AutoCloner

Multiple sequence alignment - TraesCS3B01G457000

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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	TraesCS3B01G457000	chr3B	100.000	2945	0	0	1	2945	698407391	698410335	0.000000e+00	5439.0
1	TraesCS3B01G457000	chr3B	86.616	1188	138	16	859	2029	442639390	442638207	0.000000e+00	1293.0
2	TraesCS3B01G457000	chr3B	93.590	78	2	2	2046	2120	470852026	470852103	2.400000e-21	113.0
3	TraesCS3B01G457000	chr3D	93.614	2349	111	18	613	2945	528151357	528153682	0.000000e+00	3470.0
4	TraesCS3B01G457000	chr3D	92.308	78	3	3	2046	2120	136418856	136418779	1.120000e-19	108.0
5	TraesCS3B01G457000	chr2B	96.034	580	22	1	1	579	665917136	665917715	0.000000e+00	942.0
6	TraesCS3B01G457000	chr3A	89.384	763	48	18	2161	2909	662791633	662792376	0.000000e+00	929.0
7	TraesCS3B01G457000	chr3A	89.733	711	68	5	608	1315	662711053	662711761	0.000000e+00	904.0
8	TraesCS3B01G457000	chr3A	92.412	514	39	0	1313	1826	662789450	662789963	0.000000e+00	734.0
9	TraesCS3B01G457000	chr3A	94.776	134	7	0	1912	2045	662791022	662791155	2.970000e-50	209.0
10	TraesCS3B01G457000	chr4B	95.377	584	25	1	1	582	568734626	568735209	0.000000e+00	928.0
11	TraesCS3B01G457000	chr4B	95.197	583	26	2	1	582	5275758	5276339	0.000000e+00	920.0
12	TraesCS3B01G457000	chr4B	94.719	587	26	2	1	582	657437595	657437009	0.000000e+00	907.0
13	TraesCS3B01G457000	chr1B	95.205	584	27	1	1	583	667349537	667350120	0.000000e+00	922.0
14	TraesCS3B01G457000	chr1B	95.034	584	26	3	1	582	549443020	549443602	0.000000e+00	915.0
15	TraesCS3B01G457000	chr1B	94.872	585	27	3	1	582	120652532	120653116	0.000000e+00	911.0
16	TraesCS3B01G457000	chr4A	95.197	583	27	1	1	582	664504606	664505188	0.000000e+00	920.0
17	TraesCS3B01G457000	chr7B	95.009	581	27	2	1	580	637698266	637697687	0.000000e+00	911.0
18	TraesCS3B01G457000	chr2A	90.000	90	4	4	2046	2131	618434225	618434137	8.630000e-21	111.0
19	TraesCS3B01G457000	chr1A	88.764	89	7	2	2046	2131	303782950	303782862	4.010000e-19	106.0
20	TraesCS3B01G457000	chr6B	88.636	88	7	3	2046	2130	45585627	45585540	1.440000e-18	104.0
21	TraesCS3B01G457000	chr5D	89.286	84	6	2	2046	2126	112955951	112955868	5.190000e-18	102.0
22	TraesCS3B01G457000	chr2D	91.026	78	2	3	2046	2120	114515502	114515577	1.870000e-17	100.0
23	TraesCS3B01G457000	chr2D	87.805	82	5	3	2048	2126	114515579	114515500	1.120000e-14	91.6

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	TraesCS3B01G457000	chr3B	698407391	698410335	2944	False	5439	5439	100.000000	1	2945	1	chr3B.!!$F2	2944
1	TraesCS3B01G457000	chr3B	442638207	442639390	1183	True	1293	1293	86.616000	859	2029	1	chr3B.!!$R1	1170
2	TraesCS3B01G457000	chr3D	528151357	528153682	2325	False	3470	3470	93.614000	613	2945	1	chr3D.!!$F1	2332
3	TraesCS3B01G457000	chr2B	665917136	665917715	579	False	942	942	96.034000	1	579	1	chr2B.!!$F1	578
4	TraesCS3B01G457000	chr3A	662711053	662711761	708	False	904	904	89.733000	608	1315	1	chr3A.!!$F1	707
5	TraesCS3B01G457000	chr3A	662789450	662792376	2926	False	624	929	92.190667	1313	2909	3	chr3A.!!$F2	1596
6	TraesCS3B01G457000	chr4B	568734626	568735209	583	False	928	928	95.377000	1	582	1	chr4B.!!$F2	581
7	TraesCS3B01G457000	chr4B	5275758	5276339	581	False	920	920	95.197000	1	582	1	chr4B.!!$F1	581
8	TraesCS3B01G457000	chr4B	657437009	657437595	586	True	907	907	94.719000	1	582	1	chr4B.!!$R1	581
9	TraesCS3B01G457000	chr1B	667349537	667350120	583	False	922	922	95.205000	1	583	1	chr1B.!!$F3	582
10	TraesCS3B01G457000	chr1B	549443020	549443602	582	False	915	915	95.034000	1	582	1	chr1B.!!$F2	581
11	TraesCS3B01G457000	chr1B	120652532	120653116	584	False	911	911	94.872000	1	582	1	chr1B.!!$F1	581
12	TraesCS3B01G457000	chr4A	664504606	664505188	582	False	920	920	95.197000	1	582	1	chr4A.!!$F1	581
13	TraesCS3B01G457000	chr7B	637697687	637698266	579	True	911	911	95.009000	1	580	1	chr7B.!!$R1	579

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
704	715	0.399075	CCAAAACCCTAGGTCACCGT	59.601	55.0	8.29	0.0	33.12	4.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2489	3935	0.105964	CTCCCCGTTCACACTTCACA	59.894	55.0	0.0	0.0	0.0	3.58	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
141	146	1.291132	GGAGCGAGCATTACCTTCAC	58.709	55.000	0.00	0.00	0.00	3.18
224	230	2.501610	GATTCTTCCGCCTCCGCT	59.498	61.111	0.00	0.00	0.00	5.52
264	270	3.507622	CCTTCTCCTCCAATGGTTTGAAC	59.492	47.826	0.00	0.00	34.60	3.18
292	300	2.784356	GGTTGTGCCAGCAACTGCA	61.784	57.895	4.22	0.00	45.69	4.41
359	369	1.518792	TGTTTGACGACAACCGCGA	60.519	52.632	8.23	0.00	43.32	5.87
494	504	1.153647	CTCGTCCTATGTGGCGCAA	60.154	57.895	10.83	0.00	36.05	4.85
546	556	2.882137	CACAAAGTACCCAACGGTGATT	59.118	45.455	0.00	0.00	44.40	2.57
587	597	4.783667	ACGCCCACACGTACATTT	57.216	50.000	0.00	0.00	46.19	2.32
588	598	2.535588	ACGCCCACACGTACATTTC	58.464	52.632	0.00	0.00	46.19	2.17
589	599	0.952010	ACGCCCACACGTACATTTCC	60.952	55.000	0.00	0.00	46.19	3.13
590	600	1.791662	GCCCACACGTACATTTCCG	59.208	57.895	0.00	0.00	0.00	4.30
591	601	0.952010	GCCCACACGTACATTTCCGT	60.952	55.000	0.00	0.00	37.90	4.69
592	602	1.515081	CCCACACGTACATTTCCGTT	58.485	50.000	0.00	0.00	34.59	4.44
593	603	1.874872	CCCACACGTACATTTCCGTTT	59.125	47.619	0.00	0.00	34.59	3.60
594	604	2.291190	CCCACACGTACATTTCCGTTTT	59.709	45.455	0.00	0.00	34.59	2.43
595	605	3.243134	CCCACACGTACATTTCCGTTTTT	60.243	43.478	0.00	0.00	34.59	1.94
630	640	7.122204	AGGTATAGAATACCACTTGTTTTTGCC	59.878	37.037	16.40	0.00	39.99	4.52
644	655	2.731691	TTTGCCTGTCAGTCCTCGCC	62.732	60.000	0.00	0.00	0.00	5.54
704	715	0.399075	CCAAAACCCTAGGTCACCGT	59.601	55.000	8.29	0.00	33.12	4.83
734	745	2.440501	GCTGCAAATCGGAACATAACG	58.559	47.619	0.00	0.00	0.00	3.18
977	999	1.109920	CCGATCCCAGGACATCTCGT	61.110	60.000	6.66	0.00	0.00	4.18
1074	1096	0.168128	GCAACGCACCCATTGACTAC	59.832	55.000	0.00	0.00	0.00	2.73
1178	1200	4.849329	GCTACCGGTCGGCGACAG	62.849	72.222	37.13	33.09	39.32	3.51
1198	1220	1.139058	GGATCTATGCCCTGACACGTT	59.861	52.381	0.00	0.00	0.00	3.99
1200	1222	2.953466	TCTATGCCCTGACACGTTAC	57.047	50.000	0.00	0.00	0.00	2.50
1233	1255	1.409661	GGGGGTATCAATTTCGTGCCT	60.410	52.381	0.00	0.00	0.00	4.75
1240	1262	1.611491	TCAATTTCGTGCCTTGGTTCC	59.389	47.619	0.00	0.00	0.00	3.62
1366	1388	1.813859	CACTACATCTTCCCGCCGA	59.186	57.895	0.00	0.00	0.00	5.54
1390	1412	2.572104	GTCAGGGTCAGGTCCTTTGTAT	59.428	50.000	0.00	0.00	31.06	2.29
1459	1481	3.548818	GCACATGTTCAACTTGGAGACAC	60.549	47.826	8.21	0.00	42.67	3.67
1479	1501	1.197721	CAGCAATGGTCGAAACTGGAC	59.802	52.381	0.00	0.00	0.00	4.02
1527	1549	3.813724	GTCCCTCATGGCCCCCTG	61.814	72.222	0.00	0.00	0.00	4.45
1556	1578	1.860326	CTTTTCAACTGCCGCCAAAAG	59.140	47.619	0.00	0.00	0.00	2.27
1588	1610	1.071299	AACATCACAGTCTGCGCCA	59.929	52.632	4.18	0.00	0.00	5.69
1625	1647	2.976490	GCATCACAGCAGGGTCCCT	61.976	63.158	3.85	3.85	0.00	4.20
1651	1673	3.328382	TGTCAATTACTGAGTTCCCGG	57.672	47.619	0.00	0.00	33.60	5.73
1707	1729	1.337728	GGCAAATTTGTTTCCCTCGGG	60.338	52.381	19.03	0.00	0.00	5.14
1755	1777	2.460330	CACCGATGACCTTGTGCTC	58.540	57.895	0.00	0.00	0.00	4.26
1827	2411	3.971245	GAGGAACACCTCTCACAAGAT	57.029	47.619	8.77	0.00	44.74	2.40
1862	2446	1.132453	TCGCAACGTAGTGATCTCCAG	59.868	52.381	0.00	0.00	45.00	3.86
1867	2451	1.899814	ACGTAGTGATCTCCAGCCAAA	59.100	47.619	0.00	0.00	42.51	3.28
2120	3131	5.070446	AGCGACAACTAATATGGAATGGAGA	59.930	40.000	0.00	0.00	0.00	3.71
2277	3723	6.372381	ACCATATACAAACAGAAAACCGTACC	59.628	38.462	0.00	0.00	0.00	3.34
2278	3724	6.596497	CCATATACAAACAGAAAACCGTACCT	59.404	38.462	0.00	0.00	0.00	3.08
2279	3725	7.201582	CCATATACAAACAGAAAACCGTACCTC	60.202	40.741	0.00	0.00	0.00	3.85
2280	3726	2.867975	ACAAACAGAAAACCGTACCTCG	59.132	45.455	0.00	0.00	39.52	4.63
2281	3727	3.125316	CAAACAGAAAACCGTACCTCGA	58.875	45.455	0.00	0.00	42.86	4.04
2282	3728	2.719426	ACAGAAAACCGTACCTCGAG	57.281	50.000	5.13	5.13	42.86	4.04
2283	3729	1.959282	ACAGAAAACCGTACCTCGAGT	59.041	47.619	12.31	2.17	42.86	4.18
2284	3730	2.030451	ACAGAAAACCGTACCTCGAGTC	60.030	50.000	12.31	0.00	42.86	3.36
2320	3766	8.331740	TCTTTTTCTCCAGAAATGATATCCAGT	58.668	33.333	2.59	0.00	42.83	4.00
2328	3774	6.125029	CAGAAATGATATCCAGTGAACCCTT	58.875	40.000	0.00	0.00	0.00	3.95
2440	3886	5.489249	TCAGACTCGTTCACTATAGACAGT	58.511	41.667	6.78	1.60	0.00	3.55
2441	3887	6.637657	TCAGACTCGTTCACTATAGACAGTA	58.362	40.000	6.78	0.00	0.00	2.74
2493	3939	2.702592	AAAAAGGACGAGTGGTGTGA	57.297	45.000	0.00	0.00	0.00	3.58
2494	3940	2.702592	AAAAGGACGAGTGGTGTGAA	57.297	45.000	0.00	0.00	0.00	3.18
2934	4393	6.602410	TGGCATTTTATTGTCAAAGGATGA	57.398	33.333	0.00	0.00	35.05	2.92
2935	4394	7.002250	TGGCATTTTATTGTCAAAGGATGAA	57.998	32.000	0.00	0.00	40.50	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
224	230	3.068691	CGAGGGGAGAAGGCGACA	61.069	66.667	0.00	0.00	0.00	4.35
264	270	2.639286	GCACAACCCACTTCGCTG	59.361	61.111	0.00	0.00	0.00	5.18
292	300	0.331616	GGTGCCATTTACTCACCCCT	59.668	55.000	0.00	0.00	43.27	4.79
546	556	1.663388	ATCTCGAACGCACGCAACA	60.663	52.632	0.00	0.00	0.00	3.33
603	613	9.169592	GCAAAAACAAGTGGTATTCTATACCTA	57.830	33.333	14.97	2.02	38.39	3.08
604	614	7.122204	GGCAAAAACAAGTGGTATTCTATACCT	59.878	37.037	14.97	0.00	38.39	3.08
605	615	7.122204	AGGCAAAAACAAGTGGTATTCTATACC	59.878	37.037	8.59	8.59	38.07	2.73
606	616	7.968405	CAGGCAAAAACAAGTGGTATTCTATAC	59.032	37.037	0.00	0.00	0.00	1.47
607	617	7.668052	ACAGGCAAAAACAAGTGGTATTCTATA	59.332	33.333	0.00	0.00	0.00	1.31
608	618	6.493458	ACAGGCAAAAACAAGTGGTATTCTAT	59.507	34.615	0.00	0.00	0.00	1.98
609	619	5.830991	ACAGGCAAAAACAAGTGGTATTCTA	59.169	36.000	0.00	0.00	0.00	2.10
610	620	4.649218	ACAGGCAAAAACAAGTGGTATTCT	59.351	37.500	0.00	0.00	0.00	2.40
611	621	4.944048	ACAGGCAAAAACAAGTGGTATTC	58.056	39.130	0.00	0.00	0.00	1.75
630	640	2.888863	GGAGGCGAGGACTGACAG	59.111	66.667	0.00	0.00	0.00	3.51
644	655	2.633488	GGGAAAAGGTGAGAATCGGAG	58.367	52.381	0.00	0.00	38.61	4.63
690	701	3.066814	GCGACGGTGACCTAGGGT	61.067	66.667	14.81	0.00	39.44	4.34
704	715	1.992233	GATTTGCAGCGGGATTGCGA	61.992	55.000	0.00	0.00	44.40	5.10
784	795	1.303970	GGCTTCAGCTTCTTGCCCT	60.304	57.895	0.00	0.00	44.23	5.19
817	828	1.666011	GCGATCTGGCGAGGGATTA	59.334	57.895	0.00	0.00	0.00	1.75
853	864	3.834799	CACCGACGGAGGCCCTAC	61.835	72.222	23.38	0.00	33.69	3.18
856	867	4.139234	GTACACCGACGGAGGCCC	62.139	72.222	23.38	0.96	33.69	5.80
954	976	2.900546	GAGATGTCCTGGGATCGGTATT	59.099	50.000	0.00	0.00	0.00	1.89
1178	1200	0.753262	ACGTGTCAGGGCATAGATCC	59.247	55.000	0.00	0.00	0.00	3.36
1221	1243	1.339610	TGGAACCAAGGCACGAAATTG	59.660	47.619	0.00	0.00	0.00	2.32
1233	1255	0.036388	GATCGAGCACCTGGAACCAA	60.036	55.000	0.00	0.00	0.00	3.67
1240	1262	1.039785	TGGGAGAGATCGAGCACCTG	61.040	60.000	2.38	0.00	0.00	4.00
1366	1388	0.178861	AAGGACCTGACCCTGACCAT	60.179	55.000	0.00	0.00	33.55	3.55
1390	1412	1.219124	GAATGCAGGAGCTCACGGA	59.781	57.895	17.19	7.20	42.74	4.69
1459	1481	1.197721	GTCCAGTTTCGACCATTGCTG	59.802	52.381	0.00	0.00	0.00	4.41
1479	1501	2.096496	GGTGAATGGCAGATTCTTGTCG	59.904	50.000	8.64	0.00	0.00	4.35
1486	1508	0.107017	CCTCCGGTGAATGGCAGATT	60.107	55.000	4.76	0.00	0.00	2.40
1527	1549	2.473816	GCAGTTGAAAAGCCAAGGAAC	58.526	47.619	0.00	0.00	0.00	3.62
1556	1578	0.582005	GATGTTGTAAGCGGCGATCC	59.418	55.000	12.98	0.00	0.00	3.36
1588	1610	2.397413	CTTGGGCTTGGTGAGTCGGT	62.397	60.000	0.00	0.00	0.00	4.69
1625	1647	6.629515	CGGGAACTCAGTAATTGACAAGGATA	60.630	42.308	0.00	0.00	0.00	2.59
1651	1673	2.273449	CCCTGCCTCATCCACCAC	59.727	66.667	0.00	0.00	0.00	4.16
1707	1729	1.523758	ACGAACAGAAGCCATGGTTC	58.476	50.000	14.67	15.08	39.92	3.62
1755	1777	2.451132	CGTGTATGCTCAAGAGTACCG	58.549	52.381	0.00	0.00	0.00	4.02
1827	2411	0.750249	TGCGAACAGACTTGAGGTGA	59.250	50.000	0.00	0.00	0.00	4.02
1862	2446	3.860754	GCTGTAAACCTGTTCCATTTGGC	60.861	47.826	0.00	0.00	34.44	4.52
1867	2451	2.423577	GACGCTGTAAACCTGTTCCAT	58.576	47.619	0.00	0.00	0.00	3.41
1899	2483	1.497309	ATGGCCAAGAAAGTCCCCGA	61.497	55.000	10.96	0.00	0.00	5.14
2032	3039	3.244457	ACGGAGGGAGGAACTAAAACTTG	60.244	47.826	0.00	0.00	41.55	3.16
2230	3675	2.250031	TGGTCGGGACTAAGCAAGTTA	58.750	47.619	0.00	0.00	39.07	2.24
2280	3726	3.007074	AGAAAAAGAAGGGTCGAGGACTC	59.993	47.826	0.00	0.00	32.35	3.36
2281	3727	2.973406	AGAAAAAGAAGGGTCGAGGACT	59.027	45.455	0.00	0.00	32.47	3.85
2282	3728	3.327626	GAGAAAAAGAAGGGTCGAGGAC	58.672	50.000	0.00	0.00	0.00	3.85
2283	3729	2.302157	GGAGAAAAAGAAGGGTCGAGGA	59.698	50.000	0.00	0.00	0.00	3.71
2284	3730	2.038557	TGGAGAAAAAGAAGGGTCGAGG	59.961	50.000	0.00	0.00	0.00	4.63
2328	3774	0.533491	CTCGGATAACGTCCCCAACA	59.467	55.000	0.00	0.00	44.77	3.33
2349	3795	3.457903	GACGGCAACCAACGCGTTT	62.458	57.895	24.21	5.95	0.00	3.60
2488	3934	0.179067	TCCCCGTTCACACTTCACAC	60.179	55.000	0.00	0.00	0.00	3.82
2489	3935	0.105964	CTCCCCGTTCACACTTCACA	59.894	55.000	0.00	0.00	0.00	3.58
2490	3936	0.602905	CCTCCCCGTTCACACTTCAC	60.603	60.000	0.00	0.00	0.00	3.18
2491	3937	0.761323	TCCTCCCCGTTCACACTTCA	60.761	55.000	0.00	0.00	0.00	3.02
2492	3938	0.613777	ATCCTCCCCGTTCACACTTC	59.386	55.000	0.00	0.00	0.00	3.01
2493	3939	0.324943	CATCCTCCCCGTTCACACTT	59.675	55.000	0.00	0.00	0.00	3.16
2494	3940	1.553690	CCATCCTCCCCGTTCACACT	61.554	60.000	0.00	0.00	0.00	3.55
2910	4368	7.002250	TCATCCTTTGACAATAAAATGCCAA	57.998	32.000	0.00	0.00	0.00	4.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.