AutoCloner

Multiple sequence alignment - TraesCS5A01G134700

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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	TraesCS5A01G134700	chr5A	100.000	4358	0	0	1	4358	304541612	304537255	0.000000e+00	8048
1	TraesCS5A01G134700	chr5A	82.822	163	25	2	4198	4358	531895856	531896017	4.540000e-30	143
2	TraesCS5A01G134700	chr5B	96.083	4366	118	17	1	4358	250236805	250232485	0.000000e+00	7066
3	TraesCS5A01G134700	chr5D	96.968	4057	93	8	306	4358	222737271	222741301	0.000000e+00	6783
4	TraesCS5A01G134700	chr5D	95.406	283	13	0	1	283	222736993	222737275	6.650000e-123	451
5	TraesCS5A01G134700	chr3D	79.278	748	122	30	2388	3120	581114580	581113851	3.920000e-135	492
6	TraesCS5A01G134700	chr3D	92.667	150	11	0	1019	1168	581116131	581115982	2.640000e-52	217
7	TraesCS5A01G134700	chr3A	78.961	751	128	28	2388	3120	716758250	716758988	6.550000e-133	484
8	TraesCS5A01G134700	chr3A	91.195	159	14	0	1010	1168	716756679	716756837	2.640000e-52	217
9	TraesCS5A01G134700	chr3B	78.429	751	132	28	2388	3120	777580272	777581010	3.070000e-126	462
10	TraesCS5A01G134700	chr3B	90.566	159	15	0	1010	1168	777578686	777578844	1.230000e-50	211
11	TraesCS5A01G134700	chr7D	87.681	138	11	5	4198	4330	119564313	119564449	5.840000e-34	156
12	TraesCS5A01G134700	chr7A	87.931	116	13	1	4244	4358	540869214	540869099	7.600000e-28	135
13	TraesCS5A01G134700	chr7A	80.435	184	27	9	4181	4358	559196523	559196343	9.830000e-27	132
14	TraesCS5A01G134700	chr6B	84.783	138	17	4	4223	4358	22434125	22434260	7.600000e-28	135
15	TraesCS5A01G134700	chr6B	84.783	138	16	4	4198	4330	56969398	56969535	2.730000e-27	134
16	TraesCS5A01G134700	chr2B	82.857	140	22	2	4220	4358	637872926	637873064	1.650000e-24	124

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	TraesCS5A01G134700	chr5A	304537255	304541612	4357	True	8048.0	8048	100.0000	1	4358	1	chr5A.!!$R1	4357
1	TraesCS5A01G134700	chr5B	250232485	250236805	4320	True	7066.0	7066	96.0830	1	4358	1	chr5B.!!$R1	4357
2	TraesCS5A01G134700	chr5D	222736993	222741301	4308	False	3617.0	6783	96.1870	1	4358	2	chr5D.!!$F1	4357
3	TraesCS5A01G134700	chr3D	581113851	581116131	2280	True	354.5	492	85.9725	1019	3120	2	chr3D.!!$R1	2101
4	TraesCS5A01G134700	chr3A	716756679	716758988	2309	False	350.5	484	85.0780	1010	3120	2	chr3A.!!$F1	2110
5	TraesCS5A01G134700	chr3B	777578686	777581010	2324	False	336.5	462	84.4975	1010	3120	2	chr3B.!!$F1	2110

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
746	748	0.478507	GAGAGAGAGGGAGAGAGGGG	59.521	65.0	0.0	0.0	0.0	4.79	F
2133	2642	0.105593	CACATCCATCTCCACCTCCG	59.894	60.0	0.0	0.0	0.0	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2220	2729	0.744057	TACCATGACATGCTGCACGG	60.744	55.000	3.57	2.6	0.0	4.94	R
3967	4788	1.336795	GGACGGAAAAATTGCCACAGG	60.337	52.381	0.00	0.0	0.0	4.00	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
49	50	0.668535	GAAAGGTTGAGCACACCCAC	59.331	55.000	0.00	0.00	30.66	4.61
237	238	2.576191	CAGATGACCACCTTTTCCCCTA	59.424	50.000	0.00	0.00	0.00	3.53
242	243	3.464080	TGACCACCTTTTCCCCTAAAGAA	59.536	43.478	0.00	0.00	37.31	2.52
296	297	8.357402	GTTGTAAATACATGTGAAAAAGGGTCT	58.643	33.333	9.11	0.00	35.89	3.85
373	375	0.897621	CCAAGCCCACCTCAAAATCC	59.102	55.000	0.00	0.00	0.00	3.01
405	407	6.386897	CGAGATCTATCGAATCAACCAATG	57.613	41.667	0.00	0.00	45.56	2.82
463	465	2.976271	ACGAAAACCTAACGTGCGT	58.024	47.368	0.00	0.00	38.79	5.24
498	500	0.535335	CCGGCAGTACCACTACACAT	59.465	55.000	0.00	0.00	39.03	3.21
530	532	3.239712	CACGTACGCATACACATACACAG	59.760	47.826	16.72	0.00	0.00	3.66
734	736	5.103728	AGAGAGAGAGAGAGAGAGAGAGAGA	60.104	48.000	0.00	0.00	0.00	3.10
735	737	5.139727	AGAGAGAGAGAGAGAGAGAGAGAG	58.860	50.000	0.00	0.00	0.00	3.20
736	738	4.222336	AGAGAGAGAGAGAGAGAGAGAGG	58.778	52.174	0.00	0.00	0.00	3.69
737	739	3.312890	AGAGAGAGAGAGAGAGAGAGGG	58.687	54.545	0.00	0.00	0.00	4.30
738	740	3.051803	AGAGAGAGAGAGAGAGAGAGGGA	60.052	52.174	0.00	0.00	0.00	4.20
739	741	3.312890	AGAGAGAGAGAGAGAGAGGGAG	58.687	54.545	0.00	0.00	0.00	4.30
740	742	3.051803	AGAGAGAGAGAGAGAGAGGGAGA	60.052	52.174	0.00	0.00	0.00	3.71
741	743	3.312890	AGAGAGAGAGAGAGAGGGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
742	744	3.051803	AGAGAGAGAGAGAGAGGGAGAGA	60.052	52.174	0.00	0.00	0.00	3.10
743	745	3.312890	AGAGAGAGAGAGAGGGAGAGAG	58.687	54.545	0.00	0.00	0.00	3.20
744	746	2.370189	GAGAGAGAGAGAGGGAGAGAGG	59.630	59.091	0.00	0.00	0.00	3.69
745	747	1.421646	GAGAGAGAGAGGGAGAGAGGG	59.578	61.905	0.00	0.00	0.00	4.30
746	748	0.478507	GAGAGAGAGGGAGAGAGGGG	59.521	65.000	0.00	0.00	0.00	4.79
747	749	0.998945	AGAGAGAGGGAGAGAGGGGG	60.999	65.000	0.00	0.00	0.00	5.40
748	750	0.996762	GAGAGAGGGAGAGAGGGGGA	60.997	65.000	0.00	0.00	0.00	4.81
749	751	0.998945	AGAGAGGGAGAGAGGGGGAG	60.999	65.000	0.00	0.00	0.00	4.30
750	752	2.018086	AGAGGGAGAGAGGGGGAGG	61.018	68.421	0.00	0.00	0.00	4.30
1494	1622	2.736995	CGCTCCTTTGGCGTCGAA	60.737	61.111	0.00	0.00	46.37	3.71
1556	1684	4.332543	TCATTCGAATTTCCATGTCTTCCG	59.667	41.667	8.21	0.00	0.00	4.30
2133	2642	0.105593	CACATCCATCTCCACCTCCG	59.894	60.000	0.00	0.00	0.00	4.63
2191	2700	1.517832	GGACACTGATCCAGTCCCG	59.482	63.158	14.25	0.45	43.43	5.14
2220	2729	4.608890	CGTCATTTCCAACAAAATTGCTGC	60.609	41.667	0.00	0.00	0.00	5.25
2949	3770	3.259374	CAGATATGGTATCCGTGCTCCTT	59.741	47.826	0.00	0.00	0.00	3.36
2970	3791	4.715523	CACCACGCCGACCCCAAT	62.716	66.667	0.00	0.00	0.00	3.16
3048	3869	2.577059	CTCTTCAAGGGCGCCGTA	59.423	61.111	23.92	4.47	0.00	4.02
3458	4279	0.816018	TCCTCTGGCTCTCGATCGAC	60.816	60.000	15.15	5.01	0.00	4.20
3850	4671	2.094026	CCCCTTTATGCAGCTTTTGGTC	60.094	50.000	0.00	0.00	0.00	4.02
3967	4788	5.052481	GCCCTTGCATTTCTCCAATTATTC	58.948	41.667	0.00	0.00	37.47	1.75
3973	4794	5.127519	TGCATTTCTCCAATTATTCCTGTGG	59.872	40.000	0.00	0.00	0.00	4.17
3992	4813	2.230992	TGGCAATTTTTCCGTCCATCAG	59.769	45.455	0.00	0.00	0.00	2.90
4042	4863	4.903045	AGAGAACTTCCCCAAAACGATA	57.097	40.909	0.00	0.00	0.00	2.92
4171	4995	9.567848	AAATATAAGCAAACGTTATTTCCACAG	57.432	29.630	0.00	0.00	0.00	3.66
4183	5007	6.914215	CGTTATTTCCACAGAGCGTATAGTTA	59.086	38.462	0.00	0.00	0.00	2.24
4195	5019	9.915629	CAGAGCGTATAGTTATTTCTTCCTATT	57.084	33.333	0.00	0.00	0.00	1.73
4214	5038	2.568696	TCAAGAAAGAGGCGATCTCG	57.431	50.000	0.00	0.00	46.82	4.04
4314	5138	2.066340	GGGTCACCAGATCCACACA	58.934	57.895	0.00	0.00	44.95	3.72
4335	5159	6.430000	ACACATGTGGATAGTTTTAGACCAAC	59.570	38.462	28.64	0.00	32.32	3.77

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	5.337491	CCAAGAATTCAGGTTTATTGTGGGG	60.337	44.000	8.44	0.00	0.00	4.96
117	118	4.170256	TGAAACTCAACTTGTTTTTCCGC	58.830	39.130	11.88	0.00	37.70	5.54
296	297	5.652014	CCTGGGCAAAGATGTAAAACTATGA	59.348	40.000	0.00	0.00	0.00	2.15
343	345	1.752694	GGGCTTGGGCTTCGCATAA	60.753	57.895	0.00	0.00	38.73	1.90
373	375	4.912528	TCGATAGATCTCGATCAACTCG	57.087	45.455	0.00	12.32	45.02	4.18
463	465	2.270257	CGGTACCGGGTGACTGTGA	61.270	63.158	27.00	0.00	35.56	3.58
498	500	6.202570	TGTGTATGCGTACGTGTATCTGTATA	59.797	38.462	17.90	0.34	33.36	1.47
530	532	4.261825	CCACAGGCTATAGCTCTAGTGTTC	60.262	50.000	23.53	4.34	41.70	3.18
710	712	5.103728	TCTCTCTCTCTCTCTCTCTCTCTCT	60.104	48.000	0.00	0.00	0.00	3.10
734	736	3.039526	CCCTCCCCCTCTCTCCCT	61.040	72.222	0.00	0.00	0.00	4.20
735	737	3.036959	TCCCTCCCCCTCTCTCCC	61.037	72.222	0.00	0.00	0.00	4.30
736	738	2.612251	CTCCCTCCCCCTCTCTCC	59.388	72.222	0.00	0.00	0.00	3.71
737	739	2.612251	CCTCCCTCCCCCTCTCTC	59.388	72.222	0.00	0.00	0.00	3.20
738	740	3.039526	CCCTCCCTCCCCCTCTCT	61.040	72.222	0.00	0.00	0.00	3.10
739	741	4.179599	CCCCTCCCTCCCCCTCTC	62.180	77.778	0.00	0.00	0.00	3.20
740	742	4.761304	TCCCCTCCCTCCCCCTCT	62.761	72.222	0.00	0.00	0.00	3.69
741	743	4.179599	CTCCCCTCCCTCCCCCTC	62.180	77.778	0.00	0.00	0.00	4.30
746	748	4.741239	TGTGGCTCCCCTCCCTCC	62.741	72.222	0.00	0.00	0.00	4.30
747	749	1.789576	TTTTGTGGCTCCCCTCCCTC	61.790	60.000	0.00	0.00	0.00	4.30
748	750	1.778383	TTTTGTGGCTCCCCTCCCT	60.778	57.895	0.00	0.00	0.00	4.20
749	751	1.304464	CTTTTGTGGCTCCCCTCCC	60.304	63.158	0.00	0.00	0.00	4.30
750	752	0.322906	CTCTTTTGTGGCTCCCCTCC	60.323	60.000	0.00	0.00	0.00	4.30
1329	1457	1.103398	GGAACTGCAACACCAGCACT	61.103	55.000	0.00	0.00	37.02	4.40
1556	1684	2.541120	GCTCGCAGCATGGATGGAC	61.541	63.158	0.00	0.00	41.89	4.02
1685	1980	3.848726	CCATGTTAATGTCACAAAGGGC	58.151	45.455	0.00	0.00	31.27	5.19
1716	2011	2.169352	TGATTCTTCTGACCTGCTAGCC	59.831	50.000	13.29	0.00	0.00	3.93
1877	2246	1.279271	AGAAAATGGACTGACGAGGGG	59.721	52.381	0.00	0.00	0.00	4.79
2133	2642	2.180017	CAATCGCAAGCAGTGGGC	59.820	61.111	0.00	0.00	45.30	5.36
2191	2700	3.347958	TTGTTGGAAATGACGCTGTTC	57.652	42.857	0.00	0.00	0.00	3.18
2220	2729	0.744057	TACCATGACATGCTGCACGG	60.744	55.000	3.57	2.60	0.00	4.94
2928	3749	3.176924	AGGAGCACGGATACCATATCT	57.823	47.619	0.00	0.00	0.00	1.98
3331	4152	2.369394	GAAGCCATTGGGGAAGTACAG	58.631	52.381	4.53	0.00	40.01	2.74
3458	4279	7.821359	ACAGAATTAATCATCACCATAGATCGG	59.179	37.037	0.00	0.00	0.00	4.18
3521	4342	2.039418	TCCCTAGCGATACAGTTGCAT	58.961	47.619	0.00	0.00	39.90	3.96
3584	4405	6.721208	ACATCAAATACCATCAAGTTCTTGGT	59.279	34.615	11.82	10.35	45.48	3.67
3850	4671	2.674177	CGTCCAAAGCCCTACTACAGTG	60.674	54.545	0.00	0.00	0.00	3.66
3960	4781	5.874261	CGGAAAAATTGCCACAGGAATAATT	59.126	36.000	0.00	0.00	0.00	1.40
3967	4788	1.336795	GGACGGAAAAATTGCCACAGG	60.337	52.381	0.00	0.00	0.00	4.00
3973	4794	3.848272	TCTGATGGACGGAAAAATTGC	57.152	42.857	0.00	0.00	0.00	3.56
4042	4863	9.420118	TGCCATTTGACAATTATTCCTAGTTAT	57.580	29.630	0.00	0.00	0.00	1.89
4152	4976	3.058224	GCTCTGTGGAAATAACGTTTGCT	60.058	43.478	5.91	0.00	0.00	3.91
4162	4986	8.204836	AGAAATAACTATACGCTCTGTGGAAAT	58.795	33.333	0.00	0.00	0.00	2.17
4171	4995	9.909644	TGAATAGGAAGAAATAACTATACGCTC	57.090	33.333	0.00	0.00	0.00	5.03
4183	5007	6.317391	CGCCTCTTTCTTGAATAGGAAGAAAT	59.683	38.462	13.27	0.00	45.80	2.17
4195	5019	2.568696	CGAGATCGCCTCTTTCTTGA	57.431	50.000	0.00	0.00	39.78	3.02
4279	5103	3.075005	CCCCTCACCACCGACGAT	61.075	66.667	0.00	0.00	0.00	3.73
4314	5138	5.801380	ACGTTGGTCTAAAACTATCCACAT	58.199	37.500	0.00	0.00	0.00	3.21

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.