AutoCloner

Multiple sequence alignment - TraesCS6D01G258900

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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	TraesCS6D01G258900	chr6D	100.000	4295	0	0	1	4295	365274600	365278894	0.000000e+00	7932.0
1	TraesCS6D01G258900	chr6D	99.291	282	1	1	1	281	417479386	417479667	3.830000e-140	508.0
2	TraesCS6D01G258900	chr6D	99.288	281	1	1	1	280	28328941	28328661	1.380000e-139	507.0
3	TraesCS6D01G258900	chr6D	99.286	280	2	0	1	280	436115708	436115987	1.380000e-139	507.0
4	TraesCS6D01G258900	chr6D	98.929	280	3	0	1	280	194012756	194013035	6.410000e-138	501.0
5	TraesCS6D01G258900	chr6B	95.514	1984	72	11	2318	4287	550075622	550077602	0.000000e+00	3155.0
6	TraesCS6D01G258900	chr6B	89.861	1371	73	29	678	2017	550073934	550075269	0.000000e+00	1701.0
7	TraesCS6D01G258900	chr6B	89.011	455	46	4	281	733	550054364	550054816	1.040000e-155	560.0
8	TraesCS6D01G258900	chr6B	92.135	267	13	3	2028	2294	550075249	550075507	1.890000e-98	370.0
9	TraesCS6D01G258900	chr6A	96.886	1156	34	2	3132	4287	506234745	506235898	0.000000e+00	1934.0
10	TraesCS6D01G258900	chr6A	91.063	1421	79	26	635	2013	506232007	506233421	0.000000e+00	1877.0
11	TraesCS6D01G258900	chr6A	94.458	830	31	8	2319	3133	506233792	506234621	0.000000e+00	1264.0
12	TraesCS6D01G258900	chr6A	92.989	271	16	3	2027	2295	506233404	506233673	4.030000e-105	392.0
13	TraesCS6D01G258900	chr2D	100.000	280	0	0	1	280	591542177	591541898	6.370000e-143	518.0
14	TraesCS6D01G258900	chr2D	98.947	285	1	2	1	284	631556179	631556462	3.830000e-140	508.0
15	TraesCS6D01G258900	chr2D	90.449	356	31	2	281	633	517266985	517266630	2.340000e-127	466.0
16	TraesCS6D01G258900	chr7D	99.288	281	1	1	1	280	469890792	469890512	1.380000e-139	507.0
17	TraesCS6D01G258900	chr7D	80.982	163	29	2	1087	1248	507420393	507420554	1.250000e-25	128.0
18	TraesCS6D01G258900	chr5D	98.932	281	2	1	1	280	279149956	279149676	6.410000e-138	501.0
19	TraesCS6D01G258900	chr4D	98.932	281	2	1	1	280	65118741	65119021	6.410000e-138	501.0
20	TraesCS6D01G258900	chr4D	89.665	358	36	1	281	637	498379080	498379437	5.060000e-124	455.0
21	TraesCS6D01G258900	chr3D	90.652	353	33	0	281	633	553333899	553334251	1.810000e-128	470.0
22	TraesCS6D01G258900	chr7B	89.916	357	33	2	281	637	189686439	189686086	1.410000e-124	457.0
23	TraesCS6D01G258900	chr7B	90.057	352	35	0	281	632	738782536	738782887	1.410000e-124	457.0
24	TraesCS6D01G258900	chr7B	81.098	164	27	4	1087	1248	535822661	535822822	1.250000e-25	128.0
25	TraesCS6D01G258900	chr5B	89.474	361	35	3	281	638	568185969	568185609	1.820000e-123	453.0
26	TraesCS6D01G258900	chr5B	89.802	353	36	0	281	633	700196519	700196871	1.820000e-123	453.0
27	TraesCS6D01G258900	chr1D	89.474	361	34	2	281	638	11804121	11804480	1.820000e-123	453.0
28	TraesCS6D01G258900	chr7A	80.368	163	30	2	1087	1248	577223165	577223326	5.830000e-24	122.0
29	TraesCS6D01G258900	chr7A	82.075	106	11	5	1180	1284	93143318	93143416	2.750000e-12	84.2
30	TraesCS6D01G258900	chr7A	86.957	69	9	0	1180	1248	94035666	94035734	1.280000e-10	78.7
31	TraesCS6D01G258900	chr3A	82.524	103	12	3	1182	1284	681734640	681734736	7.650000e-13	86.1
32	TraesCS6D01G258900	chr1A	81.905	105	13	3	1180	1284	5950110	5950208	2.750000e-12	84.2
33	TraesCS6D01G258900	chr4A	87.324	71	5	4	1180	1248	613941637	613941705	1.280000e-10	78.7

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	TraesCS6D01G258900	chr6D	365274600	365278894	4294	False	7932.00	7932	100.000000	1	4295	1	chr6D.!!$F2	4294
1	TraesCS6D01G258900	chr6B	550073934	550077602	3668	False	1742.00	3155	92.503333	678	4287	3	chr6B.!!$F2	3609
2	TraesCS6D01G258900	chr6A	506232007	506235898	3891	False	1366.75	1934	93.849000	635	4287	4	chr6A.!!$F1	3652

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
447	448	0.031721	ACGACGACTTCCCAACTGTC	59.968	55.0	0.0	0.0	0.0	3.51	F
1743	1766	0.108041	CCCCCATCATGTTGCAAAGC	60.108	55.0	0.0	0.0	0.0	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1908	1950	0.036765	GTCGGTGCTGACCATAACCA	60.037	55.0	0.00	0.0	43.33	3.67	R
3580	3865	0.253160	ATGGGCCCAGTAAGGAGACA	60.253	55.0	31.97	0.5	41.22	3.41	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	6.840075	CAGAAGCTCCTTCAGATTAAGTTTG	58.160	40.000	7.62	0.00	42.37	2.93
25	26	6.429385	CAGAAGCTCCTTCAGATTAAGTTTGT	59.571	38.462	7.62	0.00	42.37	2.83
26	27	7.001073	AGAAGCTCCTTCAGATTAAGTTTGTT	58.999	34.615	7.62	0.00	42.37	2.83
27	28	7.503902	AGAAGCTCCTTCAGATTAAGTTTGTTT	59.496	33.333	7.62	0.00	42.37	2.83
28	29	7.208225	AGCTCCTTCAGATTAAGTTTGTTTC	57.792	36.000	0.00	0.00	0.00	2.78
29	30	7.001073	AGCTCCTTCAGATTAAGTTTGTTTCT	58.999	34.615	0.00	0.00	0.00	2.52
30	31	7.503902	AGCTCCTTCAGATTAAGTTTGTTTCTT	59.496	33.333	0.00	0.00	0.00	2.52
31	32	7.805542	GCTCCTTCAGATTAAGTTTGTTTCTTC	59.194	37.037	0.00	0.00	0.00	2.87
32	33	7.861630	TCCTTCAGATTAAGTTTGTTTCTTCG	58.138	34.615	0.00	0.00	0.00	3.79
33	34	7.713507	TCCTTCAGATTAAGTTTGTTTCTTCGA	59.286	33.333	0.00	0.00	0.00	3.71
34	35	8.342634	CCTTCAGATTAAGTTTGTTTCTTCGAA	58.657	33.333	0.00	0.00	0.00	3.71
35	36	9.374960	CTTCAGATTAAGTTTGTTTCTTCGAAG	57.625	33.333	19.35	19.35	0.00	3.79
36	37	7.861630	TCAGATTAAGTTTGTTTCTTCGAAGG	58.138	34.615	24.37	6.79	0.00	3.46
37	38	7.713507	TCAGATTAAGTTTGTTTCTTCGAAGGA	59.286	33.333	24.37	14.37	0.00	3.36
38	39	8.507249	CAGATTAAGTTTGTTTCTTCGAAGGAT	58.493	33.333	24.37	1.98	0.00	3.24
39	40	8.722394	AGATTAAGTTTGTTTCTTCGAAGGATC	58.278	33.333	24.37	15.69	0.00	3.36
40	41	7.795482	TTAAGTTTGTTTCTTCGAAGGATCA	57.205	32.000	24.37	18.12	0.00	2.92
41	42	5.931441	AGTTTGTTTCTTCGAAGGATCAG	57.069	39.130	24.37	0.00	0.00	2.90
42	43	4.214332	AGTTTGTTTCTTCGAAGGATCAGC	59.786	41.667	24.37	16.12	0.00	4.26
43	44	3.685139	TGTTTCTTCGAAGGATCAGCT	57.315	42.857	24.37	0.00	0.00	4.24
44	45	4.008074	TGTTTCTTCGAAGGATCAGCTT	57.992	40.909	24.37	0.00	0.00	3.74
45	46	3.748048	TGTTTCTTCGAAGGATCAGCTTG	59.252	43.478	24.37	0.00	0.00	4.01
46	47	2.015736	TCTTCGAAGGATCAGCTTGC	57.984	50.000	24.37	0.00	0.00	4.01
47	48	1.552337	TCTTCGAAGGATCAGCTTGCT	59.448	47.619	24.37	0.00	0.00	3.91
48	49	1.664659	CTTCGAAGGATCAGCTTGCTG	59.335	52.381	17.70	15.74	0.00	4.41

Showing 1 to 25 of 528 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	6.429385	ACAAACTTAATCTGAAGGAGCTTCTG	59.571	38.462	0.00	0.00	40.73	3.02
2	3	6.809630	ACAAACTTAATCTGAAGGAGCTTC	57.190	37.500	0.00	0.00	40.54	3.86
3	4	7.503902	AGAAACAAACTTAATCTGAAGGAGCTT	59.496	33.333	0.00	0.00	0.00	3.74
4	5	7.001073	AGAAACAAACTTAATCTGAAGGAGCT	58.999	34.615	0.00	0.00	0.00	4.09
5	6	7.208225	AGAAACAAACTTAATCTGAAGGAGC	57.792	36.000	0.00	0.00	0.00	4.70
6	7	8.012241	CGAAGAAACAAACTTAATCTGAAGGAG	58.988	37.037	0.00	0.00	0.00	3.69
7	8	7.713507	TCGAAGAAACAAACTTAATCTGAAGGA	59.286	33.333	0.00	0.00	0.00	3.36
8	9	7.861630	TCGAAGAAACAAACTTAATCTGAAGG	58.138	34.615	0.00	0.00	0.00	3.46
9	10	9.374960	CTTCGAAGAAACAAACTTAATCTGAAG	57.625	33.333	20.74	0.00	45.90	3.02
10	11	8.342634	CCTTCGAAGAAACAAACTTAATCTGAA	58.657	33.333	26.61	0.00	45.90	3.02
11	12	7.713507	TCCTTCGAAGAAACAAACTTAATCTGA	59.286	33.333	26.61	5.79	45.90	3.27
12	13	7.861630	TCCTTCGAAGAAACAAACTTAATCTG	58.138	34.615	26.61	3.42	45.90	2.90
13	14	8.622948	ATCCTTCGAAGAAACAAACTTAATCT	57.377	30.769	26.61	0.00	45.90	2.40
14	15	8.504005	TGATCCTTCGAAGAAACAAACTTAATC	58.496	33.333	26.61	10.64	45.90	1.75
15	16	8.391075	TGATCCTTCGAAGAAACAAACTTAAT	57.609	30.769	26.61	2.59	45.90	1.40
16	17	7.519970	GCTGATCCTTCGAAGAAACAAACTTAA	60.520	37.037	26.61	0.00	45.90	1.85
17	18	6.073222	GCTGATCCTTCGAAGAAACAAACTTA	60.073	38.462	26.61	1.10	45.90	2.24
18	19	5.278022	GCTGATCCTTCGAAGAAACAAACTT	60.278	40.000	26.61	0.00	45.90	2.66
19	20	4.214332	GCTGATCCTTCGAAGAAACAAACT	59.786	41.667	26.61	1.57	45.90	2.66
20	21	4.214332	AGCTGATCCTTCGAAGAAACAAAC	59.786	41.667	26.61	15.06	45.90	2.93
21	22	4.389374	AGCTGATCCTTCGAAGAAACAAA	58.611	39.130	26.61	5.98	45.90	2.83
22	23	4.008074	AGCTGATCCTTCGAAGAAACAA	57.992	40.909	26.61	6.67	45.90	2.83
23	24	3.685139	AGCTGATCCTTCGAAGAAACA	57.315	42.857	26.61	18.93	45.90	2.83
24	25	3.425492	GCAAGCTGATCCTTCGAAGAAAC	60.425	47.826	26.61	15.69	45.90	2.78
25	26	2.744202	GCAAGCTGATCCTTCGAAGAAA	59.256	45.455	26.61	14.12	45.90	2.52

Showing 1 to 25 of 510 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.