AutoCloner

Multiple sequence alignment - TraesCS1B01G179000

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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	TraesCS1B01G179000	chr1B	100.000	3110	0	0	1	3110	324600161	324603270	0.000000e+00	5744
1	TraesCS1B01G179000	chr1B	87.255	714	89	2	8	720	530782519	530781807	0.000000e+00	813
2	TraesCS1B01G179000	chr1A	95.089	2423	65	20	714	3110	291566135	291563741	0.000000e+00	3766
3	TraesCS1B01G179000	chr1D	97.781	1577	27	3	873	2442	224575364	224573789	0.000000e+00	2712
4	TraesCS1B01G179000	chr1D	90.972	720	64	1	1	719	383794827	383794108	0.000000e+00	968
5	TraesCS1B01G179000	chr1D	85.980	699	37	20	2424	3110	224573253	224572604	0.000000e+00	691
6	TraesCS1B01G179000	chr1D	92.000	175	2	4	714	878	224575752	224575580	5.190000e-58	235
7	TraesCS1B01G179000	chr5D	90.720	722	61	2	1	721	330293301	330292585	0.000000e+00	957
8	TraesCS1B01G179000	chr3A	90.556	720	65	3	4	722	470155950	470155233	0.000000e+00	950
9	TraesCS1B01G179000	chrUn	88.227	722	82	3	1	721	39510653	39511372	0.000000e+00	859
10	TraesCS1B01G179000	chrUn	88.227	722	82	3	1	721	287244459	287245178	0.000000e+00	859
11	TraesCS1B01G179000	chrUn	88.227	722	82	3	1	721	287256774	287257493	0.000000e+00	859
12	TraesCS1B01G179000	chrUn	88.227	722	82	3	1	721	333255236	333254517	0.000000e+00	859
13	TraesCS1B01G179000	chr3B	80.169	711	131	7	25	729	813592108	813591402	9.880000e-145	523

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	TraesCS1B01G179000	chr1B	324600161	324603270	3109	False	5744.000000	5744	100.000000	1	3110	1	chr1B.!!$F1	3109
1	TraesCS1B01G179000	chr1B	530781807	530782519	712	True	813.000000	813	87.255000	8	720	1	chr1B.!!$R1	712
2	TraesCS1B01G179000	chr1A	291563741	291566135	2394	True	3766.000000	3766	95.089000	714	3110	1	chr1A.!!$R1	2396
3	TraesCS1B01G179000	chr1D	224572604	224575752	3148	True	1212.666667	2712	91.920333	714	3110	3	chr1D.!!$R2	2396
4	TraesCS1B01G179000	chr1D	383794108	383794827	719	True	968.000000	968	90.972000	1	719	1	chr1D.!!$R1	718
5	TraesCS1B01G179000	chr5D	330292585	330293301	716	True	957.000000	957	90.720000	1	721	1	chr5D.!!$R1	720
6	TraesCS1B01G179000	chr3A	470155233	470155950	717	True	950.000000	950	90.556000	4	722	1	chr3A.!!$R1	718
7	TraesCS1B01G179000	chrUn	39510653	39511372	719	False	859.000000	859	88.227000	1	721	1	chrUn.!!$F1	720
8	TraesCS1B01G179000	chrUn	287244459	287245178	719	False	859.000000	859	88.227000	1	721	1	chrUn.!!$F2	720
9	TraesCS1B01G179000	chrUn	287256774	287257493	719	False	859.000000	859	88.227000	1	721	1	chrUn.!!$F3	720
10	TraesCS1B01G179000	chrUn	333254517	333255236	719	True	859.000000	859	88.227000	1	721	1	chrUn.!!$R1	720
11	TraesCS1B01G179000	chr3B	813591402	813592108	706	True	523.000000	523	80.169000	25	729	1	chr3B.!!$R1	704

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
474	478	0.034186	ATCTGAATTTGGGCGGCAGA	60.034	50.000	12.47	2.99	39.61	4.26	F
1596	1834	1.068741	GAGAACGATCCCAACCGCTAT	59.931	52.381	0.00	0.00	0.00	2.97	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2006	2247	0.751277	CTGTGGTGTTTGACCTGCCA	60.751	55.0	0.0	0.0	46.32	4.92	R
2742	3547	0.034670	GGCAAAGCTCATCCCTGACT	60.035	55.0	0.0	0.0	0.00	3.41	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
100	101	1.137086	CTTGGGAGTGTACCTGATCCG	59.863	57.143	0.00	0.00	32.30	4.18
120	121	3.174375	CGAAAGGCAAAAATGCTCTAGC	58.826	45.455	0.40	0.00	42.50	3.42
154	155	0.994247	ATGCAGTTCATGGACCCAGA	59.006	50.000	0.00	0.00	33.26	3.86
176	178	2.047061	TGTGTATACATGGGGAGGAGC	58.953	52.381	9.18	0.00	0.00	4.70
215	217	1.620515	TCAGTGGGATCCCCTAGAGA	58.379	55.000	28.58	15.31	45.70	3.10
242	244	7.096551	GGGTACAGTTAAACTTAACACGGATA	58.903	38.462	13.38	0.00	44.14	2.59
245	247	9.143631	GTACAGTTAAACTTAACACGGATACAT	57.856	33.333	13.38	0.00	44.14	2.29
247	249	7.658575	ACAGTTAAACTTAACACGGATACATGT	59.341	33.333	13.38	2.69	44.14	3.21
450	454	4.604114	GATTGCAAAGCCTTGGCC	57.396	55.556	1.71	0.00	32.76	5.36
474	478	0.034186	ATCTGAATTTGGGCGGCAGA	60.034	50.000	12.47	2.99	39.61	4.26
483	487	1.971167	GGGCGGCAGATGTTTGTCA	60.971	57.895	12.47	0.00	0.00	3.58
570	574	2.568623	ACGCCAACAGGAAGAAGAAT	57.431	45.000	0.00	0.00	0.00	2.40
798	802	6.696411	ACAAAATTCAAACCAAACTCTGACA	58.304	32.000	0.00	0.00	0.00	3.58
843	852	7.001099	TCAATCGGAAACTAACTAACCTCTT	57.999	36.000	0.00	0.00	0.00	2.85
1596	1834	1.068741	GAGAACGATCCCAACCGCTAT	59.931	52.381	0.00	0.00	0.00	2.97
1770	2008	1.939974	TCTACCACGCAGATTGCATC	58.060	50.000	1.69	0.00	45.36	3.91
1948	2189	2.041405	GGGAGGAGAGTGGGGAGG	60.041	72.222	0.00	0.00	0.00	4.30
1987	2228	5.909621	AAGGAGATTCAATGTGTCATTGG	57.090	39.130	18.26	4.80	0.00	3.16
1989	2230	3.698040	GGAGATTCAATGTGTCATTGGCT	59.302	43.478	18.26	13.99	0.00	4.75
2006	2247	1.815817	GCTTGGCCGTTTGGTGGATT	61.816	55.000	0.00	0.00	37.67	3.01
2145	2386	7.092891	TGTGATCAGTTGGAGGTATTTACATCT	60.093	37.037	0.00	0.00	37.20	2.90
2147	2388	8.328758	TGATCAGTTGGAGGTATTTACATCTTT	58.671	33.333	0.00	0.00	37.20	2.52
2148	2389	9.832445	GATCAGTTGGAGGTATTTACATCTTTA	57.168	33.333	2.81	0.00	37.20	1.85
2221	2467	8.946085	CCTGTTAATAACTCTTTGATTGTAGCA	58.054	33.333	4.67	0.00	0.00	3.49
2279	2525	5.979288	TGACTAGTGGAGAAAGAACTACC	57.021	43.478	0.00	0.00	0.00	3.18
2283	2529	4.559862	AGTGGAGAAAGAACTACCCATG	57.440	45.455	0.00	0.00	0.00	3.66
2376	2622	7.841956	AGATGCTATAGTACAAACTTGACTGT	58.158	34.615	0.84	0.00	37.15	3.55
2398	2644	6.798482	TGTTCACATCAATTTCAGGCATATC	58.202	36.000	0.00	0.00	0.00	1.63
2405	2651	7.175119	ACATCAATTTCAGGCATATCTCTGATG	59.825	37.037	0.00	0.00	41.26	3.07
2509	3309	8.142551	AGCTATTCGTATTAAACAGTAGGAAGG	58.857	37.037	0.00	0.00	30.95	3.46
2590	3390	6.206829	ACTTATAGAGGTTTGTTGGTTTGCTC	59.793	38.462	0.00	0.00	0.00	4.26
2598	3398	4.902443	TTGTTGGTTTGCTCGAAACATA	57.098	36.364	1.25	0.00	45.15	2.29
2690	3493	6.830838	GTGGATGATTTAGGAAGAGGAACAAT	59.169	38.462	0.00	0.00	0.00	2.71
2741	3546	1.146637	CTGATGCAGATCTTAGGCGC	58.853	55.000	0.00	0.00	32.44	6.53
2742	3547	0.465287	TGATGCAGATCTTAGGCGCA	59.535	50.000	10.83	7.09	36.95	6.09
2758	3563	0.392193	CGCAGTCAGGGATGAGCTTT	60.392	55.000	0.00	0.00	0.00	3.51
2774	3579	4.873810	TTGCCAGTGGTGCGCACT	62.874	61.111	36.84	17.75	31.88	4.40
2803	3608	4.168101	CCCTAGGCATCTAAGTTCCCATA	58.832	47.826	2.05	0.00	0.00	2.74
2881	3686	6.212955	TCTGGCCGTTTTCTCTTTTATTTTG	58.787	36.000	0.00	0.00	0.00	2.44
2882	3687	6.039941	TCTGGCCGTTTTCTCTTTTATTTTGA	59.960	34.615	0.00	0.00	0.00	2.69
2883	3688	5.980715	TGGCCGTTTTCTCTTTTATTTTGAC	59.019	36.000	0.00	0.00	0.00	3.18
2884	3689	6.183360	TGGCCGTTTTCTCTTTTATTTTGACT	60.183	34.615	0.00	0.00	0.00	3.41
2885	3690	7.013464	TGGCCGTTTTCTCTTTTATTTTGACTA	59.987	33.333	0.00	0.00	0.00	2.59
2886	3691	7.537649	GGCCGTTTTCTCTTTTATTTTGACTAG	59.462	37.037	0.00	0.00	0.00	2.57
2887	3692	8.287503	GCCGTTTTCTCTTTTATTTTGACTAGA	58.712	33.333	0.00	0.00	0.00	2.43
2969	3774	7.728083	TGCCCATATTTGGTAAGCACTTATTAT	59.272	33.333	1.26	0.00	41.91	1.28
3027	3832	4.701437	ATGGTGGGGCAGGGAGGT	62.701	66.667	0.00	0.00	0.00	3.85
3028	3833	2.798760	AATGGTGGGGCAGGGAGGTA	62.799	60.000	0.00	0.00	0.00	3.08
3036	3841	2.409570	GGGCAGGGAGGTAGTCTTTAT	58.590	52.381	0.00	0.00	0.00	1.40
3063	3868	6.555812	AAAACCGATAGAAAAACCAGAGAC	57.444	37.500	0.00	0.00	39.76	3.36

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	2.808919	TCGACAGATTGACTCCTTCCT	58.191	47.619	0.00	0.00	0.00	3.36
72	73	1.806542	GTACACTCCCAAGCACACATG	59.193	52.381	0.00	0.00	0.00	3.21
80	81	1.137086	CGGATCAGGTACACTCCCAAG	59.863	57.143	0.00	0.00	0.00	3.61
100	101	3.515630	GGCTAGAGCATTTTTGCCTTTC	58.484	45.455	3.54	0.00	44.36	2.62
120	121	0.839277	TGCATCATGTCCTACCTGGG	59.161	55.000	0.00	0.00	36.20	4.45
154	155	3.309296	CTCCTCCCCATGTATACACACT	58.691	50.000	7.96	0.00	37.54	3.55
176	178	4.478371	TGATGCAGGCGCCTCAGG	62.478	66.667	30.29	17.87	37.79	3.86
215	217	4.744631	CGTGTTAAGTTTAACTGTACCCGT	59.255	41.667	13.99	0.00	42.61	5.28
299	301	1.056660	GAGAAGAGAACCACACCCCA	58.943	55.000	0.00	0.00	0.00	4.96
343	346	4.100189	GCCTCAGCTTCCTCTACAGATTTA	59.900	45.833	0.00	0.00	35.50	1.40
450	454	2.350772	GCCGCCCAAATTCAGATTATCG	60.351	50.000	0.00	0.00	0.00	2.92
474	478	1.001378	GGAAAGCACGCTGACAAACAT	60.001	47.619	0.00	0.00	0.00	2.71
483	487	1.016130	CGATCACTGGAAAGCACGCT	61.016	55.000	0.00	0.00	0.00	5.07
642	646	3.637273	AGGTCGCCCAACAGGTCC	61.637	66.667	0.00	0.00	38.26	4.46
798	802	3.374220	TTCGATTACAACACGTCAGGT	57.626	42.857	0.00	0.00	0.00	4.00
843	852	2.909965	GGTGTTTCCTTGCGGCCA	60.910	61.111	2.24	0.00	0.00	5.36
910	1148	5.066764	GCTCTCAGTATCTCGTTTAGTCCTT	59.933	44.000	0.00	0.00	0.00	3.36
1770	2008	1.218316	GAGCTCCAACCAGGGTACG	59.782	63.158	0.87	0.00	38.24	3.67
1948	2189	1.809567	CTTTCCACCACCCTTGCAGC	61.810	60.000	0.00	0.00	0.00	5.25
1987	2228	1.815817	AATCCACCAAACGGCCAAGC	61.816	55.000	2.24	0.00	0.00	4.01
1989	2230	1.467678	CCAATCCACCAAACGGCCAA	61.468	55.000	2.24	0.00	0.00	4.52
2006	2247	0.751277	CTGTGGTGTTTGACCTGCCA	60.751	55.000	0.00	0.00	46.32	4.92
2127	2368	9.836076	GTGTTTAAAGATGTAAATACCTCCAAC	57.164	33.333	0.00	0.00	32.12	3.77
2145	2386	5.531659	TCCGATACAAAAGGCTGTGTTTAAA	59.468	36.000	9.15	0.00	0.00	1.52
2147	2388	4.643463	TCCGATACAAAAGGCTGTGTTTA	58.357	39.130	9.15	0.00	0.00	2.01
2148	2389	3.482436	TCCGATACAAAAGGCTGTGTTT	58.518	40.909	9.15	2.35	0.00	2.83
2221	2467	7.955918	AGTAAACAGGAATTGAAGCAATTTCT	58.044	30.769	7.67	7.67	46.86	2.52
2342	2588	6.485830	TGTACTATAGCATCTCCAGCTTTT	57.514	37.500	0.00	0.00	43.25	2.27
2376	2622	7.012989	CAGAGATATGCCTGAAATTGATGTGAA	59.987	37.037	0.00	0.00	32.37	3.18
2398	2644	2.951642	ACACAAAACCACCACATCAGAG	59.048	45.455	0.00	0.00	0.00	3.35
2405	2651	3.518634	ACAATGACACAAAACCACCAC	57.481	42.857	0.00	0.00	0.00	4.16
2509	3309	8.926715	TCAGTAGTGTATCATTGTGATAACAC	57.073	34.615	16.27	16.27	40.64	3.32
2550	3350	7.672239	ACCTCTATAAGTAGAAGATAGGCTTGG	59.328	40.741	0.00	0.00	36.54	3.61
2699	3502	3.501828	CGTGTTGTGATCATTCTGGGAAA	59.498	43.478	0.00	0.00	0.00	3.13
2700	3503	3.073678	CGTGTTGTGATCATTCTGGGAA	58.926	45.455	0.00	0.00	0.00	3.97
2701	3504	2.698803	CGTGTTGTGATCATTCTGGGA	58.301	47.619	0.00	0.00	0.00	4.37
2741	3546	1.093159	GCAAAGCTCATCCCTGACTG	58.907	55.000	0.00	0.00	0.00	3.51
2742	3547	0.034670	GGCAAAGCTCATCCCTGACT	60.035	55.000	0.00	0.00	0.00	3.41
2803	3608	4.574674	TTGATGATTAACTGGAGCCACT	57.425	40.909	0.00	0.00	0.00	4.00
3027	3832	9.947433	TTTCTATCGGTTTTTCCATAAAGACTA	57.053	29.630	0.00	0.00	31.91	2.59
3028	3833	8.857694	TTTCTATCGGTTTTTCCATAAAGACT	57.142	30.769	0.00	0.00	31.91	3.24
3036	3841	5.828859	TCTGGTTTTTCTATCGGTTTTTCCA	59.171	36.000	0.00	0.00	35.57	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.