AutoCloner

Multiple sequence alignment - TraesCS3B01G148300

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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	TraesCS3B01G148300	chr3B	100.000	3822	0	0	1	3822	139773788	139777609	0.000000e+00	7059
1	TraesCS3B01G148300	chr3B	95.082	122	5	1	3141	3262	790640589	790640709	1.400000e-44	191
2	TraesCS3B01G148300	chr3D	85.954	3161	258	92	121	3144	90368627	90371738	0.000000e+00	3206
3	TraesCS3B01G148300	chr3D	90.476	546	36	6	3278	3822	90371749	90372279	0.000000e+00	706
4	TraesCS3B01G148300	chr3D	94.531	128	5	2	3135	3262	165446905	165447030	3.010000e-46	196
5	TraesCS3B01G148300	chr3A	86.781	1755	132	36	779	2463	106657333	106659057	0.000000e+00	1864
6	TraesCS3B01G148300	chr3A	94.662	562	22	4	3261	3822	106659784	106660337	0.000000e+00	865
7	TraesCS3B01G148300	chr3A	88.906	640	61	7	2504	3139	106659165	106659798	0.000000e+00	780
8	TraesCS3B01G148300	chr1D	96.774	124	3	1	3134	3257	108838876	108838754	5.000000e-49	206
9	TraesCS3B01G148300	chr5A	95.968	124	4	1	3140	3262	581473541	581473664	2.330000e-47	200
10	TraesCS3B01G148300	chr2D	95.238	126	6	0	3137	3262	556022244	556022119	2.330000e-47	200
11	TraesCS3B01G148300	chr2D	93.023	129	8	1	3134	3262	558937198	558937071	1.810000e-43	187
12	TraesCS3B01G148300	chr5D	95.238	126	5	1	3138	3262	361399972	361400097	8.370000e-47	198
13	TraesCS3B01G148300	chr5D	89.928	139	11	2	3124	3262	528280099	528280234	3.920000e-40	176
14	TraesCS3B01G148300	chr4D	92.913	127	7	2	3136	3262	396195509	396195385	2.350000e-42	183
15	TraesCS3B01G148300	chr7D	95.161	62	3	0	1136	1197	448756345	448756406	8.740000e-17	99
16	TraesCS3B01G148300	chr7B	95.161	62	3	0	1136	1197	466046991	466047052	8.740000e-17	99
17	TraesCS3B01G148300	chr7A	95.161	62	3	0	1136	1197	547337356	547337295	8.740000e-17	99

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	TraesCS3B01G148300	chr3B	139773788	139777609	3821	False	7059.000000	7059	100.000000	1	3822	1	chr3B.!!$F1	3821
1	TraesCS3B01G148300	chr3D	90368627	90372279	3652	False	1956.000000	3206	88.215000	121	3822	2	chr3D.!!$F2	3701
2	TraesCS3B01G148300	chr3A	106657333	106660337	3004	False	1169.666667	1864	90.116333	779	3822	3	chr3A.!!$F1	3043

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	End Stability	Orientation
40	41	0.241749	AATGGCTTGCACGTGTGATG	59.758	50.0	18.38	7.71	3.07	F
43	44	0.523072	GGCTTGCACGTGTGATGAAT	59.477	50.0	18.38	0.00	2.57	F
1354	1449	0.534203	GGTGAGTCTTGTTTCCGCCA	60.534	55.0	0.00	0.00	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1525	1662	0.034896	GTCCCAAAAGTCTCCAGCGA	59.965	55.0	0.00	0.00	4.93	R
1910	2051	0.771127	CCTGTCAAGGTTCTTGGGGA	59.229	55.0	7.67	38.96	4.81	R
3224	3483	0.322816	GGCAAGTCTGAAGCATGGGA	60.323	55.0	0.00	0.00	4.37	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
24	25	7.756395	AGACCTATTGCCATTGATCTTAATG	57.244	36.000	0.00	0.00	37.70	1.90
33	34	3.763097	TTGATCTTAATGGCTTGCACG	57.237	42.857	0.00	0.00	0.00	5.34
34	35	2.710377	TGATCTTAATGGCTTGCACGT	58.290	42.857	0.00	0.00	0.00	4.49
35	36	2.419673	TGATCTTAATGGCTTGCACGTG	59.580	45.455	12.28	12.28	0.00	4.49
36	37	1.890876	TCTTAATGGCTTGCACGTGT	58.109	45.000	18.38	0.00	0.00	4.49
37	38	1.535028	TCTTAATGGCTTGCACGTGTG	59.465	47.619	18.38	9.04	0.00	3.82
38	39	1.535028	CTTAATGGCTTGCACGTGTGA	59.465	47.619	18.38	5.11	0.00	3.58
39	40	1.819928	TAATGGCTTGCACGTGTGAT	58.180	45.000	18.38	0.00	0.00	3.06
40	41	0.241749	AATGGCTTGCACGTGTGATG	59.758	50.000	18.38	7.71	0.00	3.07
41	42	0.606130	ATGGCTTGCACGTGTGATGA	60.606	50.000	18.38	0.00	0.00	2.92
42	43	0.817229	TGGCTTGCACGTGTGATGAA	60.817	50.000	18.38	2.06	0.00	2.57
43	44	0.523072	GGCTTGCACGTGTGATGAAT	59.477	50.000	18.38	0.00	0.00	2.57
44	45	1.466360	GGCTTGCACGTGTGATGAATC	60.466	52.381	18.38	0.00	0.00	2.52
45	46	1.197492	GCTTGCACGTGTGATGAATCA	59.803	47.619	18.38	0.33	0.00	2.57
46	47	2.350676	GCTTGCACGTGTGATGAATCAA	60.351	45.455	18.38	8.92	38.75	2.57
47	48	3.852939	GCTTGCACGTGTGATGAATCAAA	60.853	43.478	18.38	0.00	38.75	2.69
48	49	3.266541	TGCACGTGTGATGAATCAAAC	57.733	42.857	18.38	3.84	40.78	2.93
49	50	2.031245	TGCACGTGTGATGAATCAAACC	60.031	45.455	18.38	0.00	41.05	3.27
50	51	2.031245	GCACGTGTGATGAATCAAACCA	60.031	45.455	18.38	0.00	41.05	3.67
51	52	3.554524	CACGTGTGATGAATCAAACCAC	58.445	45.455	7.58	5.53	41.05	4.16
52	53	2.552315	ACGTGTGATGAATCAAACCACC	59.448	45.455	7.82	3.46	41.05	4.61
53	54	2.095263	CGTGTGATGAATCAAACCACCC	60.095	50.000	7.82	0.84	41.05	4.61
54	55	2.890311	GTGTGATGAATCAAACCACCCA	59.110	45.455	2.62	0.00	38.76	4.51
55	56	3.511146	GTGTGATGAATCAAACCACCCAT	59.489	43.478	2.62	0.00	38.76	4.00
56	57	3.763360	TGTGATGAATCAAACCACCCATC	59.237	43.478	9.90	0.00	38.75	3.51

Showing 1 to 25 of 268 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.718454	CCATTAAGATCAATGGCAATAGGTCT	59.282	38.462	10.88	0.00	46.28	3.85
1	2	6.917533	CCATTAAGATCAATGGCAATAGGTC	58.082	40.000	10.88	0.00	46.28	3.85
2	3	6.906157	CCATTAAGATCAATGGCAATAGGT	57.094	37.500	10.88	0.00	46.28	3.08
11	12	4.039703	CGTGCAAGCCATTAAGATCAATG	58.960	43.478	0.00	0.00	35.97	2.82
12	13	3.696051	ACGTGCAAGCCATTAAGATCAAT	59.304	39.130	0.00	0.00	0.00	2.57
13	14	3.081061	ACGTGCAAGCCATTAAGATCAA	58.919	40.909	0.00	0.00	0.00	2.57
14	15	2.419673	CACGTGCAAGCCATTAAGATCA	59.580	45.455	0.82	0.00	0.00	2.92
15	16	2.420022	ACACGTGCAAGCCATTAAGATC	59.580	45.455	17.22	0.00	0.00	2.75
16	17	2.162208	CACACGTGCAAGCCATTAAGAT	59.838	45.455	17.22	0.00	0.00	2.40
17	18	1.535028	CACACGTGCAAGCCATTAAGA	59.465	47.619	17.22	0.00	0.00	2.10
18	19	1.535028	TCACACGTGCAAGCCATTAAG	59.465	47.619	17.22	0.00	0.00	1.85
19	20	1.598882	TCACACGTGCAAGCCATTAA	58.401	45.000	17.22	0.00	0.00	1.40
20	21	1.468127	CATCACACGTGCAAGCCATTA	59.532	47.619	17.22	0.00	0.00	1.90
21	22	0.241749	CATCACACGTGCAAGCCATT	59.758	50.000	17.22	0.00	0.00	3.16
22	23	0.606130	TCATCACACGTGCAAGCCAT	60.606	50.000	17.22	0.00	0.00	4.40
23	24	0.817229	TTCATCACACGTGCAAGCCA	60.817	50.000	17.22	0.00	0.00	4.75
24	25	0.523072	ATTCATCACACGTGCAAGCC	59.477	50.000	17.22	0.00	0.00	4.35
25	26	1.197492	TGATTCATCACACGTGCAAGC	59.803	47.619	17.22	4.38	0.00	4.01
26	27	3.541071	TTGATTCATCACACGTGCAAG	57.459	42.857	17.22	6.16	36.36	4.01
27	28	3.549827	GGTTTGATTCATCACACGTGCAA	60.550	43.478	17.22	6.16	38.13	4.08
28	29	2.031245	GGTTTGATTCATCACACGTGCA	60.031	45.455	17.22	2.20	38.13	4.57
29	30	2.031245	TGGTTTGATTCATCACACGTGC	60.031	45.455	17.22	0.00	38.13	5.34
30	31	3.554524	GTGGTTTGATTCATCACACGTG	58.445	45.455	15.48	15.48	38.13	4.49
31	32	2.552315	GGTGGTTTGATTCATCACACGT	59.448	45.455	13.51	0.00	38.13	4.49
32	33	2.095263	GGGTGGTTTGATTCATCACACG	60.095	50.000	13.51	0.00	38.13	4.49

Showing 1 to 25 of 267 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.