AutoCloner

Multiple sequence alignment - TraesCS3B01G153800

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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	TraesCS3B01G153800	chr3B	100.000	3560	0	0	1	3560	146184204	146180645	0.000000e+00	6575.0
1	TraesCS3B01G153800	chr3B	80.836	694	127	6	1084	1774	534965466	534964776	1.120000e-149	540.0
2	TraesCS3B01G153800	chr3B	78.544	261	52	4	1431	1689	729415073	729415331	6.110000e-38	169.0
3	TraesCS3B01G153800	chr3D	94.160	3082	103	38	1	3035	95247590	95244539	0.000000e+00	4623.0
4	TraesCS3B01G153800	chr3D	80.980	694	126	6	1084	1774	409021999	409021309	2.420000e-151	545.0
5	TraesCS3B01G153800	chr3D	90.361	249	19	4	3197	3441	276000125	275999878	4.430000e-84	322.0
6	TraesCS3B01G153800	chr3A	90.802	3044	157	51	4	2984	113343453	113340470	0.000000e+00	3956.0
7	TraesCS3B01G153800	chr3A	80.980	694	126	6	1084	1774	542202773	542203463	2.420000e-151	545.0
8	TraesCS3B01G153800	chr3A	87.903	248	26	4	3196	3441	691743509	691743264	4.500000e-74	289.0
9	TraesCS3B01G153800	chr3A	87.037	54	7	0	3063	3116	35669042	35668989	1.070000e-05	62.1
10	TraesCS3B01G153800	chr1A	82.403	699	112	10	1081	1774	521629150	521629842	1.830000e-167	599.0
11	TraesCS3B01G153800	chr1D	82.822	652	102	9	1128	1774	426587031	426587677	3.080000e-160	575.0
12	TraesCS3B01G153800	chr1B	81.583	695	120	8	1084	1774	576205534	576206224	5.160000e-158	568.0
13	TraesCS3B01G153800	chr6D	89.516	248	22	4	3197	3441	436237769	436238015	9.600000e-81	311.0
14	TraesCS3B01G153800	chr6D	100.000	37	0	0	3464	3500	11915177	11915141	6.380000e-08	69.4
15	TraesCS3B01G153800	chr7D	84.337	332	29	12	3197	3505	101080173	101080504	1.610000e-78	303.0
16	TraesCS3B01G153800	chr2D	90.351	228	18	3	3213	3436	557640292	557640065	2.690000e-76	296.0
17	TraesCS3B01G153800	chr2D	86.364	242	30	3	3197	3436	651065984	651065744	9.800000e-66	261.0
18	TraesCS3B01G153800	chrUn	86.290	248	30	4	3197	3441	51477341	51477587	2.110000e-67	267.0
19	TraesCS3B01G153800	chrUn	86.290	248	30	4	3197	3441	322554761	322555007	2.110000e-67	267.0
20	TraesCS3B01G153800	chr2B	85.484	248	32	4	3197	3441	133820876	133820630	4.560000e-64	255.0
21	TraesCS3B01G153800	chr7B	86.441	59	8	0	3078	3136	126178326	126178268	8.250000e-07	65.8
22	TraesCS3B01G153800	chr7B	92.683	41	3	0	3078	3118	126175455	126175495	3.840000e-05	60.2
23	TraesCS3B01G153800	chr7B	92.683	41	3	0	3078	3118	126175497	126175537	3.840000e-05	60.2
24	TraesCS3B01G153800	chr7B	92.683	41	3	0	3078	3118	126178368	126178328	3.840000e-05	60.2
25	TraesCS3B01G153800	chr7B	92.683	41	3	0	3078	3118	126221542	126221582	3.840000e-05	60.2
26	TraesCS3B01G153800	chr7B	92.683	41	3	0	3078	3118	126221584	126221624	3.840000e-05	60.2
27	TraesCS3B01G153800	chr7B	100.000	28	0	0	3078	3105	358499429	358499456	6.000000e-03	52.8
28	TraesCS3B01G153800	chr7A	87.234	47	6	0	3059	3105	339893014	339893060	2.000000e-03	54.7

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	TraesCS3B01G153800	chr3B	146180645	146184204	3559	True	6575	6575	100.000	1	3560	1	chr3B.!!$R1	3559
1	TraesCS3B01G153800	chr3B	534964776	534965466	690	True	540	540	80.836	1084	1774	1	chr3B.!!$R2	690
2	TraesCS3B01G153800	chr3D	95244539	95247590	3051	True	4623	4623	94.160	1	3035	1	chr3D.!!$R1	3034
3	TraesCS3B01G153800	chr3D	409021309	409021999	690	True	545	545	80.980	1084	1774	1	chr3D.!!$R3	690
4	TraesCS3B01G153800	chr3A	113340470	113343453	2983	True	3956	3956	90.802	4	2984	1	chr3A.!!$R2	2980
5	TraesCS3B01G153800	chr3A	542202773	542203463	690	False	545	545	80.980	1084	1774	1	chr3A.!!$F1	690
6	TraesCS3B01G153800	chr1A	521629150	521629842	692	False	599	599	82.403	1081	1774	1	chr1A.!!$F1	693
7	TraesCS3B01G153800	chr1D	426587031	426587677	646	False	575	575	82.822	1128	1774	1	chr1D.!!$F1	646
8	TraesCS3B01G153800	chr1B	576205534	576206224	690	False	568	568	81.583	1084	1774	1	chr1B.!!$F1	690

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
519	542	0.683412	TGGATCGGCCTCTCATCATG	59.317	55.000	0.00	0.00	37.63	3.07	F
520	543	0.683973	GGATCGGCCTCTCATCATGT	59.316	55.000	0.00	0.00	0.00	3.21	F
796	852	1.519455	CCTTTAGAGTCCAGCGCGG	60.519	63.158	8.83	11.37	0.00	6.46	F
1710	1786	1.679977	CCTACCGTTCCAGGACCGA	60.680	63.158	8.21	0.00	33.42	4.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1710	1786	0.390735	GGTACATGCCGACGAGGTTT	60.391	55.000	0.00	0.00	43.70	3.27	R
2001	2077	3.275832	TTGCTGATCGGTCGCGTCA	62.276	57.895	5.77	0.21	0.00	4.35	R
2169	2245	3.744719	CCGCCGTCCTCGAACAGA	61.745	66.667	0.00	0.00	39.71	3.41	R
3174	3293	0.034337	GGCCCGCCAATTCTCGTATA	59.966	55.000	0.00	0.00	35.81	1.47	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	3.038017	CAAGTGCAACGTGTGAGAAATG	58.962	45.455	0.00	0.00	45.86	2.32
115	119	8.515473	ACTAACGCATTTTTGGTTTCTATTTC	57.485	30.769	0.00	0.00	0.00	2.17
121	125	7.360017	CGCATTTTTGGTTTCTATTTCCTTTCC	60.360	37.037	0.00	0.00	0.00	3.13
129	133	6.258947	GGTTTCTATTTCCTTTCCAGATCTCG	59.741	42.308	0.00	0.00	0.00	4.04
178	182	0.750850	GGTGGCATCTAAGGACGCTA	59.249	55.000	0.00	0.00	30.74	4.26
214	219	8.050778	TCTTGACTAACACAAGAAATTGTTGT	57.949	30.769	2.45	2.45	46.68	3.32
404	415	7.356089	TCCGACTAAATAACAGTACCATCAT	57.644	36.000	0.00	0.00	0.00	2.45
471	485	3.659089	CTCGGAACCGACGGCCAAT	62.659	63.158	15.39	0.00	44.01	3.16
497	519	6.778834	AGCATCATAATCCACAAATGAACA	57.221	33.333	0.00	0.00	33.60	3.18
500	522	7.037438	GCATCATAATCCACAAATGAACAGTT	58.963	34.615	0.00	0.00	33.60	3.16
519	542	0.683412	TGGATCGGCCTCTCATCATG	59.317	55.000	0.00	0.00	37.63	3.07
520	543	0.683973	GGATCGGCCTCTCATCATGT	59.316	55.000	0.00	0.00	0.00	3.21
573	598	8.976471	CATATTCAGATACTCTAACTGTGCAAG	58.024	37.037	0.00	0.00	33.93	4.01
649	705	5.291293	ACTTATTTGCGCGTTAATTCACT	57.709	34.783	8.43	0.00	0.00	3.41
650	706	6.411630	ACTTATTTGCGCGTTAATTCACTA	57.588	33.333	8.43	0.00	0.00	2.74
651	707	7.011828	ACTTATTTGCGCGTTAATTCACTAT	57.988	32.000	8.43	0.00	0.00	2.12
781	837	7.977789	TTTTCTTTTTGAAACTCTTTGCCTT	57.022	28.000	0.00	0.00	43.55	4.35
782	838	7.977789	TTTCTTTTTGAAACTCTTTGCCTTT	57.022	28.000	0.00	0.00	39.50	3.11
791	847	4.278975	ACTCTTTGCCTTTAGAGTCCAG	57.721	45.455	0.00	0.00	46.06	3.86
795	851	2.167861	GCCTTTAGAGTCCAGCGCG	61.168	63.158	0.00	0.00	0.00	6.86
796	852	1.519455	CCTTTAGAGTCCAGCGCGG	60.519	63.158	8.83	11.37	0.00	6.46
829	892	2.806244	CCTCGGGGCATCTATTTAAACG	59.194	50.000	0.00	0.00	0.00	3.60
864	927	4.746466	TCCATTCTATTCTCTCCTCTCCC	58.254	47.826	0.00	0.00	0.00	4.30
880	943	4.963878	CCCCCATTCAGTTCTCCG	57.036	61.111	0.00	0.00	0.00	4.63
907	970	6.458232	TCTTTTGTCGAAGGGAAATTTTCA	57.542	33.333	11.09	0.00	0.00	2.69

Showing 1 to 25 of 326 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	4.799428	GCAGTCTTAACTCGGAGTTCATAC	59.201	45.833	25.51	19.72	39.51	2.39
115	119	2.763448	ACTCTTCCGAGATCTGGAAAGG	59.237	50.000	20.26	17.70	44.52	3.11
121	125	6.687081	ACTACTTAACTCTTCCGAGATCTG	57.313	41.667	0.00	0.00	39.74	2.90
129	133	4.020485	TCCTGGCAACTACTTAACTCTTCC	60.020	45.833	0.00	0.00	37.61	3.46
178	182	5.359576	TGTGTTAGTCAAGAAACTTTGGCAT	59.640	36.000	0.00	0.00	35.16	4.40
209	214	3.444388	GGGTCACCACTTAAACAACAACA	59.556	43.478	0.00	0.00	36.50	3.33
210	215	3.444388	TGGGTCACCACTTAAACAACAAC	59.556	43.478	0.00	0.00	43.37	3.32
211	216	3.698289	TGGGTCACCACTTAAACAACAA	58.302	40.909	0.00	0.00	43.37	2.83
212	217	3.367646	TGGGTCACCACTTAAACAACA	57.632	42.857	0.00	0.00	43.37	3.33
332	342	8.814931	TCATTTGACAATTGGATGGAAACTAAT	58.185	29.630	10.83	0.00	0.00	1.73
333	343	8.187913	TCATTTGACAATTGGATGGAAACTAA	57.812	30.769	10.83	0.00	0.00	2.24
374	384	9.590451	TGGTACTGTTATTTAGTCGGAAAATAG	57.410	33.333	0.00	0.00	32.10	1.73
391	401	6.711277	TCTTTTCTGCTATGATGGTACTGTT	58.289	36.000	0.00	0.00	0.00	3.16
404	415	6.040955	TCAGTTCAGAGTTCTCTTTTCTGCTA	59.959	38.462	0.00	0.00	38.52	3.49
471	485	9.571816	TGTTCATTTGTGGATTATGATGCTATA	57.428	29.630	0.00	0.00	0.00	1.31
497	519	0.755686	GATGAGAGGCCGATCCAACT	59.244	55.000	0.00	0.00	37.29	3.16
500	522	0.683412	CATGATGAGAGGCCGATCCA	59.317	55.000	0.00	0.00	37.29	3.41
519	542	3.753797	GCCTAGAGCTAATTTGGGCATAC	59.246	47.826	8.78	0.00	38.99	2.39
520	543	4.021102	GCCTAGAGCTAATTTGGGCATA	57.979	45.455	8.78	0.00	38.99	3.14
573	598	6.783892	TTTTGCATTGTAGAATTTGCCTTC	57.216	33.333	0.00	0.00	34.20	3.46
651	707	9.638239	GATTTTGCATTTCTTTACTCCATTGTA	57.362	29.630	0.00	0.00	0.00	2.41
759	815	8.527810	TCTAAAGGCAAAGAGTTTCAAAAAGAA	58.472	29.630	0.00	0.00	0.00	2.52
777	833	2.167861	CGCGCTGGACTCTAAAGGC	61.168	63.158	5.56	0.00	0.00	4.35
779	835	0.526524	CTCCGCGCTGGACTCTAAAG	60.527	60.000	15.44	2.79	43.74	1.85
781	837	3.064987	GCTCCGCGCTGGACTCTAA	62.065	63.158	15.44	0.00	43.74	2.10

Showing 1 to 25 of 301 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.