AutoCloner

Multiple sequence alignment - TraesCS6D01G191200

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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	TraesCS6D01G191200	chr6D	100.000	2486	0	0	1	2486	263964067	263961582	0.000000e+00	4591
1	TraesCS6D01G191200	chr6A	93.192	1836	101	10	1	1815	371328876	371330708	0.000000e+00	2676
2	TraesCS6D01G191200	chr6B	91.008	1846	109	31	1	1816	405061171	405059353	0.000000e+00	2436
3	TraesCS6D01G191200	chr4D	90.429	700	16	8	1811	2486	348306639	348307311	0.000000e+00	874
4	TraesCS6D01G191200	chr1D	90.129	699	16	9	1814	2486	474917412	474916741	0.000000e+00	859
5	TraesCS6D01G191200	chr2D	89.872	701	18	9	1812	2486	56189392	56188719	0.000000e+00	852
6	TraesCS6D01G191200	chr2D	89.542	459	12	2	1814	2236	33946576	33946118	1.300000e-152	549
7	TraesCS6D01G191200	chr7D	89.868	681	31	14	1814	2486	293591210	293591860	0.000000e+00	841
8	TraesCS6D01G191200	chr7D	89.383	697	23	8	1814	2486	276474041	276474710	0.000000e+00	830
9	TraesCS6D01G191200	chr7D	91.611	453	14	7	1813	2241	52618179	52618631	2.730000e-169	604
10	TraesCS6D01G191200	chr7D	94.615	260	12	2	2227	2486	52618563	52618820	3.850000e-108	401
11	TraesCS6D01G191200	chr5D	89.362	705	22	12	1808	2486	213074538	213075215	0.000000e+00	837
12	TraesCS6D01G191200	chr5D	88.858	709	16	8	1814	2486	563593625	563592944	0.000000e+00	813
13	TraesCS6D01G191200	chr1A	90.909	396	28	6	1843	2236	47816578	47816967	2.190000e-145	525
14	TraesCS6D01G191200	chr1A	100.000	63	0	0	933	995	285504124	285504186	1.560000e-22	117
15	TraesCS6D01G191200	chr2A	92.164	268	18	2	2220	2486	36028928	36029193	2.330000e-100	375

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	TraesCS6D01G191200	chr6D	263961582	263964067	2485	True	4591.0	4591	100.000	1	2486	1	chr6D.!!$R1	2485
1	TraesCS6D01G191200	chr6A	371328876	371330708	1832	False	2676.0	2676	93.192	1	1815	1	chr6A.!!$F1	1814
2	TraesCS6D01G191200	chr6B	405059353	405061171	1818	True	2436.0	2436	91.008	1	1816	1	chr6B.!!$R1	1815
3	TraesCS6D01G191200	chr4D	348306639	348307311	672	False	874.0	874	90.429	1811	2486	1	chr4D.!!$F1	675
4	TraesCS6D01G191200	chr1D	474916741	474917412	671	True	859.0	859	90.129	1814	2486	1	chr1D.!!$R1	672
5	TraesCS6D01G191200	chr2D	56188719	56189392	673	True	852.0	852	89.872	1812	2486	1	chr2D.!!$R2	674
6	TraesCS6D01G191200	chr7D	293591210	293591860	650	False	841.0	841	89.868	1814	2486	1	chr7D.!!$F2	672
7	TraesCS6D01G191200	chr7D	276474041	276474710	669	False	830.0	830	89.383	1814	2486	1	chr7D.!!$F1	672
8	TraesCS6D01G191200	chr7D	52618179	52618820	641	False	502.5	604	93.113	1813	2486	2	chr7D.!!$F3	673
9	TraesCS6D01G191200	chr5D	213074538	213075215	677	False	837.0	837	89.362	1808	2486	1	chr5D.!!$F1	678
10	TraesCS6D01G191200	chr5D	563592944	563593625	681	True	813.0	813	88.858	1814	2486	1	chr5D.!!$R1	672

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
349	351	0.468585	AGGTGGTGTGGTGTAGACGA	60.469	55.0	0.0	0.0	0.0	4.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1949	2007	1.555967	GTGGGAGAGAAGCAGAGAGT	58.444	55.0	0.0	0.0	0.0	3.24	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
114	115	2.123854	TCCATCTACGGAGGCGCT	60.124	61.111	7.64	0.00	0.00	5.92
147	148	2.885644	CGTCGCCGGACAAGATGG	60.886	66.667	5.05	0.00	43.61	3.51
349	351	0.468585	AGGTGGTGTGGTGTAGACGA	60.469	55.000	0.00	0.00	0.00	4.20
376	378	2.373540	ACCGTGCTTAAATAGACGCA	57.626	45.000	0.00	0.00	0.00	5.24
433	444	2.683867	CCGGAGTAGACTTCTCGATTGT	59.316	50.000	0.00	0.00	33.26	2.71
436	447	4.035792	CGGAGTAGACTTCTCGATTGTCAT	59.964	45.833	12.76	1.97	33.56	3.06
439	450	6.274157	AGTAGACTTCTCGATTGTCATGTT	57.726	37.500	12.76	0.00	33.56	2.71
443	454	3.997021	ACTTCTCGATTGTCATGTTGACC	59.003	43.478	5.27	0.00	46.40	4.02
533	544	3.507162	TCCATTCTGGAACAAGCTGAA	57.493	42.857	0.00	0.00	45.00	3.02
579	590	2.754375	GCGGAGAGGGTTTTGGGA	59.246	61.111	0.00	0.00	0.00	4.37
666	679	2.030893	TGTCTTGCTTGCAGAATTTCGG	60.031	45.455	0.00	0.00	0.00	4.30
682	695	2.027003	TCGGAAAACCAAACACGTCT	57.973	45.000	0.00	0.00	0.00	4.18
705	718	4.412933	CCGATGTGGTATCGCGTT	57.587	55.556	5.77	0.00	39.95	4.84
716	729	2.268298	GTATCGCGTTGGATGACTTGT	58.732	47.619	5.77	0.00	0.00	3.16
725	738	1.804151	TGGATGACTTGTAGCGTTTGC	59.196	47.619	0.00	0.00	43.24	3.68
737	750	1.006832	GCGTTTGCACATATCGGTCT	58.993	50.000	0.00	0.00	42.15	3.85
741	754	3.124466	CGTTTGCACATATCGGTCTGAAA	59.876	43.478	0.00	0.00	0.00	2.69
780	796	1.302192	CGCGTTGGAAAAGGGAGGA	60.302	57.895	0.00	0.00	40.47	3.71
792	808	3.790089	AAGGGAGGACGTTGAAAGATT	57.210	42.857	0.00	0.00	0.00	2.40
837	853	2.289257	GGTCCCCGTATAGATTTTCCCG	60.289	54.545	0.00	0.00	0.00	5.14
867	883	1.135083	ACGCTTCCTCTACATGTTCCG	60.135	52.381	2.30	0.00	0.00	4.30
882	898	2.434185	CCGTACCGCAGCACACAT	60.434	61.111	0.00	0.00	0.00	3.21
944	960	1.634702	AAAGATCTCGCACTCGAAGC	58.365	50.000	0.00	0.00	44.98	3.86
1032	1048	0.741915	GCGTTCTCCTAGAGACCCAG	59.258	60.000	0.00	0.00	38.51	4.45
1110	1126	0.417437	TCTCCTCATCCCCTTGGTCA	59.583	55.000	0.00	0.00	0.00	4.02
1251	1271	2.349886	GCTGCATCAAGAAACTACCTCG	59.650	50.000	0.00	0.00	0.00	4.63
1279	1299	1.749063	TCGATGCACAACCGATCTAGT	59.251	47.619	0.00	0.00	0.00	2.57
1839	1882	3.494398	CCCTCCGTTCCGAAATACATGAT	60.494	47.826	0.00	0.00	0.00	2.45
1949	2007	1.826921	GTCTCCCTCGCCCGTATCA	60.827	63.158	0.00	0.00	0.00	2.15
2095	2176	0.854037	CTCTTTCTCTCGCGTCGTCG	60.854	60.000	5.77	0.00	40.37	5.12
2160	2241	1.452145	CTCGAGTAGGAGGAGCTGCC	61.452	65.000	3.62	0.00	0.00	4.85
2221	2329	3.324930	CTGTGGGGAGCTGCTGGA	61.325	66.667	7.01	0.00	0.00	3.86
2222	2330	2.611800	TGTGGGGAGCTGCTGGAT	60.612	61.111	7.01	0.00	0.00	3.41
2223	2331	2.191641	GTGGGGAGCTGCTGGATC	59.808	66.667	7.01	0.00	0.00	3.36
2224	2332	2.041762	TGGGGAGCTGCTGGATCT	59.958	61.111	7.01	0.00	0.00	2.75
2225	2333	2.372890	TGGGGAGCTGCTGGATCTG	61.373	63.158	7.01	0.00	0.00	2.90
2226	2334	2.373707	GGGGAGCTGCTGGATCTGT	61.374	63.158	7.01	0.00	0.00	3.41
2227	2335	1.153208	GGGAGCTGCTGGATCTGTG	60.153	63.158	7.01	0.00	0.00	3.66
2228	2336	1.818785	GGAGCTGCTGGATCTGTGC	60.819	63.158	7.01	0.00	0.00	4.57
2229	2337	2.125229	AGCTGCTGGATCTGTGCG	60.125	61.111	0.00	0.00	0.00	5.34
2230	2338	3.200593	GCTGCTGGATCTGTGCGG	61.201	66.667	8.76	8.76	36.28	5.69
2233	2341	3.200593	GCTGGATCTGTGCGGCTG	61.201	66.667	0.00	0.00	43.95	4.85
2234	2342	2.267006	CTGGATCTGTGCGGCTGT	59.733	61.111	0.00	0.00	0.00	4.40
2235	2343	2.046988	TGGATCTGTGCGGCTGTG	60.047	61.111	0.00	0.00	0.00	3.66
2236	2344	2.821366	GGATCTGTGCGGCTGTGG	60.821	66.667	0.00	0.00	0.00	4.17
2237	2345	2.821366	GATCTGTGCGGCTGTGGG	60.821	66.667	0.00	0.00	0.00	4.61
2238	2346	4.415150	ATCTGTGCGGCTGTGGGG	62.415	66.667	0.00	0.00	0.00	4.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	62	4.036971	GTGATCGCTCTAGTACCACAATCT	59.963	45.833	0.00	0.00	0.00	2.40
112	113	3.731653	GAGGAGGAGCGGCAGAAGC	62.732	68.421	1.45	0.00	41.10	3.86
114	115	3.452786	CGAGGAGGAGCGGCAGAA	61.453	66.667	1.45	0.00	0.00	3.02
147	148	2.585153	GAGAAGGAGGGGGTTCGC	59.415	66.667	0.00	0.00	0.00	4.70
214	216	1.147376	CCGGACCTTGGTGTCACAA	59.853	57.895	5.12	0.00	36.97	3.33
239	241	2.575893	TTCTTCGTGCCGGCAGGTA	61.576	57.895	39.26	31.88	40.50	3.08
303	305	1.070134	TCCGCTCACATTATGGCTACC	59.930	52.381	0.00	0.00	0.00	3.18
349	351	5.123344	GTCTATTTAAGCACGGTTCCAATGT	59.877	40.000	0.00	0.00	0.00	2.71
376	378	1.227734	CCCGTCCGTTTGTCTGGTT	60.228	57.895	0.00	0.00	0.00	3.67
433	444	1.810151	GCCGCTTTAAGGTCAACATGA	59.190	47.619	0.00	0.00	0.00	3.07
436	447	0.533308	ACGCCGCTTTAAGGTCAACA	60.533	50.000	0.00	0.00	0.00	3.33
439	450	1.735198	CGACGCCGCTTTAAGGTCA	60.735	57.895	0.00	0.00	0.00	4.02
463	474	2.974489	GAGCGACAAGACCGGACGA	61.974	63.158	9.46	0.00	0.00	4.20
516	527	2.154462	CCGTTCAGCTTGTTCCAGAAT	58.846	47.619	0.00	0.00	0.00	2.40
666	679	5.164022	CGGTCTATAGACGTGTTTGGTTTTC	60.164	44.000	23.35	6.79	45.65	2.29
705	718	1.804151	GCAAACGCTACAAGTCATCCA	59.196	47.619	0.00	0.00	0.00	3.41
716	729	2.159156	AGACCGATATGTGCAAACGCTA	60.159	45.455	0.00	0.00	0.00	4.26
725	738	6.092670	ACACAAATCTTTCAGACCGATATGTG	59.907	38.462	0.00	0.00	39.21	3.21
737	750	8.286800	CGGACTAAAATGTACACAAATCTTTCA	58.713	33.333	0.00	0.00	0.00	2.69
741	754	5.163893	CGCGGACTAAAATGTACACAAATCT	60.164	40.000	0.00	0.00	0.00	2.40
748	761	2.737783	CCAACGCGGACTAAAATGTACA	59.262	45.455	12.47	0.00	36.56	2.90
780	796	0.591170	CCCGTGCAATCTTTCAACGT	59.409	50.000	0.00	0.00	0.00	3.99
792	808	2.137425	CTGACGTGTCTACCCGTGCA	62.137	60.000	0.00	0.00	37.44	4.57
837	853	5.997385	TGTAGAGGAAGCGTTTGATTTTTC	58.003	37.500	0.00	0.00	0.00	2.29
867	883	1.278238	GAGTATGTGTGCTGCGGTAC	58.722	55.000	6.84	6.84	0.00	3.34
882	898	5.955959	TGGTGCTTATAAAGAGTGAGGAGTA	59.044	40.000	0.00	0.00	0.00	2.59
944	960	2.439507	ACTCTCTCCTAGCTCCTCTCTG	59.560	54.545	0.00	0.00	0.00	3.35
1243	1263	6.373495	TGTGCATCGATTATATACGAGGTAGT	59.627	38.462	0.00	0.00	41.26	2.73
1251	1271	6.752351	AGATCGGTTGTGCATCGATTATATAC	59.248	38.462	14.82	0.00	42.65	1.47
1279	1299	6.481976	ACATCAGACATGAACGAACAAACTAA	59.518	34.615	0.00	0.00	39.39	2.24
1757	1793	6.183360	CGAAGAGAGGAGAGACGTGATATATG	60.183	46.154	0.00	0.00	0.00	1.78
1887	1930	4.157105	CGGTCGAGGGTAAAAATGGAAAAT	59.843	41.667	0.00	0.00	0.00	1.82
1949	2007	1.555967	GTGGGAGAGAAGCAGAGAGT	58.444	55.000	0.00	0.00	0.00	3.24
2095	2176	2.357034	TTGGGACGACGAAGCAGC	60.357	61.111	0.00	0.00	0.00	5.25
2160	2241	1.738099	CGCCACAGTTCCTCTTCCG	60.738	63.158	0.00	0.00	0.00	4.30
2218	2326	2.046988	CACAGCCGCACAGATCCA	60.047	61.111	0.00	0.00	0.00	3.41
2219	2327	2.821366	CCACAGCCGCACAGATCC	60.821	66.667	0.00	0.00	0.00	3.36
2220	2328	2.821366	CCCACAGCCGCACAGATC	60.821	66.667	0.00	0.00	0.00	2.75
2221	2329	4.415150	CCCCACAGCCGCACAGAT	62.415	66.667	0.00	0.00	0.00	2.90
2233	2341	4.554036	GATCCGGCAGCTCCCCAC	62.554	72.222	0.00	0.00	0.00	4.61
2234	2342	4.804420	AGATCCGGCAGCTCCCCA	62.804	66.667	0.00	0.00	0.00	4.96
2235	2343	4.247380	CAGATCCGGCAGCTCCCC	62.247	72.222	0.00	0.00	0.00	4.81
2236	2344	3.474570	ACAGATCCGGCAGCTCCC	61.475	66.667	0.00	0.00	0.00	4.30
2237	2345	2.202987	CACAGATCCGGCAGCTCC	60.203	66.667	0.00	0.00	0.00	4.70
2238	2346	2.894387	GCACAGATCCGGCAGCTC	60.894	66.667	0.00	0.00	0.00	4.09
2239	2347	4.827087	CGCACAGATCCGGCAGCT	62.827	66.667	0.00	0.00	0.00	4.24
2244	2352	4.457496	ACAGCCGCACAGATCCGG	62.457	66.667	0.00	0.00	46.94	5.14
2387	2495	2.713894	GGTGTACGACGCGCTCAAC	61.714	63.158	5.73	0.00	0.00	3.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.