AutoCloner

Multiple sequence alignment - TraesCS4B01G159400

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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	TraesCS4B01G159400	chr4B	100.000	3073	0	0	1	3073	308694748	308697820	0	5675
1	TraesCS4B01G159400	chr3D	96.826	3088	75	10	1	3073	589281275	589278196	0	5138
2	TraesCS4B01G159400	chr1A	96.666	3089	75	9	1	3073	554510521	554513597	0	5108
3	TraesCS4B01G159400	chr5D	96.534	3087	90	6	1	3073	6187206	6190289	0	5092
4	TraesCS4B01G159400	chr5D	96.469	3087	91	7	1	3073	503279959	503276877	0	5081
5	TraesCS4B01G159400	chr5D	95.563	3088	116	10	1	3073	432405229	432402148	0	4924
6	TraesCS4B01G159400	chr5D	96.859	2802	69	7	287	3073	503216770	503219567	0	4669
7	TraesCS4B01G159400	chr1D	96.277	3089	94	11	1	3073	254399844	254396761	0	5048
8	TraesCS4B01G159400	chr5A	95.372	3090	120	11	1	3073	607272665	607275748	0	4892
9	TraesCS4B01G159400	chr3B	96.789	2803	69	9	287	3073	201525576	201528373	0	4658
10	TraesCS4B01G159400	chr6D	96.753	2803	71	8	287	3073	168253477	168256275	0	4654
11	TraesCS4B01G159400	chr6D	95.318	1196	39	6	1	1180	45517836	45519030	0	1882
12	TraesCS4B01G159400	chrUn	96.718	2803	70	10	287	3073	93411079	93408283	0	4647
13	TraesCS4B01G159400	chrUn	96.539	2803	76	8	287	3073	216520051	216517254	0	4619
14	TraesCS4B01G159400	chrUn	97.009	535	16	0	1	535	239345998	239345464	0	900
15	TraesCS4B01G159400	chr3A	96.148	2804	86	8	287	3073	672911457	672908659	0	4560

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	TraesCS4B01G159400	chr4B	308694748	308697820	3072	False	5675	5675	100.000	1	3073	1	chr4B.!!$F1	3072
1	TraesCS4B01G159400	chr3D	589278196	589281275	3079	True	5138	5138	96.826	1	3073	1	chr3D.!!$R1	3072
2	TraesCS4B01G159400	chr1A	554510521	554513597	3076	False	5108	5108	96.666	1	3073	1	chr1A.!!$F1	3072
3	TraesCS4B01G159400	chr5D	6187206	6190289	3083	False	5092	5092	96.534	1	3073	1	chr5D.!!$F1	3072
4	TraesCS4B01G159400	chr5D	503276877	503279959	3082	True	5081	5081	96.469	1	3073	1	chr5D.!!$R2	3072
5	TraesCS4B01G159400	chr5D	432402148	432405229	3081	True	4924	4924	95.563	1	3073	1	chr5D.!!$R1	3072
6	TraesCS4B01G159400	chr5D	503216770	503219567	2797	False	4669	4669	96.859	287	3073	1	chr5D.!!$F2	2786
7	TraesCS4B01G159400	chr1D	254396761	254399844	3083	True	5048	5048	96.277	1	3073	1	chr1D.!!$R1	3072
8	TraesCS4B01G159400	chr5A	607272665	607275748	3083	False	4892	4892	95.372	1	3073	1	chr5A.!!$F1	3072
9	TraesCS4B01G159400	chr3B	201525576	201528373	2797	False	4658	4658	96.789	287	3073	1	chr3B.!!$F1	2786
10	TraesCS4B01G159400	chr6D	168253477	168256275	2798	False	4654	4654	96.753	287	3073	1	chr6D.!!$F2	2786
11	TraesCS4B01G159400	chr6D	45517836	45519030	1194	False	1882	1882	95.318	1	1180	1	chr6D.!!$F1	1179
12	TraesCS4B01G159400	chrUn	93408283	93411079	2796	True	4647	4647	96.718	287	3073	1	chrUn.!!$R1	2786
13	TraesCS4B01G159400	chrUn	216517254	216520051	2797	True	4619	4619	96.539	287	3073	1	chrUn.!!$R2	2786
14	TraesCS4B01G159400	chrUn	239345464	239345998	534	True	900	900	97.009	1	535	1	chrUn.!!$R3	534
15	TraesCS4B01G159400	chr3A	672908659	672911457	2798	True	4560	4560	96.148	287	3073	1	chr3A.!!$R1	2786

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
521	525	1.447643	GCTAGATGCACGGGACCAT	59.552	57.895	0.00	0.0	42.31	3.55	F
757	779	1.747206	GCGGATGTAGCCAAGTGGATT	60.747	52.381	0.18	0.0	37.39	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1703	1731	0.387565	GCGCCCCTTGTTTCAAAGAA	59.612	50.000	0.0	0.0	0.0	2.52	R
2181	2209	1.903183	GCATAGAGGGGGAGGTCATAC	59.097	57.143	0.0	0.0	0.0	2.39	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
78	79	5.745294	TGATAGTCAAGGTCGCGTTATTAAC	59.255	40.000	5.77	0.00	0.00	2.01
167	168	4.325084	ACTTCCCTCTAGACTTAGCTGT	57.675	45.455	0.00	0.00	0.00	4.40
183	184	3.554934	AGCTGTTGTTGAAGTTCCATCA	58.445	40.909	0.00	0.00	0.00	3.07
268	270	9.474313	AAATACCCAATATCTTGCTAGAACAAA	57.526	29.630	0.99	0.00	33.20	2.83
521	525	1.447643	GCTAGATGCACGGGACCAT	59.552	57.895	0.00	0.00	42.31	3.55
671	692	5.529800	TGTCCAATATCTCGATCGAAGTACA	59.470	40.000	19.92	11.36	0.00	2.90
683	704	5.449314	CGATCGAAGTACAGAGGTCAGAATT	60.449	44.000	10.26	0.00	0.00	2.17
757	779	1.747206	GCGGATGTAGCCAAGTGGATT	60.747	52.381	0.18	0.00	37.39	3.01
773	795	4.227300	AGTGGATTAAGGCAGTGGATTGTA	59.773	41.667	0.00	0.00	0.00	2.41
928	953	7.492352	TTTTCCTTTTCCTAGTTCTTCTTCG	57.508	36.000	0.00	0.00	0.00	3.79
936	961	2.086054	AGTTCTTCTTCGAAGCGCAT	57.914	45.000	20.56	0.00	0.00	4.73
1117	1143	2.090999	ACCCCAACATTACCCACTTGTT	60.091	45.455	0.00	0.00	34.03	2.83
1126	1152	2.413310	ACCCACTTGTTCGACTGTTT	57.587	45.000	0.00	0.00	0.00	2.83
1168	1194	2.361085	ACTTACCTCCCCAGATGGTT	57.639	50.000	0.00	0.00	35.48	3.67
1172	1198	1.821088	ACCTCCCCAGATGGTTATCC	58.179	55.000	0.00	0.00	33.64	2.59
1180	1206	4.166144	CCCCAGATGGTTATCCTAAAGTGT	59.834	45.833	0.00	0.00	33.64	3.55
1181	1207	5.340027	CCCCAGATGGTTATCCTAAAGTGTT	60.340	44.000	0.00	0.00	33.64	3.32
1203	1229	5.975693	TCGATTTACCCTCTTTTGCAATT	57.024	34.783	0.00	0.00	0.00	2.32
1211	1237	4.022329	ACCCTCTTTTGCAATTAGTTTCGG	60.022	41.667	0.00	3.22	0.00	4.30
1360	1388	6.461509	CCAAACTGTACAAGCTTCTTCCAAAT	60.462	38.462	0.00	0.00	0.00	2.32
1442	1470	7.069826	TCATATGATGAAGTACCACATGAGTGA	59.930	37.037	0.00	5.57	41.42	3.41
1516	1544	2.028130	CATCCTAGGTCTCTGCGTTCT	58.972	52.381	9.08	0.00	0.00	3.01
1661	1689	4.773323	ACCACTGCTTAGCTTTCAATTC	57.227	40.909	5.60	0.00	0.00	2.17
1668	1696	3.871594	GCTTAGCTTTCAATTCGCCTCTA	59.128	43.478	0.00	0.00	0.00	2.43
1703	1731	2.262637	TGTGAATAACCCGTCCTCCTT	58.737	47.619	0.00	0.00	0.00	3.36
1969	1997	3.134574	TCAAACCGCACTCAAAGGTAT	57.865	42.857	0.00	0.00	37.26	2.73
2108	2136	5.029807	TGTATGCATTTCGATTAGGGTCA	57.970	39.130	3.54	0.00	0.00	4.02
2181	2209	6.946229	AATCTATTTTACAGTATAGGCGCG	57.054	37.500	0.00	0.00	0.00	6.86
2263	2291	1.431488	CGGTGCCGTCCATGAATCAG	61.431	60.000	1.93	0.00	34.35	2.90
2272	2300	5.239306	GCCGTCCATGAATCAGATTATTTCA	59.761	40.000	0.00	0.00	34.18	2.69
2299	2327	6.547510	GGATTGGATTTAACTTGCCTGTCTAT	59.452	38.462	0.00	0.00	0.00	1.98
2462	2491	3.117550	TGCATTGTATGGCCCAGAATAGT	60.118	43.478	0.00	0.00	0.00	2.12
2802	2832	4.591072	GGATAGAGAGCCAGTTCCAATAGT	59.409	45.833	0.00	0.00	0.00	2.12
2892	2922	0.523335	GCGCTTTAACCATTCAGCCG	60.523	55.000	0.00	0.00	0.00	5.52
2915	2945	3.459227	TGGATGCTTAACAGGGATCATCA	59.541	43.478	0.00	0.00	34.04	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	4.825546	GTTGATGATATCAGCCCAAGTG	57.174	45.455	17.90	0.0	40.94	3.16
512	516	4.563140	AACAATAGTAACATGGTCCCGT	57.437	40.909	0.00	0.0	0.00	5.28
521	525	7.974504	AGGAGGAGAAAGAAACAATAGTAACA	58.025	34.615	0.00	0.0	0.00	2.41
623	644	7.669722	ACATAGAATGGCACTCTTTAAAAAGGA	59.330	33.333	2.86	0.0	34.00	3.36
639	660	6.694844	CGATCGAGATATTGGACATAGAATGG	59.305	42.308	10.26	0.0	33.60	3.16
728	750	0.685097	GCTACATCCGCCCCTTATCA	59.315	55.000	0.00	0.0	0.00	2.15
757	779	5.186256	TGGATTTACAATCCACTGCCTTA	57.814	39.130	13.25	0.0	42.81	2.69
928	953	1.334869	CTTGGGGTTATCATGCGCTTC	59.665	52.381	9.73	0.0	0.00	3.86
936	961	1.076350	CACAACCCCTTGGGGTTATCA	59.924	52.381	34.97	0.0	42.24	2.15
1045	1071	6.351966	GGATCTAAGTGTTGGCTAGGTAAACT	60.352	42.308	0.00	0.0	0.00	2.66
1117	1143	4.272504	CCAAAACTGCTTAGAAACAGTCGA	59.727	41.667	0.00	0.0	46.17	4.20
1126	1152	7.686434	AGTTTAGTATCCCAAAACTGCTTAGA	58.314	34.615	0.00	0.0	40.85	2.10
1151	1177	3.050564	AGGATAACCATCTGGGGAGGTAA	60.051	47.826	0.54	0.0	42.91	2.85
1152	1178	2.527057	AGGATAACCATCTGGGGAGGTA	59.473	50.000	0.54	0.0	42.91	3.08
1168	1194	7.343833	AGAGGGTAAATCGAACACTTTAGGATA	59.656	37.037	0.00	0.0	28.36	2.59
1172	1198	7.668525	AAAGAGGGTAAATCGAACACTTTAG	57.331	36.000	0.00	0.0	28.36	1.85
1180	1206	5.975693	ATTGCAAAAGAGGGTAAATCGAA	57.024	34.783	1.71	0.0	0.00	3.71
1181	1207	5.975693	AATTGCAAAAGAGGGTAAATCGA	57.024	34.783	1.71	0.0	0.00	3.59
1360	1388	8.459635	GTCATATACATCTAGAAAGCCGTATGA	58.540	37.037	0.00	4.5	0.00	2.15
1455	1483	2.348872	CGATTCGGCAGATTTGGATTCG	60.349	50.000	0.00	0.0	0.00	3.34
1516	1544	5.164620	TGAAGAACATAAGCCAGATGACA	57.835	39.130	0.00	0.0	0.00	3.58
1661	1689	6.692681	CACATTTAATTTGATGGTTAGAGGCG	59.307	38.462	5.92	0.0	0.00	5.52
1668	1696	9.665719	GGGTTATTCACATTTAATTTGATGGTT	57.334	29.630	0.00	0.0	0.00	3.67
1703	1731	0.387565	GCGCCCCTTGTTTCAAAGAA	59.612	50.000	0.00	0.0	0.00	2.52
1801	1829	6.017605	CAGCAAGTGATTGAGTTCAGTAGTTT	60.018	38.462	0.00	0.0	0.00	2.66
1931	1959	7.215007	GCGGTTTGAACTATTGATTTACGTAAC	59.785	37.037	7.70	0.0	0.00	2.50
1969	1997	5.597430	TCCTATATCAATGGGAAATGCCA	57.403	39.130	0.00	0.0	39.63	4.92
2067	2095	8.203485	TGCATACATTTGTCTCATACACTATGA	58.797	33.333	0.00	0.0	42.56	2.15
2108	2136	9.529823	TCTGGTAGAATCGTAACCATAGAATAT	57.470	33.333	5.80	0.0	42.23	1.28
2181	2209	1.903183	GCATAGAGGGGGAGGTCATAC	59.097	57.143	0.00	0.0	0.00	2.39
2272	2300	5.025453	ACAGGCAAGTTAAATCCAATCCAT	58.975	37.500	0.00	0.0	0.00	3.41
2285	2313	3.073274	GGAACCATAGACAGGCAAGTT	57.927	47.619	0.00	0.0	0.00	2.66
2892	2922	3.281727	TGATCCCTGTTAAGCATCCAC	57.718	47.619	0.00	0.0	0.00	4.02
2960	2990	8.342634	TCTCGGGATATTTTCGATTTCATTTTC	58.657	33.333	0.00	0.0	32.32	2.29
2980	3010	1.806542	CCGAATATTTGCCATCTCGGG	59.193	52.381	0.40	0.0	41.61	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.