AutoCloner

Multiple sequence alignment - TraesCS6D01G311600

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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	TraesCS6D01G311600	chr6D	100.000	2508	0	0	1	2508	420955649	420958156	0.000000e+00	4632.0
1	TraesCS6D01G311600	chr6D	84.606	799	52	32	767	1506	420935527	420936313	0.000000e+00	728.0
2	TraesCS6D01G311600	chr6D	83.777	789	69	20	770	1506	420898985	420899766	0.000000e+00	693.0
3	TraesCS6D01G311600	chr6D	77.561	205	19	14	1503	1686	420936367	420936565	5.710000e-17	99.0
4	TraesCS6D01G311600	chr6B	90.683	1610	94	29	918	2508	634329949	634331521	0.000000e+00	2091.0
5	TraesCS6D01G311600	chr6B	84.171	796	61	25	767	1506	634321721	634322507	0.000000e+00	712.0
6	TraesCS6D01G311600	chr6B	82.685	797	72	25	766	1506	634315501	634316287	0.000000e+00	647.0
7	TraesCS6D01G311600	chr6B	95.205	146	6	1	712	857	634329602	634329746	1.940000e-56	230.0
8	TraesCS6D01G311600	chr6B	97.115	104	1	1	188	291	634327625	634327726	9.220000e-40	174.0
9	TraesCS6D01G311600	chr6B	91.057	123	9	1	290	412	634329425	634329545	5.550000e-37	165.0
10	TraesCS6D01G311600	chr6B	100.000	38	0	0	887	924	634329899	634329936	1.240000e-08	71.3
11	TraesCS6D01G311600	chr6A	89.790	999	50	23	767	1751	564259894	564260854	0.000000e+00	1232.0
12	TraesCS6D01G311600	chr6A	91.942	695	35	8	1821	2508	564269178	564269858	0.000000e+00	953.0
13	TraesCS6D01G311600	chr6A	86.951	774	57	24	767	1506	564132256	564133019	0.000000e+00	830.0
14	TraesCS6D01G311600	chr6A	86.194	775	60	21	767	1506	564238510	564239272	0.000000e+00	795.0
15	TraesCS6D01G311600	chr6A	86.047	774	62	17	767	1506	564191055	564191816	0.000000e+00	789.0
16	TraesCS6D01G311600	chr6A	83.396	795	72	21	766	1506	564117683	564118471	0.000000e+00	682.0
17	TraesCS6D01G311600	chr6A	88.293	205	18	5	196	398	564259451	564259651	8.960000e-60	241.0
18	TraesCS6D01G311600	chr7D	97.326	187	5	0	1	187	460078337	460078151	4.030000e-83	318.0
19	TraesCS6D01G311600	chr1D	97.326	187	5	0	1	187	225904491	225904677	4.030000e-83	318.0
20	TraesCS6D01G311600	chr1D	95.812	191	8	0	1	191	225919155	225919345	2.420000e-80	309.0
21	TraesCS6D01G311600	chr1D	96.757	185	6	0	1	185	486285203	486285019	2.420000e-80	309.0
22	TraesCS6D01G311600	chr1D	96.257	187	7	0	1	187	486290773	486290587	8.710000e-80	307.0
23	TraesCS6D01G311600	chr1D	82.412	199	32	3	441	637	453968134	453967937	1.190000e-38	171.0
24	TraesCS6D01G311600	chr5D	97.326	187	4	1	1	187	527870447	527870632	1.450000e-82	316.0
25	TraesCS6D01G311600	chr2A	97.326	187	4	1	1	187	769664018	769664203	1.450000e-82	316.0
26	TraesCS6D01G311600	chr2A	96.791	187	6	0	1	187	769742955	769743141	1.870000e-81	313.0
27	TraesCS6D01G311600	chr2A	94.924	197	9	1	1	196	52049873	52050069	8.710000e-80	307.0
28	TraesCS6D01G311600	chr3D	82.500	160	27	1	448	606	266633697	266633538	3.360000e-29	139.0
29	TraesCS6D01G311600	chr3D	78.414	227	39	7	1041	1259	604447907	604448131	3.360000e-29	139.0
30	TraesCS6D01G311600	chr3B	78.059	237	39	10	1033	1259	811496735	811496968	1.210000e-28	137.0
31	TraesCS6D01G311600	chr5B	93.846	65	4	0	642	706	506695223	506695159	5.710000e-17	99.0
32	TraesCS6D01G311600	chr5B	93.846	65	4	0	642	706	506728237	506728173	5.710000e-17	99.0
33	TraesCS6D01G311600	chr7A	92.063	63	5	0	642	704	189506699	189506637	3.440000e-14	89.8
34	TraesCS6D01G311600	chr7A	90.625	64	6	0	642	705	726995691	726995628	4.440000e-13	86.1
35	TraesCS6D01G311600	chr5A	85.057	87	12	1	554	639	14852053	14852139	1.240000e-13	87.9
36	TraesCS6D01G311600	chrUn	90.625	64	6	0	642	705	83668083	83668020	4.440000e-13	86.1
37	TraesCS6D01G311600	chrUn	94.444	36	0	2	376	411	3917891	3917924	1.000000e-03	54.7
38	TraesCS6D01G311600	chr4B	94.545	55	3	0	642	696	453235494	453235548	4.440000e-13	86.1
39	TraesCS6D01G311600	chr4A	90.625	64	6	0	642	705	608078173	608078236	4.440000e-13	86.1
40	TraesCS6D01G311600	chr1B	90.625	64	6	0	642	705	433452963	433452900	4.440000e-13	86.1
41	TraesCS6D01G311600	chr1B	90.625	64	6	0	642	705	665690196	665690133	4.440000e-13	86.1

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	TraesCS6D01G311600	chr6D	420955649	420958156	2507	False	4632.00	4632	100.0000	1	2508	1	chr6D.!!$F2	2507
1	TraesCS6D01G311600	chr6D	420898985	420899766	781	False	693.00	693	83.7770	770	1506	1	chr6D.!!$F1	736
2	TraesCS6D01G311600	chr6D	420935527	420936565	1038	False	413.50	728	81.0835	767	1686	2	chr6D.!!$F3	919
3	TraesCS6D01G311600	chr6B	634321721	634322507	786	False	712.00	712	84.1710	767	1506	1	chr6B.!!$F2	739
4	TraesCS6D01G311600	chr6B	634315501	634316287	786	False	647.00	647	82.6850	766	1506	1	chr6B.!!$F1	740
5	TraesCS6D01G311600	chr6B	634327625	634331521	3896	False	546.26	2091	94.8120	188	2508	5	chr6B.!!$F3	2320
6	TraesCS6D01G311600	chr6A	564269178	564269858	680	False	953.00	953	91.9420	1821	2508	1	chr6A.!!$F5	687
7	TraesCS6D01G311600	chr6A	564132256	564133019	763	False	830.00	830	86.9510	767	1506	1	chr6A.!!$F2	739
8	TraesCS6D01G311600	chr6A	564238510	564239272	762	False	795.00	795	86.1940	767	1506	1	chr6A.!!$F4	739
9	TraesCS6D01G311600	chr6A	564191055	564191816	761	False	789.00	789	86.0470	767	1506	1	chr6A.!!$F3	739
10	TraesCS6D01G311600	chr6A	564259451	564260854	1403	False	736.50	1232	89.0415	196	1751	2	chr6A.!!$F6	1555
11	TraesCS6D01G311600	chr6A	564117683	564118471	788	False	682.00	682	83.3960	766	1506	1	chr6A.!!$F1	740

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
568	2319	0.036732	AGTCCAGAAGCGCCAATGAA	59.963	50.0	2.29	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2173	4228	0.03467	GAGATGCTTCCCTGTTGCCT	60.035	55.0	0.0	0.0	0.0	4.75	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
20	21	3.340337	GGTTCTGTCACAACTTCTTGC	57.660	47.619	0.00	4.01
21	22	2.945668	GGTTCTGTCACAACTTCTTGCT	59.054	45.455	0.00	3.91
22	23	3.002759	GGTTCTGTCACAACTTCTTGCTC	59.997	47.826	0.00	4.26
23	24	3.827008	TCTGTCACAACTTCTTGCTCT	57.173	42.857	0.00	4.09
24	25	4.937201	TCTGTCACAACTTCTTGCTCTA	57.063	40.909	0.00	2.43
25	26	4.876125	TCTGTCACAACTTCTTGCTCTAG	58.124	43.478	0.00	2.43
26	27	4.342378	TCTGTCACAACTTCTTGCTCTAGT	59.658	41.667	0.00	2.57
27	28	4.371786	TGTCACAACTTCTTGCTCTAGTG	58.628	43.478	0.00	2.74
28	29	4.141937	TGTCACAACTTCTTGCTCTAGTGT	60.142	41.667	0.00	3.55
29	30	4.446051	GTCACAACTTCTTGCTCTAGTGTC	59.554	45.833	0.00	3.67
30	31	4.342378	TCACAACTTCTTGCTCTAGTGTCT	59.658	41.667	0.00	3.41
31	32	4.447054	CACAACTTCTTGCTCTAGTGTCTG	59.553	45.833	0.00	3.51
32	33	4.100189	ACAACTTCTTGCTCTAGTGTCTGT	59.900	41.667	0.00	3.41
33	34	4.946478	ACTTCTTGCTCTAGTGTCTGTT	57.054	40.909	0.00	3.16
34	35	4.877282	ACTTCTTGCTCTAGTGTCTGTTC	58.123	43.478	0.00	3.18
35	36	4.586841	ACTTCTTGCTCTAGTGTCTGTTCT	59.413	41.667	0.00	3.01
36	37	5.770663	ACTTCTTGCTCTAGTGTCTGTTCTA	59.229	40.000	0.00	2.10
37	38	5.888691	TCTTGCTCTAGTGTCTGTTCTAG	57.111	43.478	36.10	2.43
38	39	5.561679	TCTTGCTCTAGTGTCTGTTCTAGA	58.438	41.667	39.84	2.43
47	48	2.582687	GTCTGTTCTAGACGTGTTCGG	58.417	52.381	45.77	4.30
48	49	2.031333	GTCTGTTCTAGACGTGTTCGGT	60.031	50.000	45.77	4.69
49	50	2.620115	TCTGTTCTAGACGTGTTCGGTT	59.380	45.455	41.85	4.44
50	51	2.978489	CTGTTCTAGACGTGTTCGGTTC	59.022	50.000	41.85	3.62
51	52	2.620115	TGTTCTAGACGTGTTCGGTTCT	59.380	45.455	41.85	3.01
52	53	3.814842	TGTTCTAGACGTGTTCGGTTCTA	59.185	43.478	41.85	2.10

Showing 1 to 25 of 336 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	3.873952	AGAGCAAGAAGTTGTGACAGAAC	59.126	43.478	7.37	7.37	35.92	3.01
2	3	4.142609	AGAGCAAGAAGTTGTGACAGAA	57.857	40.909	0.00	0.00	35.92	3.02
4	5	4.447054	CACTAGAGCAAGAAGTTGTGACAG	59.553	45.833	0.00	0.00	35.92	3.51
5	6	4.141937	ACACTAGAGCAAGAAGTTGTGACA	60.142	41.667	0.00	0.00	35.92	3.58
7	8	4.342378	AGACACTAGAGCAAGAAGTTGTGA	59.658	41.667	0.00	0.00	35.92	3.58
8	9	4.447054	CAGACACTAGAGCAAGAAGTTGTG	59.553	45.833	0.00	0.00	35.92	3.33
9	10	4.100189	ACAGACACTAGAGCAAGAAGTTGT	59.900	41.667	0.00	0.00	35.92	3.32
10	11	4.626042	ACAGACACTAGAGCAAGAAGTTG	58.374	43.478	0.00	0.00	36.67	3.16
11	12	4.946478	ACAGACACTAGAGCAAGAAGTT	57.054	40.909	0.00	0.00	0.00	2.66
12	13	4.586841	AGAACAGACACTAGAGCAAGAAGT	59.413	41.667	0.00	0.00	0.00	3.01
13	14	5.132897	AGAACAGACACTAGAGCAAGAAG	57.867	43.478	0.00	0.00	0.00	2.85
14	15	6.004574	TCTAGAACAGACACTAGAGCAAGAA	58.995	40.000	0.00	0.00	39.71	2.52
15	16	5.561679	TCTAGAACAGACACTAGAGCAAGA	58.438	41.667	0.00	0.00	39.71	3.02
16	17	5.888691	TCTAGAACAGACACTAGAGCAAG	57.111	43.478	0.00	0.00	39.71	4.01
28	29	2.224606	ACCGAACACGTCTAGAACAGA	58.775	47.619	0.00	0.00	0.00	3.41
29	30	2.701073	ACCGAACACGTCTAGAACAG	57.299	50.000	0.00	0.00	0.00	3.16
30	31	2.620115	AGAACCGAACACGTCTAGAACA	59.380	45.455	0.00	0.00	0.00	3.18
31	32	3.279853	AGAACCGAACACGTCTAGAAC	57.720	47.619	0.00	0.00	0.00	3.01
32	33	4.067896	ACTAGAACCGAACACGTCTAGAA	58.932	43.478	17.49	0.00	41.34	2.10
33	34	3.668447	ACTAGAACCGAACACGTCTAGA	58.332	45.455	17.49	0.00	41.34	2.43
34	35	4.083643	TGAACTAGAACCGAACACGTCTAG	60.084	45.833	0.00	12.35	43.42	2.43
35	36	3.814842	TGAACTAGAACCGAACACGTCTA	59.185	43.478	0.00	0.00	0.00	2.59
36	37	2.620115	TGAACTAGAACCGAACACGTCT	59.380	45.455	0.00	0.00	0.00	4.18
37	38	3.004024	TGAACTAGAACCGAACACGTC	57.996	47.619	0.00	0.00	0.00	4.34
38	39	3.655276	ATGAACTAGAACCGAACACGT	57.345	42.857	0.00	0.00	0.00	4.49

Showing 1 to 25 of 355 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.