AutoCloner

Multiple sequence alignment - TraesCS4B01G018000

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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	TraesCS4B01G018000	chr4B	100.000	2692	0	0	1	2692	13276411	13279102	0.000000e+00	4972
1	TraesCS4B01G018000	chr4D	88.821	1798	114	44	211	1956	7408647	7410409	0.000000e+00	2126
2	TraesCS4B01G018000	chr4D	93.023	215	14	1	1	214	374099514	374099728	2.010000e-81	313
3	TraesCS4B01G018000	chr4D	90.955	199	15	3	2181	2379	7411049	7411244	5.710000e-67	265
4	TraesCS4B01G018000	chr4A	83.460	1312	113	58	617	1870	596239625	596238360	0.000000e+00	1125
5	TraesCS4B01G018000	chr4A	86.489	1051	75	32	741	1746	596214781	596215809	0.000000e+00	1092
6	TraesCS4B01G018000	chr4A	86.329	790	63	24	617	1375	596207675	596208450	0.000000e+00	819
7	TraesCS4B01G018000	chr4A	86.329	790	63	24	617	1375	596211322	596212097	0.000000e+00	819
8	TraesCS4B01G018000	chr4A	88.971	680	44	20	709	1375	596204141	596204802	0.000000e+00	811
9	TraesCS4B01G018000	chr4A	90.119	253	19	5	285	532	596211027	596211278	9.300000e-85	324
10	TraesCS4B01G018000	chr4A	89.723	253	20	5	285	532	596207380	596207631	4.320000e-83	318
11	TraesCS4B01G018000	chr4A	91.866	209	17	0	1	209	546578222	546578014	2.620000e-75	292
12	TraesCS4B01G018000	chr2B	95.673	208	9	0	1	208	152133727	152133520	4.290000e-88	335
13	TraesCS4B01G018000	chr7B	93.237	207	14	0	1	207	531261733	531261939	3.370000e-79	305
14	TraesCS4B01G018000	chr7B	92.344	209	11	1	1	209	22543421	22543218	2.620000e-75	292
15	TraesCS4B01G018000	chr7B	91.346	208	18	0	1	208	22545650	22545857	4.390000e-73	285
16	TraesCS4B01G018000	chr2A	92.823	209	15	0	1	209	697069614	697069406	1.210000e-78	303
17	TraesCS4B01G018000	chr7A	92.308	208	16	0	1	208	239764646	239764853	2.030000e-76	296
18	TraesCS4B01G018000	chr6A	91.866	209	17	0	1	209	581457096	581457304	2.620000e-75	292

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	TraesCS4B01G018000	chr4B	13276411	13279102	2691	False	4972.000000	4972	100.000000	1	2692	1	chr4B.!!$F1	2691
1	TraesCS4B01G018000	chr4D	7408647	7411244	2597	False	1195.500000	2126	89.888000	211	2379	2	chr4D.!!$F2	2168
2	TraesCS4B01G018000	chr4A	596238360	596239625	1265	True	1125.000000	1125	83.460000	617	1870	1	chr4A.!!$R2	1253
3	TraesCS4B01G018000	chr4A	596204141	596215809	11668	False	697.166667	1092	87.993333	285	1746	6	chr4A.!!$F1	1461

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
263	267	0.036732	ACAAAGGCTGAGGCGAATGA	59.963	50.0	13.62	0.0	39.81	2.57	F
1391	11374	0.179076	CCATGCCAGCGACATACTGA	60.179	55.0	0.00	0.0	37.32	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1424	11420	0.097499	CTGCACACACACACACACAG	59.903	55.0	0.00	0.0	0.00	3.66	R
2482	12962	0.034756	TGAGTGGTGACCATTGTCGG	59.965	55.0	7.94	0.0	44.86	4.79	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
22	23	3.806949	TTAAAGAAGATGGCAGGGTGT	57.193	42.857	0.00	0.00	0.00	4.16
23	24	2.683211	AAAGAAGATGGCAGGGTGTT	57.317	45.000	0.00	0.00	0.00	3.32
25	26	2.206576	AGAAGATGGCAGGGTGTTTC	57.793	50.000	0.00	0.00	0.00	2.78
26	27	1.707427	AGAAGATGGCAGGGTGTTTCT	59.293	47.619	0.00	0.00	0.00	2.52
29	30	0.244721	GATGGCAGGGTGTTTCTTGC	59.755	55.000	0.00	0.00	0.00	4.01
30	31	0.469705	ATGGCAGGGTGTTTCTTGCA	60.470	50.000	0.00	0.00	0.00	4.08
31	32	0.685785	TGGCAGGGTGTTTCTTGCAA	60.686	50.000	0.00	0.00	0.00	4.08
33	34	1.134551	GGCAGGGTGTTTCTTGCAAAA	60.135	47.619	0.00	0.00	0.00	2.44
34	35	2.626840	GCAGGGTGTTTCTTGCAAAAA	58.373	42.857	0.00	1.75	0.00	1.94
36	37	3.002553	GCAGGGTGTTTCTTGCAAAAATG	59.997	43.478	0.00	1.46	0.00	2.32
37	38	3.002553	CAGGGTGTTTCTTGCAAAAATGC	59.997	43.478	0.00	0.00	0.00	3.56
38	39	2.032979	GGGTGTTTCTTGCAAAAATGCG	60.033	45.455	0.00	0.00	37.69	4.73
39	40	2.032979	GGTGTTTCTTGCAAAAATGCGG	60.033	45.455	0.00	0.00	37.69	5.69
40	41	2.032979	GTGTTTCTTGCAAAAATGCGGG	60.033	45.455	0.00	0.00	37.69	6.13
41	42	1.069973	GTTTCTTGCAAAAATGCGGGC	60.070	47.619	0.00	0.00	37.69	6.13
42	43	0.943359	TTCTTGCAAAAATGCGGGCG	60.943	50.000	0.00	0.00	37.69	6.13
43	44	1.372748	CTTGCAAAAATGCGGGCGA	60.373	52.632	0.00	0.00	37.69	5.54
44	45	0.943359	CTTGCAAAAATGCGGGCGAA	60.943	50.000	0.00	0.00	37.69	4.70
45	46	0.943359	TTGCAAAAATGCGGGCGAAG	60.943	50.000	0.00	0.00	37.69	3.79
46	47	1.080839	GCAAAAATGCGGGCGAAGA	60.081	52.632	0.00	0.00	0.00	2.87
47	48	1.344226	GCAAAAATGCGGGCGAAGAC	61.344	55.000	0.00	0.00	0.00	3.01
58	59	3.691342	CGAAGACCGGTCCAGCCA	61.691	66.667	30.82	0.00	36.97	4.75
59	60	2.047179	GAAGACCGGTCCAGCCAC	60.047	66.667	30.82	12.00	36.97	5.01
60	61	3.607370	GAAGACCGGTCCAGCCACC	62.607	68.421	30.82	4.01	36.97	4.61
62	63	4.394712	GACCGGTCCAGCCACCTG	62.395	72.222	24.75	0.00	38.85	4.00

Showing 1 to 25 of 389 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	4.322057	ACACCCTGCCATCTTCTTTAAT	57.678	40.909	0.00	0.00	0.00	1.40
2	3	3.806949	ACACCCTGCCATCTTCTTTAA	57.193	42.857	0.00	0.00	0.00	1.52
3	4	3.806949	AACACCCTGCCATCTTCTTTA	57.193	42.857	0.00	0.00	0.00	1.85
5	6	2.108952	AGAAACACCCTGCCATCTTCTT	59.891	45.455	0.00	0.00	0.00	2.52
6	7	1.707427	AGAAACACCCTGCCATCTTCT	59.293	47.619	0.00	0.00	0.00	2.85
7	8	2.206576	AGAAACACCCTGCCATCTTC	57.793	50.000	0.00	0.00	0.00	2.87
9	10	1.915141	CAAGAAACACCCTGCCATCT	58.085	50.000	0.00	0.00	0.00	2.90
10	11	0.244721	GCAAGAAACACCCTGCCATC	59.755	55.000	0.00	0.00	0.00	3.51
11	12	0.469705	TGCAAGAAACACCCTGCCAT	60.470	50.000	0.00	0.00	0.00	4.40
12	13	0.685785	TTGCAAGAAACACCCTGCCA	60.686	50.000	0.00	0.00	0.00	4.92
13	14	0.463620	TTTGCAAGAAACACCCTGCC	59.536	50.000	0.00	0.00	0.00	4.85
14	15	2.307934	TTTTGCAAGAAACACCCTGC	57.692	45.000	0.00	0.00	0.00	4.85
16	17	3.205338	GCATTTTTGCAAGAAACACCCT	58.795	40.909	6.49	0.00	34.41	4.34
17	18	2.032979	CGCATTTTTGCAAGAAACACCC	60.033	45.455	6.49	0.00	34.41	4.61
19	20	2.032979	CCCGCATTTTTGCAAGAAACAC	60.033	45.455	6.49	0.00	34.41	3.32
21	22	1.069973	GCCCGCATTTTTGCAAGAAAC	60.070	47.619	6.49	1.68	34.41	2.78
22	23	1.224965	GCCCGCATTTTTGCAAGAAA	58.775	45.000	6.49	7.71	34.41	2.52
23	24	0.943359	CGCCCGCATTTTTGCAAGAA	60.943	50.000	4.71	4.71	34.41	2.52
25	26	0.943359	TTCGCCCGCATTTTTGCAAG	60.943	50.000	0.00	0.00	34.41	4.01
26	27	0.943359	CTTCGCCCGCATTTTTGCAA	60.943	50.000	0.00	0.00	34.41	4.08
29	30	0.732538	GGTCTTCGCCCGCATTTTTG	60.733	55.000	0.00	0.00	0.00	2.44
30	31	1.584495	GGTCTTCGCCCGCATTTTT	59.416	52.632	0.00	0.00	0.00	1.94
31	32	2.686816	CGGTCTTCGCCCGCATTTT	61.687	57.895	0.00	0.00	38.85	1.82
38	39	4.452733	CTGGACCGGTCTTCGCCC	62.453	72.222	32.52	17.26	37.59	6.13
41	42	3.691342	TGGCTGGACCGGTCTTCG	61.691	66.667	32.52	21.15	43.94	3.79

Showing 1 to 25 of 378 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.