AutoCloner

Multiple sequence alignment - TraesCS5B01G050200

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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	TraesCS5B01G050200	chr5B	100.000	5020	0	0	1	5020	55370502	55375521	0.000000e+00	9271.0
1	TraesCS5B01G050200	chr5D	97.434	4872	62	18	158	5020	52280781	52285598	0.000000e+00	8246.0
2	TraesCS5B01G050200	chr5D	96.316	1113	36	4	3912	5020	52287745	52288856	0.000000e+00	1823.0
3	TraesCS5B01G050200	chr5D	95.667	300	12	1	3616	3915	52286818	52287116	9.770000e-132	481.0
4	TraesCS5B01G050200	chr5D	99.145	117	1	0	1	117	52280373	52280489	1.420000e-50	211.0
5	TraesCS5B01G050200	chr5A	92.228	1737	89	19	3115	4825	41426611	41428327	0.000000e+00	2418.0
6	TraesCS5B01G050200	chr5A	91.831	1726	96	14	1416	3119	41424796	41426498	0.000000e+00	2364.0
7	TraesCS5B01G050200	chr5A	91.186	1248	72	19	1	1218	41423441	41424680	0.000000e+00	1661.0
8	TraesCS5B01G050200	chr5A	91.444	187	9	6	4839	5020	41428388	41428572	3.000000e-62	250.0
9	TraesCS5B01G050200	chr5A	94.872	117	5	1	1251	1366	41424681	41424797	1.110000e-41	182.0
10	TraesCS5B01G050200	chrUn	100.000	412	0	0	2763	3174	477541978	477541567	0.000000e+00	761.0
11	TraesCS5B01G050200	chrUn	94.828	58	2	1	1366	1422	88110483	88110426	6.920000e-14	89.8
12	TraesCS5B01G050200	chr2A	93.805	113	7	0	437	549	170470391	170470503	2.400000e-38	171.0
13	TraesCS5B01G050200	chr2A	92.523	107	8	0	437	543	559118410	559118516	2.420000e-33	154.0
14	TraesCS5B01G050200	chr7A	94.393	107	6	0	437	543	48103180	48103074	1.120000e-36	165.0
15	TraesCS5B01G050200	chr2B	94.393	107	6	0	437	543	216462808	216462914	1.120000e-36	165.0
16	TraesCS5B01G050200	chr1A	94.393	107	6	0	437	543	106228075	106228181	1.120000e-36	165.0
17	TraesCS5B01G050200	chr1A	91.935	62	5	0	4758	4819	527789695	527789634	2.490000e-13	87.9
18	TraesCS5B01G050200	chr1B	93.458	107	7	0	437	543	160325218	160325324	5.200000e-35	159.0
19	TraesCS5B01G050200	chr1B	98.113	53	1	0	1365	1417	411211926	411211874	5.350000e-15	93.5
20	TraesCS5B01G050200	chr1B	98.113	53	0	1	1365	1417	579608120	579608069	1.920000e-14	91.6
21	TraesCS5B01G050200	chr2D	90.000	120	10	1	430	547	380407788	380407669	2.420000e-33	154.0
22	TraesCS5B01G050200	chr2D	98.113	53	1	0	1365	1417	61804625	61804677	5.350000e-15	93.5
23	TraesCS5B01G050200	chr6D	98.113	53	1	0	1365	1417	382725639	382725587	5.350000e-15	93.5
24	TraesCS5B01G050200	chr7D	93.333	60	2	2	1365	1423	123053392	123053450	2.490000e-13	87.9
25	TraesCS5B01G050200	chr3D	89.855	69	1	3	1361	1424	435451254	435451321	3.220000e-12	84.2
26	TraesCS5B01G050200	chr3D	88.732	71	1	5	1362	1426	74197562	74197493	4.170000e-11	80.5

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	TraesCS5B01G050200	chr5B	55370502	55375521	5019	False	9271.00	9271	100.0000	1	5020	1	chr5B.!!$F1	5019
1	TraesCS5B01G050200	chr5D	52280373	52288856	8483	False	2690.25	8246	97.1405	1	5020	4	chr5D.!!$F1	5019
2	TraesCS5B01G050200	chr5A	41423441	41428572	5131	False	1375.00	2418	92.3122	1	5020	5	chr5A.!!$F1	5019

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	Hairpin	End Stability	Orientation
134	147	0.597118	TGTTCAAGCAAATGCACGGC	60.597	50.000	8.28	45.16	5.68	F
1461	1739	0.376152	CGCCTGCTTTGATGCTACAG	59.624	55.000	0.00	0.00	2.74	F
1971	2268	3.053768	TGCATGTTGGATTCTGATACCCA	60.054	43.478	0.00	0.00	4.51	F
2280	2578	3.191078	AGGAGCAGGAAAGATTCGATG	57.809	47.619	0.00	0.00	3.84	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1677	1966	2.041701	ACATGCAAAGCTTTTGAGGGT	58.958	42.857	9.53	1.80	0.00	4.34	R
2412	2711	2.571202	TGTCAATGGTATGTCTGGCAGA	59.429	45.455	14.43	14.43	0.00	4.26	R
3857	4301	1.127567	AGTAGCCACAGCACTCCCAA	61.128	55.000	0.00	0.00	43.56	4.12	R
4182	4626	4.082081	CAGCAAGCTTTATTCATCAACCCA	60.082	41.667	0.00	0.00	0.00	4.51	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
132	133	1.001487	TCCTGTTCAAGCAAATGCACG	60.001	47.619	8.28	0.00	45.16	5.34
134	147	0.597118	TGTTCAAGCAAATGCACGGC	60.597	50.000	8.28	0.00	45.16	5.68
156	169	2.035783	GGTGGGGGCTGTTCCTTC	59.964	66.667	0.00	0.00	34.39	3.46
210	476	8.049117	TGATGCAGTTTCTAGGTTAGATGATTT	58.951	33.333	0.00	0.00	34.22	2.17
304	576	1.608590	AGGATGTTTTCGTTGGCACTG	59.391	47.619	0.00	0.00	0.00	3.66
305	577	1.606668	GGATGTTTTCGTTGGCACTGA	59.393	47.619	0.00	0.00	0.00	3.41
306	578	2.034053	GGATGTTTTCGTTGGCACTGAA	59.966	45.455	0.00	0.00	0.00	3.02
307	579	2.842208	TGTTTTCGTTGGCACTGAAG	57.158	45.000	0.00	0.00	0.00	3.02
308	580	2.360844	TGTTTTCGTTGGCACTGAAGA	58.639	42.857	0.00	0.00	0.00	2.87
309	581	2.948979	TGTTTTCGTTGGCACTGAAGAT	59.051	40.909	0.00	0.00	0.00	2.40
317	589	1.417517	TGGCACTGAAGATATGCGGAT	59.582	47.619	0.00	0.00	40.37	4.18
322	594	4.559502	GCACTGAAGATATGCGGATACAGA	60.560	45.833	15.91	0.00	0.00	3.41
1461	1739	0.376152	CGCCTGCTTTGATGCTACAG	59.624	55.000	0.00	0.00	0.00	2.74
1665	1954	5.733620	TTACCGTCTTGGAATAGAACAGT	57.266	39.130	0.00	0.00	42.00	3.55
1677	1966	7.619965	TGGAATAGAACAGTGTGAACATGATA	58.380	34.615	0.00	0.00	0.00	2.15
1768	2057	7.259088	AGGTTTGTATTACCTGAGAGTTCAT	57.741	36.000	0.00	0.00	44.25	2.57
1924	2221	5.455326	CCCCCTAATTCTTGTGTCCTAGATG	60.455	48.000	0.00	0.00	0.00	2.90
1969	2266	3.947196	TGTGCATGTTGGATTCTGATACC	59.053	43.478	0.00	0.00	0.00	2.73
1970	2267	3.316308	GTGCATGTTGGATTCTGATACCC	59.684	47.826	0.00	0.00	0.00	3.69
1971	2268	3.053768	TGCATGTTGGATTCTGATACCCA	60.054	43.478	0.00	0.00	0.00	4.51
1972	2269	3.953612	GCATGTTGGATTCTGATACCCAA	59.046	43.478	0.00	0.00	36.43	4.12
1973	2270	4.402155	GCATGTTGGATTCTGATACCCAAA	59.598	41.667	0.00	0.00	40.00	3.28
1974	2271	5.679638	GCATGTTGGATTCTGATACCCAAAC	60.680	44.000	0.00	3.58	40.00	2.93
1975	2272	4.006989	TGTTGGATTCTGATACCCAAACG	58.993	43.478	0.00	0.00	40.00	3.60
1976	2273	3.275617	TGGATTCTGATACCCAAACGG	57.724	47.619	0.00	0.00	37.81	4.44
2266	2564	4.536090	TGGGAAATAAGAGAGAAAGGAGCA	59.464	41.667	0.00	0.00	0.00	4.26
2280	2578	3.191078	AGGAGCAGGAAAGATTCGATG	57.809	47.619	0.00	0.00	0.00	3.84
2443	2742	7.063898	CAGACATACCATTGACAGTCTGTTAAG	59.936	40.741	14.69	5.93	44.69	1.85
3621	4065	4.998033	TGTTCACGAGCACCAATGTAAATA	59.002	37.500	0.00	0.00	0.00	1.40
3781	4225	9.003112	CATCTCTAAACAAATGTTTTATCAGCG	57.997	33.333	15.92	4.07	45.07	5.18
3795	4239	5.734855	TTATCAGCGAAGGAATTGTTAGC	57.265	39.130	0.00	0.00	0.00	3.09
3802	4246	5.086727	GCGAAGGAATTGTTAGCTGTTAAC	58.913	41.667	7.37	7.37	41.68	2.01
3857	4301	0.605860	CTGGCTGCTGTCTTTCTGCT	60.606	55.000	0.00	0.00	40.79	4.24
4005	4449	2.162681	TCTGCTGCGCTATAGCTGATA	58.837	47.619	21.98	5.24	41.97	2.15
4324	8004	9.903682	CATTTCTGTGAGACATTGAATTACTTT	57.096	29.630	0.00	0.00	0.00	2.66
4367	8052	3.769536	CAGGTGACTTGGTTTGTTTCAC	58.230	45.455	0.00	0.00	40.21	3.18
4574	8259	3.507924	GCATCGGCCGCAACATCA	61.508	61.111	23.51	0.16	0.00	3.07
4587	8272	1.002792	CAACATCATGAGGCAGCATCG	60.003	52.381	7.40	0.00	0.00	3.84
4606	8291	2.039216	TCGGATTCAGCAGGGTTTGTTA	59.961	45.455	0.00	0.00	0.00	2.41
4747	8434	4.967084	TTGGACAGTAAGCCAGTTTCTA	57.033	40.909	0.00	0.00	35.23	2.10
4764	8451	2.585330	TCTAGTGTGTGACGGTGGTAA	58.415	47.619	0.00	0.00	0.00	2.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
138	151	3.585525	GAAGGAACAGCCCCCACCC	62.586	68.421	0.00	0.00	37.37	4.61
140	153	0.251787	ATTGAAGGAACAGCCCCCAC	60.252	55.000	0.00	0.00	37.37	4.61
141	154	0.486879	AATTGAAGGAACAGCCCCCA	59.513	50.000	0.00	0.00	37.37	4.96
147	160	6.430925	TCCACACAAGATAATTGAAGGAACAG	59.569	38.462	0.00	0.00	0.00	3.16
153	166	5.885230	TGCTCCACACAAGATAATTGAAG	57.115	39.130	0.00	0.00	0.00	3.02
156	169	6.263344	CAGATTGCTCCACACAAGATAATTG	58.737	40.000	0.00	0.00	0.00	2.32
304	576	3.502920	CCGTCTGTATCCGCATATCTTC	58.497	50.000	0.00	0.00	0.00	2.87
305	577	2.352814	GCCGTCTGTATCCGCATATCTT	60.353	50.000	0.00	0.00	0.00	2.40
306	578	1.202582	GCCGTCTGTATCCGCATATCT	59.797	52.381	0.00	0.00	0.00	1.98
307	579	1.067846	TGCCGTCTGTATCCGCATATC	60.068	52.381	0.00	0.00	0.00	1.63
308	580	0.966179	TGCCGTCTGTATCCGCATAT	59.034	50.000	0.00	0.00	0.00	1.78
309	581	0.966179	ATGCCGTCTGTATCCGCATA	59.034	50.000	0.00	0.00	0.00	3.14
589	862	0.250597	ACCGAAACAGTAACCCAGGC	60.251	55.000	0.00	0.00	0.00	4.85
1461	1739	5.438761	ACTTCAGTATTCCAAACTGCAAC	57.561	39.130	0.00	0.00	43.30	4.17
1665	1954	4.458989	GCTTTTGAGGGTATCATGTTCACA	59.541	41.667	0.00	0.00	37.89	3.58
1677	1966	2.041701	ACATGCAAAGCTTTTGAGGGT	58.958	42.857	9.53	1.80	0.00	4.34
1768	2057	9.056005	GTGCCATGATAACTCATAAAGATTGTA	57.944	33.333	0.00	0.00	40.20	2.41
1924	2221	9.900264	CACAAGCAAATGTTTAAAGTTACTTTC	57.100	29.630	14.03	0.99	35.21	2.62
2033	2331	3.174779	ACTGAGGAAGGGAAGAGGTTAC	58.825	50.000	0.00	0.00	0.00	2.50
2266	2564	8.432805	ACCACTATTATTCATCGAATCTTTCCT	58.567	33.333	0.00	0.00	33.95	3.36
2412	2711	2.571202	TGTCAATGGTATGTCTGGCAGA	59.429	45.455	14.43	14.43	0.00	4.26
2508	2807	7.331687	CCATTCAAAACCAATTATTCCAGTCAC	59.668	37.037	0.00	0.00	0.00	3.67
2607	2906	3.680490	TGGCCGAACTTGTCATATTTCA	58.320	40.909	0.00	0.00	0.00	2.69
3174	3594	4.389374	ACCACCAGACAACTAAATGAGTG	58.611	43.478	0.00	0.00	38.87	3.51
3621	4065	3.568430	TCACTCACTACATCGACAAGTGT	59.432	43.478	18.05	8.62	41.12	3.55
3779	4223	3.831715	AACAGCTAACAATTCCTTCGC	57.168	42.857	0.00	0.00	0.00	4.70
3781	4225	6.655425	AGAGGTTAACAGCTAACAATTCCTTC	59.345	38.462	8.10	0.00	41.60	3.46
3795	4239	6.391227	AAATCAAACACCAGAGGTTAACAG	57.609	37.500	8.10	0.00	31.02	3.16
3802	4246	5.070001	TCACCTAAAATCAAACACCAGAGG	58.930	41.667	0.00	0.00	0.00	3.69
3857	4301	1.127567	AGTAGCCACAGCACTCCCAA	61.128	55.000	0.00	0.00	43.56	4.12
4173	4617	7.630242	TTTATTCATCAACCCAGATGTCTTC	57.370	36.000	0.00	0.00	44.46	2.87
4182	4626	4.082081	CAGCAAGCTTTATTCATCAACCCA	60.082	41.667	0.00	0.00	0.00	4.51
4259	7939	7.608153	TCTGTAAACTGCAAATGTAGTAGCTA	58.392	34.615	4.56	0.00	40.09	3.32
4324	8004	7.459795	CTGCTATATCACAGGATCAGTTCTA	57.540	40.000	0.00	0.00	34.89	2.10
4349	8034	3.168193	CACGTGAAACAAACCAAGTCAC	58.832	45.455	10.90	0.00	35.74	3.67
4367	8052	0.040067	GCCTTCTGAAGCAAACCACG	60.040	55.000	11.93	0.00	0.00	4.94
4461	8146	4.457466	TCTTTGAACTCCCAGTTACAACC	58.543	43.478	0.00	0.00	38.80	3.77
4467	8152	6.306987	ACATACAATCTTTGAACTCCCAGTT	58.693	36.000	0.00	0.00	41.95	3.16
4504	8189	5.506686	TGCACAACTTATAACTGCAACAA	57.493	34.783	0.00	0.00	34.97	2.83
4574	8259	0.471191	TGAATCCGATGCTGCCTCAT	59.529	50.000	5.78	0.00	0.00	2.90
4587	8272	3.153919	TGTAACAAACCCTGCTGAATCC	58.846	45.455	0.00	0.00	0.00	3.01
4747	8434	2.922740	AATTACCACCGTCACACACT	57.077	45.000	0.00	0.00	0.00	3.55
4784	8471	5.587289	GCCATGGCAATTCGTTTAAATCTA	58.413	37.500	32.08	0.00	41.49	1.98
4836	8524	8.245195	ACTTTTAAAGCCATTAGAAAAGGACA	57.755	30.769	4.42	0.00	30.57	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.