AutoCloner

Multiple sequence alignment - TraesCS1D01G233800

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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	TraesCS1D01G233800	chr1D	100.000	2477	0	0	1	2477	322164112	322166588	0.000000e+00	4575.0
1	TraesCS1D01G233800	chr1D	91.935	186	15	0	2290	2475	278944335	278944520	6.790000e-66	261.0
2	TraesCS1D01G233800	chr1D	89.610	77	5	2	1132	1208	322262810	322262883	7.290000e-16	95.3
3	TraesCS1D01G233800	chr1B	95.199	2437	69	16	72	2475	434834461	434836882	0.000000e+00	3808.0
4	TraesCS1D01G233800	chr1B	95.833	72	2	1	1	72	434834362	434834432	5.600000e-22	115.0
5	TraesCS1D01G233800	chr1B	89.189	74	5	3	1135	1208	435043015	435043085	3.390000e-14	89.8
6	TraesCS1D01G233800	chr1A	91.599	1595	81	19	725	2290	405868715	405870285	0.000000e+00	2154.0
7	TraesCS1D01G233800	chr1A	86.416	692	40	21	82	742	405868024	405868692	0.000000e+00	708.0
8	TraesCS1D01G233800	chr1A	89.610	77	5	2	1132	1208	406143322	406143395	7.290000e-16	95.3
9	TraesCS1D01G233800	chr1A	72.954	281	68	6	1987	2265	36128924	36129198	9.430000e-15	91.6
10	TraesCS1D01G233800	chr6D	93.011	186	13	0	2289	2474	298970653	298970838	3.140000e-69	272.0
11	TraesCS1D01G233800	chr6D	92.432	185	13	1	2292	2475	97813584	97813768	1.890000e-66	263.0
12	TraesCS1D01G233800	chr6D	75.701	214	47	5	2072	2280	156452054	156452267	4.360000e-18	102.0
13	TraesCS1D01G233800	chr3D	93.085	188	9	4	2290	2474	24107000	24106814	3.140000e-69	272.0
14	TraesCS1D01G233800	chr3D	92.473	186	11	3	2290	2474	517553458	517553641	1.890000e-66	263.0
15	TraesCS1D01G233800	chr5D	91.979	187	13	2	2289	2474	455619636	455619821	6.790000e-66	261.0
16	TraesCS1D01G233800	chr5B	91.935	186	15	0	2289	2474	132594251	132594436	6.790000e-66	261.0
17	TraesCS1D01G233800	chr4D	91.935	186	15	0	2289	2474	128586469	128586284	6.790000e-66	261.0
18	TraesCS1D01G233800	chr7B	75.465	269	56	9	2014	2276	737020299	737020035	3.350000e-24	122.0
19	TraesCS1D01G233800	chr7B	74.825	286	62	10	2014	2294	737747443	737747163	1.200000e-23	121.0
20	TraesCS1D01G233800	chr7B	75.093	269	57	9	2014	2276	737320827	737320563	1.560000e-22	117.0
21	TraesCS1D01G233800	chr7B	74.126	286	64	10	2014	2294	736971501	736971221	2.600000e-20	110.0
22	TraesCS1D01G233800	chr7B	73.776	286	65	10	2014	2294	737304540	737304260	1.210000e-18	104.0
23	TraesCS1D01G233800	chrUn	80.000	80	13	3	1987	2065	23399823	23399900	3.440000e-04	56.5

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	TraesCS1D01G233800	chr1D	322164112	322166588	2476	False	4575.0	4575	100.0000	1	2477	1	chr1D.!!$F2	2476
1	TraesCS1D01G233800	chr1B	434834362	434836882	2520	False	1961.5	3808	95.5160	1	2475	2	chr1B.!!$F2	2474
2	TraesCS1D01G233800	chr1A	405868024	405870285	2261	False	1431.0	2154	89.0075	82	2290	2	chr1A.!!$F3	2208

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
937	1040	0.340208	TCCCTCTTTCCCCCTCTCTC	59.66	60.0	0.0	0.0	0.0	3.2	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1952	2094	0.032678	CGACCTATGGCTCGCTGATT	59.967	55.0	0.0	0.0	0.0	2.57	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
22	23	1.523758	AACATTTGAGACGGGTCTGC	58.476	50.000	5.98	0.00	40.61	4.26
577	636	4.321230	GGTCCATTCTTCTGATTTTTGCGT	60.321	41.667	0.00	0.00	0.00	5.24
669	733	7.538678	GGACTTTGAATTGTATTTGCACTAGTG	59.461	37.037	18.93	18.93	0.00	2.74
930	1033	0.983905	GTCTCCCTCCCTCTTTCCCC	60.984	65.000	0.00	0.00	0.00	4.81
931	1034	1.694525	CTCCCTCCCTCTTTCCCCC	60.695	68.421	0.00	0.00	0.00	5.40
932	1035	2.191846	TCCCTCCCTCTTTCCCCCT	61.192	63.158	0.00	0.00	0.00	4.79
933	1036	1.694525	CCCTCCCTCTTTCCCCCTC	60.695	68.421	0.00	0.00	0.00	4.30
934	1037	1.398234	CCTCCCTCTTTCCCCCTCT	59.602	63.158	0.00	0.00	0.00	3.69
935	1038	0.692756	CCTCCCTCTTTCCCCCTCTC	60.693	65.000	0.00	0.00	0.00	3.20
936	1039	0.341609	CTCCCTCTTTCCCCCTCTCT	59.658	60.000	0.00	0.00	0.00	3.10
937	1040	0.340208	TCCCTCTTTCCCCCTCTCTC	59.660	60.000	0.00	0.00	0.00	3.20
938	1041	0.341609	CCCTCTTTCCCCCTCTCTCT	59.658	60.000	0.00	0.00	0.00	3.10
939	1042	1.691163	CCCTCTTTCCCCCTCTCTCTC	60.691	61.905	0.00	0.00	0.00	3.20
1293	1402	2.357569	GCCAAAGTTCAGGATGGAGGAT	60.358	50.000	0.00	0.00	36.16	3.24
1629	1751	8.567285	ACTGACATAGAATTTTAAGTTCCCTG	57.433	34.615	0.00	0.00	0.00	4.45
1637	1759	7.200455	AGAATTTTAAGTTCCCTGAAAACACG	58.800	34.615	0.00	0.00	34.52	4.49
1638	1760	6.702716	ATTTTAAGTTCCCTGAAAACACGA	57.297	33.333	0.00	0.00	34.52	4.35
1702	1840	7.771183	ACAAATAATTATGCCGAATTCACTGT	58.229	30.769	6.22	0.00	31.51	3.55
1758	1897	6.461110	AACATATGATTCAAGAAAGGGCAG	57.539	37.500	10.38	0.00	0.00	4.85
1831	1970	8.534333	TGTCTACTGTGTTTATTCATGACTTC	57.466	34.615	0.00	0.00	0.00	3.01
1837	1976	7.009179	TGTGTTTATTCATGACTTCCTCTCT	57.991	36.000	0.00	0.00	0.00	3.10
1857	1996	1.076841	TGGGCATTTTCCAGACCATCA	59.923	47.619	0.00	0.00	38.22	3.07
1858	1997	1.478105	GGGCATTTTCCAGACCATCAC	59.522	52.381	0.00	0.00	31.39	3.06
1870	2009	3.127376	CAGACCATCACGAAATGCATGAA	59.873	43.478	0.00	0.00	0.00	2.57
1871	2010	3.758023	AGACCATCACGAAATGCATGAAA	59.242	39.130	0.00	0.00	0.00	2.69
1898	2040	2.483188	GGCTCGAATGGTACGATTCCTT	60.483	50.000	20.77	0.00	39.02	3.36
1899	2041	3.195661	GCTCGAATGGTACGATTCCTTT	58.804	45.455	20.77	0.00	39.02	3.11
1952	2094	4.107311	AGGACAAATTCTCCCCAAGGTTTA	59.893	41.667	0.00	0.00	0.00	2.01
1953	2095	4.836175	GGACAAATTCTCCCCAAGGTTTAA	59.164	41.667	0.00	0.00	0.00	1.52
1956	2098	6.081356	ACAAATTCTCCCCAAGGTTTAATCA	58.919	36.000	0.00	0.00	0.00	2.57
1968	2111	2.808543	GGTTTAATCAGCGAGCCATAGG	59.191	50.000	0.00	0.00	0.00	2.57
1988	2131	0.392706	TCGCTTCCTCTTTGTCTGCA	59.607	50.000	0.00	0.00	0.00	4.41
2012	2155	1.612395	GCAGGGAGGAGAGTCACAGG	61.612	65.000	0.00	0.00	0.00	4.00
2041	2184	5.185249	TCACTCCAGCTAGTAGTTTAGGTTG	59.815	44.000	0.00	0.00	29.37	3.77
2068	2211	2.902608	TCTAATCCTCACAGGTGTGGT	58.097	47.619	17.29	5.05	45.65	4.16
2093	2236	1.748879	GGCAGATGGCGGCACTTAA	60.749	57.895	16.34	0.00	46.16	1.85
2113	2256	8.830580	CACTTAATCTTTGAGTTTGTCTTCTGA	58.169	33.333	0.00	0.00	0.00	3.27
2222	2365	1.949525	GGGTTCTTATCGTGCATGCAT	59.050	47.619	25.64	10.90	0.00	3.96
2276	2420	2.762535	ATTCAAGGGTCAACGACGAT	57.237	45.000	0.00	0.00	32.65	3.73
2298	2442	1.271379	ACCGCAGCTCCATACAAGTTT	60.271	47.619	0.00	0.00	0.00	2.66
2316	2460	3.262151	AGTTTTGGAGCCTCCTCTAGTTC	59.738	47.826	12.94	0.00	37.46	3.01
2328	2472	8.675096	AGCCTCCTCTAGTTCTTATAGTTCTAT	58.325	37.037	0.00	0.00	0.00	1.98
2359	2503	6.466885	TGGTCCTAGTTGACTAATTAGAGC	57.533	41.667	19.38	10.64	35.54	4.09
2398	2542	8.603898	TTGTCCTCATAATTAGAACCTCAGTA	57.396	34.615	0.00	0.00	0.00	2.74
2415	2559	7.306013	ACCTCAGTATGGTTCTAATATCCTCA	58.694	38.462	0.00	0.00	36.16	3.86
2447	2591	0.595310	GGCGACGATTAGCTCTGGAC	60.595	60.000	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.739338	GATGGATCGCAGACCCGTCT	61.739	60.000	4.46	0.00	42.51	4.18
15	16	0.249657	GACAGATGGATCGCAGACCC	60.250	60.000	0.00	0.00	42.51	4.46
22	23	0.033228	GCCAGGAGACAGATGGATCG	59.967	60.000	0.00	0.00	36.09	3.69
577	636	2.254152	ATGAACCTGGCTAGTCTCCA	57.746	50.000	0.00	0.00	0.00	3.86
930	1033	1.869754	CGCGAGAGAGAGAGAGAGAGG	60.870	61.905	0.00	0.00	0.00	3.69
931	1034	1.491670	CGCGAGAGAGAGAGAGAGAG	58.508	60.000	0.00	0.00	0.00	3.20
932	1035	0.529773	GCGCGAGAGAGAGAGAGAGA	60.530	60.000	12.10	0.00	0.00	3.10
933	1036	1.821241	CGCGCGAGAGAGAGAGAGAG	61.821	65.000	28.94	0.00	31.43	3.20
934	1037	1.880796	CGCGCGAGAGAGAGAGAGA	60.881	63.158	28.94	0.00	31.43	3.10
935	1038	2.625906	CGCGCGAGAGAGAGAGAG	59.374	66.667	28.94	0.00	31.43	3.20
936	1039	3.568743	GCGCGCGAGAGAGAGAGA	61.569	66.667	37.18	0.00	31.43	3.10
1748	1887	4.581309	TCTCATTCATTCTGCCCTTTCT	57.419	40.909	0.00	0.00	0.00	2.52
1758	1897	8.834749	TTCTGATCAGATCATCTCATTCATTC	57.165	34.615	25.64	0.00	38.85	2.67
1824	1963	1.890552	ATGCCCAGAGAGGAAGTCAT	58.109	50.000	0.00	0.00	41.22	3.06
1831	1970	3.985410	TGGAAAATGCCCAGAGAGG	57.015	52.632	0.00	0.00	37.03	3.69
1837	1976	1.076841	TGATGGTCTGGAAAATGCCCA	59.923	47.619	0.00	0.00	0.00	5.36
1898	2040	1.645710	GGAAGAGAGAGGGGTGACAA	58.354	55.000	0.00	0.00	0.00	3.18
1899	2041	0.252284	GGGAAGAGAGAGGGGTGACA	60.252	60.000	0.00	0.00	0.00	3.58
1952	2094	0.032678	CGACCTATGGCTCGCTGATT	59.967	55.000	0.00	0.00	0.00	2.57
1953	2095	1.662608	CGACCTATGGCTCGCTGAT	59.337	57.895	0.00	0.00	0.00	2.90
1968	2111	0.793250	GCAGACAAAGAGGAAGCGAC	59.207	55.000	0.00	0.00	0.00	5.19
1988	2131	2.040278	CTCTCCTCCCTGCCACCT	59.960	66.667	0.00	0.00	0.00	4.00
2012	2155	1.410882	CTACTAGCTGGAGTGAAGGCC	59.589	57.143	3.17	0.00	0.00	5.19
2041	2184	2.422093	CCTGTGAGGATTAGAAAGCCCC	60.422	54.545	0.00	0.00	37.67	5.80
2093	2236	6.148480	CGGATTCAGAAGACAAACTCAAAGAT	59.852	38.462	0.00	0.00	0.00	2.40
2113	2256	3.700038	ACAAACTCGAGTAGGATCGGATT	59.300	43.478	20.39	2.76	42.93	3.01
2222	2365	4.126437	ACTGACACAACATTTCGTGATCA	58.874	39.130	0.00	0.00	36.91	2.92
2231	2374	3.947196	TCTGAAGCAACTGACACAACATT	59.053	39.130	0.00	0.00	0.00	2.71
2276	2420	0.108186	CTTGTATGGAGCTGCGGTCA	60.108	55.000	0.00	0.00	0.00	4.02
2280	2424	2.414559	CCAAAACTTGTATGGAGCTGCG	60.415	50.000	0.00	0.00	36.27	5.18
2298	2442	2.930109	AGAACTAGAGGAGGCTCCAA	57.070	50.000	33.86	18.14	39.61	3.53
2328	2472	7.844493	TTAGTCAACTAGGACCAACTAGAAA	57.156	36.000	7.20	0.00	42.40	2.52
2391	2535	7.453126	AGTGAGGATATTAGAACCATACTGAGG	59.547	40.741	0.00	0.00	0.00	3.86
2415	2559	0.381089	CGTCGCCGGAGAATTAGAGT	59.619	55.000	10.32	0.00	0.00	3.24
2439	2583	2.876645	CGCTTCGTCGTCCAGAGC	60.877	66.667	0.00	0.00	0.00	4.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.