AutoCloner

Multiple sequence alignment - TraesCS5B01G033500

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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	TraesCS5B01G033500	chr5B	100.000	4279	0	0	1	4279	36719490	36723768	0.000000e+00	7902.0
1	TraesCS5B01G033500	chr5B	94.047	3511	145	24	818	4279	535111100	535114595	0.000000e+00	5267.0
2	TraesCS5B01G033500	chr5B	93.863	2379	78	18	827	3187	36767815	36765487	0.000000e+00	3522.0
3	TraesCS5B01G033500	chr5B	90.758	844	54	3	1	834	36771991	36771162	0.000000e+00	1105.0
4	TraesCS5B01G033500	chr5B	97.710	131	3	0	3921	4051	36765090	36764960	4.310000e-55	226.0
5	TraesCS5B01G033500	chr5B	93.919	148	8	1	3748	3895	36765233	36765087	5.570000e-54	222.0
6	TraesCS5B01G033500	chr5B	88.356	146	5	3	3205	3348	36765366	36765231	9.520000e-37	165.0
7	TraesCS5B01G033500	chr5B	97.500	80	2	0	4151	4230	36764965	36764886	2.080000e-28	137.0
8	TraesCS5B01G033500	chr5A	90.648	4213	248	56	148	4279	30403684	30407831	0.000000e+00	5463.0
9	TraesCS5B01G033500	chr5A	94.131	3510	143	21	818	4279	555770530	555774024	0.000000e+00	5282.0
10	TraesCS5B01G033500	chr5D	94.361	3511	140	21	818	4279	440160183	440163684	0.000000e+00	5334.0
11	TraesCS5B01G033500	chr5D	94.037	3522	117	37	812	4279	42016656	42020138	0.000000e+00	5254.0
12	TraesCS5B01G033500	chr5D	88.020	1561	131	19	275	1793	42054072	42052526	0.000000e+00	1796.0
13	TraesCS5B01G033500	chr5D	95.968	620	16	3	1818	2437	42052528	42051918	0.000000e+00	998.0
14	TraesCS5B01G033500	chr5D	89.744	741	61	5	1	730	42015892	42016628	0.000000e+00	933.0
15	TraesCS5B01G033500	chr3A	86.885	122	16	0	281	402	695644623	695644502	2.080000e-28	137.0
16	TraesCS5B01G033500	chr2D	86.885	122	16	0	281	402	272808010	272808131	2.080000e-28	137.0
17	TraesCS5B01G033500	chrUn	86.066	122	17	0	281	402	392770448	392770327	9.650000e-27	132.0
18	TraesCS5B01G033500	chr7B	86.066	122	17	0	281	402	622433732	622433853	9.650000e-27	132.0
19	TraesCS5B01G033500	chr3D	86.066	122	17	0	281	402	581040656	581040535	9.650000e-27	132.0
20	TraesCS5B01G033500	chr3D	86.066	122	17	0	281	402	589259290	589259411	9.650000e-27	132.0
21	TraesCS5B01G033500	chr3D	95.122	41	2	0	602	642	45963479	45963519	9.930000e-07	65.8

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	TraesCS5B01G033500	chr5B	36719490	36723768	4278	False	7902.000000	7902	100.000000	1	4279	1	chr5B.!!$F1	4278
1	TraesCS5B01G033500	chr5B	535111100	535114595	3495	False	5267.000000	5267	94.047000	818	4279	1	chr5B.!!$F2	3461
2	TraesCS5B01G033500	chr5B	36764886	36771991	7105	True	896.166667	3522	93.684333	1	4230	6	chr5B.!!$R1	4229
3	TraesCS5B01G033500	chr5A	30403684	30407831	4147	False	5463.000000	5463	90.648000	148	4279	1	chr5A.!!$F1	4131
4	TraesCS5B01G033500	chr5A	555770530	555774024	3494	False	5282.000000	5282	94.131000	818	4279	1	chr5A.!!$F2	3461
5	TraesCS5B01G033500	chr5D	440160183	440163684	3501	False	5334.000000	5334	94.361000	818	4279	1	chr5D.!!$F1	3461
6	TraesCS5B01G033500	chr5D	42015892	42020138	4246	False	3093.500000	5254	91.890500	1	4279	2	chr5D.!!$F2	4278
7	TraesCS5B01G033500	chr5D	42051918	42054072	2154	True	1397.000000	1796	91.994000	275	2437	2	chr5D.!!$R1	2162

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	Hairpin	End Stability	Orientation
168	170	0.321653	CCAAAGCCGCTGAGGTAGTT	60.322	55.000	0.00	43.70	2.24	F
1109	4547	0.812549	GGAGAACTCGTCCAGGAGAC	59.187	60.000	3.32	42.54	3.36	F
1593	5031	1.081242	GGCGGTGAATGTGCTTGTG	60.081	57.895	0.00	0.00	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1616	5054	0.669318	CCGGTCGCTAAACTCAAGCA	60.669	55.0	40.08	3.91	R
2030	5468	0.700564	AATCTCCTTTGCCTCAGCCA	59.299	50.0	38.69	4.75	R
3462	7054	0.417437	TCCCTCCATTGTCTCCTCCA	59.583	55.0	0.00	3.86	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
62	63	1.823295	ACAGGCACGACAACTGTCT	59.177	52.632	8.16	0.00	41.27	3.41
91	92	2.774234	TCTATGAAGAAGCCCAGGAAGG	59.226	50.000	0.00	0.00	37.03	3.46
138	139	0.394216	CCCCCTGCACAAATCGATCA	60.394	55.000	0.00	0.00	0.00	2.92
168	170	0.321653	CCAAAGCCGCTGAGGTAGTT	60.322	55.000	0.00	0.00	43.70	2.24
186	188	1.067821	GTTGCCGGAGACATAGGAGAG	59.932	57.143	5.05	0.00	0.00	3.20
229	234	1.064906	CAGGAGGGCATCATCACTGTT	60.065	52.381	0.08	0.00	0.00	3.16
326	332	3.137728	ACCCACTTTGTACTTTGCTACCT	59.862	43.478	0.00	0.00	0.00	3.08
337	343	4.959723	ACTTTGCTACCTAACGTTTACCA	58.040	39.130	5.91	0.00	0.00	3.25
357	363	4.594920	ACCATAGGCATGATAACTAGCACT	59.405	41.667	0.00	0.00	33.67	4.40
451	457	4.125695	GACCTCGTAACCGGCGCT	62.126	66.667	7.64	0.00	33.95	5.92
543	558	2.572095	TTATCCCACGAGCCAGCACG	62.572	60.000	7.93	7.93	36.19	5.34
587	602	2.098233	CATCCCCGAACACGAACCG	61.098	63.158	0.00	0.00	0.00	4.44
598	613	1.227556	ACGAACCGCACTGCTCTTT	60.228	52.632	0.00	0.00	0.00	2.52
712	740	7.272978	TGTTAGAGTTGCTCTTAAAAGACAGT	58.727	34.615	3.87	0.00	41.50	3.55
724	777	3.409026	AAAGACAGTGCAAGACTAGGG	57.591	47.619	0.00	0.00	31.73	3.53
764	817	5.128008	AGTTGAAGATGGAGAAGCTAGGTAC	59.872	44.000	0.00	0.00	0.00	3.34
787	840	3.888930	TGTTTCTCCTTCACATGGGTTTC	59.111	43.478	0.00	0.00	0.00	2.78
834	4242	5.491982	GAGAAGTGGAGATCCTAGCAAAAA	58.508	41.667	0.00	0.00	36.82	1.94
836	4244	4.227864	AGTGGAGATCCTAGCAAAAAGG	57.772	45.455	0.00	0.00	36.82	3.11
843	4251	6.372937	GGAGATCCTAGCAAAAAGGTATATGC	59.627	42.308	0.00	0.00	39.06	3.14
979	4399	1.247567	CCACCAAACGCATTTCCTCT	58.752	50.000	0.00	0.00	0.00	3.69
1109	4547	0.812549	GGAGAACTCGTCCAGGAGAC	59.187	60.000	3.32	0.00	42.54	3.36
1467	4905	2.343758	GGGACTCAGCAGTTCGCA	59.656	61.111	0.00	0.00	46.13	5.10
1593	5031	1.081242	GGCGGTGAATGTGCTTGTG	60.081	57.895	0.00	0.00	0.00	3.33
1599	5037	1.518102	GTGAATGTGCTTGTGTTTGCG	59.482	47.619	0.00	0.00	0.00	4.85
1616	5054	4.778143	GGGGCGCATCGACAAGGT	62.778	66.667	10.83	0.00	36.10	3.50
1641	5079	2.202824	TTTAGCGACCGGATGCGG	60.203	61.111	25.41	25.41	35.87	5.69
1735	5173	1.986882	TGAGGCGCTAGAGATGATCA	58.013	50.000	7.64	0.00	0.00	2.92
2029	5467	2.644299	TCTTTCTGCTTGAATGGGAGGA	59.356	45.455	0.00	0.00	34.24	3.71
2030	5468	3.267812	TCTTTCTGCTTGAATGGGAGGAT	59.732	43.478	0.00	0.00	34.24	3.24
2031	5469	2.723322	TCTGCTTGAATGGGAGGATG	57.277	50.000	0.00	0.00	0.00	3.51
2032	5470	1.213678	TCTGCTTGAATGGGAGGATGG	59.786	52.381	0.00	0.00	0.00	3.51
2033	5471	0.396139	TGCTTGAATGGGAGGATGGC	60.396	55.000	0.00	0.00	0.00	4.40
2034	5472	0.106318	GCTTGAATGGGAGGATGGCT	60.106	55.000	0.00	0.00	0.00	4.75
2035	5473	1.688772	CTTGAATGGGAGGATGGCTG	58.311	55.000	0.00	0.00	0.00	4.85
2036	5474	1.213678	CTTGAATGGGAGGATGGCTGA	59.786	52.381	0.00	0.00	0.00	4.26
2037	5475	0.841961	TGAATGGGAGGATGGCTGAG	59.158	55.000	0.00	0.00	0.00	3.35
2038	5476	0.110104	GAATGGGAGGATGGCTGAGG	59.890	60.000	0.00	0.00	0.00	3.86
2039	5477	2.004408	AATGGGAGGATGGCTGAGGC	62.004	60.000	0.00	0.00	37.82	4.70
2040	5478	3.092511	GGGAGGATGGCTGAGGCA	61.093	66.667	12.23	12.23	43.52	4.75
2041	5479	2.683465	GGGAGGATGGCTGAGGCAA	61.683	63.158	14.16	0.00	42.43	4.52
2042	5480	1.304282	GGAGGATGGCTGAGGCAAA	59.696	57.895	14.16	0.00	42.43	3.68
2043	5481	0.750911	GGAGGATGGCTGAGGCAAAG	60.751	60.000	14.16	0.00	42.43	2.77
2044	5482	0.750911	GAGGATGGCTGAGGCAAAGG	60.751	60.000	14.16	0.00	42.43	3.11
2364	5818	7.253422	GGAAACTAAAGGAATCATGTGATGTG	58.747	38.462	0.00	0.00	34.49	3.21
2445	5899	2.290641	CCATGCGTTATGTAAGGAAGGC	59.709	50.000	0.00	0.00	37.06	4.35
2446	5900	2.032680	TGCGTTATGTAAGGAAGGCC	57.967	50.000	0.00	0.00	35.98	5.19
3123	6577	9.634021	AAGTTTTTAGAAAGAGGTCTTCTGAAT	57.366	29.630	0.00	0.00	35.91	2.57
3124	6578	9.278978	AGTTTTTAGAAAGAGGTCTTCTGAATC	57.721	33.333	0.00	0.00	35.91	2.52
3195	6761	7.709947	CATGTATTTATGACATGCTGGAAAGT	58.290	34.615	0.00	0.00	45.52	2.66
3213	6781	8.978874	TGGAAAGTAACAGATGCATTACATAT	57.021	30.769	0.00	0.00	39.84	1.78
3604	7196	2.676121	CGGCTGGCATTGTGGGAA	60.676	61.111	1.08	0.00	0.00	3.97
3688	7280	1.291877	GCCTCGTCACGCAGATGTTT	61.292	55.000	0.00	0.00	34.73	2.83
3778	7370	3.321111	CCTACGGCATCATGGTAACTAGT	59.679	47.826	0.00	0.00	37.61	2.57
3780	7372	3.793559	ACGGCATCATGGTAACTAGTTC	58.206	45.455	12.39	4.04	37.61	3.01
3781	7373	3.451178	ACGGCATCATGGTAACTAGTTCT	59.549	43.478	12.39	0.00	37.61	3.01
3787	7380	2.649331	TGGTAACTAGTTCTGCTCGC	57.351	50.000	12.39	0.00	37.61	5.03
3809	7402	6.932960	TCGCTCTTGCACTATGTAGTATAGTA	59.067	38.462	0.00	0.00	39.64	1.82
3847	7440	3.265070	ACGACGTCTTCTCACTTGTAC	57.735	47.619	14.70	0.00	0.00	2.90
4005	7628	4.382147	GCTTTCTTCTACTGGTACTCTGGG	60.382	50.000	0.00	0.00	0.00	4.45
4155	7778	3.632080	ATCGTCAACCCCGTGGCA	61.632	61.111	0.00	0.00	33.59	4.92

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
60	61	5.491982	GGCTTCTTCATAGAGTTTCCAAGA	58.508	41.667	0.00	0.00	0.00	3.02
62	63	4.042809	TGGGCTTCTTCATAGAGTTTCCAA	59.957	41.667	0.00	0.00	0.00	3.53
112	113	0.116143	TTTGTGCAGGGGGCCTAATT	59.884	50.000	0.84	0.00	43.89	1.40
144	146	1.526887	CTCAGCGGCTTTGGGGATA	59.473	57.895	0.00	0.00	0.00	2.59
168	170	0.468214	CCTCTCCTATGTCTCCGGCA	60.468	60.000	0.00	0.00	0.00	5.69
186	188	4.381411	GCTATGACAATGAAGGAGGTACC	58.619	47.826	2.73	2.73	39.35	3.34
305	311	3.751518	AGGTAGCAAAGTACAAAGTGGG	58.248	45.455	0.00	0.00	0.00	4.61
326	332	7.502696	AGTTATCATGCCTATGGTAAACGTTA	58.497	34.615	0.00	0.00	40.55	3.18
337	343	4.840680	TGGAGTGCTAGTTATCATGCCTAT	59.159	41.667	0.00	0.00	0.00	2.57
357	363	1.679944	CGGGAAGGACGTACTACTGGA	60.680	57.143	0.00	0.00	0.00	3.86
451	457	2.789213	TCTCGATTTTGTCAATGGGCA	58.211	42.857	0.00	0.00	0.00	5.36
543	558	2.359850	TTGCAGCCCATGACGGTC	60.360	61.111	0.00	0.00	0.00	4.79
587	602	1.508632	TCGTGGTTAAAGAGCAGTGC	58.491	50.000	7.13	7.13	36.22	4.40
598	613	3.055021	TGTTGCCTCCATAATCGTGGTTA	60.055	43.478	0.00	0.00	40.27	2.85
689	717	6.202954	GCACTGTCTTTTAAGAGCAACTCTAA	59.797	38.462	0.00	0.00	40.28	2.10
712	740	0.835971	TGCTCCACCCTAGTCTTGCA	60.836	55.000	0.00	0.00	0.00	4.08
724	777	3.206150	TCAACTCTTTTGTCTGCTCCAC	58.794	45.455	0.00	0.00	0.00	4.02
764	817	3.146104	ACCCATGTGAAGGAGAAACAG	57.854	47.619	0.00	0.00	0.00	3.16
787	840	5.248087	CAGTAGTCGTACGATTTTGCAATG	58.752	41.667	22.57	7.73	33.97	2.82
834	4242	1.121407	TCAGGGCAGCGCATATACCT	61.121	55.000	11.47	6.76	0.00	3.08
836	4244	1.284982	CGTCAGGGCAGCGCATATAC	61.285	60.000	11.47	3.18	0.00	1.47
1467	4905	2.158986	GCTGTATGAGAGCATGAGGTGT	60.159	50.000	0.00	0.00	36.40	4.16
1599	5037	4.778143	ACCTTGTCGATGCGCCCC	62.778	66.667	4.18	0.00	0.00	5.80
1616	5054	0.669318	CCGGTCGCTAAACTCAAGCA	60.669	55.000	0.00	0.00	40.08	3.91
1735	5173	2.899256	ACCCATTTTGCAGCATTACACT	59.101	40.909	0.00	0.00	0.00	3.55
1832	5270	1.925255	TCCTCATCCTCCCAAGCAAAT	59.075	47.619	0.00	0.00	0.00	2.32
2029	5467	0.924823	ATCTCCTTTGCCTCAGCCAT	59.075	50.000	0.00	0.00	38.69	4.40
2030	5468	0.700564	AATCTCCTTTGCCTCAGCCA	59.299	50.000	0.00	0.00	38.69	4.75
2031	5469	1.101331	CAATCTCCTTTGCCTCAGCC	58.899	55.000	0.00	0.00	38.69	4.85
2032	5470	1.831580	ACAATCTCCTTTGCCTCAGC	58.168	50.000	0.00	0.00	40.48	4.26
2033	5471	4.394300	CACTTACAATCTCCTTTGCCTCAG	59.606	45.833	0.00	0.00	0.00	3.35
2034	5472	4.041567	TCACTTACAATCTCCTTTGCCTCA	59.958	41.667	0.00	0.00	0.00	3.86
2035	5473	4.579869	TCACTTACAATCTCCTTTGCCTC	58.420	43.478	0.00	0.00	0.00	4.70
2036	5474	4.287067	TCTCACTTACAATCTCCTTTGCCT	59.713	41.667	0.00	0.00	0.00	4.75
2037	5475	4.579869	TCTCACTTACAATCTCCTTTGCC	58.420	43.478	0.00	0.00	0.00	4.52
2038	5476	5.877012	TCATCTCACTTACAATCTCCTTTGC	59.123	40.000	0.00	0.00	0.00	3.68
2039	5477	7.986320	AGATCATCTCACTTACAATCTCCTTTG	59.014	37.037	0.00	0.00	0.00	2.77
2040	5478	8.088463	AGATCATCTCACTTACAATCTCCTTT	57.912	34.615	0.00	0.00	0.00	3.11
2041	5479	7.673641	AGATCATCTCACTTACAATCTCCTT	57.326	36.000	0.00	0.00	0.00	3.36
2042	5480	7.288810	GAGATCATCTCACTTACAATCTCCT	57.711	40.000	10.02	0.00	42.90	3.69
3119	6573	8.225603	AGCTTACTTTTCTTGTTTCAGATTCA	57.774	30.769	0.00	0.00	0.00	2.57
3123	6577	8.076178	GCAATAGCTTACTTTTCTTGTTTCAGA	58.924	33.333	0.00	0.00	37.91	3.27
3124	6578	8.220618	GCAATAGCTTACTTTTCTTGTTTCAG	57.779	34.615	0.00	0.00	37.91	3.02
3183	6749	3.441222	TGCATCTGTTACTTTCCAGCATG	59.559	43.478	0.00	0.00	0.00	4.06
3184	6750	3.689347	TGCATCTGTTACTTTCCAGCAT	58.311	40.909	0.00	0.00	0.00	3.79
3187	6753	6.741992	TGTAATGCATCTGTTACTTTCCAG	57.258	37.500	0.00	0.00	33.17	3.86
3189	6755	9.669353	CAATATGTAATGCATCTGTTACTTTCC	57.331	33.333	0.00	0.00	38.94	3.13
3191	6757	9.407380	TCCAATATGTAATGCATCTGTTACTTT	57.593	29.630	0.00	0.00	38.94	2.66
3192	6758	8.978874	TCCAATATGTAATGCATCTGTTACTT	57.021	30.769	0.00	0.72	38.94	2.24
3195	6761	8.352201	GCTTTCCAATATGTAATGCATCTGTTA	58.648	33.333	0.00	0.00	38.94	2.41
3213	6781	6.357367	AGAAGAAAGTGAGTAAGCTTTCCAA	58.643	36.000	3.20	0.00	46.92	3.53
3458	7050	2.355513	CCTCCATTGTCTCCTCCACTTG	60.356	54.545	0.00	0.00	0.00	3.16
3462	7054	0.417437	TCCCTCCATTGTCTCCTCCA	59.583	55.000	0.00	0.00	0.00	3.86
3557	7149	2.356278	GAATGGCACTGGCTCCCA	59.644	61.111	3.97	0.00	40.87	4.37
3565	7157	2.029288	CAGCACGTCGAATGGCACT	61.029	57.895	0.00	0.00	0.00	4.40
3688	7280	1.152777	CTCACCAAGGTGGCCAACA	60.153	57.895	25.90	0.00	42.67	3.33
3778	7370	0.603065	TAGTGCAAGAGCGAGCAGAA	59.397	50.000	0.00	0.00	46.23	3.02
3780	7372	0.928922	CATAGTGCAAGAGCGAGCAG	59.071	55.000	0.00	0.00	46.23	4.24
3781	7373	0.247460	ACATAGTGCAAGAGCGAGCA	59.753	50.000	0.00	0.00	46.23	4.26
3809	7402	3.002348	GTCGTTTCTAAGCAGCACAAAGT	59.998	43.478	0.00	0.00	0.00	2.66
4155	7778	0.813184	GCACAGCAAGCACCATGTAT	59.187	50.000	0.00	0.00	0.00	2.29

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.