AutoCloner

Multiple sequence alignment - TraesCS5B01G258500

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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	TraesCS5B01G258500	chr5B	100.000	2672	0	0	1	2672	440562810	440560139	0.000000e+00	4935.0
1	TraesCS5B01G258500	chr5B	99.775	2672	6	0	1	2672	440552001	440549330	0.000000e+00	4902.0
2	TraesCS5B01G258500	chr5B	79.717	424	59	14	1192	1594	441407943	441408360	5.630000e-72	281.0
3	TraesCS5B01G258500	chr5B	78.824	425	73	10	1892	2313	304333323	304332913	1.220000e-68	270.0
4	TraesCS5B01G258500	chr5B	77.386	482	63	26	676	1127	441407317	441407782	7.390000e-61	244.0
5	TraesCS5B01G258500	chr5D	95.652	1196	26	6	7	1182	371283795	371282606	0.000000e+00	1897.0
6	TraesCS5B01G258500	chr5D	95.624	1074	40	3	1602	2672	371281096	371280027	0.000000e+00	1716.0
7	TraesCS5B01G258500	chr5D	92.342	666	43	5	1856	2516	371016905	371017567	0.000000e+00	941.0
8	TraesCS5B01G258500	chr5D	90.332	693	33	14	1195	1869	371015087	371015763	0.000000e+00	878.0
9	TraesCS5B01G258500	chr5D	86.496	822	41	21	414	1179	371014151	371014958	0.000000e+00	839.0
10	TraesCS5B01G258500	chr5D	83.478	460	70	6	1870	2326	125962251	125961795	8.840000e-115	424.0
11	TraesCS5B01G258500	chr5D	96.721	122	4	0	2551	2672	371017568	371017689	1.250000e-48	204.0
12	TraesCS5B01G258500	chr5D	87.619	105	10	3	1078	1179	371011183	371011287	4.670000e-23	119.0
13	TraesCS5B01G258500	chrUn	100.000	797	0	0	1876	2672	340767284	340768080	0.000000e+00	1472.0
14	TraesCS5B01G258500	chr5A	85.047	642	55	19	570	1182	474144776	474144147	1.360000e-172	616.0
15	TraesCS5B01G258500	chr5A	85.047	642	55	19	570	1182	474256324	474256953	1.360000e-172	616.0
16	TraesCS5B01G258500	chr5A	84.424	642	59	14	570	1182	473982456	473983085	6.370000e-166	593.0
17	TraesCS5B01G258500	chr5A	91.214	387	33	1	25	411	474145450	474145065	2.360000e-145	525.0
18	TraesCS5B01G258500	chr5A	91.214	387	33	1	25	411	474255650	474256035	2.360000e-145	525.0
19	TraesCS5B01G258500	chr5A	90.956	387	34	1	25	411	473981781	473982166	1.100000e-143	520.0
20	TraesCS5B01G258500	chr5A	84.914	232	9	9	1254	1467	474287466	474287689	7.490000e-51	211.0
21	TraesCS5B01G258500	chr5A	84.483	232	10	9	1254	1467	474021917	474022140	3.490000e-49	206.0
22	TraesCS5B01G258500	chr5A	84.483	232	10	9	1254	1467	474155291	474155514	3.490000e-49	206.0
23	TraesCS5B01G258500	chr6D	83.656	465	60	9	1866	2326	67870855	67871307	8.840000e-115	424.0
24	TraesCS5B01G258500	chr6D	80.477	461	81	6	1872	2326	417460613	417460156	7.080000e-91	344.0
25	TraesCS5B01G258500	chr7B	83.405	464	63	9	1873	2326	680352682	680353141	4.110000e-113	418.0
26	TraesCS5B01G258500	chr2D	82.432	296	46	6	1892	2182	134462507	134462213	1.230000e-63	254.0
27	TraesCS5B01G258500	chr6B	84.962	133	17	2	2196	2326	628901348	628901479	6.000000e-27	132.0
28	TraesCS5B01G258500	chr1A	74.783	345	53	22	622	937	483648860	483648521	1.000000e-24	124.0
29	TraesCS5B01G258500	chr1B	79.870	154	27	4	784	937	514605394	514605245	2.810000e-20	110.0
30	TraesCS5B01G258500	chr2B	82.857	105	9	3	1354	1449	228911704	228911600	4.740000e-13	86.1
31	TraesCS5B01G258500	chr1D	100.000	28	0	0	1357	1384	383722504	383722477	5.000000e-03	52.8

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	TraesCS5B01G258500	chr5B	440560139	440562810	2671	True	4935.0	4935	100.0000	1	2672	1	chr5B.!!$R3	2671
1	TraesCS5B01G258500	chr5B	440549330	440552001	2671	True	4902.0	4902	99.7750	1	2672	1	chr5B.!!$R2	2671
2	TraesCS5B01G258500	chr5B	441407317	441408360	1043	False	262.5	281	78.5515	676	1594	2	chr5B.!!$F1	918
3	TraesCS5B01G258500	chr5D	371280027	371283795	3768	True	1806.5	1897	95.6380	7	2672	2	chr5D.!!$R2	2665
4	TraesCS5B01G258500	chr5D	371011183	371017689	6506	False	596.2	941	90.7020	414	2672	5	chr5D.!!$F1	2258
5	TraesCS5B01G258500	chrUn	340767284	340768080	796	False	1472.0	1472	100.0000	1876	2672	1	chrUn.!!$F1	796
6	TraesCS5B01G258500	chr5A	474144147	474145450	1303	True	570.5	616	88.1305	25	1182	2	chr5A.!!$R1	1157
7	TraesCS5B01G258500	chr5A	474255650	474256953	1303	False	570.5	616	88.1305	25	1182	2	chr5A.!!$F5	1157
8	TraesCS5B01G258500	chr5A	473981781	473983085	1304	False	556.5	593	87.6900	25	1182	2	chr5A.!!$F4	1157

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
360	361	0.107703	ATGATGTCGCCATTGACGGT	60.108	50.0	0.0	0.0	41.87	4.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	6908	4.372656	ACTAGGAGCTCGAATGTAATTGC	58.627	43.478	7.83	0.0	36.07	3.56	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
334	335	1.476891	TCGTCAACATAGAGGCTCACC	59.523	52.381	18.26	0.00	0.00	4.02
337	338	0.537188	CAACATAGAGGCTCACCCGT	59.463	55.000	18.26	5.19	39.21	5.28
338	339	1.754803	CAACATAGAGGCTCACCCGTA	59.245	52.381	18.26	0.00	39.21	4.02
339	340	2.154567	ACATAGAGGCTCACCCGTAA	57.845	50.000	18.26	0.00	39.21	3.18
340	341	2.679082	ACATAGAGGCTCACCCGTAAT	58.321	47.619	18.26	0.00	39.21	1.89
341	342	3.840991	ACATAGAGGCTCACCCGTAATA	58.159	45.455	18.26	0.00	39.21	0.98
342	343	4.417437	ACATAGAGGCTCACCCGTAATAT	58.583	43.478	18.26	0.00	39.21	1.28
345	346	3.511477	AGAGGCTCACCCGTAATATGAT	58.489	45.455	18.26	0.00	39.21	2.45
347	348	2.972713	AGGCTCACCCGTAATATGATGT	59.027	45.455	0.00	0.00	39.21	3.06
349	350	2.987149	GCTCACCCGTAATATGATGTCG	59.013	50.000	0.00	0.00	0.00	4.35
350	351	2.987149	CTCACCCGTAATATGATGTCGC	59.013	50.000	0.00	0.00	0.00	5.19
352	353	1.689813	ACCCGTAATATGATGTCGCCA	59.310	47.619	0.00	0.00	0.00	5.69
353	354	2.301870	ACCCGTAATATGATGTCGCCAT	59.698	45.455	0.00	0.00	0.00	4.40
354	355	3.244422	ACCCGTAATATGATGTCGCCATT	60.244	43.478	0.00	0.00	0.00	3.16
355	356	3.125146	CCCGTAATATGATGTCGCCATTG	59.875	47.826	0.00	0.00	0.00	2.82
358	359	4.432892	CGTAATATGATGTCGCCATTGACG	60.433	45.833	0.00	0.00	41.87	4.35
360	361	0.107703	ATGATGTCGCCATTGACGGT	60.108	50.000	0.00	0.00	41.87	4.83
362	363	1.003839	ATGTCGCCATTGACGGTGT	60.004	52.632	0.00	0.00	41.87	4.16
365	366	3.487202	CGCCATTGACGGTGTCGG	61.487	66.667	0.00	0.00	41.39	4.79
366	367	3.799755	GCCATTGACGGTGTCGGC	61.800	66.667	0.00	0.00	46.45	5.54
396	397	2.822255	GCCGTTGCCGCCTGAATA	60.822	61.111	0.00	0.00	0.00	1.75
397	398	2.403378	GCCGTTGCCGCCTGAATAA	61.403	57.895	0.00	0.00	0.00	1.40
398	399	1.724582	GCCGTTGCCGCCTGAATAAT	61.725	55.000	0.00	0.00	0.00	1.28
400	401	0.732571	CGTTGCCGCCTGAATAATGT	59.267	50.000	0.00	0.00	0.00	2.71
401	402	1.531677	CGTTGCCGCCTGAATAATGTG	60.532	52.381	0.00	0.00	0.00	3.21

Showing 1 to 25 of 34 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
345	346	1.666553	GACACCGTCAATGGCGACA	60.667	57.895	9.51	0.00	37.33	4.35
349	350	3.799755	GCCGACACCGTCAATGGC	61.800	66.667	0.00	0.00	31.73	4.40
350	351	2.358125	TGCCGACACCGTCAATGG	60.358	61.111	0.00	0.00	32.09	3.16
352	353	2.742372	GCTGCCGACACCGTCAAT	60.742	61.111	0.00	0.00	32.09	2.57
353	354	4.228567	TGCTGCCGACACCGTCAA	62.229	61.111	0.00	0.00	32.09	3.18
354	355	4.662961	CTGCTGCCGACACCGTCA	62.663	66.667	0.00	0.00	32.09	4.35
382	383	1.742831	TCACATTATTCAGGCGGCAAC	59.257	47.619	13.08	0.00	0.00	4.17
383	384	2.121291	TCACATTATTCAGGCGGCAA	57.879	45.000	13.08	0.00	0.00	4.52
384	385	1.948834	CATCACATTATTCAGGCGGCA	59.051	47.619	13.08	0.00	0.00	5.69
386	387	1.948834	TGCATCACATTATTCAGGCGG	59.051	47.619	0.00	0.00	0.00	6.13
387	388	2.603892	GCTGCATCACATTATTCAGGCG	60.604	50.000	0.00	0.00	0.00	5.52
388	389	2.359848	TGCTGCATCACATTATTCAGGC	59.640	45.455	0.00	0.00	0.00	4.85
389	390	3.550233	GCTGCTGCATCACATTATTCAGG	60.550	47.826	11.11	0.00	39.41	3.86
392	393	3.703286	TGCTGCTGCATCACATTATTC	57.297	42.857	14.93	0.00	45.31	1.75
406	407	2.678934	CAATGGGGTGCTGCTGCT	60.679	61.111	17.00	0.00	40.48	4.24
413	414	1.194218	ATACCAAAGCAATGGGGTGC	58.806	50.000	11.91	0.00	45.18	5.01
415	416	1.554617	GCAATACCAAAGCAATGGGGT	59.445	47.619	11.91	2.29	45.18	4.95
416	417	1.554160	TGCAATACCAAAGCAATGGGG	59.446	47.619	11.91	0.00	45.18	4.96
417	418	2.028294	TGTGCAATACCAAAGCAATGGG	60.028	45.455	11.91	0.00	45.18	4.00
1874	6908	4.372656	ACTAGGAGCTCGAATGTAATTGC	58.627	43.478	7.83	0.00	36.07	3.56

Showing 1 to 20 of 20 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.