AutoCloner

Multiple sequence alignment - TraesCS6B01G429900

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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	TraesCS6B01G429900	chr6B	100.000	5384	0	0	1	5384	697712426	697707043	0.000000e+00	9943.0
1	TraesCS6B01G429900	chr6B	90.273	2817	247	16	2052	4848	697674511	697671702	0.000000e+00	3659.0
2	TraesCS6B01G429900	chr6B	82.558	1634	213	46	13	1616	697676092	697674501	0.000000e+00	1373.0
3	TraesCS6B01G429900	chr6B	79.814	431	86	1	2774	3203	696854830	696855260	4.050000e-81	313.0
4	TraesCS6B01G429900	chr6B	87.607	234	25	2	5153	5382	697660778	697660545	8.890000e-68	268.0
5	TraesCS6B01G429900	chr6B	80.756	291	39	14	355	642	663650819	663651095	1.520000e-50	211.0
6	TraesCS6B01G429900	chr6D	96.990	5416	125	20	1	5384	458745733	458740324	0.000000e+00	9064.0
7	TraesCS6B01G429900	chr6D	88.832	3125	276	33	2052	5153	458716320	458713246	0.000000e+00	3770.0
8	TraesCS6B01G429900	chr6D	83.001	1606	208	39	32	1616	458717871	458716310	0.000000e+00	1393.0
9	TraesCS6B01G429900	chr6D	86.752	234	27	2	5153	5382	458691289	458691056	1.920000e-64	257.0
10	TraesCS6B01G429900	chr6A	95.743	5191	181	26	1	5162	604954806	604959985	0.000000e+00	8325.0
11	TraesCS6B01G429900	chr6A	95.531	179	5	3	5209	5384	604960272	604960450	3.170000e-72	283.0
12	TraesCS6B01G429900	chr6A	81.443	97	15	3	482	577	609830351	609830445	5.780000e-10	76.8
13	TraesCS6B01G429900	chr2B	73.810	504	89	30	69	550	276119483	276119001	5.580000e-35	159.0
14	TraesCS6B01G429900	chr2B	84.783	138	19	2	479	614	445248299	445248436	2.620000e-28	137.0
15	TraesCS6B01G429900	chr1D	74.413	426	61	30	174	572	438587916	438588320	7.270000e-29	139.0
16	TraesCS6B01G429900	chr1B	75.137	366	53	17	231	572	594494619	594494970	2.620000e-28	137.0
17	TraesCS6B01G429900	chr5A	74.238	361	67	19	208	554	458702129	458702477	1.570000e-25	128.0
18	TraesCS6B01G429900	chr5A	76.812	207	32	13	364	563	483537086	483536889	9.540000e-18	102.0
19	TraesCS6B01G429900	chr2D	84.884	86	7	5	470	554	630612901	630612821	1.240000e-11	82.4
20	TraesCS6B01G429900	chr3D	81.000	100	13	6	481	577	367913465	367913369	2.080000e-09	75.0

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	TraesCS6B01G429900	chr6B	697707043	697712426	5383	True	9943.0	9943	100.0000	1	5384	1	chr6B.!!$R2	5383
1	TraesCS6B01G429900	chr6B	697671702	697676092	4390	True	2516.0	3659	86.4155	13	4848	2	chr6B.!!$R3	4835
2	TraesCS6B01G429900	chr6D	458740324	458745733	5409	True	9064.0	9064	96.9900	1	5384	1	chr6D.!!$R2	5383
3	TraesCS6B01G429900	chr6D	458713246	458717871	4625	True	2581.5	3770	85.9165	32	5153	2	chr6D.!!$R3	5121
4	TraesCS6B01G429900	chr6A	604954806	604960450	5644	False	4304.0	8325	95.6370	1	5384	2	chr6A.!!$F2	5383

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
907	971	1.440618	TCCAGTTGGCCCAGTAGAAA	58.559	50.000	0.00	0.00	34.44	2.52	F
1212	1279	0.392461	CGGGATTCTTCCGGCTTTCA	60.392	55.000	0.00	0.00	43.63	2.69	F
2531	2615	2.999331	TCATACCCAGCTTTTAGGTGC	58.001	47.619	5.03	0.00	42.05	5.01	F
3359	3443	4.761975	AGGAACAATGCCTGCAAATATTG	58.238	39.130	12.36	12.36	36.77	1.90	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2813	2897	0.179127	AGTGTGCTGATCCGATCACG	60.179	55.000	7.00	5.44	35.06	4.35	R
2878	2962	0.957395	AACCAGTCATTGCTGCCTCG	60.957	55.000	0.00	0.00	35.28	4.63	R
3875	3959	3.317993	ACATAACTGTTGTCAAACCAGCC	59.682	43.478	2.69	0.00	35.25	4.85	R
5299	5659	0.534412	TTGCACAACCCCAAACTGTG	59.466	50.000	0.00	0.00	42.70	3.66	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
166	185	9.516546	TTCTAGTCTTTTCCTTTTTCCCTATTC	57.483	33.333	0.00	0.00	0.00	1.75
624	688	4.607778	CGCGCTGTGAATCTATCAATTGAG	60.608	45.833	14.54	1.16	40.50	3.02
632	696	7.708322	TGTGAATCTATCAATTGAGCTCACTAC	59.292	37.037	18.03	15.67	40.50	2.73
706	770	4.619760	CACTCGCACGTCACTTTATCTAAA	59.380	41.667	0.00	0.00	0.00	1.85
907	971	1.440618	TCCAGTTGGCCCAGTAGAAA	58.559	50.000	0.00	0.00	34.44	2.52
970	1035	1.651770	TCCCCTCTCCCTGTCTAATGT	59.348	52.381	0.00	0.00	0.00	2.71
1111	1176	0.676466	CCATGGTTGCCGCTTAGACA	60.676	55.000	2.57	0.00	0.00	3.41
1119	1184	2.108168	TGCCGCTTAGACAACTAGGAT	58.892	47.619	0.00	0.00	0.00	3.24
1212	1279	0.392461	CGGGATTCTTCCGGCTTTCA	60.392	55.000	0.00	0.00	43.63	2.69
1305	1372	8.872845	GTGCTTTGTTTGAAGGAATATATTTGG	58.127	33.333	0.00	0.00	0.00	3.28
1311	1378	8.783093	TGTTTGAAGGAATATATTTGGCTATCG	58.217	33.333	0.00	0.00	0.00	2.92
1550	1620	6.131264	TGCTATCAAACATTCCTTGATCCAT	58.869	36.000	1.51	0.00	41.50	3.41
1697	1768	8.480643	AACTCTTGAGATATGGTTACTTTTCG	57.519	34.615	4.49	0.00	0.00	3.46
1725	1796	8.691797	GGGCCAAATATATGAGTTAAGAACAAA	58.308	33.333	4.39	0.00	0.00	2.83
1769	1840	3.634568	TGGTGCTTGATTTGTTAACCG	57.365	42.857	2.48	0.00	0.00	4.44
1962	2034	7.879677	CCTTTCTTAATGCAAGGGAGAATTTTT	59.120	33.333	0.00	0.00	35.78	1.94
2531	2615	2.999331	TCATACCCAGCTTTTAGGTGC	58.001	47.619	5.03	0.00	42.05	5.01
2554	2638	7.916450	GTGCCGTATTAGTTGCCAATTATAAAA	59.084	33.333	0.00	0.00	0.00	1.52
2878	2962	9.521503	GAAATTCTTTCCCTAATGACAATAAGC	57.478	33.333	0.00	0.00	33.56	3.09
3120	3204	4.778213	TCAGATTCCCATTAACCTCAGG	57.222	45.455	0.00	0.00	0.00	3.86
3358	3442	6.736110	ATAGGAACAATGCCTGCAAATATT	57.264	33.333	0.00	0.00	36.96	1.28
3359	3443	4.761975	AGGAACAATGCCTGCAAATATTG	58.238	39.130	12.36	12.36	36.77	1.90
4000	4084	6.811253	TGGCCTACATGTAAGTTTTACAAG	57.189	37.500	3.32	4.57	0.00	3.16
4467	4557	7.708322	TGAACTTGATGCATCTTATAGTCAGAC	59.292	37.037	26.32	14.86	0.00	3.51
4507	4597	5.183140	GCTTAATTCTCCTGGTTTGCTACAA	59.817	40.000	0.00	0.00	0.00	2.41
4617	4708	8.495949	ACGTTTAGTCACTAAATTCTTGATGTG	58.504	33.333	13.18	0.00	38.07	3.21
4669	4760	0.902984	ACACCTGATCCACACGCCTA	60.903	55.000	0.00	0.00	0.00	3.93
4786	4902	6.552350	AGCATATGCAAGATATTTGTCCCTTT	59.448	34.615	28.62	0.00	45.16	3.11
4844	4961	4.036852	GTGATATTCTTTTAGGGGCAGCAC	59.963	45.833	0.00	0.00	0.00	4.40
4867	4984	4.499183	GAGGTCATACACTCAAAGTCTGG	58.501	47.826	0.00	0.00	33.95	3.86
4964	5083	7.814264	ATATTTTTCTGAGCGAAATGGATCT	57.186	32.000	0.00	0.00	41.04	2.75
5051	5170	1.575304	ACTTGGGATGGGCCATGTATT	59.425	47.619	26.77	0.00	38.95	1.89
5076	5195	5.047188	CCTTTGTTTTCAACATACACCCAC	58.953	41.667	0.00	0.00	41.79	4.61
5206	5331	6.099341	GCCTGTTTTAATTGGATGGTGTAAG	58.901	40.000	0.00	0.00	0.00	2.34
5295	5655	5.458041	AACTGATGAAATGAAACTGTGGG	57.542	39.130	0.00	0.00	0.00	4.61
5296	5656	4.473444	ACTGATGAAATGAAACTGTGGGT	58.527	39.130	0.00	0.00	0.00	4.51
5298	5658	6.068010	ACTGATGAAATGAAACTGTGGGTAA	58.932	36.000	0.00	0.00	0.00	2.85
5299	5659	6.016276	ACTGATGAAATGAAACTGTGGGTAAC	60.016	38.462	0.00	0.00	0.00	2.50
5356	5719	9.894783	TTAGAAATATCAAGCGCTACTAGTTAG	57.105	33.333	12.05	0.00	0.00	2.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
72	73	7.703058	AAGAGAAAAGAAAAACTGACAGGAA	57.297	32.000	7.51	0.00	0.00	3.36
624	688	7.869429	TGTAACTAACCAACTTAAGTAGTGAGC	59.131	37.037	17.45	8.84	37.12	4.26
907	971	5.048713	GTGCTAAGTAGTGTGGCTTCAATTT	60.049	40.000	0.00	0.00	0.00	1.82
970	1035	1.590610	GCAGTCTGGCTCGACTCTCA	61.591	60.000	1.14	0.00	42.10	3.27
1111	1176	4.078571	TGGATCAGTGGACCTATCCTAGTT	60.079	45.833	8.74	0.00	46.43	2.24
1119	1184	2.504920	CGCTGGATCAGTGGACCTA	58.495	57.895	0.00	0.00	38.21	3.08
1212	1279	4.588951	TGACCATCTATAACCTGCTTCGAT	59.411	41.667	0.00	0.00	0.00	3.59
1305	1372	4.360563	TGACGAGAATTTCCTTCGATAGC	58.639	43.478	13.14	3.17	38.98	2.97
1311	1378	5.924475	TCAAACTGACGAGAATTTCCTTC	57.076	39.130	0.00	0.00	0.00	3.46
1473	1543	4.592942	TGAGTGGATGGAAAATTCTCCTG	58.407	43.478	0.00	0.00	36.35	3.86
1697	1768	5.887754	TCTTAACTCATATATTTGGCCCCC	58.112	41.667	0.00	0.00	0.00	5.40
1769	1840	1.351350	AGCCGGATATTTTAGGAGGGC	59.649	52.381	5.05	0.00	39.56	5.19
1829	1900	8.716646	AAGCTACAAAAATAAATTGTATGGCC	57.283	30.769	0.00	0.00	41.13	5.36
1962	2034	3.574396	CCTCTCGCATGACCTAAGGATTA	59.426	47.826	0.00	0.00	0.00	1.75
2221	2299	7.510675	TTAACCCATAGAGGAAATCAACTCT	57.489	36.000	0.00	0.00	45.45	3.24
2270	2354	3.556633	CCTGTTGGCCATTGCATTTAACA	60.557	43.478	6.09	3.18	40.13	2.41
2271	2355	3.002102	CCTGTTGGCCATTGCATTTAAC	58.998	45.455	6.09	0.00	40.13	2.01
2349	2433	5.343307	AATTCCTTGCCGCATTAAATTCT	57.657	34.783	0.00	0.00	0.00	2.40
2350	2434	5.580297	TCAAATTCCTTGCCGCATTAAATTC	59.420	36.000	0.00	0.00	34.76	2.17
2531	2615	9.405587	CCATTTTATAATTGGCAACTAATACGG	57.594	33.333	0.00	0.00	37.61	4.02
2554	2638	5.104776	TGAAGCTCTGCACTTATTCTACCAT	60.105	40.000	0.00	0.00	0.00	3.55
2813	2897	0.179127	AGTGTGCTGATCCGATCACG	60.179	55.000	7.00	5.44	35.06	4.35
2878	2962	0.957395	AACCAGTCATTGCTGCCTCG	60.957	55.000	0.00	0.00	35.28	4.63
3120	3204	3.501445	GTGATCCAGATTAGAAGCATGGC	59.499	47.826	0.00	0.00	0.00	4.40
3358	3442	6.410388	GGGATTTAAGATATGAGAACCCACCA	60.410	42.308	0.00	0.00	34.43	4.17
3359	3443	6.004574	GGGATTTAAGATATGAGAACCCACC	58.995	44.000	0.00	0.00	34.43	4.61
3875	3959	3.317993	ACATAACTGTTGTCAAACCAGCC	59.682	43.478	2.69	0.00	35.25	4.85
4467	4557	8.336801	AGAATTAAGCTAGTACCAAAACAAGG	57.663	34.615	0.00	0.00	0.00	3.61
4617	4708	1.678101	GGAGGCAAGGACATATTGTGC	59.322	52.381	0.00	0.00	39.13	4.57
4844	4961	4.169508	CAGACTTTGAGTGTATGACCTCG	58.830	47.826	0.00	0.00	0.00	4.63
4867	4984	8.236586	TCATGCTAGATTGTGTTGTATTGTTTC	58.763	33.333	0.00	0.00	0.00	2.78
4978	5097	3.307512	TCGACGCGTTAAATATTGCATGT	59.692	39.130	15.53	0.00	0.00	3.21
5076	5195	2.558378	CCATACTGGACAGCTCACATG	58.442	52.381	0.00	0.00	40.96	3.21
5206	5331	2.570302	TGTACTAGGAGGGGTTTCAAGC	59.430	50.000	0.00	0.00	0.00	4.01
5295	5655	2.480587	GCACAACCCCAAACTGTGTTAC	60.481	50.000	3.63	0.00	41.99	2.50
5296	5656	1.751924	GCACAACCCCAAACTGTGTTA	59.248	47.619	3.63	0.00	41.99	2.41
5298	5658	0.613292	TGCACAACCCCAAACTGTGT	60.613	50.000	3.63	0.00	41.99	3.72
5299	5659	0.534412	TTGCACAACCCCAAACTGTG	59.466	50.000	0.00	0.00	42.70	3.66
5301	5661	2.211806	CATTTGCACAACCCCAAACTG	58.788	47.619	0.00	0.00	34.18	3.16
5302	5662	1.836802	ACATTTGCACAACCCCAAACT	59.163	42.857	0.00	0.00	34.18	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.