AutoCloner

Multiple sequence alignment - TraesCS3B01G263900

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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	TraesCS3B01G263900	chr3B	100.000	2411	0	0	1	2411	422514092	422511682	0.000000e+00	4453
1	TraesCS3B01G263900	chr3D	95.894	1656	47	9	7	1652	326869883	326871527	0.000000e+00	2662
2	TraesCS3B01G263900	chr3D	83.443	761	109	13	1661	2411	26308428	26307675	0.000000e+00	691
3	TraesCS3B01G263900	chr3D	81.641	768	118	16	1652	2411	545791818	545791066	1.220000e-172	616
4	TraesCS3B01G263900	chr3D	81.061	528	81	17	1645	2160	595284106	595284626	1.040000e-108	403
5	TraesCS3B01G263900	chr3D	79.497	517	75	26	1638	2138	556628630	556629131	2.970000e-89	339
6	TraesCS3B01G263900	chr3A	92.338	1788	82	17	180	1957	440607099	440608841	0.000000e+00	2492
7	TraesCS3B01G263900	chr3A	85.392	753	97	10	1651	2394	552530698	552529950	0.000000e+00	769
8	TraesCS3B01G263900	chr3A	81.889	773	121	16	1650	2411	86383261	86382497	3.380000e-178	634
9	TraesCS3B01G263900	chr3A	90.826	109	7	1	74	179	440606835	440606943	2.500000e-30	143
10	TraesCS3B01G263900	chr5D	84.928	763	80	12	1651	2408	232006868	232007600	0.000000e+00	739
11	TraesCS3B01G263900	chr1A	83.798	753	109	9	1649	2394	8227946	8228692	0.000000e+00	702
12	TraesCS3B01G263900	chr1D	87.288	118	6	4	521	629	2194719	2194602	2.520000e-25	126

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	TraesCS3B01G263900	chr3B	422511682	422514092	2410	True	4453.0	4453	100.000	1	2411	1	chr3B.!!$R1	2410
1	TraesCS3B01G263900	chr3D	326869883	326871527	1644	False	2662.0	2662	95.894	7	1652	1	chr3D.!!$F1	1645
2	TraesCS3B01G263900	chr3D	26307675	26308428	753	True	691.0	691	83.443	1661	2411	1	chr3D.!!$R1	750
3	TraesCS3B01G263900	chr3D	545791066	545791818	752	True	616.0	616	81.641	1652	2411	1	chr3D.!!$R2	759
4	TraesCS3B01G263900	chr3D	595284106	595284626	520	False	403.0	403	81.061	1645	2160	1	chr3D.!!$F3	515
5	TraesCS3B01G263900	chr3D	556628630	556629131	501	False	339.0	339	79.497	1638	2138	1	chr3D.!!$F2	500
6	TraesCS3B01G263900	chr3A	440606835	440608841	2006	False	1317.5	2492	91.582	74	1957	2	chr3A.!!$F1	1883
7	TraesCS3B01G263900	chr3A	552529950	552530698	748	True	769.0	769	85.392	1651	2394	1	chr3A.!!$R2	743
8	TraesCS3B01G263900	chr3A	86382497	86383261	764	True	634.0	634	81.889	1650	2411	1	chr3A.!!$R1	761
9	TraesCS3B01G263900	chr5D	232006868	232007600	732	False	739.0	739	84.928	1651	2408	1	chr5D.!!$F1	757
10	TraesCS3B01G263900	chr1A	8227946	8228692	746	False	702.0	702	83.798	1649	2394	1	chr1A.!!$F1	745

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
115	116	0.172803	AATGTAGGACTGTCGCGGTC	59.827	55.0	6.13	5.77	38.88	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2060	2239	0.038166	TCCCTGCATCTTTTTCGGCT	59.962	50.0	0.0	0.0	0.0	5.52	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
72	73	6.183359	CGAACTATAATGCACTTGCTATCTCG	60.183	42.308	2.33	0.68	42.66	4.04
115	116	0.172803	AATGTAGGACTGTCGCGGTC	59.827	55.000	6.13	5.77	38.88	4.79
123	127	3.553437	CTGTCGCGGTCTTGTCGGT	62.553	63.158	6.13	0.00	0.00	4.69
169	173	6.949715	ACGGGGAGTTTAGTTTGAATGTATA	58.050	36.000	0.00	0.00	0.00	1.47
245	404	5.048991	ACCTTTCGTACTGGTTATTTGCTTG	60.049	40.000	0.00	0.00	0.00	4.01
280	439	5.359860	TGATGATAAGTAAAGGCTCACTCGA	59.640	40.000	2.54	0.00	0.00	4.04
356	515	8.963725	TGTTGATATTGATTTGCTTCTGAATCT	58.036	29.630	0.00	0.00	34.24	2.40
371	530	3.141398	TGAATCTTGTCTGTCCAAGCAC	58.859	45.455	0.00	0.00	41.29	4.40
376	535	1.279840	GTCTGTCCAAGCACAACGC	59.720	57.895	0.00	0.00	42.91	4.84
402	566	4.603231	TTGACAAATATTTCCGCGGTAC	57.397	40.909	27.15	1.00	0.00	3.34
516	682	2.777972	CGGGAATCCTACGTGGCGA	61.778	63.158	0.00	0.00	35.26	5.54
594	760	1.348064	AGGGATTTGACGTCACCAGA	58.652	50.000	19.90	0.00	0.00	3.86
660	826	1.131315	TGACAGCGACTCGATTCTCAG	59.869	52.381	1.63	0.00	0.00	3.35
741	907	1.065401	TCCACAAAGCAAGCGTTTCAG	59.935	47.619	0.00	0.00	0.00	3.02
896	1062	1.300963	GGTCATGCCTCCTGCTTCA	59.699	57.895	0.00	0.00	42.00	3.02
948	1114	1.913778	TGCAATGCAACCTCAGACAT	58.086	45.000	5.01	0.00	34.76	3.06
1350	1516	0.673644	CCACCGGCAAGATCGTCTTT	60.674	55.000	0.00	0.00	33.78	2.52
1455	1621	2.660900	CGTATTTATACCGCGGCTTTGC	60.661	50.000	28.58	7.08	0.00	3.68
1591	1757	6.025896	ACTATCGTATCGTTACAAGTGTGTG	58.974	40.000	4.63	0.00	38.82	3.82
1592	1758	2.981805	TCGTATCGTTACAAGTGTGTGC	59.018	45.455	4.63	0.00	38.82	4.57
1599	1765	1.662517	TACAAGTGTGTGCCAGTGTG	58.337	50.000	0.00	0.00	38.82	3.82
1600	1766	0.322456	ACAAGTGTGTGCCAGTGTGT	60.322	50.000	0.00	0.00	36.31	3.72
1613	1779	2.538737	CCAGTGTGTGCGTTGTACTTTG	60.539	50.000	0.00	0.00	0.00	2.77
1770	1940	2.291465	GTGAGCATTGTGTCTGAAGCAA	59.709	45.455	0.00	0.00	0.00	3.91
1772	1942	3.380954	TGAGCATTGTGTCTGAAGCAAAA	59.619	39.130	0.00	0.00	0.00	2.44
1880	2056	2.103771	CGACCAACATCTCCAGATCCAT	59.896	50.000	0.00	0.00	31.21	3.41
1911	2087	2.094659	CGCGAGCAACCAAGACGAT	61.095	57.895	0.00	0.00	0.00	3.73
1920	2096	0.396435	ACCAAGACGATGCCTTCACA	59.604	50.000	0.00	0.00	0.00	3.58
1933	2109	1.581934	CTTCACAAAGGAGCACGACA	58.418	50.000	0.00	0.00	0.00	4.35
2087	2273	0.257039	AAGATGCAGGGATTTCGCCT	59.743	50.000	0.00	0.00	0.00	5.52
2099	2285	2.050836	TTTCGCCTTGGCCTGAGTCA	62.051	55.000	3.32	0.00	0.00	3.41
2182	2371	1.296392	CACAGGAATGGGAGCGACA	59.704	57.895	0.00	0.00	0.00	4.35
2227	2416	3.485346	GAGGGACAAACGGGGCACA	62.485	63.158	0.00	0.00	0.00	4.57
2281	2470	3.001902	GCGGTGGAGGATGTGACGA	62.002	63.158	0.00	0.00	0.00	4.20
2311	2500	2.490148	CCGAGCGAGCCAGTATCCA	61.490	63.158	0.00	0.00	0.00	3.41
2317	2506	1.467678	CGAGCCAGTATCCAGAGGGG	61.468	65.000	0.00	0.00	38.37	4.79
2318	2507	1.074167	AGCCAGTATCCAGAGGGGG	60.074	63.158	0.00	0.00	37.22	5.40
2353	2542	0.106918	ACCAGGACCGAAGCAACAAA	60.107	50.000	0.00	0.00	0.00	2.83
2376	2565	1.303398	TCGACAAGTCCGAGGAGCT	60.303	57.895	0.00	0.00	0.00	4.09
2389	2580	4.722700	GAGCTGGAAGGGGCGCAA	62.723	66.667	10.83	0.00	0.00	4.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	22	4.090066	CGCATACACTGATATAGCGGTTTC	59.910	45.833	0.00	0.00	40.00	2.78
24	25	2.557056	ACGCATACACTGATATAGCGGT	59.443	45.455	8.76	0.00	46.96	5.68
25	26	3.217599	ACGCATACACTGATATAGCGG	57.782	47.619	8.76	0.00	46.96	5.52
72	73	1.882623	CTTGTTGCTCCTTCAGGTTCC	59.117	52.381	0.00	0.00	36.34	3.62
115	116	1.719780	GCGAACTAGTTGACCGACAAG	59.280	52.381	14.14	0.00	39.30	3.16
123	127	6.347079	CCGTTTAATTCTTGCGAACTAGTTGA	60.347	38.462	14.14	0.17	30.67	3.18
142	146	6.063404	ACATTCAAACTAAACTCCCCGTTTA	58.937	36.000	0.00	0.00	43.75	2.01
245	404	6.624352	TTACTTATCATCATCAGGCAAAGC	57.376	37.500	0.00	0.00	0.00	3.51
280	439	2.093553	GCTCAGAGCCATCTTCAGAAGT	60.094	50.000	11.84	0.00	34.48	3.01
356	515	1.013596	CGTTGTGCTTGGACAGACAA	58.986	50.000	0.00	0.00	0.00	3.18
371	530	7.600039	CGGAAATATTTGTCAAAATAGCGTTG	58.400	34.615	5.17	0.00	40.65	4.10
376	535	6.262601	ACCGCGGAAATATTTGTCAAAATAG	58.737	36.000	35.90	0.00	40.65	1.73
377	536	6.197364	ACCGCGGAAATATTTGTCAAAATA	57.803	33.333	35.90	0.00	41.37	1.40
378	537	5.066968	ACCGCGGAAATATTTGTCAAAAT	57.933	34.783	35.90	0.00	39.38	1.82
402	566	7.526186	CGTCAAACAGTGTTATAACTCGAAAAG	59.474	37.037	16.33	6.64	0.00	2.27
489	655	2.292267	GTAGGATTCCCGTACTCGTCA	58.708	52.381	0.00	0.00	37.58	4.35
594	760	3.058293	TGCGATTGAGAATTCTGCGTTTT	60.058	39.130	14.00	0.00	0.00	2.43
660	826	1.270252	CCATTGGTCAGTTTTGCACCC	60.270	52.381	0.00	0.00	0.00	4.61
741	907	1.792949	CTACTTCTGTGTGTTGCGACC	59.207	52.381	0.45	0.00	0.00	4.79
896	1062	2.105993	GGGGTTTATAAGGCGTGGAGAT	59.894	50.000	0.00	0.00	0.00	2.75
948	1114	0.937699	GCTCGTGTCGTGTGTGCTTA	60.938	55.000	0.00	0.00	0.00	3.09
1062	1228	1.293498	GAACTCCTCCAGCAGCGAA	59.707	57.895	0.00	0.00	0.00	4.70
1455	1621	6.740411	AGTAGTAGTAGTCTTCAACGAAGG	57.260	41.667	4.02	0.00	39.82	3.46
1502	1668	1.169661	AACGAATGCACCCGCTTCAA	61.170	50.000	9.18	0.00	39.64	2.69
1511	1677	3.157510	TCGCGAAATTAAACGAATGCAC	58.842	40.909	6.20	0.00	0.00	4.57
1591	1757	1.157870	AGTACAACGCACACACTGGC	61.158	55.000	0.00	0.00	0.00	4.85
1592	1758	1.295792	AAGTACAACGCACACACTGG	58.704	50.000	0.00	0.00	0.00	4.00
1599	1765	1.328374	ACGGTTCAAAGTACAACGCAC	59.672	47.619	0.00	0.00	0.00	5.34
1600	1766	1.328069	CACGGTTCAAAGTACAACGCA	59.672	47.619	0.00	0.00	0.00	5.24
1657	1823	7.764695	TGATACATAAGTTGTGTATTCGTGG	57.235	36.000	21.76	0.00	41.50	4.94
1772	1942	1.901833	GGGTTGAGCATCCCATGTTTT	59.098	47.619	10.97	0.00	42.95	2.43
1774	1944	3.288099	GGGTTGAGCATCCCATGTT	57.712	52.632	10.97	0.00	42.95	2.71
1814	1987	2.427453	TCTCAGGATGACGAGTTTAGCC	59.573	50.000	0.00	0.00	42.56	3.93
1880	2056	1.880894	CTCGCGGTGTCCTCAGTTA	59.119	57.895	6.13	0.00	0.00	2.24
1920	2096	1.006102	CTCGGTGTCGTGCTCCTTT	60.006	57.895	0.00	0.00	37.69	3.11
1927	2103	3.626680	ATGGCGTCTCGGTGTCGTG	62.627	63.158	0.00	0.00	37.69	4.35
1933	2109	4.129737	CGGTGATGGCGTCTCGGT	62.130	66.667	8.40	0.00	0.00	4.69
1976	2152	1.839994	TCTTCGAGCATCAGGGGAAAT	59.160	47.619	0.00	0.00	33.17	2.17
2003	2179	0.598158	GTTGTCACGGCCGTTGTCTA	60.598	55.000	32.11	15.50	0.00	2.59
2060	2239	0.038166	TCCCTGCATCTTTTTCGGCT	59.962	50.000	0.00	0.00	0.00	5.52
2061	2240	1.106285	ATCCCTGCATCTTTTTCGGC	58.894	50.000	0.00	0.00	0.00	5.54
2063	2242	3.429085	CGAAATCCCTGCATCTTTTTCG	58.571	45.455	15.50	15.50	39.31	3.46
2065	2244	2.094026	GGCGAAATCCCTGCATCTTTTT	60.094	45.455	0.00	0.00	0.00	1.94
2087	2273	0.694771	ATTGCTCTGACTCAGGCCAA	59.305	50.000	5.01	9.71	30.52	4.52
2099	2285	0.465097	CGATGGCTTGGGATTGCTCT	60.465	55.000	0.00	0.00	0.00	4.09
2160	2349	1.685224	GCTCCCATTCCTGTGGTCA	59.315	57.895	0.00	0.00	37.57	4.02
2245	2434	3.901797	CTTCCCGTTCCGCCAAGCT	62.902	63.158	0.00	0.00	0.00	3.74
2257	2446	3.470888	ATCCTCCACCGCTTCCCG	61.471	66.667	0.00	0.00	0.00	5.14
2317	2506	1.221021	GTGACCCGGATCTTCACCC	59.779	63.158	0.73	0.00	34.72	4.61
2318	2507	4.934989	GTGACCCGGATCTTCACC	57.065	61.111	0.73	0.00	34.72	4.02
2320	2509	1.264749	CCTGGTGACCCGGATCTTCA	61.265	60.000	6.16	0.00	39.78	3.02
2322	2511	1.080354	TCCTGGTGACCCGGATCTT	59.920	57.895	11.01	0.00	39.78	2.40
2353	2542	1.575576	CCTCGGACTTGTCGACGTCT	61.576	60.000	18.90	1.53	32.86	4.18
2376	2565	4.344865	GGAGTTGCGCCCCTTCCA	62.345	66.667	4.18	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.