AutoCloner

Multiple sequence alignment - TraesCS5D01G075800

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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	TraesCS5D01G075800	chr5D	100.000	2417	0	0	1	2417	75271614	75274030	0.000000e+00	4464.0
1	TraesCS5D01G075800	chr5D	98.901	182	2	0	421	602	186314690	186314871	2.320000e-85	326.0
2	TraesCS5D01G075800	chr5D	98.370	184	3	0	421	604	188350263	188350080	8.330000e-85	324.0
3	TraesCS5D01G075800	chr5D	82.308	130	21	2	599	726	291901505	291901634	7.060000e-21	111.0
4	TraesCS5D01G075800	chr5B	94.103	1645	70	13	781	2417	83611772	83613397	0.000000e+00	2475.0
5	TraesCS5D01G075800	chr5B	86.614	127	15	2	604	729	524527046	524527171	3.240000e-29	139.0
6	TraesCS5D01G075800	chr5B	81.746	126	21	2	604	728	87972823	87972699	1.180000e-18	104.0
7	TraesCS5D01G075800	chr5A	93.896	1622	57	14	818	2417	70453947	70455548	0.000000e+00	2409.0
8	TraesCS5D01G075800	chr5A	94.554	202	7	4	421	622	253400623	253400426	2.330000e-80	309.0
9	TraesCS5D01G075800	chr5A	81.383	188	33	2	2	187	476302281	476302468	4.160000e-33	152.0
10	TraesCS5D01G075800	chr5A	86.538	104	11	3	91	192	681257144	681257042	7.060000e-21	111.0
11	TraesCS5D01G075800	chr5A	91.176	68	5	1	121	187	681092326	681092259	9.200000e-15	91.6
12	TraesCS5D01G075800	chr2D	98.696	230	3	0	194	423	269641790	269641561	2.240000e-110	409.0
13	TraesCS5D01G075800	chr2D	96.842	190	4	1	421	610	269414048	269413861	1.390000e-82	316.0
14	TraesCS5D01G075800	chr2D	96.842	190	5	1	421	610	317772914	317773102	1.390000e-82	316.0
15	TraesCS5D01G075800	chr2D	85.484	124	16	2	606	728	293711819	293711941	7.010000e-26	128.0
16	TraesCS5D01G075800	chr6D	97.095	241	5	2	184	423	213635345	213635106	2.890000e-109	405.0
17	TraesCS5D01G075800	chr6D	97.021	235	7	0	189	423	168798084	168797850	1.740000e-106	396.0
18	TraesCS5D01G075800	chr6D	96.354	192	7	0	421	612	214870328	214870137	1.390000e-82	316.0
19	TraesCS5D01G075800	chr6D	97.222	36	1	0	697	732	25674534	25674499	7.220000e-06	62.1
20	TraesCS5D01G075800	chr3D	98.268	231	4	0	193	423	240996573	240996343	2.890000e-109	405.0
21	TraesCS5D01G075800	chr3D	82.292	192	33	1	1	192	295288092	295288282	5.350000e-37	165.0
22	TraesCS5D01G075800	chr3D	84.127	126	17	3	606	729	551001749	551001625	4.220000e-23	119.0
23	TraesCS5D01G075800	chr3D	94.286	35	0	2	701	733	452589138	452589104	4.000000e-03	52.8
24	TraesCS5D01G075800	chr1D	98.268	231	4	0	193	423	175164802	175164572	2.890000e-109	405.0
25	TraesCS5D01G075800	chr1D	97.845	232	5	0	193	424	110718668	110718437	3.740000e-108	401.0
26	TraesCS5D01G075800	chr1D	97.046	237	5	2	187	423	173472312	173472546	4.840000e-107	398.0
27	TraesCS5D01G075800	chr1D	97.838	185	4	0	421	605	175467019	175467203	1.080000e-83	320.0
28	TraesCS5D01G075800	chr1D	87.736	106	11	2	622	726	447448403	447448299	3.260000e-24	122.0
29	TraesCS5D01G075800	chr1D	100.000	28	0	0	702	729	487509925	487509898	4.000000e-03	52.8
30	TraesCS5D01G075800	chr7D	97.854	233	5	0	191	423	340762613	340762845	1.040000e-108	403.0
31	TraesCS5D01G075800	chr7D	96.281	242	9	0	182	423	341090891	341091132	4.840000e-107	398.0
32	TraesCS5D01G075800	chr7D	85.385	130	18	1	600	728	148241138	148241267	1.510000e-27	134.0
33	TraesCS5D01G075800	chrUn	97.253	182	5	0	421	602	294033864	294034045	2.330000e-80	309.0
34	TraesCS5D01G075800	chrUn	97.253	182	5	0	421	602	294044495	294044676	2.330000e-80	309.0
35	TraesCS5D01G075800	chrUn	97.253	182	5	0	421	602	399461825	399462006	2.330000e-80	309.0
36	TraesCS5D01G075800	chr4B	83.957	187	27	3	2	187	600912197	600912381	2.470000e-40	176.0
37	TraesCS5D01G075800	chr4A	82.143	196	30	4	1	194	429402334	429402526	1.920000e-36	163.0
38	TraesCS5D01G075800	chr3B	81.915	188	27	5	1	186	389484504	389484686	4.160000e-33	152.0
39	TraesCS5D01G075800	chr1A	80.851	188	23	7	1	186	448925652	448925476	4.190000e-28	135.0
40	TraesCS5D01G075800	chr4D	89.773	88	8	1	91	177	500405027	500404940	7.060000e-21	111.0
41	TraesCS5D01G075800	chr2B	85.567	97	14	0	98	194	759529990	759529894	4.250000e-18	102.0
42	TraesCS5D01G075800	chr6A	86.301	73	9	1	660	731	591389852	591389924	7.160000e-11	78.7
43	TraesCS5D01G075800	chr7B	87.273	55	7	0	660	714	484280382	484280328	2.010000e-06	63.9
44	TraesCS5D01G075800	chr7B	100.000	29	0	0	689	717	641546962	641546934	1.000000e-03	54.7
45	TraesCS5D01G075800	chr1B	100.000	28	0	0	691	718	573068842	573068815	4.000000e-03	52.8

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	TraesCS5D01G075800	chr5D	75271614	75274030	2416	False	4464	4464	100.000	1	2417	1	chr5D.!!$F1	2416
1	TraesCS5D01G075800	chr5B	83611772	83613397	1625	False	2475	2475	94.103	781	2417	1	chr5B.!!$F1	1636
2	TraesCS5D01G075800	chr5A	70453947	70455548	1601	False	2409	2409	93.896	818	2417	1	chr5A.!!$F1	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
697	698	0.040425	AACAGACAAAATGCGCGTCC	60.04	50.0	8.43	0.0	0.0	4.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1600	1621	0.770499	TGGGCTCACTGAAACATCCA	59.23	50.0	0.0	0.0	0.0	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
25	26	3.792047	CATGTGTGCCGGTCGCTG	61.792	66.667	1.90	1.14	38.78	5.18
28	29	4.980805	GTGTGCCGGTCGCTGGAA	62.981	66.667	1.90	0.00	38.78	3.53
29	30	4.243008	TGTGCCGGTCGCTGGAAA	62.243	61.111	1.90	0.00	38.78	3.13
30	31	3.423154	GTGCCGGTCGCTGGAAAG	61.423	66.667	1.90	0.00	38.78	2.62
31	32	3.936203	TGCCGGTCGCTGGAAAGT	61.936	61.111	1.90	0.00	38.78	2.66
32	33	2.668550	GCCGGTCGCTGGAAAGTT	60.669	61.111	1.90	0.00	29.82	2.66
33	34	2.258726	GCCGGTCGCTGGAAAGTTT	61.259	57.895	1.90	0.00	29.82	2.66
34	35	1.574428	CCGGTCGCTGGAAAGTTTG	59.426	57.895	0.00	0.00	29.82	2.93
35	36	1.164041	CCGGTCGCTGGAAAGTTTGT	61.164	55.000	0.00	0.00	29.82	2.83
36	37	0.234884	CGGTCGCTGGAAAGTTTGTC	59.765	55.000	0.00	0.00	0.00	3.18
37	38	1.305201	GGTCGCTGGAAAGTTTGTCA	58.695	50.000	0.00	0.00	0.00	3.58
38	39	1.264288	GGTCGCTGGAAAGTTTGTCAG	59.736	52.381	9.86	9.86	0.00	3.51
39	40	0.944386	TCGCTGGAAAGTTTGTCAGC	59.056	50.000	21.50	21.50	46.32	4.26
54	55	1.596603	TCAGCATGAACTGTGTGGTG	58.403	50.000	0.00	11.61	45.97	4.17
55	56	0.594602	CAGCATGAACTGTGTGGTGG	59.405	55.000	0.00	0.00	39.69	4.61
56	57	0.538057	AGCATGAACTGTGTGGTGGG	60.538	55.000	0.00	0.00	0.00	4.61
57	58	0.823356	GCATGAACTGTGTGGTGGGT	60.823	55.000	0.00	0.00	0.00	4.51
58	59	1.691196	CATGAACTGTGTGGTGGGTT	58.309	50.000	0.00	0.00	0.00	4.11
59	60	2.031120	CATGAACTGTGTGGTGGGTTT	58.969	47.619	0.00	0.00	0.00	3.27
60	61	2.223803	TGAACTGTGTGGTGGGTTTT	57.776	45.000	0.00	0.00	0.00	2.43
61	62	2.530701	TGAACTGTGTGGTGGGTTTTT	58.469	42.857	0.00	0.00	0.00	1.94
80	81	5.999205	TTTTTGAGGATGGCATTGTATGT	57.001	34.783	0.00	0.00	0.00	2.29
81	82	5.581126	TTTTGAGGATGGCATTGTATGTC	57.419	39.130	0.00	0.00	34.88	3.06
82	83	2.837498	TGAGGATGGCATTGTATGTCG	58.163	47.619	0.00	0.00	37.81	4.35
83	84	2.146342	GAGGATGGCATTGTATGTCGG	58.854	52.381	0.00	0.00	37.81	4.79

Showing 1 to 25 of 501 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	2.258726	AAACTTTCCAGCGACCGGC	61.259	57.895	0.00	0.00	44.05	6.13
16	17	1.164041	ACAAACTTTCCAGCGACCGG	61.164	55.000	0.00	0.00	0.00	5.28
17	18	0.234884	GACAAACTTTCCAGCGACCG	59.765	55.000	0.00	0.00	0.00	4.79
18	19	1.264288	CTGACAAACTTTCCAGCGACC	59.736	52.381	0.00	0.00	0.00	4.79
19	20	1.334149	GCTGACAAACTTTCCAGCGAC	60.334	52.381	0.00	0.00	41.86	5.19
20	21	0.944386	GCTGACAAACTTTCCAGCGA	59.056	50.000	0.00	0.00	41.86	4.93
21	22	3.461843	GCTGACAAACTTTCCAGCG	57.538	52.632	0.00	0.00	41.86	5.18
23	24	4.037208	AGTTCATGCTGACAAACTTTCCAG	59.963	41.667	0.00	0.00	0.00	3.86
24	25	3.953612	AGTTCATGCTGACAAACTTTCCA	59.046	39.130	0.00	0.00	0.00	3.53
25	26	4.202050	ACAGTTCATGCTGACAAACTTTCC	60.202	41.667	7.27	0.00	39.62	3.13
26	27	4.736793	CACAGTTCATGCTGACAAACTTTC	59.263	41.667	7.27	0.00	39.62	2.62
27	28	4.158394	ACACAGTTCATGCTGACAAACTTT	59.842	37.500	7.27	0.00	39.62	2.66
28	29	3.696051	ACACAGTTCATGCTGACAAACTT	59.304	39.130	7.27	0.00	39.62	2.66
29	30	3.065786	CACACAGTTCATGCTGACAAACT	59.934	43.478	7.27	0.00	39.62	2.66
30	31	3.365832	CACACAGTTCATGCTGACAAAC	58.634	45.455	7.27	0.00	39.62	2.93
31	32	2.358582	CCACACAGTTCATGCTGACAAA	59.641	45.455	7.27	0.00	39.62	2.83
32	33	1.948834	CCACACAGTTCATGCTGACAA	59.051	47.619	7.27	0.00	39.62	3.18
33	34	1.134128	ACCACACAGTTCATGCTGACA	60.134	47.619	7.27	0.00	39.62	3.58
34	35	1.265095	CACCACACAGTTCATGCTGAC	59.735	52.381	7.27	0.00	39.62	3.51
35	36	1.596603	CACCACACAGTTCATGCTGA	58.403	50.000	7.27	0.00	39.62	4.26
36	37	0.594602	CCACCACACAGTTCATGCTG	59.405	55.000	0.00	0.00	41.92	4.41
37	38	0.538057	CCCACCACACAGTTCATGCT	60.538	55.000	0.00	0.00	0.00	3.79
38	39	0.823356	ACCCACCACACAGTTCATGC	60.823	55.000	0.00	0.00	0.00	4.06
39	40	1.691196	AACCCACCACACAGTTCATG	58.309	50.000	0.00	0.00	0.00	3.07
40	41	2.452600	AAACCCACCACACAGTTCAT	57.547	45.000	0.00	0.00	0.00	2.57

Showing 1 to 25 of 554 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.