AutoCloner

Multiple sequence alignment - TraesCS6D01G390400

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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	TraesCS6D01G390400	chr6D	100.000	2608	0	0	1	2608	465377207	465374600	0.000000	4817.0
1	TraesCS6D01G390400	chr6D	97.550	2612	36	11	1	2608	28107680	28105093	0.000000	4444.0
2	TraesCS6D01G390400	chr6D	97.583	2607	38	10	1	2605	62913911	62916494	0.000000	4442.0
3	TraesCS6D01G390400	chr6D	94.872	39	2	0	488	526	2771898	2771936	0.000008	62.1
4	TraesCS6D01G390400	chr6D	100.000	33	0	0	494	526	6286369	6286337	0.000008	62.1
5	TraesCS6D01G390400	chr1D	98.005	2607	28	10	1	2605	411212262	411214846	0.000000	4505.0
6	TraesCS6D01G390400	chr1D	97.812	2605	34	10	1	2603	38762413	38764996	0.000000	4473.0
7	TraesCS6D01G390400	chr1D	97.775	2607	34	11	1	2605	2184220	2186804	0.000000	4471.0
8	TraesCS6D01G390400	chr7D	97.852	2607	32	9	1	2605	17198676	17201260	0.000000	4482.0
9	TraesCS6D01G390400	chr7D	97.433	2610	45	8	1	2608	52435736	52433147	0.000000	4429.0
10	TraesCS6D01G390400	chr3D	97.778	2610	35	9	1	2608	530288314	530285726	0.000000	4477.0
11	TraesCS6D01G390400	chr3D	97.733	2603	35	10	1	2601	522531783	522534363	0.000000	4458.0
12	TraesCS6D01G390400	chr2D	97.738	2608	35	11	1	2605	431410470	431413056	0.000000	4468.0
13	TraesCS6D01G390400	chr2D	97.660	2607	34	13	1	2605	5604375	5606956	0.000000	4451.0
14	TraesCS6D01G390400	chr2D	97.468	2607	43	9	1	2605	559267738	559270323	0.000000	4427.0
15	TraesCS6D01G390400	chr5D	97.699	2607	34	12	1	2605	8250492	8253074	0.000000	4458.0
16	TraesCS6D01G390400	chr5D	97.920	1635	13	9	1	1635	16176498	16174885	0.000000	2811.0
17	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	24566363	24566331	0.000008	62.1
18	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	194103085	194103053	0.000008	62.1
19	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	264700865	264700833	0.000008	62.1
20	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	307407836	307407804	0.000008	62.1
21	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	369545189	369545157	0.000008	62.1
22	TraesCS6D01G390400	chrUn	94.872	39	2	0	488	526	425372519	425372557	0.000008	62.1
23	TraesCS6D01G390400	chrUn	100.000	33	0	0	494	526	465140658	465140626	0.000008	62.1

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	TraesCS6D01G390400	chr6D	465374600	465377207	2607	True	4817	4817	100.000	1	2608	1	chr6D.!!$R3	2607
1	TraesCS6D01G390400	chr6D	28105093	28107680	2587	True	4444	4444	97.550	1	2608	1	chr6D.!!$R2	2607
2	TraesCS6D01G390400	chr6D	62913911	62916494	2583	False	4442	4442	97.583	1	2605	1	chr6D.!!$F2	2604
3	TraesCS6D01G390400	chr1D	411212262	411214846	2584	False	4505	4505	98.005	1	2605	1	chr1D.!!$F3	2604
4	TraesCS6D01G390400	chr1D	38762413	38764996	2583	False	4473	4473	97.812	1	2603	1	chr1D.!!$F2	2602
5	TraesCS6D01G390400	chr1D	2184220	2186804	2584	False	4471	4471	97.775	1	2605	1	chr1D.!!$F1	2604
6	TraesCS6D01G390400	chr7D	17198676	17201260	2584	False	4482	4482	97.852	1	2605	1	chr7D.!!$F1	2604
7	TraesCS6D01G390400	chr7D	52433147	52435736	2589	True	4429	4429	97.433	1	2608	1	chr7D.!!$R1	2607
8	TraesCS6D01G390400	chr3D	530285726	530288314	2588	True	4477	4477	97.778	1	2608	1	chr3D.!!$R1	2607
9	TraesCS6D01G390400	chr3D	522531783	522534363	2580	False	4458	4458	97.733	1	2601	1	chr3D.!!$F1	2600
10	TraesCS6D01G390400	chr2D	431410470	431413056	2586	False	4468	4468	97.738	1	2605	1	chr2D.!!$F2	2604
11	TraesCS6D01G390400	chr2D	5604375	5606956	2581	False	4451	4451	97.660	1	2605	1	chr2D.!!$F1	2604
12	TraesCS6D01G390400	chr2D	559267738	559270323	2585	False	4427	4427	97.468	1	2605	1	chr2D.!!$F3	2604
13	TraesCS6D01G390400	chr5D	8250492	8253074	2582	False	4458	4458	97.699	1	2605	1	chr5D.!!$F1	2604
14	TraesCS6D01G390400	chr5D	16174885	16176498	1613	True	2811	2811	97.920	1	1635	1	chr5D.!!$R1	1634

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
502	503	0.105709	TGCTCCTCCCATCACGGATA	60.106	55.0	0.0	0.0	36.56	2.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1814	1819	2.303549	GACTGGGGACTCTGCCATCG	62.304	65.0	0.0	0.0	0.0	3.84	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
490	491	1.373570	CCCAAAAGATCGTGCTCCTC	58.626	55.000	0.00	0.00	0.00	3.71
491	492	1.373570	CCAAAAGATCGTGCTCCTCC	58.626	55.000	0.00	0.00	0.00	4.30
494	495	1.207791	AAAGATCGTGCTCCTCCCAT	58.792	50.000	0.00	0.00	0.00	4.00
495	496	0.755686	AAGATCGTGCTCCTCCCATC	59.244	55.000	0.00	0.00	0.00	3.51
497	498	0.249657	GATCGTGCTCCTCCCATCAC	60.250	60.000	0.00	0.00	0.00	3.06
498	499	2.202797	CGTGCTCCTCCCATCACG	60.203	66.667	0.00	0.00	44.62	4.35
499	500	2.187946	GTGCTCCTCCCATCACGG	59.812	66.667	0.00	0.00	0.00	4.94
501	502	1.383109	TGCTCCTCCCATCACGGAT	60.383	57.895	0.00	0.00	36.56	4.18
502	503	0.105709	TGCTCCTCCCATCACGGATA	60.106	55.000	0.00	0.00	36.56	2.59
504	505	2.225267	TGCTCCTCCCATCACGGATATA	60.225	50.000	0.00	0.00	36.56	0.86
505	506	3.034635	GCTCCTCCCATCACGGATATAT	58.965	50.000	0.00	0.00	36.56	0.86
506	507	4.215908	GCTCCTCCCATCACGGATATATA	58.784	47.826	0.00	0.00	36.56	0.86
507	508	4.038162	GCTCCTCCCATCACGGATATATAC	59.962	50.000	0.00	0.00	36.56	1.47
508	509	4.543689	TCCTCCCATCACGGATATATACC	58.456	47.826	0.00	0.00	36.56	2.73
509	510	4.232122	TCCTCCCATCACGGATATATACCT	59.768	45.833	0.00	0.00	36.56	3.08
510	511	4.962995	CCTCCCATCACGGATATATACCTT	59.037	45.833	0.00	0.00	36.56	3.50
511	512	5.069251	CCTCCCATCACGGATATATACCTTC	59.931	48.000	0.00	0.00	36.56	3.46
512	513	4.960469	TCCCATCACGGATATATACCTTCC	59.040	45.833	0.00	0.00	36.56	3.46
513	514	4.101119	CCCATCACGGATATATACCTTCCC	59.899	50.000	0.00	0.00	36.56	3.97
514	515	4.714802	CCATCACGGATATATACCTTCCCA	59.285	45.833	0.00	0.00	36.56	4.37
515	516	5.366768	CCATCACGGATATATACCTTCCCAT	59.633	44.000	0.00	0.00	36.56	4.00
516	517	6.126768	CCATCACGGATATATACCTTCCCATT	60.127	42.308	0.00	0.00	36.56	3.16
517	518	6.540438	TCACGGATATATACCTTCCCATTC	57.460	41.667	0.00	0.00	0.00	2.67
518	519	6.261435	TCACGGATATATACCTTCCCATTCT	58.739	40.000	0.00	0.00	0.00	2.40
519	520	7.415908	TCACGGATATATACCTTCCCATTCTA	58.584	38.462	0.00	0.00	0.00	2.10
520	521	7.341256	TCACGGATATATACCTTCCCATTCTAC	59.659	40.741	0.00	0.00	0.00	2.59
521	522	6.610425	ACGGATATATACCTTCCCATTCTACC	59.390	42.308	0.00	0.00	0.00	3.18
841	842	5.794894	AGTAGTTCTGGTGTAATTGGAGTG	58.205	41.667	0.00	0.00	0.00	3.51
1092	1093	2.270352	TGAAGGTGCAAAAGGATCGT	57.730	45.000	0.00	0.00	0.00	3.73
1780	1785	9.114952	CCTTTTAAAATTTGTGTGTAAACCCAT	57.885	29.630	0.09	0.00	0.00	4.00
1814	1819	1.076332	ACGCAGGATAAGAAACGTGC	58.924	50.000	0.00	0.00	42.10	5.34
1871	1876	6.038271	GGATACATTCCACATAACAAGGTGAC	59.962	42.308	0.00	0.00	44.74	3.67
1997	2002	6.495181	TGTTTGCCCCTTTACTCATTTAATGA	59.505	34.615	7.46	7.46	37.76	2.57
2510	2516	1.273886	AGAGAGTTGGCGGAGAAAGAC	59.726	52.381	0.00	0.00	0.00	3.01
2605	2611	1.289109	CCGACGCAATCTCCAACGTT	61.289	55.000	0.00	0.00	39.16	3.99

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
490	491	4.101119	GGGAAGGTATATATCCGTGATGGG	59.899	50.000	0.0	0.00	38.76	4.00
491	492	4.714802	TGGGAAGGTATATATCCGTGATGG	59.285	45.833	0.0	0.00	40.09	3.51
494	495	6.261435	AGAATGGGAAGGTATATATCCGTGA	58.739	40.000	0.0	0.00	33.90	4.35
495	496	6.546428	AGAATGGGAAGGTATATATCCGTG	57.454	41.667	0.0	0.00	33.90	4.94
497	498	6.238953	CGGTAGAATGGGAAGGTATATATCCG	60.239	46.154	0.0	0.00	33.90	4.18
498	499	6.462628	GCGGTAGAATGGGAAGGTATATATCC	60.463	46.154	0.0	0.00	0.00	2.59
499	500	6.097839	TGCGGTAGAATGGGAAGGTATATATC	59.902	42.308	0.0	0.00	0.00	1.63
501	502	5.335261	TGCGGTAGAATGGGAAGGTATATA	58.665	41.667	0.0	0.00	0.00	0.86
502	503	4.164981	TGCGGTAGAATGGGAAGGTATAT	58.835	43.478	0.0	0.00	0.00	0.86
504	505	2.404559	TGCGGTAGAATGGGAAGGTAT	58.595	47.619	0.0	0.00	0.00	2.73
505	506	1.868713	TGCGGTAGAATGGGAAGGTA	58.131	50.000	0.0	0.00	0.00	3.08
506	507	1.141053	GATGCGGTAGAATGGGAAGGT	59.859	52.381	0.0	0.00	0.00	3.50
507	508	1.140852	TGATGCGGTAGAATGGGAAGG	59.859	52.381	0.0	0.00	0.00	3.46
508	509	2.620251	TGATGCGGTAGAATGGGAAG	57.380	50.000	0.0	0.00	0.00	3.46
509	510	3.278574	CTTTGATGCGGTAGAATGGGAA	58.721	45.455	0.0	0.00	0.00	3.97
510	511	2.917933	CTTTGATGCGGTAGAATGGGA	58.082	47.619	0.0	0.00	0.00	4.37
511	512	1.334869	GCTTTGATGCGGTAGAATGGG	59.665	52.381	0.0	0.00	0.00	4.00
512	513	2.763249	GCTTTGATGCGGTAGAATGG	57.237	50.000	0.0	0.00	0.00	3.16
841	842	0.381089	GCTCTTGCATGACATCCTGC	59.619	55.000	0.0	2.52	39.41	4.85
920	921	8.153221	TCCAACTAATTCCTAACAATACCAGA	57.847	34.615	0.0	0.00	0.00	3.86
921	922	8.840321	CATCCAACTAATTCCTAACAATACCAG	58.160	37.037	0.0	0.00	0.00	4.00
1092	1093	6.605471	TTGAGTTTCTTATCTACCTCAGCA	57.395	37.500	0.0	0.00	0.00	4.41
1558	1561	3.742369	GGTTGCCACAAATTGAAGATGTG	59.258	43.478	0.0	6.25	43.10	3.21
1814	1819	2.303549	GACTGGGGACTCTGCCATCG	62.304	65.000	0.0	0.00	0.00	3.84
1871	1876	3.367703	GGATTGTGCCATCTCAAACCTTG	60.368	47.826	0.0	0.00	36.39	3.61
1895	1900	5.269189	TGTATCCTTCATGTGGAGTGACTA	58.731	41.667	13.7	1.79	36.99	2.59
1997	2002	9.427821	ACCTAGTATCTCACATCAGAGTTAATT	57.572	33.333	0.0	0.00	36.97	1.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.