AutoCloner

Multiple sequence alignment - TraesCS2D01G499900

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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	TraesCS2D01G499900	chr2D	100.000	2875	0	0	1	2875	594572658	594569784	0.000000e+00	5310.0
1	TraesCS2D01G499900	chr1B	94.297	754	43	0	1	754	216519288	216520041	0.000000e+00	1155.0
2	TraesCS2D01G499900	chr1D	93.907	755	46	0	1	755	477260432	477259678	0.000000e+00	1140.0
3	TraesCS2D01G499900	chr1D	93.245	755	50	1	1	754	302902062	302901308	0.000000e+00	1110.0
4	TraesCS2D01G499900	chr6B	92.573	754	54	1	1	754	674957725	674956974	0.000000e+00	1081.0
5	TraesCS2D01G499900	chr5D	90.344	756	71	2	1	754	550426468	550425713	0.000000e+00	990.0
6	TraesCS2D01G499900	chr5A	89.920	754	76	0	1	754	673561902	673561149	0.000000e+00	972.0
7	TraesCS2D01G499900	chr3B	87.192	851	101	6	2028	2875	545081551	545082396	0.000000e+00	961.0
8	TraesCS2D01G499900	chr3B	85.989	728	87	8	1261	1975	813809664	813808939	0.000000e+00	765.0
9	TraesCS2D01G499900	chr3B	85.989	728	87	8	1261	1975	813836382	813835657	0.000000e+00	765.0
10	TraesCS2D01G499900	chr3B	83.188	458	75	2	1613	2069	545081097	545081553	4.430000e-113	418.0
11	TraesCS2D01G499900	chr4A	89.243	753	81	0	1	753	673129381	673128629	0.000000e+00	942.0
12	TraesCS2D01G499900	chr4A	81.876	629	104	6	2229	2852	735565310	735565933	3.280000e-144	521.0
13	TraesCS2D01G499900	chr7A	88.360	756	84	3	1	755	19446068	19446820	0.000000e+00	905.0
14	TraesCS2D01G499900	chr7A	90.291	103	10	0	2773	2875	39478637	39478535	5.000000e-28	135.0
15	TraesCS2D01G499900	chr7B	88.095	756	86	3	1	755	494242778	494243530	0.000000e+00	894.0
16	TraesCS2D01G499900	chr7B	76.815	496	98	14	2354	2842	100008992	100009477	2.200000e-66	263.0
17	TraesCS2D01G499900	chr7B	74.037	493	117	11	2355	2843	6389318	6388833	1.050000e-44	191.0
18	TraesCS2D01G499900	chr3A	77.642	1306	263	21	1585	2875	547128187	547126896	0.000000e+00	767.0
19	TraesCS2D01G499900	chr2B	82.035	629	103	6	2229	2852	711154683	711155306	7.060000e-146	527.0
20	TraesCS2D01G499900	chr2B	76.866	134	25	6	1618	1748	68187384	68187514	1.430000e-08	71.3
21	TraesCS2D01G499900	chr6A	76.145	524	91	25	909	1408	529573173	529573686	7.960000e-61	244.0
22	TraesCS2D01G499900	chr6A	72.241	580	122	28	916	1466	494495365	494495934	2.990000e-30	143.0
23	TraesCS2D01G499900	chr4B	75.356	491	114	5	2354	2842	404791405	404790920	2.230000e-56	230.0
24	TraesCS2D01G499900	chr4B	90.000	50	2	1	913	962	115065679	115065725	8.600000e-06	62.1
25	TraesCS2D01G499900	chrUn	79.077	325	65	3	2357	2681	30362478	30362157	1.340000e-53	220.0
26	TraesCS2D01G499900	chr3D	74.606	508	114	14	2354	2855	271438747	271439245	2.900000e-50	209.0

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	TraesCS2D01G499900	chr2D	594569784	594572658	2874	True	5310.0	5310	100.000	1	2875	1	chr2D.!!$R1	2874
1	TraesCS2D01G499900	chr1B	216519288	216520041	753	False	1155.0	1155	94.297	1	754	1	chr1B.!!$F1	753
2	TraesCS2D01G499900	chr1D	477259678	477260432	754	True	1140.0	1140	93.907	1	755	1	chr1D.!!$R2	754
3	TraesCS2D01G499900	chr1D	302901308	302902062	754	True	1110.0	1110	93.245	1	754	1	chr1D.!!$R1	753
4	TraesCS2D01G499900	chr6B	674956974	674957725	751	True	1081.0	1081	92.573	1	754	1	chr6B.!!$R1	753
5	TraesCS2D01G499900	chr5D	550425713	550426468	755	True	990.0	990	90.344	1	754	1	chr5D.!!$R1	753
6	TraesCS2D01G499900	chr5A	673561149	673561902	753	True	972.0	972	89.920	1	754	1	chr5A.!!$R1	753
7	TraesCS2D01G499900	chr3B	813808939	813809664	725	True	765.0	765	85.989	1261	1975	1	chr3B.!!$R1	714
8	TraesCS2D01G499900	chr3B	813835657	813836382	725	True	765.0	765	85.989	1261	1975	1	chr3B.!!$R2	714
9	TraesCS2D01G499900	chr3B	545081097	545082396	1299	False	689.5	961	85.190	1613	2875	2	chr3B.!!$F1	1262
10	TraesCS2D01G499900	chr4A	673128629	673129381	752	True	942.0	942	89.243	1	753	1	chr4A.!!$R1	752
11	TraesCS2D01G499900	chr4A	735565310	735565933	623	False	521.0	521	81.876	2229	2852	1	chr4A.!!$F1	623
12	TraesCS2D01G499900	chr7A	19446068	19446820	752	False	905.0	905	88.360	1	755	1	chr7A.!!$F1	754
13	TraesCS2D01G499900	chr7B	494242778	494243530	752	False	894.0	894	88.095	1	755	1	chr7B.!!$F2	754
14	TraesCS2D01G499900	chr3A	547126896	547128187	1291	True	767.0	767	77.642	1585	2875	1	chr3A.!!$R1	1290
15	TraesCS2D01G499900	chr2B	711154683	711155306	623	False	527.0	527	82.035	2229	2852	1	chr2B.!!$F2	623
16	TraesCS2D01G499900	chr6A	529573173	529573686	513	False	244.0	244	76.145	909	1408	1	chr6A.!!$F2	499

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
842	843	0.035725	GGGTTTTTCCGACCCGATCT	60.036	55.0	0.0	0.0	46.71	2.75	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2565	2653	0.174845	TACCTTCAGGATTCCACGCG	59.825	55.0	3.53	3.53	38.94	6.01	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
70	71	3.253432	GTCTCTTCCAACGGAGCAATTTT	59.747	43.478	0.00	0.00	31.21	1.82
95	96	4.280436	TGATGATCGTTACTTTGTGGGT	57.720	40.909	0.00	0.00	0.00	4.51
138	139	7.449247	GGAAAGCTATACATGAGGAGATCTTT	58.551	38.462	0.00	0.11	0.00	2.52
172	173	3.066621	TGCCACTGACAACTTCATCAAAC	59.933	43.478	0.00	0.00	32.17	2.93
216	217	4.962155	TCTTGAAGAAGAAGGAGAACACC	58.038	43.478	0.00	0.00	35.14	4.16
224	225	1.134438	AAGGAGAACACCCAGGGGAC	61.134	60.000	11.37	0.00	38.96	4.46
324	325	4.776647	GGCATGTTTGGCGCGGTC	62.777	66.667	8.83	0.00	38.79	4.79
447	448	0.403271	AGGCACTGGCACTTTCAGAT	59.597	50.000	5.25	0.00	43.71	2.90
558	559	2.496899	TTGTCCAAGAGATCAAGGCC	57.503	50.000	0.00	0.00	0.00	5.19
573	574	0.615850	AGGCCAGAGCAACTACCTTC	59.384	55.000	5.01	0.00	42.56	3.46
711	712	6.574350	CGACCTTCTCTTTGTACCTATGAAT	58.426	40.000	0.00	0.00	0.00	2.57
771	772	2.844839	GGCAGAGTCCGCCCCTAT	60.845	66.667	6.05	0.00	44.22	2.57
772	773	1.533273	GGCAGAGTCCGCCCCTATA	60.533	63.158	6.05	0.00	44.22	1.31
773	774	1.536943	GGCAGAGTCCGCCCCTATAG	61.537	65.000	6.05	0.00	44.22	1.31
774	775	1.536943	GCAGAGTCCGCCCCTATAGG	61.537	65.000	12.27	12.27	0.00	2.57
775	776	0.178958	CAGAGTCCGCCCCTATAGGT	60.179	60.000	17.72	0.00	0.00	3.08
776	777	0.178958	AGAGTCCGCCCCTATAGGTG	60.179	60.000	17.72	7.51	37.15	4.00
781	782	2.847715	GCCCCTATAGGTGGCGGT	60.848	66.667	26.14	0.00	40.16	5.68
782	783	2.449450	GCCCCTATAGGTGGCGGTT	61.449	63.158	26.14	0.00	40.16	4.44
783	784	1.991339	GCCCCTATAGGTGGCGGTTT	61.991	60.000	26.14	0.00	40.16	3.27
784	785	0.108019	CCCCTATAGGTGGCGGTTTC	59.892	60.000	17.72	0.00	0.00	2.78
785	786	0.108019	CCCTATAGGTGGCGGTTTCC	59.892	60.000	17.72	0.00	0.00	3.13
797	798	2.894307	CGGTTTCCGTTTCTTCATCC	57.106	50.000	0.00	0.00	42.73	3.51
798	799	1.127951	CGGTTTCCGTTTCTTCATCCG	59.872	52.381	0.00	0.00	42.73	4.18
799	800	2.419667	GGTTTCCGTTTCTTCATCCGA	58.580	47.619	0.00	0.00	0.00	4.55

Showing 1 to 25 of 277 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	71	4.387559	CCACAAAGTAACGATCATCAACGA	59.612	41.667	0.00	0.00	0.00	3.85
95	96	1.153647	CGCCGTGCACTCCAGATAA	60.154	57.895	16.19	0.00	0.00	1.75
138	139	1.699083	TCAGTGGCAAATGGAGTCTGA	59.301	47.619	0.00	0.00	0.00	3.27
172	173	7.164230	AGAACTCTATGTCTGACAAGTAAGG	57.836	40.000	15.31	6.04	0.00	2.69
216	217	1.918293	TGGTACTGCTGTCCCCTGG	60.918	63.158	0.00	0.00	0.00	4.45
224	225	1.733041	CGTGGTCGTGGTACTGCTG	60.733	63.158	0.00	0.00	0.00	4.41
321	322	2.551912	CCTGCAAACCACACCGACC	61.552	63.158	0.00	0.00	0.00	4.79
324	325	1.603455	ATCCCTGCAAACCACACCG	60.603	57.895	0.00	0.00	0.00	4.94
447	448	7.275183	CCAGTATTTGGTTGATGTAGAGATCA	58.725	38.462	0.00	0.00	42.41	2.92
756	757	0.178958	ACCTATAGGGGCGGACTCTG	60.179	60.000	22.91	0.00	40.27	3.35
757	758	0.178958	CACCTATAGGGGCGGACTCT	60.179	60.000	22.91	0.00	40.27	3.24
758	759	1.186267	CCACCTATAGGGGCGGACTC	61.186	65.000	22.91	0.00	37.25	3.36
759	760	1.152312	CCACCTATAGGGGCGGACT	60.152	63.158	22.91	0.00	37.25	3.85
760	761	2.880380	GCCACCTATAGGGGCGGAC	61.880	68.421	26.14	14.84	40.16	4.79
761	762	2.525877	GCCACCTATAGGGGCGGA	60.526	66.667	26.14	0.00	40.16	5.54
764	765	1.991339	AAACCGCCACCTATAGGGGC	61.991	60.000	28.49	28.49	43.63	5.80
765	766	0.108019	GAAACCGCCACCTATAGGGG	59.892	60.000	22.91	19.11	41.66	4.79
766	767	0.108019	GGAAACCGCCACCTATAGGG	59.892	60.000	22.91	11.41	40.27	3.53
767	768	0.249741	CGGAAACCGCCACCTATAGG	60.250	60.000	17.73	17.73	41.17	2.57
768	769	3.284197	CGGAAACCGCCACCTATAG	57.716	57.895	0.00	0.00	41.17	1.31
779	780	2.159037	GTCGGATGAAGAAACGGAAACC	59.841	50.000	0.00	0.00	0.00	3.27
780	781	2.159881	CGTCGGATGAAGAAACGGAAAC	60.160	50.000	0.00	0.00	0.00	2.78
781	782	2.063266	CGTCGGATGAAGAAACGGAAA	58.937	47.619	0.00	0.00	0.00	3.13
782	783	1.270274	TCGTCGGATGAAGAAACGGAA	59.730	47.619	0.00	0.00	34.30	4.30
783	784	0.883153	TCGTCGGATGAAGAAACGGA	59.117	50.000	0.00	0.00	34.30	4.69

Showing 1 to 25 of 252 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.