AutoCloner

Multiple sequence alignment - TraesCS2A01G427800

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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	TraesCS2A01G427800	chr2A	100.000	9003	0	0	1	9003	680371424	680362422	0.000000e+00	16626
1	TraesCS2A01G427800	chr2A	87.385	325	41	0	3351	3675	680367750	680367426	3.070000e-99	374
2	TraesCS2A01G427800	chr2A	87.385	325	41	0	3675	3999	680368074	680367750	3.070000e-99	374
3	TraesCS2A01G427800	chr2A	88.889	117	13	0	3052	3168	680368259	680368143	2.620000e-30	145
4	TraesCS2A01G427800	chr2A	88.889	117	13	0	3166	3282	680368373	680368257	2.620000e-30	145
5	TraesCS2A01G427800	chr2B	93.787	7629	265	72	661	8188	640991124	640983604	0.000000e+00	11269
6	TraesCS2A01G427800	chr2B	85.917	845	61	28	8199	9003	640981938	640981112	0.000000e+00	848
7	TraesCS2A01G427800	chr2B	84.118	510	64	10	1	503	640991732	640991233	2.270000e-130	477
8	TraesCS2A01G427800	chr2B	76.993	439	89	9	1	431	163562092	163562526	3.250000e-59	241
9	TraesCS2A01G427800	chr2B	88.889	117	13	0	3052	3168	640988626	640988510	2.620000e-30	145
10	TraesCS2A01G427800	chr2B	88.889	117	13	0	3166	3282	640988740	640988624	2.620000e-30	145
11	TraesCS2A01G427800	chr2D	95.556	6526	185	33	726	7201	538069110	538062640	0.000000e+00	10347
12	TraesCS2A01G427800	chr2D	88.972	1741	97	45	7315	9003	538062289	538060592	0.000000e+00	2063
13	TraesCS2A01G427800	chr2D	87.077	325	42	0	3351	3675	538066168	538065844	1.430000e-97	368
14	TraesCS2A01G427800	chr2D	87.077	325	42	0	3675	3999	538066492	538066168	1.430000e-97	368
15	TraesCS2A01G427800	chr2D	88.034	117	14	0	3052	3168	538066677	538066561	1.220000e-28	139
16	TraesCS2A01G427800	chr2D	88.034	117	14	0	3166	3282	538066791	538066675	1.220000e-28	139
17	TraesCS2A01G427800	chr6D	86.813	455	31	6	6926	7354	438125465	438125014	1.760000e-131	481
18	TraesCS2A01G427800	chr3D	83.589	457	68	5	1	451	24569257	24569712	1.080000e-113	422
19	TraesCS2A01G427800	chr7A	83.040	454	69	6	1	447	10359300	10359752	1.090000e-108	405
20	TraesCS2A01G427800	chr7A	90.106	283	19	4	6926	7202	22644423	22644702	8.590000e-95	359
21	TraesCS2A01G427800	chr7A	76.890	463	84	18	1	447	670686171	670686626	3.250000e-59	241
22	TraesCS2A01G427800	chr7A	87.730	163	12	1	7200	7354	22644734	22644896	5.550000e-42	183
23	TraesCS2A01G427800	chr7D	91.930	285	16	3	6924	7202	50325935	50326218	8.470000e-105	392
24	TraesCS2A01G427800	chr7D	77.263	453	90	7	7	451	25058424	25057977	4.170000e-63	254
25	TraesCS2A01G427800	chr7D	88.095	168	12	1	7196	7355	50326246	50326413	9.220000e-45	193
26	TraesCS2A01G427800	chr1A	90.106	283	19	4	6926	7202	67650582	67650861	8.590000e-95	359
27	TraesCS2A01G427800	chr1A	86.228	167	15	1	7196	7354	67650889	67651055	3.340000e-39	174
28	TraesCS2A01G427800	chr6B	89.046	283	22	4	6926	7202	698552868	698552589	8.660000e-90	342
29	TraesCS2A01G427800	chr6B	86.585	164	14	1	7199	7354	698552558	698552395	3.340000e-39	174
30	TraesCS2A01G427800	chr4D	77.996	459	82	17	1	447	99207163	99207614	4.140000e-68	270
31	TraesCS2A01G427800	chr1B	79.284	391	71	10	1	384	47628083	47628470	1.930000e-66	265
32	TraesCS2A01G427800	chrUn	76.623	462	86	18	1	447	434813945	434814399	1.510000e-57	235

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	TraesCS2A01G427800	chr2A	680362422	680371424	9002	True	3532.800000	16626	90.5096	1	9003	5	chr2A.!!$R1	9002
1	TraesCS2A01G427800	chr2B	640981112	640991732	10620	True	2576.800000	11269	88.3200	1	9003	5	chr2B.!!$R1	9002
2	TraesCS2A01G427800	chr2D	538060592	538069110	8518	True	2237.333333	10347	89.1250	726	9003	6	chr2D.!!$R1	8277

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
530	564	0.251608	AATTTTGAGGACGGGGGTGG	60.252	55.000	0.00	0.00	0.00	4.61	F
645	679	0.388907	CAAAGGGTTGCATTGGAGCG	60.389	55.000	0.00	0.00	37.31	5.03	F
992	1036	0.389166	AGAACAGTAGCGCTCACAGC	60.389	55.000	16.34	0.00	38.02	4.40	F
1828	1875	0.036010	CAGAGTTGAGGATTGCCGGT	60.036	55.000	1.90	0.00	39.96	5.28	F
2113	2188	0.814457	GTCGATCTCTGACTGGCTGT	59.186	55.000	0.00	0.00	33.54	4.40	F
2982	3078	0.464373	GCCCATTCATTCAGAGCCGA	60.464	55.000	0.00	0.00	0.00	5.54	F
3503	3614	0.107456	CTACCGAGCATGGGCAGATT	59.893	55.000	0.00	0.00	44.61	2.40	F
4367	4478	1.122019	AGAACCACTCGGAGCAGGTT	61.122	55.000	26.21	26.21	46.39	3.50	F
4781	4892	1.281656	GTAACTGTTGTGCCGCCAC	59.718	57.895	2.69	0.00	42.40	5.01	F
6308	6421	0.323629	ATGGGTCCGTTGTGTCGATT	59.676	50.000	0.00	0.00	0.00	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1490	1534	0.168128	GCATCGTAGCAACAACCACC	59.832	55.000	0.0	0.00	4.61	R
1727	1773	0.249398	AAAATCGTGGAGACGGGGAG	59.751	55.000	0.0	46.11	4.30	R
2977	3073	0.179032	TTGTTGTCCATGTGTCGGCT	60.179	50.000	0.0	0.00	5.52	R
2978	3074	0.881118	ATTGTTGTCCATGTGTCGGC	59.119	50.000	0.0	0.00	5.54	R
3365	3476	1.350684	TCTGTGGGCATAACTTGAGCA	59.649	47.619	0.0	0.00	4.26	R
4367	4478	1.290324	GCTGTGAGGCTTGAGTCGA	59.710	57.895	0.0	0.00	4.20	R
5218	5331	0.389391	ACGGCCGATAATGAGTCCTG	59.611	55.000	35.9	0.00	3.86	R
5566	5679	1.097232	TGCATCCTGAAATTGCTCGG	58.903	50.000	0.0	37.28	4.63	R
6773	6886	2.354259	CTCCTGTGTGAATCTTGGCTC	58.646	52.381	0.0	0.00	4.70	R
8217	10316	0.179111	GATGAGACGATCCAACGCCA	60.179	55.000	0.0	36.70	5.69	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
29	30	3.087906	TTCTTCCCGCCTAGCCCC	61.088	66.667	0.00	0.00	0.00	5.80
73	74	4.329545	TTGAGGGCGTGTGGAGGC	62.330	66.667	0.00	0.00	0.00	4.70
80	81	2.029073	CGTGTGGAGGCGTGTCTT	59.971	61.111	0.00	0.00	0.00	3.01
91	92	1.352156	GCGTGTCTTCGGCGAATCTT	61.352	55.000	23.96	0.00	0.00	2.40
95	96	1.270094	TGTCTTCGGCGAATCTTGTGT	60.270	47.619	23.96	0.00	0.00	3.72
107	108	0.669318	TCTTGTGTGATTCGGTCGGC	60.669	55.000	0.00	0.00	0.00	5.54
115	116	1.963190	GATTCGGTCGGCGTTTGTCC	61.963	60.000	6.85	2.47	0.00	4.02
117	118	3.110178	CGGTCGGCGTTTGTCCTC	61.110	66.667	6.85	0.00	0.00	3.71
119	120	1.301479	GGTCGGCGTTTGTCCTCTT	60.301	57.895	6.85	0.00	0.00	2.85
130	131	4.480480	TCCTCTTTGGATCCGCCT	57.520	55.556	7.39	0.00	40.56	5.52
131	132	1.907739	TCCTCTTTGGATCCGCCTG	59.092	57.895	7.39	0.00	40.56	4.85
132	133	0.617535	TCCTCTTTGGATCCGCCTGA	60.618	55.000	7.39	2.00	40.56	3.86
133	134	0.253044	CCTCTTTGGATCCGCCTGAA	59.747	55.000	7.39	0.00	38.35	3.02
134	135	1.133976	CCTCTTTGGATCCGCCTGAAT	60.134	52.381	7.39	0.00	38.35	2.57
135	136	2.216898	CTCTTTGGATCCGCCTGAATC	58.783	52.381	7.39	0.00	37.63	2.52
136	137	1.134098	TCTTTGGATCCGCCTGAATCC	60.134	52.381	7.39	0.00	37.63	3.01
137	138	0.463654	TTTGGATCCGCCTGAATCCG	60.464	55.000	7.39	0.00	36.02	4.18
138	139	2.031163	GGATCCGCCTGAATCCGG	59.969	66.667	0.00	0.00	45.64	5.14
139	140	2.808206	GGATCCGCCTGAATCCGGT	61.808	63.158	0.00	0.00	44.63	5.28
140	141	1.301009	GATCCGCCTGAATCCGGTC	60.301	63.158	0.00	0.00	44.63	4.79
141	142	1.749334	GATCCGCCTGAATCCGGTCT	61.749	60.000	0.00	0.00	44.63	3.85
142	143	1.338136	ATCCGCCTGAATCCGGTCTT	61.338	55.000	0.00	0.00	44.63	3.01
143	144	1.521681	CCGCCTGAATCCGGTCTTC	60.522	63.158	0.00	6.96	39.67	2.87
144	145	1.218047	CGCCTGAATCCGGTCTTCA	59.782	57.895	17.32	17.32	0.00	3.02
153	154	2.288961	TCCGGTCTTCATTCGCTTAC	57.711	50.000	0.00	0.00	0.00	2.34

Showing 1 to 25 of 315 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	4.530857	CTGAACGGGGGCTAGGCG	62.531	72.222	10.58	0.00	0.00	5.52
29	30	1.466167	CTTGAAGCATCACCTGAACGG	59.534	52.381	0.00	0.00	34.61	4.44
30	31	1.135859	GCTTGAAGCATCACCTGAACG	60.136	52.381	13.09	0.00	41.89	3.95
55	56	2.046892	CCTCCACACGCCCTCAAG	60.047	66.667	0.00	0.00	0.00	3.02
73	74	0.366871	CAAGATTCGCCGAAGACACG	59.633	55.000	5.52	0.00	0.00	4.49
76	77	1.126846	CACACAAGATTCGCCGAAGAC	59.873	52.381	5.52	2.20	0.00	3.01
80	81	1.999735	GAATCACACAAGATTCGCCGA	59.000	47.619	0.00	0.00	42.96	5.54
86	87	2.346803	CCGACCGAATCACACAAGATT	58.653	47.619	0.00	0.00	40.75	2.40
91	92	2.431771	CGCCGACCGAATCACACA	60.432	61.111	0.00	0.00	40.02	3.72
95	96	1.286354	GACAAACGCCGACCGAATCA	61.286	55.000	0.00	0.00	41.02	2.57
101	102	0.883370	AAAGAGGACAAACGCCGACC	60.883	55.000	0.00	0.00	0.00	4.79
115	116	2.216898	GATTCAGGCGGATCCAAAGAG	58.783	52.381	13.41	0.00	37.29	2.85
117	118	1.312815	GGATTCAGGCGGATCCAAAG	58.687	55.000	13.41	0.00	37.29	2.77
119	120	1.146041	CGGATTCAGGCGGATCCAA	59.854	57.895	13.41	0.00	37.29	3.53
128	129	2.205074	CGAATGAAGACCGGATTCAGG	58.795	52.381	24.05	15.48	39.86	3.86
129	130	1.594862	GCGAATGAAGACCGGATTCAG	59.405	52.381	24.05	15.53	39.86	3.02
130	131	1.207089	AGCGAATGAAGACCGGATTCA	59.793	47.619	22.80	22.80	40.72	2.57
131	132	1.941325	AGCGAATGAAGACCGGATTC	58.059	50.000	9.46	12.95	0.00	2.52
132	133	2.403252	AAGCGAATGAAGACCGGATT	57.597	45.000	9.46	1.40	0.00	3.01
133	134	2.798499	CGTAAGCGAATGAAGACCGGAT	60.798	50.000	9.46	0.00	41.33	4.18
134	135	1.468565	CGTAAGCGAATGAAGACCGGA	60.469	52.381	9.46	0.00	41.33	5.14
135	136	0.921347	CGTAAGCGAATGAAGACCGG	59.079	55.000	0.00	0.00	41.33	5.28
136	137	1.582502	GACGTAAGCGAATGAAGACCG	59.417	52.381	0.00	0.00	45.62	4.79
137	138	2.599082	CAGACGTAAGCGAATGAAGACC	59.401	50.000	0.00	0.00	45.62	3.85
138	139	3.059570	CACAGACGTAAGCGAATGAAGAC	59.940	47.826	0.00	0.00	45.62	3.01

Showing 1 to 25 of 279 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.