AutoCloner

Multiple sequence alignment - TraesCS5B01G152200

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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	TraesCS5B01G152200	chr5B	100.000	4712	0	0	1	4712	281582655	281577944	0	8702
1	TraesCS5B01G152200	chr5A	94.706	2701	95	22	7	2675	331111917	331114601	0	4152
2	TraesCS5B01G152200	chr5A	96.441	1995	45	8	2719	4712	331114847	331116816	0	3267
3	TraesCS5B01G152200	chr5D	97.139	1992	32	6	2721	4712	247074627	247076593	0	3339
4	TraesCS5B01G152200	chr5D	94.875	1834	68	7	877	2700	247072525	247074342	0	2843
5	TraesCS5B01G152200	chr5D	95.023	864	21	11	5	847	247071353	247072215	0	1338
6	TraesCS5B01G152200	chr3A	90.020	1012	76	9	2783	3788	95945634	95944642	0	1286
7	TraesCS5B01G152200	chr3A	84.712	1040	120	17	991	1993	95948646	95947609	0	1003
8	TraesCS5B01G152200	chr3B	89.631	1003	82	7	2793	3792	127856285	127855302	0	1256
9	TraesCS5B01G152200	chr3B	85.481	1040	112	16	991	1993	127862519	127861482	0	1048
10	TraesCS5B01G152200	chr3D	88.495	1043	94	9	2751	3786	81693319	81692296	0	1238
11	TraesCS5B01G152200	chr3D	85.243	1030	115	14	991	1985	81696338	81695311	0	1026

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	TraesCS5B01G152200	chr5B	281577944	281582655	4711	True	8702.000000	8702	100.0000	1	4712	1	chr5B.!!$R1	4711
1	TraesCS5B01G152200	chr5A	331111917	331116816	4899	False	3709.500000	4152	95.5735	7	4712	2	chr5A.!!$F1	4705
2	TraesCS5B01G152200	chr5D	247071353	247076593	5240	False	2506.666667	3339	95.6790	5	4712	3	chr5D.!!$F1	4707
3	TraesCS5B01G152200	chr3A	95944642	95948646	4004	True	1144.500000	1286	87.3660	991	3788	2	chr3A.!!$R1	2797
4	TraesCS5B01G152200	chr3B	127855302	127856285	983	True	1256.000000	1256	89.6310	2793	3792	1	chr3B.!!$R1	999
5	TraesCS5B01G152200	chr3B	127861482	127862519	1037	True	1048.000000	1048	85.4810	991	1993	1	chr3B.!!$R2	1002
6	TraesCS5B01G152200	chr3D	81692296	81696338	4042	True	1132.000000	1238	86.8690	991	3786	2	chr3D.!!$R1	2795

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
592	596	0.389296	TCGCCACCATGTCGTACAAG	60.389	55.0	0.00	0.00	0.00	3.16	F
1221	1572	0.391793	TCACGTCCACACTGCACAAA	60.392	50.0	0.00	0.00	0.00	2.83	F
1287	1638	0.615331	AGCAGAAGATTGCCGAGGAA	59.385	50.0	0.00	0.00	45.18	3.36	F
2691	3580	1.436600	CACTGCTGCAGTACCAAGAG	58.563	55.0	32.51	16.13	43.43	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2406	3196	0.036388	TCGGATCTTGCTGGTGTTCC	60.036	55.000	0.00	0.00	0.00	3.62	R
2662	3551	1.975407	GCAGCAGTGGGTCAGCATT	60.975	57.895	0.00	0.00	0.00	3.56	R
2716	4337	5.707495	AGAAGTGGTTATCTCCTAGGTAGG	58.293	45.833	9.08	0.00	45.02	3.18	R
4074	5748	0.702316	AAGGGAAAGGTACGCCCATT	59.298	50.000	12.44	1.36	44.55	3.16	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
30	31	2.360350	ACACCCCTTGCATCAGCG	60.360	61.111	0.00	0.00	46.23	5.18
37	38	0.729116	CCTTGCATCAGCGGTTACAG	59.271	55.000	0.00	0.00	46.23	2.74
196	199	3.077484	ACATGCCATCAGTAAACAGCT	57.923	42.857	0.00	0.00	0.00	4.24
592	596	0.389296	TCGCCACCATGTCGTACAAG	60.389	55.000	0.00	0.00	0.00	3.16
702	707	5.052298	CCATTTATCTGGGCTGAGCATCAT	61.052	45.833	6.82	0.00	37.25	2.45
705	710	9.178630	CCATTTATCTGGGCTGAGCATCATAAC	62.179	44.444	6.82	0.00	37.25	1.89
720	730	9.294030	GAGCATCATAACAGAAATTTTGTTAGG	57.706	33.333	19.98	19.98	42.40	2.69
732	742	7.619302	AGAAATTTTGTTAGGGATGCATAAGGA	59.381	33.333	0.00	0.00	0.00	3.36
853	1162	1.956678	GGGCCGCGCTTAATCTCTC	60.957	63.158	5.56	0.00	0.00	3.20
855	1164	1.956678	GCCGCGCTTAATCTCTCCC	60.957	63.158	5.56	0.00	0.00	4.30
982	1294	2.196229	CCACGAAAACCCCCACCA	59.804	61.111	0.00	0.00	0.00	4.17
1217	1568	2.279186	CGTCACGTCCACACTGCA	60.279	61.111	0.00	0.00	0.00	4.41
1221	1572	0.391793	TCACGTCCACACTGCACAAA	60.392	50.000	0.00	0.00	0.00	2.83
1287	1638	0.615331	AGCAGAAGATTGCCGAGGAA	59.385	50.000	0.00	0.00	45.18	3.36
1520	1871	2.507452	CATCTCCCGCATGCTCCA	59.493	61.111	17.13	0.00	0.00	3.86
1530	1881	1.919600	GCATGCTCCAGGAGAAGGGT	61.920	60.000	21.89	0.00	0.00	4.34
1644	1995	2.591429	CTGGTGTTCGTGCTGCCA	60.591	61.111	0.00	0.00	0.00	4.92
1689	2040	2.548707	GGAGATGCTGATGCCGATTGTA	60.549	50.000	0.00	0.00	38.71	2.41
2125	2908	3.127589	TCTGATCTTCACGAAAAACGCA	58.872	40.909	0.00	0.00	46.94	5.24
2137	2920	4.201783	ACGAAAAACGCAGGATACATTAGC	60.202	41.667	0.00	0.00	46.94	3.09
2184	2967	8.927675	TTTCTAATGGGTAAAACTTAAGAGCA	57.072	30.769	10.09	0.00	0.00	4.26
2189	2972	3.434641	GGGTAAAACTTAAGAGCACGGTC	59.565	47.826	10.09	0.00	0.00	4.79
2304	3094	6.351711	GGATGTAGGAGGAATATGAGACCATG	60.352	46.154	0.00	0.00	34.31	3.66
2406	3196	4.263462	TGTTATATTGCAGGCCCTCCTATG	60.263	45.833	0.00	0.00	41.93	2.23
2505	3366	4.813296	AACGACAATTTCAGTGTCCTTC	57.187	40.909	0.00	0.00	42.00	3.46
2507	3368	2.411547	CGACAATTTCAGTGTCCTTCGC	60.412	50.000	0.00	0.00	42.00	4.70
2573	3462	9.102757	AGCAATGTAGATGTAAACTTGTCTATG	57.897	33.333	0.00	0.00	0.00	2.23
2691	3580	1.436600	CACTGCTGCAGTACCAAGAG	58.563	55.000	32.51	16.13	43.43	2.85
3342	5011	3.777106	TTCCCTGATATCCAGCATGTC	57.223	47.619	0.00	0.00	41.57	3.06
3378	5047	2.030628	GCCTGCCGAGATAGAGAACTAC	60.031	54.545	0.00	0.00	0.00	2.73
3820	5493	6.980978	CCTTACCTTACATGTGTAGACATCAG	59.019	42.308	9.11	0.05	41.12	2.90
3865	5538	6.342111	CAGATACAGTAGGGAACTCCTTTTC	58.658	44.000	0.00	0.00	45.47	2.29
4074	5748	6.569127	TGTAGGGATCTTTAAAGGCATACA	57.431	37.500	15.13	14.86	0.00	2.29
4083	5757	2.428544	AAAGGCATACAATGGGCGTA	57.571	45.000	0.00	0.00	34.32	4.42
4188	5862	6.694447	ACTTTCAAATCCATCTGGTTCATTG	58.306	36.000	0.00	0.00	36.34	2.82
4447	6121	2.596452	CTTGCTTCTCTAGAACGCGAA	58.404	47.619	15.93	0.00	33.77	4.70
4524	6198	3.438087	CAGACAGTAGTCCAAAGCAATGG	59.562	47.826	1.50	1.50	46.15	3.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
30	31	7.596248	TGTCGTATACAAAGAAAGACTGTAACC	59.404	37.037	3.32	0.00	34.29	2.85
37	38	7.404139	AACTGTGTCGTATACAAAGAAAGAC	57.596	36.000	3.32	1.18	45.18	3.01
196	199	4.678256	AGTAGAGGAGAAGAATGTGGTGA	58.322	43.478	0.00	0.00	0.00	4.02
373	377	2.048503	CCCGACGTCTGGAACACC	60.049	66.667	20.35	0.00	0.00	4.16
592	596	2.476051	CTCAACCACGACATGCGC	59.524	61.111	0.00	0.00	46.04	6.09
702	707	7.531857	TGCATCCCTAACAAAATTTCTGTTA	57.468	32.000	17.37	17.37	38.05	2.41
705	710	7.707893	CCTTATGCATCCCTAACAAAATTTCTG	59.292	37.037	0.19	0.00	0.00	3.02
717	727	5.593909	CACACATTTTCCTTATGCATCCCTA	59.406	40.000	0.19	0.00	0.00	3.53
720	730	5.104374	CACACACATTTTCCTTATGCATCC	58.896	41.667	0.19	0.00	0.00	3.51
809	840	2.575532	CAGACCCAACAGTGTCATGTT	58.424	47.619	0.00	0.00	44.12	2.71
982	1294	0.921256	ATGGCTGGGGTTTAGAGGCT	60.921	55.000	0.00	0.00	33.56	4.58
1031	1343	1.546834	GTAGTTGTCCTCGTCATCGC	58.453	55.000	0.00	0.00	36.96	4.58
1195	1546	1.105167	AGTGTGGACGTGACGAGGAA	61.105	55.000	13.70	0.00	0.00	3.36
1231	1582	4.176752	GGTGGGGGTGATCTCCGC	62.177	72.222	19.63	19.63	39.30	5.54
1287	1638	3.450115	GTCGTGCGGTAGGAGGCT	61.450	66.667	0.00	0.00	0.00	4.58
1320	1671	1.134699	GTGATGTCCTTGGCGATCTCA	60.135	52.381	0.00	0.00	0.00	3.27
1520	1871	1.115467	CTGCACGATACCCTTCTCCT	58.885	55.000	0.00	0.00	0.00	3.69
1644	1995	1.450848	CAGCGCCACCATGATGAGT	60.451	57.895	2.29	0.00	0.00	3.41
1804	2155	0.108138	ATGCAGAGCAAGGGTCGTAC	60.108	55.000	0.00	0.00	43.62	3.67
2094	2875	4.449068	TCGTGAAGATCAGAAAAAGACAGC	59.551	41.667	0.00	0.00	0.00	4.40
2125	2908	1.416401	CCACCCACGCTAATGTATCCT	59.584	52.381	0.00	0.00	0.00	3.24
2184	2967	0.535335	ATAGACACGCCAATGACCGT	59.465	50.000	0.00	0.00	38.35	4.83
2189	2972	6.944557	TCGATAATTATAGACACGCCAATG	57.055	37.500	4.34	0.00	0.00	2.82
2304	3094	5.445964	TCTGAATTATTTTCTACCCAGGCC	58.554	41.667	0.00	0.00	0.00	5.19
2406	3196	0.036388	TCGGATCTTGCTGGTGTTCC	60.036	55.000	0.00	0.00	0.00	3.62
2505	3366	3.666883	TTGTAATCGTTGGCATTAGCG	57.333	42.857	0.00	0.00	43.41	4.26
2507	3368	5.238432	TGCCTATTGTAATCGTTGGCATTAG	59.762	40.000	0.00	0.00	43.09	1.73
2573	3462	9.965824	CAATGATGGGGATTAGTTGTTTAATAC	57.034	33.333	0.00	0.00	0.00	1.89
2662	3551	1.975407	GCAGCAGTGGGTCAGCATT	60.975	57.895	0.00	0.00	0.00	3.56
2716	4337	5.707495	AGAAGTGGTTATCTCCTAGGTAGG	58.293	45.833	9.08	0.00	45.02	3.18
2717	4338	7.663043	AAAGAAGTGGTTATCTCCTAGGTAG	57.337	40.000	9.08	5.31	0.00	3.18
3342	5011	5.178061	TCGGCAGGCATATCATAGTTAATG	58.822	41.667	0.00	0.00	36.88	1.90
3654	5323	1.280133	TCTCTTCTGGAACCAGCCATG	59.720	52.381	15.20	6.68	43.31	3.66
3820	5493	7.615582	TCTGGATTGTCATCTCATTGTTTAC	57.384	36.000	0.00	0.00	0.00	2.01
3865	5538	5.165961	TGTGAATACCCTCCAGAAAAGAG	57.834	43.478	0.00	0.00	0.00	2.85
4074	5748	0.702316	AAGGGAAAGGTACGCCCATT	59.298	50.000	12.44	1.36	44.55	3.16
4083	5757	8.499288	TGAAACCATTAAATAAAGGGAAAGGT	57.501	30.769	0.00	0.00	41.79	3.50
4245	5919	1.235724	GGACCTTTGAAACCTCCGTG	58.764	55.000	0.00	0.00	0.00	4.94
4524	6198	4.678509	TTTACGACAATGCAACCATCTC	57.321	40.909	0.00	0.00	0.00	2.75
4529	6203	3.987220	AGCAATTTTACGACAATGCAACC	59.013	39.130	0.00	0.00	0.00	3.77
4589	6263	6.508030	TTTCCTGCCATATGAGTAATGGTA	57.492	37.500	3.65	0.00	44.87	3.25
4622	6296	7.599998	ACATCAGGTGATTAAAAGTTGCATTTC	59.400	33.333	0.00	0.00	31.21	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.