AutoCloner

Multiple sequence alignment - TraesCS3B01G468300

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	TraesCS3B01G468300	chr3B	100.000	3128	0	0	1	3128	712755966	712752839	0.000000e+00	5777.0
1	TraesCS3B01G468300	chr3D	89.842	2028	69	55	682	2640	537941661	537939702	0.000000e+00	2477.0
2	TraesCS3B01G468300	chr3D	79.887	532	51	28	1	502	537942304	537941799	3.860000e-89	339.0
3	TraesCS3B01G468300	chr3D	97.143	35	1	0	630	664	537941730	537941696	3.370000e-05	60.2
4	TraesCS3B01G468300	chr3D	100.000	28	0	0	2760	2787	10309500	10309473	6.000000e-03	52.8
5	TraesCS3B01G468300	chr3A	85.556	2077	113	58	630	2638	673478035	673476078	0.000000e+00	2001.0
6	TraesCS3B01G468300	chr3A	84.392	551	49	25	48	592	673478555	673478036	1.000000e-139	507.0
7	TraesCS3B01G468300	chr3A	98.507	67	1	0	2521	2587	673476187	673476121	5.480000e-23	119.0
8	TraesCS3B01G468300	chr4B	97.561	451	11	0	2678	3128	60071178	60070728	0.000000e+00	773.0
9	TraesCS3B01G468300	chr7B	99.716	352	1	0	2777	3128	593917640	593917289	0.000000e+00	645.0
10	TraesCS3B01G468300	chr7B	89.583	48	4	1	870	916	646245544	646245591	3.370000e-05	60.2
11	TraesCS3B01G468300	chr7B	85.185	54	6	2	2735	2787	724478400	724478452	2.000000e-03	54.7
12	TraesCS3B01G468300	chr7A	100.000	29	0	0	2759	2787	39037425	39037397	2.000000e-03	54.7
13	TraesCS3B01G468300	chr4A	100.000	29	0	0	2759	2787	36007117	36007089	2.000000e-03	54.7
14	TraesCS3B01G468300	chr2B	100.000	29	0	0	2759	2787	706375915	706375887	2.000000e-03	54.7
15	TraesCS3B01G468300	chr1A	100.000	29	0	0	2759	2787	562885287	562885259	2.000000e-03	54.7

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	TraesCS3B01G468300	chr3B	712752839	712755966	3127	True	5777.000000	5777	100.000000	1	3128	1	chr3B.!!$R1	3127
1	TraesCS3B01G468300	chr3D	537939702	537942304	2602	True	958.733333	2477	88.957333	1	2640	3	chr3D.!!$R2	2639
2	TraesCS3B01G468300	chr3A	673476078	673478555	2477	True	875.666667	2001	89.485000	48	2638	3	chr3A.!!$R1	2590

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
669	719	0.108041	GGTAATTCCCGGCGAGTGAA	60.108	55.0	9.3	8.77	0.0	3.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2157	2310	0.107165	GTACATTCAGTGAGGGGGCC	60.107	60.0	0.0	0.0	0.0	5.8	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
37	38	1.535226	GCCCCAACGTGTTTGAACTTC	60.535	52.381	0.00	0.00	37.39	3.01
95	103	2.769195	TAGGGCCCGGCGGTTATT	60.769	61.111	26.32	10.24	0.00	1.40
112	130	7.254852	GCGGTTATTTAATTGGAGTTGATTGA	58.745	34.615	0.00	0.00	0.00	2.57
123	141	0.455815	GTTGATTGATTCCACCGCCC	59.544	55.000	0.00	0.00	0.00	6.13
149	168	4.337274	CCGTCAAAAACTAAACTGGAAGGT	59.663	41.667	0.00	0.00	39.30	3.50
199	219	1.828660	CCCCAGCGTACTCCTCGAT	60.829	63.158	0.00	0.00	0.00	3.59
375	419	1.343821	CGCACGTTAACTGATCCGC	59.656	57.895	3.71	0.00	0.00	5.54
427	475	3.695606	GAGGCCTCGCACTGTGGA	61.696	66.667	19.06	4.53	32.77	4.02
430	478	2.646175	GGCCTCGCACTGTGGACTA	61.646	63.158	10.21	0.00	36.26	2.59
432	480	1.215647	CCTCGCACTGTGGACTACC	59.784	63.158	10.21	0.00	32.77	3.18
433	481	1.532604	CCTCGCACTGTGGACTACCA	61.533	60.000	10.21	0.00	44.76	3.25
490	539	4.314440	GACTGCCACCTCCGTGCA	62.314	66.667	0.00	0.00	38.79	4.57
586	636	4.422506	CAGCTGTTTAACTGCGCG	57.577	55.556	18.46	0.00	45.97	6.86
592	642	0.810426	TGTTTAACTGCGCGGTGACA	60.810	50.000	25.11	23.26	0.00	3.58
593	643	0.110823	GTTTAACTGCGCGGTGACAG	60.111	55.000	25.11	9.25	39.86	3.51
594	644	1.837538	TTTAACTGCGCGGTGACAGC	61.838	55.000	25.11	0.00	37.42	4.40
620	670	3.056328	GCCTTCCCGCTTCGCTTT	61.056	61.111	0.00	0.00	0.00	3.51
621	671	2.626780	GCCTTCCCGCTTCGCTTTT	61.627	57.895	0.00	0.00	0.00	2.27
622	672	1.210155	CCTTCCCGCTTCGCTTTTG	59.790	57.895	0.00	0.00	0.00	2.44
623	673	1.442688	CTTCCCGCTTCGCTTTTGC	60.443	57.895	0.00	0.00	43.23	3.68
624	674	1.856265	CTTCCCGCTTCGCTTTTGCT	61.856	55.000	0.00	0.00	44.80	3.91
625	675	1.852067	TTCCCGCTTCGCTTTTGCTC	61.852	55.000	0.00	0.00	44.80	4.26
626	676	2.176792	CCGCTTCGCTTTTGCTCC	59.823	61.111	0.00	0.00	44.80	4.70
627	677	2.328099	CCGCTTCGCTTTTGCTCCT	61.328	57.895	0.00	0.00	44.80	3.69
628	678	1.154338	CGCTTCGCTTTTGCTCCTG	60.154	57.895	0.00	0.00	44.80	3.86

Showing 1 to 25 of 438 entries

Previous1 2 3 4 5…18Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
37	38	2.432628	GACCTGGCCACGTCGAAG	60.433	66.667	17.50	0.00	0.00	3.79
84	92	2.946990	ACTCCAATTAAATAACCGCCGG	59.053	45.455	0.00	0.00	0.00	6.13
95	103	6.127758	CGGTGGAATCAATCAACTCCAATTAA	60.128	38.462	0.00	0.00	39.62	1.40
123	141	2.603652	CCAGTTTAGTTTTTGACGGGCG	60.604	50.000	0.00	0.00	0.00	6.13
132	151	7.612633	TGTCAAACTACCTTCCAGTTTAGTTTT	59.387	33.333	3.43	0.00	42.79	2.43
199	219	5.512942	TGAAACCATCCCAATTGTCTCTA	57.487	39.130	4.43	0.00	0.00	2.43
207	227	5.959594	TCAAGAATGATGAAACCATCCCAAT	59.040	36.000	0.00	0.00	39.67	3.16
241	262	2.029288	CGCAGGGTGCACACTAGTG	61.029	63.158	23.88	21.44	45.36	2.74
243	264	1.446792	CTCGCAGGGTGCACACTAG	60.447	63.158	23.88	18.84	45.36	2.57
352	396	3.784412	CAGTTAACGTGCGGCCGG	61.784	66.667	29.38	13.36	0.00	6.13
353	397	2.020836	GATCAGTTAACGTGCGGCCG	62.021	60.000	24.05	24.05	0.00	6.13
354	398	1.702491	GGATCAGTTAACGTGCGGCC	61.702	60.000	0.00	0.00	0.00	6.13
355	399	1.713830	GGATCAGTTAACGTGCGGC	59.286	57.895	0.00	0.00	0.00	6.53
356	400	1.995991	CGGATCAGTTAACGTGCGG	59.004	57.895	12.27	1.26	0.00	5.69
375	419	4.351938	TCAAGGCGACGTCCGTGG	62.352	66.667	10.58	2.56	41.15	4.94
427	475	1.865788	TTAAGTCGCGGCGTGGTAGT	61.866	55.000	22.90	2.52	0.00	2.73
430	478	0.952010	AAATTAAGTCGCGGCGTGGT	60.952	50.000	22.90	10.63	0.00	4.16
432	480	1.136197	TGAAAATTAAGTCGCGGCGTG	60.136	47.619	22.90	15.42	0.00	5.34
433	481	1.136169	GTGAAAATTAAGTCGCGGCGT	60.136	47.619	22.90	4.10	0.00	5.68
435	483	1.789054	CGGTGAAAATTAAGTCGCGGC	60.789	52.381	0.21	0.21	0.00	6.53
437	485	1.789054	GCCGGTGAAAATTAAGTCGCG	60.789	52.381	1.90	0.00	0.00	5.87
440	488	1.198178	TGCGCCGGTGAAAATTAAGTC	59.802	47.619	21.76	0.00	0.00	3.01
441	489	1.240256	TGCGCCGGTGAAAATTAAGT	58.760	45.000	21.76	0.00	0.00	2.24
442	490	1.982913	GTTGCGCCGGTGAAAATTAAG	59.017	47.619	21.76	0.00	0.00	1.85
502	551	1.440060	CGGCGGCAGTGGAGTAATA	59.560	57.895	10.53	0.00	0.00	0.98

Showing 1 to 25 of 423 entries

Previous1 2 3 4 5…17Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.