AutoCloner

Multiple sequence alignment - TraesCS3B01G230300

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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	TraesCS3B01G230300	chr3B	100.000	3450	0	0	1	3450	344281770	344278321	0.000000e+00	6372.0
1	TraesCS3B01G230300	chr1B	98.844	2854	18	7	612	3450	400295118	400297971	0.000000e+00	5073.0
2	TraesCS3B01G230300	chr1B	99.033	2792	23	2	663	3450	641515707	641512916	0.000000e+00	5003.0
3	TraesCS3B01G230300	chr3A	98.807	2849	24	2	612	3450	648036386	648033538	0.000000e+00	5064.0
4	TraesCS3B01G230300	chr3A	98.532	2861	19	9	612	3450	639500582	639497723	0.000000e+00	5029.0
5	TraesCS3B01G230300	chr3A	92.416	567	30	9	49	611	329528202	329528759	0.000000e+00	797.0
6	TraesCS3B01G230300	chr3A	95.833	48	2	0	1	48	329528174	329528221	1.030000e-10	78.7
7	TraesCS3B01G230300	chr5A	98.705	2857	19	5	612	3450	593169434	593166578	0.000000e+00	5055.0
8	TraesCS3B01G230300	chr5A	99.175	2789	18	3	666	3450	506137752	506134965	0.000000e+00	5018.0
9	TraesCS3B01G230300	chr2A	98.770	2846	27	5	611	3450	310415269	310412426	0.000000e+00	5055.0
10	TraesCS3B01G230300	chr2A	98.392	2861	24	3	612	3450	84594387	84591527	0.000000e+00	5009.0
11	TraesCS3B01G230300	chr2A	94.500	200	0	2	612	800	84589509	84589310	7.240000e-77	298.0
12	TraesCS3B01G230300	chr2A	90.732	205	1	1	612	798	310410241	310410037	1.230000e-64	257.0
13	TraesCS3B01G230300	chr7B	98.601	2859	20	8	612	3450	312341953	312339095	0.000000e+00	5040.0
14	TraesCS3B01G230300	chr7B	99.176	2792	18	3	663	3450	244398064	244400854	0.000000e+00	5024.0
15	TraesCS3B01G230300	chr3D	93.122	567	30	6	49	611	228171444	228170883	0.000000e+00	822.0
16	TraesCS3B01G230300	chr3D	100.000	32	0	0	1	32	228171472	228171441	3.720000e-05	60.2

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	TraesCS3B01G230300	chr3B	344278321	344281770	3449	True	6372.00	6372	100.0000	1	3450	1	chr3B.!!$R1	3449
1	TraesCS3B01G230300	chr1B	400295118	400297971	2853	False	5073.00	5073	98.8440	612	3450	1	chr1B.!!$F1	2838
2	TraesCS3B01G230300	chr1B	641512916	641515707	2791	True	5003.00	5003	99.0330	663	3450	1	chr1B.!!$R1	2787
3	TraesCS3B01G230300	chr3A	648033538	648036386	2848	True	5064.00	5064	98.8070	612	3450	1	chr3A.!!$R2	2838
4	TraesCS3B01G230300	chr3A	639497723	639500582	2859	True	5029.00	5029	98.5320	612	3450	1	chr3A.!!$R1	2838
5	TraesCS3B01G230300	chr3A	329528174	329528759	585	False	437.85	797	94.1245	1	611	2	chr3A.!!$F1	610
6	TraesCS3B01G230300	chr5A	593166578	593169434	2856	True	5055.00	5055	98.7050	612	3450	1	chr5A.!!$R2	2838
7	TraesCS3B01G230300	chr5A	506134965	506137752	2787	True	5018.00	5018	99.1750	666	3450	1	chr5A.!!$R1	2784
8	TraesCS3B01G230300	chr2A	310410037	310415269	5232	True	2656.00	5055	94.7510	611	3450	2	chr2A.!!$R2	2839
9	TraesCS3B01G230300	chr2A	84589310	84594387	5077	True	2653.50	5009	96.4460	612	3450	2	chr2A.!!$R1	2838
10	TraesCS3B01G230300	chr7B	312339095	312341953	2858	True	5040.00	5040	98.6010	612	3450	1	chr7B.!!$R1	2838
11	TraesCS3B01G230300	chr7B	244398064	244400854	2790	False	5024.00	5024	99.1760	663	3450	1	chr7B.!!$F1	2787
12	TraesCS3B01G230300	chr3D	228170883	228171472	589	True	441.10	822	96.5610	1	611	2	chr3D.!!$R1	610

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
541	542	0.030638	CCCACGCAACTCCTTTTGTG	59.969	55.0	0.0	0.0	41.8	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2499	2835	4.386711	ACTCCAACTAGTACAGCCAAAAC	58.613	43.478	0.0	0.0	0.0	2.43	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 end TH	Hairpin	End Stability
42	43	3.033114	CTCAAGTGCTGAGCGAGAG	57.967	57.895	0.35	45.11	3.20
43	44	0.243365	CTCAAGTGCTGAGCGAGAGT	59.757	55.000	0.00	45.11	3.24
44	45	0.676184	TCAAGTGCTGAGCGAGAGTT	59.324	50.000	0.00	0.00	3.01
45	46	1.886542	TCAAGTGCTGAGCGAGAGTTA	59.113	47.619	0.00	0.00	2.24
46	47	2.296190	TCAAGTGCTGAGCGAGAGTTAA	59.704	45.455	0.00	0.00	2.01
47	48	3.056536	TCAAGTGCTGAGCGAGAGTTAAT	60.057	43.478	0.00	0.00	1.40
48	49	4.157840	TCAAGTGCTGAGCGAGAGTTAATA	59.842	41.667	0.00	0.00	0.98
49	50	4.300189	AGTGCTGAGCGAGAGTTAATAG	57.700	45.455	0.00	0.00	1.73
50	51	3.697045	AGTGCTGAGCGAGAGTTAATAGT	59.303	43.478	0.00	0.00	2.12
51	52	3.794028	GTGCTGAGCGAGAGTTAATAGTG	59.206	47.826	0.00	0.00	2.74
52	53	3.444034	TGCTGAGCGAGAGTTAATAGTGT	59.556	43.478	0.00	0.00	3.55
53	54	4.082190	TGCTGAGCGAGAGTTAATAGTGTT	60.082	41.667	0.00	0.00	3.32
54	55	4.266502	GCTGAGCGAGAGTTAATAGTGTTG	59.733	45.833	0.00	0.00	3.33
55	56	5.638596	TGAGCGAGAGTTAATAGTGTTGA	57.361	39.130	0.00	0.00	3.18
56	57	5.641709	TGAGCGAGAGTTAATAGTGTTGAG	58.358	41.667	0.00	0.00	3.02
57	58	4.425520	AGCGAGAGTTAATAGTGTTGAGC	58.574	43.478	0.00	0.00	4.26
58	59	3.240861	GCGAGAGTTAATAGTGTTGAGCG	59.759	47.826	0.00	0.00	5.03
59	60	4.659088	CGAGAGTTAATAGTGTTGAGCGA	58.341	43.478	0.00	0.00	4.93
102	103	3.181465	CCACACTATGGCTAGGGTAACAG	60.181	52.174	0.00	39.68	3.16
103	104	3.039011	ACACTATGGCTAGGGTAACAGG	58.961	50.000	0.00	39.90	4.00
104	105	3.039011	CACTATGGCTAGGGTAACAGGT	58.961	50.000	0.00	39.74	4.00
105	106	4.220724	CACTATGGCTAGGGTAACAGGTA	58.779	47.826	0.00	39.74	3.08
106	107	4.652421	CACTATGGCTAGGGTAACAGGTAA	59.348	45.833	0.00	39.74	2.85
107	108	4.652881	ACTATGGCTAGGGTAACAGGTAAC	59.347	45.833	0.00	39.74	2.50
108	109	2.190538	TGGCTAGGGTAACAGGTAACC	58.809	52.381	0.00	40.33	2.85

Showing 1 to 25 of 423 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	5.642686	ACTCTCGCTCAACACTATTAACTC	58.357	41.667	0.00	0.00	0.00	3.01
41	42	5.646577	ACTCTCGCTCAACACTATTAACT	57.353	39.130	0.00	0.00	0.00	2.24
42	43	7.807687	TTAACTCTCGCTCAACACTATTAAC	57.192	36.000	0.00	0.00	0.00	2.01
43	44	8.869897	CAATTAACTCTCGCTCAACACTATTAA	58.130	33.333	0.00	0.00	0.00	1.40
44	45	7.010183	GCAATTAACTCTCGCTCAACACTATTA	59.990	37.037	0.00	0.00	0.00	0.98
45	46	6.183360	GCAATTAACTCTCGCTCAACACTATT	60.183	38.462	0.00	0.00	0.00	1.73
46	47	5.292101	GCAATTAACTCTCGCTCAACACTAT	59.708	40.000	0.00	0.00	0.00	2.12
47	48	4.625742	GCAATTAACTCTCGCTCAACACTA	59.374	41.667	0.00	0.00	0.00	2.74
48	49	3.433615	GCAATTAACTCTCGCTCAACACT	59.566	43.478	0.00	0.00	0.00	3.55
49	50	3.433615	AGCAATTAACTCTCGCTCAACAC	59.566	43.478	0.00	0.00	0.00	3.32
50	51	3.664107	AGCAATTAACTCTCGCTCAACA	58.336	40.909	0.00	0.00	0.00	3.33
51	52	4.251960	GAGCAATTAACTCTCGCTCAAC	57.748	45.455	4.90	0.00	46.55	3.18
55	56	3.876274	TCTGAGCAATTAACTCTCGCT	57.124	42.857	8.63	0.00	35.12	4.93
56	57	3.062774	GGTTCTGAGCAATTAACTCTCGC	59.937	47.826	8.63	0.00	35.12	5.03
57	58	4.092091	GTGGTTCTGAGCAATTAACTCTCG	59.908	45.833	8.63	1.98	34.60	4.04
58	59	4.393371	GGTGGTTCTGAGCAATTAACTCTC	59.607	45.833	8.63	0.83	34.60	3.20
59	60	4.202461	TGGTGGTTCTGAGCAATTAACTCT	60.202	41.667	8.63	0.00	34.60	3.24
103	104	7.206687	TGAATTTTGTCAGAATTGGTGGTTAC	58.793	34.615	6.09	0.00	0.00	2.50
104	105	7.353414	TGAATTTTGTCAGAATTGGTGGTTA	57.647	32.000	6.09	0.00	0.00	2.85
105	106	6.232581	TGAATTTTGTCAGAATTGGTGGTT	57.767	33.333	6.09	0.00	0.00	3.67
106	107	5.867903	TGAATTTTGTCAGAATTGGTGGT	57.132	34.783	6.09	0.00	0.00	4.16
107	108	8.830201	TTATTGAATTTTGTCAGAATTGGTGG	57.170	30.769	6.09	0.00	0.00	4.61
115	116	9.658799	TGGTTGTTTTTATTGAATTTTGTCAGA	57.341	25.926	0.00	0.00	0.00	3.27
116	117	9.701355	GTGGTTGTTTTTATTGAATTTTGTCAG	57.299	29.630	0.00	0.00	0.00	3.51
117	118	9.442047	AGTGGTTGTTTTTATTGAATTTTGTCA	57.558	25.926	0.00	0.00	0.00	3.58

Showing 1 to 25 of 448 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.