AutoCloner

Multiple sequence alignment - TraesCS1D01G307700

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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	TraesCS1D01G307700	chr1D	100.000	4025	0	0	1	4025	403949102	403945078	0.000000e+00	7433.0
1	TraesCS1D01G307700	chr1D	88.175	2723	274	23	747	3448	446708254	446705559	0.000000e+00	3201.0
2	TraesCS1D01G307700	chr1B	94.396	4015	177	17	1	3980	543469781	543465780	0.000000e+00	6124.0
3	TraesCS1D01G307700	chr1B	87.771	2723	278	27	747	3448	611523270	611525958	0.000000e+00	3133.0
4	TraesCS1D01G307700	chr1B	86.667	90	11	1	23	112	611521741	611521829	9.210000e-17	99.0
5	TraesCS1D01G307700	chr1B	93.846	65	3	1	1102	1166	543469515	543469452	3.310000e-16	97.1
6	TraesCS1D01G307700	chr1B	100.000	46	0	0	3980	4025	543464473	543464428	7.170000e-13	86.1
7	TraesCS1D01G307700	chr1A	96.078	3315	99	16	731	4025	499623905	499620602	0.000000e+00	5373.0
8	TraesCS1D01G307700	chr1A	88.037	2725	273	28	747	3448	542440251	542437557	0.000000e+00	3177.0
9	TraesCS1D01G307700	chr1A	97.945	584	11	1	149	732	499624648	499624066	0.000000e+00	1011.0
10	TraesCS1D01G307700	chr1A	98.013	151	3	0	1	151	499624825	499624675	3.090000e-66	263.0

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	TraesCS1D01G307700	chr1D	403945078	403949102	4024	True	7433.000000	7433	100.000000	1	4025	1	chr1D.!!$R1	4024
1	TraesCS1D01G307700	chr1D	446705559	446708254	2695	True	3201.000000	3201	88.175000	747	3448	1	chr1D.!!$R2	2701
2	TraesCS1D01G307700	chr1B	543464428	543469781	5353	True	2102.400000	6124	96.080667	1	4025	3	chr1B.!!$R1	4024
3	TraesCS1D01G307700	chr1B	611521741	611525958	4217	False	1616.000000	3133	87.219000	23	3448	2	chr1B.!!$F1	3425
4	TraesCS1D01G307700	chr1A	542437557	542440251	2694	True	3177.000000	3177	88.037000	747	3448	1	chr1A.!!$R1	2701
5	TraesCS1D01G307700	chr1A	499620602	499624825	4223	True	2215.666667	5373	97.345333	1	4025	3	chr1A.!!$R2	4024

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	Hairpin	End Stability	Orientation
374	405	2.689034	CCCCCTCCCTCTGTGACC	60.689	72.222	0.00	4.02	F
1797	2994	1.418334	ATGGCGAGGATTCTGTAGCT	58.582	50.000	0.00	3.32	F
2131	3328	2.267006	AGCGTGATGGAGCTGTGG	59.733	61.111	42.82	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1833	3030	0.642291	GCGTGTCTGTGTCATCATCG	59.358	55.0	0.00	0.0	3.84	R
2820	4017	0.032615	TTGGGGAGCAACTGTGGTTT	60.033	50.0	0.00	35.0	3.27	R
3856	5081	1.095600	CTGACGCTAGCCTACACAGA	58.904	55.0	9.66	0.0	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
145	146	6.421801	CCCATTTCAAACACAAATGAGACTTC	59.578	38.462	6.70	0.00	41.81	3.01
374	405	2.689034	CCCCCTCCCTCTGTGACC	60.689	72.222	0.00	0.00	0.00	4.02
611	1376	5.416271	TGGTGTCCTAGTAATTCTTCCAC	57.584	43.478	0.00	0.00	0.00	4.02
691	1710	4.516698	ACGTCTTGTTTAGTACTCGGAAGA	59.483	41.667	0.00	0.59	39.12	2.87
842	2033	4.154918	CAGGTGAGATTTTAGCTTGGTGTC	59.845	45.833	0.00	0.00	0.00	3.67
860	2051	4.278419	GGTGTCTTACTTTCATGCTGGTTT	59.722	41.667	0.00	0.00	0.00	3.27
1028	2222	3.149981	GGGCTAGGAATTTCATACCTGC	58.850	50.000	0.00	0.00	35.52	4.85
1686	2883	4.141251	ACTGTTCCTGGTGTTGAAATAGGT	60.141	41.667	0.00	0.00	0.00	3.08
1797	2994	1.418334	ATGGCGAGGATTCTGTAGCT	58.582	50.000	0.00	0.00	0.00	3.32
1833	3030	2.945668	GGCAGGTGGTTATGAGAATGAC	59.054	50.000	0.00	0.00	0.00	3.06
1887	3084	2.543635	TCAGGGGGTAACAGTAGGAAC	58.456	52.381	0.00	0.00	39.74	3.62
2131	3328	2.267006	AGCGTGATGGAGCTGTGG	59.733	61.111	0.00	0.00	42.82	4.17
2318	3515	2.293122	CGAGACCTCTAAGCTCCATGAG	59.707	54.545	0.00	0.00	0.00	2.90
2573	3770	2.359975	GGGTCTTCGCTGTTGGGG	60.360	66.667	0.00	0.00	0.00	4.96
2959	4156	7.822822	AGTTAACTTATGACTATGGTGTGGTTC	59.177	37.037	1.12	0.00	0.00	3.62
2977	4174	2.262915	GAGCTGGGACCAGTCGTG	59.737	66.667	18.86	0.00	45.24	4.35
3313	4527	3.623960	TGTAATTACTTGGCACCGCATAC	59.376	43.478	16.33	0.00	0.00	2.39
3314	4528	2.411628	ATTACTTGGCACCGCATACA	57.588	45.000	0.00	0.00	0.00	2.29
3333	4548	7.011669	CGCATACATATGATGATGATAGGCAAA	59.988	37.037	10.38	0.00	35.75	3.68
3334	4549	8.680001	GCATACATATGATGATGATAGGCAAAA	58.320	33.333	10.38	0.00	35.75	2.44
3336	4551	7.154435	ACATATGATGATGATAGGCAAAAGC	57.846	36.000	10.38	0.00	0.00	3.51
3337	4552	6.717997	ACATATGATGATGATAGGCAAAAGCA	59.282	34.615	10.38	0.00	0.00	3.91
3370	4586	3.762288	AGTCTTGAAATGCTGCACATCAT	59.238	39.130	16.81	3.21	38.34	2.45
3413	4635	6.428385	AAGCTGCATCTGTGTTTATACTTC	57.572	37.500	1.02	0.00	0.00	3.01
3420	4642	8.040727	TGCATCTGTGTTTATACTTCATACAGT	58.959	33.333	0.00	0.00	36.40	3.55
3441	4663	4.876679	AGTATAAGAAAGGCTTCGCTTTCC	59.123	41.667	17.03	8.38	39.60	3.13
3464	4686	5.390567	CCGCGTCTCAAAAGTATTTAAAGCT	60.391	40.000	4.92	0.00	37.28	3.74
3465	4687	6.183360	CCGCGTCTCAAAAGTATTTAAAGCTA	60.183	38.462	4.92	0.00	37.28	3.32
3466	4688	6.677411	CGCGTCTCAAAAGTATTTAAAGCTAC	59.323	38.462	0.00	0.00	37.28	3.58
3467	4689	7.411588	CGCGTCTCAAAAGTATTTAAAGCTACT	60.412	37.037	0.00	0.00	37.28	2.57
3468	4690	7.688578	GCGTCTCAAAAGTATTTAAAGCTACTG	59.311	37.037	2.92	1.78	37.28	2.74
3638	4860	8.783660	ACCTAGATTCTACCAATGTCAGATTA	57.216	34.615	0.00	0.00	0.00	1.75
3640	4862	8.865090	CCTAGATTCTACCAATGTCAGATTAGT	58.135	37.037	0.00	0.00	0.00	2.24
3670	4892	5.404667	GGAAGATGGTTAATAATCGGTCGTC	59.595	44.000	0.00	0.00	0.00	4.20
3811	5036	0.874390	GTGGATGCGTGTGTTGATGT	59.126	50.000	0.00	0.00	0.00	3.06
3814	5039	3.126858	GTGGATGCGTGTGTTGATGTATT	59.873	43.478	0.00	0.00	0.00	1.89
3856	5081	1.614317	CCTTCTCCTTGCCATCCGTTT	60.614	52.381	0.00	0.00	0.00	3.60
3918	5144	0.390860	AGCTGCGACTTGTCAAGACT	59.609	50.000	19.53	0.00	0.00	3.24

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	0.630673	AGCATGGGTTGATGGGCTTA	59.369	50.000	0.00	0.00	0.00	3.09
145	146	7.307493	TGATCCTACTTCATCAATGAAAACG	57.693	36.000	6.85	0.00	45.26	3.60
374	405	1.656652	ACTCTTTCCATCGATTGCCG	58.343	50.000	0.00	0.00	40.25	5.69
413	444	6.127168	CCATGCAGATTAATATTGCCATCCAT	60.127	38.462	17.22	5.60	37.03	3.41
691	1710	8.186821	GCAGTTATCAACTAGATGAAGCATTTT	58.813	33.333	6.80	0.00	40.46	1.82
842	2033	6.251376	GCGATTAAAACCAGCATGAAAGTAAG	59.749	38.462	0.00	0.00	39.69	2.34
860	2051	6.247727	TGAAAAAGTACTGCATGCGATTAA	57.752	33.333	14.09	0.00	0.00	1.40
1256	2450	1.476488	GGGTAACATCAATGGGCACAC	59.524	52.381	0.00	0.00	39.74	3.82
1686	2883	8.443176	AGCTCCATCCTGAAATAGAAAATATCA	58.557	33.333	0.00	0.00	0.00	2.15
1797	2994	2.297880	ACCTGCCGCGACAATACATATA	59.702	45.455	8.23	0.00	0.00	0.86
1833	3030	0.642291	GCGTGTCTGTGTCATCATCG	59.358	55.000	0.00	0.00	0.00	3.84
1887	3084	1.142748	GTCATGCCTCTCCTCGGTG	59.857	63.158	0.00	0.00	0.00	4.94
2129	3326	0.824109	CTGCGTCCTCTTCCATACCA	59.176	55.000	0.00	0.00	0.00	3.25
2131	3328	0.872021	CGCTGCGTCCTCTTCCATAC	60.872	60.000	14.93	0.00	0.00	2.39
2573	3770	2.384203	GCACCAGCACGAATAGGAC	58.616	57.895	0.00	0.00	41.58	3.85
2634	3831	9.342308	TCATCTTCACTATCATCCAAATTAACC	57.658	33.333	0.00	0.00	0.00	2.85
2820	4017	0.032615	TTGGGGAGCAACTGTGGTTT	60.033	50.000	0.00	0.00	35.00	3.27
3313	4527	7.027760	GTGCTTTTGCCTATCATCATCATATG	58.972	38.462	0.00	0.00	46.87	1.78
3314	4528	6.717997	TGTGCTTTTGCCTATCATCATCATAT	59.282	34.615	0.00	0.00	46.87	1.78
3333	4548	3.070159	TCAAGACTACAAGAGCTGTGCTT	59.930	43.478	0.00	0.00	39.88	3.91
3334	4549	2.630098	TCAAGACTACAAGAGCTGTGCT	59.370	45.455	0.00	0.00	43.88	4.40
3336	4551	5.616424	GCATTTCAAGACTACAAGAGCTGTG	60.616	44.000	0.00	0.00	39.20	3.66
3337	4552	4.453819	GCATTTCAAGACTACAAGAGCTGT	59.546	41.667	0.00	0.00	42.47	4.40
3441	4663	5.618561	AGCTTTAAATACTTTTGAGACGCG	58.381	37.500	3.53	3.53	0.00	6.01
3495	4717	6.038271	GGTATATGAACCCACAAGTAAAGCAG	59.962	42.308	0.00	0.00	33.02	4.24
3496	4718	5.883673	GGTATATGAACCCACAAGTAAAGCA	59.116	40.000	0.00	0.00	33.02	3.91
3570	4792	1.895798	TGAGCAGACAAGTAGTGAGGG	59.104	52.381	0.00	0.00	0.00	4.30
3571	4793	2.353208	GGTGAGCAGACAAGTAGTGAGG	60.353	54.545	0.00	0.00	0.00	3.86
3638	4860	6.652205	TTATTAACCATCTTCCCAGGAACT	57.348	37.500	0.00	0.00	43.88	3.01
3640	4862	6.296026	CGATTATTAACCATCTTCCCAGGAA	58.704	40.000	0.00	0.00	0.00	3.36
3670	4892	2.724977	TACTGTCTTCGCAGTTCCAG	57.275	50.000	4.01	0.00	46.45	3.86
3705	4927	2.170397	TGACACGACATGGGCATTCTAT	59.830	45.455	0.00	0.00	0.00	1.98
3772	4997	4.380867	CCACCAAGTATCTGAACAAATGGC	60.381	45.833	0.00	0.00	0.00	4.40
3811	5036	5.620738	AGACAGATTAGCAGCAGGAAATA	57.379	39.130	0.00	0.00	0.00	1.40
3814	5039	3.369892	GGAAGACAGATTAGCAGCAGGAA	60.370	47.826	0.00	0.00	0.00	3.36
3856	5081	1.095600	CTGACGCTAGCCTACACAGA	58.904	55.000	9.66	0.00	0.00	3.41
3918	5144	2.292016	CCACATGTTTTTACAGCACCGA	59.708	45.455	0.00	0.00	0.00	4.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.