AutoCloner

Multiple sequence alignment - TraesCS2B01G133900

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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	TraesCS2B01G133900	chr2B	100.000	3617	0	0	1	3617	100081729	100078113	0.000000e+00	6680
1	TraesCS2B01G133900	chr2D	96.216	2854	81	14	772	3617	64068244	64065410	0.000000e+00	4647
2	TraesCS2B01G133900	chr2D	85.000	300	39	5	480	773	64068634	64068335	2.110000e-77	300
3	TraesCS2B01G133900	chr2A	95.676	2775	93	14	848	3617	65522067	65519315	0.000000e+00	4434

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	TraesCS2B01G133900	chr2B	100078113	100081729	3616	True	6680.0	6680	100.000	1	3617	1	chr2B.!!$R1	3616
1	TraesCS2B01G133900	chr2D	64065410	64068634	3224	True	2473.5	4647	90.608	480	3617	2	chr2D.!!$R1	3137
2	TraesCS2B01G133900	chr2A	65519315	65522067	2752	True	4434.0	4434	95.676	848	3617	1	chr2A.!!$R1	2769

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
469	470	0.095245	CGTATGCGTGCTTCCACAAG	59.905	55.000	0.00	0.0	42.17	3.16	F
955	1057	0.965866	CGGCCCAGTCTGACTAGTCA	60.966	60.000	23.80	23.8	38.06	3.41	F
1524	1627	1.134699	TGCTGCTATAACTCGCTGCTT	60.135	47.619	12.87	0.0	46.83	3.91	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2289	2392	0.534203	TTTTGAACCGCTCGGCTTCT	60.534	50.0	8.41	39.32	2.85	R
2483	2586	0.388659	CTCCTCTGATCTGCCTTCCG	59.611	60.0	0.00	0.00	4.30	R
2741	2844	0.468226	GGATCCCCGTAGCACATCAA	59.532	55.0	0.00	0.00	2.57	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
61	62	9.979578	AGTTTATGCAACTTGTTTTATGATTCA	57.020	25.926	0.00	0.00	43.89	2.57
67	68	9.624697	TGCAACTTGTTTTATGATTCAGAATAC	57.375	29.630	7.42	7.42	0.00	1.89
68	69	9.624697	GCAACTTGTTTTATGATTCAGAATACA	57.375	29.630	11.61	11.61	28.34	2.29
79	80	6.962686	TGATTCAGAATACACTTATGCATGC	58.037	36.000	11.82	11.82	0.00	4.06
80	81	6.769341	TGATTCAGAATACACTTATGCATGCT	59.231	34.615	20.33	7.07	0.00	3.79
81	82	7.283807	TGATTCAGAATACACTTATGCATGCTT	59.716	33.333	20.33	15.55	0.00	3.91
82	83	6.609237	TCAGAATACACTTATGCATGCTTC	57.391	37.500	20.33	10.58	0.00	3.86
83	84	6.351711	TCAGAATACACTTATGCATGCTTCT	58.648	36.000	20.33	12.72	0.00	2.85
84	85	6.259387	TCAGAATACACTTATGCATGCTTCTG	59.741	38.462	23.88	23.88	38.74	3.02
85	86	6.259387	CAGAATACACTTATGCATGCTTCTGA	59.741	38.462	24.87	5.99	39.21	3.27
86	87	6.825213	AGAATACACTTATGCATGCTTCTGAA	59.175	34.615	20.33	3.25	0.00	3.02
87	88	7.501559	AGAATACACTTATGCATGCTTCTGAAT	59.498	33.333	20.33	5.16	0.00	2.57
88	89	8.681486	AATACACTTATGCATGCTTCTGAATA	57.319	30.769	20.33	4.09	0.00	1.75
89	90	8.681486	ATACACTTATGCATGCTTCTGAATAA	57.319	30.769	20.33	11.83	0.00	1.40
90	91	7.578310	ACACTTATGCATGCTTCTGAATAAT	57.422	32.000	20.33	2.82	28.46	1.28
91	92	7.423199	ACACTTATGCATGCTTCTGAATAATG	58.577	34.615	20.33	13.72	28.46	1.90
92	93	6.861572	CACTTATGCATGCTTCTGAATAATGG	59.138	38.462	20.33	5.31	28.46	3.16
93	94	6.774170	ACTTATGCATGCTTCTGAATAATGGA	59.226	34.615	20.33	10.22	28.46	3.41
94	95	7.450634	ACTTATGCATGCTTCTGAATAATGGAT	59.549	33.333	20.33	17.35	34.30	3.41
95	96	6.665992	ATGCATGCTTCTGAATAATGGATT	57.334	33.333	20.33	0.00	0.00	3.01
96	97	6.474140	TGCATGCTTCTGAATAATGGATTT	57.526	33.333	20.33	0.00	0.00	2.17
97	98	7.585579	TGCATGCTTCTGAATAATGGATTTA	57.414	32.000	20.33	0.00	0.00	1.40
98	99	7.654568	TGCATGCTTCTGAATAATGGATTTAG	58.345	34.615	20.33	0.00	33.42	1.85
99	100	7.503230	TGCATGCTTCTGAATAATGGATTTAGA	59.497	33.333	20.33	0.00	38.14	2.10
100	101	8.355169	GCATGCTTCTGAATAATGGATTTAGAA	58.645	33.333	11.37	4.92	43.96	2.10

Showing 1 to 25 of 300 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	9.624697	GTATTCTGAATCATAAAACAAGTTGCA	57.375	29.630	6.10	0.00	0.00	4.08
42	43	9.624697	TGTATTCTGAATCATAAAACAAGTTGC	57.375	29.630	6.10	0.00	0.00	4.17
53	54	8.724229	GCATGCATAAGTGTATTCTGAATCATA	58.276	33.333	14.21	0.00	0.00	2.15
54	55	7.447545	AGCATGCATAAGTGTATTCTGAATCAT	59.552	33.333	21.98	0.00	0.00	2.45
55	56	6.769341	AGCATGCATAAGTGTATTCTGAATCA	59.231	34.615	21.98	2.67	0.00	2.57
56	57	7.199541	AGCATGCATAAGTGTATTCTGAATC	57.800	36.000	21.98	0.06	0.00	2.52
57	58	7.501559	AGAAGCATGCATAAGTGTATTCTGAAT	59.498	33.333	21.98	8.14	0.00	2.57
58	59	6.825213	AGAAGCATGCATAAGTGTATTCTGAA	59.175	34.615	21.98	0.00	0.00	3.02
59	60	6.259387	CAGAAGCATGCATAAGTGTATTCTGA	59.741	38.462	24.87	0.00	40.15	3.27
60	61	6.259387	TCAGAAGCATGCATAAGTGTATTCTG	59.741	38.462	23.88	23.88	39.68	3.02
61	62	6.351711	TCAGAAGCATGCATAAGTGTATTCT	58.648	36.000	21.98	13.34	0.00	2.40
62	63	6.609237	TCAGAAGCATGCATAAGTGTATTC	57.391	37.500	21.98	11.19	0.00	1.75
63	64	7.578310	ATTCAGAAGCATGCATAAGTGTATT	57.422	32.000	21.98	1.00	0.00	1.89
64	65	8.681486	TTATTCAGAAGCATGCATAAGTGTAT	57.319	30.769	21.98	10.80	0.00	2.29
65	66	8.562052	CATTATTCAGAAGCATGCATAAGTGTA	58.438	33.333	21.98	4.06	0.00	2.90
66	67	7.423199	CATTATTCAGAAGCATGCATAAGTGT	58.577	34.615	21.98	3.40	0.00	3.55
67	68	6.861572	CCATTATTCAGAAGCATGCATAAGTG	59.138	38.462	21.98	9.64	0.00	3.16
68	69	6.774170	TCCATTATTCAGAAGCATGCATAAGT	59.226	34.615	21.98	0.00	0.00	2.24
69	70	7.210718	TCCATTATTCAGAAGCATGCATAAG	57.789	36.000	21.98	7.18	0.00	1.73
70	71	7.770366	ATCCATTATTCAGAAGCATGCATAA	57.230	32.000	21.98	13.75	0.00	1.90
71	72	7.770366	AATCCATTATTCAGAAGCATGCATA	57.230	32.000	21.98	4.69	0.00	3.14
72	73	6.665992	AATCCATTATTCAGAAGCATGCAT	57.334	33.333	21.98	8.13	0.00	3.96
73	74	6.474140	AAATCCATTATTCAGAAGCATGCA	57.526	33.333	21.98	0.00	0.00	3.96
74	75	7.879070	TCTAAATCCATTATTCAGAAGCATGC	58.121	34.615	10.51	10.51	0.00	4.06
90	91	9.964354	AGCATGCATAAGTATATTCTAAATCCA	57.036	29.630	21.98	0.00	0.00	3.41

Showing 1 to 25 of 371 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.