AutoCloner

Multiple sequence alignment - TraesCS5B01G167800

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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	TraesCS5B01G167800	chr5B	100.000	2429	0	0	1	2429	310050158	310052586	0	4486
1	TraesCS5B01G167800	chr1D	93.962	2418	140	5	1	2414	370318154	370315739	0	3651
2	TraesCS5B01G167800	chr1D	88.386	2428	258	22	1	2414	136959446	136957029	0	2900
3	TraesCS5B01G167800	chr1D	88.206	2425	270	10	1	2414	9832966	9835385	0	2880
4	TraesCS5B01G167800	chr5D	92.497	2279	161	6	144	2414	445706985	445704709	0	3253
5	TraesCS5B01G167800	chr7D	87.836	2417	279	14	1	2407	22677619	22680030	0	2820
6	TraesCS5B01G167800	chr7D	84.072	2436	353	32	1	2414	277561595	277559173	0	2316
7	TraesCS5B01G167800	chr7A	90.971	2060	176	4	364	2414	289137995	289135937	0	2765
8	TraesCS5B01G167800	chr3A	86.897	2427	293	22	1	2414	539362903	539360489	0	2697
9	TraesCS5B01G167800	chr2D	84.082	2425	364	19	1	2414	81842753	81840340	0	2320

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	TraesCS5B01G167800	chr5B	310050158	310052586	2428	False	4486	4486	100.000	1	2429	1	chr5B.!!$F1	2428
1	TraesCS5B01G167800	chr1D	370315739	370318154	2415	True	3651	3651	93.962	1	2414	1	chr1D.!!$R2	2413
2	TraesCS5B01G167800	chr1D	136957029	136959446	2417	True	2900	2900	88.386	1	2414	1	chr1D.!!$R1	2413
3	TraesCS5B01G167800	chr1D	9832966	9835385	2419	False	2880	2880	88.206	1	2414	1	chr1D.!!$F1	2413
4	TraesCS5B01G167800	chr5D	445704709	445706985	2276	True	3253	3253	92.497	144	2414	1	chr5D.!!$R1	2270
5	TraesCS5B01G167800	chr7D	22677619	22680030	2411	False	2820	2820	87.836	1	2407	1	chr7D.!!$F1	2406
6	TraesCS5B01G167800	chr7D	277559173	277561595	2422	True	2316	2316	84.072	1	2414	1	chr7D.!!$R1	2413
7	TraesCS5B01G167800	chr7A	289135937	289137995	2058	True	2765	2765	90.971	364	2414	1	chr7A.!!$R1	2050
8	TraesCS5B01G167800	chr3A	539360489	539362903	2414	True	2697	2697	86.897	1	2414	1	chr3A.!!$R1	2413
9	TraesCS5B01G167800	chr2D	81840340	81842753	2413	True	2320	2320	84.082	1	2414	1	chr2D.!!$R1	2413

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
287	290	0.249073	CATGAGGTCCGGTCTAAGCG	60.249	60.0	0.0	0.0	39.06	4.68	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1625	1631	0.181114	TGATGGAGAATTGGCCGGAG	59.819	55.0	5.05	0.0	0.0	4.63	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
85	86	0.462759	CGCTCATCCCCAAAGTCTCC	60.463	60.000	0.00	0.00	0.00	3.71
111	114	1.447838	CGACATCCACCAGTTCCGG	60.448	63.158	0.00	0.00	0.00	5.14
261	264	2.660064	GGTGCTGGTCCTCCACGAT	61.660	63.158	0.00	0.00	39.03	3.73
287	290	0.249073	CATGAGGTCCGGTCTAAGCG	60.249	60.000	0.00	0.00	39.06	4.68
291	294	2.577593	GTCCGGTCTAAGCGCCTT	59.422	61.111	2.29	0.00	37.85	4.35
418	421	0.809636	CCGCGTAATGCAGATGGTGA	60.810	55.000	4.92	0.00	46.97	4.02
496	499	1.426251	ATGTGGGGTCTGTCAAGGCA	61.426	55.000	0.00	0.00	0.00	4.75
555	558	2.194056	CTTGCCGCCATCCTGGAT	59.806	61.111	2.57	2.57	40.96	3.41
579	582	1.941668	GCTAAGGCTGCGGGACATATC	60.942	57.143	0.00	0.00	35.22	1.63
713	716	2.122768	CCTCCTCCTATGCTTCCAACT	58.877	52.381	0.00	0.00	0.00	3.16
726	729	3.690460	CTTCCAACTAATGTCTGGCCTT	58.310	45.455	3.32	0.00	0.00	4.35
1026	1029	0.803117	TCTACAGCCTTCACGAGACG	59.197	55.000	0.00	0.00	0.00	4.18
1042	1045	0.460811	GACGCTGCACCATGAGATCA	60.461	55.000	0.00	0.00	0.00	2.92
1051	1054	2.674852	CACCATGAGATCACCAAAGTCG	59.325	50.000	0.00	0.00	0.00	4.18
1318	1323	1.068333	CCCAGTTTTGGCAGTCGATTG	60.068	52.381	3.12	3.12	43.58	2.67
1425	1430	4.483243	GATTCCCCCTTCGCGGCA	62.483	66.667	6.13	0.00	0.00	5.69
1432	1437	1.524621	CCCTTCGCGGCATGATTCT	60.525	57.895	6.13	0.00	0.00	2.40
1625	1631	0.035739	TTAGGTGGCGTCTTGAACCC	59.964	55.000	0.00	0.00	32.85	4.11
1642	1648	1.533711	CCTCCGGCCAATTCTCCAT	59.466	57.895	2.24	0.00	0.00	3.41
1659	1665	2.314852	TCCATCAAGTCCCTCTACCAGA	59.685	50.000	0.00	0.00	0.00	3.86
1679	1687	2.109799	ATTGCTCCCTCCATCGCG	59.890	61.111	0.00	0.00	0.00	5.87
1718	1731	1.488705	TTGGTCCATCCGTCTGCCTT	61.489	55.000	0.00	0.00	39.52	4.35
1726	1739	2.859165	TCCGTCTGCCTTTGAAGATT	57.141	45.000	0.00	0.00	0.00	2.40
1782	1795	2.283676	GTCTGGGGTCGAGGTCCA	60.284	66.667	0.00	0.00	0.00	4.02
1858	1871	5.047731	AGACTCGAATCACATCTTCTTCACA	60.048	40.000	0.00	0.00	0.00	3.58
1939	1952	1.280998	CATACCAACTTCCCCGACCTT	59.719	52.381	0.00	0.00	0.00	3.50
1980	1993	1.141053	CCCCCTACTATCTTGCCACAC	59.859	57.143	0.00	0.00	0.00	3.82
2072	2085	4.394712	CTCTTCGGCGGGCCACTT	62.395	66.667	7.21	0.00	35.37	3.16
2104	2117	9.294030	CTATTCAAATTATCTGGTTTCTTGCAC	57.706	33.333	0.00	0.00	0.00	4.57
2170	2183	2.752640	TTCATCGCCGACCTCCGA	60.753	61.111	0.00	0.00	41.76	4.55
2237	2250	1.519719	CCTGACTAGGGCTGCTGTC	59.480	63.158	0.00	4.39	40.63	3.51
2245	2258	4.687215	GGCTGCTGTCAGTCGCCA	62.687	66.667	22.08	4.24	42.29	5.69
2309	2336	3.957288	GCCCTCAGCAGAACCTTTA	57.043	52.632	0.00	0.00	42.97	1.85
2348	2381	2.208132	TGGGTGTGTGTGTTGAACTT	57.792	45.000	0.00	0.00	0.00	2.66
2351	2385	2.490115	GGGTGTGTGTGTTGAACTTTGA	59.510	45.455	0.00	0.00	0.00	2.69
2362	2396	8.126074	GTGTGTTGAACTTTGATTGTATGTGTA	58.874	33.333	0.00	0.00	0.00	2.90
2415	2450	2.606717	CGAAAGCCTTTTTCGGTACC	57.393	50.000	12.72	0.16	45.17	3.34
2416	2451	1.874872	CGAAAGCCTTTTTCGGTACCA	59.125	47.619	13.54	0.00	45.17	3.25
2417	2452	2.486592	CGAAAGCCTTTTTCGGTACCAT	59.513	45.455	13.54	0.00	45.17	3.55
2418	2453	3.425758	CGAAAGCCTTTTTCGGTACCATC	60.426	47.826	13.54	0.00	45.17	3.51
2419	2454	2.871096	AGCCTTTTTCGGTACCATCA	57.129	45.000	13.54	0.00	0.00	3.07
2420	2455	3.149005	AGCCTTTTTCGGTACCATCAA	57.851	42.857	13.54	0.00	0.00	2.57
2421	2456	2.817844	AGCCTTTTTCGGTACCATCAAC	59.182	45.455	13.54	0.00	0.00	3.18
2422	2457	2.817844	GCCTTTTTCGGTACCATCAACT	59.182	45.455	13.54	0.00	0.00	3.16
2423	2458	3.254903	GCCTTTTTCGGTACCATCAACTT	59.745	43.478	13.54	0.00	0.00	2.66
2424	2459	4.794169	CCTTTTTCGGTACCATCAACTTG	58.206	43.478	13.54	0.00	0.00	3.16
2425	2460	4.517453	CCTTTTTCGGTACCATCAACTTGA	59.483	41.667	13.54	0.00	0.00	3.02
2426	2461	5.334879	CCTTTTTCGGTACCATCAACTTGAG	60.335	44.000	13.54	0.00	0.00	3.02
2427	2462	3.328382	TTCGGTACCATCAACTTGAGG	57.672	47.619	13.54	0.00	0.00	3.86
2428	2463	2.531771	TCGGTACCATCAACTTGAGGA	58.468	47.619	13.54	0.00	27.97	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
10	11	2.232941	GGACCCAACGTAGAACTCATCA	59.767	50.000	0.00	0.00	0.00	3.07
43	44	4.160329	AGATGATCCCATAGTTAAGGCGA	58.840	43.478	0.00	0.00	32.09	5.54
111	114	0.096976	CGTTGATCACCGTGATTGGC	59.903	55.000	15.20	3.87	37.20	4.52
178	181	0.621082	TGGGTAATGTGATCGGCCAA	59.379	50.000	2.24	0.00	0.00	4.52
287	290	5.860090	CTTAAGGAAGACCGCCCTAAGGC	62.860	56.522	0.00	0.00	45.05	4.35
291	294	2.537633	TCTTAAGGAAGACCGCCCTA	57.462	50.000	1.85	0.00	36.75	3.53
487	490	1.004745	GGAGAAGGGATTGCCTTGACA	59.995	52.381	14.87	0.00	0.00	3.58
496	499	2.929043	ACAAGAATGGGGAGAAGGGATT	59.071	45.455	0.00	0.00	0.00	3.01
555	558	1.687840	TCCCGCAGCCTTAGCCTTA	60.688	57.895	0.00	0.00	41.25	2.69
681	684	1.981495	AGGAGGAGGAACTTGAGGTTG	59.019	52.381	0.00	0.00	41.55	3.77
713	716	7.012327	CGAAATTGATCTTAAGGCCAGACATTA	59.988	37.037	5.01	0.00	0.00	1.90
948	951	0.757561	TGATAAGGATCGTCCGGGCA	60.758	55.000	6.96	0.00	42.75	5.36
1026	1029	0.393402	TGGTGATCTCATGGTGCAGC	60.393	55.000	9.47	9.47	0.00	5.25
1042	1045	0.674534	AAGCGAGACTCGACTTTGGT	59.325	50.000	28.43	7.14	43.74	3.67
1051	1054	0.101579	GCCCAGTAGAAGCGAGACTC	59.898	60.000	0.00	0.00	0.00	3.36
1227	1232	8.202461	ACTTATTCCGGATGATATCTAACCAA	57.798	34.615	4.15	0.00	0.00	3.67
1296	1301	0.400213	TCGACTGCCAAAACTGGGAT	59.600	50.000	0.00	0.00	0.00	3.85
1425	1430	3.636679	TGGAGAAGAGGTCGAGAATCAT	58.363	45.455	0.00	0.00	33.17	2.45
1432	1437	1.205655	CAGCAATGGAGAAGAGGTCGA	59.794	52.381	0.00	0.00	0.00	4.20
1594	1600	0.546747	CCACCTAACCTGGTCTGGGA	60.547	60.000	18.29	0.00	38.45	4.37
1625	1631	0.181114	TGATGGAGAATTGGCCGGAG	59.819	55.000	5.05	0.00	0.00	4.63
1642	1648	1.431633	TGGTCTGGTAGAGGGACTTGA	59.568	52.381	0.00	0.00	41.55	3.02
1659	1665	1.528824	CGATGGAGGGAGCAATGGT	59.471	57.895	0.00	0.00	0.00	3.55
1726	1739	2.291365	CATTGCCACATGAAGATCCGA	58.709	47.619	0.00	0.00	0.00	4.55
1858	1871	5.009710	CCATTGAAACTGAGCAGATATGCAT	59.990	40.000	15.82	3.79	37.25	3.96
1878	1891	2.843113	ACCTCTCTAAAGCAGCTCCATT	59.157	45.455	0.00	0.00	0.00	3.16
1939	1952	0.959553	AGAGCTGGAGTTCGTCGAAA	59.040	50.000	9.70	0.00	0.00	3.46
1944	1957	1.985116	GGGGAGAGCTGGAGTTCGT	60.985	63.158	0.00	0.00	0.00	3.85
1980	1993	2.813354	GCCCCAATCTCAAGCCATCTAG	60.813	54.545	0.00	0.00	0.00	2.43
2072	2085	8.958119	AAACCAGATAATTTGAATAGAGCGTA	57.042	30.769	0.00	0.00	0.00	4.42
2104	2117	4.899239	CTAAGCGGCCGCCAGAGG	62.899	72.222	44.47	26.02	43.17	3.69
2170	2183	2.833582	AGACGGACGGCCATCGAT	60.834	61.111	8.76	0.00	42.43	3.59
2231	2244	2.340078	GAGTGGCGACTGACAGCA	59.660	61.111	5.94	0.00	29.71	4.41
2309	2336	4.307432	CCAAGTCTCACGACACAAAGTAT	58.693	43.478	0.00	0.00	42.73	2.12
2348	2381	5.065859	CCGCCAAGAATACACATACAATCAA	59.934	40.000	0.00	0.00	0.00	2.57
2351	2385	4.523083	ACCGCCAAGAATACACATACAAT	58.477	39.130	0.00	0.00	0.00	2.71
2362	2396	5.852282	ATATAAAGCAAACCGCCAAGAAT	57.148	34.783	0.00	0.00	44.04	2.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.