AutoCloner

Multiple sequence alignment - TraesCS1A01G277700

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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	TraesCS1A01G277700	chr1A	100.000	6354	0	0	1	6354	473036634	473042987	0.000000e+00	11734.0
1	TraesCS1A01G277700	chr1A	93.890	1784	79	16	2124	3886	70692448	70694222	0.000000e+00	2663.0
2	TraesCS1A01G277700	chr1A	89.374	1788	170	19	2121	3896	533738740	533740519	0.000000e+00	2231.0
3	TraesCS1A01G277700	chr1A	86.658	772	98	5	1	769	521875567	521876336	0.000000e+00	850.0
4	TraesCS1A01G277700	chr1A	89.535	86	7	1	5491	5574	560251594	560251679	2.420000e-19	108.0
5	TraesCS1A01G277700	chr5A	94.949	1762	78	7	2128	3888	567886860	567888611	0.000000e+00	2750.0
6	TraesCS1A01G277700	chr5A	85.227	88	9	3	5492	5576	622203936	622203850	3.160000e-13	87.9
7	TraesCS1A01G277700	chr7A	94.895	1763	76	8	2127	3887	647310941	647309191	0.000000e+00	2745.0
8	TraesCS1A01G277700	chr7A	94.457	1768	92	5	2121	3886	476297248	476299011	0.000000e+00	2717.0
9	TraesCS1A01G277700	chr7A	94.498	1763	79	9	2127	3887	609635422	609633676	0.000000e+00	2702.0
10	TraesCS1A01G277700	chr7A	93.850	1805	81	15	2119	3906	642156402	642154611	0.000000e+00	2691.0
11	TraesCS1A01G277700	chr7A	94.976	1453	69	3	2435	3886	33356656	33358105	0.000000e+00	2276.0
12	TraesCS1A01G277700	chr4A	94.662	1761	81	9	2128	3887	236003877	236002129	0.000000e+00	2719.0
13	TraesCS1A01G277700	chr3A	93.931	1796	82	11	2120	3897	499237955	499239741	0.000000e+00	2687.0
14	TraesCS1A01G277700	chr3A	89.744	156	14	2	6199	6354	376751347	376751194	1.400000e-46	198.0
15	TraesCS1A01G277700	chr3A	87.838	74	9	0	5501	5574	410084520	410084447	3.160000e-13	87.9
16	TraesCS1A01G277700	chr3A	87.838	74	9	0	5501	5574	410090184	410090111	3.160000e-13	87.9
17	TraesCS1A01G277700	chr3A	87.838	74	9	0	5501	5574	410096471	410096398	3.160000e-13	87.9
18	TraesCS1A01G277700	chr7D	92.897	1774	104	19	2128	3887	558926987	558928752	0.000000e+00	2558.0
19	TraesCS1A01G277700	chr7D	86.658	772	93	7	1	769	490898583	490897819	0.000000e+00	846.0
20	TraesCS1A01G277700	chr7D	88.462	156	17	1	6199	6354	364967480	364967634	3.020000e-43	187.0
21	TraesCS1A01G277700	chr1D	95.095	1631	58	7	3880	5495	373431183	373432806	0.000000e+00	2549.0
22	TraesCS1A01G277700	chr1D	90.620	1322	56	29	826	2127	373429924	373431197	0.000000e+00	1692.0
23	TraesCS1A01G277700	chr1D	93.482	629	32	4	5584	6205	373433734	373434360	0.000000e+00	926.0
24	TraesCS1A01G277700	chr1D	89.466	731	71	6	1	726	426866878	426867607	0.000000e+00	918.0
25	TraesCS1A01G277700	chr1D	87.067	750	85	8	1	745	438999487	439000229	0.000000e+00	837.0
26	TraesCS1A01G277700	chr1D	92.073	328	16	5	5584	5904	373432866	373433190	2.700000e-123	453.0
27	TraesCS1A01G277700	chr1D	90.411	146	13	1	6203	6348	137880498	137880642	2.340000e-44	191.0
28	TraesCS1A01G277700	chr1D	89.933	149	14	1	6206	6354	379658115	379657968	2.340000e-44	191.0
29	TraesCS1A01G277700	chr1B	94.468	1627	63	9	3889	5495	498706999	498708618	0.000000e+00	2481.0
30	TraesCS1A01G277700	chr1B	89.940	1332	62	33	826	2128	498705718	498707006	0.000000e+00	1652.0
31	TraesCS1A01G277700	chr1B	94.299	421	19	2	5939	6354	498728655	498729075	1.930000e-179	640.0
32	TraesCS1A01G277700	chr1B	93.151	365	19	4	5584	5943	498708678	498709041	1.210000e-146	531.0
33	TraesCS1A01G277700	chr1B	88.636	88	8	1	5492	5577	543504309	543504396	8.710000e-19	106.0
34	TraesCS1A01G277700	chr3D	87.183	749	91	5	1	745	527142058	527141311	0.000000e+00	846.0
35	TraesCS1A01G277700	chr3D	90.604	149	13	1	6206	6354	298456608	298456461	5.030000e-46	196.0
36	TraesCS1A01G277700	chr3D	93.506	77	5	0	5498	5574	417424008	417424084	1.450000e-21	115.0
37	TraesCS1A01G277700	chr3B	86.898	748	87	6	1	745	3627358	3628097	0.000000e+00	828.0
38	TraesCS1A01G277700	chr4D	85.824	783	96	11	1	775	465023360	465024135	0.000000e+00	817.0
39	TraesCS1A01G277700	chrUn	86.622	740	88	5	1	737	94263548	94264279	0.000000e+00	808.0
40	TraesCS1A01G277700	chr6A	85.401	774	100	8	1	769	573824101	573823336	0.000000e+00	791.0
41	TraesCS1A01G277700	chr6B	86.465	495	40	11	1003	1496	494395577	494395109	9.440000e-143	518.0
42	TraesCS1A01G277700	chr2A	91.096	146	12	1	6203	6348	144661029	144661173	5.030000e-46	196.0
43	TraesCS1A01G277700	chr2D	88.125	160	17	2	6195	6354	261229259	261229102	8.410000e-44	189.0
44	TraesCS1A01G277700	chr2D	87.500	160	18	2	6195	6354	261155442	261155285	3.910000e-42	183.0
45	TraesCS1A01G277700	chr5D	86.517	89	8	4	5490	5575	264634959	264635046	1.890000e-15	95.3
46	TraesCS1A01G277700	chr5B	85.882	85	10	1	5492	5574	499376966	499376882	8.770000e-14	89.8

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	TraesCS1A01G277700	chr1A	473036634	473042987	6353	False	11734.000000	11734	100.000000	1	6354	1	chr1A.!!$F2	6353
1	TraesCS1A01G277700	chr1A	70692448	70694222	1774	False	2663.000000	2663	93.890000	2124	3886	1	chr1A.!!$F1	1762
2	TraesCS1A01G277700	chr1A	533738740	533740519	1779	False	2231.000000	2231	89.374000	2121	3896	1	chr1A.!!$F4	1775
3	TraesCS1A01G277700	chr1A	521875567	521876336	769	False	850.000000	850	86.658000	1	769	1	chr1A.!!$F3	768
4	TraesCS1A01G277700	chr5A	567886860	567888611	1751	False	2750.000000	2750	94.949000	2128	3888	1	chr5A.!!$F1	1760
5	TraesCS1A01G277700	chr7A	647309191	647310941	1750	True	2745.000000	2745	94.895000	2127	3887	1	chr7A.!!$R3	1760
6	TraesCS1A01G277700	chr7A	476297248	476299011	1763	False	2717.000000	2717	94.457000	2121	3886	1	chr7A.!!$F2	1765
7	TraesCS1A01G277700	chr7A	609633676	609635422	1746	True	2702.000000	2702	94.498000	2127	3887	1	chr7A.!!$R1	1760
8	TraesCS1A01G277700	chr7A	642154611	642156402	1791	True	2691.000000	2691	93.850000	2119	3906	1	chr7A.!!$R2	1787
9	TraesCS1A01G277700	chr7A	33356656	33358105	1449	False	2276.000000	2276	94.976000	2435	3886	1	chr7A.!!$F1	1451
10	TraesCS1A01G277700	chr4A	236002129	236003877	1748	True	2719.000000	2719	94.662000	2128	3887	1	chr4A.!!$R1	1759
11	TraesCS1A01G277700	chr3A	499237955	499239741	1786	False	2687.000000	2687	93.931000	2120	3897	1	chr3A.!!$F1	1777
12	TraesCS1A01G277700	chr7D	558926987	558928752	1765	False	2558.000000	2558	92.897000	2128	3887	1	chr7D.!!$F2	1759
13	TraesCS1A01G277700	chr7D	490897819	490898583	764	True	846.000000	846	86.658000	1	769	1	chr7D.!!$R1	768
14	TraesCS1A01G277700	chr1D	373429924	373434360	4436	False	1405.000000	2549	92.817500	826	6205	4	chr1D.!!$F4	5379
15	TraesCS1A01G277700	chr1D	426866878	426867607	729	False	918.000000	918	89.466000	1	726	1	chr1D.!!$F2	725
16	TraesCS1A01G277700	chr1D	438999487	439000229	742	False	837.000000	837	87.067000	1	745	1	chr1D.!!$F3	744
17	TraesCS1A01G277700	chr1B	498705718	498709041	3323	False	1554.666667	2481	92.519667	826	5943	3	chr1B.!!$F3	5117
18	TraesCS1A01G277700	chr3D	527141311	527142058	747	True	846.000000	846	87.183000	1	745	1	chr3D.!!$R2	744
19	TraesCS1A01G277700	chr3B	3627358	3628097	739	False	828.000000	828	86.898000	1	745	1	chr3B.!!$F1	744
20	TraesCS1A01G277700	chr4D	465023360	465024135	775	False	817.000000	817	85.824000	1	775	1	chr4D.!!$F1	774
21	TraesCS1A01G277700	chrUn	94263548	94264279	731	False	808.000000	808	86.622000	1	737	1	chrUn.!!$F1	736
22	TraesCS1A01G277700	chr6A	573823336	573824101	765	True	791.000000	791	85.401000	1	769	1	chr6A.!!$R1	768

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
521	537	0.038892	AAACTCCTACGAAAGCGCGA	60.039	50.0	12.10	0.0	42.48	5.87	F
954	987	0.107643	GCTCCTCCCATAGCCAGAAC	59.892	60.0	0.00	0.0	32.40	3.01	F
2463	2539	0.036765	TCCGCCACGCTTCAATAACT	60.037	50.0	0.00	0.0	0.00	2.24	F
3726	3861	0.114168	ACAATGGGCCCTTGCTACAA	59.886	50.0	25.70	0.0	37.74	2.41	F
4458	4615	0.244721	GGCTTGTCCACAAATGCTCC	59.755	55.0	4.29	0.0	35.15	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1747	1811	0.512952	GTCTGCAACCTGTTACAGCG	59.487	55.0	6.88	3.2	34.71	5.18	R
2659	2740	0.621082	TCATTGTGGCCGGATGGTTA	59.379	50.0	5.05	0.0	37.67	2.85	R
3827	3962	0.951558	GGTCAGTTTGGTGCACGAAT	59.048	50.0	15.36	0.0	0.00	3.34	R
4865	5022	0.391661	CCTCCCACGTCATCACTTGG	60.392	60.0	0.00	0.0	40.89	3.61	R
5741	5904	0.803768	CAACGGAGACATGAGAGCGG	60.804	60.0	0.00	0.0	0.00	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
91	92	5.163933	GGTGTTCGCAAAGTAATCGACATAA	60.164	40.000	0.00	0.00	31.48	1.90
114	123	2.419739	GGGCGTGACCTCTCTCTCC	61.420	68.421	0.00	0.00	39.10	3.71
120	131	0.539669	TGACCTCTCTCTCCGTTGCA	60.540	55.000	0.00	0.00	0.00	4.08
170	182	1.265454	CCCCTGTACCGAGGAAGCTT	61.265	60.000	0.00	0.00	34.69	3.74
417	430	0.458716	GCACTCGACAGAAGCTACCC	60.459	60.000	0.00	0.00	0.00	3.69
452	468	2.571216	CCGGCGATCGTATCCCCTT	61.571	63.158	17.81	0.00	37.11	3.95
498	514	0.895530	AAATCTCCTCCAAGCGACGA	59.104	50.000	0.00	0.00	0.00	4.20
521	537	0.038892	AAACTCCTACGAAAGCGCGA	60.039	50.000	12.10	0.00	42.48	5.87
548	564	1.311859	AACGGCCATATCGAGACGTA	58.688	50.000	2.24	0.00	33.85	3.57
564	580	2.170166	ACGTAGTTTGGTATGGACGGA	58.830	47.619	0.00	0.00	37.78	4.69
565	581	2.762327	ACGTAGTTTGGTATGGACGGAT	59.238	45.455	0.00	0.00	37.78	4.18
569	585	2.704065	AGTTTGGTATGGACGGATAGGG	59.296	50.000	0.00	0.00	0.00	3.53
570	586	2.701951	GTTTGGTATGGACGGATAGGGA	59.298	50.000	0.00	0.00	0.00	4.20
594	616	1.915769	GGGTGAGCTGTGAGGAGGT	60.916	63.158	0.00	0.00	0.00	3.85
644	666	1.995626	GGTAGGGCAGGGAAGAGCA	60.996	63.158	0.00	0.00	0.00	4.26
658	680	3.240134	GAGCAGGTGGAGGCGTTGA	62.240	63.158	0.00	0.00	34.54	3.18
685	710	2.506065	GGACTGCTAGTGTCCCGAT	58.494	57.895	19.74	0.00	46.01	4.18
688	713	2.573369	GACTGCTAGTGTCCCGATAGA	58.427	52.381	6.72	0.00	39.76	1.98
707	733	1.450211	CGGGCCACGGGAGAATAAT	59.550	57.895	4.39	0.00	39.42	1.28
717	743	1.014352	GGAGAATAATGGCGTGCGTT	58.986	50.000	0.00	0.00	0.00	4.84
745	771	1.671328	TCCACGCGATGTTTGTTTCAA	59.329	42.857	15.93	0.00	0.00	2.69
747	773	3.049206	CCACGCGATGTTTGTTTCAATT	58.951	40.909	15.93	0.00	0.00	2.32
748	774	3.489047	CCACGCGATGTTTGTTTCAATTT	59.511	39.130	15.93	0.00	0.00	1.82
759	785	6.369065	TGTTTGTTTCAATTTAAACTTGGCGT	59.631	30.769	14.56	0.00	39.57	5.68
773	799	3.921677	CTTGGCGTAAGTTTAGGTCAGA	58.078	45.455	0.12	0.00	35.03	3.27

Showing 1 to 25 of 238 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	2.415357	CGTTTTCGTATGGCAAGGCATT	60.415	45.455	14.49	0.00	38.65	3.56
91	92	2.925170	AGAGGTCACGCCCTGCTT	60.925	61.111	0.00	0.00	38.26	3.91
114	123	0.958091	TCCCAACCTGAATTGCAACG	59.042	50.000	0.00	0.00	0.00	4.10
120	131	0.609131	CCGTGCTCCCAACCTGAATT	60.609	55.000	0.00	0.00	0.00	2.17
174	186	1.778334	TCGTTCACGACCACATTGAG	58.222	50.000	0.00	0.00	44.22	3.02
197	209	2.592102	AGATCTTGTGGTGGTTGCAT	57.408	45.000	0.00	0.00	0.00	3.96
241	253	6.851609	TCTTCCACCATTTCATTTATTCGTG	58.148	36.000	0.00	0.00	0.00	4.35
243	255	8.755696	TTTTCTTCCACCATTTCATTTATTCG	57.244	30.769	0.00	0.00	0.00	3.34
272	284	4.660303	ACAAAGGCATGGATAGTGGAGATA	59.340	41.667	0.00	0.00	0.00	1.98
417	430	1.006102	GGCGACGGATATGGACCAG	60.006	63.158	0.00	0.00	0.00	4.00
452	468	4.728102	CGTCGTAGCCGGTGCCAA	62.728	66.667	1.90	0.00	38.69	4.52
478	494	2.097036	TCGTCGCTTGGAGGAGATTTA	58.903	47.619	0.00	0.00	34.77	1.40
498	514	2.140717	CGCTTTCGTAGGAGTTTTGGT	58.859	47.619	0.00	0.00	0.00	3.67
521	537	0.249741	GATATGGCCGTTACCACGCT	60.250	55.000	0.77	0.00	45.72	5.07
529	545	1.266175	CTACGTCTCGATATGGCCGTT	59.734	52.381	0.77	0.00	0.00	4.44
530	546	0.873054	CTACGTCTCGATATGGCCGT	59.127	55.000	1.35	1.35	0.00	5.68
538	554	3.949754	TCCATACCAAACTACGTCTCGAT	59.050	43.478	0.00	0.00	0.00	3.59
548	564	2.704065	CCCTATCCGTCCATACCAAACT	59.296	50.000	0.00	0.00	0.00	2.66
584	606	4.631740	TCCGGCCACCTCCTCACA	62.632	66.667	2.24	0.00	0.00	3.58
594	616	1.971505	CTGCCACTATTCTCCGGCCA	61.972	60.000	2.24	0.00	44.22	5.36
629	651	3.013932	CCTGCTCTTCCCTGCCCT	61.014	66.667	0.00	0.00	0.00	5.19
638	660	2.520536	AACGCCTCCACCTGCTCTT	61.521	57.895	0.00	0.00	0.00	2.85
644	666	2.750350	CCTTCAACGCCTCCACCT	59.250	61.111	0.00	0.00	0.00	4.00
658	680	0.905357	ACTAGCAGTCCATTCGCCTT	59.095	50.000	0.00	0.00	0.00	4.35
685	710	2.866523	ATTCTCCCGTGGCCCGTCTA	62.867	60.000	0.00	0.00	33.66	2.59

Showing 1 to 25 of 249 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.