AutoCloner

Multiple sequence alignment - TraesCS3B01G108900

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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	TraesCS3B01G108900	chr3B	100.000	2450	0	0	1	2450	74830718	74828269	0.000000e+00	4525
1	TraesCS3B01G108900	chr3B	89.163	2473	225	30	1	2450	71908846	71911298	0.000000e+00	3042
2	TraesCS3B01G108900	chr3B	87.616	2471	261	34	1	2449	645181933	645184380	0.000000e+00	2826
3	TraesCS3B01G108900	chr3B	92.908	141	8	2	2308	2447	321733783	321733644	1.150000e-48	204
4	TraesCS3B01G108900	chr4B	89.971	2453	219	21	1	2434	569592067	569594511	0.000000e+00	3142
5	TraesCS3B01G108900	chr6B	91.935	2170	157	12	1	2160	680646385	680648546	0.000000e+00	3022
6	TraesCS3B01G108900	chr5B	88.880	2473	230	32	1	2450	370324522	370322072	0.000000e+00	3001
7	TraesCS3B01G108900	chr7B	90.147	2314	204	18	1	2297	363002688	363004994	0.000000e+00	2988
8	TraesCS3B01G108900	chr7B	89.552	2297	223	13	1	2289	594481663	594479376	0.000000e+00	2896
9	TraesCS3B01G108900	chr1B	90.069	2306	200	22	1	2289	556072807	556070514	0.000000e+00	2963
10	TraesCS3B01G108900	chr1B	89.853	2316	207	21	1	2297	465588042	465585736	0.000000e+00	2950
11	TraesCS3B01G108900	chr2B	97.288	295	6	1	2156	2450	545609926	545609634	1.310000e-137	499
12	TraesCS3B01G108900	chr2B	89.916	238	22	2	2213	2450	465449102	465448867	3.060000e-79	305
13	TraesCS3B01G108900	chr2B	91.489	141	10	2	2308	2447	337502678	337502817	2.490000e-45	193

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	TraesCS3B01G108900	chr3B	74828269	74830718	2449	True	4525	4525	100.000	1	2450	1	chr3B.!!$R1	2449
1	TraesCS3B01G108900	chr3B	71908846	71911298	2452	False	3042	3042	89.163	1	2450	1	chr3B.!!$F1	2449
2	TraesCS3B01G108900	chr3B	645181933	645184380	2447	False	2826	2826	87.616	1	2449	1	chr3B.!!$F2	2448
3	TraesCS3B01G108900	chr4B	569592067	569594511	2444	False	3142	3142	89.971	1	2434	1	chr4B.!!$F1	2433
4	TraesCS3B01G108900	chr6B	680646385	680648546	2161	False	3022	3022	91.935	1	2160	1	chr6B.!!$F1	2159
5	TraesCS3B01G108900	chr5B	370322072	370324522	2450	True	3001	3001	88.880	1	2450	1	chr5B.!!$R1	2449
6	TraesCS3B01G108900	chr7B	363002688	363004994	2306	False	2988	2988	90.147	1	2297	1	chr7B.!!$F1	2296
7	TraesCS3B01G108900	chr7B	594479376	594481663	2287	True	2896	2896	89.552	1	2289	1	chr7B.!!$R1	2288
8	TraesCS3B01G108900	chr1B	556070514	556072807	2293	True	2963	2963	90.069	1	2289	1	chr1B.!!$R2	2288
9	TraesCS3B01G108900	chr1B	465585736	465588042	2306	True	2950	2950	89.853	1	2297	1	chr1B.!!$R1	2296

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
948	953	0.033366	AACCAGAAACGCATTTGCCC	59.967	50.0	0.0	0.0	37.91	5.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1887	1902	0.396435	TGCTCTCAACGGGAACACAT	59.604	50.0	0.0	0.0	0.0	3.21	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
67	68	2.991190	CGGCAGCGAGAAGTAGTTTTTA	59.009	45.455	0.00	0.0	0.00	1.52
141	142	3.885297	CTCCTACTTGCCATATTTGTGGG	59.115	47.826	0.00	0.0	39.73	4.61
194	196	0.820871	GGCTACTCTCACACTCCAGG	59.179	60.000	0.00	0.0	0.00	4.45
413	415	4.825634	TCCTACTCATATACCTCAACACCG	59.174	45.833	0.00	0.0	0.00	4.94
420	422	2.832643	TACCTCAACACCGGGAGATA	57.167	50.000	6.32	0.0	32.87	1.98
448	450	3.713826	TGGAGTTAAATGGTCCTCCAC	57.286	47.619	6.22	0.0	46.45	4.02
475	477	2.948979	CAACCAACAACTCCAGCAACTA	59.051	45.455	0.00	0.0	0.00	2.24
478	480	3.389983	ACCAACAACTCCAGCAACTACTA	59.610	43.478	0.00	0.0	0.00	1.82
550	552	3.969287	AGCTCACATTGCTTAGTCTCA	57.031	42.857	0.00	0.0	37.52	3.27
853	858	3.387374	AGATGATCCAGAGCTCGAACAAT	59.613	43.478	8.37	0.0	0.00	2.71
890	895	9.420118	AGTTGAAGACTCATCATCTATTACTCT	57.580	33.333	0.00	0.0	31.20	3.24
899	904	9.195411	CTCATCATCTATTACTCTTGAAGAAGC	57.805	37.037	0.00	0.0	0.00	3.86
901	906	9.322773	CATCATCTATTACTCTTGAAGAAGCAA	57.677	33.333	0.00	0.0	0.00	3.91
908	913	7.865706	TTACTCTTGAAGAAGCAAAAGAAGT	57.134	32.000	0.00	0.0	0.00	3.01
911	916	6.375455	ACTCTTGAAGAAGCAAAAGAAGTTGA	59.625	34.615	0.00	0.0	0.00	3.18
915	920	6.267817	TGAAGAAGCAAAAGAAGTTGATGTG	58.732	36.000	0.00	0.0	0.00	3.21
916	921	6.095300	TGAAGAAGCAAAAGAAGTTGATGTGA	59.905	34.615	0.00	0.0	0.00	3.58
938	943	7.080724	GTGATTGAAGATGAAGAACCAGAAAC	58.919	38.462	0.00	0.0	0.00	2.78
939	944	5.673337	TTGAAGATGAAGAACCAGAAACG	57.327	39.130	0.00	0.0	0.00	3.60
948	953	0.033366	AACCAGAAACGCATTTGCCC	59.967	50.000	0.00	0.0	37.91	5.36
968	973	2.530177	CATCGTCATACAAGAGCGTGT	58.470	47.619	0.00	0.0	35.43	4.49
970	975	3.021269	TCGTCATACAAGAGCGTGTTT	57.979	42.857	0.00	0.0	32.75	2.83
972	977	4.548494	TCGTCATACAAGAGCGTGTTTTA	58.452	39.130	0.00	0.0	32.75	1.52
1003	1008	3.548770	TCCAATCCTCTTGATGACATGC	58.451	45.455	0.00	0.0	32.68	4.06
1005	1010	3.952323	CCAATCCTCTTGATGACATGCTT	59.048	43.478	0.00	0.0	32.68	3.91
1014	1019	6.053650	TCTTGATGACATGCTTCCTTATGAG	58.946	40.000	0.00	0.0	0.00	2.90
1015	1020	5.619132	TGATGACATGCTTCCTTATGAGA	57.381	39.130	0.00	0.0	0.00	3.27
1024	1029	4.880120	TGCTTCCTTATGAGATCTTTGCTG	59.120	41.667	0.00	0.0	0.00	4.41
1029	1034	5.365025	TCCTTATGAGATCTTTGCTGCTACT	59.635	40.000	0.00	0.0	0.00	2.57
1030	1035	5.466058	CCTTATGAGATCTTTGCTGCTACTG	59.534	44.000	0.00	0.0	0.00	2.74
1032	1037	3.854666	TGAGATCTTTGCTGCTACTGTC	58.145	45.455	0.00	0.0	0.00	3.51
1038	1043	2.566833	TTGCTGCTACTGTCCATTGT	57.433	45.000	0.00	0.0	0.00	2.71
1039	1044	1.812235	TGCTGCTACTGTCCATTGTG	58.188	50.000	0.00	0.0	0.00	3.33
1041	1046	2.154462	GCTGCTACTGTCCATTGTGTT	58.846	47.619	0.00	0.0	0.00	3.32
1237	1242	4.338012	TCCTCATGTTAGTGTCGACCTTA	58.662	43.478	14.12	2.4	0.00	2.69
1245	1250	5.924254	TGTTAGTGTCGACCTTACTGATTTG	59.076	40.000	14.12	0.0	0.00	2.32
1344	1349	4.154918	CCTACCACTTGCATTGTCTCTTTC	59.845	45.833	0.00	0.0	0.00	2.62
1345	1350	3.554934	ACCACTTGCATTGTCTCTTTCA	58.445	40.909	0.00	0.0	0.00	2.69
1365	1370	4.067896	TCATTGAGTGCTCTTTCAGGTTC	58.932	43.478	0.68	0.0	0.00	3.62
1403	1408	3.402110	CACTACATGCTGACCAAGTTCA	58.598	45.455	0.00	0.0	0.00	3.18
1490	1499	1.973515	TGAAGAGAGAAGCTGGAGCAA	59.026	47.619	0.65	0.0	45.16	3.91
1847	1862	8.767478	AATCATTTTCTGCTTTTACCTTGATG	57.233	30.769	0.00	0.0	0.00	3.07
1853	1868	3.230134	TGCTTTTACCTTGATGCACCTT	58.770	40.909	0.00	0.0	0.00	3.50
1885	1900	5.009610	ACGTTTAGATGTTGAATTTGTGCCT	59.990	36.000	0.00	0.0	0.00	4.75
1887	1902	7.081349	CGTTTAGATGTTGAATTTGTGCCTAA	58.919	34.615	0.00	0.0	0.00	2.69
1897	1912	1.529226	TTGTGCCTAATGTGTTCCCG	58.471	50.000	0.00	0.0	0.00	5.14
2002	2017	9.023962	AGTGATGATTCCTATTTTTGTGCTTAA	57.976	29.630	0.00	0.0	0.00	1.85
2118	2140	4.470602	GGGTTAGCTTGGGCAGTAATTAT	58.529	43.478	0.00	0.0	41.70	1.28
2274	2303	4.567747	GGTGGTATGTTCCTTTGGTGAGAT	60.568	45.833	0.00	0.0	0.00	2.75
2275	2304	4.636206	GTGGTATGTTCCTTTGGTGAGATC	59.364	45.833	0.00	0.0	0.00	2.75
2338	2368	8.450578	TGAACTGATCACAAGTTTATGTTCTT	57.549	30.769	15.44	0.0	34.31	2.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
67	68	4.801164	TCGTAAGAACTAGGCCTATCCTT	58.199	43.478	14.30	17.47	44.22	3.36
194	196	2.053627	CGAAGCTCATGCCAAAACAAC	58.946	47.619	0.00	0.00	40.80	3.32
413	415	3.515602	ACTCCATTGGCAATATCTCCC	57.484	47.619	13.23	0.00	0.00	4.30
420	422	4.162131	GGACCATTTAACTCCATTGGCAAT	59.838	41.667	6.96	6.96	0.00	3.56
475	477	4.155462	CACTTGCACATGAGATTGCTTAGT	59.845	41.667	0.00	4.35	39.62	2.24
478	480	2.352421	GCACTTGCACATGAGATTGCTT	60.352	45.455	0.00	0.00	39.62	3.91
620	622	5.045286	ACTTCATCCACTAGCTCTTTTCCAT	60.045	40.000	0.00	0.00	0.00	3.41
853	858	8.150296	TGATGAGTCTTCAACTTGATCACTTTA	58.850	33.333	6.26	0.00	38.74	1.85
890	895	6.753279	CACATCAACTTCTTTTGCTTCTTCAA	59.247	34.615	0.00	0.00	0.00	2.69
899	904	8.912658	CATCTTCAATCACATCAACTTCTTTTG	58.087	33.333	0.00	0.00	0.00	2.44
901	906	8.400184	TCATCTTCAATCACATCAACTTCTTT	57.600	30.769	0.00	0.00	0.00	2.52
908	913	6.716173	TGGTTCTTCATCTTCAATCACATCAA	59.284	34.615	0.00	0.00	0.00	2.57
911	916	6.479006	TCTGGTTCTTCATCTTCAATCACAT	58.521	36.000	0.00	0.00	0.00	3.21
915	920	6.310197	CGTTTCTGGTTCTTCATCTTCAATC	58.690	40.000	0.00	0.00	0.00	2.67
916	921	5.335191	GCGTTTCTGGTTCTTCATCTTCAAT	60.335	40.000	0.00	0.00	0.00	2.57
938	943	0.943673	TATGACGATGGGCAAATGCG	59.056	50.000	0.00	0.00	43.26	4.73
939	944	1.675483	TGTATGACGATGGGCAAATGC	59.325	47.619	0.00	0.00	41.14	3.56
948	953	2.530177	ACACGCTCTTGTATGACGATG	58.470	47.619	0.00	0.00	0.00	3.84
968	973	6.731467	AGAGGATTGGATAAACCTGCTAAAA	58.269	36.000	0.00	0.00	38.99	1.52
970	975	5.975988	AGAGGATTGGATAAACCTGCTAA	57.024	39.130	0.00	0.00	38.99	3.09
972	977	4.228210	TCAAGAGGATTGGATAAACCTGCT	59.772	41.667	0.00	0.00	38.99	4.24
1003	1008	5.124645	AGCAGCAAAGATCTCATAAGGAAG	58.875	41.667	0.00	0.00	0.00	3.46
1005	1010	4.767578	AGCAGCAAAGATCTCATAAGGA	57.232	40.909	0.00	0.00	0.00	3.36
1014	1019	2.977914	TGGACAGTAGCAGCAAAGATC	58.022	47.619	0.00	0.00	0.00	2.75
1015	1020	3.641434	ATGGACAGTAGCAGCAAAGAT	57.359	42.857	0.00	0.00	0.00	2.40
1024	1029	5.424757	TGGTATAACACAATGGACAGTAGC	58.575	41.667	0.00	0.00	0.00	3.58
1029	1034	7.953005	AATTGATGGTATAACACAATGGACA	57.047	32.000	15.02	0.00	32.66	4.02
1030	1035	9.950680	CTTAATTGATGGTATAACACAATGGAC	57.049	33.333	15.02	0.00	32.66	4.02
1032	1037	8.632679	AGCTTAATTGATGGTATAACACAATGG	58.367	33.333	15.02	11.12	32.66	3.16
1245	1250	5.897377	AAAGCACATGTTTAGGATGGTAC	57.103	39.130	0.00	0.00	0.00	3.34
1344	1349	4.070716	AGAACCTGAAAGAGCACTCAATG	58.929	43.478	0.00	0.00	34.07	2.82
1345	1350	4.363991	AGAACCTGAAAGAGCACTCAAT	57.636	40.909	0.00	0.00	34.07	2.57
1403	1408	1.566231	GGTCCCAGGGAATGTCATCTT	59.434	52.381	10.89	0.00	31.38	2.40
1490	1499	4.444591	CCTTTGCTTCTCTATCCTCATGCT	60.445	45.833	0.00	0.00	0.00	3.79
1847	1862	0.951558	AAACGTGGTGATCAAGGTGC	59.048	50.000	0.00	0.00	0.00	5.01
1853	1868	4.888917	TCAACATCTAAACGTGGTGATCA	58.111	39.130	0.00	0.00	37.15	2.92
1885	1900	2.037902	TGCTCTCAACGGGAACACATTA	59.962	45.455	0.00	0.00	0.00	1.90
1887	1902	0.396435	TGCTCTCAACGGGAACACAT	59.604	50.000	0.00	0.00	0.00	3.21
1897	1912	3.437049	GTGGTTAGGTGATTGCTCTCAAC	59.563	47.826	0.00	0.00	34.60	3.18
2223	2252	3.383505	CGAGAACATGGTATACACCTGGA	59.616	47.826	0.00	0.00	45.98	3.86
2338	2368	3.159472	AGCATGATCCAGAGCACAAAAA	58.841	40.909	0.00	0.00	0.00	1.94
2345	2380	2.914695	AAGAGAGCATGATCCAGAGC	57.085	50.000	7.49	0.00	0.00	4.09
2348	2383	4.952071	TCCTAAAGAGAGCATGATCCAG	57.048	45.455	7.49	0.00	0.00	3.86
2349	2384	4.141620	GGTTCCTAAAGAGAGCATGATCCA	60.142	45.833	7.49	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.