AutoCloner

Multiple sequence alignment - TraesCS3B01G438700

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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	TraesCS3B01G438700	chr3B	100.000	4709	0	0	1	4709	677993025	677997733	0.000000e+00	8696.0
1	TraesCS3B01G438700	chr3B	100.000	180	0	0	710	889	25477074	25476895	2.720000e-87	333.0
2	TraesCS3B01G438700	chr3A	89.551	1627	106	24	2093	3709	649809729	649811301	0.000000e+00	2004.0
3	TraesCS3B01G438700	chr3A	88.119	808	52	19	890	1679	649808523	649809304	0.000000e+00	920.0
4	TraesCS3B01G438700	chr3A	88.547	585	44	13	4138	4706	649812003	649812580	0.000000e+00	688.0
5	TraesCS3B01G438700	chr3A	89.701	301	25	4	3824	4122	649811493	649811789	3.440000e-101	379.0
6	TraesCS3B01G438700	chr3A	87.500	184	11	6	1915	2098	649809419	649809590	7.990000e-48	202.0
7	TraesCS3B01G438700	chr3A	92.391	92	7	0	1838	1929	649809304	649809395	1.060000e-26	132.0
8	TraesCS3B01G438700	chr3A	93.478	46	2	1	664	709	649808488	649808532	3.040000e-07	67.6
9	TraesCS3B01G438700	chr3D	91.379	870	62	10	1916	2782	515258091	515258950	0.000000e+00	1179.0
10	TraesCS3B01G438700	chr3D	88.160	777	45	11	914	1680	515257240	515257979	0.000000e+00	881.0
11	TraesCS3B01G438700	chr3D	92.091	569	33	7	2726	3293	515258949	515259506	0.000000e+00	791.0
12	TraesCS3B01G438700	chr3D	88.367	490	40	10	3300	3785	515260900	515261376	1.470000e-159	573.0
13	TraesCS3B01G438700	chr3D	89.513	267	23	3	3860	4126	515261490	515261751	2.720000e-87	333.0
14	TraesCS3B01G438700	chr3D	89.744	117	9	3	4366	4482	515262035	515262148	3.800000e-31	147.0
15	TraesCS3B01G438700	chr3D	94.505	91	5	0	1839	1929	515257976	515258066	1.770000e-29	141.0
16	TraesCS3B01G438700	chr3D	95.652	46	1	1	664	709	515257191	515257235	6.540000e-09	73.1
17	TraesCS3B01G438700	chr6B	87.449	494	52	9	147	632	290269511	290269020	1.140000e-155	560.0
18	TraesCS3B01G438700	chr6B	87.247	494	53	9	147	632	290205506	290205997	5.320000e-154	555.0
19	TraesCS3B01G438700	chr6B	83.838	495	65	9	147	632	255878558	255879046	1.540000e-124	457.0
20	TraesCS3B01G438700	chr7A	87.247	494	50	9	147	632	523629823	523630311	6.890000e-153	551.0
21	TraesCS3B01G438700	chr7A	98.378	185	3	0	706	890	670503323	670503507	4.540000e-85	326.0
22	TraesCS3B01G438700	chr7D	86.749	483	55	8	155	630	334112234	334112714	3.230000e-146	529.0
23	TraesCS3B01G438700	chr7D	84.306	497	60	14	147	632	145412285	145411796	1.980000e-128	470.0
24	TraesCS3B01G438700	chr7B	85.979	485	59	8	155	632	208148915	208148433	1.170000e-140	510.0
25	TraesCS3B01G438700	chr6A	85.193	493	63	10	147	630	483539719	483540210	9.100000e-137	497.0
26	TraesCS3B01G438700	chr6A	92.818	181	9	4	1673	1852	105042079	105041902	4.670000e-65	259.0
27	TraesCS3B01G438700	chr4D	88.283	367	39	4	147	510	399171424	399171789	2.010000e-118	436.0
28	TraesCS3B01G438700	chr4D	94.253	174	9	1	1675	1847	93338039	93338212	1.000000e-66	265.0
29	TraesCS3B01G438700	chr4D	90.132	152	14	1	1	151	444518239	444518390	3.720000e-46	196.0
30	TraesCS3B01G438700	chr5A	100.000	181	0	0	710	890	709468079	709467899	7.550000e-88	335.0
31	TraesCS3B01G438700	chr5A	99.451	182	1	0	709	890	534843765	534843584	9.770000e-87	331.0
32	TraesCS3B01G438700	chr5A	89.899	198	15	5	1678	1873	362179181	362178987	2.810000e-62	250.0
33	TraesCS3B01G438700	chr2A	100.000	181	0	0	710	890	356519094	356519274	7.550000e-88	335.0
34	TraesCS3B01G438700	chr2A	92.857	182	11	2	1672	1851	94112557	94112376	3.610000e-66	263.0
35	TraesCS3B01G438700	chr1A	99.451	182	1	0	710	891	151542930	151543111	9.770000e-87	331.0
36	TraesCS3B01G438700	chr1A	87.121	132	17	0	1161	1292	458564177	458564308	2.940000e-32	150.0
37	TraesCS3B01G438700	chrUn	99.448	181	1	0	710	890	330934131	330934311	3.510000e-86	329.0
38	TraesCS3B01G438700	chr5B	98.895	181	1	1	710	890	505216824	505216645	5.880000e-84	322.0
39	TraesCS3B01G438700	chr5B	97.561	164	4	0	1678	1841	291840757	291840594	9.980000e-72	281.0
40	TraesCS3B01G438700	chr5B	94.253	174	9	1	1674	1847	268089568	268089396	1.000000e-66	265.0
41	TraesCS3B01G438700	chr1B	97.790	181	4	0	710	890	152289717	152289897	3.540000e-81	313.0
42	TraesCS3B01G438700	chr1B	93.407	182	10	2	1669	1849	316758536	316758716	7.770000e-68	268.0
43	TraesCS3B01G438700	chr2D	93.855	179	9	2	1667	1843	560959661	560959483	7.770000e-68	268.0
44	TraesCS3B01G438700	chr2D	81.081	111	21	0	1178	1288	635768865	635768975	6.490000e-14	89.8
45	TraesCS3B01G438700	chr5D	93.258	178	10	2	1666	1842	181626287	181626111	1.300000e-65	261.0

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	TraesCS3B01G438700	chr3B	677993025	677997733	4708	False	8696.000000	8696	100.000000	1	4709	1	chr3B.!!$F1	4708
1	TraesCS3B01G438700	chr3A	649808488	649812580	4092	False	627.514286	2004	89.898143	664	4706	7	chr3A.!!$F1	4042
2	TraesCS3B01G438700	chr3D	515257191	515262148	4957	False	514.762500	1179	91.176375	664	4482	8	chr3D.!!$F1	3818

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
531	532	0.029567	TTTTGCGTGGTTAGGCGTTG	59.970	50.000	0.00	0.00	40.46	4.10	F
744	745	0.108945	ACGAAAGGTGCTACGTAGGC	60.109	55.000	23.47	15.70	37.22	3.93	F
1364	1380	0.237761	GTATCGATCGTGGAGTCCCG	59.762	60.000	15.94	10.13	34.29	5.14	F
1561	1580	0.452122	CCGTGCGGTTCGTGAAATTC	60.452	55.000	1.93	0.00	0.00	2.17	F
2557	2765	1.065854	GCTGTGGGTATGTGAGAGCTT	60.066	52.381	0.00	0.00	0.00	3.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1570	1589	0.034896	AACCAACACTCGCTCGGAAT	59.965	50.000	0.00	0.00	0.00	3.01	R
2537	2745	0.539051	AGCTCTCACATACCCACAGC	59.461	55.000	0.00	0.00	0.00	4.40	R
2581	2789	1.065854	AGCACTGCCCAAGTATCTGAC	60.066	52.381	0.00	0.00	36.83	3.51	R
3536	5191	0.763035	ACTGTTTTAGGACCGTGGCT	59.237	50.000	0.00	0.00	0.00	4.75	R
3826	5578	0.172578	TACGAGCTAGCATGCGTGTT	59.827	50.000	28.59	7.05	37.56	3.32	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	End Stability
20	21	3.942130	GGTCTTTATGTGGCAAGCTTT	57.058	42.857	0.00	0.00	3.51
21	22	3.838120	GGTCTTTATGTGGCAAGCTTTC	58.162	45.455	0.00	0.00	2.62
22	23	3.507622	GGTCTTTATGTGGCAAGCTTTCT	59.492	43.478	0.00	0.00	2.52
23	24	4.479619	GTCTTTATGTGGCAAGCTTTCTG	58.520	43.478	0.00	0.00	3.02
24	25	4.022849	GTCTTTATGTGGCAAGCTTTCTGT	60.023	41.667	0.00	0.00	3.41
25	26	3.921119	TTATGTGGCAAGCTTTCTGTG	57.079	42.857	0.00	0.00	3.66
26	27	0.963962	ATGTGGCAAGCTTTCTGTGG	59.036	50.000	0.00	0.00	4.17
27	28	1.108727	TGTGGCAAGCTTTCTGTGGG	61.109	55.000	0.00	0.00	4.61
28	29	2.202395	TGGCAAGCTTTCTGTGGGC	61.202	57.895	0.00	0.00	5.36
29	30	2.256461	GCAAGCTTTCTGTGGGCG	59.744	61.111	0.00	0.00	6.13
30	31	2.555547	GCAAGCTTTCTGTGGGCGT	61.556	57.895	0.00	0.00	5.68
31	32	1.576421	CAAGCTTTCTGTGGGCGTC	59.424	57.895	0.00	0.00	5.19
32	33	0.886490	CAAGCTTTCTGTGGGCGTCT	60.886	55.000	0.00	0.00	4.18
33	34	0.179018	AAGCTTTCTGTGGGCGTCTT	60.179	50.000	0.00	0.00	3.01
34	35	0.603975	AGCTTTCTGTGGGCGTCTTC	60.604	55.000	0.00	0.00	2.87
35	36	0.603975	GCTTTCTGTGGGCGTCTTCT	60.604	55.000	0.00	0.00	2.85
36	37	1.151668	CTTTCTGTGGGCGTCTTCTG	58.848	55.000	0.00	0.00	3.02
37	38	0.250295	TTTCTGTGGGCGTCTTCTGG	60.250	55.000	0.00	0.00	3.86
38	39	2.731691	TTCTGTGGGCGTCTTCTGGC	62.732	60.000	0.00	0.00	4.85
39	40	3.535629	CTGTGGGCGTCTTCTGGCA	62.536	63.158	0.00	0.00	4.92
40	41	2.743928	GTGGGCGTCTTCTGGCAG	60.744	66.667	8.58	8.58	4.85
41	42	4.704833	TGGGCGTCTTCTGGCAGC	62.705	66.667	10.34	0.00	5.25
42	43	4.400961	GGGCGTCTTCTGGCAGCT	62.401	66.667	10.34	0.00	4.24
43	44	3.123620	GGCGTCTTCTGGCAGCTG	61.124	66.667	10.11	10.11	4.24
44	45	2.047844	GCGTCTTCTGGCAGCTGA	60.048	61.111	20.43	7.40	4.26

Showing 1 to 25 of 898 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	End Stability
0	1	3.507622	AGAAAGCTTGCCACATAAAGACC	59.492	43.478	3.85
1	2	4.022849	ACAGAAAGCTTGCCACATAAAGAC	60.023	41.667	3.01
2	3	4.022935	CACAGAAAGCTTGCCACATAAAGA	60.023	41.667	2.52
3	4	4.232221	CACAGAAAGCTTGCCACATAAAG	58.768	43.478	1.85
5	6	2.557924	CCACAGAAAGCTTGCCACATAA	59.442	45.455	1.90
6	7	2.161855	CCACAGAAAGCTTGCCACATA	58.838	47.619	2.29
7	8	0.963962	CCACAGAAAGCTTGCCACAT	59.036	50.000	3.21
8	9	1.108727	CCCACAGAAAGCTTGCCACA	61.109	55.000	4.17
9	10	1.662044	CCCACAGAAAGCTTGCCAC	59.338	57.895	5.01
10	11	2.202395	GCCCACAGAAAGCTTGCCA	61.202	57.895	4.92
11	12	2.653115	GCCCACAGAAAGCTTGCC	59.347	61.111	4.52
12	13	2.256461	CGCCCACAGAAAGCTTGC	59.744	61.111	4.01
13	14	0.886490	AGACGCCCACAGAAAGCTTG	60.886	55.000	4.01
14	15	0.179018	AAGACGCCCACAGAAAGCTT	60.179	50.000	3.74
15	16	0.603975	GAAGACGCCCACAGAAAGCT	60.604	55.000	3.74
16	17	0.603975	AGAAGACGCCCACAGAAAGC	60.604	55.000	3.51
17	18	1.151668	CAGAAGACGCCCACAGAAAG	58.848	55.000	2.62
18	19	0.250295	CCAGAAGACGCCCACAGAAA	60.250	55.000	2.52
19	20	1.371183	CCAGAAGACGCCCACAGAA	59.629	57.895	3.02
20	21	3.059982	CCAGAAGACGCCCACAGA	58.940	61.111	3.41
21	22	2.743928	GCCAGAAGACGCCCACAG	60.744	66.667	3.66
22	23	3.535629	CTGCCAGAAGACGCCCACA	62.536	63.158	4.17
23	24	2.743928	CTGCCAGAAGACGCCCAC	60.744	66.667	4.61
24	25	4.704833	GCTGCCAGAAGACGCCCA	62.705	66.667	5.36
25	26	4.400961	AGCTGCCAGAAGACGCCC	62.401	66.667	6.13

Showing 1 to 25 of 838 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.