AutoCloner

Multiple sequence alignment - TraesCS5D01G372000

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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	TraesCS5D01G372000	chr5D	100.000	2141	0	0	1	2141	446174025	446176165	0.000000e+00	3954
1	TraesCS5D01G372000	chr5D	99.168	1924	16	0	218	2141	503218676	503220599	0.000000e+00	3465
2	TraesCS5D01G372000	chr5D	98.805	1924	23	0	218	2141	503277768	503275845	0.000000e+00	3426
3	TraesCS5D01G372000	chr5D	97.000	200	3	3	1	199	446186587	446186784	1.220000e-87	333
4	TraesCS5D01G372000	chr1A	99.220	1924	15	0	218	2141	554512706	554514629	0.000000e+00	3470
5	TraesCS5D01G372000	chr1A	95.349	86	4	0	3	88	450805718	450805803	1.030000e-28	137
6	TraesCS5D01G372000	chr2D	99.116	1924	17	0	218	2141	272564413	272566336	0.000000e+00	3459
7	TraesCS5D01G372000	chr3D	98.960	1924	19	1	218	2141	589279086	589277164	0.000000e+00	3441
8	TraesCS5D01G372000	chr3B	98.909	1924	21	0	218	2141	201527482	201529405	0.000000e+00	3437
9	TraesCS5D01G372000	chr6D	98.753	1924	24	0	218	2141	168255384	168257307	0.000000e+00	3421
10	TraesCS5D01G372000	chr3A	98.701	1924	23	2	218	2141	672909549	672907628	0.000000e+00	3413
11	TraesCS5D01G372000	chr3A	95.349	86	4	0	3	88	512573982	512574067	1.030000e-28	137
12	TraesCS5D01G372000	chr3A	94.186	86	5	0	3	88	519312626	519312711	4.790000e-27	132
13	TraesCS5D01G372000	chr3A	89.524	105	9	2	92	196	732251237	732251135	4.790000e-27	132
14	TraesCS5D01G372000	chr1D	98.649	1924	23	3	218	2141	254397651	254395731	0.000000e+00	3406
15	TraesCS5D01G372000	chr7D	93.011	186	13	0	3	188	208870428	208870613	2.710000e-69	272
16	TraesCS5D01G372000	chr7D	90.385	104	7	3	92	195	523231852	523231952	1.330000e-27	134
17	TraesCS5D01G372000	chr7A	90.476	105	8	2	92	196	727657632	727657734	1.030000e-28	137
18	TraesCS5D01G372000	chr7A	90.476	105	8	2	92	196	727666157	727666259	1.030000e-28	137
19	TraesCS5D01G372000	chr4A	95.349	86	4	0	3	88	186674589	186674674	1.030000e-28	137
20	TraesCS5D01G372000	chr4A	95.349	86	4	0	3	88	717702097	717702012	1.030000e-28	137
21	TraesCS5D01G372000	chr2B	90.476	105	8	2	92	196	94308648	94308546	1.030000e-28	137
22	TraesCS5D01G372000	chr2B	94.186	86	5	0	3	88	435443054	435443139	4.790000e-27	132
23	TraesCS5D01G372000	chr2A	90.476	105	8	2	92	196	593704831	593704933	1.030000e-28	137
24	TraesCS5D01G372000	chr2A	89.524	105	9	2	92	196	53491298	53491400	4.790000e-27	132
25	TraesCS5D01G372000	chr5B	94.186	86	5	0	3	88	637756467	637756382	4.790000e-27	132

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	TraesCS5D01G372000	chr5D	446174025	446176165	2140	False	3954	3954	100.000	1	2141	1	chr5D.!!$F1	2140
1	TraesCS5D01G372000	chr5D	503218676	503220599	1923	False	3465	3465	99.168	218	2141	1	chr5D.!!$F3	1923
2	TraesCS5D01G372000	chr5D	503275845	503277768	1923	True	3426	3426	98.805	218	2141	1	chr5D.!!$R1	1923
3	TraesCS5D01G372000	chr1A	554512706	554514629	1923	False	3470	3470	99.220	218	2141	1	chr1A.!!$F2	1923
4	TraesCS5D01G372000	chr2D	272564413	272566336	1923	False	3459	3459	99.116	218	2141	1	chr2D.!!$F1	1923
5	TraesCS5D01G372000	chr3D	589277164	589279086	1922	True	3441	3441	98.960	218	2141	1	chr3D.!!$R1	1923
6	TraesCS5D01G372000	chr3B	201527482	201529405	1923	False	3437	3437	98.909	218	2141	1	chr3B.!!$F1	1923
7	TraesCS5D01G372000	chr6D	168255384	168257307	1923	False	3421	3421	98.753	218	2141	1	chr6D.!!$F1	1923
8	TraesCS5D01G372000	chr3A	672907628	672909549	1921	True	3413	3413	98.701	218	2141	1	chr3A.!!$R1	1923
9	TraesCS5D01G372000	chr1D	254395731	254397651	1920	True	3406	3406	98.649	218	2141	1	chr1D.!!$R1	1923

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
152	153	0.037232	CTGTTCCTTCTCCCCGACAC	60.037	60.0	0.0	0.0	0.0	3.67	F
211	212	0.865362	GTCCCCCTCCCTACCATCTA	59.135	60.0	0.0	0.0	0.0	1.98	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1017	1018	3.320826	TCTCCGAATATTTGCCATCTCGA	59.679	43.478	0.0	0.0	0.0	4.04	R
1917	1919	5.296035	TCTCGTTAATCTCTTCATGCTCGTA	59.704	40.000	0.0	0.0	0.0	3.43	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
48	49	4.899239	CTCCCGACCGCTGCCATC	62.899	72.222	0.00	0.00	0.00	3.51
76	77	3.333189	CTCGCCGCATCGTGGATG	61.333	66.667	0.00	1.29	42.37	3.51
77	78	3.773262	CTCGCCGCATCGTGGATGA	62.773	63.158	9.66	0.00	42.09	2.92
78	79	3.333189	CGCCGCATCGTGGATGAG	61.333	66.667	9.66	6.12	42.09	2.90
79	80	3.643978	GCCGCATCGTGGATGAGC	61.644	66.667	9.66	7.39	42.09	4.26
80	81	2.969238	CCGCATCGTGGATGAGCC	60.969	66.667	9.66	0.00	42.09	4.70
81	82	2.969238	CGCATCGTGGATGAGCCC	60.969	66.667	9.66	0.00	42.09	5.19
82	83	2.969238	GCATCGTGGATGAGCCCG	60.969	66.667	9.66	0.00	42.09	6.13
83	84	2.814604	CATCGTGGATGAGCCCGA	59.185	61.111	3.05	3.05	42.09	5.14
84	85	1.592669	CATCGTGGATGAGCCCGAC	60.593	63.158	2.64	0.00	42.09	4.79
85	86	2.797278	ATCGTGGATGAGCCCGACC	61.797	63.158	2.64	0.00	40.48	4.79
86	87	4.530857	CGTGGATGAGCCCGACCC	62.531	72.222	0.00	0.00	33.75	4.46
87	88	4.176752	GTGGATGAGCCCGACCCC	62.177	72.222	0.00	0.00	34.97	4.95
88	89	4.414956	TGGATGAGCCCGACCCCT	62.415	66.667	0.00	0.00	34.97	4.79
89	90	3.551407	GGATGAGCCCGACCCCTC	61.551	72.222	0.00	0.00	0.00	4.30
90	91	2.764128	GATGAGCCCGACCCCTCA	60.764	66.667	0.00	0.00	41.81	3.86
91	92	3.083997	ATGAGCCCGACCCCTCAC	61.084	66.667	0.00	0.00	40.55	3.51
118	119	4.152964	CCTGCTCGCCTGCTGCTA	62.153	66.667	0.00	0.00	38.05	3.49
119	120	2.889503	CTGCTCGCCTGCTGCTAC	60.890	66.667	0.00	0.00	38.05	3.58
120	121	4.457496	TGCTCGCCTGCTGCTACC	62.457	66.667	0.00	0.00	38.05	3.18
141	142	2.204306	CCCCCTCCCCTGTTCCTT	60.204	66.667	0.00	0.00	0.00	3.36
142	143	2.309504	CCCCCTCCCCTGTTCCTTC	61.310	68.421	0.00	0.00	0.00	3.46
143	144	1.229984	CCCCTCCCCTGTTCCTTCT	60.230	63.158	0.00	0.00	0.00	2.85
144	145	1.275421	CCCCTCCCCTGTTCCTTCTC	61.275	65.000	0.00	0.00	0.00	2.87
145	146	1.275421	CCCTCCCCTGTTCCTTCTCC	61.275	65.000	0.00	0.00	0.00	3.71
146	147	1.275421	CCTCCCCTGTTCCTTCTCCC	61.275	65.000	0.00	0.00	0.00	4.30
147	148	1.229853	TCCCCTGTTCCTTCTCCCC	60.230	63.158	0.00	0.00	0.00	4.81
148	149	2.670148	CCCCTGTTCCTTCTCCCCG	61.670	68.421	0.00	0.00	0.00	5.73
149	150	1.612442	CCCTGTTCCTTCTCCCCGA	60.612	63.158	0.00	0.00	0.00	5.14
150	151	1.597461	CCTGTTCCTTCTCCCCGAC	59.403	63.158	0.00	0.00	0.00	4.79
151	152	1.192146	CCTGTTCCTTCTCCCCGACA	61.192	60.000	0.00	0.00	0.00	4.35
152	153	0.037232	CTGTTCCTTCTCCCCGACAC	60.037	60.000	0.00	0.00	0.00	3.67
153	154	1.080025	GTTCCTTCTCCCCGACACG	60.080	63.158	0.00	0.00	0.00	4.49
155	156	4.452733	CCTTCTCCCCGACACGGC	62.453	72.222	4.57	0.00	46.86	5.68
156	157	3.382832	CTTCTCCCCGACACGGCT	61.383	66.667	4.57	0.00	46.86	5.52
157	158	3.358076	CTTCTCCCCGACACGGCTC	62.358	68.421	4.57	0.00	46.86	4.70
158	159	4.671590	TCTCCCCGACACGGCTCA	62.672	66.667	4.57	0.00	46.86	4.26
159	160	4.436998	CTCCCCGACACGGCTCAC	62.437	72.222	4.57	0.00	46.86	3.51
207	208	4.791069	GCGTCCCCCTCCCTACCA	62.791	72.222	0.00	0.00	0.00	3.25
208	209	2.285868	CGTCCCCCTCCCTACCAT	59.714	66.667	0.00	0.00	0.00	3.55
209	210	1.837499	CGTCCCCCTCCCTACCATC	60.837	68.421	0.00	0.00	0.00	3.51
210	211	1.632740	GTCCCCCTCCCTACCATCT	59.367	63.158	0.00	0.00	0.00	2.90
211	212	0.865362	GTCCCCCTCCCTACCATCTA	59.135	60.000	0.00	0.00	0.00	1.98
212	213	1.437547	GTCCCCCTCCCTACCATCTAT	59.562	57.143	0.00	0.00	0.00	1.98
213	214	1.437149	TCCCCCTCCCTACCATCTATG	59.563	57.143	0.00	0.00	0.00	2.23
214	215	1.152271	CCCCCTCCCTACCATCTATGT	59.848	57.143	0.00	0.00	0.00	2.29
215	216	2.541466	CCCCTCCCTACCATCTATGTC	58.459	57.143	0.00	0.00	0.00	3.06
216	217	2.112691	CCCCTCCCTACCATCTATGTCT	59.887	54.545	0.00	0.00	0.00	3.41
298	299	4.108902	CGGTGTCGTCCATGGATG	57.891	61.111	25.71	25.71	0.00	3.51
542	543	3.898123	AGGTAGTCGATGGCTATTCACAT	59.102	43.478	0.00	0.00	0.00	3.21
871	872	1.667830	CCGTTCGTGTGCATCCAGT	60.668	57.895	0.00	0.00	0.00	4.00
934	935	4.584325	GCTTTAACCATTCAGCCATGGATA	59.416	41.667	18.40	0.00	46.18	2.59
1462	1464	4.881273	TGGACGATCCTATTTGGTCAAATG	59.119	41.667	16.52	8.34	37.24	2.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	4.899239	GATGGCAGCGGTCGGGAG	62.899	72.222	0.00	0.00	0.00	4.30
59	60	3.333189	CATCCACGATGCGGCGAG	61.333	66.667	12.98	0.04	33.17	5.03
60	61	3.773262	CTCATCCACGATGCGGCGA	62.773	63.158	12.98	0.00	39.63	5.54
61	62	3.333189	CTCATCCACGATGCGGCG	61.333	66.667	0.51	0.51	39.63	6.46
62	63	3.643978	GCTCATCCACGATGCGGC	61.644	66.667	0.00	0.00	39.63	6.53
63	64	2.969238	GGCTCATCCACGATGCGG	60.969	66.667	0.00	0.00	39.63	5.69
64	65	2.969238	GGGCTCATCCACGATGCG	60.969	66.667	0.00	0.00	39.63	4.73
65	66	2.969238	CGGGCTCATCCACGATGC	60.969	66.667	0.00	0.00	39.63	3.91
66	67	1.592669	GTCGGGCTCATCCACGATG	60.593	63.158	0.00	0.00	41.00	3.84
67	68	2.797278	GGTCGGGCTCATCCACGAT	61.797	63.158	0.00	0.00	38.89	3.73
68	69	3.458163	GGTCGGGCTCATCCACGA	61.458	66.667	0.00	0.00	35.93	4.35
69	70	4.530857	GGGTCGGGCTCATCCACG	62.531	72.222	0.00	0.00	36.21	4.94
70	71	4.176752	GGGGTCGGGCTCATCCAC	62.177	72.222	0.00	0.00	36.21	4.02
71	72	4.414956	AGGGGTCGGGCTCATCCA	62.415	66.667	0.00	0.00	36.21	3.41
72	73	3.551407	GAGGGGTCGGGCTCATCC	61.551	72.222	0.00	0.00	0.00	3.51
73	74	2.764128	TGAGGGGTCGGGCTCATC	60.764	66.667	0.00	0.00	0.00	2.92
74	75	3.083997	GTGAGGGGTCGGGCTCAT	61.084	66.667	0.00	0.00	0.00	2.90
124	125	2.204306	AAGGAACAGGGGAGGGGG	60.204	66.667	0.00	0.00	0.00	5.40
125	126	1.229984	AGAAGGAACAGGGGAGGGG	60.230	63.158	0.00	0.00	0.00	4.79
126	127	1.275421	GGAGAAGGAACAGGGGAGGG	61.275	65.000	0.00	0.00	0.00	4.30
127	128	1.275421	GGGAGAAGGAACAGGGGAGG	61.275	65.000	0.00	0.00	0.00	4.30
128	129	1.275421	GGGGAGAAGGAACAGGGGAG	61.275	65.000	0.00	0.00	0.00	4.30
129	130	1.229853	GGGGAGAAGGAACAGGGGA	60.230	63.158	0.00	0.00	0.00	4.81
130	131	2.670148	CGGGGAGAAGGAACAGGGG	61.670	68.421	0.00	0.00	0.00	4.79
131	132	1.612442	TCGGGGAGAAGGAACAGGG	60.612	63.158	0.00	0.00	0.00	4.45
132	133	1.192146	TGTCGGGGAGAAGGAACAGG	61.192	60.000	0.00	0.00	0.00	4.00
133	134	0.037232	GTGTCGGGGAGAAGGAACAG	60.037	60.000	0.00	0.00	0.00	3.16
134	135	1.812686	CGTGTCGGGGAGAAGGAACA	61.813	60.000	0.00	0.00	0.00	3.18
135	136	1.080025	CGTGTCGGGGAGAAGGAAC	60.080	63.158	0.00	0.00	0.00	3.62
136	137	2.280552	CCGTGTCGGGGAGAAGGAA	61.281	63.158	0.00	0.00	44.15	3.36
137	138	2.678934	CCGTGTCGGGGAGAAGGA	60.679	66.667	0.00	0.00	44.15	3.36
190	191	4.791069	TGGTAGGGAGGGGGACGC	62.791	72.222	0.00	0.00	43.76	5.19
191	192	1.837499	GATGGTAGGGAGGGGGACG	60.837	68.421	0.00	0.00	0.00	4.79
192	193	0.865362	TAGATGGTAGGGAGGGGGAC	59.135	60.000	0.00	0.00	0.00	4.46
193	194	1.437149	CATAGATGGTAGGGAGGGGGA	59.563	57.143	0.00	0.00	0.00	4.81
194	195	1.152271	ACATAGATGGTAGGGAGGGGG	59.848	57.143	0.00	0.00	0.00	5.40
195	196	2.112691	AGACATAGATGGTAGGGAGGGG	59.887	54.545	0.00	0.00	0.00	4.79
196	197	3.076785	AGAGACATAGATGGTAGGGAGGG	59.923	52.174	0.00	0.00	0.00	4.30
197	198	4.396357	AGAGACATAGATGGTAGGGAGG	57.604	50.000	0.00	0.00	0.00	4.30
198	199	7.122055	GTCATAAGAGACATAGATGGTAGGGAG	59.878	44.444	0.00	0.00	38.40	4.30
199	200	6.948886	GTCATAAGAGACATAGATGGTAGGGA	59.051	42.308	0.00	0.00	38.40	4.20
200	201	6.153680	GGTCATAAGAGACATAGATGGTAGGG	59.846	46.154	0.00	0.00	40.29	3.53
201	202	6.951198	AGGTCATAAGAGACATAGATGGTAGG	59.049	42.308	0.00	0.00	40.29	3.18
202	203	7.122055	GGAGGTCATAAGAGACATAGATGGTAG	59.878	44.444	0.00	0.00	40.29	3.18
203	204	6.948886	GGAGGTCATAAGAGACATAGATGGTA	59.051	42.308	0.00	0.00	40.29	3.25
204	205	5.777732	GGAGGTCATAAGAGACATAGATGGT	59.222	44.000	0.00	0.00	40.29	3.55
205	206	5.186797	GGGAGGTCATAAGAGACATAGATGG	59.813	48.000	0.00	0.00	40.29	3.51
206	207	5.186797	GGGGAGGTCATAAGAGACATAGATG	59.813	48.000	0.00	0.00	40.29	2.90
207	208	5.337788	GGGGAGGTCATAAGAGACATAGAT	58.662	45.833	0.00	0.00	40.29	1.98
208	209	4.449376	GGGGGAGGTCATAAGAGACATAGA	60.449	50.000	0.00	0.00	40.29	1.98
209	210	3.835395	GGGGGAGGTCATAAGAGACATAG	59.165	52.174	0.00	0.00	40.29	2.23
210	211	3.471306	AGGGGGAGGTCATAAGAGACATA	59.529	47.826	0.00	0.00	40.29	2.29
211	212	2.251338	AGGGGGAGGTCATAAGAGACAT	59.749	50.000	0.00	0.00	40.29	3.06
212	213	1.651770	AGGGGGAGGTCATAAGAGACA	59.348	52.381	0.00	0.00	40.29	3.41
213	214	2.090999	AGAGGGGGAGGTCATAAGAGAC	60.091	54.545	0.00	0.00	37.80	3.36
214	215	2.227703	AGAGGGGGAGGTCATAAGAGA	58.772	52.381	0.00	0.00	0.00	3.10
215	216	2.785357	AGAGGGGGAGGTCATAAGAG	57.215	55.000	0.00	0.00	0.00	2.85
216	217	3.758787	GCATAGAGGGGGAGGTCATAAGA	60.759	52.174	0.00	0.00	0.00	2.10
286	287	5.820423	ACGAAATAATTTCATCCATGGACGA	59.180	36.000	18.99	12.63	39.63	4.20
298	299	8.807581	GTGAAATCCAATCCACGAAATAATTTC	58.192	33.333	0.00	0.00	36.32	2.17
542	543	5.367352	TCTTCTTTGGTGTTAAGGTGGTAGA	59.633	40.000	0.00	0.00	0.00	2.59
871	872	6.782988	TGGTAAATTTGTGGGTTCAATTCCTA	59.217	34.615	0.00	0.00	0.00	2.94
885	886	7.102993	GCCCAACTCATAATTGGTAAATTTGT	58.897	34.615	0.00	0.00	44.46	2.83
934	935	5.507482	CGATGTACGATGATCCCTGTTAAGT	60.507	44.000	0.00	0.00	45.77	2.24
1017	1018	3.320826	TCTCCGAATATTTGCCATCTCGA	59.679	43.478	0.00	0.00	0.00	4.04
1462	1464	7.025365	AGGAAAATCGTAATTTTTCGTTAGGC	58.975	34.615	0.00	0.00	43.48	3.93
1917	1919	5.296035	TCTCGTTAATCTCTTCATGCTCGTA	59.704	40.000	0.00	0.00	0.00	3.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.