AutoCloner

Multiple sequence alignment - TraesCS2D01G111100

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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	TraesCS2D01G111100	chr2D	100.000	3104	0	0	1	3104	61811658	61808555	0.000000e+00	5733.0
1	TraesCS2D01G111100	chr2B	87.569	1094	76	20	1338	2398	96630498	96629432	0.000000e+00	1212.0
2	TraesCS2D01G111100	chr2B	94.304	474	18	6	827	1293	96630974	96630503	0.000000e+00	717.0
3	TraesCS2D01G111100	chr2B	87.395	238	21	7	2871	3101	96629086	96628851	6.600000e-67	265.0
4	TraesCS2D01G111100	chr2A	87.079	890	85	19	1528	2411	62277826	62276961	0.000000e+00	979.0
5	TraesCS2D01G111100	chr2A	95.368	475	10	6	827	1292	62278436	62277965	0.000000e+00	745.0
6	TraesCS2D01G111100	chr2A	86.957	161	17	4	2752	2909	62276757	62276598	8.850000e-41	178.0
7	TraesCS2D01G111100	chr2A	91.667	96	7	1	1338	1432	62277959	62277864	6.980000e-27	132.0
8	TraesCS2D01G111100	chr7B	89.922	258	18	6	998	1248	443859350	443859094	2.990000e-85	326.0
9	TraesCS2D01G111100	chr7B	100.000	30	0	0	679	708	500218077	500218048	4.320000e-04	56.5
10	TraesCS2D01G111100	chr7D	89.535	258	19	6	998	1248	426752973	426752717	1.390000e-83	320.0
11	TraesCS2D01G111100	chr7A	89.535	258	19	6	998	1248	506489045	506489301	1.390000e-83	320.0
12	TraesCS2D01G111100	chr4A	77.624	362	57	16	212	558	633061616	633061968	6.790000e-47	198.0
13	TraesCS2D01G111100	chr4A	84.615	78	10	2	632	708	464771801	464771877	3.320000e-10	76.8
14	TraesCS2D01G111100	chr6D	85.185	81	6	6	2	77	122237244	122237165	9.230000e-11	78.7
15	TraesCS2D01G111100	chr1B	91.379	58	3	2	15	70	191012858	191012801	9.230000e-11	78.7
16	TraesCS2D01G111100	chr5A	86.207	58	4	3	649	704	437228985	437229040	3.340000e-05	60.2

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	TraesCS2D01G111100	chr2D	61808555	61811658	3103	True	5733.000000	5733	100.00000	1	3104	1	chr2D.!!$R1	3103
1	TraesCS2D01G111100	chr2B	96628851	96630974	2123	True	731.333333	1212	89.75600	827	3101	3	chr2B.!!$R1	2274
2	TraesCS2D01G111100	chr2A	62276598	62278436	1838	True	508.500000	979	90.26775	827	2909	4	chr2A.!!$R1	2082

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
427	428	0.105224	CACGTAAGGTGTGGTGTCCA	59.895	55.0	0.0	0.0	41.89	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2419	2460	0.179043	GAAGGGGGAGAATTCGAGCC	60.179	60.0	0.0	3.31	0.0	4.7	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
85	86	9.617523	AAAAAGTCATCAGTTTTGGAAATGATT	57.382	25.926	0.00	0.00	45.37	2.57
86	87	9.617523	AAAAGTCATCAGTTTTGGAAATGATTT	57.382	25.926	0.00	0.00	45.37	2.17
87	88	9.617523	AAAGTCATCAGTTTTGGAAATGATTTT	57.382	25.926	0.00	0.00	45.37	1.82
88	89	8.597662	AGTCATCAGTTTTGGAAATGATTTTG	57.402	30.769	0.00	0.00	45.37	2.44
89	90	8.423349	AGTCATCAGTTTTGGAAATGATTTTGA	58.577	29.630	0.00	0.00	45.37	2.69
90	91	9.044150	GTCATCAGTTTTGGAAATGATTTTGAA	57.956	29.630	0.00	0.00	45.37	2.69
91	92	9.610705	TCATCAGTTTTGGAAATGATTTTGAAA	57.389	25.926	0.00	0.00	45.37	2.69
133	134	9.875675	TTTTGAAAAACAGTTTGTCAATTTCTG	57.124	25.926	25.86	8.89	32.94	3.02
134	135	8.824159	TTGAAAAACAGTTTGTCAATTTCTGA	57.176	26.923	22.86	4.38	32.94	3.27
135	136	8.824159	TGAAAAACAGTTTGTCAATTTCTGAA	57.176	26.923	15.51	0.00	35.22	3.02
136	137	9.265901	TGAAAAACAGTTTGTCAATTTCTGAAA	57.734	25.926	15.51	5.15	35.22	2.69
167	168	8.652463	AGGTTTCAAAAATTGTAAAAGTTCACG	58.348	29.630	0.00	0.00	0.00	4.35
168	169	8.648968	GGTTTCAAAAATTGTAAAAGTTCACGA	58.351	29.630	0.00	0.00	0.00	4.35
171	172	8.918961	TCAAAAATTGTAAAAGTTCACGATGT	57.081	26.923	0.00	0.00	0.00	3.06
172	173	9.360093	TCAAAAATTGTAAAAGTTCACGATGTT	57.640	25.926	0.00	0.00	0.00	2.71
173	174	9.407514	CAAAAATTGTAAAAGTTCACGATGTTG	57.592	29.630	0.00	0.44	0.00	3.33
174	175	8.918961	AAAATTGTAAAAGTTCACGATGTTGA	57.081	26.923	0.00	0.00	0.00	3.18
175	176	8.918961	AAATTGTAAAAGTTCACGATGTTGAA	57.081	26.923	0.00	0.00	32.94	2.69
176	177	8.918961	AATTGTAAAAGTTCACGATGTTGAAA	57.081	26.923	0.00	0.00	37.24	2.69
177	178	8.918961	ATTGTAAAAGTTCACGATGTTGAAAA	57.081	26.923	0.00	0.00	37.24	2.29
178	179	8.744008	TTGTAAAAGTTCACGATGTTGAAAAA	57.256	26.923	0.00	0.00	37.24	1.94
179	180	8.918961	TGTAAAAGTTCACGATGTTGAAAAAT	57.081	26.923	0.00	0.00	37.24	1.82
180	181	8.802856	TGTAAAAGTTCACGATGTTGAAAAATG	58.197	29.630	0.00	0.00	37.24	2.32
181	182	7.826260	AAAAGTTCACGATGTTGAAAAATGT	57.174	28.000	0.00	0.00	37.24	2.71
182	183	7.826260	AAAGTTCACGATGTTGAAAAATGTT	57.174	28.000	0.00	0.00	37.24	2.71

Showing 1 to 25 of 690 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
59	60	9.617523	AATCATTTCCAAAACTGATGACTTTTT	57.382	25.926	0.00	0.00	35.60	1.94
60	61	9.617523	AAATCATTTCCAAAACTGATGACTTTT	57.382	25.926	0.00	0.00	35.60	2.27
61	62	9.617523	AAAATCATTTCCAAAACTGATGACTTT	57.382	25.926	0.00	0.00	35.60	2.66
62	63	9.048446	CAAAATCATTTCCAAAACTGATGACTT	57.952	29.630	0.00	0.00	35.60	3.01
63	64	8.423349	TCAAAATCATTTCCAAAACTGATGACT	58.577	29.630	0.00	0.00	35.60	3.41
64	65	8.592105	TCAAAATCATTTCCAAAACTGATGAC	57.408	30.769	0.00	0.00	35.60	3.06
65	66	9.610705	TTTCAAAATCATTTCCAAAACTGATGA	57.389	25.926	0.00	0.00	35.60	2.92
107	108	9.875675	CAGAAATTGACAAACTGTTTTTCAAAA	57.124	25.926	28.23	14.59	31.94	2.44
108	109	9.265901	TCAGAAATTGACAAACTGTTTTTCAAA	57.734	25.926	28.23	17.12	31.94	2.69
109	110	8.824159	TCAGAAATTGACAAACTGTTTTTCAA	57.176	26.923	27.27	27.27	31.94	2.69
110	111	8.824159	TTCAGAAATTGACAAACTGTTTTTCA	57.176	26.923	15.90	15.90	34.94	2.69
141	142	8.652463	CGTGAACTTTTACAATTTTTGAAACCT	58.348	29.630	0.00	0.00	0.00	3.50
142	143	8.648968	TCGTGAACTTTTACAATTTTTGAAACC	58.351	29.630	0.00	0.00	0.00	3.27
145	146	9.360093	ACATCGTGAACTTTTACAATTTTTGAA	57.640	25.926	0.00	0.00	0.00	2.69
146	147	8.918961	ACATCGTGAACTTTTACAATTTTTGA	57.081	26.923	0.00	0.00	0.00	2.69
147	148	9.407514	CAACATCGTGAACTTTTACAATTTTTG	57.592	29.630	0.00	0.00	0.00	2.44
148	149	9.360093	TCAACATCGTGAACTTTTACAATTTTT	57.640	25.926	0.00	0.00	0.00	1.94
149	150	8.918961	TCAACATCGTGAACTTTTACAATTTT	57.081	26.923	0.00	0.00	0.00	1.82
150	151	8.918961	TTCAACATCGTGAACTTTTACAATTT	57.081	26.923	0.00	0.00	32.56	1.82
151	152	8.918961	TTTCAACATCGTGAACTTTTACAATT	57.081	26.923	0.00	0.00	37.24	2.32
152	153	8.918961	TTTTCAACATCGTGAACTTTTACAAT	57.081	26.923	0.00	0.00	37.24	2.71
153	154	8.744008	TTTTTCAACATCGTGAACTTTTACAA	57.256	26.923	0.00	0.00	37.24	2.41
154	155	8.802856	CATTTTTCAACATCGTGAACTTTTACA	58.197	29.630	0.00	0.00	37.24	2.41
155	156	8.803799	ACATTTTTCAACATCGTGAACTTTTAC	58.196	29.630	0.00	0.00	37.24	2.01
156	157	8.918961	ACATTTTTCAACATCGTGAACTTTTA	57.081	26.923	0.00	0.00	37.24	1.52

Showing 1 to 25 of 675 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.