AutoCloner

Multiple sequence alignment - TraesCS5D01G254800

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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	TraesCS5D01G254800	chr5D	100.000	2858	0	0	1	2858	361206446	361209303	0.000000e+00	5278
1	TraesCS5D01G254800	chr5D	96.013	2859	107	5	1	2858	397071681	397068829	0.000000e+00	4641
2	TraesCS5D01G254800	chr3D	96.852	2859	86	3	1	2858	584823380	584820525	0.000000e+00	4778
3	TraesCS5D01G254800	chr3D	96.571	2858	95	2	1	2858	57186340	57189194	0.000000e+00	4732
4	TraesCS5D01G254800	chr3D	97.005	2638	78	1	221	2858	371448297	371445661	0.000000e+00	4433
5	TraesCS5D01G254800	chr2D	96.851	2858	88	1	1	2858	284567096	284569951	0.000000e+00	4778
6	TraesCS5D01G254800	chr1B	96.361	2858	102	2	1	2858	637509812	637512667	0.000000e+00	4700
7	TraesCS5D01G254800	chr1D	96.292	2859	87	3	1	2858	388982728	388985568	0.000000e+00	4674
8	TraesCS5D01G254800	chr4D	95.556	2858	110	4	1	2858	454415356	454418196	0.000000e+00	4558
9	TraesCS5D01G254800	chr1A	93.918	2861	163	5	1	2858	511612740	511609888	0.000000e+00	4309
10	TraesCS5D01G254800	chr7D	96.537	231	7	1	1	230	616765296	616765066	5.780000e-102	381

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	TraesCS5D01G254800	chr5D	361206446	361209303	2857	False	5278	5278	100.000	1	2858	1	chr5D.!!$F1	2857
1	TraesCS5D01G254800	chr5D	397068829	397071681	2852	True	4641	4641	96.013	1	2858	1	chr5D.!!$R1	2857
2	TraesCS5D01G254800	chr3D	584820525	584823380	2855	True	4778	4778	96.852	1	2858	1	chr3D.!!$R2	2857
3	TraesCS5D01G254800	chr3D	57186340	57189194	2854	False	4732	4732	96.571	1	2858	1	chr3D.!!$F1	2857
4	TraesCS5D01G254800	chr3D	371445661	371448297	2636	True	4433	4433	97.005	221	2858	1	chr3D.!!$R1	2637
5	TraesCS5D01G254800	chr2D	284567096	284569951	2855	False	4778	4778	96.851	1	2858	1	chr2D.!!$F1	2857
6	TraesCS5D01G254800	chr1B	637509812	637512667	2855	False	4700	4700	96.361	1	2858	1	chr1B.!!$F1	2857
7	TraesCS5D01G254800	chr1D	388982728	388985568	2840	False	4674	4674	96.292	1	2858	1	chr1D.!!$F1	2857
8	TraesCS5D01G254800	chr4D	454415356	454418196	2840	False	4558	4558	95.556	1	2858	1	chr4D.!!$F1	2857
9	TraesCS5D01G254800	chr1A	511609888	511612740	2852	True	4309	4309	93.918	1	2858	1	chr1A.!!$R1	2857

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
383	404	0.247736	GAGAACCACACTGCTCGGAT	59.752	55.0	0.0	0.0	0.0	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2332	2356	0.338814	AGGTAGGGATGGAGGACGTT	59.661	55.0	0.0	0.0	0.0	3.99	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
61	62	3.374540	AGCCAGCCCTTGGATCAATAAAT	60.375	43.478	0.00	0.00	43.77	1.40
71	74	5.509716	TGGATCAATAAATGCAAGCAGAG	57.490	39.130	0.00	0.00	0.00	3.35
72	75	5.195185	TGGATCAATAAATGCAAGCAGAGA	58.805	37.500	0.00	0.00	0.00	3.10
77	80	9.909644	GATCAATAAATGCAAGCAGAGAATATT	57.090	29.630	0.00	0.00	0.00	1.28
194	213	0.466543	AACCACGACTACAACCTGCA	59.533	50.000	0.00	0.00	0.00	4.41
232	251	2.668457	CGTGACAACTTGGTATCAGCTC	59.332	50.000	0.00	0.00	0.00	4.09
334	355	1.825341	CACGAGGATCATGAGGCCA	59.175	57.895	17.02	0.00	33.17	5.36
383	404	0.247736	GAGAACCACACTGCTCGGAT	59.752	55.000	0.00	0.00	0.00	4.18
607	629	1.151721	CCAGGGGATAGGGCTCCAT	60.152	63.158	0.00	0.00	37.01	3.41
640	662	5.896963	AGATTGATTTTCCCCTCTTTGACT	58.103	37.500	0.00	0.00	0.00	3.41
826	848	4.274950	GGACCGAGTTTCAAAAACTGATCA	59.725	41.667	9.65	0.00	32.78	2.92
916	939	1.066143	CCGTGGCAGAATACTCCAAGT	60.066	52.381	0.00	0.00	0.00	3.16
1029	1052	0.976641	AGGTCGAGATGCTGAAACCA	59.023	50.000	0.00	0.00	0.00	3.67
1151	1174	1.630126	CCCATGGCTGCACCTACTCT	61.630	60.000	6.09	0.00	40.22	3.24
1235	1258	3.627218	GGATGAACGGCGCGCTAC	61.627	66.667	32.29	18.93	0.00	3.58
1305	1328	4.211164	TGCAAACGACTGTTCTACATTCAG	59.789	41.667	0.00	0.00	37.31	3.02
1373	1396	6.459573	GCACAAATCTCACTCTTGGTTGTTAA	60.460	38.462	0.00	0.00	0.00	2.01
1414	1437	1.016130	AATGCAGGTCACTCTTCGCG	61.016	55.000	0.00	0.00	0.00	5.87
1483	1506	1.620819	ACTTCATCCACGAAGAGCTGT	59.379	47.619	7.63	0.00	44.32	4.40
1499	1522	4.077184	GTCCACCATCGTCGGGCA	62.077	66.667	0.00	0.00	0.00	5.36
1657	1680	1.888018	GGGTTCGACATCGTCCTCA	59.112	57.895	14.12	0.00	40.80	3.86
1689	1712	2.232208	CCTCAAAACTCTTGGGCCAATC	59.768	50.000	21.25	0.00	0.00	2.67
1758	1781	3.637273	GTGGAGTGGTCGGGCCTT	61.637	66.667	0.84	0.00	38.35	4.35
1777	1800	3.519930	GCTCCCTCGGACGTCCTC	61.520	72.222	30.92	7.40	0.00	3.71
1780	1803	4.753662	CCCTCGGACGTCCTCCCA	62.754	72.222	30.92	11.99	35.21	4.37
1782	1805	2.280552	CCTCGGACGTCCTCCCAAA	61.281	63.158	30.92	9.32	35.21	3.28
1855	1878	1.366111	CGATGTTTTCGCCGACCCAT	61.366	55.000	0.00	0.00	41.69	4.00
1891	1914	0.028505	GCGTGCACATGACCATCATC	59.971	55.000	18.64	0.00	34.28	2.92
1934	1957	2.358737	GGTTGCTGTCCGTCCCTG	60.359	66.667	0.00	0.00	0.00	4.45
2095	2118	2.093288	TGTATCGACTACCGTGGTCTCT	60.093	50.000	12.61	3.17	39.75	3.10
2121	2144	3.476552	TGTCACCATCAAGGACAAGTTC	58.523	45.455	0.00	0.00	41.22	3.01
2332	2356	1.872952	CGTTCCAAGCACTCATGAACA	59.127	47.619	0.00	0.00	36.07	3.18
2342	2366	1.691976	ACTCATGAACAACGTCCTCCA	59.308	47.619	0.00	0.00	0.00	3.86
2405	2429	4.152284	TCTTGATCTACAGCTCGTCCTA	57.848	45.455	0.00	0.00	0.00	2.94
2420	2444	2.744166	CGTCCTAGTCGGATCACCTACA	60.744	54.545	0.00	0.00	45.44	2.74
2425	2449	5.013808	TCCTAGTCGGATCACCTACATCATA	59.986	44.000	0.00	0.00	36.69	2.15
2433	2457	6.471146	GGATCACCTACATCATATCAAGCTT	58.529	40.000	0.00	0.00	0.00	3.74
2463	2487	1.933181	GCTATGCGCACACATCAACTA	59.067	47.619	14.90	0.00	38.92	2.24
2493	2517	1.813862	CGCTCCAAGTGTTCCTTTGGA	60.814	52.381	5.88	5.88	32.74	3.53
2528	2552	3.430929	GCTTATCTGGGACACGTCATCTT	60.431	47.826	0.00	0.00	0.00	2.40
2568	2592	0.179045	ACAGCGACAAGGTTCTTGCT	60.179	50.000	7.48	0.00	0.00	3.91
2651	2675	3.181469	GGATACTACCGCAAGTTCATCCA	60.181	47.826	10.22	0.00	35.78	3.41
2783	2807	2.033757	CCCTGTGCTTCAGCTGCT	59.966	61.111	9.47	0.00	42.38	4.24
2794	2818	2.495155	TCAGCTGCTGGATTTTGCTA	57.505	45.000	27.79	3.81	32.29	3.49

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	5.586243	GGTTGTAGAATATTCTCTGCTTGCA	59.414	40.000	21.17	4.21	38.70	4.08
71	74	5.841783	AGGGAGGAGAGGTTGTAGAATATTC	59.158	44.000	7.41	7.41	0.00	1.75
72	75	5.793967	AGGGAGGAGAGGTTGTAGAATATT	58.206	41.667	0.00	0.00	0.00	1.28
77	80	2.821437	CAAGGGAGGAGAGGTTGTAGA	58.179	52.381	0.00	0.00	0.00	2.59
232	251	4.271816	CGCTGGGATCGACGAGGG	62.272	72.222	3.01	0.00	0.00	4.30
334	355	1.238439	CTGTTCAAAGTGGCGACCAT	58.762	50.000	0.00	0.00	35.28	3.55
586	608	0.476611	GGAGCCCTATCCCCTGGATT	60.477	60.000	0.15	0.00	39.79	3.01
607	629	4.949856	GGGAAAATCAATCTTGTAGAGGCA	59.050	41.667	0.00	0.00	0.00	4.75
826	848	2.424302	CGGTCCGAAGTGGTTGGT	59.576	61.111	4.91	0.00	39.52	3.67
1208	1231	1.226974	CGTTCATCCATCTCGGCGT	60.227	57.895	6.85	0.00	33.14	5.68
1235	1258	1.466167	CACAATTGAAGCAGAGACCCG	59.534	52.381	13.59	0.00	0.00	5.28
1343	1366	3.777106	AGAGTGAGATTTGTGCTTCCA	57.223	42.857	0.00	0.00	0.00	3.53
1373	1396	2.046314	CGCTGGTGGGAATTCCGT	60.046	61.111	18.30	0.00	38.76	4.69
1483	1506	3.770040	CTGCCCGACGATGGTGGA	61.770	66.667	0.00	0.00	0.00	4.02
1499	1522	0.618968	ACGATTGGAGGAGAAGGGCT	60.619	55.000	0.00	0.00	0.00	5.19
1503	1526	2.656560	AACGACGATTGGAGGAGAAG	57.343	50.000	0.00	0.00	0.00	2.85
1657	1680	5.470047	AGAGTTTTGAGGAATCGTGTACT	57.530	39.130	0.00	0.00	0.00	2.73
1689	1712	1.207089	TGCGTAGTGAAATCCCAGAGG	59.793	52.381	0.00	0.00	0.00	3.69
1777	1800	2.554272	GCACGCGTGTAGTTTGGG	59.446	61.111	36.80	11.99	0.00	4.12
1780	1803	1.554042	CCTTCGCACGCGTGTAGTTT	61.554	55.000	36.80	0.00	40.74	2.66
1782	1805	2.430244	CCTTCGCACGCGTGTAGT	60.430	61.111	36.80	0.00	40.74	2.73
1891	1914	3.877508	GGTGTCCCGGAAATAAGATGAAG	59.122	47.826	0.73	0.00	0.00	3.02
1934	1957	1.022451	TTGAATCGTTGGGTAGCGGC	61.022	55.000	0.00	0.00	0.00	6.53
2121	2144	2.710377	TCATCGACAACAGGAATTGGG	58.290	47.619	0.00	0.00	33.63	4.12
2332	2356	0.338814	AGGTAGGGATGGAGGACGTT	59.661	55.000	0.00	0.00	0.00	3.99
2342	2366	1.206371	CAAACCGACGAAGGTAGGGAT	59.794	52.381	6.97	0.00	45.21	3.85
2405	2429	5.325239	TGATATGATGTAGGTGATCCGACT	58.675	41.667	0.00	0.00	39.54	4.18
2420	2444	5.163478	GCCTCCAAAACAAGCTTGATATGAT	60.163	40.000	32.50	6.30	0.00	2.45
2425	2449	2.601905	AGCCTCCAAAACAAGCTTGAT	58.398	42.857	32.50	18.98	0.00	2.57
2433	2457	2.179764	GCGCATAGCCTCCAAAACA	58.820	52.632	0.30	0.00	40.81	2.83
2463	2487	1.808945	CACTTGGAGCGCTTGAGAAAT	59.191	47.619	13.26	0.00	0.00	2.17
2493	2517	3.117738	CCAGATAAGCCATGGTTTCCTCT	60.118	47.826	18.02	16.86	0.00	3.69
2568	2592	1.823169	GAACCGGCCAGTCTACCACA	61.823	60.000	0.00	0.00	0.00	4.17
2783	2807	7.549842	CCACAATGAATGAAATAGCAAAATCCA	59.450	33.333	0.00	0.00	0.00	3.41
2794	2818	6.627243	CATCACACTCCACAATGAATGAAAT	58.373	36.000	0.00	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.