AutoCloner

Multiple sequence alignment - TraesCS6D01G314200

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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	TraesCS6D01G314200	chr6D	100.000	3449	0	0	1	3449	422604103	422607551	0.000000e+00	6370.0
1	TraesCS6D01G314200	chr6B	92.037	2675	137	44	808	3449	636795382	636798013	0.000000e+00	3690.0
2	TraesCS6D01G314200	chr6B	87.815	476	44	8	1	464	636767742	636768215	2.340000e-151	545.0
3	TraesCS6D01G314200	chr6A	92.941	1020	55	15	1667	2672	565344039	565345055	0.000000e+00	1469.0
4	TraesCS6D01G314200	chr6A	92.209	783	36	7	567	1346	565343076	565343836	0.000000e+00	1085.0
5	TraesCS6D01G314200	chr6A	86.914	619	60	18	2675	3285	565345134	565345739	0.000000e+00	675.0
6	TraesCS6D01G314200	chr2D	83.854	192	20	10	3188	3371	117250669	117250857	4.580000e-39	172.0
7	TraesCS6D01G314200	chr7D	84.024	169	12	14	3187	3348	132159528	132159688	7.710000e-32	148.0
8	TraesCS6D01G314200	chr4D	90.196	51	5	0	3098	3148	314635607	314635657	2.220000e-07	67.6

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	TraesCS6D01G314200	chr6D	422604103	422607551	3448	False	6370.000000	6370	100.000	1	3449	1	chr6D.!!$F1	3448
1	TraesCS6D01G314200	chr6B	636795382	636798013	2631	False	3690.000000	3690	92.037	808	3449	1	chr6B.!!$F2	2641
2	TraesCS6D01G314200	chr6A	565343076	565345739	2663	False	1076.333333	1469	90.688	567	3285	3	chr6A.!!$F1	2718

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
630	631	0.028902	GAAGTTGTGTGCGTGGGTTC	59.971	55.0	0.0	0.0	0.00	3.62	F
2277	2343	0.512952	AGAGCGAATGCACAAACGTC	59.487	50.0	0.0	0.0	46.23	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2379	2445	1.447489	CTGCTCAAGCTCACTCCCG	60.447	63.158	3.32	0.0	42.66	5.14	R
3372	3540	0.039798	CGGTTGAAGACGAAGACGGA	60.040	55.000	0.00	0.0	44.46	4.69	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	Hairpin	End Stability
17	18	3.081554	AGCGATCCAAACAGCCCT	58.918	55.556	0.00	5.19
18	19	2.296920	AGCGATCCAAACAGCCCTA	58.703	52.632	0.00	3.53
19	20	0.839946	AGCGATCCAAACAGCCCTAT	59.160	50.000	0.00	2.57
20	21	2.047061	AGCGATCCAAACAGCCCTATA	58.953	47.619	0.00	1.31
21	22	2.037772	AGCGATCCAAACAGCCCTATAG	59.962	50.000	0.00	1.31
22	23	2.224305	GCGATCCAAACAGCCCTATAGT	60.224	50.000	0.00	2.12
23	24	3.654414	CGATCCAAACAGCCCTATAGTC	58.346	50.000	0.00	2.59
24	25	3.069586	CGATCCAAACAGCCCTATAGTCA	59.930	47.826	0.00	3.41
25	26	4.442893	CGATCCAAACAGCCCTATAGTCAA	60.443	45.833	0.00	3.18
26	27	4.919774	TCCAAACAGCCCTATAGTCAAA	57.080	40.909	0.00	2.69
27	28	4.843728	TCCAAACAGCCCTATAGTCAAAG	58.156	43.478	0.00	2.77
28	29	4.288626	TCCAAACAGCCCTATAGTCAAAGT	59.711	41.667	0.00	2.66
29	30	4.396166	CCAAACAGCCCTATAGTCAAAGTG	59.604	45.833	0.00	3.16
30	31	4.910458	AACAGCCCTATAGTCAAAGTGT	57.090	40.909	0.00	3.55
31	32	4.473477	ACAGCCCTATAGTCAAAGTGTC	57.527	45.455	0.00	3.67
32	33	3.838317	ACAGCCCTATAGTCAAAGTGTCA	59.162	43.478	0.00	3.58
33	34	4.286032	ACAGCCCTATAGTCAAAGTGTCAA	59.714	41.667	0.00	3.18
34	35	5.221843	ACAGCCCTATAGTCAAAGTGTCAAA	60.222	40.000	0.00	2.69
35	36	5.122396	CAGCCCTATAGTCAAAGTGTCAAAC	59.878	44.000	0.00	2.93
36	37	5.013183	AGCCCTATAGTCAAAGTGTCAAACT	59.987	40.000	42.60	2.66
37	38	6.212791	AGCCCTATAGTCAAAGTGTCAAACTA	59.787	38.462	38.56	2.24
38	39	6.313164	GCCCTATAGTCAAAGTGTCAAACTAC	59.687	42.308	38.56	2.73
39	40	7.612677	CCCTATAGTCAAAGTGTCAAACTACT	58.387	38.462	38.56	2.57
40	41	8.746530	CCCTATAGTCAAAGTGTCAAACTACTA	58.253	37.037	38.56	1.82
44	45	7.304497	AGTCAAAGTGTCAAACTACTATCCT	57.696	36.000	38.56	3.24

Showing 1 to 25 of 412 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
0	1	0.839946	ATAGGGCTGTTTGGATCGCT	59.160	50.000	0.00	0.00	4.93
1	2	2.224305	ACTATAGGGCTGTTTGGATCGC	60.224	50.000	4.43	0.00	4.58
2	3	3.069586	TGACTATAGGGCTGTTTGGATCG	59.930	47.826	4.43	0.00	3.69
3	4	4.689612	TGACTATAGGGCTGTTTGGATC	57.310	45.455	4.43	0.00	3.36
4	5	5.044846	ACTTTGACTATAGGGCTGTTTGGAT	60.045	40.000	4.43	0.00	3.41
5	6	4.288626	ACTTTGACTATAGGGCTGTTTGGA	59.711	41.667	4.43	0.00	3.53
6	7	4.396166	CACTTTGACTATAGGGCTGTTTGG	59.604	45.833	4.43	0.00	3.28
7	8	5.003804	ACACTTTGACTATAGGGCTGTTTG	58.996	41.667	4.43	0.00	2.93
8	9	5.221843	TGACACTTTGACTATAGGGCTGTTT	60.222	40.000	4.43	0.00	2.83
9	10	4.286032	TGACACTTTGACTATAGGGCTGTT	59.714	41.667	4.43	0.00	3.16
10	11	3.838317	TGACACTTTGACTATAGGGCTGT	59.162	43.478	4.43	0.00	4.40
11	12	4.471904	TGACACTTTGACTATAGGGCTG	57.528	45.455	4.43	0.00	4.85
12	13	5.013183	AGTTTGACACTTTGACTATAGGGCT	59.987	40.000	4.43	27.32	5.19
13	14	5.246307	AGTTTGACACTTTGACTATAGGGC	58.754	41.667	4.43	27.32	5.19
14	15	7.612677	AGTAGTTTGACACTTTGACTATAGGG	58.387	38.462	4.43	36.88	3.53
18	19	9.036980	AGGATAGTAGTTTGACACTTTGACTAT	57.963	33.333	0.00	37.45	2.12
19	20	8.418597	AGGATAGTAGTTTGACACTTTGACTA	57.581	34.615	0.00	36.88	2.59
20	21	7.304497	AGGATAGTAGTTTGACACTTTGACT	57.696	36.000	0.00	36.88	3.41
21	22	7.964604	AAGGATAGTAGTTTGACACTTTGAC	57.035	36.000	0.00	36.88	3.18
22	23	8.974060	AAAAGGATAGTAGTTTGACACTTTGA	57.026	30.769	0.00	36.88	2.69
55	56	9.709600	GCTTCACTATAGAAAAAGATAGTTTGC	57.290	33.333	6.78	36.87	3.68
132	133	9.507329	GAGCATTAGGTGGAATAGATCAAAATA	57.493	33.333	0.00	0.00	1.40
133	134	8.000709	TGAGCATTAGGTGGAATAGATCAAAAT	58.999	33.333	0.00	0.00	1.82
134	135	7.345691	TGAGCATTAGGTGGAATAGATCAAAA	58.654	34.615	0.00	0.00	2.44
135	136	6.899089	TGAGCATTAGGTGGAATAGATCAAA	58.101	36.000	0.00	0.00	2.69

Showing 1 to 25 of 416 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.