AutoCloner

Multiple sequence alignment - TraesCS1B01G388500

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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	TraesCS1B01G388500	chr1B	100.000	2798	0	0	1	2798	622357754	622360551	0.000000e+00	5168
1	TraesCS1B01G388500	chr1B	95.927	2799	102	4	1	2798	622312114	622314901	0.000000e+00	4527
2	TraesCS1B01G388500	chr1B	93.194	2160	109	22	646	2798	622217993	622220121	0.000000e+00	3140
3	TraesCS1B01G388500	chr1A	92.210	1810	80	20	622	2390	547238878	547237089	0.000000e+00	2505
4	TraesCS1B01G388500	chr1A	92.108	1812	80	20	622	2390	547216982	547215191	0.000000e+00	2495
5	TraesCS1B01G388500	chr1D	91.816	1784	104	18	622	2390	452262540	452260784	0.000000e+00	2447
6	TraesCS1B01G388500	chr1D	91.921	1374	79	19	644	2005	452270299	452268946	0.000000e+00	1893
7	TraesCS1B01G388500	chr1D	91.138	1388	87	21	628	2005	452265414	452264053	0.000000e+00	1849
8	TraesCS1B01G388500	chr1D	92.118	1053	70	9	961	2005	452337954	452336907	0.000000e+00	1472
9	TraesCS1B01G388500	chr1D	89.834	541	46	8	1	532	132862936	132862396	0.000000e+00	686
10	TraesCS1B01G388500	chr1D	94.203	138	7	1	1966	2102	452264047	452263910	2.820000e-50	209
11	TraesCS1B01G388500	chr1D	92.857	140	7	2	1966	2102	452268940	452268801	1.700000e-47	200
12	TraesCS1B01G388500	chrUn	92.544	1529	70	11	622	2124	246249905	246248395	0.000000e+00	2152
13	TraesCS1B01G388500	chrUn	92.375	1036	49	13	1379	2390	416393732	416394761	0.000000e+00	1448
14	TraesCS1B01G388500	chrUn	93.061	245	10	3	622	861	362688419	362688661	4.430000e-93	351
15	TraesCS1B01G388500	chr2D	86.615	650	58	8	1	621	646431173	646431822	0.000000e+00	691
16	TraesCS1B01G388500	chr7D	86.399	647	63	14	1	636	91566397	91565765	0.000000e+00	684
17	TraesCS1B01G388500	chr7D	86.068	646	57	18	1	633	618329976	618329351	0.000000e+00	664
18	TraesCS1B01G388500	chr7D	82.315	311	51	3	2490	2798	428978699	428979007	1.650000e-67	267
19	TraesCS1B01G388500	chr3B	86.614	635	64	8	3	627	710395542	710394919	0.000000e+00	682
20	TraesCS1B01G388500	chr3B	77.708	637	82	36	3	617	97081509	97080911	4.470000e-88	335
21	TraesCS1B01G388500	chr3B	84.713	314	23	12	48	358	657536932	657537223	9.800000e-75	291
22	TraesCS1B01G388500	chr3D	84.592	649	68	9	1	617	348273277	348272629	1.420000e-172	616
23	TraesCS1B01G388500	chr6B	86.458	576	55	9	50	615	506550562	506551124	6.630000e-171	610
24	TraesCS1B01G388500	chr6B	83.387	313	46	6	2489	2798	518677005	518676696	4.560000e-73	285
25	TraesCS1B01G388500	chr7B	85.161	620	55	22	1	598	43562105	43562709	3.990000e-168	601
26	TraesCS1B01G388500	chr7B	82.595	316	50	5	2485	2798	104298643	104298955	9.870000e-70	274
27	TraesCS1B01G388500	chr5D	84.044	633	73	16	1	624	168637143	168636530	4.020000e-163	584
28	TraesCS1B01G388500	chr6D	83.544	316	42	7	2485	2798	428978509	428978816	1.270000e-73	287
29	TraesCS1B01G388500	chr6D	83.013	312	51	2	2488	2798	20134782	20134472	5.900000e-72	281
30	TraesCS1B01G388500	chr6A	82.540	315	51	4	2485	2798	573641598	573641909	9.870000e-70	274
31	TraesCS1B01G388500	chr4D	82.166	314	50	5	2488	2798	46027109	46026799	5.940000e-67	265

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	TraesCS1B01G388500	chr1B	622357754	622360551	2797	False	5168.0	5168	100.000	1	2798	1	chr1B.!!$F3	2797
1	TraesCS1B01G388500	chr1B	622312114	622314901	2787	False	4527.0	4527	95.927	1	2798	1	chr1B.!!$F2	2797
2	TraesCS1B01G388500	chr1B	622217993	622220121	2128	False	3140.0	3140	93.194	646	2798	1	chr1B.!!$F1	2152
3	TraesCS1B01G388500	chr1A	547237089	547238878	1789	True	2505.0	2505	92.210	622	2390	1	chr1A.!!$R2	1768
4	TraesCS1B01G388500	chr1A	547215191	547216982	1791	True	2495.0	2495	92.108	622	2390	1	chr1A.!!$R1	1768
5	TraesCS1B01G388500	chr1D	452336907	452337954	1047	True	1472.0	1472	92.118	961	2005	1	chr1D.!!$R2	1044
6	TraesCS1B01G388500	chr1D	452260784	452270299	9515	True	1319.6	2447	92.387	622	2390	5	chr1D.!!$R3	1768
7	TraesCS1B01G388500	chr1D	132862396	132862936	540	True	686.0	686	89.834	1	532	1	chr1D.!!$R1	531
8	TraesCS1B01G388500	chrUn	246248395	246249905	1510	True	2152.0	2152	92.544	622	2124	1	chrUn.!!$R1	1502
9	TraesCS1B01G388500	chrUn	416393732	416394761	1029	False	1448.0	1448	92.375	1379	2390	1	chrUn.!!$F2	1011
10	TraesCS1B01G388500	chr2D	646431173	646431822	649	False	691.0	691	86.615	1	621	1	chr2D.!!$F1	620
11	TraesCS1B01G388500	chr7D	91565765	91566397	632	True	684.0	684	86.399	1	636	1	chr7D.!!$R1	635
12	TraesCS1B01G388500	chr7D	618329351	618329976	625	True	664.0	664	86.068	1	633	1	chr7D.!!$R2	632
13	TraesCS1B01G388500	chr3B	710394919	710395542	623	True	682.0	682	86.614	3	627	1	chr3B.!!$R2	624
14	TraesCS1B01G388500	chr3B	97080911	97081509	598	True	335.0	335	77.708	3	617	1	chr3B.!!$R1	614
15	TraesCS1B01G388500	chr3D	348272629	348273277	648	True	616.0	616	84.592	1	617	1	chr3D.!!$R1	616
16	TraesCS1B01G388500	chr6B	506550562	506551124	562	False	610.0	610	86.458	50	615	1	chr6B.!!$F1	565
17	TraesCS1B01G388500	chr7B	43562105	43562709	604	False	601.0	601	85.161	1	598	1	chr7B.!!$F1	597
18	TraesCS1B01G388500	chr5D	168636530	168637143	613	True	584.0	584	84.044	1	624	1	chr5D.!!$R1	623

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
523	597	3.056678	TGCAATACAGGCAACCAATCAAG	60.057	43.478	0.0	0.0	38.54	3.02	F
1021	1120	1.518572	GCGACTACCACCATGTCCG	60.519	63.158	0.0	0.0	0.00	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1475	1574	1.544093	CGACTTGGCATGCCCAGATAT	60.544	52.381	37.16	19.91	46.39	1.63	R
2542	10442	1.065199	TGTCTAGTATCGTCGGTGGGT	60.065	52.381	0.00	0.00	0.00	4.51	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
362	435	3.423867	GTGTGTGTTGTGTGTTGTCAAAC	59.576	43.478	0.00	0.00	36.78	2.93
523	597	3.056678	TGCAATACAGGCAACCAATCAAG	60.057	43.478	0.00	0.00	38.54	3.02
534	608	5.458891	GCAACCAATCAAGATGCAGATATC	58.541	41.667	0.00	0.00	37.00	1.63
590	665	6.594159	CCAGTTAGGACAAGTATGTAAAGTGG	59.406	42.308	9.06	9.06	40.74	4.00
604	680	5.121811	TGTAAAGTGGCAAAAACAATGCAT	58.878	33.333	0.00	0.00	45.60	3.96
617	693	4.757799	ACAATGCATGTAACTAAACGCA	57.242	36.364	0.00	0.00	41.63	5.24
957	1056	3.309682	CACACTCGCTCTTCAGTTTTCAA	59.690	43.478	0.00	0.00	0.00	2.69
1021	1120	1.518572	GCGACTACCACCATGTCCG	60.519	63.158	0.00	0.00	0.00	4.79
1306	1405	1.954362	GCTCGAGGTGATCCACTGCT	61.954	60.000	15.58	0.00	34.40	4.24
1864	1979	3.384816	CTGCACACAGTGGTTCAGA	57.615	52.632	5.31	0.00	39.22	3.27
1865	1980	1.667236	CTGCACACAGTGGTTCAGAA	58.333	50.000	5.31	0.00	39.22	3.02
1866	1981	1.331756	CTGCACACAGTGGTTCAGAAC	59.668	52.381	5.31	4.52	39.22	3.01
1867	1982	1.065491	TGCACACAGTGGTTCAGAACT	60.065	47.619	13.13	0.00	33.64	3.01
1868	1983	2.017049	GCACACAGTGGTTCAGAACTT	58.983	47.619	13.13	0.00	33.64	2.66
1869	1984	2.423538	GCACACAGTGGTTCAGAACTTT	59.576	45.455	13.13	0.00	33.64	2.66
1884	1999	9.813080	GTTCAGAACTTTAGATTGTAACATCAC	57.187	33.333	6.00	0.00	0.00	3.06
1899	2014	8.325421	TGTAACATCACGGTGTAAATTACAAT	57.675	30.769	7.48	0.00	40.93	2.71
1964	2080	1.271325	TGGATGTAGCCTGTGTGTTGG	60.271	52.381	0.00	0.00	0.00	3.77
2354	10249	4.452455	GGATGGAGGCATAGACGTATTTTG	59.548	45.833	0.00	0.00	0.00	2.44
2409	10309	1.069513	ACTAGCAAATATACCCGCGCA	59.930	47.619	8.75	0.00	0.00	6.09
2434	10334	3.664025	GCAACGGAAGAAAAAGATTGACG	59.336	43.478	0.00	0.00	0.00	4.35
2437	10337	4.377897	ACGGAAGAAAAAGATTGACGACT	58.622	39.130	0.00	0.00	0.00	4.18
2448	10348	8.553459	AAAAGATTGACGACTCTTGATTACAT	57.447	30.769	0.00	0.00	32.20	2.29
2542	10442	1.005037	GGAGACACGCATCCACACA	60.005	57.895	0.00	0.00	35.54	3.72
2571	10471	2.011947	CGATACTAGACACACCACCGA	58.988	52.381	0.00	0.00	0.00	4.69
2576	10476	3.899726	ACTAGACACACCACCGAGATAT	58.100	45.455	0.00	0.00	0.00	1.63
2589	10489	1.613520	CGAGATATGGGCTAGACGGGA	60.614	57.143	0.00	0.00	0.00	5.14
2612	10512	5.234466	AGAATCTTATTCCATCTTCCGGG	57.766	43.478	0.00	0.00	0.00	5.73
2633	10534	1.801913	CCGCCTTCGTCTCGTCTTG	60.802	63.158	0.00	0.00	0.00	3.02
2668	10569	3.185797	CGGAACCTAACAAAACTCGAAGG	59.814	47.826	0.00	0.00	0.00	3.46
2685	10586	7.373493	ACTCGAAGGAACGTCTAAAAATAGAA	58.627	34.615	0.00	0.00	33.85	2.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
583	657	5.121811	ACATGCATTGTTTTTGCCACTTTA	58.878	33.333	0.00	0.00	39.39	1.85
590	665	6.785164	CGTTTAGTTACATGCATTGTTTTTGC	59.215	34.615	0.00	0.00	39.87	3.68
604	680	4.202243	ACAGTAAGGGTGCGTTTAGTTACA	60.202	41.667	0.00	0.00	0.00	2.41
617	693	1.045407	TGCAACGAGACAGTAAGGGT	58.955	50.000	0.00	0.00	0.00	4.34
957	1056	7.680730	AGGTGTACTGTATGTTCTCAAAAGAT	58.319	34.615	0.00	0.00	0.00	2.40
971	1070	2.320681	AAGGCAGGAGGTGTACTGTA	57.679	50.000	0.00	0.00	37.07	2.74
1021	1120	3.398353	CGGCGAAGGTCGAGGAGAC	62.398	68.421	0.00	0.00	46.20	3.36
1257	1356	2.747686	GCAAAGGTCTCGGGGTCA	59.252	61.111	0.00	0.00	0.00	4.02
1306	1405	2.687200	ACCGAGCATAGCCCACCA	60.687	61.111	0.00	0.00	0.00	4.17
1475	1574	1.544093	CGACTTGGCATGCCCAGATAT	60.544	52.381	37.16	19.91	46.39	1.63
1862	1977	7.117812	CACCGTGATGTTACAATCTAAAGTTCT	59.882	37.037	0.00	0.00	0.00	3.01
1863	1978	7.095355	ACACCGTGATGTTACAATCTAAAGTTC	60.095	37.037	5.28	0.00	0.00	3.01
1864	1979	6.708949	ACACCGTGATGTTACAATCTAAAGTT	59.291	34.615	5.28	0.00	0.00	2.66
1865	1980	6.228258	ACACCGTGATGTTACAATCTAAAGT	58.772	36.000	5.28	0.00	0.00	2.66
1866	1981	6.721571	ACACCGTGATGTTACAATCTAAAG	57.278	37.500	5.28	0.00	0.00	1.85
1867	1982	8.604640	TTTACACCGTGATGTTACAATCTAAA	57.395	30.769	5.28	0.00	33.85	1.85
1868	1983	8.780846	ATTTACACCGTGATGTTACAATCTAA	57.219	30.769	5.28	0.00	33.85	2.10
1869	1984	8.780846	AATTTACACCGTGATGTTACAATCTA	57.219	30.769	5.28	0.00	33.85	1.98
1884	1999	6.972328	CCCAAAGATCATTGTAATTTACACCG	59.028	38.462	8.75	3.83	38.63	4.94
1899	2014	4.487804	TCAAACCATTTCCCCAAAGATCA	58.512	39.130	0.00	0.00	0.00	2.92
1964	2080	3.372206	CACCGTTCTCATTTCTCATGGAC	59.628	47.826	0.00	0.00	0.00	4.02
2354	10249	3.492337	AGAGCTAGCTATACCTGTCCAC	58.508	50.000	19.38	0.00	0.00	4.02
2409	10309	5.691754	GTCAATCTTTTTCTTCCGTTGCAAT	59.308	36.000	0.59	0.00	0.00	3.56
2434	10334	5.233050	CACGTCCATCATGTAATCAAGAGTC	59.767	44.000	0.00	0.00	0.00	3.36
2437	10337	4.441792	CCACGTCCATCATGTAATCAAGA	58.558	43.478	0.00	0.00	0.00	3.02
2448	10348	2.048597	GTGTCGCCACGTCCATCA	60.049	61.111	0.00	0.00	0.00	3.07
2542	10442	1.065199	TGTCTAGTATCGTCGGTGGGT	60.065	52.381	0.00	0.00	0.00	4.51
2571	10471	2.110188	TCTTCCCGTCTAGCCCATATCT	59.890	50.000	0.00	0.00	0.00	1.98
2576	10476	1.120530	GATTCTTCCCGTCTAGCCCA	58.879	55.000	0.00	0.00	0.00	5.36
2589	10489	5.369699	TCCCGGAAGATGGAATAAGATTCTT	59.630	40.000	0.73	4.03	0.00	2.52
2633	10534	1.282875	GTTCCGTGTCCTGCTTTGC	59.717	57.895	0.00	0.00	0.00	3.68
2668	10569	5.583854	GGGAGGGTTCTATTTTTAGACGTTC	59.416	44.000	0.00	0.00	0.00	3.95
2685	10586	3.322466	CCTTGCAGACGGGAGGGT	61.322	66.667	0.00	0.00	28.71	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.