AutoCloner

Multiple sequence alignment - TraesCS1A01G202400

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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	TraesCS1A01G202400	chr1A	100.000	3266	0	0	1	3266	363602982	363599717	0.000000e+00	6032
1	TraesCS1A01G202400	chr1A	95.320	3269	142	9	3	3266	118198329	118195067	0.000000e+00	5179
2	TraesCS1A01G202400	chr1A	90.453	1016	67	14	3	1015	548052323	548053311	0.000000e+00	1312
3	TraesCS1A01G202400	chr7A	95.903	3271	120	10	3	3266	93310877	93314140	0.000000e+00	5286
4	TraesCS1A01G202400	chr7A	95.350	3269	138	11	3	3266	499950724	499953983	0.000000e+00	5182
5	TraesCS1A01G202400	chr2A	95.838	3268	127	9	3	3266	53575668	53572406	0.000000e+00	5273
6	TraesCS1A01G202400	chr2A	95.656	3269	127	10	3	3266	697151056	697154314	0.000000e+00	5236
7	TraesCS1A01G202400	chr2A	90.443	1716	98	32	3	1711	728981195	728982851	0.000000e+00	2200
8	TraesCS1A01G202400	chr2A	87.664	608	51	4	2683	3266	307019695	307019088	0.000000e+00	686
9	TraesCS1A01G202400	chr6A	95.566	3270	133	10	3	3266	594022903	594026166	0.000000e+00	5225
10	TraesCS1A01G202400	chr6A	95.073	1502	65	8	3	1501	616507633	616506138	0.000000e+00	2355
11	TraesCS1A01G202400	chr5A	95.439	3267	138	10	3	3266	689846366	689843108	0.000000e+00	5197
12	TraesCS1A01G202400	chr3A	95.774	3100	119	9	172	3266	535603338	535606430	0.000000e+00	4988
13	TraesCS1A01G202400	chr4D	93.119	3299	183	17	6	3266	482669896	482666604	0.000000e+00	4795
14	TraesCS1A01G202400	chr3D	90.431	418	28	9	6	415	516359889	516359476	1.030000e-149	540

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	TraesCS1A01G202400	chr1A	363599717	363602982	3265	True	6032	6032	100.000	1	3266	1	chr1A.!!$R2	3265
1	TraesCS1A01G202400	chr1A	118195067	118198329	3262	True	5179	5179	95.320	3	3266	1	chr1A.!!$R1	3263
2	TraesCS1A01G202400	chr1A	548052323	548053311	988	False	1312	1312	90.453	3	1015	1	chr1A.!!$F1	1012
3	TraesCS1A01G202400	chr7A	93310877	93314140	3263	False	5286	5286	95.903	3	3266	1	chr7A.!!$F1	3263
4	TraesCS1A01G202400	chr7A	499950724	499953983	3259	False	5182	5182	95.350	3	3266	1	chr7A.!!$F2	3263
5	TraesCS1A01G202400	chr2A	53572406	53575668	3262	True	5273	5273	95.838	3	3266	1	chr2A.!!$R1	3263
6	TraesCS1A01G202400	chr2A	697151056	697154314	3258	False	5236	5236	95.656	3	3266	1	chr2A.!!$F1	3263
7	TraesCS1A01G202400	chr2A	728981195	728982851	1656	False	2200	2200	90.443	3	1711	1	chr2A.!!$F2	1708
8	TraesCS1A01G202400	chr2A	307019088	307019695	607	True	686	686	87.664	2683	3266	1	chr2A.!!$R2	583
9	TraesCS1A01G202400	chr6A	594022903	594026166	3263	False	5225	5225	95.566	3	3266	1	chr6A.!!$F1	3263
10	TraesCS1A01G202400	chr6A	616506138	616507633	1495	True	2355	2355	95.073	3	1501	1	chr6A.!!$R1	1498
11	TraesCS1A01G202400	chr5A	689843108	689846366	3258	True	5197	5197	95.439	3	3266	1	chr5A.!!$R1	3263
12	TraesCS1A01G202400	chr3A	535603338	535606430	3092	False	4988	4988	95.774	172	3266	1	chr3A.!!$F1	3094
13	TraesCS1A01G202400	chr4D	482666604	482669896	3292	True	4795	4795	93.119	6	3266	1	chr4D.!!$R1	3260

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
674	694	0.464554	TGCAACATTGGTCGTGTGGA	60.465	50.0	0.0	0.0	0.0	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2648	2674	1.009829	CATGCCGGTGACTCTAAAGC	58.99	55.0	1.9	0.0	0.0	3.51	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
126	130	3.861276	TTGACGGTGTGTATCTCGAAT	57.139	42.857	0.00	0.00	0.00	3.34
255	264	2.426522	TCGAGATTTTGCTGTGGAAGG	58.573	47.619	0.00	0.00	0.00	3.46
321	330	5.680619	TGGAACAAAGTATCAACTCTGTGT	58.319	37.500	0.00	0.00	35.83	3.72
323	332	5.758296	GGAACAAAGTATCAACTCTGTGTGA	59.242	40.000	0.00	0.00	35.83	3.58
325	334	7.602644	GGAACAAAGTATCAACTCTGTGTGATA	59.397	37.037	0.00	0.00	35.83	2.15
326	335	7.891183	ACAAAGTATCAACTCTGTGTGATAC	57.109	36.000	13.44	13.44	35.55	2.24
327	336	7.671302	ACAAAGTATCAACTCTGTGTGATACT	58.329	34.615	16.74	16.74	43.44	2.12
328	337	8.150945	ACAAAGTATCAACTCTGTGTGATACTT	58.849	33.333	23.63	23.63	46.58	2.24
330	339	8.539770	AAGTATCAACTCTGTGTGATACTTTG	57.460	34.615	23.63	5.89	44.99	2.77
358	375	0.601057	TCAAGATTCGTGTCGCCTGA	59.399	50.000	0.00	0.00	0.00	3.86
575	595	3.075998	CACGTGAGAGTGATGCGC	58.924	61.111	10.90	0.00	44.43	6.09
589	609	3.292159	GCGCCGGGAAGTTTGGTT	61.292	61.111	2.18	0.00	0.00	3.67
674	694	0.464554	TGCAACATTGGTCGTGTGGA	60.465	50.000	0.00	0.00	0.00	4.02
721	741	5.390613	GTGCGAGCAATAACATTTGTTACT	58.609	37.500	5.34	0.00	42.55	2.24
743	763	3.591023	TGCTTAATCGGACGATTTGACA	58.409	40.909	22.82	15.53	41.55	3.58
780	800	3.120385	CGCGAGCATTGCCACTCA	61.120	61.111	0.00	0.00	44.79	3.41
781	801	2.679934	CGCGAGCATTGCCACTCAA	61.680	57.895	0.00	0.00	44.79	3.02
823	843	1.153745	GACGAGCGCATGTCTTCCT	60.154	57.895	20.65	0.00	32.37	3.36
948	968	3.935203	ACTATTGCTGTTCCATCTCAACG	59.065	43.478	0.00	0.00	0.00	4.10
1140	1160	0.958822	ACATCCACGGCAAGGAAAAC	59.041	50.000	0.00	0.00	38.93	2.43
1590	1611	6.429078	TGTTCTAGCGTACTTTCTGTTCTAGA	59.571	38.462	0.00	0.00	33.44	2.43
1970	1995	0.032540	AACCCCGACAAGTACGTCAC	59.967	55.000	0.00	0.00	35.54	3.67
1978	2003	1.968493	ACAAGTACGTCACCATCCAGT	59.032	47.619	0.00	0.00	0.00	4.00
2098	2124	9.432982	AGGATAAGATTGATAGAGTTGAAGACT	57.567	33.333	0.00	0.00	42.70	3.24
2143	2169	3.445096	ACTGCCAAATTACCTCATTGAGC	59.555	43.478	8.23	0.00	0.00	4.26
2337	2363	5.008118	GCTTGTCCTTTCTATTGTATCAGGC	59.992	44.000	0.00	0.00	0.00	4.85
2542	2568	3.197265	ACAACAAAATGCAAAGCAGTCC	58.803	40.909	0.00	0.00	43.65	3.85
2648	2674	1.228367	AGAGGCACAGGTTTGCAGG	60.228	57.895	0.00	0.00	44.94	4.85
2741	2767	9.529823	CTCCTAATACATAGTTATAGGGTCACA	57.470	37.037	0.00	0.00	0.00	3.58
2769	2800	1.070758	AGTGAGTCAAGGTTGTGCGAT	59.929	47.619	0.00	0.00	0.00	4.58
2811	2842	4.455533	GTCATGGCAAGTGTAATGTGAGAA	59.544	41.667	0.00	0.00	0.00	2.87
2828	2859	0.620556	GAAAGGCACCTGGATCCAGA	59.379	55.000	38.37	7.53	46.30	3.86
2869	2900	0.892755	ACTTCTCGATGCACGGGTAA	59.107	50.000	8.13	2.45	43.73	2.85
2870	2901	1.480954	ACTTCTCGATGCACGGGTAAT	59.519	47.619	8.13	0.00	43.73	1.89
2885	2916	2.429478	GGTAATAACGTTGTGGGTGCT	58.571	47.619	11.99	0.00	0.00	4.40
2892	2923	1.346395	ACGTTGTGGGTGCTCAATAGA	59.654	47.619	0.00	0.00	0.00	1.98
3036	3068	1.210478	AGATGCAGTTACGGAAGGCAT	59.790	47.619	17.01	17.01	46.91	4.40
3046	3078	0.322456	CGGAAGGCATGGAGGTGAAA	60.322	55.000	0.00	0.00	0.00	2.69
3139	3190	4.891756	TCCGAATACGAATTTAGGGAGTCT	59.108	41.667	0.00	0.00	42.66	3.24
3234	3285	4.101119	GCATTACTGGCTCTTAACCCTCTA	59.899	45.833	0.00	0.00	0.00	2.43
3253	3304	0.112995	AGATGCATGGTGGTGTGGTT	59.887	50.000	2.46	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.517037	AAAACGAACAGACAGAATCGATC	57.483	39.130	0.00	0.00	38.59	3.69
1	2	5.924475	AAAAACGAACAGACAGAATCGAT	57.076	34.783	0.00	0.00	38.59	3.59
41	45	0.817634	CAAGGACTTCAACACCGCCA	60.818	55.000	0.00	0.00	0.00	5.69
126	130	4.278513	CGCCAACCACCCTCCCAA	62.279	66.667	0.00	0.00	0.00	4.12
255	264	3.028130	CCACTACTCTCTTCCTTCCTCC	58.972	54.545	0.00	0.00	0.00	4.30
306	315	7.671302	ACAAAGTATCACACAGAGTTGATACT	58.329	34.615	15.38	15.38	44.34	2.12
307	316	7.891183	ACAAAGTATCACACAGAGTTGATAC	57.109	36.000	11.98	11.98	39.21	2.24
309	318	7.807977	AAACAAAGTATCACACAGAGTTGAT	57.192	32.000	0.00	0.00	0.00	2.57
311	320	8.612619	ACTAAAACAAAGTATCACACAGAGTTG	58.387	33.333	0.00	0.00	0.00	3.16
313	322	9.998106	ATACTAAAACAAAGTATCACACAGAGT	57.002	29.630	0.00	0.00	35.70	3.24
325	334	9.052759	ACACGAATCTTGATACTAAAACAAAGT	57.947	29.630	0.00	0.00	0.00	2.66
326	335	9.530129	GACACGAATCTTGATACTAAAACAAAG	57.470	33.333	0.00	0.00	0.00	2.77
327	336	8.218441	CGACACGAATCTTGATACTAAAACAAA	58.782	33.333	0.00	0.00	0.00	2.83
328	337	7.620600	GCGACACGAATCTTGATACTAAAACAA	60.621	37.037	0.00	0.00	0.00	2.83
329	338	6.183360	GCGACACGAATCTTGATACTAAAACA	60.183	38.462	0.00	0.00	0.00	2.83
330	339	6.176453	GCGACACGAATCTTGATACTAAAAC	58.824	40.000	0.00	0.00	0.00	2.43
532	552	2.051638	CGACACACGCTCGTAACTG	58.948	57.895	0.00	0.00	34.51	3.16
575	595	2.354805	CCTCTAGAACCAAACTTCCCGG	60.355	54.545	0.00	0.00	0.00	5.73
654	674	0.597568	CCACACGACCAATGTTGCAT	59.402	50.000	0.00	0.00	0.00	3.96
692	712	2.778299	TGTTATTGCTCGCACCTTTCT	58.222	42.857	0.00	0.00	0.00	2.52
721	741	3.997681	TGTCAAATCGTCCGATTAAGCAA	59.002	39.130	14.61	0.00	43.26	3.91
743	763	1.138859	GGTTGGCAGGAAAAAGCAACT	59.861	47.619	0.00	0.00	0.00	3.16
780	800	4.595538	TGCGTCGAGGCAACCGTT	62.596	61.111	28.85	0.00	40.59	4.44
823	843	0.107800	CTCGTCGTGGTAGAGAGGGA	60.108	60.000	0.00	0.00	34.13	4.20
918	938	4.130857	TGGAACAGCAATAGTGTTTTCGA	58.869	39.130	0.00	0.00	38.26	3.71
948	968	3.132646	ACAGAGATTGTGAGGAGATGCTC	59.867	47.826	0.00	0.00	38.99	4.26
1140	1160	0.177836	TGGTGCATACGACATCCAGG	59.822	55.000	0.00	0.00	0.00	4.45
1744	1766	6.202516	TGGACGAAAACATTTCAGAAACTT	57.797	33.333	0.00	0.00	0.00	2.66
1803	1825	9.396022	ACATTTAAGGTCGATTCATCAAGTATT	57.604	29.630	0.00	0.00	0.00	1.89
1970	1995	2.022195	CTCTCCATTTGCACTGGATGG	58.978	52.381	15.72	12.70	41.83	3.51
1978	2003	3.831323	TGAAAGGAACTCTCCATTTGCA	58.169	40.909	0.00	0.00	45.24	4.08
2143	2169	1.388093	GTACGCATCTATCGCTGCATG	59.612	52.381	0.00	0.00	38.30	4.06
2337	2363	7.293745	TCGTTCTAACAGAAGTAAACTACGAG	58.706	38.462	0.00	0.00	34.42	4.18
2542	2568	3.609103	AAAGTGTACTCAGCGCAAAAG	57.391	42.857	11.47	6.13	0.00	2.27
2648	2674	1.009829	CATGCCGGTGACTCTAAAGC	58.990	55.000	1.90	0.00	0.00	3.51
2741	2767	3.933861	ACCTTGACTCACTTCCAAACT	57.066	42.857	0.00	0.00	0.00	2.66
2769	2800	1.915489	ACTCTTACATGCCCCATGACA	59.085	47.619	11.78	0.00	43.81	3.58
2811	2842	1.771255	GTATCTGGATCCAGGTGCCTT	59.229	52.381	35.95	18.56	43.75	4.35
2828	2859	1.095228	CAATCCCGTGCCTTGCGTAT	61.095	55.000	0.00	0.00	0.00	3.06
2869	2900	2.264005	TTGAGCACCCACAACGTTAT	57.736	45.000	0.00	0.00	0.00	1.89
2870	2901	2.264005	ATTGAGCACCCACAACGTTA	57.736	45.000	0.00	0.00	0.00	3.18
2885	2916	3.027412	GCCTCTCAGACCACTCTATTGA	58.973	50.000	0.00	0.00	0.00	2.57
2892	2923	0.612229	CACATGCCTCTCAGACCACT	59.388	55.000	0.00	0.00	0.00	4.00
3036	3068	1.144913	CCTCTTGGGTTTTCACCTCCA	59.855	52.381	0.00	0.00	43.65	3.86
3046	3078	1.073199	CTTCCGTGCCTCTTGGGTT	59.927	57.895	0.00	0.00	37.43	4.11
3139	3190	1.819288	CTCTAGAGGCTTCACAACCGA	59.181	52.381	12.27	0.00	0.00	4.69
3234	3285	0.112995	AACCACACCACCATGCATCT	59.887	50.000	0.00	0.00	0.00	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.