AutoCloner

Multiple sequence alignment - TraesCS6B01G261200

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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	TraesCS6B01G261200	chr6B	100.000	3331	0	0	1	3331	471169448	471166118	0.000000e+00	6152
1	TraesCS6B01G261200	chr1A	95.685	1993	78	7	1	1991	530705747	530703761	0.000000e+00	3197
2	TraesCS6B01G261200	chr1A	94.260	1359	55	4	1991	3331	530694439	530693086	0.000000e+00	2056
3	TraesCS6B01G261200	chr6A	94.972	1949	84	6	1	1937	100259315	100257369	0.000000e+00	3044
4	TraesCS6B01G261200	chr6A	93.552	853	32	6	1931	2762	100247985	100247135	0.000000e+00	1249
5	TraesCS6B01G261200	chr6A	91.707	627	48	2	2707	3331	100247137	100246513	0.000000e+00	867
6	TraesCS6B01G261200	chr7B	81.521	2511	381	62	91	2563	673520255	673522720	0.000000e+00	1989
7	TraesCS6B01G261200	chr2B	80.070	2283	362	63	98	2331	793164126	793161888	0.000000e+00	1609
8	TraesCS6B01G261200	chr2B	77.419	217	41	8	3117	3331	793161012	793160802	4.510000e-24	122
9	TraesCS6B01G261200	chr5A	78.895	2028	328	78	402	2376	603381294	603379314	0.000000e+00	1282
10	TraesCS6B01G261200	chr5A	73.719	917	199	38	1435	2331	414013445	414014339	1.490000e-83	320
11	TraesCS6B01G261200	chr5A	82.870	216	34	2	66	281	603381607	603381395	1.220000e-44	191
12	TraesCS6B01G261200	chr4B	78.836	2027	331	76	402	2376	127722145	127720165	0.000000e+00	1277
13	TraesCS6B01G261200	chr4B	82.870	216	34	2	66	281	127722458	127722246	1.220000e-44	191
14	TraesCS6B01G261200	chr2A	73.744	796	153	43	1148	1914	705790270	705791038	9.170000e-66	261
15	TraesCS6B01G261200	chrUn	82.870	216	34	2	66	281	391668380	391668592	1.220000e-44	191

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	TraesCS6B01G261200	chr6B	471166118	471169448	3330	True	6152.0	6152	100.0000	1	3331	1	chr6B.!!$R1	3330
1	TraesCS6B01G261200	chr1A	530703761	530705747	1986	True	3197.0	3197	95.6850	1	1991	1	chr1A.!!$R2	1990
2	TraesCS6B01G261200	chr1A	530693086	530694439	1353	True	2056.0	2056	94.2600	1991	3331	1	chr1A.!!$R1	1340
3	TraesCS6B01G261200	chr6A	100257369	100259315	1946	True	3044.0	3044	94.9720	1	1937	1	chr6A.!!$R1	1936
4	TraesCS6B01G261200	chr6A	100246513	100247985	1472	True	1058.0	1249	92.6295	1931	3331	2	chr6A.!!$R2	1400
5	TraesCS6B01G261200	chr7B	673520255	673522720	2465	False	1989.0	1989	81.5210	91	2563	1	chr7B.!!$F1	2472
6	TraesCS6B01G261200	chr2B	793160802	793164126	3324	True	865.5	1609	78.7445	98	3331	2	chr2B.!!$R1	3233
7	TraesCS6B01G261200	chr5A	603379314	603381607	2293	True	736.5	1282	80.8825	66	2376	2	chr5A.!!$R1	2310
8	TraesCS6B01G261200	chr5A	414013445	414014339	894	False	320.0	320	73.7190	1435	2331	1	chr5A.!!$F1	896
9	TraesCS6B01G261200	chr4B	127720165	127722458	2293	True	734.0	1277	80.8530	66	2376	2	chr4B.!!$R1	2310
10	TraesCS6B01G261200	chr2A	705790270	705791038	768	False	261.0	261	73.7440	1148	1914	1	chr2A.!!$F1	766

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
542	554	0.608035	ACCATCGCCGACCAATTGTT	60.608	50.0	4.43	0.0	0.00	2.83	F
1440	1483	0.108615	GACATGCTAGTGTCACGCCT	60.109	55.0	8.27	0.0	46.04	5.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2286	2397	0.108186	TCATTCAGAGCGTCGGCAAT	60.108	50.0	0.00	0.0	43.41	3.56	R
2949	3304	0.248866	GGGTGCCAAGTTTTCACACG	60.249	55.0	6.59	0.0	32.69	4.49	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
188	190	5.531634	TGAAATGAGAAGGAACATTGCAAC	58.468	37.500	0.00	0.00	38.57	4.17
259	261	2.547642	CCAAATTTGACAACACCCGCAT	60.548	45.455	19.86	0.00	0.00	4.73
309	311	2.140792	ACCAGGCGTCAGTGGTTCT	61.141	57.895	0.00	0.00	45.17	3.01
322	324	2.158295	AGTGGTTCTGGTACTCTCCACT	60.158	50.000	16.51	16.51	46.91	4.00
527	539	2.586425	CAAACCAGTGGTCTTGACCAT	58.414	47.619	23.20	11.16	42.41	3.55
542	554	0.608035	ACCATCGCCGACCAATTGTT	60.608	50.000	4.43	0.00	0.00	2.83
728	749	5.063438	CGAATTGGACATAGACGAACACAAT	59.937	40.000	0.00	0.00	0.00	2.71
734	755	4.569943	ACATAGACGAACACAATGAAGCT	58.430	39.130	0.00	0.00	0.00	3.74
761	782	3.756434	CGCCTGTTAAGAAGGATGGAAAA	59.244	43.478	8.10	0.00	36.91	2.29
782	803	2.093973	AGCCACTCTGATTTCACCTACG	60.094	50.000	0.00	0.00	0.00	3.51
784	805	3.512680	CCACTCTGATTTCACCTACGTC	58.487	50.000	0.00	0.00	0.00	4.34
837	858	2.951642	GGCCAGCTAATGATGCTTAACA	59.048	45.455	0.00	0.00	38.92	2.41
954	975	1.003355	CCATGGTCGAGCAACTGGT	60.003	57.895	22.64	0.91	0.00	4.00
1068	1100	5.416013	AGGTACTTTCCAAAGATAAGCAAGC	59.584	40.000	6.05	0.00	39.31	4.01
1074	1106	2.159517	CCAAAGATAAGCAAGCGTGGAC	60.160	50.000	0.79	0.00	0.00	4.02
1140	1173	1.433064	CCCCGATGCCATTTTCACG	59.567	57.895	0.00	0.00	0.00	4.35
1141	1174	1.029408	CCCCGATGCCATTTTCACGA	61.029	55.000	0.00	0.00	0.00	4.35
1146	1179	3.130633	CGATGCCATTTTCACGAGGATA	58.869	45.455	0.00	0.00	0.00	2.59
1212	1245	3.762823	TGCCATCAAGTCACAAATATGCA	59.237	39.130	0.00	0.00	0.00	3.96
1358	1391	4.034048	GCGGTATGAAATCACAACTACAGG	59.966	45.833	0.00	0.00	0.00	4.00
1440	1483	0.108615	GACATGCTAGTGTCACGCCT	60.109	55.000	8.27	0.00	46.04	5.52
1485	1528	6.860080	AGAATCATGTCAATACAAAGGCAAG	58.140	36.000	0.00	0.00	39.58	4.01
1492	1541	4.391830	GTCAATACAAAGGCAAGTCATCGA	59.608	41.667	0.00	0.00	0.00	3.59
1781	1859	3.366577	GGACACAACACGGAAAACTTGTT	60.367	43.478	0.00	0.00	41.66	2.83
1795	1873	2.419667	ACTTGTTTTATGTACGCGGCT	58.580	42.857	12.47	0.00	0.00	5.52
1880	1958	4.248859	CAGACATTCATGGACGAAGAAGT	58.751	43.478	0.00	0.00	0.00	3.01
2244	2355	2.034124	TCATCGAGCTGATCCACATGA	58.966	47.619	0.00	0.00	34.13	3.07
2286	2397	1.174783	GCTAGAAGGACTCGACACCA	58.825	55.000	0.00	0.00	0.00	4.17
2288	2399	2.166664	GCTAGAAGGACTCGACACCATT	59.833	50.000	0.00	0.00	0.00	3.16
2497	2663	2.724174	GCAGCGTCCAAACAATAACAAC	59.276	45.455	0.00	0.00	0.00	3.32
2505	2671	6.415573	CGTCCAAACAATAACAACTTGGTAAC	59.584	38.462	0.00	0.00	38.16	2.50
2510	2676	7.633193	AACAATAACAACTTGGTAACTGTCA	57.367	32.000	5.74	0.00	37.61	3.58
2729	2916	1.135689	ACTCCACATTCGCGCATTTTC	60.136	47.619	8.75	0.00	0.00	2.29
2782	3025	1.379710	ACCCACAAGCACAACTGCA	60.380	52.632	0.00	0.00	46.97	4.41
2813	3056	0.108138	GCGGTTACTGTGCCTCATCT	60.108	55.000	0.00	0.00	0.00	2.90
2949	3304	3.683365	AGGCACAAACAAATCCAATCC	57.317	42.857	0.00	0.00	0.00	3.01
2953	3308	3.798548	GCACAAACAAATCCAATCCGTGT	60.799	43.478	0.00	0.00	0.00	4.49
3143	3529	7.228706	CCAACTTGTCTCAATAAACTACCAGTT	59.771	37.037	0.00	0.00	40.80	3.16
3278	3665	5.507650	GGTTCGCAAATACTTAAAACACCCA	60.508	40.000	0.00	0.00	0.00	4.51
3281	3668	4.261656	CGCAAATACTTAAAACACCCACCA	60.262	41.667	0.00	0.00	0.00	4.17

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	50	4.740822	GGTGGCCCGCACCAATCT	62.741	66.667	0.00	0.00	42.70	2.40
219	221	4.062677	TGGTTTGACAGTGTACACCTAC	57.937	45.455	22.28	13.47	0.00	3.18
259	261	0.867746	GCGCGATAAGATGCATTGGA	59.132	50.000	12.10	0.00	0.00	3.53
309	311	1.390926	GGGGGAGTGGAGAGTACCA	59.609	63.158	0.00	0.00	37.63	3.25
322	324	3.494254	GGGTGTGTGTGTGGGGGA	61.494	66.667	0.00	0.00	0.00	4.81
379	390	6.952773	AACAACACATTTTAGTTCAGGCTA	57.047	33.333	0.00	0.00	0.00	3.93
527	539	0.533085	TGTGAACAATTGGTCGGCGA	60.533	50.000	18.35	4.99	33.57	5.54
542	554	1.272807	GCCCCTAGTAGGTGTTGTGA	58.727	55.000	15.26	0.00	31.93	3.58
728	749	3.760151	TCTTAACAGGCGTACTAGCTTCA	59.240	43.478	0.00	0.00	37.29	3.02
734	755	4.098960	CCATCCTTCTTAACAGGCGTACTA	59.901	45.833	0.00	0.00	0.00	1.82
761	782	2.093973	CGTAGGTGAAATCAGAGTGGCT	60.094	50.000	0.00	0.00	0.00	4.75
782	803	0.874607	AGTGTGTCTTTGTCGCCGAC	60.875	55.000	10.96	10.96	0.00	4.79
784	805	0.874175	TGAGTGTGTCTTTGTCGCCG	60.874	55.000	0.00	0.00	0.00	6.46
837	858	2.169352	CCTCGGTGTCTCCAATCTCATT	59.831	50.000	0.00	0.00	35.57	2.57
973	996	3.002791	CTCTGATGGCTTTTAGAACGCA	58.997	45.455	0.00	0.00	0.00	5.24
978	1001	5.698741	TCCATTCTCTGATGGCTTTTAGA	57.301	39.130	0.00	0.00	45.07	2.10
1212	1245	4.141287	TCGTGGTCCAATTCAGAACAATT	58.859	39.130	0.00	0.00	31.43	2.32
1358	1391	1.537202	GGCAAGAATGTGGACAGTGTC	59.463	52.381	15.24	15.24	0.00	3.67
1440	1483	2.964209	TGTGGTATTTTCCCCTGCAAA	58.036	42.857	0.00	0.00	0.00	3.68
1485	1528	4.848299	GCACTTCACTTCATTTTCGATGAC	59.152	41.667	0.00	0.00	0.00	3.06
1492	1541	4.977963	CGATGTTGCACTTCACTTCATTTT	59.022	37.500	0.00	0.00	0.00	1.82
1781	1859	1.996898	CTTGTCAGCCGCGTACATAAA	59.003	47.619	4.92	0.00	0.00	1.40
1795	1873	1.810755	AGAGCGTCGTGTATCTTGTCA	59.189	47.619	0.00	0.00	0.00	3.58
1880	1958	3.801307	TGTGGTAGACAGTAGAGGTGA	57.199	47.619	0.00	0.00	0.00	4.02
2286	2397	0.108186	TCATTCAGAGCGTCGGCAAT	60.108	50.000	0.00	0.00	43.41	3.56
2288	2399	1.153765	CTCATTCAGAGCGTCGGCA	60.154	57.895	0.00	0.00	43.41	5.69
2435	2598	9.809096	TGTAAATGTTGCTGATTACAAGAAAAA	57.191	25.926	0.00	0.00	35.84	1.94
2497	2663	8.352201	TCAATGAAAATCTTGACAGTTACCAAG	58.648	33.333	0.00	0.00	40.68	3.61
2729	2916	1.746615	CACTCATTCTGGTGCGGGG	60.747	63.158	0.00	0.00	0.00	5.73
2782	3025	1.926489	TAACCGCTTCCACCCCCAT	60.926	57.895	0.00	0.00	0.00	4.00
2845	3088	4.550422	CGGATGATGTACAGTACCTGATG	58.450	47.826	8.30	0.00	35.18	3.07
2949	3304	0.248866	GGGTGCCAAGTTTTCACACG	60.249	55.000	6.59	0.00	32.69	4.49
2953	3308	1.110442	CTGTGGGTGCCAAGTTTTCA	58.890	50.000	0.00	0.00	34.18	2.69
3042	3397	6.365520	ACTGGTTATTTCCTGTCTTCAGTTT	58.634	36.000	0.00	0.00	39.82	2.66
3091	3446	3.548587	CGACATTGCTGAACAGTTCAAG	58.451	45.455	16.85	11.72	39.58	3.02
3143	3529	6.520272	CATGGTTTTGTTTTTCCCATGTCTA	58.480	36.000	8.46	0.00	44.79	2.59
3278	3665	3.265995	CCCAGTTACTATCCCAGTTTGGT	59.734	47.826	0.00	0.00	38.80	3.67
3281	3668	2.916934	TGCCCAGTTACTATCCCAGTTT	59.083	45.455	0.00	0.00	38.80	2.66

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.