AutoCloner

Multiple sequence alignment - TraesCS4B01G159800

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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	TraesCS4B01G159800	chr4B	100.000	2350	0	0	1	2350	310467318	310464969	0	4340
1	TraesCS4B01G159800	chr6B	95.964	2354	82	9	1	2350	128890874	128888530	0	3808
2	TraesCS4B01G159800	chr7B	95.839	2355	84	9	1	2350	716796730	716794385	0	3794
3	TraesCS4B01G159800	chr7B	95.794	2354	84	9	1	2350	742936591	742938933	0	3784
4	TraesCS4B01G159800	chr7A	95.837	2354	85	8	1	2350	60097089	60094745	0	3792
5	TraesCS4B01G159800	chrUn	96.543	2285	72	6	69	2350	257943290	257945570	0	3775
6	TraesCS4B01G159800	chr5B	95.669	2355	87	10	1	2350	713094874	713097218	0	3770
7	TraesCS4B01G159800	chr5B	95.667	2354	88	9	1	2350	713113853	713111510	0	3770
8	TraesCS4B01G159800	chr1B	95.497	2354	92	9	1	2350	583549419	583551762	0	3747
9	TraesCS4B01G159800	chr1B	95.248	2357	96	11	1	2350	49816953	49819300	0	3718

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	TraesCS4B01G159800	chr4B	310464969	310467318	2349	True	4340	4340	100.000	1	2350	1	chr4B.!!$R1	2349
1	TraesCS4B01G159800	chr6B	128888530	128890874	2344	True	3808	3808	95.964	1	2350	1	chr6B.!!$R1	2349
2	TraesCS4B01G159800	chr7B	716794385	716796730	2345	True	3794	3794	95.839	1	2350	1	chr7B.!!$R1	2349
3	TraesCS4B01G159800	chr7B	742936591	742938933	2342	False	3784	3784	95.794	1	2350	1	chr7B.!!$F1	2349
4	TraesCS4B01G159800	chr7A	60094745	60097089	2344	True	3792	3792	95.837	1	2350	1	chr7A.!!$R1	2349
5	TraesCS4B01G159800	chrUn	257943290	257945570	2280	False	3775	3775	96.543	69	2350	1	chrUn.!!$F1	2281
6	TraesCS4B01G159800	chr5B	713094874	713097218	2344	False	3770	3770	95.669	1	2350	1	chr5B.!!$F1	2349
7	TraesCS4B01G159800	chr5B	713111510	713113853	2343	True	3770	3770	95.667	1	2350	1	chr5B.!!$R1	2349
8	TraesCS4B01G159800	chr1B	583549419	583551762	2343	False	3747	3747	95.497	1	2350	1	chr1B.!!$F2	2349
9	TraesCS4B01G159800	chr1B	49816953	49819300	2347	False	3718	3718	95.248	1	2350	1	chr1B.!!$F1	2349

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
58	59	0.323178	CAGAATCTGCCTGGTGCCTT	60.323	55.0	0.0	0.0	40.16	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1765	1773	0.393808	GTTGGCGGCAAGGAAGGATA	60.394	55.0	26.22	0.0	0.0	2.59	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
58	59	0.323178	CAGAATCTGCCTGGTGCCTT	60.323	55.000	0.00	0.00	40.16	4.35
92	93	6.120905	CCCATTGGATCAATTTGCCATTTAA	58.879	36.000	3.62	0.00	31.05	1.52
127	128	7.395772	TGATCTTCATGTGGGCAACTTTTATTA	59.604	33.333	0.00	0.00	0.00	0.98
157	158	5.458041	ACAAATGCAATCCTGTATATGCC	57.542	39.130	0.00	0.00	38.00	4.40
308	313	4.360951	AACAAATAGGTGGTCTTTCCGA	57.639	40.909	0.00	0.00	39.52	4.55
384	389	6.295236	CGTTATTTCGTAATCCCCAGGGTATA	60.295	42.308	4.22	0.00	36.47	1.47
444	449	8.181904	TCATTACTTTGGCTCTTTCATTTTCT	57.818	30.769	0.00	0.00	0.00	2.52
476	481	4.035017	GGCATTACGATTGTTGGATTTCG	58.965	43.478	0.00	0.00	37.60	3.46
491	496	2.859165	TTTCGAAGACATGGGCTTCT	57.141	45.000	21.02	3.89	39.60	2.85
673	678	7.338449	GTGGGTTTTCTTGGACTATGCTATTTA	59.662	37.037	0.00	0.00	0.00	1.40
750	755	5.191722	AGCATTAACCAGTCTGGAATTAGGA	59.808	40.000	26.18	1.44	40.96	2.94
766	771	9.154632	TGGAATTAGGAGTAGCTATATCACAAA	57.845	33.333	0.00	0.00	0.00	2.83
888	893	2.040442	TAGGGGGCTACAGCTGCA	59.960	61.111	15.27	0.00	41.70	4.41
914	919	1.608055	CAGCACTGAACATGGTTCCA	58.392	50.000	6.64	0.00	0.00	3.53
987	992	1.270893	GCCGAGAAGACCAGGAAAAGT	60.271	52.381	0.00	0.00	0.00	2.66
991	996	5.246307	CCGAGAAGACCAGGAAAAGTTAAT	58.754	41.667	0.00	0.00	0.00	1.40
1116	1122	6.978338	TCAGCTTCGTTATCGATTAGGTATT	58.022	36.000	1.71	0.00	45.65	1.89
1187	1193	7.277098	CCAAATTGAACAAATGATAGCTCAAGG	59.723	37.037	0.00	0.00	34.37	3.61
1225	1232	4.325344	GGGAATTGAAAGGGGAGAATGAGA	60.325	45.833	0.00	0.00	0.00	3.27
1344	1351	4.771684	CTCGCAAGCAAATTCGGG	57.228	55.556	0.00	0.00	37.18	5.14
1448	1455	6.053632	TGGTACTTGTCTGATCAATCACAT	57.946	37.500	0.00	0.00	32.50	3.21
1504	1511	4.927425	GTCTTGAACCGCTTACTAATCACA	59.073	41.667	0.00	0.00	0.00	3.58
1538	1546	3.636231	CCCCTTCGCCAGTCCACA	61.636	66.667	0.00	0.00	0.00	4.17
1673	1681	9.814899	GTAGTAGTTGTCTCTATGTAGTAGTCA	57.185	37.037	0.00	0.00	0.00	3.41
1692	1700	1.537202	CAGCCTTTGTTAAGCTTCGCT	59.463	47.619	0.00	0.00	42.56	4.93
1729	1737	3.553917	GCTACTCGAATGCCTCTTTCTTC	59.446	47.826	0.00	0.00	0.00	2.87
1765	1773	6.013725	TGTGTATGGTCTAGTCTTTCCAATGT	60.014	38.462	0.00	0.00	33.55	2.71
1766	1774	7.179516	TGTGTATGGTCTAGTCTTTCCAATGTA	59.820	37.037	0.00	0.00	33.55	2.29
2097	2107	3.916989	GGGGTCAGGAGGGAAATATATGT	59.083	47.826	0.00	0.00	0.00	2.29
2120	2130	3.007506	TGTTTTCTATCAGTCCCAAGCGA	59.992	43.478	0.00	0.00	0.00	4.93
2156	2166	3.534941	GGTCCGCTTACCGAGGAT	58.465	61.111	0.00	0.00	43.78	3.24
2236	2246	0.909610	GTGGGGGTGACAGAGGATGA	60.910	60.000	0.00	0.00	0.00	2.92
2270	2280	7.878127	CGGTTCATAGTTGGGTATGATATTCTT	59.122	37.037	0.00	0.00	38.83	2.52
2278	2288	8.723365	AGTTGGGTATGATATTCTTGTGGATTA	58.277	33.333	0.00	0.00	0.00	1.75
2286	2296	9.833179	ATGATATTCTTGTGGATTATTGGGAAT	57.167	29.630	0.00	0.00	0.00	3.01
2298	2308	9.797732	TGGATTATTGGGAATGTCCTCTATATA	57.202	33.333	0.00	0.00	36.57	0.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
58	59	3.961239	TGATCCAATGGGGTATTAGGGA	58.039	45.455	0.00	0.00	38.11	4.20
92	93	5.069516	GCCCACATGAAGATCAATTATTGGT	59.930	40.000	0.00	0.00	0.00	3.67
144	145	2.028658	CAGTGAGCGGCATATACAGGAT	60.029	50.000	1.45	0.00	0.00	3.24
147	148	2.398498	GACAGTGAGCGGCATATACAG	58.602	52.381	1.45	0.00	0.00	2.74
157	158	0.232303	GACCAAAACGACAGTGAGCG	59.768	55.000	0.00	2.60	0.00	5.03
205	210	1.421646	CACTGACTTTCCACCTCCCTT	59.578	52.381	0.00	0.00	0.00	3.95
335	340	6.292703	CGAAAAAGTAAAAGTGACCGAGATGT	60.293	38.462	0.00	0.00	0.00	3.06
384	389	9.614792	CTTGTTACTATGAAGCTAAAGGGTATT	57.385	33.333	0.00	0.00	0.00	1.89
405	410	7.653311	GCCAAAGTAATGAGAAAATGACTTGTT	59.347	33.333	0.00	0.00	32.46	2.83
465	470	3.081061	CCCATGTCTTCGAAATCCAACA	58.919	45.455	0.00	0.00	0.00	3.33
736	741	8.394822	TGATATAGCTACTCCTAATTCCAGACT	58.605	37.037	0.00	0.00	0.00	3.24
854	859	3.303938	CCCTAGAATCTTCAGCTCCTCA	58.696	50.000	0.00	0.00	0.00	3.86
862	867	3.309296	CTGTAGCCCCCTAGAATCTTCA	58.691	50.000	0.00	0.00	0.00	3.02
888	893	2.223876	CCATGTTCAGTGCTGCAAAAGT	60.224	45.455	2.77	0.00	0.00	2.66
914	919	5.351465	CACAAACGCAATATCTTGAGTACCT	59.649	40.000	0.80	0.00	43.46	3.08
1116	1122	6.070021	ACTCATTCATCTTGATGTTCCCACTA	60.070	38.462	10.01	0.00	0.00	2.74
1187	1193	5.782047	TCAATTCCCAATGAACAACATGAC	58.218	37.500	0.00	0.00	39.39	3.06
1344	1351	4.935808	TCTTTCGGTAGCCTTCTTTCATTC	59.064	41.667	0.00	0.00	0.00	2.67
1473	1480	1.144969	GCGGTTCAAGACATCGAACA	58.855	50.000	0.00	0.00	42.67	3.18
1504	1511	5.453158	GAAGGGGGCCTACTATACGTATAT	58.547	45.833	15.42	8.74	31.13	0.86
1538	1546	2.990479	GACCAAGACGGGCCAGAT	59.010	61.111	10.86	0.00	36.36	2.90
1615	1623	1.751924	GATAGTGAAGCCGTCAGAGGT	59.248	52.381	0.00	0.00	36.74	3.85
1710	1718	3.971245	AGAAGAAAGAGGCATTCGAGT	57.029	42.857	0.00	0.00	32.04	4.18
1712	1720	6.525578	TTAGTAGAAGAAAGAGGCATTCGA	57.474	37.500	0.00	0.00	32.04	3.71
1765	1773	0.393808	GTTGGCGGCAAGGAAGGATA	60.394	55.000	26.22	0.00	0.00	2.59
1766	1774	1.678970	GTTGGCGGCAAGGAAGGAT	60.679	57.895	26.22	0.00	0.00	3.24
1823	1831	3.120442	AGCTACCGTTTAACGAATGCAAC	60.120	43.478	19.61	1.87	46.05	4.17
1850	1858	3.574074	GAAGCAGGCAGGAAGGGCA	62.574	63.158	0.00	0.00	35.46	5.36
2097	2107	3.751175	CGCTTGGGACTGATAGAAAACAA	59.249	43.478	0.00	0.00	0.00	2.83
2120	2130	0.541863	CGTGGAAGCTGGGGAGTATT	59.458	55.000	0.00	0.00	0.00	1.89
2156	2166	2.764128	GGGTCCTCCCGCATCTCA	60.764	66.667	0.00	0.00	44.74	3.27
2236	2246	2.159282	CCAACTATGAACCGTACGAGCT	60.159	50.000	18.76	0.00	0.00	4.09
2270	2280	4.478317	AGAGGACATTCCCAATAATCCACA	59.522	41.667	0.00	0.00	37.19	4.17
2278	2288	8.609617	TCGAATATATAGAGGACATTCCCAAT	57.390	34.615	0.00	0.00	37.19	3.16
2286	2296	9.201989	AGGCATATTTCGAATATATAGAGGACA	57.798	33.333	0.00	0.00	0.00	4.02
2298	2308	5.049129	GCTGCTAGAAAGGCATATTTCGAAT	60.049	40.000	0.00	0.00	42.73	3.34
2299	2309	4.273480	GCTGCTAGAAAGGCATATTTCGAA	59.727	41.667	0.00	0.00	42.73	3.71
2319	2329	1.526041	GAGCTGCAGATCGTAATGCTG	59.474	52.381	20.43	6.69	42.98	4.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.