AutoCloner

Multiple sequence alignment - TraesCS6B01G048800

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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	TraesCS6B01G048800	chr6B	100.000	2619	0	0	1	2619	28721444	28724062	0.000000e+00	4837.0
1	TraesCS6B01G048800	chr6B	95.426	1618	46	15	698	2289	28942206	28943821	0.000000e+00	2553.0
2	TraesCS6B01G048800	chr6B	85.435	1689	121	63	123	1759	28514292	28512677	0.000000e+00	1640.0
3	TraesCS6B01G048800	chr6B	89.397	896	74	18	717	1605	59298737	59299618	0.000000e+00	1109.0
4	TraesCS6B01G048800	chr6B	85.423	1029	93	34	768	1761	29044506	29045512	0.000000e+00	1016.0
5	TraesCS6B01G048800	chr6B	96.296	270	5	4	2351	2619	28511401	28511136	3.090000e-119	438.0
6	TraesCS6B01G048800	chr6B	91.489	282	17	3	2288	2569	28943896	28944170	5.290000e-102	381.0
7	TraesCS6B01G048800	chr6B	81.865	386	44	19	1787	2153	28512478	28512100	4.240000e-78	302.0
8	TraesCS6B01G048800	chr6B	90.336	238	11	6	2286	2521	59300311	59300538	4.240000e-78	302.0
9	TraesCS6B01G048800	chr6B	83.881	335	33	6	1	321	29043961	29044288	1.520000e-77	300.0
10	TraesCS6B01G048800	chr6B	83.448	290	37	8	1785	2068	29045625	29045909	2.590000e-65	259.0
11	TraesCS6B01G048800	chr6B	85.955	178	22	2	342	519	28940781	28940955	1.240000e-43	187.0
12	TraesCS6B01G048800	chr6B	85.484	124	17	1	2462	2585	27941061	27941183	7.610000e-26	128.0
13	TraesCS6B01G048800	chr3A	91.765	1020	68	13	742	1751	66253793	66254806	0.000000e+00	1404.0
14	TraesCS6B01G048800	chr3A	83.971	418	42	9	3	406	66252915	66253321	6.840000e-101	377.0
15	TraesCS6B01G048800	chr3A	88.364	275	21	5	1801	2068	66254805	66255075	1.170000e-83	320.0
16	TraesCS6B01G048800	chr3A	94.949	99	5	0	2055	2153	66255031	66255129	3.490000e-34	156.0
17	TraesCS6B01G048800	chr6D	87.220	1072	76	30	747	1769	16514334	16515393	0.000000e+00	1164.0
18	TraesCS6B01G048800	chr6D	87.354	1028	73	33	778	1761	16386780	16385766	0.000000e+00	1125.0
19	TraesCS6B01G048800	chr6D	84.181	531	49	11	1	515	16513624	16514135	1.410000e-132	483.0
20	TraesCS6B01G048800	chr6D	87.542	297	19	2	2290	2586	16384439	16384161	6.990000e-86	327.0
21	TraesCS6B01G048800	chr6D	79.124	388	48	22	1785	2153	16385571	16385198	1.210000e-58	237.0
22	TraesCS6B01G048800	chr6D	81.757	296	37	12	1785	2068	16515546	16515836	5.640000e-57	231.0
23	TraesCS6B01G048800	chr6A	86.857	1088	81	37	733	1769	16705057	16706133	0.000000e+00	1160.0
24	TraesCS6B01G048800	chr6A	87.475	998	80	31	754	1724	16656002	16655023	0.000000e+00	1109.0
25	TraesCS6B01G048800	chr6A	81.765	510	66	18	16	510	16704323	16704820	4.060000e-108	401.0
26	TraesCS6B01G048800	chr6A	80.879	387	46	22	1785	2153	16654711	16654335	1.980000e-71	279.0
27	TraesCS6B01G048800	chr6A	81.787	291	41	9	1785	2068	16706287	16706572	1.570000e-57	233.0
28	TraesCS6B01G048800	chr6A	92.784	97	7	0	2470	2566	16456672	16456768	9.770000e-30	141.0
29	TraesCS6B01G048800	chr6A	90.000	90	6	2	1979	2068	16654476	16654390	2.130000e-21	113.0
30	TraesCS6B01G048800	chr1B	83.824	204	19	5	1788	1978	587500417	587500215	5.760000e-42	182.0
31	TraesCS6B01G048800	chrUn	79.528	254	19	19	1527	1761	163376400	163376639	1.620000e-32	150.0
32	TraesCS6B01G048800	chr7B	84.906	53	7	1	405	457	665001482	665001533	5.000000e-03	52.8

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	TraesCS6B01G048800	chr6B	28721444	28724062	2618	False	4837.000000	4837	100.000000	1	2619	1	chr6B.!!$F2	2618
1	TraesCS6B01G048800	chr6B	28940781	28944170	3389	False	1040.333333	2553	90.956667	342	2569	3	chr6B.!!$F3	2227
2	TraesCS6B01G048800	chr6B	28511136	28514292	3156	True	793.333333	1640	87.865333	123	2619	3	chr6B.!!$R1	2496
3	TraesCS6B01G048800	chr6B	59298737	59300538	1801	False	705.500000	1109	89.866500	717	2521	2	chr6B.!!$F5	1804
4	TraesCS6B01G048800	chr6B	29043961	29045909	1948	False	525.000000	1016	84.250667	1	2068	3	chr6B.!!$F4	2067
5	TraesCS6B01G048800	chr3A	66252915	66255129	2214	False	564.250000	1404	89.762250	3	2153	4	chr3A.!!$F1	2150
6	TraesCS6B01G048800	chr6D	16513624	16515836	2212	False	626.000000	1164	84.386000	1	2068	3	chr6D.!!$F1	2067
7	TraesCS6B01G048800	chr6D	16384161	16386780	2619	True	563.000000	1125	84.673333	778	2586	3	chr6D.!!$R1	1808
8	TraesCS6B01G048800	chr6A	16704323	16706572	2249	False	598.000000	1160	83.469667	16	2068	3	chr6A.!!$F2	2052
9	TraesCS6B01G048800	chr6A	16654335	16656002	1667	True	500.333333	1109	86.118000	754	2153	3	chr6A.!!$R1	1399

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
282	302	0.102844	CTTGTGGGTTGTGGCTTGTG	59.897	55.0	0.0	0.0	0.0	3.33	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2043	3981	0.60864	ACCTAGTGTGGCAGTGCTAC	59.391	55.0	23.46	23.46	40.44	3.58	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
45	46	1.460699	GGGGGTTGCTTGAGTCCTT	59.539	57.895	0.00	0.00	0.00	3.36
65	66	1.304381	GGCTTGGAGGGTGATGCAA	60.304	57.895	0.00	0.00	0.00	4.08
130	131	1.208706	TGTTGGAGGTGTCAAGGTGA	58.791	50.000	0.00	0.00	0.00	4.02
138	139	3.515901	GAGGTGTCAAGGTGATAGTCCTT	59.484	47.826	0.00	0.00	44.93	3.36
244	263	2.270923	CTCTTGATGGCATCGTTTCGA	58.729	47.619	21.65	11.96	41.13	3.71
270	290	2.663196	GTCGGAGGGACTTGTGGG	59.337	66.667	0.00	0.00	41.55	4.61
277	297	2.200337	GGGACTTGTGGGTTGTGGC	61.200	63.158	0.00	0.00	0.00	5.01
278	298	1.152756	GGACTTGTGGGTTGTGGCT	60.153	57.895	0.00	0.00	0.00	4.75
279	299	0.755327	GGACTTGTGGGTTGTGGCTT	60.755	55.000	0.00	0.00	0.00	4.35
280	300	0.385390	GACTTGTGGGTTGTGGCTTG	59.615	55.000	0.00	0.00	0.00	4.01
281	301	0.324275	ACTTGTGGGTTGTGGCTTGT	60.324	50.000	0.00	0.00	0.00	3.16
282	302	0.102844	CTTGTGGGTTGTGGCTTGTG	59.897	55.000	0.00	0.00	0.00	3.33
283	303	1.326213	TTGTGGGTTGTGGCTTGTGG	61.326	55.000	0.00	0.00	0.00	4.17
314	334	2.470257	GTGACGACTAGTGTGTTTTCGG	59.530	50.000	0.00	0.00	33.97	4.30
350	384	1.001887	TGAATTGGGCGGTGGGTAC	60.002	57.895	0.00	0.00	0.00	3.34
430	566	1.873591	GGATCGAAGCGGCATATGTTT	59.126	47.619	1.45	0.00	0.00	2.83
433	569	2.351455	TCGAAGCGGCATATGTTTGAA	58.649	42.857	1.45	0.00	0.00	2.69
436	572	4.104776	CGAAGCGGCATATGTTTGAATTT	58.895	39.130	1.45	0.00	0.00	1.82
444	580	6.574832	CGGCATATGTTTGAATTTATCAGACG	59.425	38.462	4.29	0.00	44.13	4.18
463	599	1.789506	GTATCATTCCTCTCTGGCGC	58.210	55.000	0.00	0.00	35.26	6.53
622	2044	0.405198	TTGAGCATCCTCCAGCCAAA	59.595	50.000	0.00	0.00	37.29	3.28
623	2045	0.405198	TGAGCATCCTCCAGCCAAAA	59.595	50.000	0.00	0.00	37.29	2.44
624	2046	1.203038	TGAGCATCCTCCAGCCAAAAA	60.203	47.619	0.00	0.00	37.29	1.94
647	2107	8.552083	AAAAACAAACTCTTGAGCATCTTTTT	57.448	26.923	0.00	1.90	36.33	1.94
648	2108	7.529880	AAACAAACTCTTGAGCATCTTTTTG	57.470	32.000	0.00	3.27	36.33	2.44
657	2117	1.334054	GCATCTTTTTGTGCTCTGCG	58.666	50.000	0.00	0.00	38.30	5.18
803	2290	2.277949	CACGTCATCGATCCGCGT	60.278	61.111	4.92	11.85	41.80	6.01
913	2413	3.947041	ACAGCCCACCTCCCTCCT	61.947	66.667	0.00	0.00	0.00	3.69
920	2422	1.394151	CACCTCCCTCCTTCCTCCT	59.606	63.158	0.00	0.00	0.00	3.69
1241	2770	2.113774	CTGAAGCAGGTGCACCCA	59.886	61.111	32.29	20.57	45.16	4.51
1382	2911	1.231641	CCGGGAGATCCAGACCTCT	59.768	63.158	0.00	0.00	37.91	3.69
2048	3986	8.685838	ACACTAGGTAATTTTTCTTTGTAGCA	57.314	30.769	0.00	0.00	0.00	3.49
2049	3987	8.565416	ACACTAGGTAATTTTTCTTTGTAGCAC	58.435	33.333	0.00	0.00	0.00	4.40
2050	3988	8.784043	CACTAGGTAATTTTTCTTTGTAGCACT	58.216	33.333	0.00	0.00	0.00	4.40
2051	3989	8.784043	ACTAGGTAATTTTTCTTTGTAGCACTG	58.216	33.333	0.00	0.00	0.00	3.66
2052	3990	6.447162	AGGTAATTTTTCTTTGTAGCACTGC	58.553	36.000	0.00	0.00	0.00	4.40
2053	3991	5.633601	GGTAATTTTTCTTTGTAGCACTGCC	59.366	40.000	0.00	0.00	0.00	4.85
2054	3992	4.935352	ATTTTTCTTTGTAGCACTGCCA	57.065	36.364	0.00	0.00	0.00	4.92
2055	3993	3.708563	TTTTCTTTGTAGCACTGCCAC	57.291	42.857	0.00	0.00	0.00	5.01
2056	3994	2.340210	TTCTTTGTAGCACTGCCACA	57.660	45.000	0.00	0.00	0.00	4.17
2057	3995	1.593196	TCTTTGTAGCACTGCCACAC	58.407	50.000	1.36	0.00	0.00	3.82
2058	3996	1.140852	TCTTTGTAGCACTGCCACACT	59.859	47.619	1.36	0.00	0.00	3.55
2116	4086	0.669318	TTGTGATCACGAAGCGACCC	60.669	55.000	20.54	0.00	0.00	4.46

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
45	46	3.089838	CATCACCCTCCAAGCCCA	58.910	61.111	0.00	0.00	0.00	5.36
130	131	4.405036	GTCGGGAGGAAAAGTAAGGACTAT	59.595	45.833	0.00	0.00	33.58	2.12
138	139	1.975680	AGCTTGTCGGGAGGAAAAGTA	59.024	47.619	0.00	0.00	41.36	2.24
215	234	0.464373	GCCATCAAGAGGGAATGCGA	60.464	55.000	4.73	0.00	33.27	5.10
270	290	0.385390	CCAACTCCACAAGCCACAAC	59.615	55.000	0.00	0.00	0.00	3.32
277	297	2.113139	ACCGGCCAACTCCACAAG	59.887	61.111	0.00	0.00	0.00	3.16
278	298	2.203280	CACCGGCCAACTCCACAA	60.203	61.111	0.00	0.00	0.00	3.33
279	299	3.164977	TCACCGGCCAACTCCACA	61.165	61.111	0.00	0.00	0.00	4.17
280	300	2.668550	GTCACCGGCCAACTCCAC	60.669	66.667	0.00	0.00	0.00	4.02
281	301	4.308458	CGTCACCGGCCAACTCCA	62.308	66.667	0.00	0.00	0.00	3.86
282	302	3.998672	TCGTCACCGGCCAACTCC	61.999	66.667	0.00	0.00	33.95	3.85
283	303	1.870055	TAGTCGTCACCGGCCAACTC	61.870	60.000	0.00	0.00	40.30	3.01
430	566	8.642432	AGAGGAATGATACGTCTGATAAATTCA	58.358	33.333	0.00	0.00	32.48	2.57
433	569	8.303156	CAGAGAGGAATGATACGTCTGATAAAT	58.697	37.037	0.00	0.00	33.28	1.40
436	572	5.707764	CCAGAGAGGAATGATACGTCTGATA	59.292	44.000	0.00	0.00	41.22	2.15
444	580	1.606737	GGCGCCAGAGAGGAATGATAC	60.607	57.143	24.80	0.00	41.22	2.24
463	599	2.732094	GTCCACGAACCACGACGG	60.732	66.667	0.00	0.00	45.77	4.79
622	2044	8.445493	CAAAAAGATGCTCAAGAGTTTGTTTTT	58.555	29.630	12.03	12.03	35.73	1.94
623	2045	7.603784	ACAAAAAGATGCTCAAGAGTTTGTTTT	59.396	29.630	7.84	6.16	35.10	2.43
624	2046	7.063780	CACAAAAAGATGCTCAAGAGTTTGTTT	59.936	33.333	9.93	2.74	36.18	2.83
626	2048	6.038356	CACAAAAAGATGCTCAAGAGTTTGT	58.962	36.000	7.84	7.84	38.20	2.83
627	2049	5.051240	GCACAAAAAGATGCTCAAGAGTTTG	60.051	40.000	0.00	3.59	38.84	2.93
628	2050	5.045872	GCACAAAAAGATGCTCAAGAGTTT	58.954	37.500	0.00	0.00	38.84	2.66
629	2051	4.614946	GCACAAAAAGATGCTCAAGAGTT	58.385	39.130	0.00	0.00	38.84	3.01
630	2052	4.234530	GCACAAAAAGATGCTCAAGAGT	57.765	40.909	0.00	0.00	38.84	3.24
727	2189	2.099831	GACTCCCGCGTACTCGTG	59.900	66.667	4.92	0.00	45.59	4.35
903	2403	1.394151	CAGGAGGAAGGAGGGAGGT	59.606	63.158	0.00	0.00	0.00	3.85
913	2413	3.039011	GTTATGTAGGGAGCAGGAGGAA	58.961	50.000	0.00	0.00	0.00	3.36
920	2422	0.750850	GCGAGGTTATGTAGGGAGCA	59.249	55.000	0.00	0.00	0.00	4.26
1241	2770	2.060980	GGAGGAGATGCCCACGTCT	61.061	63.158	0.00	0.00	45.10	4.18
2028	3966	6.447162	GCAGTGCTACAAAGAAAAATTACCT	58.553	36.000	8.18	0.00	0.00	3.08
2029	3967	5.633601	GGCAGTGCTACAAAGAAAAATTACC	59.366	40.000	16.11	0.00	0.00	2.85
2030	3968	6.143919	GTGGCAGTGCTACAAAGAAAAATTAC	59.856	38.462	25.01	0.00	39.80	1.89
2031	3969	6.183360	TGTGGCAGTGCTACAAAGAAAAATTA	60.183	34.615	29.48	3.89	46.28	1.40
2032	3970	5.049828	GTGGCAGTGCTACAAAGAAAAATT	58.950	37.500	25.01	0.00	39.80	1.82
2033	3971	4.099266	TGTGGCAGTGCTACAAAGAAAAAT	59.901	37.500	29.48	0.00	46.28	1.82
2034	3972	3.445450	TGTGGCAGTGCTACAAAGAAAAA	59.555	39.130	29.48	5.90	46.28	1.94
2035	3973	3.020274	TGTGGCAGTGCTACAAAGAAAA	58.980	40.909	29.48	6.65	46.28	2.29
2036	3974	2.649190	TGTGGCAGTGCTACAAAGAAA	58.351	42.857	29.48	7.39	46.28	2.52
2037	3975	2.340210	TGTGGCAGTGCTACAAAGAA	57.660	45.000	29.48	8.14	46.28	2.52
2043	3981	0.608640	ACCTAGTGTGGCAGTGCTAC	59.391	55.000	23.46	23.46	40.44	3.58
2044	3982	2.225382	TACCTAGTGTGGCAGTGCTA	57.775	50.000	16.11	5.94	0.00	3.49
2045	3983	1.348064	TTACCTAGTGTGGCAGTGCT	58.652	50.000	16.11	0.00	0.00	4.40
2046	3984	2.403252	ATTACCTAGTGTGGCAGTGC	57.597	50.000	6.55	6.55	0.00	4.40
2047	3985	5.473504	AGAAAAATTACCTAGTGTGGCAGTG	59.526	40.000	0.00	0.00	0.00	3.66
2048	3986	5.631119	AGAAAAATTACCTAGTGTGGCAGT	58.369	37.500	0.00	0.00	0.00	4.40
2049	3987	6.575162	AAGAAAAATTACCTAGTGTGGCAG	57.425	37.500	0.00	0.00	0.00	4.85
2050	3988	6.322712	ACAAAGAAAAATTACCTAGTGTGGCA	59.677	34.615	0.00	0.00	0.00	4.92
2051	3989	6.745116	ACAAAGAAAAATTACCTAGTGTGGC	58.255	36.000	0.00	0.00	0.00	5.01
2052	3990	9.063615	ACTACAAAGAAAAATTACCTAGTGTGG	57.936	33.333	0.00	0.00	0.00	4.17
2116	4086	2.472816	ACTTTGCGCCTTCACAAAATG	58.527	42.857	4.18	0.00	35.49	2.32
2414	5056	9.461312	AGTTGTATTGGTTCTTGCATATAAGAA	57.539	29.630	0.00	0.00	42.63	2.52
2415	5057	9.461312	AAGTTGTATTGGTTCTTGCATATAAGA	57.539	29.630	0.00	0.00	35.02	2.10
2416	5058	9.507280	CAAGTTGTATTGGTTCTTGCATATAAG	57.493	33.333	0.00	0.00	31.19	1.73
2417	5059	9.237187	TCAAGTTGTATTGGTTCTTGCATATAA	57.763	29.630	2.11	0.00	36.47	0.98
2418	5060	8.800370	TCAAGTTGTATTGGTTCTTGCATATA	57.200	30.769	2.11	0.00	36.47	0.86
2424	5066	7.687941	ATACCTCAAGTTGTATTGGTTCTTG	57.312	36.000	14.12	0.00	37.44	3.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.