AutoCloner

Multiple sequence alignment - TraesCS3A01G092400

Loading Multiple Alignment...

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	TraesCS3A01G092400	chr3A	100.000	4006	0	0	1	4006	57961372	57957367	0.000000e+00	7398.0
1	TraesCS3A01G092400	chr3B	95.077	3169	75	20	892	4006	72935457	72938598	0.000000e+00	4913.0
2	TraesCS3A01G092400	chr3B	88.449	909	52	13	1	869	72934572	72935467	0.000000e+00	1048.0
3	TraesCS3A01G092400	chr3D	94.029	3182	98	25	892	4006	46554080	46557236	0.000000e+00	4739.0
4	TraesCS3A01G092400	chr3D	87.015	670	34	15	1	657	46553218	46553847	0.000000e+00	706.0
5	TraesCS3A01G092400	chr3D	94.170	223	7	4	653	872	46553874	46554093	6.420000e-88	335.0
6	TraesCS3A01G092400	chr3D	87.086	302	32	6	2527	2822	369413408	369413708	6.420000e-88	335.0
7	TraesCS3A01G092400	chr7B	89.869	306	27	2	2521	2822	13823711	13823406	1.350000e-104	390.0
8	TraesCS3A01G092400	chr7B	86.688	308	34	5	2522	2823	616539803	616540109	6.420000e-88	335.0
9	TraesCS3A01G092400	chr7B	92.216	167	13	0	1012	1178	147586614	147586448	1.860000e-58	237.0
10	TraesCS3A01G092400	chr5D	89.542	306	27	3	2522	2822	115401775	115401470	2.260000e-102	383.0
11	TraesCS3A01G092400	chr5B	89.542	306	27	3	2522	2822	126598771	126598466	2.260000e-102	383.0
12	TraesCS3A01G092400	chr5A	88.925	307	28	3	2522	2822	121412055	121411749	1.360000e-99	374.0
13	TraesCS3A01G092400	chr4D	85.759	316	36	9	2517	2826	421335522	421335210	3.860000e-85	326.0
14	TraesCS3A01G092400	chr2D	90.950	221	18	1	1012	1232	196365211	196365429	3.030000e-76	296.0
15	TraesCS3A01G092400	chr6A	91.617	167	14	0	1012	1178	576945102	576944936	8.660000e-57	231.0
16	TraesCS3A01G092400	chrUn	91.018	167	15	0	1012	1178	50316819	50316653	4.030000e-55	226.0
17	TraesCS3A01G092400	chrUn	91.018	167	15	0	1012	1178	307457563	307457397	4.030000e-55	226.0
18	TraesCS3A01G092400	chr6B	83.333	228	32	5	281	504	157774322	157774547	5.250000e-49	206.0
19	TraesCS3A01G092400	chr7A	80.435	92	13	5	281	370	25858208	25858120	9.290000e-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	TraesCS3A01G092400	chr3A	57957367	57961372	4005	True	7398.000000	7398	100.000	1	4006	1	chr3A.!!$R1	4005
1	TraesCS3A01G092400	chr3B	72934572	72938598	4026	False	2980.500000	4913	91.763	1	4006	2	chr3B.!!$F1	4005
2	TraesCS3A01G092400	chr3D	46553218	46557236	4018	False	1926.666667	4739	91.738	1	4006	3	chr3D.!!$F2	4005

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	End Stability	Orientation
72	76	0.323360	GGTTCAGGGGTTAGCATGCA	60.323	55.000	21.98	2.77	3.96	F
469	487	1.341156	CCCCACACCTCATCTCTCCC	61.341	65.000	0.00	0.00	4.30	F
482	500	1.653918	TCTCTCCCCCTCTTCCATTCT	59.346	52.381	0.00	0.00	2.40	F
2015	2095	2.072298	GCAAATCGAGAGCTTCACAGT	58.928	47.619	0.00	0.00	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1837	1917	1.467734	CAGTGCAGACTTTCAGCATCC	59.532	52.381	40.92	3.51	R
2082	2163	0.179009	AACATGTGCCAGTGCTCAGT	60.179	50.000	43.52	3.41	R
2093	2174	4.516698	CACCAGATAATCCCTAACATGTGC	59.483	45.833	0.00	4.57	R
3005	3100	1.377856	GCTTGGGTTCCTCAGCCTC	60.378	63.158	44.37	4.70	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
43	47	6.771267	GGGCTGGTAGTTAGTAGCAAATTTAT	59.229	38.462	0.57	0.00	38.67	1.40
70	74	0.625849	AGGGTTCAGGGGTTAGCATG	59.374	55.000	0.00	0.00	0.00	4.06
71	75	1.037579	GGGTTCAGGGGTTAGCATGC	61.038	60.000	10.51	10.51	0.00	4.06
72	76	0.323360	GGTTCAGGGGTTAGCATGCA	60.323	55.000	21.98	2.77	0.00	3.96
73	77	1.686115	GGTTCAGGGGTTAGCATGCAT	60.686	52.381	21.98	7.68	0.00	3.96
266	280	5.636837	CAGTAAGAGTCTAAGAGAGCACAC	58.363	45.833	0.00	0.00	0.00	3.82
311	325	7.363880	GCATCTCTAACCGATCCCTTATAATCA	60.364	40.741	0.00	0.00	0.00	2.57
337	352	9.620259	AGTTAGAGGAGGATAAAATCATGTTTC	57.380	33.333	0.00	0.00	0.00	2.78
458	476	2.490509	CGGAGTAAAAATTCCCCACACC	59.509	50.000	0.00	0.00	0.00	4.16
459	477	3.774734	GGAGTAAAAATTCCCCACACCT	58.225	45.455	0.00	0.00	0.00	4.00
462	480	5.010708	AGTAAAAATTCCCCACACCTCAT	57.989	39.130	0.00	0.00	0.00	2.90
469	487	1.341156	CCCCACACCTCATCTCTCCC	61.341	65.000	0.00	0.00	0.00	4.30
482	500	1.653918	TCTCTCCCCCTCTTCCATTCT	59.346	52.381	0.00	0.00	0.00	2.40
559	577	3.377759	CCCCGCCGCCAAAAATGA	61.378	61.111	0.00	0.00	0.00	2.57
567	585	2.094675	CCGCCAAAAATGACTGGATCT	58.905	47.619	0.00	0.00	34.35	2.75
592	610	6.721208	TGGCCATTTTAAGTGAAGAAATCTCT	59.279	34.615	0.00	0.00	33.37	3.10
627	645	4.136796	AGTCTAGCTGTGTTGATTTTGCA	58.863	39.130	0.00	0.00	0.00	4.08
666	715	8.654997	AGTGGTCTGCTAATTATGATAATCACT	58.345	33.333	0.00	2.78	0.00	3.41
699	748	6.925165	CCTTTTTGACTGTGCAAATACTTCAT	59.075	34.615	0.00	0.00	37.57	2.57
751	803	7.613022	ACAGAGTTTGGATGATTTATGTCACAT	59.387	33.333	0.00	0.00	0.00	3.21
772	824	7.714813	TCACATTCACTTCATTCTTCAACAGTA	59.285	33.333	0.00	0.00	0.00	2.74
903	955	2.311124	GCTACGGCTTTGGATACAGT	57.689	50.000	0.00	0.00	41.47	3.55
904	956	2.629051	GCTACGGCTTTGGATACAGTT	58.371	47.619	0.00	0.00	41.47	3.16
905	957	2.608090	GCTACGGCTTTGGATACAGTTC	59.392	50.000	0.00	0.00	41.47	3.01
906	958	3.925530	GCTACGGCTTTGGATACAGTTCA	60.926	47.826	0.00	0.00	41.47	3.18

Showing 1 to 25 of 60 entries

Previous1 2 3Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	47	1.207488	CCCCTGAACCCTGATGTCCA	61.207	60.000	0.00	0.00	0.00	4.02
70	74	4.446413	GCACTGGGGCAGCAATGC	62.446	66.667	0.00	0.00	34.37	3.56
71	75	2.992689	TGCACTGGGGCAGCAATG	60.993	61.111	0.00	0.00	39.25	2.82
266	280	6.821388	AGATGCTCTAACATAACTAACCCTG	58.179	40.000	0.00	0.00	0.00	4.45
311	325	9.620259	GAAACATGATTTTATCCTCCTCTAACT	57.380	33.333	0.00	0.00	0.00	2.24
328	343	5.189180	GCACTTTAGAGGAGGAAACATGAT	58.811	41.667	0.00	0.00	0.00	2.45
332	347	3.496160	GGTGCACTTTAGAGGAGGAAACA	60.496	47.826	17.98	0.00	0.00	2.83
337	352	3.369576	GGTTAGGTGCACTTTAGAGGAGG	60.370	52.174	17.98	0.00	0.00	4.30
411	426	2.152016	GGGCGGAGTATATTTGAAGGC	58.848	52.381	0.00	0.00	0.00	4.35
416	431	1.876416	CGGGTGGGCGGAGTATATTTG	60.876	57.143	0.00	0.00	0.00	2.32
420	435	3.228759	GCGGGTGGGCGGAGTATA	61.229	66.667	0.00	0.00	0.00	1.47
458	476	1.062581	TGGAAGAGGGGGAGAGATGAG	60.063	57.143	0.00	0.00	0.00	2.90
459	477	1.018840	TGGAAGAGGGGGAGAGATGA	58.981	55.000	0.00	0.00	0.00	2.92
462	480	1.653918	AGAATGGAAGAGGGGGAGAGA	59.346	52.381	0.00	0.00	0.00	3.10
469	487	1.821332	GCGGCAGAATGGAAGAGGG	60.821	63.158	0.00	0.00	35.86	4.30
559	577	4.019174	CACTTAAAATGGCCAGATCCAGT	58.981	43.478	13.05	7.75	39.89	4.00
567	585	6.721208	AGAGATTTCTTCACTTAAAATGGCCA	59.279	34.615	8.56	8.56	0.00	5.36
592	610	6.183360	ACACAGCTAGACTCACTTAAAACTCA	60.183	38.462	0.00	0.00	0.00	3.41
666	715	1.210967	ACAGTCAAAAAGGTCACCCGA	59.789	47.619	0.00	0.00	35.12	5.14
711	760	8.862325	TCCAAACTCTGTATAACACAATGAAT	57.138	30.769	0.00	0.00	36.48	2.57
751	803	9.119418	TGATTTACTGTTGAAGAATGAAGTGAA	57.881	29.630	0.00	0.00	0.00	3.18
772	824	6.299805	TCAGTATTCTGCACCTACTGATTT	57.700	37.500	17.87	0.00	43.81	2.17
884	936	2.311124	ACTGTATCCAAAGCCGTAGC	57.689	50.000	0.00	0.00	40.32	3.58
885	937	3.857052	TGAACTGTATCCAAAGCCGTAG	58.143	45.455	0.00	0.00	0.00	3.51
886	938	3.965379	TGAACTGTATCCAAAGCCGTA	57.035	42.857	0.00	0.00	0.00	4.02

Showing 1 to 25 of 63 entries

Previous1 2 3Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.