AutoCloner

Multiple sequence alignment - TraesCS6B01G392600

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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	TraesCS6B01G392600	chr6B	100.000	2933	0	0	1	2933	667801140	667798208	0.000000e+00	5417
1	TraesCS6B01G392600	chr6D	94.336	2931	119	14	31	2932	441812451	441809539	0.000000e+00	4449
2	TraesCS6B01G392600	chr6D	86.842	152	18	2	364	514	20769528	20769678	5.030000e-38	169
3	TraesCS6B01G392600	chr6A	93.755	2706	141	9	248	2932	591091309	591088611	0.000000e+00	4036
4	TraesCS6B01G392600	chr6A	85.490	1723	215	22	1020	2722	591208345	591206638	0.000000e+00	1764
5	TraesCS6B01G392600	chr6A	86.971	307	30	6	693	992	591208644	591208341	1.300000e-88	337
6	TraesCS6B01G392600	chr6A	93.443	183	10	2	2750	2932	591206523	591206343	1.340000e-68	270
7	TraesCS6B01G392600	chr6A	93.056	72	5	0	2	73	591099501	591099430	4.000000e-19	106
8	TraesCS6B01G392600	chr1A	87.485	2437	241	21	516	2932	54362051	54359659	0.000000e+00	2752
9	TraesCS6B01G392600	chr1D	88.842	1174	95	17	1781	2932	56039261	56038102	0.000000e+00	1410
10	TraesCS6B01G392600	chr1D	86.984	1260	144	7	516	1774	56040460	56039220	0.000000e+00	1400
11	TraesCS6B01G392600	chr7D	88.889	153	14	2	364	514	261805471	261805320	4.990000e-43	185
12	TraesCS6B01G392600	chrUn	92.593	81	6	0	78	158	454753093	454753013	1.850000e-22	117

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	TraesCS6B01G392600	chr6B	667798208	667801140	2932	True	5417.000000	5417	100.000000	1	2933	1	chr6B.!!$R1	2932
1	TraesCS6B01G392600	chr6D	441809539	441812451	2912	True	4449.000000	4449	94.336000	31	2932	1	chr6D.!!$R1	2901
2	TraesCS6B01G392600	chr6A	591088611	591091309	2698	True	4036.000000	4036	93.755000	248	2932	1	chr6A.!!$R1	2684
3	TraesCS6B01G392600	chr6A	591206343	591208644	2301	True	790.333333	1764	88.634667	693	2932	3	chr6A.!!$R3	2239
4	TraesCS6B01G392600	chr1A	54359659	54362051	2392	True	2752.000000	2752	87.485000	516	2932	1	chr1A.!!$R1	2416
5	TraesCS6B01G392600	chr1D	56038102	56040460	2358	True	1405.000000	1410	87.913000	516	2932	2	chr1D.!!$R1	2416

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
389	391	0.390866	CTCTGCACACGATTGGCTCT	60.391	55.0	0.0	0.0	0.0	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2230	2274	0.675633	ACAAAAAGAGCAGGCGCAAT	59.324	45.0	10.83	0.0	42.27	3.56	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
60	61	3.458831	AGAACACTCATCCTGATCCCTT	58.541	45.455	0.00	0.00	0.00	3.95
62	63	1.211457	ACACTCATCCTGATCCCTTGC	59.789	52.381	0.00	0.00	0.00	4.01
101	102	5.957771	ATCACCCTGACTACACATGTAAT	57.042	39.130	0.00	0.00	0.00	1.89
106	107	7.040755	TCACCCTGACTACACATGTAATTTTTG	60.041	37.037	0.00	0.00	0.00	2.44
247	248	4.264172	TGCTTTGGGGGTACATAAATCTGT	60.264	41.667	0.00	0.00	0.00	3.41
249	250	5.186992	GCTTTGGGGGTACATAAATCTGTTT	59.813	40.000	0.00	0.00	0.00	2.83
348	350	1.338674	TGTGGGACCGCATTCAGTTAG	60.339	52.381	0.00	0.00	0.00	2.34
362	364	6.251376	GCATTCAGTTAGCGTATTGGAAAAAG	59.749	38.462	0.00	0.00	0.00	2.27
367	369	7.013464	TCAGTTAGCGTATTGGAAAAAGGAAAA	59.987	33.333	0.00	0.00	0.00	2.29
389	391	0.390866	CTCTGCACACGATTGGCTCT	60.391	55.000	0.00	0.00	0.00	4.09
412	414	4.128388	GATTTGCGGCCAACGGGG	62.128	66.667	2.24	0.00	44.51	5.73
439	441	5.044846	AGGAGCCACACAGATTAAATAACCT	60.045	40.000	0.00	0.00	0.00	3.50
514	516	1.469767	CGTGTGCATAGCAGTGCTCTA	60.470	52.381	23.64	5.25	45.27	2.43
520	522	4.033817	GTGCATAGCAGTGCTCTAGAAAAG	59.966	45.833	23.64	0.51	45.27	2.27
534	536	6.403092	GCTCTAGAAAAGATTGGCAGAACTTC	60.403	42.308	0.00	0.00	32.41	3.01
550	552	7.008357	GGCAGAACTTCAGTATTTTTAATTCGC	59.992	37.037	0.00	0.00	0.00	4.70
877	901	3.244422	ACCTCCTTATTTTGTGAGCGTGA	60.244	43.478	0.00	0.00	0.00	4.35
956	980	1.607467	CTCCCCACCTGGCCAAAAG	60.607	63.158	7.01	0.35	0.00	2.27
1254	1285	2.234300	TCAAGAAGACGGTGAACCAC	57.766	50.000	0.00	0.00	35.14	4.16
1351	1382	0.677731	GCTACACAAGGCCATGCTCA	60.678	55.000	8.15	0.00	0.00	4.26
1719	1750	3.069318	GGAAGGGACCTCGACGCT	61.069	66.667	0.00	0.00	0.00	5.07
1883	1914	1.374125	GGTTTGGTTGGCAATCGGC	60.374	57.895	1.92	0.00	43.74	5.54
1924	1955	4.292186	TCATCTTGGAGTCTTTTCCCTG	57.708	45.455	0.00	0.00	36.35	4.45
1958	1990	4.171234	AGGATGGAGAGAAGTCTTTTCCA	58.829	43.478	14.31	14.31	41.23	3.53
1972	2004	0.391228	TTTCCAGTAGCGTGCAGTGA	59.609	50.000	0.00	0.00	0.00	3.41
1973	2005	0.038251	TTCCAGTAGCGTGCAGTGAG	60.038	55.000	0.00	0.00	0.00	3.51
1974	2006	2.097038	CCAGTAGCGTGCAGTGAGC	61.097	63.158	0.00	0.00	45.96	4.26
1975	2007	1.080230	CAGTAGCGTGCAGTGAGCT	60.080	57.895	11.81	11.81	45.94	4.09
1976	2008	0.171231	CAGTAGCGTGCAGTGAGCTA	59.829	55.000	10.15	10.15	45.94	3.32
1978	2010	2.263153	TAGCGTGCAGTGAGCTACA	58.737	52.632	10.15	0.00	45.94	2.74
1979	2011	0.817654	TAGCGTGCAGTGAGCTACAT	59.182	50.000	10.15	0.00	45.94	2.29
1991	2030	3.330766	GCTACATGCGTCTCGTCTT	57.669	52.632	0.00	0.00	0.00	3.01
1992	2031	2.470196	GCTACATGCGTCTCGTCTTA	57.530	50.000	0.00	0.00	0.00	2.10
2047	2086	6.208797	AGGAAAGGCAACCTTAATAAGTTGAC	59.791	38.462	14.13	12.02	43.92	3.18
2200	2244	6.239396	TCTTCCATGGTCCGTTTGTTTAATA	58.761	36.000	12.58	0.00	0.00	0.98
2230	2274	4.566545	TCAGTTGGTCGTAACTCGTAAA	57.433	40.909	0.00	0.00	38.78	2.01
2314	2358	8.445193	ACTTCTTATTTACTCTTAACACGTCG	57.555	34.615	0.00	0.00	0.00	5.12
2345	2389	6.127054	CCAAGTATGAAGAGTCCACTCCAATA	60.127	42.308	2.96	0.00	43.88	1.90
2476	2526	4.248859	CAGATCCAAAGTGAACATCGTCT	58.751	43.478	0.00	0.00	0.00	4.18
2568	2629	3.380637	AGTGCTCTGGGTATTGTAGTACG	59.619	47.826	0.00	0.00	0.00	3.67
2571	2632	3.550436	GCTCTGGGTATTGTAGTACGAGC	60.550	52.174	6.75	6.75	32.48	5.03
2575	2636	3.131577	TGGGTATTGTAGTACGAGCCAAG	59.868	47.826	14.71	0.00	0.00	3.61
2674	2736	1.089920	GCATAATCATAGCGCCCAGG	58.910	55.000	2.29	0.00	0.00	4.45
2679	2741	3.865383	CATAGCGCCCAGGCCAGA	61.865	66.667	5.01	0.00	37.98	3.86
2704	2766	5.070685	CCCCCATGCCTACTAAGATAAAAC	58.929	45.833	0.00	0.00	0.00	2.43
2748	2884	6.325286	ACCTAAAAGCCAATTACCAAACAAGA	59.675	34.615	0.00	0.00	0.00	3.02
2905	3057	5.331876	AGAGTTTCCCTCGTTAAGATGAG	57.668	43.478	0.00	0.00	45.44	2.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
70	71	5.531287	GTGTAGTCAGGGTGATTGTTCTTTT	59.469	40.000	0.00	0.00	0.00	2.27
133	134	2.159028	AGCTAAGCTAACTAGTGCTGCC	60.159	50.000	8.37	1.43	39.71	4.85
249	250	9.817365	CATGTTCACACAAATTGTAAACAAAAA	57.183	25.926	18.20	3.34	35.67	1.94
254	256	8.265998	GCTAACATGTTCACACAAATTGTAAAC	58.734	33.333	15.85	4.97	35.67	2.01
273	275	0.608130	TGACGCTGGTGAGCTAACAT	59.392	50.000	2.93	0.00	43.77	2.71
348	350	4.929211	AGCATTTTCCTTTTTCCAATACGC	59.071	37.500	0.00	0.00	0.00	4.42
362	364	0.874390	TCGTGTGCAGAGCATTTTCC	59.126	50.000	0.00	0.00	41.91	3.13
367	369	1.651240	GCCAATCGTGTGCAGAGCAT	61.651	55.000	0.00	0.00	41.91	3.79
389	391	2.281831	TGGCCGCAAATCGTCCAA	60.282	55.556	0.00	0.00	43.95	3.53
406	408	1.844289	TGTGGCTCCTAACCCCGTT	60.844	57.895	0.00	0.00	0.00	4.44
412	414	7.201705	GGTTATTTAATCTGTGTGGCTCCTAAC	60.202	40.741	0.00	0.00	0.00	2.34
439	441	6.246919	GTCAGGTAGACCATAGGATTAGCTA	58.753	44.000	0.66	0.00	41.56	3.32
514	516	5.136105	ACTGAAGTTCTGCCAATCTTTTCT	58.864	37.500	9.48	0.00	0.00	2.52
520	522	9.860898	ATTAAAAATACTGAAGTTCTGCCAATC	57.139	29.630	9.48	0.00	0.00	2.67
630	632	9.029368	TGGTTATTCAAAATTGTACATCATCCA	57.971	29.630	0.00	0.00	0.00	3.41
708	723	7.912250	GCATCTTATCCGGATATGCTTATTTTG	59.088	37.037	30.65	18.81	0.00	2.44
819	838	8.747471	TCATAAATGCATCATCAAACCAAGTAA	58.253	29.630	0.00	0.00	0.00	2.24
877	901	9.315525	GAGGCTATATCGAGAAACTTTTAACTT	57.684	33.333	0.00	0.00	0.00	2.66
956	980	5.077134	AGAAATGGAAATTAGGTTGCTGC	57.923	39.130	0.00	0.00	0.00	5.25
1254	1285	0.739112	GCTGGCTGAGGAAGTCTTCG	60.739	60.000	6.50	0.00	0.00	3.79
1398	1429	1.133199	AGGATCTCCTCCAGCCTACTG	60.133	57.143	0.00	0.00	44.77	2.74
1774	1805	4.602259	GGTGCTATAGCCGGCGCA	62.602	66.667	23.20	21.85	40.26	6.09
1883	1914	2.278857	CTTCAGGATCGACGCCGG	60.279	66.667	0.00	0.00	36.24	6.13
1924	1955	2.972713	TCTCCATCCTACCTTACATGGC	59.027	50.000	0.00	0.00	36.49	4.40
1958	1990	2.568003	TAGCTCACTGCACGCTACT	58.432	52.632	0.00	0.00	45.94	2.57
1972	2004	0.811915	AAGACGAGACGCATGTAGCT	59.188	50.000	0.00	0.00	42.61	3.32
1973	2005	2.470196	TAAGACGAGACGCATGTAGC	57.530	50.000	0.00	0.00	40.87	3.58
1974	2006	5.034797	TCAAATAAGACGAGACGCATGTAG	58.965	41.667	0.00	0.00	0.00	2.74
1975	2007	4.989044	TCAAATAAGACGAGACGCATGTA	58.011	39.130	0.00	0.00	0.00	2.29
1976	2008	3.845178	TCAAATAAGACGAGACGCATGT	58.155	40.909	0.00	0.00	0.00	3.21
1978	2010	6.292381	GCTAAATCAAATAAGACGAGACGCAT	60.292	38.462	0.00	0.00	0.00	4.73
1979	2011	5.005394	GCTAAATCAAATAAGACGAGACGCA	59.995	40.000	0.00	0.00	0.00	5.24
1982	2014	7.402640	CCAAGCTAAATCAAATAAGACGAGAC	58.597	38.462	0.00	0.00	0.00	3.36
1983	2015	6.037172	GCCAAGCTAAATCAAATAAGACGAGA	59.963	38.462	0.00	0.00	0.00	4.04
2114	2153	4.576463	GCGACCATGGAAGAAATTCATAGT	59.424	41.667	21.47	0.00	0.00	2.12
2115	2154	4.023707	GGCGACCATGGAAGAAATTCATAG	60.024	45.833	21.47	0.00	0.00	2.23
2120	2159	2.214376	TGGCGACCATGGAAGAAATT	57.786	45.000	21.47	0.00	0.00	1.82
2200	2244	2.639065	ACGACCAACTGAACAACACAT	58.361	42.857	0.00	0.00	0.00	3.21
2230	2274	0.675633	ACAAAAAGAGCAGGCGCAAT	59.324	45.000	10.83	0.00	42.27	3.56
2290	2334	7.462462	GCCGACGTGTTAAGAGTAAATAAGAAG	60.462	40.741	0.00	0.00	0.00	2.85
2293	2337	5.275602	CGCCGACGTGTTAAGAGTAAATAAG	60.276	44.000	0.00	0.00	33.53	1.73
2313	2357	2.223829	ACTCTTCATACTTGGATCGCCG	60.224	50.000	0.00	0.00	36.79	6.46
2314	2358	3.385577	GACTCTTCATACTTGGATCGCC	58.614	50.000	0.00	0.00	0.00	5.54
2345	2389	5.262588	TGTGTGCATCTAGATACGTCAAT	57.737	39.130	4.54	0.00	0.00	2.57
2556	2606	5.919141	CCATACTTGGCTCGTACTACAATAC	59.081	44.000	0.00	0.00	35.85	1.89
2568	2629	1.952296	CATTGGCTCCATACTTGGCTC	59.048	52.381	0.00	0.00	43.29	4.70
2571	2632	0.664761	CGCATTGGCTCCATACTTGG	59.335	55.000	0.00	0.00	45.15	3.61
2575	2636	1.948104	TGTACGCATTGGCTCCATAC	58.052	50.000	0.00	0.00	38.10	2.39
2642	2704	3.437428	TGATTATGCATGAACGCTTTGC	58.563	40.909	10.16	0.00	36.91	3.68
2645	2707	4.377738	CGCTATGATTATGCATGAACGCTT	60.378	41.667	10.16	0.00	0.00	4.68
2647	2709	3.410850	CGCTATGATTATGCATGAACGC	58.589	45.455	10.16	0.00	0.00	4.84
2748	2884	4.875536	TGTCATGCATAACTTGTATTCGCT	59.124	37.500	0.00	0.00	0.00	4.93
2838	2988	6.313164	GGGAGTAGCAATGTTGTTTCTACTAC	59.687	42.308	10.41	10.41	39.76	2.73
2905	3057	7.735326	TTCCTATGGTATTTATCTAGAGGGC	57.265	40.000	0.00	0.00	0.00	5.19

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.