AutoCloner

Multiple sequence alignment - TraesCS3D01G151500

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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	TraesCS3D01G151500	chr3D	100.000	3395	0	0	1	3395	116041453	116044847	0.000000e+00	6270.0
1	TraesCS3D01G151500	chr3D	73.364	642	159	12	1034	1669	409021983	409021348	9.480000e-56	228.0
2	TraesCS3D01G151500	chr3B	96.517	2900	70	12	1	2885	169627671	169630554	0.000000e+00	4767.0
3	TraesCS3D01G151500	chr3B	95.680	463	12	5	2934	3395	169630570	169631025	0.000000e+00	737.0
4	TraesCS3D01G151500	chr3B	75.870	431	98	6	1034	1461	534965450	534965023	7.380000e-52	215.0
5	TraesCS3D01G151500	chr3A	94.280	2937	99	34	1	2885	112956433	112959352	0.000000e+00	4429.0
6	TraesCS3D01G151500	chr3A	93.737	463	23	4	2934	3395	112959368	112959825	0.000000e+00	689.0
7	TraesCS3D01G151500	chr3A	73.435	655	160	14	1022	1669	542202777	542203424	2.040000e-57	233.0
8	TraesCS3D01G151500	chr2B	76.013	617	142	6	1049	1662	91836508	91837121	7.070000e-82	315.0
9	TraesCS3D01G151500	chr2B	91.379	58	5	0	2882	2939	725734864	725734807	2.810000e-11	80.5
10	TraesCS3D01G151500	chr2B	90.323	62	5	1	2885	2945	750112633	750112572	2.810000e-11	80.5
11	TraesCS3D01G151500	chr2A	75.840	625	147	4	1049	1671	59323948	59323326	7.070000e-82	315.0
12	TraesCS3D01G151500	chr2D	75.365	617	146	6	1049	1662	59007124	59007737	3.310000e-75	292.0
13	TraesCS3D01G151500	chr2D	90.164	61	5	1	2881	2941	58891228	58891169	1.010000e-10	78.7
14	TraesCS3D01G151500	chr1A	96.364	55	2	0	2882	2936	238868708	238868762	1.300000e-14	91.6
15	TraesCS3D01G151500	chr1D	96.296	54	2	0	2882	2935	12070151	12070098	4.670000e-14	89.8
16	TraesCS3D01G151500	chr1D	92.593	54	4	0	2885	2938	393111926	393111873	1.010000e-10	78.7
17	TraesCS3D01G151500	chr4D	92.727	55	4	0	2882	2936	310484182	310484236	2.810000e-11	80.5
18	TraesCS3D01G151500	chr1B	91.379	58	5	0	2882	2939	416582987	416582930	2.810000e-11	80.5
19	TraesCS3D01G151500	chr7A	87.879	66	6	2	2882	2945	547951725	547951660	3.630000e-10	76.8

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	TraesCS3D01G151500	chr3D	116041453	116044847	3394	False	6270	6270	100.0000	1	3395	1	chr3D.!!$F1	3394
1	TraesCS3D01G151500	chr3D	409021348	409021983	635	True	228	228	73.3640	1034	1669	1	chr3D.!!$R1	635
2	TraesCS3D01G151500	chr3B	169627671	169631025	3354	False	2752	4767	96.0985	1	3395	2	chr3B.!!$F1	3394
3	TraesCS3D01G151500	chr3A	112956433	112959825	3392	False	2559	4429	94.0085	1	3395	2	chr3A.!!$F2	3394
4	TraesCS3D01G151500	chr3A	542202777	542203424	647	False	233	233	73.4350	1022	1669	1	chr3A.!!$F1	647
5	TraesCS3D01G151500	chr2B	91836508	91837121	613	False	315	315	76.0130	1049	1662	1	chr2B.!!$F1	613
6	TraesCS3D01G151500	chr2A	59323326	59323948	622	True	315	315	75.8400	1049	1671	1	chr2A.!!$R1	622
7	TraesCS3D01G151500	chr2D	59007124	59007737	613	False	292	292	75.3650	1049	1662	1	chr2D.!!$F1	613

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
598	618	0.109342	GGCTAGGATGTGTGGATGGG	59.891	60.000	0.00	0.00	0.0	4.00	F
2268	2300	1.719780	GAGTACGAACGGTTCTGCAAG	59.280	52.381	17.94	5.39	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2307	2339	0.034896	GCTTTTCCTCTGACGGACCA	59.965	55.000	0.00	0.0	31.44	4.02	R
3093	3155	2.358898	GTGGCTTGTTTCTGCTGAAGAA	59.641	45.455	6.13	0.0	43.37	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
37	38	2.044793	AGGGTCAATGTCCTGGAAGA	57.955	50.000	0.00	0.00	34.07	2.87
72	73	5.796935	CGTCCATTTGTCAGCTAAAAATGAG	59.203	40.000	20.98	14.31	41.64	2.90
78	79	7.581213	TTTGTCAGCTAAAAATGAGAAAGGA	57.419	32.000	0.00	0.00	34.78	3.36
105	109	3.629398	CACCTATTGCCAGGATTCAGAAC	59.371	47.826	3.30	0.00	39.18	3.01
127	131	4.573607	ACGAAAGAAAAGTACCACCTGAAC	59.426	41.667	0.00	0.00	0.00	3.18
151	155	1.647545	ATGTACAGCATGCGTGTGGC	61.648	55.000	24.18	18.55	42.53	5.01
189	197	4.999950	TGGAGAAGTGAGAATTCTTCAAGC	59.000	41.667	9.87	0.00	38.95	4.01
196	204	6.276091	AGTGAGAATTCTTCAAGCAAAAACC	58.724	36.000	9.87	0.00	0.00	3.27
303	322	2.947652	CACCCCAGAAACATATGCTCAG	59.052	50.000	1.58	0.00	0.00	3.35
347	366	2.550978	CTCGGCAAACTGGTCGATTAT	58.449	47.619	0.00	0.00	44.72	1.28
361	380	5.644636	TGGTCGATTATGGAAAACCTAACAC	59.355	40.000	0.00	0.00	0.00	3.32
431	451	2.597510	GTCACCAGCCCAACACCC	60.598	66.667	0.00	0.00	0.00	4.61
445	465	4.959460	ACCCCACCCACCCCACAT	62.959	66.667	0.00	0.00	0.00	3.21
598	618	0.109342	GGCTAGGATGTGTGGATGGG	59.891	60.000	0.00	0.00	0.00	4.00
674	694	2.126888	GCCATCCAACGCAACGTG	60.127	61.111	0.00	0.00	39.99	4.49
952	978	2.167487	ACGCTTGTGAACACCCAATTTT	59.833	40.909	2.46	0.00	0.00	1.82
953	979	3.381908	ACGCTTGTGAACACCCAATTTTA	59.618	39.130	2.46	0.00	0.00	1.52
955	981	4.055360	GCTTGTGAACACCCAATTTTACC	58.945	43.478	2.46	0.00	0.00	2.85
956	982	4.202212	GCTTGTGAACACCCAATTTTACCT	60.202	41.667	2.46	0.00	0.00	3.08
958	984	3.892588	TGTGAACACCCAATTTTACCTCC	59.107	43.478	2.46	0.00	0.00	4.30
959	985	3.892588	GTGAACACCCAATTTTACCTCCA	59.107	43.478	0.00	0.00	0.00	3.86
960	986	3.892588	TGAACACCCAATTTTACCTCCAC	59.107	43.478	0.00	0.00	0.00	4.02
1015	1041	2.366640	TAGGATGGAGAGGAAGTCCG	57.633	55.000	0.00	0.00	42.08	4.79
1746	1772	2.589610	TATCCAGGCTGCTCGACCCT	62.590	60.000	9.56	0.00	0.00	4.34
1887	1919	3.744559	GCTTTCAGCACGGACCAA	58.255	55.556	0.00	0.00	41.89	3.67
2268	2300	1.719780	GAGTACGAACGGTTCTGCAAG	59.280	52.381	17.94	5.39	0.00	4.01
2307	2339	2.842496	TCTCAAGGACATCTGCTGGAAT	59.158	45.455	0.00	0.00	0.00	3.01
2412	2444	6.480320	GCATTTAAGTGTGATATCTTCCGAGT	59.520	38.462	3.98	0.00	0.00	4.18
2477	2509	2.926778	AGCTGAGACTTTGCTCACTT	57.073	45.000	0.00	0.00	39.84	3.16
2478	2510	2.492012	AGCTGAGACTTTGCTCACTTG	58.508	47.619	0.00	0.00	39.84	3.16
2479	2511	2.103771	AGCTGAGACTTTGCTCACTTGA	59.896	45.455	0.00	0.00	39.84	3.02
2480	2512	2.479656	GCTGAGACTTTGCTCACTTGAG	59.520	50.000	1.56	1.56	39.84	3.02
2733	2795	6.295236	GCAGATAGCATAGAACAGATTCCTCT	60.295	42.308	0.00	0.00	44.79	3.69
2734	2796	7.315142	CAGATAGCATAGAACAGATTCCTCTC	58.685	42.308	0.00	0.00	35.18	3.20
2735	2797	7.177216	CAGATAGCATAGAACAGATTCCTCTCT	59.823	40.741	0.00	0.00	35.18	3.10
2736	2798	5.534207	AGCATAGAACAGATTCCTCTCTG	57.466	43.478	0.00	0.00	46.59	3.35
2757	2819	4.699637	TGTGTCATATTCCCGGTATGTTC	58.300	43.478	0.00	1.90	32.63	3.18
2829	2891	6.764308	ACAGATGCATTAAACAAGTAGCAT	57.236	33.333	0.00	0.00	44.50	3.79
2843	2905	3.484407	AGTAGCATGGATTTGATGGAGC	58.516	45.455	0.00	0.00	0.00	4.70
2885	2947	9.868277	TGAAGTGCCCAACAATTATTTATTTAG	57.132	29.630	0.00	0.00	36.53	1.85
2886	2948	9.869757	GAAGTGCCCAACAATTATTTATTTAGT	57.130	29.630	0.00	0.00	36.53	2.24
2913	2975	9.174166	ACAAAGTTAGTACAAAATTGAGTCACT	57.826	29.630	0.00	0.00	0.00	3.41
2916	2978	8.732746	AGTTAGTACAAAATTGAGTCACTTGT	57.267	30.769	15.21	15.21	34.71	3.16
2917	2979	9.174166	AGTTAGTACAAAATTGAGTCACTTGTT	57.826	29.630	15.79	5.89	32.69	2.83
2918	2980	9.783256	GTTAGTACAAAATTGAGTCACTTGTTT	57.217	29.630	15.79	9.86	32.69	2.83
2920	2982	8.687824	AGTACAAAATTGAGTCACTTGTTTTG	57.312	30.769	19.90	19.90	40.48	2.44
2921	2983	6.966435	ACAAAATTGAGTCACTTGTTTTGG	57.034	33.333	22.65	12.90	39.54	3.28
2922	2984	5.874261	ACAAAATTGAGTCACTTGTTTTGGG	59.126	36.000	22.65	9.98	39.54	4.12
2923	2985	5.930837	AAATTGAGTCACTTGTTTTGGGA	57.069	34.783	0.00	0.00	0.00	4.37
2924	2986	4.918810	ATTGAGTCACTTGTTTTGGGAC	57.081	40.909	0.00	0.00	0.00	4.46
2925	2987	2.285083	TGAGTCACTTGTTTTGGGACG	58.715	47.619	0.00	0.00	33.84	4.79
2926	2988	1.602377	GAGTCACTTGTTTTGGGACGG	59.398	52.381	0.00	0.00	33.84	4.79
2927	2989	1.210967	AGTCACTTGTTTTGGGACGGA	59.789	47.619	0.00	0.00	33.84	4.69
2928	2990	1.602377	GTCACTTGTTTTGGGACGGAG	59.398	52.381	0.00	0.00	0.00	4.63
3047	3109	3.510753	TGGTGATGTTACAAATGCATGCT	59.489	39.130	20.33	0.00	0.00	3.79
3093	3155	8.383175	TCTGGTCAAACAACTTAGGATAAGAAT	58.617	33.333	3.64	0.00	0.00	2.40
3307	3372	8.760569	CAAACCAGTTGACATACAAAATAAACC	58.239	33.333	0.00	0.00	39.87	3.27
3308	3373	7.589958	ACCAGTTGACATACAAAATAAACCA	57.410	32.000	0.00	0.00	40.36	3.67
3309	3374	8.012957	ACCAGTTGACATACAAAATAAACCAA	57.987	30.769	0.00	0.00	40.36	3.67
3310	3375	7.923878	ACCAGTTGACATACAAAATAAACCAAC	59.076	33.333	0.00	0.00	40.36	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	3.941483	GACAAATGGACGATGGTGAGAAT	59.059	43.478	0.00	0.00	0.00	2.40
72	73	2.952310	GGCAATAGGTGTCCATCCTTTC	59.048	50.000	0.00	0.00	36.60	2.62
78	79	1.595311	TCCTGGCAATAGGTGTCCAT	58.405	50.000	0.00	0.00	38.99	3.41
105	109	4.318546	CGTTCAGGTGGTACTTTTCTTTCG	60.319	45.833	0.00	0.00	0.00	3.46
151	155	4.220382	ACTTCTCCACAATCAGAGACAGAG	59.780	45.833	0.00	0.00	38.83	3.35
326	345	1.298859	AATCGACCAGTTTGCCGAGC	61.299	55.000	0.00	0.00	34.40	5.03
347	366	3.219281	GAGCAAGGTGTTAGGTTTTCCA	58.781	45.455	0.00	0.00	43.73	3.53
361	380	0.809241	GCTGATGTCTCCGAGCAAGG	60.809	60.000	0.00	0.00	0.00	3.61
431	451	1.304381	CAAGATGTGGGGTGGGTGG	60.304	63.158	0.00	0.00	0.00	4.61
598	618	1.372087	CCGGCCTGCTCTGAATGAAC	61.372	60.000	0.00	0.00	0.00	3.18
674	694	1.084289	CGCCTAATAATAAGCCGGGC	58.916	55.000	12.11	12.11	35.33	6.13
952	978	1.538876	AGCAAGCTGGGTGGAGGTA	60.539	57.895	0.00	0.00	0.00	3.08
953	979	2.856000	AGCAAGCTGGGTGGAGGT	60.856	61.111	0.00	0.00	0.00	3.85
955	981	3.060615	GCAGCAAGCTGGGTGGAG	61.061	66.667	21.52	0.00	43.77	3.86
1015	1041	1.940613	GTACCGGTTCATGAGAATGGC	59.059	52.381	15.04	0.00	36.27	4.40
1746	1772	6.356556	CATGGTGATCCTAGTGTTTGGATTA	58.643	40.000	0.00	0.00	42.56	1.75
1887	1919	3.165071	CCTGTTGCCTTTACCATCCTTT	58.835	45.455	0.00	0.00	0.00	3.11
1897	1929	0.396974	TGTTCTGCCCTGTTGCCTTT	60.397	50.000	0.00	0.00	0.00	3.11
2307	2339	0.034896	GCTTTTCCTCTGACGGACCA	59.965	55.000	0.00	0.00	31.44	4.02
2412	2444	8.489489	AGAGAGGAGAATAGATTGTAATTGCAA	58.511	33.333	11.51	11.51	0.00	4.08
2701	2755	3.969287	TCTATGCTATCTGCCATGGTC	57.031	47.619	14.67	6.41	42.00	4.02
2733	2795	3.964688	ACATACCGGGAATATGACACAGA	59.035	43.478	15.43	0.00	34.65	3.41
2734	2796	4.336889	ACATACCGGGAATATGACACAG	57.663	45.455	15.43	0.00	34.65	3.66
2735	2797	4.407621	AGAACATACCGGGAATATGACACA	59.592	41.667	15.43	0.00	34.65	3.72
2736	2798	4.957296	AGAACATACCGGGAATATGACAC	58.043	43.478	15.43	7.52	34.65	3.67
2737	2799	4.899457	AGAGAACATACCGGGAATATGACA	59.101	41.667	15.43	0.00	34.65	3.58
2738	2800	5.470047	AGAGAACATACCGGGAATATGAC	57.530	43.478	15.43	9.65	34.65	3.06
2739	2801	5.741964	GCAAGAGAACATACCGGGAATATGA	60.742	44.000	15.43	0.00	34.65	2.15
2740	2802	4.452455	GCAAGAGAACATACCGGGAATATG	59.548	45.833	6.32	7.75	36.32	1.78
2829	2891	0.252761	TCTGCGCTCCATCAAATCCA	59.747	50.000	9.73	0.00	0.00	3.41
2887	2949	9.174166	AGTGACTCAATTTTGTACTAACTTTGT	57.826	29.630	0.00	0.00	0.00	2.83
2890	2952	9.174166	ACAAGTGACTCAATTTTGTACTAACTT	57.826	29.630	0.00	0.00	30.79	2.66
2892	2954	9.783256	AAACAAGTGACTCAATTTTGTACTAAC	57.217	29.630	0.00	0.00	32.18	2.34
2894	2956	9.781834	CAAAACAAGTGACTCAATTTTGTACTA	57.218	29.630	15.26	0.00	34.09	1.82
2895	2957	7.759433	CCAAAACAAGTGACTCAATTTTGTACT	59.241	33.333	18.99	0.00	36.00	2.73
2897	2959	7.038659	CCCAAAACAAGTGACTCAATTTTGTA	58.961	34.615	18.99	0.00	36.00	2.41
2899	2961	6.035975	GTCCCAAAACAAGTGACTCAATTTTG	59.964	38.462	16.01	16.01	36.99	2.44
2900	2962	6.106003	GTCCCAAAACAAGTGACTCAATTTT	58.894	36.000	0.00	0.00	0.00	1.82
2901	2963	5.660460	GTCCCAAAACAAGTGACTCAATTT	58.340	37.500	0.00	0.00	0.00	1.82
2902	2964	4.202010	CGTCCCAAAACAAGTGACTCAATT	60.202	41.667	0.00	0.00	0.00	2.32
2903	2965	3.315191	CGTCCCAAAACAAGTGACTCAAT	59.685	43.478	0.00	0.00	0.00	2.57
2904	2966	2.680841	CGTCCCAAAACAAGTGACTCAA	59.319	45.455	0.00	0.00	0.00	3.02
2905	2967	2.285083	CGTCCCAAAACAAGTGACTCA	58.715	47.619	0.00	0.00	0.00	3.41
2906	2968	1.602377	CCGTCCCAAAACAAGTGACTC	59.398	52.381	0.00	0.00	0.00	3.36
2907	2969	1.210967	TCCGTCCCAAAACAAGTGACT	59.789	47.619	0.00	0.00	0.00	3.41
2908	2970	1.602377	CTCCGTCCCAAAACAAGTGAC	59.398	52.381	0.00	0.00	0.00	3.67
2909	2971	1.210967	ACTCCGTCCCAAAACAAGTGA	59.789	47.619	0.00	0.00	0.00	3.41
2910	2972	1.333619	CACTCCGTCCCAAAACAAGTG	59.666	52.381	0.00	0.00	0.00	3.16
2911	2973	1.210967	TCACTCCGTCCCAAAACAAGT	59.789	47.619	0.00	0.00	0.00	3.16
2912	2974	1.873591	CTCACTCCGTCCCAAAACAAG	59.126	52.381	0.00	0.00	0.00	3.16
2913	2975	1.210967	ACTCACTCCGTCCCAAAACAA	59.789	47.619	0.00	0.00	0.00	2.83
2914	2976	0.834612	ACTCACTCCGTCCCAAAACA	59.165	50.000	0.00	0.00	0.00	2.83
2915	2977	2.825861	TACTCACTCCGTCCCAAAAC	57.174	50.000	0.00	0.00	0.00	2.43
2916	2978	5.687166	AATATACTCACTCCGTCCCAAAA	57.313	39.130	0.00	0.00	0.00	2.44
2917	2979	6.795144	TTAATATACTCACTCCGTCCCAAA	57.205	37.500	0.00	0.00	0.00	3.28
2918	2980	6.684613	GCTTTAATATACTCACTCCGTCCCAA	60.685	42.308	0.00	0.00	0.00	4.12
2919	2981	5.221382	GCTTTAATATACTCACTCCGTCCCA	60.221	44.000	0.00	0.00	0.00	4.37
2920	2982	5.221382	TGCTTTAATATACTCACTCCGTCCC	60.221	44.000	0.00	0.00	0.00	4.46
2921	2983	5.839621	TGCTTTAATATACTCACTCCGTCC	58.160	41.667	0.00	0.00	0.00	4.79
2922	2984	6.736123	TCTGCTTTAATATACTCACTCCGTC	58.264	40.000	0.00	0.00	0.00	4.79
2923	2985	6.710597	TCTGCTTTAATATACTCACTCCGT	57.289	37.500	0.00	0.00	0.00	4.69
2924	2986	8.594881	ATTTCTGCTTTAATATACTCACTCCG	57.405	34.615	0.00	0.00	0.00	4.63
2932	2994	9.659830	CCGTGGTTTATTTCTGCTTTAATATAC	57.340	33.333	0.00	0.00	0.00	1.47
2937	2999	5.048573	GTCCCGTGGTTTATTTCTGCTTTAA	60.049	40.000	0.00	0.00	0.00	1.52
2953	3015	8.711170	AGGTTATATATAATATTGGTCCCGTGG	58.289	37.037	8.40	0.00	0.00	4.94
3093	3155	2.358898	GTGGCTTGTTTCTGCTGAAGAA	59.641	45.455	6.13	0.00	43.37	2.52
3146	3209	7.766278	ACTTCTGGTGATGTCACTTTGTATATC	59.234	37.037	12.43	0.00	45.73	1.63
3272	3335	8.855110	TGTATGTCAACTGGTTTGATAATGTTT	58.145	29.630	0.00	0.00	46.14	2.83
3273	3336	8.402798	TGTATGTCAACTGGTTTGATAATGTT	57.597	30.769	0.00	0.00	46.14	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.