AutoCloner

Multiple sequence alignment - TraesCS1D01G207400

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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	TraesCS1D01G207400	chr1D	100.000	2859	0	0	1	2859	293616091	293613233	0.000000e+00	5280.0
1	TraesCS1D01G207400	chr1D	87.356	522	51	6	2338	2859	334465134	334464628	4.100000e-163	584.0
2	TraesCS1D01G207400	chr1A	92.012	2291	123	22	1	2262	365619965	365617706	0.000000e+00	3162.0
3	TraesCS1D01G207400	chr1A	90.385	52	5	0	2802	2853	528073528	528073579	5.110000e-08	69.4
4	TraesCS1D01G207400	chr1B	92.158	1798	72	29	505	2278	394894103	394892351	0.000000e+00	2475.0
5	TraesCS1D01G207400	chr1B	87.954	523	40	9	1	503	394896838	394896319	1.900000e-166	595.0
6	TraesCS1D01G207400	chr1B	86.679	533	51	8	2290	2813	394886450	394885929	8.890000e-160	573.0
7	TraesCS1D01G207400	chr2D	89.603	529	52	3	2332	2859	566843255	566842729	0.000000e+00	669.0
8	TraesCS1D01G207400	chr5B	86.553	528	51	10	2338	2859	45652738	45652225	5.350000e-157	564.0
9	TraesCS1D01G207400	chr3A	84.860	535	54	12	2338	2851	690077483	690076955	5.460000e-142	514.0
10	TraesCS1D01G207400	chr4D	80.864	486	76	15	1008	1485	486918669	486918193	1.620000e-97	366.0
11	TraesCS1D01G207400	chr5A	80.493	487	78	16	1008	1485	667197348	667196870	9.740000e-95	357.0
12	TraesCS1D01G207400	chr4B	80.457	481	77	14	1008	1485	621675778	621675312	4.530000e-93	351.0
13	TraesCS1D01G207400	chr6A	82.292	384	53	8	2338	2717	604452889	604452517	4.600000e-83	318.0
14	TraesCS1D01G207400	chr6A	78.261	138	15	8	1702	1838	596229566	596229443	1.100000e-09	75.0
15	TraesCS1D01G207400	chrUn	80.309	259	41	9	2603	2858	339340070	339339819	1.350000e-43	187.0
16	TraesCS1D01G207400	chr2B	80.309	259	41	9	2603	2858	6828779	6828528	1.350000e-43	187.0
17	TraesCS1D01G207400	chr2B	80.309	259	41	9	2603	2858	6916241	6915990	1.350000e-43	187.0
18	TraesCS1D01G207400	chr2B	80.315	254	40	9	2608	2858	6780798	6780552	1.750000e-42	183.0
19	TraesCS1D01G207400	chr6B	83.099	71	7	3	2791	2859	181731315	181731248	3.080000e-05	60.2

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	TraesCS1D01G207400	chr1D	293613233	293616091	2858	True	5280	5280	100.000	1	2859	1	chr1D.!!$R1	2858
1	TraesCS1D01G207400	chr1D	334464628	334465134	506	True	584	584	87.356	2338	2859	1	chr1D.!!$R2	521
2	TraesCS1D01G207400	chr1A	365617706	365619965	2259	True	3162	3162	92.012	1	2262	1	chr1A.!!$R1	2261
3	TraesCS1D01G207400	chr1B	394892351	394896838	4487	True	1535	2475	90.056	1	2278	2	chr1B.!!$R2	2277
4	TraesCS1D01G207400	chr1B	394885929	394886450	521	True	573	573	86.679	2290	2813	1	chr1B.!!$R1	523
5	TraesCS1D01G207400	chr2D	566842729	566843255	526	True	669	669	89.603	2332	2859	1	chr2D.!!$R1	527
6	TraesCS1D01G207400	chr5B	45652225	45652738	513	True	564	564	86.553	2338	2859	1	chr5B.!!$R1	521
7	TraesCS1D01G207400	chr3A	690076955	690077483	528	True	514	514	84.860	2338	2851	1	chr3A.!!$R1	513

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
850	3088	0.25316	AGGTATTGCTCCCAGACCCA	60.253	55.0	0.0	0.0	32.12	4.51	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2559	4837	0.038618	CGGAGGTTGTGTCATCGTCA	60.039	55.0	0.0	0.0	0.0	4.35	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
74	81	3.303605	GCACACTCTATGAGCGCG	58.696	61.111	0.00	0.00	35.09	6.86
93	111	2.311462	CGTTCGAGATATCGAGCCTTG	58.689	52.381	18.86	3.70	43.33	3.61
95	113	3.560503	GTTCGAGATATCGAGCCTTGAG	58.439	50.000	14.72	0.00	43.33	3.02
109	127	5.006165	CGAGCCTTGAGATTGATGAAGTTAC	59.994	44.000	0.00	0.00	0.00	2.50
116	134	6.950842	TGAGATTGATGAAGTTACCACAGAT	58.049	36.000	0.00	0.00	0.00	2.90
119	137	4.558226	TGATGAAGTTACCACAGATGCT	57.442	40.909	0.00	0.00	0.00	3.79
242	265	3.589951	ATCTTGATGGGATGGTTCCAG	57.410	47.619	0.00	0.00	44.60	3.86
354	377	6.293698	TCAGTCAGTAGTCAGTACAGTACAA	58.706	40.000	13.37	0.00	33.55	2.41
417	440	1.732941	AAAATCTGTCCGCGTGCATA	58.267	45.000	4.92	0.00	0.00	3.14
503	526	6.563422	AGTATAACGTAGCCAATGTCGTTAA	58.437	36.000	11.73	1.89	46.39	2.01
511	2748	3.687698	AGCCAATGTCGTTAATGTGGTAC	59.312	43.478	4.49	0.00	0.00	3.34
546	2784	2.953648	TCTGTCTGTTGTCACCTCGTTA	59.046	45.455	0.00	0.00	0.00	3.18
559	2797	3.679980	CACCTCGTTACCTGTTTCAGATG	59.320	47.826	0.00	0.00	32.44	2.90
566	2804	3.213206	ACCTGTTTCAGATGTTGCTCA	57.787	42.857	0.00	0.00	32.44	4.26
568	2806	3.181451	ACCTGTTTCAGATGTTGCTCAGA	60.181	43.478	0.00	0.00	32.44	3.27
569	2807	3.817084	CCTGTTTCAGATGTTGCTCAGAA	59.183	43.478	0.00	0.00	32.44	3.02
611	2849	6.727824	AAAGCAGAAGTGTCACATACATAC	57.272	37.500	5.62	0.00	41.10	2.39
732	2970	6.597672	TGCTTTAACAGTTCAGTTTCTTCTCA	59.402	34.615	0.00	0.00	33.07	3.27
763	3001	5.269459	GTTGTGGACGATATGATACATGC	57.731	43.478	0.00	0.00	0.00	4.06
850	3088	0.253160	AGGTATTGCTCCCAGACCCA	60.253	55.000	0.00	0.00	32.12	4.51
1187	3425	2.125912	CACCTTCGAGGACGGCAG	60.126	66.667	7.76	0.00	37.67	4.85
1211	3449	1.290955	CCCTCGTCGGTAAGCAACA	59.709	57.895	0.00	0.00	0.00	3.33
1242	3480	6.173339	ACAATGTCCGTAGATTTTCATCTGT	58.827	36.000	0.00	0.00	40.28	3.41
1248	3486	8.204160	TGTCCGTAGATTTTCATCTGTATGATT	58.796	33.333	0.00	0.00	41.73	2.57
1252	3490	9.034544	CGTAGATTTTCATCTGTATGATTCACA	57.965	33.333	0.00	0.00	41.73	3.58
1684	3949	1.597027	CGGCGACAAGTTCACCCTT	60.597	57.895	0.00	0.00	0.00	3.95
1687	3952	1.166531	GCGACAAGTTCACCCTTGCT	61.167	55.000	1.04	0.00	44.55	3.91
1871	4136	2.484241	CCATTCTGATCTCCATGCACGA	60.484	50.000	0.00	0.00	0.00	4.35
1950	4215	2.310349	TGCCCCACCACATACACTATTT	59.690	45.455	0.00	0.00	0.00	1.40
1951	4216	3.523972	TGCCCCACCACATACACTATTTA	59.476	43.478	0.00	0.00	0.00	1.40
1968	4233	2.983907	TTACCGTGGCATTTCCGATA	57.016	45.000	0.00	0.00	37.80	2.92
2055	4322	6.384224	TCTCGTATACGTTGTGTTCTTCATT	58.616	36.000	23.67	0.00	40.80	2.57
2088	4358	1.531602	GCCCTTGCCTTCCTGTTGT	60.532	57.895	0.00	0.00	0.00	3.32
2089	4359	1.115326	GCCCTTGCCTTCCTGTTGTT	61.115	55.000	0.00	0.00	0.00	2.83
2090	4360	0.675633	CCCTTGCCTTCCTGTTGTTG	59.324	55.000	0.00	0.00	0.00	3.33
2096	4366	1.515521	CCTTCCTGTTGTTGCGGTCC	61.516	60.000	0.00	0.00	0.00	4.46
2147	4417	6.530019	AGTGTAATAAAATGCTTTCCCCTG	57.470	37.500	0.00	0.00	0.00	4.45
2158	4430	1.344438	CTTTCCCCTGCTTTTGGTTCC	59.656	52.381	0.00	0.00	0.00	3.62
2170	4442	2.093306	TTGGTTCCGATACTGCACTG	57.907	50.000	0.00	0.00	0.00	3.66
2171	4443	1.262417	TGGTTCCGATACTGCACTGA	58.738	50.000	0.00	0.00	0.00	3.41
2207	4479	6.750501	CACGAATTTTCCGATCTGAACTAGTA	59.249	38.462	0.00	0.00	0.00	1.82
2213	4485	5.419760	TCCGATCTGAACTAGTATGAACG	57.580	43.478	0.00	5.70	0.00	3.95
2239	4512	1.200948	GTCAGCTCTGGTGCAATTTCC	59.799	52.381	0.00	0.00	34.99	3.13
2264	4537	8.748412	CCTTGGAGAATGTTAATATTTTGGTCA	58.252	33.333	0.00	0.00	0.00	4.02
2278	4551	1.595311	TGGTCATCCATTGTAGCCCT	58.405	50.000	0.00	0.00	39.03	5.19
2279	4552	2.770447	TGGTCATCCATTGTAGCCCTA	58.230	47.619	0.00	0.00	39.03	3.53
2280	4553	3.326521	TGGTCATCCATTGTAGCCCTAT	58.673	45.455	0.00	0.00	39.03	2.57
2281	4554	3.721575	TGGTCATCCATTGTAGCCCTATT	59.278	43.478	0.00	0.00	39.03	1.73
2282	4555	4.074970	GGTCATCCATTGTAGCCCTATTG	58.925	47.826	0.00	0.00	0.00	1.90
2283	4556	4.446311	GGTCATCCATTGTAGCCCTATTGT	60.446	45.833	0.00	0.00	0.00	2.71
2284	4557	5.221843	GGTCATCCATTGTAGCCCTATTGTA	60.222	44.000	0.00	0.00	0.00	2.41
2285	4558	5.934625	GTCATCCATTGTAGCCCTATTGTAG	59.065	44.000	0.00	0.00	0.00	2.74
2286	4559	5.843969	TCATCCATTGTAGCCCTATTGTAGA	59.156	40.000	0.00	0.00	0.00	2.59
2287	4560	6.328934	TCATCCATTGTAGCCCTATTGTAGAA	59.671	38.462	0.00	0.00	0.00	2.10
2288	4561	5.925509	TCCATTGTAGCCCTATTGTAGAAC	58.074	41.667	0.00	0.00	0.00	3.01
2305	4578	7.266922	TGTAGAACCTAAAACATGACAAACC	57.733	36.000	0.00	0.00	0.00	3.27
2307	4580	7.558444	TGTAGAACCTAAAACATGACAAACCTT	59.442	33.333	0.00	0.00	0.00	3.50
2379	4652	2.579207	TCTTTCCTCTAACATCCGCG	57.421	50.000	0.00	0.00	0.00	6.46
2389	4662	1.546589	AACATCCGCGGGGTCTTACA	61.547	55.000	27.83	2.60	33.83	2.41
2483	4756	5.438117	CACATATATTCTTGCAACTGAGCG	58.562	41.667	0.00	0.00	37.31	5.03

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	5.462068	TGCGTGTGTATAAGATTCTATGTGC	59.538	40.000	0.00	0.00	0.00	4.57
93	111	6.238320	GCATCTGTGGTAACTTCATCAATCTC	60.238	42.308	0.00	0.00	37.61	2.75
95	113	5.587844	AGCATCTGTGGTAACTTCATCAATC	59.412	40.000	0.00	0.00	33.52	2.67
109	127	3.553511	GTCGACTATGAAAGCATCTGTGG	59.446	47.826	8.70	0.00	35.94	4.17
116	134	2.991190	GTTTCCGTCGACTATGAAAGCA	59.009	45.455	18.86	2.97	0.00	3.91
119	137	3.287312	ACGTTTCCGTCGACTATGAAA	57.713	42.857	14.70	15.56	46.28	2.69
145	163	1.468565	CGGCGATGTTTCTTCGGTAGA	60.469	52.381	0.00	0.00	37.10	2.59
147	165	0.527113	TCGGCGATGTTTCTTCGGTA	59.473	50.000	4.99	0.00	37.10	4.02
148	166	0.320073	TTCGGCGATGTTTCTTCGGT	60.320	50.000	11.76	0.00	37.10	4.69
150	168	2.096417	ACTTTTCGGCGATGTTTCTTCG	60.096	45.455	11.76	0.00	39.55	3.79
225	245	0.703488	TGCTGGAACCATCCCATCAA	59.297	50.000	0.00	0.00	45.95	2.57
354	377	3.879295	CCATCAAGGTAAAGCATCATCGT	59.121	43.478	0.00	0.00	0.00	3.73
417	440	6.039941	GTGAGTAGCATAGGTACTGAATCTGT	59.960	42.308	12.97	0.00	45.17	3.41
503	526	3.008375	AGACAAGTCATGCAGTACCACAT	59.992	43.478	2.72	0.00	0.00	3.21
511	2748	2.994578	CAGACAGAGACAAGTCATGCAG	59.005	50.000	2.72	0.00	37.23	4.41
546	2784	3.144506	CTGAGCAACATCTGAAACAGGT	58.855	45.455	0.00	0.00	31.51	4.00
850	3088	2.606519	TTGTGTAGCCGGGAGCCT	60.607	61.111	2.18	0.00	45.47	4.58
1187	3425	2.862347	CTTACCGACGAGGGTGACGC	62.862	65.000	11.52	0.00	46.96	5.19
1211	3449	6.385649	AAATCTACGGACATTGTTTGTTGT	57.614	33.333	0.00	0.00	39.18	3.32
1252	3490	9.358872	CGCACATATCATCAACATATACTAAGT	57.641	33.333	0.00	0.00	0.00	2.24
1254	3492	8.527810	TCCGCACATATCATCAACATATACTAA	58.472	33.333	0.00	0.00	0.00	2.24
1262	3500	4.070630	TCATCCGCACATATCATCAACA	57.929	40.909	0.00	0.00	0.00	3.33
1684	3949	1.985614	CATGTGGGAGAGGTCAGCA	59.014	57.895	0.00	0.00	0.00	4.41
1687	3952	2.300967	GGGCATGTGGGAGAGGTCA	61.301	63.158	0.00	0.00	0.00	4.02
1738	4003	3.785859	GACTGGATGAGGCGGGCA	61.786	66.667	3.78	0.00	0.00	5.36
1871	4136	3.593794	GAGGAGGCGTACGGCGAT	61.594	66.667	32.36	23.03	44.92	4.58
1950	4215	1.758280	AGTATCGGAAATGCCACGGTA	59.242	47.619	0.00	0.00	35.94	4.02
1951	4216	0.539986	AGTATCGGAAATGCCACGGT	59.460	50.000	0.00	0.00	35.94	4.83
2055	4322	2.988684	GGCGAAACACCCATGCCA	60.989	61.111	0.00	0.00	45.06	4.92
2088	4358	3.153130	TCAAATGATCTTTGGACCGCAA	58.847	40.909	13.94	0.00	0.00	4.85
2089	4359	2.789213	TCAAATGATCTTTGGACCGCA	58.211	42.857	13.94	0.00	0.00	5.69
2090	4360	3.848272	TTCAAATGATCTTTGGACCGC	57.152	42.857	13.94	0.00	0.00	5.68
2126	4396	5.022787	AGCAGGGGAAAGCATTTTATTACA	58.977	37.500	0.00	0.00	39.27	2.41
2139	4409	1.419381	GGAACCAAAAGCAGGGGAAA	58.581	50.000	0.00	0.00	0.00	3.13
2142	4412	0.611896	ATCGGAACCAAAAGCAGGGG	60.612	55.000	0.00	0.00	0.00	4.79
2147	4417	1.810151	TGCAGTATCGGAACCAAAAGC	59.190	47.619	0.00	0.00	0.00	3.51
2158	4430	1.391485	GTGCTTGTCAGTGCAGTATCG	59.609	52.381	0.00	0.00	40.06	2.92
2170	4442	2.663279	AATTCGTGTTCGTGCTTGTC	57.337	45.000	0.00	0.00	38.33	3.18
2171	4443	3.359654	GAAAATTCGTGTTCGTGCTTGT	58.640	40.909	0.00	0.00	38.33	3.16
2213	4485	0.873743	GCACCAGAGCTGACGATAGC	60.874	60.000	0.00	7.43	44.01	2.97
2220	4493	1.074405	AGGAAATTGCACCAGAGCTGA	59.926	47.619	0.00	0.00	34.99	4.26
2264	4537	6.465894	GGTTCTACAATAGGGCTACAATGGAT	60.466	42.308	0.00	0.00	0.00	3.41
2279	4552	8.357402	GGTTTGTCATGTTTTAGGTTCTACAAT	58.643	33.333	0.00	0.00	0.00	2.71
2280	4553	7.558444	AGGTTTGTCATGTTTTAGGTTCTACAA	59.442	33.333	0.00	0.00	0.00	2.41
2281	4554	7.057894	AGGTTTGTCATGTTTTAGGTTCTACA	58.942	34.615	0.00	0.00	0.00	2.74
2282	4555	7.506328	AGGTTTGTCATGTTTTAGGTTCTAC	57.494	36.000	0.00	0.00	0.00	2.59
2283	4556	8.528044	AAAGGTTTGTCATGTTTTAGGTTCTA	57.472	30.769	0.00	0.00	0.00	2.10
2284	4557	7.418337	AAAGGTTTGTCATGTTTTAGGTTCT	57.582	32.000	0.00	0.00	0.00	3.01
2285	4558	8.487313	AAAAAGGTTTGTCATGTTTTAGGTTC	57.513	30.769	0.00	0.00	0.00	3.62
2320	4593	7.769044	CACCAGCTTTACCTAAGTTGTATACAT	59.231	37.037	6.36	0.00	41.85	2.29
2333	4606	3.073274	GGTTGATCACCAGCTTTACCT	57.927	47.619	0.00	0.00	46.42	3.08
2379	4652	0.618458	TGTGGCAGATGTAAGACCCC	59.382	55.000	0.00	0.00	0.00	4.95
2389	4662	1.676916	CCATGAAGACGTGTGGCAGAT	60.677	52.381	0.00	0.00	0.00	2.90
2483	4756	4.518970	TGTGGTCTATCTTTTGAAACTGGC	59.481	41.667	0.00	0.00	0.00	4.85
2559	4837	0.038618	CGGAGGTTGTGTCATCGTCA	60.039	55.000	0.00	0.00	0.00	4.35
2739	5038	1.877443	GACGGTGTTGTAGCATTGGTT	59.123	47.619	0.00	0.00	0.00	3.67
2745	5044	2.340809	CCCGACGGTGTTGTAGCA	59.659	61.111	13.94	0.00	0.00	3.49
2748	5055	1.661480	CTGACCCGACGGTGTTGTA	59.339	57.895	13.94	1.50	44.88	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.