AutoCloner

Multiple sequence alignment - TraesCS2A01G079800

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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	TraesCS2A01G079800	chr2A	100.000	3300	0	0	1	3300	36119020	36122319	0.000000e+00	6095.0
1	TraesCS2A01G079800	chr2A	100.000	982	0	0	953	1934	35469064	35468083	0.000000e+00	1814.0
2	TraesCS2A01G079800	chr2A	89.286	196	11	6	3047	3239	36058419	36058607	1.530000e-58	237.0
3	TraesCS2A01G079800	chr2A	100.000	84	0	0	3217	3300	35467364	35467281	4.410000e-34	156.0
4	TraesCS2A01G079800	chrUn	99.404	2349	10	2	953	3300	280377632	280375287	0.000000e+00	4257.0
5	TraesCS2A01G079800	chr2B	90.411	1533	100	17	460	1977	54732869	54734369	0.000000e+00	1973.0
6	TraesCS2A01G079800	chr2B	84.267	1214	111	35	2087	3275	54734353	54735511	0.000000e+00	1110.0
7	TraesCS2A01G079800	chr2B	84.868	456	42	9	18	461	54732292	54732732	5.060000e-118	435.0
8	TraesCS2A01G079800	chr2B	90.909	110	4	4	3132	3239	54555884	54555989	3.430000e-30	143.0
9	TraesCS2A01G079800	chr2B	96.970	33	1	0	3268	3300	422230597	422230565	4.600000e-04	56.5
10	TraesCS2A01G079800	chr2D	90.872	1490	89	25	518	1977	32961483	32962955	0.000000e+00	1954.0
11	TraesCS2A01G079800	chr2D	84.126	1178	132	31	2115	3266	32962990	32964138	0.000000e+00	1088.0
12	TraesCS2A01G079800	chr2D	88.496	452	31	7	18	461	32960824	32961262	8.110000e-146	527.0
13	TraesCS2A01G079800	chr2D	94.643	112	6	0	1978	2089	636430852	636430963	1.220000e-39	174.0
14	TraesCS2A01G079800	chr2D	92.958	71	5	0	460	530	32961397	32961467	1.620000e-18	104.0
15	TraesCS2A01G079800	chr3A	95.536	112	5	0	1977	2088	746096345	746096234	2.620000e-41	180.0
16	TraesCS2A01G079800	chr3A	97.059	34	1	0	3267	3300	598561959	598561926	1.280000e-04	58.4
17	TraesCS2A01G079800	chr3A	96.970	33	1	0	3268	3300	107602778	107602810	4.600000e-04	56.5
18	TraesCS2A01G079800	chr6D	95.327	107	5	0	1978	2084	466894767	466894873	1.570000e-38	171.0
19	TraesCS2A01G079800	chr6D	93.458	107	7	0	1978	2084	411789302	411789408	3.410000e-35	159.0
20	TraesCS2A01G079800	chr1A	94.545	110	6	0	1978	2087	95051960	95051851	1.570000e-38	171.0
21	TraesCS2A01G079800	chr7D	92.982	114	8	0	1978	2091	555408260	555408147	2.040000e-37	167.0
22	TraesCS2A01G079800	chr1D	95.238	105	5	0	1978	2082	295841950	295841846	2.040000e-37	167.0
23	TraesCS2A01G079800	chr4B	92.793	111	8	0	1977	2087	672102348	672102238	9.480000e-36	161.0
24	TraesCS2A01G079800	chr3D	97.143	35	1	0	3266	3300	588394894	588394860	3.560000e-05	60.2
25	TraesCS2A01G079800	chr7B	97.059	34	1	0	3267	3300	578843370	578843403	1.280000e-04	58.4
26	TraesCS2A01G079800	chr5B	100.000	30	0	0	3271	3300	294558258	294558287	4.600000e-04	56.5
27	TraesCS2A01G079800	chr4A	100.000	30	0	0	3271	3300	646986471	646986500	4.600000e-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	TraesCS2A01G079800	chr2A	36119020	36122319	3299	False	6095.000000	6095	100.000000	1	3300	1	chr2A.!!$F2	3299
1	TraesCS2A01G079800	chr2A	35467281	35469064	1783	True	985.000000	1814	100.000000	953	3300	2	chr2A.!!$R1	2347
2	TraesCS2A01G079800	chrUn	280375287	280377632	2345	True	4257.000000	4257	99.404000	953	3300	1	chrUn.!!$R1	2347
3	TraesCS2A01G079800	chr2B	54732292	54735511	3219	False	1172.666667	1973	86.515333	18	3275	3	chr2B.!!$F2	3257
4	TraesCS2A01G079800	chr2D	32960824	32964138	3314	False	918.250000	1954	89.113000	18	3266	4	chr2D.!!$F2	3248

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
302	310	1.024271	CCCGACCCTTTGTGCATATG	58.976	55.000	0.00	0.0	0.00	1.78	F
542	731	3.343941	TGCCTAAACTTCGTTATGGCT	57.656	42.857	17.43	0.0	41.27	4.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2214	2460	0.392998	GGCGCCTTTCTTGGAGATCA	60.393	55.000	22.15	0.0	0.0	2.92	R
3004	3262	4.341783	GTGCTGTGCTGGGCTCCT	62.342	66.667	0.00	0.0	0.0	3.69	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	3.164977	GCCTGCTCCTCCCTACCC	61.165	72.222	0.00	0.00	0.00	3.69
198	200	6.964370	TGTTACAGTTCAATTCGTTGTCAAAG	59.036	34.615	0.00	0.00	0.00	2.77
199	201	5.560966	ACAGTTCAATTCGTTGTCAAAGT	57.439	34.783	0.00	0.00	0.00	2.66
259	267	8.467402	TTTGTTAATTTGGTTATATTGGCACG	57.533	30.769	0.00	0.00	0.00	5.34
261	269	8.277490	TGTTAATTTGGTTATATTGGCACGTA	57.723	30.769	0.00	0.00	0.00	3.57
279	287	5.574830	GCACGTATCCTGATGAACATAGATC	59.425	44.000	0.00	0.00	0.00	2.75
282	290	6.071672	ACGTATCCTGATGAACATAGATCCAG	60.072	42.308	0.00	0.00	0.00	3.86
286	294	2.037641	TGATGAACATAGATCCAGCCCG	59.962	50.000	0.00	0.00	0.00	6.13
295	303	2.198304	GATCCAGCCCGACCCTTTGT	62.198	60.000	0.00	0.00	0.00	2.83
302	310	1.024271	CCCGACCCTTTGTGCATATG	58.976	55.000	0.00	0.00	0.00	1.78
413	434	3.472283	ACCCGTGTTGTTGTATGTACA	57.528	42.857	0.00	0.00	0.00	2.90
415	436	3.749088	ACCCGTGTTGTTGTATGTACATG	59.251	43.478	18.81	0.00	35.89	3.21
421	442	8.061857	CCGTGTTGTTGTATGTACATGATTATC	58.938	37.037	18.81	4.93	35.89	1.75
542	731	3.343941	TGCCTAAACTTCGTTATGGCT	57.656	42.857	17.43	0.00	41.27	4.75
708	909	7.817962	CCTTGGTAAGATATACTAATTCACCCG	59.182	40.741	0.00	0.00	0.00	5.28
709	910	8.481492	TTGGTAAGATATACTAATTCACCCGA	57.519	34.615	0.00	0.00	0.00	5.14
710	911	8.660295	TGGTAAGATATACTAATTCACCCGAT	57.340	34.615	0.00	0.00	0.00	4.18
711	912	9.096823	TGGTAAGATATACTAATTCACCCGATT	57.903	33.333	0.00	0.00	0.00	3.34
730	931	6.459066	CCGATTGTCAGTGGATTGATAGTAT	58.541	40.000	0.00	0.00	0.00	2.12
773	974	9.905713	TTTAAATAGGAGAATATGAACTGCAGT	57.094	29.630	15.25	15.25	0.00	4.40
850	1052	4.330620	AGTGTTTGCATTTTGTTGCTTCTG	59.669	37.500	0.00	0.00	43.18	3.02
854	1056	4.120792	TGCATTTTGTTGCTTCTGTCAA	57.879	36.364	0.00	0.00	43.18	3.18
874	1076	5.710099	GTCAAATAACTTGGATCACCCTTGA	59.290	40.000	0.00	0.00	35.56	3.02
875	1077	6.208599	GTCAAATAACTTGGATCACCCTTGAA	59.791	38.462	0.00	0.00	33.65	2.69
876	1078	6.780031	TCAAATAACTTGGATCACCCTTGAAA	59.220	34.615	0.00	0.00	33.65	2.69
877	1079	7.454380	TCAAATAACTTGGATCACCCTTGAAAT	59.546	33.333	0.00	0.00	33.65	2.17
878	1080	7.410120	AATAACTTGGATCACCCTTGAAATC	57.590	36.000	0.00	0.00	34.61	2.17
2214	2460	5.733373	GCTTTGTCAAGGAGAAATCGTTTGT	60.733	40.000	0.00	0.00	0.00	2.83
2222	2468	4.020218	AGGAGAAATCGTTTGTGATCTCCA	60.020	41.667	19.61	0.00	39.84	3.86
2424	2670	5.106317	CGTGTTTATTAACAGTCCCAATGCT	60.106	40.000	0.00	0.00	44.53	3.79
3004	3262	4.348495	GTGTGAGGGGGAGGGGGA	62.348	72.222	0.00	0.00	0.00	4.81
3157	3436	2.163211	GCCTGTGCCATTCTTCTTCTTC	59.837	50.000	0.00	0.00	0.00	2.87
3158	3437	3.683802	CCTGTGCCATTCTTCTTCTTCT	58.316	45.455	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	4.812476	TCGAATGCGGCGTCAGGG	62.812	66.667	9.37	1.26	38.28	4.45
121	123	0.542333	TCAACGTCAACCTGGAACCA	59.458	50.000	0.00	0.00	0.00	3.67
150	152	2.630889	AGAGGATGGAGAGGAACACA	57.369	50.000	0.00	0.00	0.00	3.72
157	159	3.945921	TGTAACACGTAGAGGATGGAGAG	59.054	47.826	0.00	0.00	0.00	3.20
253	261	1.552792	TGTTCATCAGGATACGTGCCA	59.447	47.619	11.25	0.00	46.39	4.92
259	267	6.105333	GCTGGATCTATGTTCATCAGGATAC	58.895	44.000	0.00	0.00	0.00	2.24
261	269	4.019501	GGCTGGATCTATGTTCATCAGGAT	60.020	45.833	0.00	0.00	0.00	3.24
279	287	2.672996	CACAAAGGGTCGGGCTGG	60.673	66.667	0.00	0.00	0.00	4.85
282	290	0.751643	ATATGCACAAAGGGTCGGGC	60.752	55.000	0.00	0.00	0.00	6.13
286	294	2.684881	CTCACCATATGCACAAAGGGTC	59.315	50.000	0.00	0.00	0.00	4.46
295	303	4.040095	CCTTCTCATCTCTCACCATATGCA	59.960	45.833	0.00	0.00	0.00	3.96
302	310	1.830477	ACAGCCTTCTCATCTCTCACC	59.170	52.381	0.00	0.00	0.00	4.02
335	344	6.665992	ACTGAACAATACTAGTCAGGTCAA	57.334	37.500	0.00	0.00	0.00	3.18
337	346	7.600065	TGTTACTGAACAATACTAGTCAGGTC	58.400	38.462	0.00	0.00	42.66	3.85
338	347	7.534723	TGTTACTGAACAATACTAGTCAGGT	57.465	36.000	0.00	0.00	42.66	4.00
413	434	8.716674	ATGGCACTAGAAAATTGGATAATCAT	57.283	30.769	0.00	0.00	0.00	2.45
415	436	9.822185	AAAATGGCACTAGAAAATTGGATAATC	57.178	29.630	0.00	0.00	0.00	1.75
421	442	5.240121	AGCAAAATGGCACTAGAAAATTGG	58.760	37.500	0.00	0.00	35.83	3.16
428	449	4.816385	GCATACTAGCAAAATGGCACTAGA	59.184	41.667	14.02	1.62	36.45	2.43
542	731	5.079689	AGCAATCATCAATGTTGCAATGA	57.920	34.783	21.32	2.52	42.14	2.57
708	909	8.768955	GTTCATACTATCAATCCACTGACAATC	58.231	37.037	0.00	0.00	0.00	2.67
709	910	8.489489	AGTTCATACTATCAATCCACTGACAAT	58.511	33.333	0.00	0.00	31.21	2.71
710	911	7.765819	CAGTTCATACTATCAATCCACTGACAA	59.234	37.037	0.00	0.00	32.52	3.18
711	912	7.124147	TCAGTTCATACTATCAATCCACTGACA	59.876	37.037	0.00	0.00	34.59	3.58
714	915	7.223582	GTGTCAGTTCATACTATCAATCCACTG	59.776	40.741	0.00	0.00	31.96	3.66
730	931	8.767085	CCTATTTAAACGTTTAGTGTCAGTTCA	58.233	33.333	19.31	0.00	0.00	3.18
773	974	9.601810	TCTCATAAATAGCTCTAATTACCCAGA	57.398	33.333	0.00	0.00	0.00	3.86
850	1052	5.710099	TCAAGGGTGATCCAAGTTATTTGAC	59.290	40.000	0.00	0.00	39.21	3.18
854	1056	6.953520	TGATTTCAAGGGTGATCCAAGTTATT	59.046	34.615	0.00	0.00	38.24	1.40
874	1076	6.701400	CACAAAATCTTCGAGGGTTTTGATTT	59.299	34.615	37.54	21.48	41.61	2.17
875	1077	6.215845	CACAAAATCTTCGAGGGTTTTGATT	58.784	36.000	37.54	22.06	41.61	2.57
876	1078	5.278957	CCACAAAATCTTCGAGGGTTTTGAT	60.279	40.000	37.54	24.56	41.61	2.57
877	1079	4.037446	CCACAAAATCTTCGAGGGTTTTGA	59.963	41.667	37.54	9.99	41.61	2.69
878	1080	4.298332	CCACAAAATCTTCGAGGGTTTTG	58.702	43.478	32.41	32.41	43.53	2.44
2103	2326	3.748048	TCAGCACAATCTCAACAAGCTAC	59.252	43.478	0.00	0.00	0.00	3.58
2214	2460	0.392998	GGCGCCTTTCTTGGAGATCA	60.393	55.000	22.15	0.00	0.00	2.92
3004	3262	4.341783	GTGCTGTGCTGGGCTCCT	62.342	66.667	0.00	0.00	0.00	3.69
3157	3436	3.677190	GCATGATGCAGACAGAAGAAG	57.323	47.619	13.36	0.00	44.26	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.