AutoCloner

Multiple sequence alignment - TraesCS2D01G451000

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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	TraesCS2D01G451000	chr2D	100.000	2303	0	0	665	2967	560933340	560935642	0.000000e+00	4253.0
1	TraesCS2D01G451000	chr2D	100.000	366	0	0	1	366	560932676	560933041	0.000000e+00	676.0
2	TraesCS2D01G451000	chr2A	85.649	439	29	7	2080	2511	700950233	700950644	5.880000e-117	431.0
3	TraesCS2D01G451000	chr2A	91.667	204	15	2	2671	2874	700950662	700950863	6.260000e-72	281.0
4	TraesCS2D01G451000	chr2A	100.000	32	0	0	2936	2967	700950864	700950895	3.190000e-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	TraesCS2D01G451000	chr2D	560932676	560935642	2966	False	2464.5	4253	100.000000	1	2967	2	chr2D.!!$F1	2966
1	TraesCS2D01G451000	chr2A	700950233	700950895	662	False	257.4	431	92.438667	2080	2967	3	chr2A.!!$F1	887

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
233	234	0.036010	CTCGATCCAGGGCAAAGTGT	60.036	55.0	0.00	0.00	0.0	3.55	F
234	235	0.036388	TCGATCCAGGGCAAAGTGTC	60.036	55.0	0.00	0.00	0.0	3.67	F
328	329	0.036765	TTCATTGTTCGGCTAGGCGT	60.037	50.0	34.02	15.29	0.0	5.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1699	1700	0.032678	ATAAGACAGCCGCGATCCTG	59.967	55.0	8.23	13.65	35.26	3.86	R
1700	1701	0.032678	CATAAGACAGCCGCGATCCT	59.967	55.0	8.23	0.00	0.00	3.24	R
2028	2029	0.034756	CGCATCCCATATCCGTTCCA	59.965	55.0	0.00	0.00	0.00	3.53	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
17	18	4.449391	AAACAGACCGACCAACCG	57.551	55.556	0.00	0.00	0.00	4.44
18	19	1.824658	AAACAGACCGACCAACCGA	59.175	52.632	0.00	0.00	0.00	4.69
19	20	0.531311	AAACAGACCGACCAACCGAC	60.531	55.000	0.00	0.00	0.00	4.79
20	21	1.397390	AACAGACCGACCAACCGACT	61.397	55.000	0.00	0.00	0.00	4.18
21	22	1.372997	CAGACCGACCAACCGACTG	60.373	63.158	0.00	0.00	0.00	3.51
22	23	2.048503	GACCGACCAACCGACTGG	60.049	66.667	1.54	1.54	42.68	4.00
23	24	4.309950	ACCGACCAACCGACTGGC	62.310	66.667	2.91	0.00	40.45	4.85
24	25	4.003788	CCGACCAACCGACTGGCT	62.004	66.667	2.91	0.00	40.45	4.75
25	26	2.642254	CCGACCAACCGACTGGCTA	61.642	63.158	2.91	0.00	40.45	3.93
26	27	1.445582	CGACCAACCGACTGGCTAC	60.446	63.158	2.91	0.00	40.45	3.58
27	28	1.445582	GACCAACCGACTGGCTACG	60.446	63.158	2.91	0.00	40.45	3.51
44	45	2.126031	GGGACGAACGAGTCAGCC	60.126	66.667	0.14	2.90	42.62	4.85
45	46	2.649034	GGACGAACGAGTCAGCCA	59.351	61.111	0.14	0.00	42.62	4.75
46	47	1.444553	GGACGAACGAGTCAGCCAG	60.445	63.158	0.14	0.00	42.62	4.85
47	48	2.049063	ACGAACGAGTCAGCCAGC	60.049	61.111	0.14	0.00	0.00	4.85
48	49	2.811317	CGAACGAGTCAGCCAGCC	60.811	66.667	0.00	0.00	0.00	4.85
49	50	2.343758	GAACGAGTCAGCCAGCCA	59.656	61.111	0.00	0.00	0.00	4.75
50	51	1.739562	GAACGAGTCAGCCAGCCAG	60.740	63.158	0.00	0.00	0.00	4.85
51	52	3.890936	AACGAGTCAGCCAGCCAGC	62.891	63.158	0.00	0.00	0.00	4.85
53	54	4.025858	GAGTCAGCCAGCCAGCCA	62.026	66.667	0.00	0.00	0.00	4.75
54	55	3.557903	GAGTCAGCCAGCCAGCCAA	62.558	63.158	0.00	0.00	0.00	4.52
55	56	3.060615	GTCAGCCAGCCAGCCAAG	61.061	66.667	0.00	0.00	0.00	3.61
56	57	4.355720	TCAGCCAGCCAGCCAAGG	62.356	66.667	0.00	0.00	0.00	3.61
63	64	2.820037	GCCAGCCAAGGCGTCTAC	60.820	66.667	5.28	0.00	46.12	2.59
74	75	4.944372	CGTCTACCGGCCCGCATC	62.944	72.222	0.00	0.00	0.00	3.91

Showing 1 to 25 of 1,393 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	0.531311	GTCGGTTGGTCGGTCTGTTT	60.531	55.000	0.00	0.00	0.00	2.83
1	2	1.068585	GTCGGTTGGTCGGTCTGTT	59.931	57.895	0.00	0.00	0.00	3.16
2	3	1.831286	AGTCGGTTGGTCGGTCTGT	60.831	57.895	0.00	0.00	0.00	3.41
3	4	1.372997	CAGTCGGTTGGTCGGTCTG	60.373	63.158	0.00	0.00	0.00	3.51
4	5	2.571216	CCAGTCGGTTGGTCGGTCT	61.571	63.158	0.00	0.00	33.38	3.85
5	6	2.048503	CCAGTCGGTTGGTCGGTC	60.049	66.667	0.00	0.00	33.38	4.79
6	7	4.309950	GCCAGTCGGTTGGTCGGT	62.310	66.667	7.74	0.00	40.49	4.69
7	8	2.642254	TAGCCAGTCGGTTGGTCGG	61.642	63.158	7.74	0.00	40.49	4.79
8	9	1.445582	GTAGCCAGTCGGTTGGTCG	60.446	63.158	7.74	0.00	40.49	4.79
9	10	1.445582	CGTAGCCAGTCGGTTGGTC	60.446	63.158	7.74	1.67	40.49	4.02
10	11	2.654877	CGTAGCCAGTCGGTTGGT	59.345	61.111	7.74	0.00	40.49	3.67
11	12	2.125673	CCGTAGCCAGTCGGTTGG	60.126	66.667	2.18	2.18	41.58	3.77
12	13	2.125673	CCCGTAGCCAGTCGGTTG	60.126	66.667	0.00	0.00	44.51	3.77
13	14	2.283388	TCCCGTAGCCAGTCGGTT	60.283	61.111	0.00	0.00	44.51	4.44
14	15	3.066814	GTCCCGTAGCCAGTCGGT	61.067	66.667	0.00	0.00	44.51	4.69
15	16	4.189188	CGTCCCGTAGCCAGTCGG	62.189	72.222	0.00	0.00	45.42	4.79
16	17	2.693762	TTCGTCCCGTAGCCAGTCG	61.694	63.158	0.00	0.00	0.00	4.18
17	18	1.153881	GTTCGTCCCGTAGCCAGTC	60.154	63.158	0.00	0.00	0.00	3.51
18	19	2.968206	GTTCGTCCCGTAGCCAGT	59.032	61.111	0.00	0.00	0.00	4.00
19	20	2.202570	CGTTCGTCCCGTAGCCAG	60.203	66.667	0.00	0.00	0.00	4.85
20	21	2.672651	TCGTTCGTCCCGTAGCCA	60.673	61.111	0.00	0.00	0.00	4.75
21	22	2.101770	CTCGTTCGTCCCGTAGCC	59.898	66.667	0.00	0.00	0.00	3.93
22	23	1.226239	GACTCGTTCGTCCCGTAGC	60.226	63.158	0.00	0.00	0.00	3.58
23	24	0.096628	CTGACTCGTTCGTCCCGTAG	59.903	60.000	0.00	0.00	32.97	3.51
24	25	1.915614	GCTGACTCGTTCGTCCCGTA	61.916	60.000	0.00	0.00	32.97	4.02

Showing 1 to 25 of 1,432 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.