AutoCloner

Multiple sequence alignment - TraesCS1B01G117800

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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	TraesCS1B01G117800	chr1B	100.000	3878	0	0	1	3878	137623738	137627615	0.000000e+00	7162.0
1	TraesCS1B01G117800	chr1B	92.937	269	18	1	3429	3696	565953459	565953727	1.310000e-104	390.0
2	TraesCS1B01G117800	chr1B	90.845	284	24	1	3429	3710	394942150	394941867	2.830000e-101	379.0
3	TraesCS1B01G117800	chr1A	93.767	1877	75	30	1294	3156	79167524	79169372	0.000000e+00	2780.0
4	TraesCS1B01G117800	chr1A	93.023	516	25	7	727	1240	79167001	79167507	0.000000e+00	743.0
5	TraesCS1B01G117800	chr1A	82.922	527	44	19	132	652	79166471	79166957	2.140000e-117	433.0
6	TraesCS1B01G117800	chr1A	93.309	269	17	1	3429	3696	584712367	584712099	2.810000e-106	396.0
7	TraesCS1B01G117800	chr1A	92.381	105	6	2	3212	3315	79169381	79169484	8.680000e-32	148.0
8	TraesCS1B01G117800	chr1D	96.815	1036	30	1	1288	2320	85180050	85181085	0.000000e+00	1727.0
9	TraesCS1B01G117800	chr1D	84.934	1135	94	33	119	1233	85178956	85180033	0.000000e+00	1077.0
10	TraesCS1B01G117800	chr1D	96.230	504	17	2	2376	2879	85181111	85181612	0.000000e+00	824.0
11	TraesCS1B01G117800	chr1D	79.602	402	46	18	2918	3294	85181622	85182012	4.970000e-64	255.0
12	TraesCS1B01G117800	chr6B	93.358	271	17	1	3429	3698	280999779	280999509	2.170000e-107	399.0
13	TraesCS1B01G117800	chr2B	93.309	269	17	1	3429	3696	216470120	216469852	2.810000e-106	396.0
14	TraesCS1B01G117800	chr2B	93.309	269	17	1	3429	3696	572570250	572569982	2.810000e-106	396.0
15	TraesCS1B01G117800	chr4B	92.989	271	18	1	3429	3698	307461995	307462265	1.010000e-105	394.0
16	TraesCS1B01G117800	chr7B	92.593	270	19	1	3429	3697	557195315	557195046	1.690000e-103	387.0
17	TraesCS1B01G117800	chr7B	75.956	183	32	12	1781	1960	429267871	429267698	2.480000e-12	84.2
18	TraesCS1B01G117800	chr3B	92.029	276	21	1	3429	3703	768574277	768574002	1.690000e-103	387.0
19	TraesCS1B01G117800	chr7D	75.956	183	32	12	1781	1960	415682954	415682781	2.480000e-12	84.2
20	TraesCS1B01G117800	chr7A	75.956	183	32	12	1781	1960	477809654	477809481	2.480000e-12	84.2
21	TraesCS1B01G117800	chr7A	96.970	33	1	0	1928	1960	511695960	511695928	5.410000e-04	56.5

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	TraesCS1B01G117800	chr1B	137623738	137627615	3877	False	7162.00	7162	100.00000	1	3878	1	chr1B.!!$F1	3877
1	TraesCS1B01G117800	chr1A	79166471	79169484	3013	False	1026.00	2780	90.52325	132	3315	4	chr1A.!!$F1	3183
2	TraesCS1B01G117800	chr1D	85178956	85182012	3056	False	970.75	1727	89.39525	119	3294	4	chr1D.!!$F1	3175

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
655	687	0.036388	GGCAACCACTCAAGATCGGA	60.036	55.000	0.0	0.00	0.0	4.55	F
1273	1316	0.029700	TGCTTCGTCGACTCGTTTCA	59.970	50.000	14.7	1.25	0.0	2.69	F
1275	1318	1.057847	GCTTCGTCGACTCGTTTCATG	59.942	52.381	14.7	0.00	0.0	3.07	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2244	2290	0.042131	TGGAGTTCTGGTACCCGGAT	59.958	55.0	10.07	0.00	38.86	4.18	R
2294	2340	0.248702	GAGCTAGAAGACGAAGGCGG	60.249	60.0	0.00	0.00	43.17	6.13	R
2956	3010	0.388778	TTGCGCATGATGCACCTTTG	60.389	50.0	18.47	0.61	45.36	2.77	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
34	35	7.722949	ATATGTTCTTGATTGGATGTTTGGT	57.277	32.000	0.00	0.00	0.00	3.67
35	36	8.821686	ATATGTTCTTGATTGGATGTTTGGTA	57.178	30.769	0.00	0.00	0.00	3.25
36	37	6.573664	TGTTCTTGATTGGATGTTTGGTAG	57.426	37.500	0.00	0.00	0.00	3.18
37	38	5.476599	TGTTCTTGATTGGATGTTTGGTAGG	59.523	40.000	0.00	0.00	0.00	3.18
38	39	4.599041	TCTTGATTGGATGTTTGGTAGGG	58.401	43.478	0.00	0.00	0.00	3.53
39	40	3.380471	TGATTGGATGTTTGGTAGGGG	57.620	47.619	0.00	0.00	0.00	4.79
40	41	2.031870	GATTGGATGTTTGGTAGGGGC	58.968	52.381	0.00	0.00	0.00	5.80
41	42	0.322997	TTGGATGTTTGGTAGGGGCG	60.323	55.000	0.00	0.00	0.00	6.13
42	43	1.301954	GGATGTTTGGTAGGGGCGT	59.698	57.895	0.00	0.00	0.00	5.68
43	44	0.542805	GGATGTTTGGTAGGGGCGTA	59.457	55.000	0.00	0.00	0.00	4.42
44	45	1.474498	GGATGTTTGGTAGGGGCGTAG	60.474	57.143	0.00	0.00	0.00	3.51
45	46	0.544697	ATGTTTGGTAGGGGCGTAGG	59.455	55.000	0.00	0.00	0.00	3.18
46	47	1.222661	GTTTGGTAGGGGCGTAGGG	59.777	63.158	0.00	0.00	0.00	3.53
47	48	2.672181	TTTGGTAGGGGCGTAGGGC	61.672	63.158	0.00	0.00	42.51	5.19
48	49	3.927817	TTGGTAGGGGCGTAGGGCA	62.928	63.158	11.36	0.00	46.16	5.36
49	50	3.085296	GGTAGGGGCGTAGGGCAA	61.085	66.667	11.36	0.00	46.16	4.52
50	51	2.449450	GGTAGGGGCGTAGGGCAAT	61.449	63.158	11.36	1.13	46.16	3.56
51	52	1.227853	GTAGGGGCGTAGGGCAATG	60.228	63.158	11.36	0.00	46.16	2.82
52	53	1.691337	TAGGGGCGTAGGGCAATGT	60.691	57.895	11.36	0.00	46.16	2.71
53	54	1.276140	TAGGGGCGTAGGGCAATGTT	61.276	55.000	11.36	0.00	46.16	2.71
54	55	1.680989	GGGGCGTAGGGCAATGTTT	60.681	57.895	11.36	0.00	46.16	2.83
55	56	1.663379	GGGGCGTAGGGCAATGTTTC	61.663	60.000	11.36	0.00	46.16	2.78
56	57	1.663379	GGGCGTAGGGCAATGTTTCC	61.663	60.000	11.36	0.00	46.16	3.13
57	58	0.679960	GGCGTAGGGCAATGTTTCCT	60.680	55.000	3.83	0.00	46.16	3.36
58	59	1.173913	GCGTAGGGCAATGTTTCCTT	58.826	50.000	0.00	0.00	42.87	3.36

Showing 1 to 25 of 564 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.425248	ACCAAACATCCAATCAAGAACATATAT	57.575	29.630	0.00	0.00	0.00	0.86
9	10	8.821686	ACCAAACATCCAATCAAGAACATATA	57.178	30.769	0.00	0.00	0.00	0.86
10	11	7.722949	ACCAAACATCCAATCAAGAACATAT	57.277	32.000	0.00	0.00	0.00	1.78
11	12	7.339212	CCTACCAAACATCCAATCAAGAACATA	59.661	37.037	0.00	0.00	0.00	2.29
12	13	6.153340	CCTACCAAACATCCAATCAAGAACAT	59.847	38.462	0.00	0.00	0.00	2.71
13	14	5.476599	CCTACCAAACATCCAATCAAGAACA	59.523	40.000	0.00	0.00	0.00	3.18
14	15	5.105756	CCCTACCAAACATCCAATCAAGAAC	60.106	44.000	0.00	0.00	0.00	3.01
15	16	5.016173	CCCTACCAAACATCCAATCAAGAA	58.984	41.667	0.00	0.00	0.00	2.52
16	17	4.569653	CCCCTACCAAACATCCAATCAAGA	60.570	45.833	0.00	0.00	0.00	3.02
17	18	3.701040	CCCCTACCAAACATCCAATCAAG	59.299	47.826	0.00	0.00	0.00	3.02
18	19	3.707316	CCCCTACCAAACATCCAATCAA	58.293	45.455	0.00	0.00	0.00	2.57
19	20	2.622977	GCCCCTACCAAACATCCAATCA	60.623	50.000	0.00	0.00	0.00	2.57
20	21	2.031870	GCCCCTACCAAACATCCAATC	58.968	52.381	0.00	0.00	0.00	2.67
21	22	1.684869	CGCCCCTACCAAACATCCAAT	60.685	52.381	0.00	0.00	0.00	3.16
22	23	0.322997	CGCCCCTACCAAACATCCAA	60.323	55.000	0.00	0.00	0.00	3.53
23	24	1.301623	CGCCCCTACCAAACATCCA	59.698	57.895	0.00	0.00	0.00	3.41
24	25	0.542805	TACGCCCCTACCAAACATCC	59.457	55.000	0.00	0.00	0.00	3.51
25	26	1.474498	CCTACGCCCCTACCAAACATC	60.474	57.143	0.00	0.00	0.00	3.06
26	27	0.544697	CCTACGCCCCTACCAAACAT	59.455	55.000	0.00	0.00	0.00	2.71
27	28	1.555477	CCCTACGCCCCTACCAAACA	61.555	60.000	0.00	0.00	0.00	2.83
28	29	1.222661	CCCTACGCCCCTACCAAAC	59.777	63.158	0.00	0.00	0.00	2.93
29	30	2.672181	GCCCTACGCCCCTACCAAA	61.672	63.158	0.00	0.00	0.00	3.28
30	31	3.085296	GCCCTACGCCCCTACCAA	61.085	66.667	0.00	0.00	0.00	3.67
31	32	3.927817	TTGCCCTACGCCCCTACCA	62.928	63.158	0.00	0.00	36.24	3.25
32	33	2.449450	ATTGCCCTACGCCCCTACC	61.449	63.158	0.00	0.00	36.24	3.18

Showing 1 to 25 of 514 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.