AutoCloner

Multiple sequence alignment - TraesCS4D01G053300

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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	TraesCS4D01G053300	chr4D	100.000	7143	0	0	1	7143	29322479	29329621	0.000000e+00	13191.0
1	TraesCS4D01G053300	chr4D	96.007	551	22	0	6588	7138	29346814	29347364	0.000000e+00	896.0
2	TraesCS4D01G053300	chr4D	93.182	44	3	0	5933	5976	259053329	259053286	1.660000e-06	65.8
3	TraesCS4D01G053300	chr4A	97.352	5930	92	15	3	5881	573892931	573887016	0.000000e+00	10021.0
4	TraesCS4D01G053300	chr4A	95.007	761	22	7	5847	6600	573886949	573886198	0.000000e+00	1181.0
5	TraesCS4D01G053300	chr4B	97.015	4623	97	19	941	5545	41778037	41782636	0.000000e+00	7734.0
6	TraesCS4D01G053300	chr4B	93.039	747	34	12	5852	6589	41783066	41783803	0.000000e+00	1075.0
7	TraesCS4D01G053300	chr4B	96.620	355	12	0	5524	5878	41782711	41783065	2.220000e-164	590.0
8	TraesCS4D01G053300	chr4B	91.899	395	27	4	4888	5280	42141373	42141764	1.350000e-151	547.0
9	TraesCS4D01G053300	chr4B	82.055	613	50	22	326	915	41777464	41778039	1.080000e-127	468.0
10	TraesCS4D01G053300	chr4B	91.343	335	19	3	1	325	41776174	41776508	3.930000e-122	449.0
11	TraesCS4D01G053300	chr4B	92.308	299	21	1	5272	5568	42144186	42144484	2.380000e-114	424.0
12	TraesCS4D01G053300	chr4B	86.207	87	10	2	4818	4904	42141272	42141356	7.630000e-15	93.5
13	TraesCS4D01G053300	chr3D	95.100	551	27	0	6588	7138	118502844	118503394	0.000000e+00	869.0
14	TraesCS4D01G053300	chr3D	94.918	551	28	0	6588	7138	75548104	75548654	0.000000e+00	863.0
15	TraesCS4D01G053300	chrUn	94.918	551	28	0	6588	7138	143842946	143843496	0.000000e+00	863.0
16	TraesCS4D01G053300	chr5D	94.918	551	28	0	6588	7138	435979781	435980331	0.000000e+00	863.0
17	TraesCS4D01G053300	chr5D	94.434	557	29	2	6585	7141	255513597	255513043	0.000000e+00	856.0
18	TraesCS4D01G053300	chr3A	94.604	556	30	0	6588	7143	469793034	469793589	0.000000e+00	861.0
19	TraesCS4D01G053300	chr3A	91.566	83	7	0	5892	5974	705926309	705926227	1.630000e-21	115.0
20	TraesCS4D01G053300	chr1D	94.909	550	28	0	6588	7137	164482554	164482005	0.000000e+00	861.0
21	TraesCS4D01G053300	chr1D	91.860	86	2	1	843	928	469030402	469030482	1.630000e-21	115.0
22	TraesCS4D01G053300	chr1D	97.872	47	1	0	5892	5938	481042121	481042075	1.650000e-11	82.4
23	TraesCS4D01G053300	chr6D	94.585	554	30	0	6588	7141	121672816	121672263	0.000000e+00	857.0
24	TraesCS4D01G053300	chr6D	95.238	42	2	0	5933	5974	423818549	423818508	4.620000e-07	67.6
25	TraesCS4D01G053300	chr7A	84.167	360	46	7	5424	5777	610205449	610205803	8.880000e-89	339.0
26	TraesCS4D01G053300	chr2A	83.708	356	46	8	5424	5773	238530331	238530680	6.910000e-85	326.0
27	TraesCS4D01G053300	chr1A	91.333	150	6	3	801	948	562004818	562004962	1.570000e-46	198.0
28	TraesCS4D01G053300	chr1A	92.308	143	4	3	805	945	562001592	562001729	5.650000e-46	196.0
29	TraesCS4D01G053300	chr1A	93.548	93	1	1	836	928	561981076	561981163	4.500000e-27	134.0
30	TraesCS4D01G053300	chr6B	95.238	42	2	0	5933	5974	15269085	15269044	4.620000e-07	67.6
31	TraesCS4D01G053300	chr6A	95.238	42	2	0	5933	5974	142074852	142074893	4.620000e-07	67.6

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	TraesCS4D01G053300	chr4D	29322479	29329621	7142	False	13191.000000	13191	100.0000	1	7143	1	chr4D.!!$F1	7142
1	TraesCS4D01G053300	chr4D	29346814	29347364	550	False	896.000000	896	96.0070	6588	7138	1	chr4D.!!$F2	550
2	TraesCS4D01G053300	chr4A	573886198	573892931	6733	True	5601.000000	10021	96.1795	3	6600	2	chr4A.!!$R1	6597
3	TraesCS4D01G053300	chr4B	41776174	41783803	7629	False	2063.200000	7734	92.0144	1	6589	5	chr4B.!!$F1	6588
4	TraesCS4D01G053300	chr4B	42141272	42144484	3212	False	354.833333	547	90.1380	4818	5568	3	chr4B.!!$F2	750
5	TraesCS4D01G053300	chr3D	118502844	118503394	550	False	869.000000	869	95.1000	6588	7138	1	chr3D.!!$F2	550
6	TraesCS4D01G053300	chr3D	75548104	75548654	550	False	863.000000	863	94.9180	6588	7138	1	chr3D.!!$F1	550
7	TraesCS4D01G053300	chrUn	143842946	143843496	550	False	863.000000	863	94.9180	6588	7138	1	chrUn.!!$F1	550
8	TraesCS4D01G053300	chr5D	435979781	435980331	550	False	863.000000	863	94.9180	6588	7138	1	chr5D.!!$F1	550
9	TraesCS4D01G053300	chr5D	255513043	255513597	554	True	856.000000	856	94.4340	6585	7141	1	chr5D.!!$R1	556
10	TraesCS4D01G053300	chr3A	469793034	469793589	555	False	861.000000	861	94.6040	6588	7143	1	chr3A.!!$F1	555
11	TraesCS4D01G053300	chr1D	164482005	164482554	549	True	861.000000	861	94.9090	6588	7137	1	chr1D.!!$R1	549
12	TraesCS4D01G053300	chr6D	121672263	121672816	553	True	857.000000	857	94.5850	6588	7141	1	chr6D.!!$R1	553

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
182	193	2.202919	CATCACCTCGCCATCGCA	60.203	61.111	0.00	0.00	35.26	5.10	F
289	300	2.226962	ATGCTGGAAGGCTTTGTGAT	57.773	45.000	0.00	0.00	0.00	3.06	F
418	1384	2.350522	GTCAAAGATGTGCCATCGTCT	58.649	47.619	8.84	0.85	35.50	4.18	F
421	1387	3.195610	TCAAAGATGTGCCATCGTCTACT	59.804	43.478	8.84	0.00	33.88	2.57	F
849	1849	4.074647	GGTTTCAACCCGGTCCAG	57.925	61.111	0.00	0.00	43.43	3.86	F
3574	4580	1.535462	AGAAAACGGAAGGCAATCACG	59.465	47.619	0.00	0.00	0.00	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1983	2988	0.314935	ACCAAGGTTGCAATTGCTCG	59.685	50.000	29.37	11.95	42.66	5.03	R
2233	3239	6.589523	TGAAGTTTGAACAGACAAAAACCATG	59.410	34.615	0.00	0.00	40.62	3.66	R
2376	3382	7.899973	ACATGAATAAAGAAGGAAAGCATGTT	58.100	30.769	0.00	0.00	40.36	2.71	R
3054	4060	9.632638	ATTCTAATGGGTGATATAACATATGGC	57.367	33.333	7.80	0.00	0.00	4.40	R
3801	4807	0.798776	CAGCCTCGAACGCAGATTTT	59.201	50.000	6.89	0.00	0.00	1.82	R
6463	10172	0.109086	ACTCCGAGCATCTTCACACG	60.109	55.000	0.00	0.00	0.00	4.49	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
60	61	6.263168	CCACCTACAAGAAGTGAAGACAAAAT	59.737	38.462	0.00	0.00	33.21	1.82
182	193	2.202919	CATCACCTCGCCATCGCA	60.203	61.111	0.00	0.00	35.26	5.10
289	300	2.226962	ATGCTGGAAGGCTTTGTGAT	57.773	45.000	0.00	0.00	0.00	3.06
364	1330	5.717178	AGATGTACCATCCTCAGCGTATATT	59.283	40.000	0.74	0.00	0.00	1.28
418	1384	2.350522	GTCAAAGATGTGCCATCGTCT	58.649	47.619	8.84	0.85	35.50	4.18
421	1387	3.195610	TCAAAGATGTGCCATCGTCTACT	59.804	43.478	8.84	0.00	33.88	2.57
459	1425	9.985730	ATCAATGCTATTAATTTTGTACCATGG	57.014	29.630	11.19	11.19	0.00	3.66
488	1454	7.458409	TCAATACCTTTTCAGTAGTCGTACT	57.542	36.000	0.00	0.00	40.38	2.73
489	1455	8.565896	TCAATACCTTTTCAGTAGTCGTACTA	57.434	34.615	0.00	0.00	37.40	1.82
567	1533	5.408299	CGATTAGGCGATTACCATTCATTCA	59.592	40.000	0.00	0.00	0.00	2.57
699	1668	5.346270	ACCCTAGATCTCTTCAACCTCTTT	58.654	41.667	0.00	0.00	0.00	2.52
849	1849	4.074647	GGTTTCAACCCGGTCCAG	57.925	61.111	0.00	0.00	43.43	3.86
1746	2751	6.913170	TCTGTTGATTTCAGATTTAACTGCC	58.087	36.000	0.00	0.00	37.07	4.85
2233	3239	7.426743	GCGTAGTCTCTTATTTTCTTGAAATGC	59.573	37.037	0.00	0.00	38.40	3.56
3054	4060	4.742167	CCTGCTCGGATTATTGCTATATCG	59.258	45.833	0.00	0.00	33.16	2.92
3574	4580	1.535462	AGAAAACGGAAGGCAATCACG	59.465	47.619	0.00	0.00	0.00	4.35
4138	5144	6.554419	TCTGAAAGACATTTTTGTCACTGTG	58.446	36.000	0.17	0.17	38.67	3.66
4879	5903	5.824904	AAGTTCAATTAGCGCATTCTGAT	57.175	34.783	11.47	0.00	0.00	2.90
4892	5947	6.816640	AGCGCATTCTGATTAGTTAAACACTA	59.183	34.615	11.47	0.00	36.88	2.74
5242	6307	5.448438	TGTTCTATTTGTGCGCTTTAACAG	58.552	37.500	9.73	0.00	0.00	3.16
5336	8843	7.545615	GCATTTATTTCCAATTTCTCGTTTCCT	59.454	33.333	0.00	0.00	0.00	3.36
5693	9298	6.128526	GCCGAGCATAATGATTCCTTAACTAC	60.129	42.308	0.00	0.00	0.00	2.73
5880	9587	9.796120	TGCCAGTAAAAACTGCAAATTATATAC	57.204	29.630	0.00	0.00	36.46	1.47
6229	9936	3.118112	CCTCAGACCAATCAGGCATAAGT	60.118	47.826	0.00	0.00	43.14	2.24
6266	9973	2.224066	GCATTCATGTAGGAGCGTACCT	60.224	50.000	7.58	7.58	43.32	3.08
6358	10066	2.813754	GCTTGTGACTGAGCCATGTTAA	59.186	45.455	0.00	0.00	32.80	2.01
6419	10128	1.128692	GCGGACTGATGTGCTTGTAAC	59.871	52.381	0.00	0.00	32.02	2.50
6463	10172	2.177173	GTCATCCTTGCGCGAATTTTC	58.823	47.619	12.10	0.00	0.00	2.29
6508	10225	9.226606	TCTTGTTCGTTTTTCCATCTATGTATT	57.773	29.630	0.00	0.00	0.00	1.89
6509	10226	9.277565	CTTGTTCGTTTTTCCATCTATGTATTG	57.722	33.333	0.00	0.00	0.00	1.90
6522	10245	8.514594	CCATCTATGTATTGTTTGTGTCTTTGT	58.485	33.333	0.00	0.00	0.00	2.83
6544	10267	1.282930	GCAAAGTCTCGACGGTGGAC	61.283	60.000	0.00	1.89	36.20	4.02
6556	10279	4.394712	GTGGACGGGTGGAGGCAG	62.395	72.222	0.00	0.00	0.00	4.85
6566	10289	2.353607	GGAGGCAGCGTCGTATCG	60.354	66.667	8.97	0.00	0.00	2.92
6580	10303	4.921515	CGTCGTATCGAATAAATGTCCCAT	59.078	41.667	0.00	0.00	37.72	4.00
6657	10380	0.179468	GTGGCAGCGGGGTCTTATTA	59.821	55.000	0.00	0.00	0.00	0.98
6658	10381	0.913205	TGGCAGCGGGGTCTTATTAA	59.087	50.000	0.00	0.00	0.00	1.40
6691	10414	8.966501	AGGGATATTAAGGCCTCCTTTTAATAA	58.033	33.333	5.23	0.00	41.69	1.40
6702	10425	6.647229	CCTCCTTTTAATAAAGTACCGGACT	58.353	40.000	9.46	4.30	39.29	3.85
6734	10457	6.115448	AGCACTTAGTGAATACCTGAACTT	57.885	37.500	17.40	0.00	35.23	2.66
6735	10458	6.534634	AGCACTTAGTGAATACCTGAACTTT	58.465	36.000	17.40	0.00	35.23	2.66
6777	10500	4.301628	GGTAAGTACCCCGATTATTGTCG	58.698	47.826	0.00	0.00	40.53	4.35
6906	10629	4.162690	GCACTCGGGCCCTAGTGG	62.163	72.222	41.87	29.19	42.72	4.00
6937	10660	7.572523	TTAAGCATAGCAAAGTCATAGCAAT	57.427	32.000	0.00	0.00	0.00	3.56
6997	10720	9.511272	AAACCCTAACAAAACTAACTCGATTAT	57.489	29.630	0.00	0.00	0.00	1.28
7036	10760	2.045926	ATCACCGTCCAGCAAGCC	60.046	61.111	0.00	0.00	0.00	4.35

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
182	193	4.841246	GGGATCATTCTAGGTGTCCTACAT	59.159	45.833	0.00	0.00	34.61	2.29
226	237	0.535553	GGGGTTAGCCGTGTTGTTCA	60.536	55.000	0.00	0.00	34.97	3.18
227	238	0.535553	TGGGGTTAGCCGTGTTGTTC	60.536	55.000	0.00	0.00	34.97	3.18
289	300	1.375396	CATGACGGTTTCCCTCGCA	60.375	57.895	0.00	0.00	0.00	5.10
364	1330	5.528043	AAAGCAACCACATTGATGTACAA	57.472	34.783	0.00	0.00	41.23	2.41
456	1422	9.533831	ACTACTGAAAAGGTATTGAAATTCCAT	57.466	29.630	2.09	0.00	0.00	3.41
459	1425	8.718734	ACGACTACTGAAAAGGTATTGAAATTC	58.281	33.333	0.00	0.00	0.00	2.17
465	1431	8.671921	TCTAGTACGACTACTGAAAAGGTATTG	58.328	37.037	0.00	0.00	34.79	1.90
489	1455	9.947189	TCCCATATACTAAATACCCGATAATCT	57.053	33.333	0.00	0.00	0.00	2.40
567	1533	6.494146	GGTAGAGCTTAATGGTGAGGTATACT	59.506	42.308	2.25	0.00	36.40	2.12
714	1704	7.420029	ACGGGAGGAGTTATACATAGGATTAT	58.580	38.462	0.00	0.00	0.00	1.28
715	1705	6.797707	ACGGGAGGAGTTATACATAGGATTA	58.202	40.000	0.00	0.00	0.00	1.75
723	1713	2.077687	GGGACGGGAGGAGTTATACA	57.922	55.000	0.00	0.00	0.00	2.29
845	1845	0.855855	TCCCCTCTCCTTCCTCTGGA	60.856	60.000	0.00	0.00	0.00	3.86
846	1846	0.043334	TTCCCCTCTCCTTCCTCTGG	59.957	60.000	0.00	0.00	0.00	3.86
847	1847	1.494960	CTTCCCCTCTCCTTCCTCTG	58.505	60.000	0.00	0.00	0.00	3.35
848	1848	0.341609	CCTTCCCCTCTCCTTCCTCT	59.658	60.000	0.00	0.00	0.00	3.69
849	1849	0.692756	CCCTTCCCCTCTCCTTCCTC	60.693	65.000	0.00	0.00	0.00	3.71
875	1875	1.067706	CCTGTGAGTGCTCTCTCTGTG	60.068	57.143	16.23	7.68	40.98	3.66
1816	2821	4.643784	CAGCAAAGAGGAAGGCAAATAGAT	59.356	41.667	0.00	0.00	0.00	1.98
1858	2863	3.918591	GCAAAATGATGAGCACTCAACTG	59.081	43.478	4.14	0.00	43.58	3.16
1975	2980	7.119116	CCAAGGTTGCAATTGCTCGTATATATA	59.881	37.037	29.37	3.82	42.66	0.86
1983	2988	0.314935	ACCAAGGTTGCAATTGCTCG	59.685	50.000	29.37	11.95	42.66	5.03
2233	3239	6.589523	TGAAGTTTGAACAGACAAAAACCATG	59.410	34.615	0.00	0.00	40.62	3.66
2376	3382	7.899973	ACATGAATAAAGAAGGAAAGCATGTT	58.100	30.769	0.00	0.00	40.36	2.71
3054	4060	9.632638	ATTCTAATGGGTGATATAACATATGGC	57.367	33.333	7.80	0.00	0.00	4.40
3801	4807	0.798776	CAGCCTCGAACGCAGATTTT	59.201	50.000	6.89	0.00	0.00	1.82
4063	5069	2.091541	TGCCTACTTGCCAATTGTAGC	58.908	47.619	4.43	2.10	34.13	3.58
4263	5287	7.601886	CAGTTGAATCTATGACCATATCCTCAC	59.398	40.741	0.00	0.00	0.00	3.51
5336	8843	7.287061	TGTCTGGGAACTAAAAGATCAAGAAA	58.713	34.615	0.00	0.00	0.00	2.52
5693	9298	2.395690	CTGCGGCTCGTTTTAGCG	59.604	61.111	0.00	0.00	43.74	4.26
5880	9587	3.925688	GCAGCTGCATCAATGAAAATG	57.074	42.857	33.36	0.00	41.59	2.32
5908	9615	4.274459	GCAAATAATGACATCTTCGCCTCT	59.726	41.667	0.00	0.00	0.00	3.69
6229	9936	7.656412	ACATGAATGCTACAACAACAACATAA	58.344	30.769	0.00	0.00	0.00	1.90
6463	10172	0.109086	ACTCCGAGCATCTTCACACG	60.109	55.000	0.00	0.00	0.00	4.49
6508	10225	3.667497	TTGCCAACAAAGACACAAACA	57.333	38.095	0.00	0.00	31.21	2.83
6522	10245	0.878523	CACCGTCGAGACTTTGCCAA	60.879	55.000	0.00	0.00	0.00	4.52
6546	10269	2.955751	GATACGACGCTGCCTCCACC	62.956	65.000	0.00	0.00	0.00	4.61
6547	10270	1.589196	GATACGACGCTGCCTCCAC	60.589	63.158	0.00	0.00	0.00	4.02
6548	10271	2.805546	GATACGACGCTGCCTCCA	59.194	61.111	0.00	0.00	0.00	3.86
6549	10272	2.332362	TTCGATACGACGCTGCCTCC	62.332	60.000	0.00	0.00	34.89	4.30
6551	10274	0.949397	TATTCGATACGACGCTGCCT	59.051	50.000	0.00	0.00	34.89	4.75
6552	10275	1.762419	TTATTCGATACGACGCTGCC	58.238	50.000	0.00	0.00	34.89	4.85
6554	10277	4.143597	GGACATTTATTCGATACGACGCTG	60.144	45.833	0.00	0.00	34.89	5.18
6556	10279	3.120782	GGGACATTTATTCGATACGACGC	59.879	47.826	0.00	0.00	34.89	5.19
6557	10280	4.292599	TGGGACATTTATTCGATACGACG	58.707	43.478	0.00	0.00	34.89	5.12
6580	10303	9.491675	TCTTTTTCATAAACACGTATAGAACCA	57.508	29.630	0.00	0.00	0.00	3.67
6657	10380	6.092346	AGGCCTTAATATCCCTCAGTTTTT	57.908	37.500	0.00	0.00	0.00	1.94
6658	10381	5.399152	GGAGGCCTTAATATCCCTCAGTTTT	60.399	44.000	6.77	0.00	44.45	2.43
6691	10414	5.640783	GTGCTAATGTTTTAGTCCGGTACTT	59.359	40.000	11.09	0.00	39.80	2.24
6702	10425	9.953565	AGGTATTCACTAAGTGCTAATGTTTTA	57.046	29.630	0.00	0.00	32.98	1.52
6706	10429	7.182817	TCAGGTATTCACTAAGTGCTAATGT	57.817	36.000	0.00	0.00	32.98	2.71
6727	10450	5.728351	TGACCGTAGTTTGAAAAGTTCAG	57.272	39.130	0.00	0.00	41.38	3.02
6777	10500	0.108041	TGATCCGTTAACCCCGAAGC	60.108	55.000	0.00	0.00	0.00	3.86
6906	10629	4.427312	ACTTTGCTATGCTTAATGCTTGC	58.573	39.130	0.00	0.00	43.37	4.01
6951	10674	8.388656	GGGTTTGATCCCTAGTATCCATTATA	57.611	38.462	0.00	0.00	43.85	0.98
6997	10720	7.884877	GTGATGGGTTGGATGAGATTTATCATA	59.115	37.037	0.00	0.00	40.02	2.15
7036	10760	4.148871	CGTGCGTGAGTAATTCCATCATAG	59.851	45.833	0.00	0.00	0.00	2.23

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.