AutoCloner

Multiple sequence alignment - TraesCS3B01G450800

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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	TraesCS3B01G450800	chr3B	100.000	3298	0	0	1	3298	691342236	691338939	0.000000e+00	6091
1	TraesCS3B01G450800	chr3B	96.863	1020	32	0	2279	3298	786464728	786465747	0.000000e+00	1707
2	TraesCS3B01G450800	chr3B	93.269	104	5	2	2178	2279	678531640	678531537	5.700000e-33	152
3	TraesCS3B01G450800	chr7D	97.105	2280	62	4	1	2279	30312808	30315084	0.000000e+00	3842
4	TraesCS3B01G450800	chr1D	97.016	2279	64	4	1	2279	58485513	58483239	0.000000e+00	3829
5	TraesCS3B01G450800	chr1D	96.713	2282	70	4	1	2279	108798530	108796251	0.000000e+00	3794
6	TraesCS3B01G450800	chr1D	96.519	2241	67	7	47	2279	10804205	10801968	0.000000e+00	3696
7	TraesCS3B01G450800	chrUn	96.361	2281	76	4	1	2279	52473335	52475610	0.000000e+00	3746
8	TraesCS3B01G450800	chr4B	96.280	2285	77	6	1	2279	539964047	539961765	0.000000e+00	3742
9	TraesCS3B01G450800	chr4D	95.744	2279	68	9	1	2279	65876431	65874182	0.000000e+00	3644
10	TraesCS3B01G450800	chr3D	95.940	2192	82	7	90	2279	175422130	175419944	0.000000e+00	3548
11	TraesCS3B01G450800	chr6B	95.898	2194	81	7	1	2191	680526233	680524046	0.000000e+00	3544
12	TraesCS3B01G450800	chr1B	97.059	1020	30	0	2279	3298	559602249	559603268	0.000000e+00	1718
13	TraesCS3B01G450800	chr1B	96.663	1019	34	0	2280	3298	348793470	348792452	0.000000e+00	1694
14	TraesCS3B01G450800	chr5B	96.860	1019	32	0	2280	3298	362536832	362535814	0.000000e+00	1705
15	TraesCS3B01G450800	chr5B	96.673	1022	34	0	2277	3298	539123797	539124818	0.000000e+00	1700
16	TraesCS3B01G450800	chr5B	96.667	1020	33	1	2279	3298	277592514	277591496	0.000000e+00	1694
17	TraesCS3B01G450800	chr5B	96.667	1020	33	1	2279	3298	575834792	575833774	0.000000e+00	1694
18	TraesCS3B01G450800	chr7B	96.765	1020	33	0	2279	3298	566566332	566565313	0.000000e+00	1701
19	TraesCS3B01G450800	chr7B	96.762	1019	33	0	2280	3298	18891153	18892171	0.000000e+00	1700

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	TraesCS3B01G450800	chr3B	691338939	691342236	3297	True	6091	6091	100.000	1	3298	1	chr3B.!!$R2	3297
1	TraesCS3B01G450800	chr3B	786464728	786465747	1019	False	1707	1707	96.863	2279	3298	1	chr3B.!!$F1	1019
2	TraesCS3B01G450800	chr7D	30312808	30315084	2276	False	3842	3842	97.105	1	2279	1	chr7D.!!$F1	2278
3	TraesCS3B01G450800	chr1D	58483239	58485513	2274	True	3829	3829	97.016	1	2279	1	chr1D.!!$R2	2278
4	TraesCS3B01G450800	chr1D	108796251	108798530	2279	True	3794	3794	96.713	1	2279	1	chr1D.!!$R3	2278
5	TraesCS3B01G450800	chr1D	10801968	10804205	2237	True	3696	3696	96.519	47	2279	1	chr1D.!!$R1	2232
6	TraesCS3B01G450800	chrUn	52473335	52475610	2275	False	3746	3746	96.361	1	2279	1	chrUn.!!$F1	2278
7	TraesCS3B01G450800	chr4B	539961765	539964047	2282	True	3742	3742	96.280	1	2279	1	chr4B.!!$R1	2278
8	TraesCS3B01G450800	chr4D	65874182	65876431	2249	True	3644	3644	95.744	1	2279	1	chr4D.!!$R1	2278
9	TraesCS3B01G450800	chr3D	175419944	175422130	2186	True	3548	3548	95.940	90	2279	1	chr3D.!!$R1	2189
10	TraesCS3B01G450800	chr6B	680524046	680526233	2187	True	3544	3544	95.898	1	2191	1	chr6B.!!$R1	2190
11	TraesCS3B01G450800	chr1B	559602249	559603268	1019	False	1718	1718	97.059	2279	3298	1	chr1B.!!$F1	1019
12	TraesCS3B01G450800	chr1B	348792452	348793470	1018	True	1694	1694	96.663	2280	3298	1	chr1B.!!$R1	1018
13	TraesCS3B01G450800	chr5B	362535814	362536832	1018	True	1705	1705	96.860	2280	3298	1	chr5B.!!$R2	1018
14	TraesCS3B01G450800	chr5B	539123797	539124818	1021	False	1700	1700	96.673	2277	3298	1	chr5B.!!$F1	1021
15	TraesCS3B01G450800	chr5B	277591496	277592514	1018	True	1694	1694	96.667	2279	3298	1	chr5B.!!$R1	1019
16	TraesCS3B01G450800	chr5B	575833774	575834792	1018	True	1694	1694	96.667	2279	3298	1	chr5B.!!$R3	1019
17	TraesCS3B01G450800	chr7B	566565313	566566332	1019	True	1701	1701	96.765	2279	3298	1	chr7B.!!$R1	1019
18	TraesCS3B01G450800	chr7B	18891153	18892171	1018	False	1700	1700	96.762	2280	3298	1	chr7B.!!$F1	1018

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
494	499	2.095853	CCACACCTATTGCAAAGCTACG	59.904	50.0	1.71	0.0	0.00	3.51	F
1284	1303	1.398958	CCAGGACTGAGCTAGGAGCC	61.399	65.0	0.00	0.0	43.77	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1410	1432	0.981183	AGAAACCCATCCGTAGTGCA	59.019	50.0	0.00	0.0	0.0	4.57	R
3275	3330	0.178958	TAATCTCTCTCGGGAGGGCC	60.179	60.0	13.54	0.0	39.8	5.80	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
38	39	6.219473	CAAACCTAAAACATGCATTGTACCA	58.781	36.000	0.00	0.00	37.68	3.25
79	80	5.504665	GCATGCTAGCCAAAACTGTAGTATG	60.505	44.000	13.29	5.41	38.15	2.39
133	136	2.172851	ACATGCATGTTGGCCAAAAG	57.827	45.000	26.61	14.05	37.90	2.27
187	190	7.928706	ACATCTATTCTAGCCAACTGAATACAC	59.071	37.037	0.00	0.00	33.24	2.90
213	216	2.553602	TGTCCAACTGAACATGCATGTC	59.446	45.455	31.45	23.19	40.80	3.06
242	245	7.012232	CCAAAAACTGAAATAAATGCAACCTGT	59.988	33.333	0.00	0.00	0.00	4.00
393	398	3.497118	CGACAGCAAAAACACAAGAACA	58.503	40.909	0.00	0.00	0.00	3.18
439	444	8.194104	GCCACAAACCATATTAACATATTCACA	58.806	33.333	0.00	0.00	0.00	3.58
493	498	2.423538	CCCACACCTATTGCAAAGCTAC	59.576	50.000	1.71	0.00	0.00	3.58
494	499	2.095853	CCACACCTATTGCAAAGCTACG	59.904	50.000	1.71	0.00	0.00	3.51
542	548	5.005586	CGGAACTAAAAACATAACGGCGATA	59.994	40.000	16.62	6.62	0.00	2.92
752	762	4.753516	TGCTCTTGCCAGCTATTTACTA	57.246	40.909	0.00	0.00	40.39	1.82
1192	1211	2.815684	ATCAGACCGTGGTGCCCCTA	62.816	60.000	0.00	0.00	0.00	3.53
1284	1303	1.398958	CCAGGACTGAGCTAGGAGCC	61.399	65.000	0.00	0.00	43.77	4.70
1289	1308	4.075793	TGAGCTAGGAGCCGGGGT	62.076	66.667	2.18	0.00	43.77	4.95
1329	1351	4.557899	AGGAGAAGAAGGAGAGGATGAT	57.442	45.455	0.00	0.00	0.00	2.45
1396	1418	4.774200	ACAGCCTTCAAATTGCTAAGGATT	59.226	37.500	15.18	2.63	42.01	3.01
1410	1432	7.361457	TGCTAAGGATTACTACAACAGCTAT	57.639	36.000	0.00	0.00	0.00	2.97
1607	1629	3.710677	AGTGATGAGGAGATGGAAGAAGG	59.289	47.826	0.00	0.00	0.00	3.46
1734	1757	1.836166	CTGATAGATGGGCGATGGGAT	59.164	52.381	0.00	0.00	0.00	3.85
1983	2010	6.449635	AAAATGACTTAACTGTGCAACTGA	57.550	33.333	0.00	0.00	39.30	3.41
2000	2027	2.644299	ACTGATGTCCAACTTCCCATGA	59.356	45.455	0.00	0.00	0.00	3.07
2009	2036	4.039004	TCCAACTTCCCATGATGTTTTGTG	59.961	41.667	0.00	0.00	36.91	3.33
2114	2141	6.040247	AGTGTTTTTAAAAAGGTGCAGCTAC	58.960	36.000	20.51	11.37	0.00	3.58
2163	2190	3.377172	GTGCCAACACATGTCCTATTACC	59.623	47.826	0.00	0.00	46.61	2.85
2174	2201	0.532862	CCTATTACCGTGCAGCTGGG	60.533	60.000	17.12	11.00	0.00	4.45
2542	2597	8.951787	TTGTAGTGATTGTAACAGTAACAACT	57.048	30.769	0.00	0.00	39.51	3.16
2573	2628	9.826574	AGTAAATAAGCGAAAACCAGTATATGA	57.173	29.630	0.00	0.00	0.00	2.15
2649	2704	8.923270	TCATCATGTAACAGTCATAACATAGGA	58.077	33.333	0.00	0.00	31.55	2.94
2704	2759	7.817478	TGTAATGTAGGCATGTATTCCGAATAG	59.183	37.037	0.81	0.00	35.15	1.73
2706	2761	5.779922	TGTAGGCATGTATTCCGAATAGTC	58.220	41.667	0.81	0.00	0.00	2.59
3150	3205	0.253044	CATCCAACCCATCACCGTCT	59.747	55.000	0.00	0.00	0.00	4.18
3275	3330	0.028242	CTCGAACGGACTCCAGATCG	59.972	60.000	10.96	10.96	0.00	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
18	19	5.160641	GTGTGGTACAATGCATGTTTTAGG	58.839	41.667	0.00	0.00	44.16	2.69
38	39	1.736645	GCATGCCGAGTACACGTGT	60.737	57.895	26.52	26.52	0.00	4.49
79	80	7.639461	CCAGAAAACATGTTTTTATTTGCACAC	59.361	33.333	31.42	17.43	42.26	3.82
133	136	3.620488	TGGCCAGGATACATTTTCTCAC	58.380	45.455	0.00	0.00	41.41	3.51
187	190	3.814842	TGCATGTTCAGTTGGACAGTTAG	59.185	43.478	0.00	0.00	0.00	2.34
213	216	4.450419	TGCATTTATTTCAGTTTTTGGCCG	59.550	37.500	0.00	0.00	0.00	6.13
242	245	5.303078	GGCTAGAATAGATGTCTCAGTTGGA	59.697	44.000	0.00	0.00	42.77	3.53
393	398	4.660789	GCTTCATTAGCCATGGACAAAT	57.339	40.909	18.40	8.36	44.48	2.32
451	456	4.263068	GGGACCAGAATATATGTGTGGGAG	60.263	50.000	11.21	0.00	32.13	4.30
493	498	9.313323	CGCTATATTGAACATATTTTTACACCG	57.687	33.333	0.00	0.00	0.00	4.94
494	499	9.607285	CCGCTATATTGAACATATTTTTACACC	57.393	33.333	0.00	0.00	0.00	4.16
517	522	3.165890	GCCGTTATGTTTTTAGTTCCGC	58.834	45.455	0.00	0.00	0.00	5.54
561	567	8.697507	AACAAGAAAGAAGAATTGTAGGACAT	57.302	30.769	0.00	0.00	34.92	3.06
752	762	6.443934	TGTTATGTTAGTTGCACAGTTTGT	57.556	33.333	0.00	0.00	0.00	2.83
960	974	2.034687	GCCACACACTCCCTGCAT	59.965	61.111	0.00	0.00	0.00	3.96
1192	1211	3.324846	TCTGACTGCAAAGACACCACTAT	59.675	43.478	0.00	0.00	0.00	2.12
1284	1303	3.047877	GCTCCGTCAACAACCCCG	61.048	66.667	0.00	0.00	0.00	5.73
1289	1308	0.746204	TTGCACAGCTCCGTCAACAA	60.746	50.000	0.00	0.00	0.00	2.83
1396	1418	4.201980	CCGTAGTGCATAGCTGTTGTAGTA	60.202	45.833	0.00	0.00	0.00	1.82
1410	1432	0.981183	AGAAACCCATCCGTAGTGCA	59.019	50.000	0.00	0.00	0.00	4.57
1547	1569	4.834406	TCTGGAATAGGGTCTAGGACAT	57.166	45.455	0.14	0.00	33.68	3.06
1554	1576	5.674035	AGATTTTGGATCTGGAATAGGGTCT	59.326	40.000	0.00	0.00	0.00	3.85
1607	1629	4.578105	CCTCTTCAGCAAATATTGGAGGTC	59.422	45.833	0.00	0.00	35.66	3.85
1734	1757	2.413796	GTCACGAACAAAGTGTGTCACA	59.586	45.455	0.18	0.18	40.60	3.58
1841	1866	2.905075	TGCAGTTATACAAGATGCGCT	58.095	42.857	9.73	0.00	39.74	5.92
1983	2010	3.744940	ACATCATGGGAAGTTGGACAT	57.255	42.857	0.00	0.00	0.00	3.06
2000	2027	7.847557	AAGCACCAAAAGTGATACACAAAACAT	60.848	33.333	4.75	0.00	46.71	2.71
2009	2036	4.739716	CACAACAAGCACCAAAAGTGATAC	59.260	41.667	0.00	0.00	46.71	2.24
2114	2141	1.086696	AATCGCAGGAAATGGACACG	58.913	50.000	0.00	0.00	0.00	4.49
2386	2440	3.316308	GGTTGAATTGACAACTCAGCTGT	59.684	43.478	14.67	0.00	46.17	4.40
2542	2597	7.708998	ACTGGTTTTCGCTTATTTACTTTTCA	58.291	30.769	0.00	0.00	0.00	2.69
2573	2628	0.393820	TCCGGTGCCTACGAGTTTTT	59.606	50.000	0.00	0.00	0.00	1.94
2649	2704	3.169099	ACTGGAGCTAGTTCTGTGTCAT	58.831	45.455	6.54	0.00	0.00	3.06
2704	2759	5.810587	TCTTTTCCATAAGCACGTATGAGAC	59.189	40.000	5.32	0.00	33.97	3.36
2706	2761	6.313905	AGTTCTTTTCCATAAGCACGTATGAG	59.686	38.462	5.32	0.00	33.97	2.90
2941	2996	5.879223	AGTTCTTGATCCTATCTTGCAAGTG	59.121	40.000	25.19	15.92	37.71	3.16
3150	3205	3.838244	AATTCCATCGTAGGCTTGCTA	57.162	42.857	0.00	0.00	0.00	3.49
3202	3257	2.644299	TCATCAACCATCCTCCAACACT	59.356	45.455	0.00	0.00	0.00	3.55
3206	3261	3.682436	CGTCATCATCAACCATCCTCCAA	60.682	47.826	0.00	0.00	0.00	3.53
3275	3330	0.178958	TAATCTCTCTCGGGAGGGCC	60.179	60.000	13.54	0.00	39.80	5.80

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.