AutoCloner

Multiple sequence alignment - TraesCS4A01G124500

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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	TraesCS4A01G124500	chr4A	100.000	2572	0	0	1	2572	157561001	157563572	0.000000e+00	4750.0
1	TraesCS4A01G124500	chr4A	92.308	39	2	1	2265	2303	690220614	690220577	1.000000e-03	54.7
2	TraesCS4A01G124500	chr4D	92.723	1704	83	11	903	2572	317198557	317196861	0.000000e+00	2422.0
3	TraesCS4A01G124500	chr4D	94.092	931	41	6	1	924	317199494	317198571	0.000000e+00	1402.0
4	TraesCS4A01G124500	chr4B	93.626	1616	63	11	875	2459	394384819	394383213	0.000000e+00	2377.0
5	TraesCS4A01G124500	chr4B	95.912	636	22	3	1	636	394385576	394384945	0.000000e+00	1027.0
6	TraesCS4A01G124500	chr4B	97.059	102	3	0	688	789	394384948	394384847	3.400000e-39	172.0
7	TraesCS4A01G124500	chr6D	82.658	888	120	20	743	1605	27521557	27520679	0.000000e+00	756.0
8	TraesCS4A01G124500	chr6B	82.589	896	117	21	743	1627	50396496	50397363	0.000000e+00	754.0
9	TraesCS4A01G124500	chr6A	82.088	910	129	21	743	1627	30466812	30467712	0.000000e+00	747.0
10	TraesCS4A01G124500	chr5B	81.752	137	18	6	2436	2571	10399634	10399504	9.730000e-20	108.0
11	TraesCS4A01G124500	chr5A	84.545	110	12	4	2462	2571	8116349	8116245	1.260000e-18	104.0
12	TraesCS4A01G124500	chr5D	90.164	61	6	0	2511	2571	10356118	10356058	2.120000e-11	80.5
13	TraesCS4A01G124500	chrUn	81.915	94	16	1	2223	2315	235115315	235115222	7.630000e-11	78.7
14	TraesCS4A01G124500	chr3D	97.143	35	0	1	2270	2303	524715669	524715703	9.940000e-05	58.4
15	TraesCS4A01G124500	chr2D	100.000	28	0	0	2281	2308	351288369	351288342	5.000000e-03	52.8

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	TraesCS4A01G124500	chr4A	157561001	157563572	2571	False	4750	4750	100.000000	1	2572	1	chr4A.!!$F1	2571
1	TraesCS4A01G124500	chr4D	317196861	317199494	2633	True	1912	2422	93.407500	1	2572	2	chr4D.!!$R1	2571
2	TraesCS4A01G124500	chr4B	394383213	394385576	2363	True	1192	2377	95.532333	1	2459	3	chr4B.!!$R1	2458
3	TraesCS4A01G124500	chr6D	27520679	27521557	878	True	756	756	82.658000	743	1605	1	chr6D.!!$R1	862
4	TraesCS4A01G124500	chr6B	50396496	50397363	867	False	754	754	82.589000	743	1627	1	chr6B.!!$F1	884
5	TraesCS4A01G124500	chr6A	30466812	30467712	900	False	747	747	82.088000	743	1627	1	chr6A.!!$F1	884

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
563	573	2.905075	TGGACGATATTCAGTGCCTTG	58.095	47.619	0.0	0.0	0.0	3.61	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2475	2629	1.254026	ACTCGACAATTCCCAGACGA	58.746	50.0	0.0	0.0	0.0	4.2	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
37	38	9.979578	AAAAATATCACATGCTTGTTACAAGAA	57.020	25.926	26.94	18.55	32.34	2.52
116	117	4.277672	GGGATATCTGTGCACGACTAAGTA	59.722	45.833	13.13	2.45	0.00	2.24
465	475	7.554835	ACAGATCTATTTACACGGCCAAAATAA	59.445	33.333	2.24	0.00	0.00	1.40
466	476	8.567948	CAGATCTATTTACACGGCCAAAATAAT	58.432	33.333	2.24	0.00	0.00	1.28
467	477	9.787435	AGATCTATTTACACGGCCAAAATAATA	57.213	29.630	2.24	0.09	0.00	0.98
488	498	7.549615	AATATCATTATGATGCTGATCCACG	57.450	36.000	17.09	0.00	37.70	4.94
563	573	2.905075	TGGACGATATTCAGTGCCTTG	58.095	47.619	0.00	0.00	0.00	3.61
626	636	5.980698	ACAAGATCTTAGTTGATGCGATG	57.019	39.130	7.86	0.00	0.00	3.84
695	705	6.823182	TCACAAAACAGGACACTATATCATGG	59.177	38.462	0.00	0.00	32.20	3.66
879	914	8.620116	TGTGAATATTGTTTCTCTTGACATGA	57.380	30.769	0.00	0.00	0.00	3.07
1011	1097	7.896811	AGAATCTATACATAATGGACGCAGAA	58.103	34.615	0.00	0.00	0.00	3.02
1089	1177	1.395954	CACACACTGCCAATGATCTCG	59.604	52.381	0.00	0.00	0.00	4.04
1137	1225	1.153524	AAACCATGACAGGCCTGCA	59.846	52.632	33.06	28.64	0.00	4.41
1170	1258	2.808206	CGACCATGGCCTAGACCCC	61.808	68.421	13.04	0.00	0.00	4.95
1232	1321	2.188817	GTGGTGAGGGTAATCCAGAGT	58.811	52.381	0.00	0.00	38.24	3.24
1323	1418	3.825160	GACCTTGCTGCGGTGTCCA	62.825	63.158	3.86	0.00	34.19	4.02
1442	1537	0.110486	ATGTGGAGAAGTTTGCCCGT	59.890	50.000	0.00	0.00	0.00	5.28
1526	1621	0.773644	ATGCACAGTGGAACCTCCTT	59.226	50.000	0.00	0.00	37.80	3.36
1605	1702	0.181114	GGCACATGACAGGCCAGATA	59.819	55.000	5.01	0.00	46.92	1.98
1608	1706	0.105593	ACATGACAGGCCAGATAGCG	59.894	55.000	5.01	0.00	0.00	4.26
1618	1716	2.356135	GCCAGATAGCGTCCTGAAAAA	58.644	47.619	4.27	0.00	32.37	1.94
1620	1718	3.600388	CCAGATAGCGTCCTGAAAAAGT	58.400	45.455	4.27	0.00	32.37	2.66
1718	1816	8.883954	TTTGCATTTTACACATTTCATCTTGA	57.116	26.923	0.00	0.00	0.00	3.02
1868	1982	0.315886	GTTTTCGCGGGGGTGATTTT	59.684	50.000	6.13	0.00	0.00	1.82
1951	2065	7.043986	CGTAAGATTATCTGGACGTCAAAGAAG	60.044	40.741	18.91	6.51	43.02	2.85
2103	2228	3.774766	GGCTGGGGTTCAAGGATTATTTT	59.225	43.478	0.00	0.00	0.00	1.82
2105	2230	5.178061	GCTGGGGTTCAAGGATTATTTTTG	58.822	41.667	0.00	0.00	0.00	2.44
2109	2234	6.995091	TGGGGTTCAAGGATTATTTTTGTTTG	59.005	34.615	0.00	0.00	0.00	2.93
2140	2265	5.013287	TGCATAAGGGGCTACCGATAATTTA	59.987	40.000	0.00	0.00	46.96	1.40
2142	2267	6.602009	GCATAAGGGGCTACCGATAATTTAAT	59.398	38.462	0.00	0.00	46.96	1.40
2144	2269	6.894339	AAGGGGCTACCGATAATTTAATTG	57.106	37.500	0.00	0.00	46.96	2.32
2145	2270	5.948842	AGGGGCTACCGATAATTTAATTGT	58.051	37.500	0.00	0.00	46.96	2.71
2146	2271	6.002082	AGGGGCTACCGATAATTTAATTGTC	58.998	40.000	4.64	4.64	46.96	3.18
2243	2397	6.688073	ATCCCTCCGATCATATTACTTGTT	57.312	37.500	0.00	0.00	0.00	2.83
2263	2417	2.671596	TGCGGCTTTAATGCAACTTTC	58.328	42.857	14.56	0.00	35.33	2.62
2308	2462	7.522073	GCTGCGATAATTAATTTGGATTGGAGA	60.522	37.037	16.57	0.00	0.00	3.71
2352	2506	4.483311	GGTCGACCTCAGTTAAGTTACAG	58.517	47.826	27.64	0.00	0.00	2.74
2365	2519	9.209175	CAGTTAAGTTACAGAGCTAAGAATTGT	57.791	33.333	0.00	0.00	0.00	2.71
2430	2584	3.066900	CCAGAACTACGACAGGTGATAGG	59.933	52.174	0.00	0.00	0.00	2.57
2459	2613	2.110420	GTAGTATGGGGCGGCACC	59.890	66.667	16.11	16.11	37.93	5.01
2494	2648	1.202582	CTCGTCTGGGAATTGTCGAGT	59.797	52.381	0.00	0.00	39.51	4.18
2505	2659	0.796870	TTGTCGAGTACAGCATCGCG	60.797	55.000	0.00	0.00	39.87	5.87
2513	2667	2.742053	AGTACAGCATCGCGTGATTTTT	59.258	40.909	9.17	0.00	30.49	1.94
2540	2694	9.729023	TGTTGAACACAACAAATATTGAGTAAG	57.271	29.630	12.33	0.00	46.80	2.34
2545	2699	9.528018	AACACAACAAATATTGAGTAAGTTTGG	57.472	29.630	0.00	0.00	33.02	3.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	6.493115	TCACAATTTCCATGGTTCATGTTAGT	59.507	34.615	12.58	0.00	39.94	2.24
116	117	6.836242	TGCCCTCCTTTTCATAAACAAAAAT	58.164	32.000	0.00	0.00	0.00	1.82
307	314	5.407995	CCAGAACTTCAACAAAGCAAACAAA	59.592	36.000	0.00	0.00	38.67	2.83
327	334	8.150827	AGCATATATTACCTTGATTAGCCAGA	57.849	34.615	0.00	0.00	0.00	3.86
368	375	9.814899	ACATTTGTTCTGTTATTGTTCAATGAA	57.185	25.926	8.11	0.00	0.00	2.57
388	395	6.187125	ACGATCCTCATCTTCAAACATTTG	57.813	37.500	0.00	0.00	39.48	2.32
465	475	6.537660	CACGTGGATCAGCATCATAATGATAT	59.462	38.462	7.95	0.00	34.28	1.63
466	476	5.870978	CACGTGGATCAGCATCATAATGATA	59.129	40.000	7.95	0.00	34.28	2.15
467	477	4.694037	CACGTGGATCAGCATCATAATGAT	59.306	41.667	7.95	0.00	37.65	2.45
488	498	3.187227	CAGAGTTGACTTGCACCATACAC	59.813	47.826	0.00	0.00	0.00	2.90
695	705	1.484356	GAAAGCGATGGATTGCATGC	58.516	50.000	11.82	11.82	39.70	4.06
1040	1126	3.389329	AGTCCAATCGCCATCTGTTATCT	59.611	43.478	0.00	0.00	0.00	1.98
1089	1177	1.546476	ACACGATCCAGTCTCTGTTCC	59.454	52.381	0.00	0.00	0.00	3.62
1170	1258	2.733026	CCAAGTAACAACGAAGTACCCG	59.267	50.000	4.02	4.02	45.00	5.28
1232	1321	2.092429	GTGCCTGGAGAAATCATACCCA	60.092	50.000	0.00	0.00	0.00	4.51
1323	1418	0.252197	GGAGGCGACATTGGGTTAGT	59.748	55.000	0.00	0.00	0.00	2.24
1442	1537	3.375922	TCTCGTATCTGTTATGCGTGACA	59.624	43.478	3.25	3.25	0.00	3.58
1526	1621	3.244770	GGGTGTAACTTTCCTCCATGACA	60.245	47.826	0.00	0.00	36.74	3.58
1605	1702	2.919228	ACAGAACTTTTTCAGGACGCT	58.081	42.857	0.00	0.00	33.72	5.07
1608	1706	5.516696	GCAAGAAACAGAACTTTTTCAGGAC	59.483	40.000	13.44	0.72	34.68	3.85
1618	1716	3.065371	CCAAACGAGCAAGAAACAGAACT	59.935	43.478	0.00	0.00	0.00	3.01
1620	1718	2.357637	CCCAAACGAGCAAGAAACAGAA	59.642	45.455	0.00	0.00	0.00	3.02
1868	1982	1.455849	CAGAGCCACAAACCCCAGA	59.544	57.895	0.00	0.00	0.00	3.86
1894	2008	3.106738	GAGGATCCATGGTTGCTGG	57.893	57.895	20.39	0.00	34.93	4.85
1951	2065	3.645268	AACCAAGCATCCCTCCCGC	62.645	63.158	0.00	0.00	0.00	6.13
2103	2228	4.878397	CCCCTTATGCAAACAAACAAACAA	59.122	37.500	0.00	0.00	0.00	2.83
2105	2230	3.249799	GCCCCTTATGCAAACAAACAAAC	59.750	43.478	0.00	0.00	0.00	2.93
2109	2234	3.368013	GGTAGCCCCTTATGCAAACAAAC	60.368	47.826	0.00	0.00	0.00	2.93
2243	2397	2.671596	GAAAGTTGCATTAAAGCCGCA	58.328	42.857	0.00	0.00	0.00	5.69
2352	2506	7.313951	ACTTTCTGCATACAATTCTTAGCTC	57.686	36.000	0.00	0.00	0.00	4.09
2390	2544	2.568956	CTGGTCAGGAAGGACTCATTGA	59.431	50.000	0.00	0.00	37.91	2.57
2430	2584	3.573110	CCCCATACTACCTGCTAGTGTAC	59.427	52.174	0.00	0.00	36.29	2.90
2475	2629	1.254026	ACTCGACAATTCCCAGACGA	58.746	50.000	0.00	0.00	0.00	4.20
2476	2630	2.094906	TGTACTCGACAATTCCCAGACG	60.095	50.000	0.00	0.00	34.15	4.18
2540	2694	4.367450	TCTTGTGCTTTGTATTGCCAAAC	58.633	39.130	0.00	0.00	31.38	2.93
2545	2699	5.362556	TTCTCTCTTGTGCTTTGTATTGC	57.637	39.130	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.