AutoCloner

Multiple sequence alignment - TraesCS6D01G257900

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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	TraesCS6D01G257900	chr6D	100.000	3165	0	0	1	3165	363465079	363461915	0.000000e+00	5845.0
1	TraesCS6D01G257900	chr6D	90.947	243	22	0	2653	2895	227008004	227007762	8.460000e-86	327.0
2	TraesCS6D01G257900	chr6B	88.110	2666	146	67	2	2597	548117166	548114602	0.000000e+00	3009.0
3	TraesCS6D01G257900	chr6A	90.975	1241	45	23	1400	2589	504472989	504471765	0.000000e+00	1609.0
4	TraesCS6D01G257900	chr6A	86.099	1374	92	47	2	1343	504474489	504473183	0.000000e+00	1387.0
5	TraesCS6D01G257900	chr6A	92.797	236	16	1	2930	3165	504471463	504471229	1.090000e-89	340.0
6	TraesCS6D01G257900	chr6A	90.400	250	20	4	2649	2896	190652677	190652430	3.040000e-85	326.0
7	TraesCS6D01G257900	chr4D	91.429	245	21	0	2651	2895	30506670	30506426	1.410000e-88	337.0
8	TraesCS6D01G257900	chr4D	87.500	288	32	4	2646	2931	325892195	325892480	2.350000e-86	329.0
9	TraesCS6D01G257900	chr4D	90.323	248	23	1	2652	2898	11504358	11504111	1.090000e-84	324.0
10	TraesCS6D01G257900	chr4D	95.122	41	2	0	2892	2932	484462757	484462717	7.330000e-07	65.8
11	TraesCS6D01G257900	chr4D	95.000	40	2	0	2892	2931	112074029	112073990	2.640000e-06	63.9
12	TraesCS6D01G257900	chr3D	91.020	245	21	1	2651	2895	511728398	511728155	2.350000e-86	329.0
13	TraesCS6D01G257900	chr3D	90.688	247	23	0	2652	2898	523192596	523192350	2.350000e-86	329.0
14	TraesCS6D01G257900	chr3D	88.806	268	24	6	2637	2902	129016840	129016577	1.090000e-84	324.0
15	TraesCS6D01G257900	chr2D	91.322	242	18	3	2655	2895	642827313	642827074	8.460000e-86	327.0
16	TraesCS6D01G257900	chr7D	89.241	158	15	2	2008	2165	190005354	190005509	2.490000e-46	196.0
17	TraesCS6D01G257900	chr7B	90.000	150	15	0	2016	2165	334487119	334487268	8.960000e-46	195.0
18	TraesCS6D01G257900	chr7A	88.608	158	16	2	2008	2165	194177270	194177115	1.160000e-44	191.0
19	TraesCS6D01G257900	chr3A	91.071	56	3	2	2603	2657	66275397	66275451	1.220000e-09	75.0
20	TraesCS6D01G257900	chr3A	91.667	48	1	3	2610	2656	540972263	540972218	2.640000e-06	63.9
21	TraesCS6D01G257900	chr3B	88.136	59	7	0	2598	2656	741635444	741635502	1.570000e-08	71.3
22	TraesCS6D01G257900	chr3B	88.136	59	7	0	2598	2656	741647662	741647720	1.570000e-08	71.3
23	TraesCS6D01G257900	chr2B	89.286	56	6	0	2602	2657	213885548	213885493	1.570000e-08	71.3
24	TraesCS6D01G257900	chr1A	90.385	52	4	1	2892	2943	583322164	583322214	2.040000e-07	67.6
25	TraesCS6D01G257900	chrUn	95.000	40	2	0	2892	2931	248124587	248124548	2.640000e-06	63.9
26	TraesCS6D01G257900	chrUn	95.000	40	2	0	2892	2931	346478602	346478641	2.640000e-06	63.9
27	TraesCS6D01G257900	chr4B	95.000	40	2	0	2892	2931	172735533	172735494	2.640000e-06	63.9
28	TraesCS6D01G257900	chr2A	89.796	49	3	2	2888	2934	76520611	76520563	9.480000e-06	62.1
29	TraesCS6D01G257900	chr5A	89.362	47	5	0	2892	2938	469275404	469275450	3.410000e-05	60.2

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	TraesCS6D01G257900	chr6D	363461915	363465079	3164	True	5845	5845	100.000	1	3165	1	chr6D.!!$R2	3164
1	TraesCS6D01G257900	chr6B	548114602	548117166	2564	True	3009	3009	88.110	2	2597	1	chr6B.!!$R1	2595
2	TraesCS6D01G257900	chr6A	504471229	504474489	3260	True	1112	1609	89.957	2	3165	3	chr6A.!!$R2	3163

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
834	852	0.031994	AGCACCAACCGAACAATTGC	59.968	50.0	5.05	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2811	3135	0.110056	TAACGAACGAGACCGACTGC	60.11	55.0	0.14	0.0	39.5	4.4	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
44	50	2.419990	CCTGTGGATAATTGGACTGCGA	60.420	50.000	0.00	0.00	0.00	5.10
134	141	3.119459	AGCGATTTAGCTCTCGTCTCAAA	60.119	43.478	12.90	0.00	45.67	2.69
135	142	3.000575	GCGATTTAGCTCTCGTCTCAAAC	60.001	47.826	12.90	0.00	37.23	2.93
136	143	4.416620	CGATTTAGCTCTCGTCTCAAACT	58.583	43.478	0.00	0.00	0.00	2.66
137	144	5.570344	CGATTTAGCTCTCGTCTCAAACTA	58.430	41.667	0.00	0.00	0.00	2.24
138	145	6.202937	CGATTTAGCTCTCGTCTCAAACTAT	58.797	40.000	0.00	0.00	0.00	2.12
142	152	9.871238	ATTTAGCTCTCGTCTCAAACTATTTTA	57.129	29.630	0.00	0.00	0.00	1.52
147	157	6.860080	TCTCGTCTCAAACTATTTTATCCGT	58.140	36.000	0.00	0.00	0.00	4.69
148	158	6.750501	TCTCGTCTCAAACTATTTTATCCGTG	59.249	38.462	0.00	0.00	0.00	4.94
175	185	6.040391	AGCACTTAGTTTGCAGTTTTTGGATA	59.960	34.615	0.00	0.00	42.83	2.59
204	214	3.119291	GCTGATACTCGGTCATTCAGTG	58.881	50.000	0.00	0.00	36.91	3.66
228	238	3.808728	TGGACCAAGCTATTCTGTATGC	58.191	45.455	0.00	0.00	0.00	3.14
279	289	0.662077	CACCGATGTCGTGTTCGTCA	60.662	55.000	1.44	0.00	39.07	4.35
327	337	4.500205	CGTAGCACGATATTCCTAAACCCA	60.500	45.833	3.04	0.00	46.05	4.51
340	350	3.831911	CCTAAACCCAATCCTCAAAAGCA	59.168	43.478	0.00	0.00	0.00	3.91
342	352	4.541973	AAACCCAATCCTCAAAAGCATC	57.458	40.909	0.00	0.00	0.00	3.91
364	374	0.607620	GCATAGCCAAACCAAAGCCA	59.392	50.000	0.00	0.00	0.00	4.75
393	403	4.081642	CGTCTTGAGAAAGTAGGAATCCCA	60.082	45.833	0.00	0.00	33.88	4.37
523	537	2.916716	GACAAATGTAAACCATGCGCAG	59.083	45.455	18.32	5.51	32.82	5.18
536	550	3.390521	CGCAGGCACCCACCTCTA	61.391	66.667	0.00	0.00	38.26	2.43
537	551	2.586792	GCAGGCACCCACCTCTAG	59.413	66.667	0.00	0.00	38.26	2.43
538	552	2.586792	CAGGCACCCACCTCTAGC	59.413	66.667	0.00	0.00	38.26	3.42
552	570	7.508636	ACCCACCTCTAGCATCATATATCTATG	59.491	40.741	0.00	1.66	36.79	2.23
560	578	6.753180	AGCATCATATATCTATGTAAGCCCG	58.247	40.000	6.49	0.00	36.80	6.13
562	580	6.459066	CATCATATATCTATGTAAGCCCGGG	58.541	44.000	19.09	19.09	36.80	5.73

Showing 1 to 25 of 230 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.883217	AGGCAATCCATATGTCATCTATGAAC	59.117	38.462	1.24	0.00	34.86	3.18
134	141	4.755266	AGTGCTCCACGGATAAAATAGT	57.245	40.909	0.00	0.00	39.64	2.12
135	142	6.281405	ACTAAGTGCTCCACGGATAAAATAG	58.719	40.000	0.00	0.00	39.64	1.73
136	143	6.229936	ACTAAGTGCTCCACGGATAAAATA	57.770	37.500	0.00	0.00	39.64	1.40
137	144	5.099042	ACTAAGTGCTCCACGGATAAAAT	57.901	39.130	0.00	0.00	39.64	1.82
138	145	4.546829	ACTAAGTGCTCCACGGATAAAA	57.453	40.909	0.00	0.00	39.64	1.52
142	152	2.699954	CAAACTAAGTGCTCCACGGAT	58.300	47.619	0.00	0.00	39.64	4.18
147	157	2.638480	ACTGCAAACTAAGTGCTCCA	57.362	45.000	0.00	0.00	42.69	3.86
148	158	3.990318	AAACTGCAAACTAAGTGCTCC	57.010	42.857	0.00	0.00	42.69	4.70
175	185	1.043816	CCGAGTATCAGCTCCACCAT	58.956	55.000	0.00	0.00	33.17	3.55
204	214	5.449177	GCATACAGAATAGCTTGGTCCAAAC	60.449	44.000	5.64	0.68	0.00	2.93
228	238	3.119708	CCAAATCTCAAAGGGAAGCTTCG	60.120	47.826	19.91	6.18	0.00	3.79
236	246	3.256631	CACAAGGTCCAAATCTCAAAGGG	59.743	47.826	0.00	0.00	0.00	3.95
299	309	1.993370	GGAATATCGTGCTACGCATCC	59.007	52.381	4.15	5.46	41.91	3.51
327	337	2.715046	TGCTCGATGCTTTTGAGGATT	58.285	42.857	8.07	0.00	43.37	3.01
340	350	2.418368	TTGGTTTGGCTATGCTCGAT	57.582	45.000	0.00	0.00	0.00	3.59
342	352	1.468054	GCTTTGGTTTGGCTATGCTCG	60.468	52.381	0.00	0.00	0.00	5.03
364	374	5.507637	TCCTACTTTCTCAAGACGGATAGT	58.492	41.667	0.00	0.00	33.72	2.12
393	403	3.440173	CCTGAATTTACGCAGGTGTGAAT	59.560	43.478	0.00	0.00	45.21	2.57
523	537	1.147153	GATGCTAGAGGTGGGTGCC	59.853	63.158	0.00	0.00	0.00	5.01
535	549	7.039714	CCGGGCTTACATAGATATATGATGCTA	60.040	40.741	14.15	0.00	0.00	3.49
536	550	6.239430	CCGGGCTTACATAGATATATGATGCT	60.239	42.308	14.15	0.00	0.00	3.79
537	551	5.928839	CCGGGCTTACATAGATATATGATGC	59.071	44.000	14.15	12.89	0.00	3.91
538	552	6.459066	CCCGGGCTTACATAGATATATGATG	58.541	44.000	8.08	4.88	0.00	3.07
552	570	3.647649	AACGTACGCCCGGGCTTAC	62.648	63.158	39.20	39.20	40.84	2.34

Showing 1 to 25 of 225 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.