AutoCloner

Multiple sequence alignment - TraesCS7D01G406900

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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	TraesCS7D01G406900	chr7D	100.000	4229	0	0	1	4229	524313913	524318141	0.000000	7810.0
1	TraesCS7D01G406900	chr7D	97.651	809	15	3	1	808	524306259	524307064	0.000000	1386.0
2	TraesCS7D01G406900	chr7D	97.528	809	19	1	1	809	524251530	524252337	0.000000	1382.0
3	TraesCS7D01G406900	chr7D	95.802	810	32	2	1	809	562199092	562199900	0.000000	1306.0
4	TraesCS7D01G406900	chr7D	89.704	709	72	1	951	1659	523544636	523545343	0.000000	904.0
5	TraesCS7D01G406900	chr7D	97.297	37	1	0	818	854	562201560	562201596	0.000004	63.9
6	TraesCS7D01G406900	chr7A	95.550	3416	121	12	827	4229	604379160	604382557	0.000000	5437.0
7	TraesCS7D01G406900	chr7A	94.815	810	39	2	1	809	604252399	604253206	0.000000	1260.0
8	TraesCS7D01G406900	chr7A	94.314	809	44	1	1	809	604257800	604258606	0.000000	1238.0
9	TraesCS7D01G406900	chr7A	93.820	809	48	2	1	809	604263180	604263986	0.000000	1216.0
10	TraesCS7D01G406900	chr7A	93.596	812	49	3	1	812	604304650	604305458	0.000000	1208.0
11	TraesCS7D01G406900	chr7B	95.442	3379	108	19	867	4224	560513760	560517113	0.000000	5345.0
12	TraesCS7D01G406900	chr7B	93.742	815	37	7	1	809	560503608	560504414	0.000000	1210.0
13	TraesCS7D01G406900	chr7B	87.671	584	71	1	1076	1659	559630150	559630732	0.000000	678.0
14	TraesCS7D01G406900	chr6A	96.919	1428	28	7	1	1413	74150757	74152183	0.000000	2379.0

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	TraesCS7D01G406900	chr7D	524313913	524318141	4228	False	7810.00	7810	100.0000	1	4229	1	chr7D.!!$F4	4228
1	TraesCS7D01G406900	chr7D	524306259	524307064	805	False	1386.00	1386	97.6510	1	808	1	chr7D.!!$F3	807
2	TraesCS7D01G406900	chr7D	524251530	524252337	807	False	1382.00	1382	97.5280	1	809	1	chr7D.!!$F2	808
3	TraesCS7D01G406900	chr7D	523544636	523545343	707	False	904.00	904	89.7040	951	1659	1	chr7D.!!$F1	708
4	TraesCS7D01G406900	chr7D	562199092	562201596	2504	False	684.95	1306	96.5495	1	854	2	chr7D.!!$F5	853
5	TraesCS7D01G406900	chr7A	604379160	604382557	3397	False	5437.00	5437	95.5500	827	4229	1	chr7A.!!$F5	3402
6	TraesCS7D01G406900	chr7A	604252399	604253206	807	False	1260.00	1260	94.8150	1	809	1	chr7A.!!$F1	808
7	TraesCS7D01G406900	chr7A	604257800	604258606	806	False	1238.00	1238	94.3140	1	809	1	chr7A.!!$F2	808
8	TraesCS7D01G406900	chr7A	604263180	604263986	806	False	1216.00	1216	93.8200	1	809	1	chr7A.!!$F3	808
9	TraesCS7D01G406900	chr7A	604304650	604305458	808	False	1208.00	1208	93.5960	1	812	1	chr7A.!!$F4	811
10	TraesCS7D01G406900	chr7B	560513760	560517113	3353	False	5345.00	5345	95.4420	867	4224	1	chr7B.!!$F3	3357
11	TraesCS7D01G406900	chr7B	560503608	560504414	806	False	1210.00	1210	93.7420	1	809	1	chr7B.!!$F2	808
12	TraesCS7D01G406900	chr7B	559630150	559630732	582	False	678.00	678	87.6710	1076	1659	1	chr7B.!!$F1	583
13	TraesCS7D01G406900	chr6A	74150757	74152183	1426	False	2379.00	2379	96.9190	1	1413	1	chr6A.!!$F1	1412

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
579	585	2.132517	TTTCACGTACGAGCGAGCCA	62.133	55.0	24.41	0.0	35.59	4.75	F
1631	3312	0.036388	TGGACTGGTTTGATCTCGGC	60.036	55.0	0.00	0.0	0.00	5.54	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1659	3340	0.961019	GGTTGAAGCAATCCACAGCA	59.039	50.0	0.00	0.0	0.00	4.41	R
3459	5144	0.687354	CAGTGAGCCAACTGGTAGGT	59.313	55.0	8.23	0.0	43.22	3.08	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
203	204	4.585526	GACGGGGATGCATCGCGA	62.586	66.667	30.44	13.09	42.00	5.87
390	391	3.643320	CACCTCTACCCTCTCATGCATTA	59.357	47.826	0.00	0.00	0.00	1.90
410	411	6.575201	GCATTATTGAGCAAATAACGAGCTAC	59.425	38.462	6.72	0.00	42.22	3.58
579	585	2.132517	TTTCACGTACGAGCGAGCCA	62.133	55.000	24.41	0.00	35.59	4.75
825	2486	6.035217	CAGCATAGAAGATGAGGTGATATCG	58.965	44.000	0.00	0.00	0.00	2.92
955	2636	8.636213	AGCCCACTTCATCATCATAAAATAAAG	58.364	33.333	0.00	0.00	0.00	1.85
1425	3106	4.819761	TCTGCCGTGCCGCTCATC	62.820	66.667	0.00	0.00	0.00	2.92
1626	3307	1.464997	GTCGCTTGGACTGGTTTGATC	59.535	52.381	0.00	0.00	42.62	2.92
1631	3312	0.036388	TGGACTGGTTTGATCTCGGC	60.036	55.000	0.00	0.00	0.00	5.54
1632	3313	0.036388	GGACTGGTTTGATCTCGGCA	60.036	55.000	0.00	0.00	0.00	5.69
1647	3328	3.929948	GCATACTCGCGTGCTGGC	61.930	66.667	11.71	7.37	38.30	4.85
1701	3382	0.171679	TGCTTTCTGATGGCATTGCG	59.828	50.000	0.00	0.00	0.00	4.85
1773	3454	3.382546	AGGATTTGGATTTTGGATGCTCG	59.617	43.478	0.00	0.00	0.00	5.03
1794	3475	2.345760	GCACATGCTGGTTGGGGAG	61.346	63.158	0.00	0.00	38.21	4.30
1796	3477	0.679002	CACATGCTGGTTGGGGAGAG	60.679	60.000	0.00	0.00	0.00	3.20
1807	3488	0.621571	TGGGGAGAGGAGGATGTTGG	60.622	60.000	0.00	0.00	0.00	3.77
1813	3494	1.905215	AGAGGAGGATGTTGGTGAGTG	59.095	52.381	0.00	0.00	0.00	3.51
1817	3498	2.613977	GGAGGATGTTGGTGAGTGACAG	60.614	54.545	0.00	0.00	0.00	3.51
1983	3664	0.937304	TTGCACGCTCTCTGTTTGAC	59.063	50.000	0.00	0.00	0.00	3.18
2469	4150	1.770658	TCATGCCTACTGGATGAAGGG	59.229	52.381	0.00	0.00	31.65	3.95
2478	4159	0.535335	TGGATGAAGGGCGTCTGTAC	59.465	55.000	0.00	0.00	32.91	2.90
2686	4367	1.339055	ACCTAGCTCGAAATGCTGCAA	60.339	47.619	6.36	0.00	41.32	4.08
2841	4522	2.009042	GCAGGTTACAGCTCGATTGCT	61.009	52.381	0.00	0.00	45.18	3.91
2852	4533	3.818787	GATTGCTGTGGCTGGGCG	61.819	66.667	0.00	0.00	39.59	6.13
2914	4595	8.720562	CACGCATAATGGAGATTATTGTAATGA	58.279	33.333	0.00	0.00	33.21	2.57
3054	4735	2.234300	CCATTGCATTTGGCCTCATC	57.766	50.000	3.32	0.00	43.89	2.92
3391	5073	7.880713	TGTGCCATTTAAGTTAGAGTGATTACA	59.119	33.333	0.00	0.00	0.00	2.41
3413	5095	6.047870	ACACATATTCATCTTCTGAGAGCAC	58.952	40.000	0.00	0.00	34.85	4.40
3459	5144	5.696270	GTCAGTTGTGTCACACTGATGAATA	59.304	40.000	26.64	11.70	37.99	1.75
3460	5145	5.696270	TCAGTTGTGTCACACTGATGAATAC	59.304	40.000	23.16	10.73	34.10	1.89
3461	5146	4.997395	AGTTGTGTCACACTGATGAATACC	59.003	41.667	9.90	0.00	35.11	2.73
3462	5147	4.890158	TGTGTCACACTGATGAATACCT	57.110	40.909	9.90	0.00	35.11	3.08
3499	5184	3.265221	TGGAAATGAGCTCCTCTTCACAT	59.735	43.478	12.15	0.00	33.77	3.21
3603	5288	0.901580	ATGGCTGCCCTTGTTTCCTG	60.902	55.000	17.53	0.00	0.00	3.86
3640	5326	5.982516	GTCACTTGTTGCCATGTTAATGAAA	59.017	36.000	0.00	0.00	35.67	2.69
3671	5358	2.564062	CGGTGACTCCAAGGGTAAGTAA	59.436	50.000	0.00	0.00	35.57	2.24
3788	5479	1.429930	TGTAGACAAAGGAGGTGGCA	58.570	50.000	0.00	0.00	0.00	4.92
3964	5656	2.368221	GCTGATAGATGCTGGGAGAAGT	59.632	50.000	0.00	0.00	0.00	3.01
3965	5657	3.554752	GCTGATAGATGCTGGGAGAAGTC	60.555	52.174	0.00	0.00	0.00	3.01
4000	5692	3.310954	ACCCAGGAGGAACTAGTCATCAT	60.311	47.826	0.00	0.00	41.55	2.45
4001	5693	3.323403	CCCAGGAGGAACTAGTCATCATC	59.677	52.174	0.00	0.00	41.55	2.92
4002	5694	3.963374	CCAGGAGGAACTAGTCATCATCA	59.037	47.826	10.47	0.00	41.55	3.07
4034	5726	1.476891	GTAGAGCTGTGGATCGAACCA	59.523	52.381	10.84	10.84	37.63	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
79	80	1.596934	GAGCGGTTCATCCCAGACA	59.403	57.895	0.00	0.00	0.00	3.41
203	204	4.287067	ACTCATGGTTGTTCCTAGTGATGT	59.713	41.667	0.00	0.00	37.07	3.06
390	391	4.430007	TCGTAGCTCGTTATTTGCTCAAT	58.570	39.130	0.00	0.00	40.80	2.57
579	585	1.210155	GCGGCGCATGAAAGAAACT	59.790	52.632	29.21	0.00	0.00	2.66
825	2486	7.703197	TCTGTTTTCAACCGGACTTTTTATTTC	59.297	33.333	9.46	0.00	0.00	2.17
870	2543	2.684001	TTGTGACACTCGACCAAACT	57.316	45.000	7.20	0.00	0.00	2.66
955	2636	0.942252	AGAAAGACGGCCGTGTTTTC	59.058	50.000	42.16	38.24	40.83	2.29
1425	3106	1.527433	TATGGATGAGAGGGCTCGCG	61.527	60.000	0.00	0.00	44.33	5.87
1497	3178	1.006102	AACCGCGTCCTTCACAGAG	60.006	57.895	4.92	0.00	0.00	3.35
1659	3340	0.961019	GGTTGAAGCAATCCACAGCA	59.039	50.000	0.00	0.00	0.00	4.41
1773	3454	2.260434	CCAACCAGCATGTGCAGC	59.740	61.111	7.83	0.00	45.16	5.25
1794	3475	1.902508	TCACTCACCAACATCCTCCTC	59.097	52.381	0.00	0.00	0.00	3.71
1796	3477	1.347707	TGTCACTCACCAACATCCTCC	59.652	52.381	0.00	0.00	0.00	4.30
1807	3488	3.491267	GCAACTACAAGTCTGTCACTCAC	59.509	47.826	0.00	0.00	36.96	3.51
1813	3494	1.721926	GAGCGCAACTACAAGTCTGTC	59.278	52.381	11.47	0.00	36.96	3.51
1817	3498	1.321743	CGATGAGCGCAACTACAAGTC	59.678	52.381	11.47	0.00	0.00	3.01
1858	3539	2.573083	CCCTTGCACGGCCAATGTT	61.573	57.895	2.24	0.00	0.00	2.71
2478	4159	3.111838	CACCAATCTCATCTCGTCGAAG	58.888	50.000	0.00	0.00	0.00	3.79
2584	4265	0.971959	ATTGGCATGGTCCGCACAAT	60.972	50.000	0.00	0.00	0.00	2.71
2661	4342	2.028112	AGCATTTCGAGCTAGGTCAACA	60.028	45.455	21.17	4.73	41.32	3.33
2664	4345	1.740380	GCAGCATTTCGAGCTAGGTCA	60.740	52.381	21.17	6.39	41.14	4.02
2667	4348	1.372582	TTGCAGCATTTCGAGCTAGG	58.627	50.000	0.00	0.00	41.14	3.02
2686	4367	4.408270	TGGCTCTAGCTTCAGAAGATGATT	59.592	41.667	14.86	0.00	41.70	2.57
2760	4441	3.530265	TTTGATGCATCTTCCCATTGC	57.470	42.857	26.32	0.00	36.91	3.56
2852	4533	5.883673	TCACCAACTATAAACTTATGCACCC	59.116	40.000	0.00	0.00	0.00	4.61
2914	4595	3.596101	ACCTGCATCTAATCTCCTCCAT	58.404	45.455	0.00	0.00	0.00	3.41
2929	4610	6.808321	ATATCCTACTGACTTTAACCTGCA	57.192	37.500	0.00	0.00	0.00	4.41
3054	4735	1.160137	GCAGGTTTGGTGCTAGACTG	58.840	55.000	0.00	0.00	37.96	3.51
3300	4982	4.081198	ACCTGAAAGCTACTCTGAAGATGG	60.081	45.833	0.00	0.00	0.00	3.51
3391	5073	6.282167	CAGTGCTCTCAGAAGATGAATATGT	58.718	40.000	0.00	0.00	37.52	2.29
3395	5077	3.682155	GCCAGTGCTCTCAGAAGATGAAT	60.682	47.826	0.00	0.00	33.82	2.57
3413	5095	5.501156	ACCTTTTCCTGATAAAGTAGCCAG	58.499	41.667	0.00	0.00	32.06	4.85
3459	5144	0.687354	CAGTGAGCCAACTGGTAGGT	59.313	55.000	8.23	0.00	43.22	3.08
3460	5145	3.540211	CAGTGAGCCAACTGGTAGG	57.460	57.895	8.23	0.00	43.22	3.18
3499	5184	6.472016	ACTATGTGTGTGATGAATGTTACCA	58.528	36.000	0.00	0.00	0.00	3.25
3603	5288	3.397482	ACAAGTGACAGAACTGCAGATC	58.603	45.455	23.35	19.17	0.00	2.75
3671	5358	3.381908	CACCTAGACTATTGACTTCGGCT	59.618	47.826	0.00	0.00	0.00	5.52
3788	5479	4.722700	GCAGGGTGCCGTGGATGT	62.723	66.667	12.13	0.00	37.42	3.06
4000	5692	9.154632	TCCACAGCTCTACCTTAATAATATTGA	57.845	33.333	0.00	0.00	0.00	2.57
4001	5693	9.950496	ATCCACAGCTCTACCTTAATAATATTG	57.050	33.333	0.00	0.00	0.00	1.90
4034	5726	1.224592	CGATGGGTTAGCCAGCCTT	59.775	57.895	13.24	0.00	44.37	4.35
4144	5846	8.137437	CACTTATTTTTCTTGTCCACAACATCT	58.863	33.333	0.00	0.00	37.82	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.