AutoCloner

Multiple sequence alignment - TraesCS6D01G223700

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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	TraesCS6D01G223700	chr6D	100.000	2700	0	0	1	2700	315749386	315752085	0.000000e+00	4987.0
1	TraesCS6D01G223700	chr6A	91.304	1656	67	27	262	1885	453551964	453553574	0.000000e+00	2189.0
2	TraesCS6D01G223700	chr6B	94.094	999	32	8	877	1874	509319514	509318542	0.000000e+00	1493.0
3	TraesCS6D01G223700	chr6B	91.542	603	36	6	275	875	509320136	509319547	0.000000e+00	817.0
4	TraesCS6D01G223700	chr6B	72.029	690	146	27	2005	2678	122953667	122954325	7.740000e-36	161.0
5	TraesCS6D01G223700	chr6B	75.113	221	51	3	2462	2681	489838908	489838691	1.710000e-17	100.0
6	TraesCS6D01G223700	chr6B	97.059	34	1	0	2288	2321	704836855	704836888	1.040000e-04	58.4
7	TraesCS6D01G223700	chr7D	78.865	511	66	29	2182	2676	99990188	99989704	9.390000e-80	307.0
8	TraesCS6D01G223700	chr2D	75.087	289	52	14	2243	2520	606756919	606756640	1.700000e-22	117.0
9	TraesCS6D01G223700	chr2D	72.414	377	75	21	2013	2381	539236229	539235874	2.860000e-15	93.5
10	TraesCS6D01G223700	chr3A	72.388	402	80	20	2296	2681	698688766	698688380	6.150000e-17	99.0

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	TraesCS6D01G223700	chr6D	315749386	315752085	2699	False	4987	4987	100.000	1	2700	1	chr6D.!!$F1	2699
1	TraesCS6D01G223700	chr6A	453551964	453553574	1610	False	2189	2189	91.304	262	1885	1	chr6A.!!$F1	1623
2	TraesCS6D01G223700	chr6B	509318542	509320136	1594	True	1155	1493	92.818	275	1874	2	chr6B.!!$R2	1599

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
106	107	0.032815	AAAATTTTGTGCCCCCGACG	59.967	50.0	1.75	0.0	0.0	5.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1879	1958	0.029834	GCCCGCATGTAAATGCTCTG	59.97	55.0	15.85	5.23	44.9	3.35	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
26	27	4.007940	CGGCGGTGGTGTCGTTTG	62.008	66.667	0.00	0.00	0.00	2.93
27	28	3.656045	GGCGGTGGTGTCGTTTGG	61.656	66.667	0.00	0.00	0.00	3.28
28	29	3.656045	GCGGTGGTGTCGTTTGGG	61.656	66.667	0.00	0.00	0.00	4.12
29	30	2.975799	CGGTGGTGTCGTTTGGGG	60.976	66.667	0.00	0.00	0.00	4.96
30	31	3.292159	GGTGGTGTCGTTTGGGGC	61.292	66.667	0.00	0.00	0.00	5.80
31	32	3.656045	GTGGTGTCGTTTGGGGCG	61.656	66.667	0.00	0.00	0.00	6.13
32	33	4.939368	TGGTGTCGTTTGGGGCGG	62.939	66.667	0.00	0.00	0.00	6.13
33	34	4.941309	GGTGTCGTTTGGGGCGGT	62.941	66.667	0.00	0.00	0.00	5.68
34	35	3.656045	GTGTCGTTTGGGGCGGTG	61.656	66.667	0.00	0.00	0.00	4.94
35	36	4.939368	TGTCGTTTGGGGCGGTGG	62.939	66.667	0.00	0.00	0.00	4.61
49	50	4.746309	GTGGCCATGGCAGGAGCA	62.746	66.667	36.56	22.45	44.61	4.26
50	51	4.435970	TGGCCATGGCAGGAGCAG	62.436	66.667	36.56	0.00	44.61	4.24
52	53	4.119363	GCCATGGCAGGAGCAGGA	62.119	66.667	32.08	0.00	44.61	3.86
53	54	2.192443	CCATGGCAGGAGCAGGAG	59.808	66.667	0.00	0.00	44.61	3.69
54	55	2.192443	CATGGCAGGAGCAGGAGG	59.808	66.667	0.00	0.00	44.61	4.30
55	56	3.095163	ATGGCAGGAGCAGGAGGG	61.095	66.667	0.00	0.00	44.61	4.30
65	66	2.770048	CAGGAGGGCGGGAGGATT	60.770	66.667	0.00	0.00	0.00	3.01
66	67	2.042930	AGGAGGGCGGGAGGATTT	59.957	61.111	0.00	0.00	0.00	2.17
67	68	1.619669	AGGAGGGCGGGAGGATTTT	60.620	57.895	0.00	0.00	0.00	1.82
68	69	1.214992	AGGAGGGCGGGAGGATTTTT	61.215	55.000	0.00	0.00	0.00	1.94
83	84	2.562953	TTTTTGGAGAGCAGGGGGA	58.437	52.632	0.00	0.00	0.00	4.81
84	85	0.856982	TTTTTGGAGAGCAGGGGGAA	59.143	50.000	0.00	0.00	0.00	3.97
85	86	1.084018	TTTTGGAGAGCAGGGGGAAT	58.916	50.000	0.00	0.00	0.00	3.01
86	87	1.084018	TTTGGAGAGCAGGGGGAATT	58.916	50.000	0.00	0.00	0.00	2.17
87	88	1.979809	TTGGAGAGCAGGGGGAATTA	58.020	50.000	0.00	0.00	0.00	1.40

Showing 1 to 25 of 627 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	4.007940	CAAACGACACCACCGCCG	62.008	66.667	0.00	0.00	0.00	6.46
10	11	3.656045	CCAAACGACACCACCGCC	61.656	66.667	0.00	0.00	0.00	6.13
11	12	3.656045	CCCAAACGACACCACCGC	61.656	66.667	0.00	0.00	0.00	5.68
12	13	2.975799	CCCCAAACGACACCACCG	60.976	66.667	0.00	0.00	0.00	4.94
13	14	3.292159	GCCCCAAACGACACCACC	61.292	66.667	0.00	0.00	0.00	4.61
14	15	3.656045	CGCCCCAAACGACACCAC	61.656	66.667	0.00	0.00	0.00	4.16
15	16	4.939368	CCGCCCCAAACGACACCA	62.939	66.667	0.00	0.00	0.00	4.17
16	17	4.941309	ACCGCCCCAAACGACACC	62.941	66.667	0.00	0.00	0.00	4.16
17	18	3.656045	CACCGCCCCAAACGACAC	61.656	66.667	0.00	0.00	0.00	3.67
18	19	4.939368	CCACCGCCCCAAACGACA	62.939	66.667	0.00	0.00	0.00	4.35
32	33	4.746309	TGCTCCTGCCATGGCCAC	62.746	66.667	33.44	17.85	41.09	5.01
33	34	4.435970	CTGCTCCTGCCATGGCCA	62.436	66.667	33.44	21.65	41.09	5.36
35	36	4.119363	TCCTGCTCCTGCCATGGC	62.119	66.667	30.54	30.54	42.35	4.40
36	37	2.192443	CTCCTGCTCCTGCCATGG	59.808	66.667	7.63	7.63	38.71	3.66
37	38	2.192443	CCTCCTGCTCCTGCCATG	59.808	66.667	0.00	0.00	38.71	3.66
38	39	3.095163	CCCTCCTGCTCCTGCCAT	61.095	66.667	0.00	0.00	38.71	4.40
48	49	1.926426	AAAATCCTCCCGCCCTCCTG	61.926	60.000	0.00	0.00	0.00	3.86
49	50	1.214992	AAAAATCCTCCCGCCCTCCT	61.215	55.000	0.00	0.00	0.00	3.69
50	51	1.306633	AAAAATCCTCCCGCCCTCC	59.693	57.895	0.00	0.00	0.00	4.30
65	66	0.856982	TTCCCCCTGCTCTCCAAAAA	59.143	50.000	0.00	0.00	0.00	1.94
66	67	1.084018	ATTCCCCCTGCTCTCCAAAA	58.916	50.000	0.00	0.00	0.00	2.44
67	68	1.084018	AATTCCCCCTGCTCTCCAAA	58.916	50.000	0.00	0.00	0.00	3.28
68	69	1.979809	TAATTCCCCCTGCTCTCCAA	58.020	50.000	0.00	0.00	0.00	3.53
69	70	1.979809	TTAATTCCCCCTGCTCTCCA	58.020	50.000	0.00	0.00	0.00	3.86
70	71	3.382083	TTTTAATTCCCCCTGCTCTCC	57.618	47.619	0.00	0.00	0.00	3.71

Showing 1 to 25 of 558 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.