AutoCloner

Multiple sequence alignment - TraesCS4B01G283300

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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	TraesCS4B01G283300	chr4B	100.000	5982	0	0	1	5982	566602901	566596920	0.000000e+00	11047.0
1	TraesCS4B01G283300	chr4D	92.061	3212	107	41	1686	4809	453226543	453223392	0.000000e+00	4383.0
2	TraesCS4B01G283300	chr4D	90.229	1351	62	27	4672	5982	453223389	453222069	0.000000e+00	1700.0
3	TraesCS4B01G283300	chr4D	94.507	892	41	6	580	1464	453227708	453226818	0.000000e+00	1369.0
4	TraesCS4B01G283300	chr4D	87.097	341	34	8	239	575	453228079	453227745	1.570000e-100	377.0
5	TraesCS4B01G283300	chr4D	87.879	132	12	2	1460	1587	453226789	453226658	1.040000e-32	152.0
6	TraesCS4B01G283300	chr4D	74.909	275	46	21	31	292	337256217	337256481	2.950000e-18	104.0
7	TraesCS4B01G283300	chr4D	91.549	71	4	2	1592	1660	453226611	453226541	4.930000e-16	97.1
8	TraesCS4B01G283300	chr4A	89.766	2306	114	52	2558	4806	14022289	14024529	0.000000e+00	2839.0
9	TraesCS4B01G283300	chr4A	91.190	1067	54	26	4939	5982	14025025	14026074	0.000000e+00	1413.0
10	TraesCS4B01G283300	chr4A	93.960	894	42	8	580	1464	14020167	14021057	0.000000e+00	1341.0
11	TraesCS4B01G283300	chr4A	84.000	1000	94	32	1586	2547	14021247	14022218	0.000000e+00	900.0
12	TraesCS4B01G283300	chr4A	86.000	150	16	3	1460	1604	14021086	14021235	8.030000e-34	156.0
13	TraesCS4B01G283300	chr3D	79.661	295	33	13	908	1198	611562855	611563126	2.850000e-43	187.0
14	TraesCS4B01G283300	chr2A	77.778	270	49	9	28	291	176557118	176557382	8.030000e-34	156.0

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	TraesCS4B01G283300	chr4B	566596920	566602901	5981	True	11047.00	11047	100.000000	1	5982	1	chr4B.!!$R1	5981
1	TraesCS4B01G283300	chr4D	453222069	453228079	6010	True	1346.35	4383	90.553667	239	5982	6	chr4D.!!$R1	5743
2	TraesCS4B01G283300	chr4A	14020167	14026074	5907	False	1329.80	2839	88.983200	580	5982	5	chr4A.!!$F1	5402

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
21	22	0.036388	AACATGACACTACCTGGCCG	60.036	55.000	0.00	0.00	0.00	6.13	F
173	174	0.108424	GCCACTTGTCTCGCTCTGAT	60.108	55.000	0.00	0.00	0.00	2.90	F
178	179	0.391661	TTGTCTCGCTCTGATTGGGC	60.392	55.000	0.00	0.00	0.00	5.36	F
229	230	0.473755	TGAGAATGGTGTGGTGCACT	59.526	50.000	17.98	0.00	46.86	4.40	F
345	348	1.072648	ACCCCCGTTGATCGAAAAAGA	59.927	47.619	0.00	0.00	42.86	2.52	F
2153	2318	1.412710	TCCACTCTGACACCTCAACAC	59.587	52.381	0.00	0.00	0.00	3.32	F
2160	2325	1.948834	TGACACCTCAACACTGCATTG	59.051	47.619	1.95	1.95	0.00	2.82	F
2409	2575	5.239087	CCCTGCTTTAACACAATGCATTTTT	59.761	36.000	9.83	6.09	33.02	1.94	F
4186	4485	1.352352	CAAGAGGTTCCACATGAGGGT	59.648	52.381	9.48	0.00	0.00	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1491	1568	1.106285	GCACTTGCCCCTAAAGATGG	58.894	55.000	0.00	0.0	34.31	3.51	R
2071	2231	1.227102	CAGATGAAATGGGCGGGGA	59.773	57.895	0.00	0.0	0.00	4.81	R
2074	2234	1.679139	TAAGCAGATGAAATGGGCGG	58.321	50.000	0.00	0.0	0.00	6.13	R
2188	2353	6.640518	ACAAGTGTACCTTATCACCATACAG	58.359	40.000	0.00	0.0	35.45	2.74	R
2233	2398	5.388944	TGCAAAACAAAGAAAATGCAACAC	58.611	33.333	0.00	0.0	40.47	3.32	R
2985	3244	1.965935	TTTCTAGCACAGCTGCAACA	58.034	45.000	15.27	0.0	46.97	3.33	R
3624	3887	2.101917	GGCATGAAACATAAGGCTGCAT	59.898	45.455	0.50	0.0	0.00	3.96	R
4255	4554	0.251341	CCTGCCCAAAAGTGTAGCCT	60.251	55.000	0.00	0.0	0.00	4.58	R
5681	6373	0.259647	CATGAAAGGGAGGGGCATCA	59.740	55.000	0.00	0.0	0.00	3.07	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
19	20	1.453155	CCAACATGACACTACCTGGC	58.547	55.000	0.00	0.00	0.00	4.85
20	21	1.453155	CAACATGACACTACCTGGCC	58.547	55.000	0.00	0.00	0.00	5.36
21	22	0.036388	AACATGACACTACCTGGCCG	60.036	55.000	0.00	0.00	0.00	6.13
22	23	1.815421	CATGACACTACCTGGCCGC	60.815	63.158	0.00	0.00	0.00	6.53
23	24	3.031417	ATGACACTACCTGGCCGCC	62.031	63.158	1.04	1.04	0.00	6.13
24	25	4.468689	GACACTACCTGGCCGCCC	62.469	72.222	7.03	0.00	0.00	6.13
26	27	3.717294	CACTACCTGGCCGCCCTT	61.717	66.667	7.03	0.00	0.00	3.95
27	28	3.717294	ACTACCTGGCCGCCCTTG	61.717	66.667	7.03	0.00	0.00	3.61
28	29	3.399181	CTACCTGGCCGCCCTTGA	61.399	66.667	7.03	0.00	0.00	3.02
29	30	2.931105	TACCTGGCCGCCCTTGAA	60.931	61.111	7.03	0.00	0.00	2.69
30	31	3.262448	TACCTGGCCGCCCTTGAAC	62.262	63.158	7.03	0.00	0.00	3.18
32	33	4.697756	CTGGCCGCCCTTGAACGA	62.698	66.667	7.03	0.00	0.00	3.85
33	34	4.257654	TGGCCGCCCTTGAACGAA	62.258	61.111	7.03	0.00	0.00	3.85
34	35	3.733960	GGCCGCCCTTGAACGAAC	61.734	66.667	0.00	0.00	0.00	3.95
35	36	4.084888	GCCGCCCTTGAACGAACG	62.085	66.667	0.00	0.00	0.00	3.95
36	37	2.356553	CCGCCCTTGAACGAACGA	60.357	61.111	0.14	0.00	0.00	3.85
37	38	1.957186	CCGCCCTTGAACGAACGAA	60.957	57.895	0.14	0.00	0.00	3.85
38	39	1.296056	CCGCCCTTGAACGAACGAAT	61.296	55.000	0.14	0.00	0.00	3.34
39	40	0.179225	CGCCCTTGAACGAACGAATG	60.179	55.000	0.14	0.00	0.00	2.67
40	41	0.454452	GCCCTTGAACGAACGAATGC	60.454	55.000	0.14	0.00	0.00	3.56
41	42	0.179225	CCCTTGAACGAACGAATGCG	60.179	55.000	0.14	0.00	44.79	4.73
42	43	0.787787	CCTTGAACGAACGAATGCGA	59.212	50.000	0.00	0.00	41.64	5.10
43	44	1.193650	CCTTGAACGAACGAATGCGAA	59.806	47.619	0.00	0.00	41.64	4.70
44	45	2.222624	CTTGAACGAACGAATGCGAAC	58.777	47.619	0.00	0.00	41.64	3.95
45	46	1.209998	TGAACGAACGAATGCGAACA	58.790	45.000	0.00	0.00	41.64	3.18

Showing 1 to 25 of 314 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	1.453155	GCCAGGTAGTGTCATGTTGG	58.547	55.000	0.00	0.00	0.00	3.77
1	2	1.453155	GGCCAGGTAGTGTCATGTTG	58.547	55.000	0.00	0.00	0.00	3.33
2	3	0.036388	CGGCCAGGTAGTGTCATGTT	60.036	55.000	2.24	0.00	0.00	2.71
3	4	1.596934	CGGCCAGGTAGTGTCATGT	59.403	57.895	2.24	0.00	0.00	3.21
4	5	1.815421	GCGGCCAGGTAGTGTCATG	60.815	63.158	2.24	0.00	0.00	3.07
5	6	2.584608	GCGGCCAGGTAGTGTCAT	59.415	61.111	2.24	0.00	0.00	3.06
6	7	3.702048	GGCGGCCAGGTAGTGTCA	61.702	66.667	15.62	0.00	0.00	3.58
7	8	4.468689	GGGCGGCCAGGTAGTGTC	62.469	72.222	25.33	0.00	0.00	3.67
9	10	3.717294	AAGGGCGGCCAGGTAGTG	61.717	66.667	31.59	0.00	0.00	2.74
10	11	3.717294	CAAGGGCGGCCAGGTAGT	61.717	66.667	31.59	4.80	0.00	2.73
11	12	2.966732	TTCAAGGGCGGCCAGGTAG	61.967	63.158	31.59	14.27	0.00	3.18
12	13	2.931105	TTCAAGGGCGGCCAGGTA	60.931	61.111	31.59	12.42	0.00	3.08
13	14	4.660938	GTTCAAGGGCGGCCAGGT	62.661	66.667	31.59	12.19	0.00	4.00
15	16	4.697756	TCGTTCAAGGGCGGCCAG	62.698	66.667	31.59	21.81	0.00	4.85
16	17	4.257654	TTCGTTCAAGGGCGGCCA	62.258	61.111	31.59	6.60	0.00	5.36
17	18	3.733960	GTTCGTTCAAGGGCGGCC	61.734	66.667	22.67	22.67	0.00	6.13
18	19	4.084888	CGTTCGTTCAAGGGCGGC	62.085	66.667	0.00	0.00	0.00	6.53
19	20	1.296056	ATTCGTTCGTTCAAGGGCGG	61.296	55.000	0.00	0.00	0.00	6.13
20	21	0.179225	CATTCGTTCGTTCAAGGGCG	60.179	55.000	0.00	0.00	0.00	6.13
21	22	0.454452	GCATTCGTTCGTTCAAGGGC	60.454	55.000	0.00	0.00	0.00	5.19
22	23	0.179225	CGCATTCGTTCGTTCAAGGG	60.179	55.000	0.00	0.00	0.00	3.95
23	24	0.787787	TCGCATTCGTTCGTTCAAGG	59.212	50.000	0.00	0.00	36.96	3.61
24	25	2.222624	GTTCGCATTCGTTCGTTCAAG	58.777	47.619	0.00	0.00	36.96	3.02
25	26	1.593469	TGTTCGCATTCGTTCGTTCAA	59.407	42.857	0.00	0.00	36.96	2.69
26	27	1.209998	TGTTCGCATTCGTTCGTTCA	58.790	45.000	0.00	0.00	36.96	3.18

Showing 1 to 25 of 325 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.