AutoCloner

Multiple sequence alignment - TraesCS6D01G271300

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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	TraesCS6D01G271300	chr6D	100.000	3666	0	0	1	3666	380559940	380563605	0.000000e+00	6770.0
1	TraesCS6D01G271300	chr6B	93.850	3236	154	21	466	3666	567820583	567823808	0.000000e+00	4831.0
2	TraesCS6D01G271300	chr6B	76.860	1210	224	33	995	2178	567844159	567845338	1.860000e-177	632.0
3	TraesCS6D01G271300	chr6B	82.301	226	25	9	3451	3666	567852241	567852461	8.090000e-42	182.0
4	TraesCS6D01G271300	chr6B	86.486	111	8	1	3263	3366	567852110	567852220	8.320000e-22	115.0
5	TraesCS6D01G271300	chr6A	92.378	1207	69	12	974	2178	521992260	521993445	0.000000e+00	1698.0
6	TraesCS6D01G271300	chr6A	88.470	954	80	11	1	952	521989703	521990628	0.000000e+00	1125.0
7	TraesCS6D01G271300	chr6A	90.732	669	42	11	1512	2178	521995211	521995861	0.000000e+00	874.0
8	TraesCS6D01G271300	chr6A	96.188	446	15	1	3223	3666	522036179	522036624	0.000000e+00	728.0
9	TraesCS6D01G271300	chr6A	77.360	1197	221	28	995	2180	522044435	522045592	0.000000e+00	664.0
10	TraesCS6D01G271300	chr6A	94.326	423	16	4	2175	2590	522032791	522033212	3.090000e-180	641.0
11	TraesCS6D01G271300	chr6A	95.385	195	9	0	3043	3237	522034599	522034793	9.890000e-81	311.0
12	TraesCS6D01G271300	chr6A	98.684	76	1	0	3043	3118	522034317	522034392	6.390000e-28	135.0
13	TraesCS6D01G271300	chr6A	83.784	111	9	5	3263	3365	522058674	522058783	3.010000e-16	97.1
14	TraesCS6D01G271300	chr1D	75.523	478	101	13	262	736	57504695	57504231	1.710000e-53	220.0

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	TraesCS6D01G271300	chr6D	380559940	380563605	3665	False	6770.000000	6770	100.000000	1	3666	1	chr6D.!!$F1	3665
1	TraesCS6D01G271300	chr6B	567820583	567823808	3225	False	4831.000000	4831	93.850000	466	3666	1	chr6B.!!$F1	3200
2	TraesCS6D01G271300	chr6B	567844159	567845338	1179	False	632.000000	632	76.860000	995	2178	1	chr6B.!!$F2	1183
3	TraesCS6D01G271300	chr6A	521989703	521995861	6158	False	1232.333333	1698	90.526667	1	2178	3	chr6A.!!$F3	2177
4	TraesCS6D01G271300	chr6A	522044435	522045592	1157	False	664.000000	664	77.360000	995	2180	1	chr6A.!!$F1	1185
5	TraesCS6D01G271300	chr6A	522032791	522036624	3833	False	453.750000	728	96.145750	2175	3666	4	chr6A.!!$F4	1491

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	Hairpin	End Stability	Orientation
262	264	0.108756	GGTAGAACTGCTCCACGACC	60.109	60.0	0.00	4.79	F
578	580	0.251341	AAAGCAGGGCTCCGAATTGT	60.251	50.0	38.25	2.71	F
2026	3685	0.888736	TTGGTGCATGGTTCGGTCAG	60.889	55.0	0.00	3.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
1857	3487	0.323629	TTGGCTCCAAGTAACCGAGG	59.676	55.000	0.00	4.63	R
2135	3794	1.228552	TTGGGAAAGCACCTGAGGC	60.229	57.895	0.00	4.70	R
3523	10079	1.010797	CACAACAGCGCAGTGTCAC	60.011	57.895	11.47	3.67	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
60	61	3.389687	AAATGACTTGAATAGCGCACG	57.610	42.857	11.47	0.00	0.00	5.34
74	75	1.352156	CGCACGAGGGACAAAGTAGC	61.352	60.000	0.00	0.00	0.00	3.58
78	79	0.458025	CGAGGGACAAAGTAGCCGTC	60.458	60.000	0.00	0.00	34.23	4.79
79	80	0.606604	GAGGGACAAAGTAGCCGTCA	59.393	55.000	0.00	0.00	36.77	4.35
85	86	3.063588	GGACAAAGTAGCCGTCAATTAGC	59.936	47.826	0.00	0.00	0.00	3.09
121	122	2.224523	TGCCCTATTCGGATTCATCACC	60.225	50.000	0.00	0.00	33.16	4.02
144	146	3.676873	CGATGCCCCTTGATTTTTCCTTG	60.677	47.826	0.00	0.00	0.00	3.61
157	159	8.647143	TGATTTTTCCTTGAAATTGAGAACAC	57.353	30.769	0.00	0.00	31.34	3.32
179	181	0.611618	TCCTTCGCATGTTGGGCATT	60.612	50.000	0.00	0.00	35.19	3.56
180	182	0.458889	CCTTCGCATGTTGGGCATTG	60.459	55.000	0.00	0.00	35.19	2.82
181	183	0.244450	CTTCGCATGTTGGGCATTGT	59.756	50.000	0.00	0.00	35.19	2.71
190	192	5.394005	GCATGTTGGGCATTGTCAATAACTA	60.394	40.000	0.00	0.00	35.19	2.24
245	247	0.460311	GACGAATCCATGGACTCGGT	59.540	55.000	39.28	27.91	46.30	4.69
250	252	3.718815	GAATCCATGGACTCGGTAGAAC	58.281	50.000	18.99	0.00	0.00	3.01
262	264	0.108756	GGTAGAACTGCTCCACGACC	60.109	60.000	0.00	0.00	0.00	4.79
288	290	7.041848	CGAATCCATCATATGTGCTTCAAAGTA	60.042	37.037	1.90	0.00	0.00	2.24
294	296	9.069078	CATCATATGTGCTTCAAAGTAAACAAG	57.931	33.333	1.90	0.00	0.00	3.16
299	301	8.770438	ATGTGCTTCAAAGTAAACAAGAAAAA	57.230	26.923	0.00	0.00	0.00	1.94
300	302	8.013236	TGTGCTTCAAAGTAAACAAGAAAAAC	57.987	30.769	0.00	0.00	0.00	2.43
301	303	7.870445	TGTGCTTCAAAGTAAACAAGAAAAACT	59.130	29.630	0.00	0.00	0.00	2.66
302	304	8.708742	GTGCTTCAAAGTAAACAAGAAAAACTT	58.291	29.630	0.00	0.00	39.70	2.66
378	380	1.597027	GGACGATAATGTGCGGGGG	60.597	63.158	0.00	0.00	0.00	5.40
379	381	2.203153	ACGATAATGTGCGGGGGC	60.203	61.111	0.00	0.00	0.00	5.80
380	382	3.345808	CGATAATGTGCGGGGGCG	61.346	66.667	0.00	0.00	0.00	6.13
411	413	3.126528	CGGCGGTTAGACTAGGGG	58.873	66.667	0.00	0.00	0.00	4.79

Showing 1 to 25 of 79 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
14	15	1.798223	TCGTCGTTTTTGGATGAGCTG	59.202	47.619	0.00	0.00	4.24
15	16	2.163818	TCGTCGTTTTTGGATGAGCT	57.836	45.000	0.00	0.00	4.09
48	49	1.141019	GTCCCTCGTGCGCTATTCA	59.859	57.895	9.73	0.00	2.57
60	61	0.606604	TGACGGCTACTTTGTCCCTC	59.393	55.000	0.00	0.00	4.30
85	86	1.518056	GGGCACGTGGGCATATGATG	61.518	60.000	18.88	45.66	3.07
97	98	0.828022	TGAATCCGAATAGGGCACGT	59.172	50.000	0.00	41.52	4.49
121	122	1.136891	GGAAAAATCAAGGGGCATCGG	59.863	52.381	0.00	0.00	4.18
144	146	3.423645	CGAAGGAGCGTGTTCTCAATTTC	60.424	47.826	0.00	34.84	2.17
157	159	2.753966	CCCAACATGCGAAGGAGCG	61.754	63.158	0.00	40.67	5.03
179	181	8.463607	TGACGATGATACTTGTAGTTATTGACA	58.536	33.333	0.00	0.00	3.58
180	182	8.851960	TGACGATGATACTTGTAGTTATTGAC	57.148	34.615	0.00	0.00	3.18
190	192	6.586344	AGGATGAAATGACGATGATACTTGT	58.414	36.000	0.00	0.00	3.16
243	245	0.108756	GGTCGTGGAGCAGTTCTACC	60.109	60.000	0.00	34.02	3.18
245	247	0.607217	TCGGTCGTGGAGCAGTTCTA	60.607	55.000	0.00	0.00	2.10
250	252	1.519455	GGATTCGGTCGTGGAGCAG	60.519	63.158	0.00	0.00	4.24
262	264	5.678132	TTGAAGCACATATGATGGATTCG	57.322	39.130	10.38	32.38	3.34
366	368	4.169696	CTCCGCCCCCGCACATTA	62.170	66.667	0.00	34.03	1.90
397	399	1.755380	CTTCCACCCCTAGTCTAACCG	59.245	57.143	0.00	0.00	4.44
411	413	1.149401	GCCTATGCCTCCCTTCCAC	59.851	63.158	0.00	0.00	4.02
424	426	1.607612	CCAACCCCGACTTGCCTAT	59.392	57.895	0.00	0.00	2.57
426	428	4.660938	GCCAACCCCGACTTGCCT	62.661	66.667	0.00	0.00	4.75
483	485	1.961394	TCACTATACCATCCACTCCGC	59.039	52.381	0.00	0.00	5.54
515	517	1.539496	GCTTTGTGTCCGTGTAGTCCA	60.539	52.381	0.00	0.00	4.02
532	534	2.044946	GTCCATCCGGCCTTGCTT	60.045	61.111	0.00	0.00	3.91
540	542	1.264749	TTCTCCCTGTGTCCATCCGG	61.265	60.000	0.00	0.00	5.14

Showing 1 to 25 of 73 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.