AutoCloner

Multiple sequence alignment - TraesCS3B01G449100

Loading Multiple Alignment...

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	TraesCS3B01G449100	chr3B	100.000	4013	0	0	1	4013	689682536	689686548	0.000000e+00	7411.0
1	TraesCS3B01G449100	chr3B	98.305	59	1	0	1	59	689670631	689670689	1.970000e-18	104.0
2	TraesCS3B01G449100	chr3B	97.778	45	1	0	61	105	689670171	689670215	1.200000e-10	78.7
3	TraesCS3B01G449100	chr3D	86.541	1694	99	65	479	2101	523168477	523170112	0.000000e+00	1746.0
4	TraesCS3B01G449100	chr3D	92.821	1170	51	21	2227	3380	523170133	523171285	0.000000e+00	1664.0
5	TraesCS3B01G449100	chr3D	88.475	564	22	14	3459	4013	523171331	523171860	3.380000e-180	641.0
6	TraesCS3B01G449100	chr3D	81.723	383	37	18	114	481	523166774	523167138	5.070000e-74	289.0
7	TraesCS3B01G449100	chr3A	88.327	1225	66	37	556	1748	657942765	657943944	0.000000e+00	1399.0
8	TraesCS3B01G449100	chr3A	91.457	995	61	15	1887	2862	657944008	657944997	0.000000e+00	1345.0
9	TraesCS3B01G449100	chr3A	91.398	558	26	12	3459	4013	657945594	657946132	0.000000e+00	745.0
10	TraesCS3B01G449100	chr3A	88.054	519	27	12	2862	3380	657945065	657945548	2.080000e-162	582.0
11	TraesCS3B01G449100	chr3A	81.328	482	34	27	94	553	657936634	657937081	1.380000e-89	340.0

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	TraesCS3B01G449100	chr3B	689682536	689686548	4012	False	7411.00	7411	100.000	1	4013	1	chr3B.!!$F1	4012
1	TraesCS3B01G449100	chr3D	523166774	523171860	5086	False	1085.00	1746	87.390	114	4013	4	chr3D.!!$F1	3899
2	TraesCS3B01G449100	chr3A	657942765	657946132	3367	False	1017.75	1399	89.809	556	4013	4	chr3A.!!$F2	3457

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
343	366	0.089516	GTACAACGAAACGGCGTACG	59.910	55.0	27.94	27.94	44.86	3.67	F
700	2087	0.322648	CGTCGTTTTTAGGGGAGGGT	59.677	55.0	0.00	0.00	0.00	4.34	F
1704	3144	0.035458	CGGGAGAGCACTCAAGGTTT	59.965	55.0	13.37	0.00	44.22	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1147	2558	0.177604	ATCACCTAGCAGCAGCAGAC	59.822	55.0	3.17	45.49	3.51	R
2566	4042	0.039617	GAGCAGATGAGACGGATCGG	60.040	60.0	0.00	0.00	4.18	R
3455	5022	0.254178	ACTGCCGCTGATGGATCTTT	59.746	50.0	4.02	0.00	2.52	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
25	26	8.945758	CTCTTTCAGATTGTGACAATTACTTG	57.054	34.615	12.62	8.97	33.71	3.16
27	28	9.554395	TCTTTCAGATTGTGACAATTACTTGTA	57.446	29.630	12.62	1.28	45.57	2.41
30	31	8.492673	TCAGATTGTGACAATTACTTGTATCC	57.507	34.615	12.62	0.00	45.57	2.59
31	32	8.100164	TCAGATTGTGACAATTACTTGTATCCA	58.900	33.333	12.62	0.00	45.57	3.41
32	33	8.393366	CAGATTGTGACAATTACTTGTATCCAG	58.607	37.037	12.62	0.00	45.57	3.86
33	34	8.103305	AGATTGTGACAATTACTTGTATCCAGT	58.897	33.333	12.62	0.00	45.57	4.00
34	35	9.378551	GATTGTGACAATTACTTGTATCCAGTA	57.621	33.333	12.62	0.00	45.57	2.74
35	36	9.733556	ATTGTGACAATTACTTGTATCCAGTAA	57.266	29.630	4.72	0.00	45.57	2.24
36	37	9.562408	TTGTGACAATTACTTGTATCCAGTAAA	57.438	29.630	0.00	0.00	45.57	2.01
37	38	9.733556	TGTGACAATTACTTGTATCCAGTAAAT	57.266	29.630	0.00	0.00	45.57	1.40
44	45	8.974060	TTACTTGTATCCAGTAAATTCATCCC	57.026	34.615	0.00	0.00	0.00	3.85
45	46	6.969043	ACTTGTATCCAGTAAATTCATCCCA	58.031	36.000	0.00	0.00	0.00	4.37
46	47	6.828785	ACTTGTATCCAGTAAATTCATCCCAC	59.171	38.462	0.00	0.00	0.00	4.61
47	48	6.575244	TGTATCCAGTAAATTCATCCCACT	57.425	37.500	0.00	0.00	0.00	4.00
48	49	6.356556	TGTATCCAGTAAATTCATCCCACTG	58.643	40.000	0.00	0.00	37.06	3.66
61	62	3.315765	CCACTGGGAGCGTAACAAA	57.684	52.632	0.00	0.00	35.59	2.83
62	63	1.600023	CCACTGGGAGCGTAACAAAA	58.400	50.000	0.00	0.00	35.59	2.44
63	64	1.950909	CCACTGGGAGCGTAACAAAAA	59.049	47.619	0.00	0.00	35.59	1.94
64	65	2.287368	CCACTGGGAGCGTAACAAAAAC	60.287	50.000	0.00	0.00	35.59	2.43
65	66	2.616842	CACTGGGAGCGTAACAAAAACT	59.383	45.455	0.00	0.00	0.00	2.66
66	67	3.810941	CACTGGGAGCGTAACAAAAACTA	59.189	43.478	0.00	0.00	0.00	2.24
67	68	4.454504	CACTGGGAGCGTAACAAAAACTAT	59.545	41.667	0.00	0.00	0.00	2.12
68	69	4.694037	ACTGGGAGCGTAACAAAAACTATC	59.306	41.667	0.00	0.00	0.00	2.08
69	70	4.643463	TGGGAGCGTAACAAAAACTATCA	58.357	39.130	0.00	0.00	0.00	2.15
70	71	5.064558	TGGGAGCGTAACAAAAACTATCAA	58.935	37.500	0.00	0.00	0.00	2.57

Showing 1 to 25 of 349 entries

Previous1 2 3 4 5…14Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	9.554395	TACAAGTAATTGTCACAATCTGAAAGA	57.446	29.630	12.49	0.00	41.17	2.52
4	5	8.946085	GGATACAAGTAATTGTCACAATCTGAA	58.054	33.333	12.49	0.00	36.44	3.02
5	6	8.492673	GGATACAAGTAATTGTCACAATCTGA	57.507	34.615	12.49	0.00	36.44	3.27
25	26	6.867662	CAGTGGGATGAATTTACTGGATAC	57.132	41.667	0.00	0.00	36.12	2.24
42	43	0.250553	TTTGTTACGCTCCCAGTGGG	60.251	55.000	23.57	23.57	46.11	4.61
43	44	1.600023	TTTTGTTACGCTCCCAGTGG	58.400	50.000	0.63	0.63	0.00	4.00
44	45	2.616842	AGTTTTTGTTACGCTCCCAGTG	59.383	45.455	0.00	0.00	0.00	3.66
45	46	2.927028	AGTTTTTGTTACGCTCCCAGT	58.073	42.857	0.00	0.00	0.00	4.00
46	47	4.693566	TGATAGTTTTTGTTACGCTCCCAG	59.306	41.667	0.00	0.00	0.00	4.45
47	48	4.643463	TGATAGTTTTTGTTACGCTCCCA	58.357	39.130	0.00	0.00	0.00	4.37
48	49	5.616488	TTGATAGTTTTTGTTACGCTCCC	57.384	39.130	0.00	0.00	0.00	4.30
49	50	5.086727	GCTTGATAGTTTTTGTTACGCTCC	58.913	41.667	0.00	0.00	0.00	4.70
50	51	5.685841	TGCTTGATAGTTTTTGTTACGCTC	58.314	37.500	0.00	0.00	0.00	5.03
51	52	5.682943	TGCTTGATAGTTTTTGTTACGCT	57.317	34.783	0.00	0.00	0.00	5.07
52	53	6.140110	TCTTGCTTGATAGTTTTTGTTACGC	58.860	36.000	0.00	0.00	0.00	4.42
53	54	8.629986	CATTCTTGCTTGATAGTTTTTGTTACG	58.370	33.333	0.00	0.00	0.00	3.18
54	55	9.677567	TCATTCTTGCTTGATAGTTTTTGTTAC	57.322	29.630	0.00	0.00	0.00	2.50
55	56	9.897744	CTCATTCTTGCTTGATAGTTTTTGTTA	57.102	29.630	0.00	0.00	0.00	2.41
56	57	8.632679	TCTCATTCTTGCTTGATAGTTTTTGTT	58.367	29.630	0.00	0.00	0.00	2.83
57	58	8.169977	TCTCATTCTTGCTTGATAGTTTTTGT	57.830	30.769	0.00	0.00	0.00	2.83
58	59	8.909671	GTTCTCATTCTTGCTTGATAGTTTTTG	58.090	33.333	0.00	0.00	0.00	2.44
59	60	8.632679	TGTTCTCATTCTTGCTTGATAGTTTTT	58.367	29.630	0.00	0.00	0.00	1.94
60	61	8.169977	TGTTCTCATTCTTGCTTGATAGTTTT	57.830	30.769	0.00	0.00	0.00	2.43
61	62	7.574592	GCTGTTCTCATTCTTGCTTGATAGTTT	60.575	37.037	0.00	0.00	0.00	2.66
62	63	6.128063	GCTGTTCTCATTCTTGCTTGATAGTT	60.128	38.462	0.00	0.00	0.00	2.24

Showing 1 to 25 of 358 entries

Previous1 2 3 4 5…15Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.