	3599	3.136123	CCCACCATTGAGCAGCGG	61.136	66.667	0.00	0.00	0.00	5.52
2857	3600	2.046023	TCCCACCATTGAGCAGCG	60.046	61.111	0.00	0.00	0.00	5.18
2858	3601	1.303561	TGTCCCACCATTGAGCAGC	60.304	57.895	0.00	0.00	0.00	5.25
2859	3602	1.310933	GCTGTCCCACCATTGAGCAG	61.311	60.000	0.00	0.00	0.00	4.24
2860	3603	1.303561	GCTGTCCCACCATTGAGCA	60.304	57.895	0.00	0.00	0.00	4.26
2861	3604	2.048603	GGCTGTCCCACCATTGAGC	61.049	63.158	0.00	0.00	0.00	4.26
2862	3605	1.379916	TGGCTGTCCCACCATTGAG	59.620	57.895	0.00	0.00	39.18	3.02
2863	3606	3.586543	TGGCTGTCCCACCATTGA	58.413	55.556	0.00	0.00	39.18	2.57
2877	3620	1.873863	GGAAAAGTACGCCTGTGGC	59.126	57.895	0.00	0.00	46.75	5.01
2878	3621	1.296056	CCGGAAAAGTACGCCTGTGG	61.296	60.000	0.00	0.00	0.00	4.17
2879	3622	0.601841	ACCGGAAAAGTACGCCTGTG	60.602	55.000	9.46	0.00	0.00	3.66
2880	3623	0.107268	AACCGGAAAAGTACGCCTGT	59.893	50.000	9.46	0.00	0.00	4.00
2881	3624	0.515564	CAACCGGAAAAGTACGCCTG	59.484	55.000	9.46	0.00	0.00	4.85
2882	3625	0.604511	CCAACCGGAAAAGTACGCCT	60.605	55.000	9.46	0.00	0.00	5.52
2883	3626	0.603439	TCCAACCGGAAAAGTACGCC	60.603	55.000	9.46	0.00	38.83	5.68
2884	3627	2.917172	TCCAACCGGAAAAGTACGC	58.083	52.632	9.46	0.00	38.83	4.42
2893	3636	2.432444	GTGATGATTGTTCCAACCGGA	58.568	47.619	9.46	0.00	40.60	5.14
2894	3637	1.472480	GGTGATGATTGTTCCAACCGG	59.528	52.381	0.00	0.00	0.00	5.28
2895	3638	2.162208	CAGGTGATGATTGTTCCAACCG	59.838	50.000	0.00	0.00	0.00	4.44
2896	3639	2.493278	CCAGGTGATGATTGTTCCAACC	59.507	50.000	0.00	0.00	0.00	3.77
2897	3640	2.094545	GCCAGGTGATGATTGTTCCAAC	60.095	50.000	0.00	0.00	0.00	3.77
2898	3641	2.170166	GCCAGGTGATGATTGTTCCAA	58.830	47.619	0.00	0.00	0.00	3.53
2899	3642	1.616725	GGCCAGGTGATGATTGTTCCA	60.617	52.381	0.00	0.00	0.00	3.53
2900	3643	1.106285	GGCCAGGTGATGATTGTTCC	58.894	55.000	0.00	0.00	0.00	3.62
2901	3644	1.747355	CTGGCCAGGTGATGATTGTTC	59.253	52.381	26.14	0.00	0.00	3.18
2902	3645	1.355381	TCTGGCCAGGTGATGATTGTT	59.645	47.619	32.23	0.00	0.00	2.83
2903	3646	0.994247	TCTGGCCAGGTGATGATTGT	59.006	50.000	32.23	0.00	0.00	2.71
2904	3647	1.064906	AGTCTGGCCAGGTGATGATTG	60.065	52.381	32.23	3.70	0.00	2.67
2905	3648	1.293062	AGTCTGGCCAGGTGATGATT	58.707	50.000	32.23	6.25	0.00	2.57
2906	3649	1.211457	GAAGTCTGGCCAGGTGATGAT	59.789	52.381	32.23	11.85	0.00	2.45
2907	3650	0.615331	GAAGTCTGGCCAGGTGATGA	59.385	55.000	32.23	9.68	0.00	2.92
2908	3651	3.165606	GAAGTCTGGCCAGGTGATG	57.834	57.895	32.23	7.03	0.00	3.07

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.