AutoCloner

Multiple sequence alignment - TraesCS5A01G128700

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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	TraesCS5A01G128700	chr5A	100.000	3179	0	0	1	3179	288262237	288259059	0.000000e+00	5871.0
1	TraesCS5A01G128700	chr5A	91.607	703	36	18	1	694	606695354	606696042	0.000000e+00	950.0
2	TraesCS5A01G128700	chr5D	94.805	2329	67	21	859	3175	217229601	217227315	0.000000e+00	3581.0
3	TraesCS5A01G128700	chr5D	89.949	587	53	6	701	1286	217285581	217285000	0.000000e+00	752.0
4	TraesCS5A01G128700	chr5D	91.667	168	14	0	701	868	217230014	217229847	1.910000e-57	233.0
5	TraesCS5A01G128700	chr5B	93.207	2488	86	26	698	3175	232661096	232663510	0.000000e+00	3581.0
6	TraesCS5A01G128700	chr7A	93.208	692	28	9	1	691	192632299	192632972	0.000000e+00	1000.0
7	TraesCS5A01G128700	chr7A	92.135	712	33	19	1	702	134602930	134603628	0.000000e+00	983.0
8	TraesCS5A01G128700	chr7A	91.607	703	37	18	1	694	124057429	124056740	0.000000e+00	952.0
9	TraesCS5A01G128700	chr7A	91.038	703	44	16	1	694	38744045	38744737	0.000000e+00	931.0
10	TraesCS5A01G128700	chr2A	91.441	701	43	13	1	698	677892337	677891651	0.000000e+00	946.0
11	TraesCS5A01G128700	chr2B	88.571	700	54	21	1	694	45601535	45602214	0.000000e+00	826.0
12	TraesCS5A01G128700	chr7B	88.051	703	54	24	1	694	130340575	130341256	0.000000e+00	806.0
13	TraesCS5A01G128700	chr4A	86.571	700	72	19	1	694	664923990	664923307	0.000000e+00	752.0
14	TraesCS5A01G128700	chr4A	100.000	28	0	0	3142	3169	121157040	121157067	6.000000e-03	52.8
15	TraesCS5A01G128700	chr2D	100.000	35	0	0	3141	3175	626926220	626926254	7.360000e-07	65.8

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	TraesCS5A01G128700	chr5A	288259059	288262237	3178	True	5871	5871	100.000	1	3179	1	chr5A.!!$R1	3178
1	TraesCS5A01G128700	chr5A	606695354	606696042	688	False	950	950	91.607	1	694	1	chr5A.!!$F1	693
2	TraesCS5A01G128700	chr5D	217227315	217230014	2699	True	1907	3581	93.236	701	3175	2	chr5D.!!$R2	2474
3	TraesCS5A01G128700	chr5D	217285000	217285581	581	True	752	752	89.949	701	1286	1	chr5D.!!$R1	585
4	TraesCS5A01G128700	chr5B	232661096	232663510	2414	False	3581	3581	93.207	698	3175	1	chr5B.!!$F1	2477
5	TraesCS5A01G128700	chr7A	192632299	192632972	673	False	1000	1000	93.208	1	691	1	chr7A.!!$F3	690
6	TraesCS5A01G128700	chr7A	134602930	134603628	698	False	983	983	92.135	1	702	1	chr7A.!!$F2	701
7	TraesCS5A01G128700	chr7A	124056740	124057429	689	True	952	952	91.607	1	694	1	chr7A.!!$R1	693
8	TraesCS5A01G128700	chr7A	38744045	38744737	692	False	931	931	91.038	1	694	1	chr7A.!!$F1	693
9	TraesCS5A01G128700	chr2A	677891651	677892337	686	True	946	946	91.441	1	698	1	chr2A.!!$R1	697
10	TraesCS5A01G128700	chr2B	45601535	45602214	679	False	826	826	88.571	1	694	1	chr2B.!!$F1	693
11	TraesCS5A01G128700	chr7B	130340575	130341256	681	False	806	806	88.051	1	694	1	chr7B.!!$F1	693
12	TraesCS5A01G128700	chr4A	664923307	664923990	683	True	752	752	86.571	1	694	1	chr4A.!!$R1	693

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
714	736	0.039437	CTAACACACGACTCGCACCT	60.039	55.0	0.0	0.0	0.0	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2407	2693	0.459489	GGTGCAGCAACAGTCCAAAA	59.541	50.0	11.86	0.0	0.0	2.44	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
93	95	6.606796	TCCTATGGACAACATATGCACAAAAT	59.393	34.615	1.58	0.00	41.07	1.82
105	107	8.885722	ACATATGCACAAAATGGAATTGATTTC	58.114	29.630	1.58	0.00	36.10	2.17
106	108	9.104965	CATATGCACAAAATGGAATTGATTTCT	57.895	29.630	0.00	0.00	36.10	2.52
131	133	7.394016	TCCTACATGTTCAACTACACATCATT	58.606	34.615	2.30	0.00	30.90	2.57
319	321	5.824624	GCCTCAGATCCACAAATTTAGATGA	59.175	40.000	0.00	0.00	0.00	2.92
392	398	3.427309	GAGAAGCCCTCTGTTCGTC	57.573	57.895	0.00	0.00	38.86	4.20
473	487	0.474854	TCCACTTACCAGGGCCAGAA	60.475	55.000	6.18	0.00	0.00	3.02
698	720	6.128117	GGTCAGAACATAATTTTGTCCGCTAA	60.128	38.462	1.83	0.00	0.00	3.09
699	721	6.741358	GTCAGAACATAATTTTGTCCGCTAAC	59.259	38.462	1.83	0.00	0.00	2.34
709	731	1.063951	GTCCGCTAACACACGACTCG	61.064	60.000	0.00	0.00	0.00	4.18
714	736	0.039437	CTAACACACGACTCGCACCT	60.039	55.000	0.00	0.00	0.00	4.00
715	737	1.198408	CTAACACACGACTCGCACCTA	59.802	52.381	0.00	0.00	0.00	3.08
761	783	4.947147	GCACCCGAACTGCCCACA	62.947	66.667	0.00	0.00	0.00	4.17
915	1192	1.418908	CCCACCCCACTGACACTCTT	61.419	60.000	0.00	0.00	0.00	2.85
980	1257	1.071471	CTAATGGCCGCGGGATCTT	59.929	57.895	29.38	4.15	0.00	2.40
1505	1782	2.049433	CGTAGGGAATAGCGGCGG	60.049	66.667	9.78	0.00	0.00	6.13
1938	2215	3.626670	ACGAGAGGTACTTCCACTATTCG	59.373	47.826	9.52	9.52	41.55	3.34
1974	2251	3.792736	GTGATGGCGCTGGGGGTA	61.793	66.667	7.64	0.00	0.00	3.69
2037	2314	1.202177	GCCAAGCACCATTATCACACG	60.202	52.381	0.00	0.00	0.00	4.49
2095	2372	2.131281	GGAGTACGATTTCTACGGCC	57.869	55.000	0.00	0.00	34.93	6.13
2181	2458	0.685097	TCAGGTTGTACTGGTGAGGC	59.315	55.000	0.00	0.00	38.98	4.70
2336	2619	2.819608	GCAGAAATGTAGGCCAGTTTGA	59.180	45.455	5.01	0.00	30.08	2.69
2337	2620	3.366374	GCAGAAATGTAGGCCAGTTTGAC	60.366	47.826	5.01	0.00	30.08	3.18
2340	2623	2.094762	ATGTAGGCCAGTTTGACGAC	57.905	50.000	5.01	0.00	0.00	4.34
2362	2645	4.005650	CCAGATGGTTATGATGGAATCCG	58.994	47.826	0.00	0.00	44.73	4.18
2363	2646	3.438087	CAGATGGTTATGATGGAATCCGC	59.562	47.826	0.00	0.00	44.73	5.54
2364	2647	3.072915	AGATGGTTATGATGGAATCCGCA	59.927	43.478	0.00	0.00	44.73	5.69
2365	2648	3.507162	TGGTTATGATGGAATCCGCAT	57.493	42.857	11.31	11.31	44.73	4.73
2366	2649	3.148412	TGGTTATGATGGAATCCGCATG	58.852	45.455	15.00	0.00	44.73	4.06
2367	2650	2.489329	GGTTATGATGGAATCCGCATGG	59.511	50.000	15.00	0.00	44.73	3.66
2368	2651	3.149196	GTTATGATGGAATCCGCATGGT	58.851	45.455	15.00	0.00	44.73	3.55
2369	2652	2.369983	ATGATGGAATCCGCATGGTT	57.630	45.000	6.65	0.00	44.73	3.67
2370	2653	3.507162	ATGATGGAATCCGCATGGTTA	57.493	42.857	6.65	0.00	44.73	2.85
2371	2654	3.507162	TGATGGAATCCGCATGGTTAT	57.493	42.857	0.00	0.00	44.73	1.89
2372	2655	3.148412	TGATGGAATCCGCATGGTTATG	58.852	45.455	0.00	0.00	44.73	1.90
2373	2656	3.181446	TGATGGAATCCGCATGGTTATGA	60.181	43.478	0.00	0.00	44.73	2.15
2374	2657	3.507162	TGGAATCCGCATGGTTATGAT	57.493	42.857	0.00	0.00	36.36	2.45
2407	2693	8.227791	CGCAAGTTCTTGTTTGTACTATTATGT	58.772	33.333	13.04	0.00	0.00	2.29
2449	2735	5.181690	TGTCAGTTGTCAAAATGGTTAGC	57.818	39.130	0.00	0.00	32.26	3.09
2614	2900	2.187351	TGTTTCGTTTCTGTTGCAGC	57.813	45.000	0.00	0.00	0.00	5.25
2615	2901	1.742831	TGTTTCGTTTCTGTTGCAGCT	59.257	42.857	1.17	0.00	0.00	4.24
2616	2902	2.939756	TGTTTCGTTTCTGTTGCAGCTA	59.060	40.909	1.17	0.00	0.00	3.32
2617	2903	3.563808	TGTTTCGTTTCTGTTGCAGCTAT	59.436	39.130	1.17	0.00	0.00	2.97
2618	2904	4.752604	TGTTTCGTTTCTGTTGCAGCTATA	59.247	37.500	1.17	0.00	0.00	1.31
2619	2905	5.411361	TGTTTCGTTTCTGTTGCAGCTATAT	59.589	36.000	1.17	0.00	0.00	0.86
2620	2906	6.072728	TGTTTCGTTTCTGTTGCAGCTATATT	60.073	34.615	1.17	0.00	0.00	1.28
2621	2907	6.494893	TTCGTTTCTGTTGCAGCTATATTT	57.505	33.333	1.17	0.00	0.00	1.40
2622	2908	6.494893	TCGTTTCTGTTGCAGCTATATTTT	57.505	33.333	1.17	0.00	0.00	1.82
2623	2909	6.908825	TCGTTTCTGTTGCAGCTATATTTTT	58.091	32.000	1.17	0.00	0.00	1.94
2669	2955	5.951148	TGATTTCTCATTACAAGATTGGCCA	59.049	36.000	0.00	0.00	0.00	5.36
2703	2989	3.258123	GGTAAGTCCAATGTGGTGCAAAT	59.742	43.478	0.00	0.00	39.03	2.32
2705	2991	3.665745	AGTCCAATGTGGTGCAAATTC	57.334	42.857	0.00	0.00	39.03	2.17
2710	2996	4.586421	TCCAATGTGGTGCAAATTCTTGTA	59.414	37.500	0.00	0.00	39.03	2.41
2719	3005	6.030228	GGTGCAAATTCTTGTAGTAGATTGC	58.970	40.000	0.00	0.00	39.16	3.56
2855	3142	8.082242	GCAGGAACAAAAATTGAAGTACTGTAT	58.918	33.333	0.00	0.00	0.00	2.29
2870	3157	2.093973	ACTGTATTACTGCTGCGCTCTT	60.094	45.455	9.73	0.00	0.00	2.85
2874	3161	4.745125	TGTATTACTGCTGCGCTCTTATTC	59.255	41.667	9.73	0.00	0.00	1.75
2875	3162	1.840181	TACTGCTGCGCTCTTATTCG	58.160	50.000	9.73	0.00	0.00	3.34
2940	3227	4.941657	TCTCTGTTGTATGAGCTATGCTG	58.058	43.478	0.00	0.00	39.88	4.41
3045	3337	9.825109	TCGGTTAATTAGATAAATGACATGACA	57.175	29.630	0.00	0.00	0.00	3.58
3064	3357	2.884639	ACATTACAATTATGCCGCCTCC	59.115	45.455	0.00	0.00	0.00	4.30
3065	3358	2.719531	TTACAATTATGCCGCCTCCA	57.280	45.000	0.00	0.00	0.00	3.86
3163	3456	2.969821	TTGCTTTTGGCTCTAGGGAA	57.030	45.000	0.00	0.00	42.39	3.97
3175	3468	4.343814	GGCTCTAGGGAATATATGCTCCTC	59.656	50.000	0.00	0.00	31.88	3.71
3176	3469	4.343814	GCTCTAGGGAATATATGCTCCTCC	59.656	50.000	0.00	0.00	31.88	4.30
3177	3470	4.537751	TCTAGGGAATATATGCTCCTCCG	58.462	47.826	4.46	0.07	31.88	4.63
3178	3471	1.834263	AGGGAATATATGCTCCTCCGC	59.166	52.381	3.91	0.00	31.88	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
93	95	7.174413	TGAACATGTAGGAGAAATCAATTCCA	58.826	34.615	0.00	0.00	38.94	3.53
105	107	6.398095	TGATGTGTAGTTGAACATGTAGGAG	58.602	40.000	0.00	0.00	37.15	3.69
106	108	6.353404	TGATGTGTAGTTGAACATGTAGGA	57.647	37.500	0.00	0.00	37.15	2.94
131	133	7.373617	TGATAGATGATTTGGTAGGCAGTAA	57.626	36.000	0.00	0.00	0.00	2.24
185	187	8.221251	ACTAGGTGATGTTAGATGAGTAGATGA	58.779	37.037	0.00	0.00	0.00	2.92
267	269	2.439507	GCATCCTTGAGGTATTCTCCCA	59.560	50.000	0.00	0.00	41.76	4.37
319	321	3.321950	CCCCTTGATCTACTCCATCCTT	58.678	50.000	0.00	0.00	0.00	3.36
547	562	4.587520	AGGAACCCTGGCATCTGA	57.412	55.556	0.00	0.00	29.57	3.27
698	720	1.170919	ACTAGGTGCGAGTCGTGTGT	61.171	55.000	15.08	2.55	0.00	3.72
699	721	0.454620	GACTAGGTGCGAGTCGTGTG	60.455	60.000	15.08	1.94	34.41	3.82
709	731	3.597255	GTCCCAAAAGTAGACTAGGTGC	58.403	50.000	0.00	0.00	0.00	5.01
714	736	5.069516	ACTCAAACGTCCCAAAAGTAGACTA	59.930	40.000	0.00	0.00	0.00	2.59
715	737	4.141779	ACTCAAACGTCCCAAAAGTAGACT	60.142	41.667	0.00	0.00	0.00	3.24
761	783	5.499004	TGGTTGGATAGTTTGTTAGCTCT	57.501	39.130	0.00	0.00	0.00	4.09
764	786	4.082408	GGGTTGGTTGGATAGTTTGTTAGC	60.082	45.833	0.00	0.00	0.00	3.09
819	841	2.814835	GGTGACCGAACTGTGGGGT	61.815	63.158	2.98	2.98	36.58	4.95
915	1192	2.050714	GTGAGTCGCCGACGTGAA	60.051	61.111	12.13	0.00	41.18	3.18
1149	1426	1.519455	GACTTGCTCGGATCCCACG	60.519	63.158	6.06	0.00	0.00	4.94
1371	1648	0.033991	CGAGGAGGAAGGAGTGGAGA	60.034	60.000	0.00	0.00	0.00	3.71
1722	1999	2.111878	GCGGGCTGGCAGATGTAT	59.888	61.111	20.86	0.00	0.00	2.29
1938	2215	1.815421	CACCGCCTGCATACCTGAC	60.815	63.158	0.00	0.00	0.00	3.51
1974	2251	1.418334	ATAGGCTCAGTTCCTCGCAT	58.582	50.000	0.00	0.00	35.21	4.73
2037	2314	1.625818	TCCAGCTCCTTCTTCTGGTTC	59.374	52.381	7.31	0.00	45.67	3.62
2181	2458	5.932303	ACAGTAATACACACAGTTAAGGCAG	59.068	40.000	0.00	0.00	0.00	4.85
2340	2623	4.005650	CGGATTCCATCATAACCATCTGG	58.994	47.826	3.09	0.00	42.17	3.86
2350	2633	2.369983	AACCATGCGGATTCCATCAT	57.630	45.000	3.09	2.77	35.59	2.45
2351	2634	3.148412	CATAACCATGCGGATTCCATCA	58.852	45.455	3.09	0.28	35.59	3.07
2356	2639	3.411446	TCCATCATAACCATGCGGATTC	58.589	45.455	0.00	0.00	31.90	2.52
2357	2640	3.507162	TCCATCATAACCATGCGGATT	57.493	42.857	0.00	0.00	31.90	3.01
2358	2641	3.507162	TTCCATCATAACCATGCGGAT	57.493	42.857	0.00	0.00	34.97	4.18
2359	2642	3.411446	GATTCCATCATAACCATGCGGA	58.589	45.455	0.00	0.00	33.84	5.54
2360	2643	2.489329	GGATTCCATCATAACCATGCGG	59.511	50.000	0.00	0.00	38.77	5.69
2361	2644	2.160219	CGGATTCCATCATAACCATGCG	59.840	50.000	3.09	0.00	31.73	4.73
2362	2645	2.095059	GCGGATTCCATCATAACCATGC	60.095	50.000	3.09	0.00	31.73	4.06
2363	2646	3.148412	TGCGGATTCCATCATAACCATG	58.852	45.455	3.09	0.00	0.00	3.66
2364	2647	3.507162	TGCGGATTCCATCATAACCAT	57.493	42.857	3.09	0.00	0.00	3.55
2365	2648	3.213506	CTTGCGGATTCCATCATAACCA	58.786	45.455	3.09	0.00	0.00	3.67
2366	2649	3.214328	ACTTGCGGATTCCATCATAACC	58.786	45.455	3.09	0.00	0.00	2.85
2367	2650	4.576463	AGAACTTGCGGATTCCATCATAAC	59.424	41.667	3.09	0.00	0.00	1.89
2368	2651	4.780815	AGAACTTGCGGATTCCATCATAA	58.219	39.130	3.09	0.00	0.00	1.90
2369	2652	4.422073	AGAACTTGCGGATTCCATCATA	57.578	40.909	3.09	0.00	0.00	2.15
2370	2653	3.287867	AGAACTTGCGGATTCCATCAT	57.712	42.857	3.09	0.00	0.00	2.45
2371	2654	2.749076	CAAGAACTTGCGGATTCCATCA	59.251	45.455	3.09	0.00	33.45	3.07
2372	2655	2.749621	ACAAGAACTTGCGGATTCCATC	59.250	45.455	13.50	0.00	44.03	3.51
2373	2656	2.795329	ACAAGAACTTGCGGATTCCAT	58.205	42.857	13.50	0.00	44.03	3.41
2374	2657	2.270352	ACAAGAACTTGCGGATTCCA	57.730	45.000	13.50	0.00	44.03	3.53
2407	2693	0.459489	GGTGCAGCAACAGTCCAAAA	59.541	50.000	11.86	0.00	0.00	2.44
2449	2735	4.495422	ACTTCGGTTATTGTCAGCTAGTG	58.505	43.478	0.00	0.00	0.00	2.74
2549	2835	8.565896	TCACTTAATGAAATCAGCACTGTATT	57.434	30.769	0.00	0.00	33.02	1.89
2703	2989	6.993079	TGACTGAAGCAATCTACTACAAGAA	58.007	36.000	0.00	0.00	0.00	2.52
2705	2991	7.840342	AATGACTGAAGCAATCTACTACAAG	57.160	36.000	0.00	0.00	0.00	3.16
2740	3026	4.973168	AGTAAGGCAATCTGTCAGACAAA	58.027	39.130	4.21	0.00	0.00	2.83
2870	3157	1.605457	GCGAGTCATGGATGCCGAATA	60.605	52.381	0.00	0.00	0.00	1.75
2874	3161	1.493950	GAAGCGAGTCATGGATGCCG	61.494	60.000	0.00	0.00	0.00	5.69
2875	3162	0.462581	TGAAGCGAGTCATGGATGCC	60.463	55.000	0.00	0.00	0.00	4.40
2940	3227	6.756542	ACTTTGATAAACAACAACCTCAAAGC	59.243	34.615	17.92	0.00	43.56	3.51
3042	3334	3.058224	GGAGGCGGCATAATTGTAATGTC	60.058	47.826	13.08	0.00	0.00	3.06
3043	3335	2.884639	GGAGGCGGCATAATTGTAATGT	59.115	45.455	13.08	0.00	0.00	2.71
3044	3336	2.884012	TGGAGGCGGCATAATTGTAATG	59.116	45.455	13.08	0.00	0.00	1.90
3045	3337	3.222173	TGGAGGCGGCATAATTGTAAT	57.778	42.857	13.08	0.00	0.00	1.89
3046	3338	2.685897	GTTGGAGGCGGCATAATTGTAA	59.314	45.455	13.08	0.00	0.00	2.41
3064	3357	8.764524	AGTTGTAGTAGCATTTCTCTAAGTTG	57.235	34.615	0.00	0.00	0.00	3.16
3065	3358	9.780186	AAAGTTGTAGTAGCATTTCTCTAAGTT	57.220	29.630	0.00	0.00	0.00	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.