AutoCloner

Multiple sequence alignment - TraesCS3B01G158600

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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	TraesCS3B01G158600	chr3B	100.000	7815	0	0	1	7815	153965221	153957407	0.000000e+00	14432
1	TraesCS3B01G158600	chr3B	93.985	133	7	1	4774	4906	153960316	153960185	4.780000e-47	200
2	TraesCS3B01G158600	chr3B	93.985	133	7	1	4906	5037	153960448	153960316	4.780000e-47	200
3	TraesCS3B01G158600	chr3D	95.242	4645	144	29	1	4604	103361660	103357052	0.000000e+00	7282
4	TraesCS3B01G158600	chr3D	91.664	3251	162	60	4608	7815	103357015	103353831	0.000000e+00	4401
5	TraesCS3B01G158600	chr3D	95.489	133	5	1	4774	4906	103356717	103356586	2.210000e-50	211
6	TraesCS3B01G158600	chr3D	95.489	133	5	1	4906	5037	103356849	103356717	2.210000e-50	211
7	TraesCS3B01G158600	chr3A	92.057	1322	87	15	2301	3615	552782689	552783999	0.000000e+00	1844
8	TraesCS3B01G158600	chr3A	89.156	1457	113	21	708	2122	552781126	552782579	0.000000e+00	1773
9	TraesCS3B01G158600	chr3A	86.846	1452	112	45	4914	6302	552785633	552787068	0.000000e+00	1550
10	TraesCS3B01G158600	chr3A	86.028	866	71	25	3888	4712	552784117	552784973	0.000000e+00	883
11	TraesCS3B01G158600	chr3A	83.388	608	51	21	6302	6864	552787107	552787709	1.160000e-142	518
12	TraesCS3B01G158600	chr3A	81.281	203	20	5	7143	7327	552787857	552788059	1.760000e-31	148
13	TraesCS3B01G158600	chr3A	82.857	140	14	6	7661	7792	552788211	552788348	4.950000e-22	117
14	TraesCS3B01G158600	chr4A	76.074	326	74	4	2867	3190	535430654	535430331	4.850000e-37	167

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	TraesCS3B01G158600	chr3B	153957407	153965221	7814	True	14432.000000	14432	100.000000	1	7815	1	chr3B.!!$R1	7814
1	TraesCS3B01G158600	chr3D	103353831	103361660	7829	True	3026.250000	7282	94.471000	1	7815	4	chr3D.!!$R1	7814
2	TraesCS3B01G158600	chr3A	552781126	552788348	7222	False	976.142857	1844	85.944714	708	7792	7	chr3A.!!$F1	7084

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	Hairpin	End Stability	Orientation
944	976	0.105709	CCCCTCTCCCTCTTCCTCTC	60.106	65.000	0.00	0.00	3.20	F
2287	2372	0.036306	TCGGGCAGAAGTCCCTTTTC	59.964	55.000	0.00	41.69	2.29	F
3045	3132	1.911057	AAAGGCACCCTTTGACTAGC	58.089	50.000	8.37	46.34	3.42	F
4553	4671	1.705186	ACCTGCAACCAGATAACCACT	59.295	47.619	0.00	41.77	4.00	F
6034	6684	0.326264	AGAAAGATGACAAGGGCGCT	59.674	50.000	7.64	0.00	5.92	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2749	2836	0.967380	GCACTAAGCACCCCTGCATT	60.967	55.000	0.00	46.97	3.56	R
3836	3933	2.233922	GGAAATGGTGACTCTCGGAGAA	59.766	50.000	9.32	34.09	2.87	R
4860	5100	1.003580	TGAAGAAGATCCCAGTGTGGC	59.996	52.381	0.00	35.79	5.01	R
6544	7266	0.104672	TGGAAGGGAAGACTGGGACA	60.105	55.000	0.00	0.00	4.02	R
7385	8222	0.044702	AGATCCAGATGACCCACCCA	59.955	55.000	0.00	0.00	4.51	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
95	96	2.355756	ACACGCAATATGCTGGAATGAC	59.644	45.455	0.43	0.00	42.25	3.06
96	97	1.949525	ACGCAATATGCTGGAATGACC	59.050	47.619	0.43	0.00	42.25	4.02
178	179	6.100279	TGTGGCTAGAGATCATAAAGGAATGT	59.900	38.462	0.00	0.00	0.00	2.71
209	210	1.621107	TCGTGCGTTTCCGTCTAATC	58.379	50.000	0.00	0.00	36.15	1.75
217	218	4.259850	GCGTTTCCGTCTAATCTGTTCATC	60.260	45.833	0.00	0.00	36.15	2.92
220	221	5.661056	TTCCGTCTAATCTGTTCATCTGT	57.339	39.130	0.00	0.00	0.00	3.41
224	231	4.672862	CGTCTAATCTGTTCATCTGTAGCG	59.327	45.833	0.00	0.00	0.00	4.26
281	288	7.043565	GGCCATGCATAATCCTATTATTTTGG	58.956	38.462	0.00	0.00	0.00	3.28
341	348	6.377429	TGATGTTTTAGACAGGTCGATACTCT	59.623	38.462	0.00	0.00	42.62	3.24
357	364	9.522804	GTCGATACTCTTTGAGTTGAAGATAAT	57.477	33.333	5.52	0.00	40.28	1.28
362	369	8.023050	ACTCTTTGAGTTGAAGATAATCGTTG	57.977	34.615	0.00	0.00	40.28	4.10
425	432	6.098695	ACATTAATTTGGATGCCAACATAGCT	59.901	34.615	0.00	0.00	43.82	3.32
483	490	2.158726	TCGGATGGGTTATTGGTTAGGC	60.159	50.000	0.00	0.00	0.00	3.93
494	501	4.568152	ATTGGTTAGGCGACAATTATGC	57.432	40.909	0.00	0.00	31.21	3.14
505	512	5.291614	GGCGACAATTATGCAACAATGATTT	59.708	36.000	0.00	0.00	0.00	2.17
508	515	8.379161	GCGACAATTATGCAACAATGATTTTTA	58.621	29.630	0.00	0.00	0.00	1.52
509	516	9.674208	CGACAATTATGCAACAATGATTTTTAC	57.326	29.630	0.00	0.00	0.00	2.01
511	518	9.723601	ACAATTATGCAACAATGATTTTTACCT	57.276	25.926	0.00	0.00	0.00	3.08
607	616	8.907222	ATGAAGAAAATAACCAACATTGCTTT	57.093	26.923	0.00	0.00	0.00	3.51
645	654	4.142687	CCATTGTCGACAAATTGACCTACC	60.143	45.833	32.69	0.00	38.35	3.18
646	655	3.755112	TGTCGACAAATTGACCTACCA	57.245	42.857	17.62	0.00	38.35	3.25
654	663	6.293955	CGACAAATTGACCTACCAATTGACTT	60.294	38.462	7.12	0.00	43.61	3.01
658	667	8.550376	CAAATTGACCTACCAATTGACTTTTTG	58.450	33.333	7.12	1.56	43.61	2.44
667	676	7.388460	ACCAATTGACTTTTTGCATGAAAAA	57.612	28.000	7.56	7.56	40.52	1.94
672	681	9.724839	AATTGACTTTTTGCATGAAAAATCAAG	57.275	25.926	23.08	16.18	41.62	3.02

Showing 1 to 25 of 264 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
22	23	1.245732	AACTCGCCTAGTCAACGACT	58.754	50.000	1.75	1.75	45.54	4.18
95	96	3.363378	GCTCGCATCGACATTAATCTTGG	60.363	47.826	0.00	0.00	0.00	3.61
96	97	3.492383	AGCTCGCATCGACATTAATCTTG	59.508	43.478	0.00	0.00	0.00	3.02
209	210	4.489810	AGAGTTTCGCTACAGATGAACAG	58.510	43.478	0.00	0.00	0.00	3.16
217	218	3.060895	CCGCTAAAAGAGTTTCGCTACAG	59.939	47.826	0.00	0.00	34.19	2.74
220	221	2.028748	ACCCGCTAAAAGAGTTTCGCTA	60.029	45.455	0.00	0.00	34.19	4.26
224	231	6.985059	ACATATAGACCCGCTAAAAGAGTTTC	59.015	38.462	0.00	0.00	31.66	2.78
341	348	5.414454	CCCCAACGATTATCTTCAACTCAAA	59.586	40.000	0.00	0.00	0.00	2.69
357	364	2.434331	CTGAAAGGCCCCCAACGA	59.566	61.111	0.00	0.00	0.00	3.85
362	369	1.341976	TGAATAAGCTGAAAGGCCCCC	60.342	52.381	0.00	0.00	0.00	5.40
425	432	4.703379	AAATTTTGCAATCTCCCCAACA	57.297	36.364	0.00	0.00	0.00	3.33
430	437	6.616774	TTGAACAAAATTTTGCAATCTCCC	57.383	33.333	26.94	10.33	41.79	4.30
431	438	7.696755	AGTTTGAACAAAATTTTGCAATCTCC	58.303	30.769	26.94	12.16	41.79	3.71
483	490	9.674208	GTAAAAATCATTGTTGCATAATTGTCG	57.326	29.630	0.00	0.00	0.00	4.35
583	592	9.474920	CTAAAGCAATGTTGGTTATTTTCTTCA	57.525	29.630	10.22	0.00	46.98	3.02
607	616	5.416639	TCGACAATGGTTAGTTAGAGTGCTA	59.583	40.000	0.00	0.00	0.00	3.49
617	626	5.048991	GGTCAATTTGTCGACAATGGTTAGT	60.049	40.000	30.10	12.59	35.55	2.24
645	654	9.504710	TTGATTTTTCATGCAAAAAGTCAATTG	57.495	25.926	21.27	0.00	45.20	2.32
646	655	9.724839	CTTGATTTTTCATGCAAAAAGTCAATT	57.275	25.926	23.51	2.14	45.54	2.32
658	667	9.537192	TGGATTTATGATCTTGATTTTTCATGC	57.463	29.630	0.00	0.00	31.59	4.06
667	676	7.723172	GGAGGAGTTTGGATTTATGATCTTGAT	59.277	37.037	0.00	0.00	0.00	2.57
672	681	9.660180	GTATAGGAGGAGTTTGGATTTATGATC	57.340	37.037	0.00	0.00	0.00	2.92
692	701	5.183522	TGTTTTTAAAGGTTGGCCGTATAGG	59.816	40.000	0.00	0.00	44.97	2.57
712	721	9.515226	AGATTGTGTATTTACTGGTATGTGTTT	57.485	29.630	0.00	0.00	0.00	2.83
713	722	9.515226	AAGATTGTGTATTTACTGGTATGTGTT	57.485	29.630	0.00	0.00	0.00	3.32

Showing 1 to 25 of 231 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.