AutoCloner

Multiple sequence alignment - TraesCS6D01G374500

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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	TraesCS6D01G374500	chr6D	100.000	3354	0	0	1	3354	458889851	458893204	0.000000	6194.0
1	TraesCS6D01G374500	chr5D	98.538	3284	47	1	71	3354	562925244	562928526	0.000000	5797.0
2	TraesCS6D01G374500	chr1A	98.477	3284	45	1	71	3354	94765533	94762255	0.000000	5782.0
3	TraesCS6D01G374500	chr2D	98.386	3284	53	0	71	3354	200935005	200938288	0.000000	5771.0
4	TraesCS6D01G374500	chr2D	97.777	3284	71	2	71	3354	604416976	604420257	0.000000	5659.0
5	TraesCS6D01G374500	chr1D	98.234	3284	56	1	71	3354	185786507	185783226	0.000000	5742.0
6	TraesCS6D01G374500	chr7A	98.203	3284	59	0	71	3354	211308177	211311460	0.000000	5738.0
7	TraesCS6D01G374500	chr7A	97.990	3284	66	0	71	3354	563544702	563547985	0.000000	5699.0
8	TraesCS6D01G374500	chr7A	94.444	36	2	0	36	71	272943669	272943704	0.000467	56.5
9	TraesCS6D01G374500	chr3D	98.056	3240	61	2	115	3354	523740066	523743303	0.000000	5633.0
10	TraesCS6D01G374500	chr7D	97.533	3284	81	0	71	3354	307118175	307114892	0.000000	5616.0
11	TraesCS6D01G374500	chr3B	100.000	32	0	0	40	71	454613833	454613864	0.000036	60.2
12	TraesCS6D01G374500	chr6A	96.970	33	1	0	39	71	48803716	48803748	0.000467	56.5
13	TraesCS6D01G374500	chr4B	100.000	30	0	0	43	72	63759335	63759364	0.000467	56.5
14	TraesCS6D01G374500	chr7B	96.875	32	1	0	40	71	50613521	50613552	0.002000	54.7
15	TraesCS6D01G374500	chr6B	96.875	32	1	0	40	71	205364702	205364733	0.002000	54.7
16	TraesCS6D01G374500	chr5B	100.000	29	0	0	43	71	46633388	46633360	0.002000	54.7
17	TraesCS6D01G374500	chr5B	100.000	28	0	0	45	72	303230989	303230962	0.006000	52.8
18	TraesCS6D01G374500	chr4A	87.500	48	5	1	25	71	562284190	562284237	0.002000	54.7

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	TraesCS6D01G374500	chr6D	458889851	458893204	3353	False	6194	6194	100.000	1	3354	1	chr6D.!!$F1	3353
1	TraesCS6D01G374500	chr5D	562925244	562928526	3282	False	5797	5797	98.538	71	3354	1	chr5D.!!$F1	3283
2	TraesCS6D01G374500	chr1A	94762255	94765533	3278	True	5782	5782	98.477	71	3354	1	chr1A.!!$R1	3283
3	TraesCS6D01G374500	chr2D	200935005	200938288	3283	False	5771	5771	98.386	71	3354	1	chr2D.!!$F1	3283
4	TraesCS6D01G374500	chr2D	604416976	604420257	3281	False	5659	5659	97.777	71	3354	1	chr2D.!!$F2	3283
5	TraesCS6D01G374500	chr1D	185783226	185786507	3281	True	5742	5742	98.234	71	3354	1	chr1D.!!$R1	3283
6	TraesCS6D01G374500	chr7A	211308177	211311460	3283	False	5738	5738	98.203	71	3354	1	chr7A.!!$F1	3283
7	TraesCS6D01G374500	chr7A	563544702	563547985	3283	False	5699	5699	97.990	71	3354	1	chr7A.!!$F3	3283
8	TraesCS6D01G374500	chr3D	523740066	523743303	3237	False	5633	5633	98.056	115	3354	1	chr3D.!!$F1	3239
9	TraesCS6D01G374500	chr7D	307114892	307118175	3283	True	5616	5616	97.533	71	3354	1	chr7D.!!$R1	3283

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
68	69	1.479730	ACTCCCTCCGTCCGAAAATAC	59.52	52.381	0.0	0.0	0.00	1.89	F
1118	1119	1.339727	GGGTTGGTTATTCGTCAGCCT	60.34	52.381	0.0	0.0	33.23	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1839	1841	1.640917	TACCTTTCGAGACCAAGCCT	58.359	50.000	0.0	0.0	0.00	4.58	R
2611	2613	1.134788	GTTGTAGGTGGATGGACCTCG	60.135	57.143	0.0	0.0	43.33	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
21	22	4.846779	GGTGTCTTAATGTCTTTTGGCA	57.153	40.909	0.00	0.00	38.97	4.92
22	23	4.546570	GGTGTCTTAATGTCTTTTGGCAC	58.453	43.478	0.00	0.00	36.59	5.01
23	24	4.278419	GGTGTCTTAATGTCTTTTGGCACT	59.722	41.667	0.00	0.00	36.59	4.40
24	25	5.221244	GGTGTCTTAATGTCTTTTGGCACTT	60.221	40.000	0.00	0.00	36.59	3.16
25	26	6.273071	GTGTCTTAATGTCTTTTGGCACTTT	58.727	36.000	0.00	0.00	36.59	2.66
26	27	6.198966	GTGTCTTAATGTCTTTTGGCACTTTG	59.801	38.462	0.00	0.00	36.59	2.77
27	28	6.096141	TGTCTTAATGTCTTTTGGCACTTTGA	59.904	34.615	0.00	0.00	36.59	2.69
28	29	6.978080	GTCTTAATGTCTTTTGGCACTTTGAA	59.022	34.615	0.00	0.00	36.59	2.69
29	30	7.168135	GTCTTAATGTCTTTTGGCACTTTGAAG	59.832	37.037	0.00	0.00	36.59	3.02
30	31	5.343307	AATGTCTTTTGGCACTTTGAAGT	57.657	34.783	0.00	0.00	36.59	3.01
31	32	4.799564	TGTCTTTTGGCACTTTGAAGTT	57.200	36.364	0.00	0.00	37.08	2.66
32	33	5.906113	TGTCTTTTGGCACTTTGAAGTTA	57.094	34.783	0.00	0.00	37.08	2.24
33	34	6.274157	TGTCTTTTGGCACTTTGAAGTTAA	57.726	33.333	0.00	0.00	37.08	2.01
34	35	6.872920	TGTCTTTTGGCACTTTGAAGTTAAT	58.127	32.000	0.00	0.00	37.08	1.40
35	36	7.327214	TGTCTTTTGGCACTTTGAAGTTAATT	58.673	30.769	0.00	0.00	37.08	1.40
36	37	8.470805	TGTCTTTTGGCACTTTGAAGTTAATTA	58.529	29.630	0.00	0.00	37.08	1.40
37	38	9.308318	GTCTTTTGGCACTTTGAAGTTAATTAA	57.692	29.630	0.00	0.00	37.08	1.40
38	39	9.528018	TCTTTTGGCACTTTGAAGTTAATTAAG	57.472	29.630	0.00	0.00	37.08	1.85
39	40	9.313118	CTTTTGGCACTTTGAAGTTAATTAAGT	57.687	29.630	0.00	0.00	37.08	2.24
40	41	9.660180	TTTTGGCACTTTGAAGTTAATTAAGTT	57.340	25.926	16.46	16.46	37.08	2.66
41	42	9.660180	TTTGGCACTTTGAAGTTAATTAAGTTT	57.340	25.926	17.32	7.07	37.08	2.66
42	43	8.641499	TGGCACTTTGAAGTTAATTAAGTTTG	57.359	30.769	17.32	12.69	37.08	2.93
43	44	8.254508	TGGCACTTTGAAGTTAATTAAGTTTGT	58.745	29.630	17.32	11.86	37.08	2.83
44	45	9.738832	GGCACTTTGAAGTTAATTAAGTTTGTA	57.261	29.630	17.32	6.89	37.08	2.41
58	59	7.902920	TTAAGTTTGTATATACTCCCTCCGT	57.097	36.000	13.89	0.00	0.00	4.69
59	60	6.402456	AAGTTTGTATATACTCCCTCCGTC	57.598	41.667	13.89	0.00	0.00	4.79
60	61	4.831710	AGTTTGTATATACTCCCTCCGTCC	59.168	45.833	13.89	0.00	0.00	4.79
61	62	3.063510	TGTATATACTCCCTCCGTCCG	57.936	52.381	13.89	0.00	0.00	4.79
62	63	2.639347	TGTATATACTCCCTCCGTCCGA	59.361	50.000	13.89	0.00	0.00	4.55
63	64	2.965671	ATATACTCCCTCCGTCCGAA	57.034	50.000	0.00	0.00	0.00	4.30
64	65	2.734755	TATACTCCCTCCGTCCGAAA	57.265	50.000	0.00	0.00	0.00	3.46
65	66	1.856629	ATACTCCCTCCGTCCGAAAA	58.143	50.000	0.00	0.00	0.00	2.29
66	67	1.856629	TACTCCCTCCGTCCGAAAAT	58.143	50.000	0.00	0.00	0.00	1.82
67	68	1.856629	ACTCCCTCCGTCCGAAAATA	58.143	50.000	0.00	0.00	0.00	1.40
68	69	1.479730	ACTCCCTCCGTCCGAAAATAC	59.520	52.381	0.00	0.00	0.00	1.89
69	70	1.755380	CTCCCTCCGTCCGAAAATACT	59.245	52.381	0.00	0.00	0.00	2.12
382	383	4.965532	AGCCTGTATCAATGAAGAGTAGGT	59.034	41.667	0.00	0.00	0.00	3.08
425	426	7.654568	AGTAAATAGTGTTTTTGTTAGCCACC	58.345	34.615	0.00	0.00	0.00	4.61
725	726	5.783875	AGAGTGAAAGGGGTTAGTAGCTAAA	59.216	40.000	0.00	0.00	0.00	1.85
820	821	3.810743	GCGGCCCCTATTGATTCTTACAT	60.811	47.826	0.00	0.00	0.00	2.29
1118	1119	1.339727	GGGTTGGTTATTCGTCAGCCT	60.340	52.381	0.00	0.00	33.23	4.58
1839	1841	4.766373	TCTTCCAGCAATGAATTGTAGCAA	59.234	37.500	5.02	0.00	39.88	3.91
1910	1912	0.968901	AATGTCGACCTACCGCTCCA	60.969	55.000	14.12	0.00	0.00	3.86
2343	2345	7.362660	GCCGACAAGGGATTTTCTTAATAACTT	60.363	37.037	0.00	0.00	41.48	2.66
2436	2438	4.837093	TCGAACCTATCCCATTTTGACT	57.163	40.909	0.00	0.00	0.00	3.41
2538	2540	3.521560	ACACGACACGCAATCTTATGAT	58.478	40.909	0.00	0.00	33.70	2.45
2611	2613	3.927758	GCGTTAGAGAAAGGAAAGGACTC	59.072	47.826	0.00	0.00	0.00	3.36
3015	3017	0.109153	ATTGCTATCATCTGCGGGCA	59.891	50.000	0.00	0.00	0.00	5.36
3038	3040	6.015180	GCAGCCCTCATTATTGAATTTATCCA	60.015	38.462	0.00	0.00	0.00	3.41
3100	3102	8.733458	GTTTATGCATGCTTCATTCCTATATCA	58.267	33.333	20.33	0.00	0.00	2.15

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.278419	AGTGCCAAAAGACATTAAGACACC	59.722	41.667	0.00	0.00	0.00	4.16
1	2	5.438761	AGTGCCAAAAGACATTAAGACAC	57.561	39.130	0.00	0.00	0.00	3.67
2	3	6.096141	TCAAAGTGCCAAAAGACATTAAGACA	59.904	34.615	0.00	0.00	0.00	3.41
3	4	6.503524	TCAAAGTGCCAAAAGACATTAAGAC	58.496	36.000	0.00	0.00	0.00	3.01
4	5	6.707440	TCAAAGTGCCAAAAGACATTAAGA	57.293	33.333	0.00	0.00	0.00	2.10
5	6	6.980397	ACTTCAAAGTGCCAAAAGACATTAAG	59.020	34.615	0.00	0.00	37.98	1.85
6	7	6.872920	ACTTCAAAGTGCCAAAAGACATTAA	58.127	32.000	0.00	0.00	37.98	1.40
7	8	6.463995	ACTTCAAAGTGCCAAAAGACATTA	57.536	33.333	0.00	0.00	37.98	1.90
8	9	5.343307	ACTTCAAAGTGCCAAAAGACATT	57.657	34.783	0.00	0.00	37.98	2.71
9	10	5.343307	AACTTCAAAGTGCCAAAAGACAT	57.657	34.783	0.00	0.00	39.66	3.06
10	11	4.799564	AACTTCAAAGTGCCAAAAGACA	57.200	36.364	0.00	0.00	39.66	3.41
11	12	7.770801	AATTAACTTCAAAGTGCCAAAAGAC	57.229	32.000	0.00	0.00	39.66	3.01
12	13	9.528018	CTTAATTAACTTCAAAGTGCCAAAAGA	57.472	29.630	0.00	0.00	39.66	2.52
13	14	9.313118	ACTTAATTAACTTCAAAGTGCCAAAAG	57.687	29.630	0.00	2.15	39.66	2.27
14	15	9.660180	AACTTAATTAACTTCAAAGTGCCAAAA	57.340	25.926	0.00	0.00	39.66	2.44
15	16	9.660180	AAACTTAATTAACTTCAAAGTGCCAAA	57.340	25.926	0.00	0.00	39.66	3.28
16	17	9.092876	CAAACTTAATTAACTTCAAAGTGCCAA	57.907	29.630	0.00	0.00	39.66	4.52
17	18	8.254508	ACAAACTTAATTAACTTCAAAGTGCCA	58.745	29.630	0.00	0.00	39.66	4.92
18	19	8.642908	ACAAACTTAATTAACTTCAAAGTGCC	57.357	30.769	0.00	0.00	39.66	5.01
32	33	8.931568	ACGGAGGGAGTATATACAAACTTAATT	58.068	33.333	15.18	0.00	0.00	1.40
33	34	8.488308	ACGGAGGGAGTATATACAAACTTAAT	57.512	34.615	15.18	0.00	0.00	1.40
34	35	7.014615	GGACGGAGGGAGTATATACAAACTTAA	59.985	40.741	15.18	0.00	0.00	1.85
35	36	6.491403	GGACGGAGGGAGTATATACAAACTTA	59.509	42.308	15.18	0.00	0.00	2.24
36	37	5.303845	GGACGGAGGGAGTATATACAAACTT	59.696	44.000	15.18	1.30	0.00	2.66
37	38	4.831710	GGACGGAGGGAGTATATACAAACT	59.168	45.833	15.18	8.90	0.00	2.66
38	39	4.320788	CGGACGGAGGGAGTATATACAAAC	60.321	50.000	15.18	6.03	0.00	2.93
39	40	3.822735	CGGACGGAGGGAGTATATACAAA	59.177	47.826	15.18	0.00	0.00	2.83
40	41	3.072915	TCGGACGGAGGGAGTATATACAA	59.927	47.826	15.18	0.00	0.00	2.41
41	42	2.639347	TCGGACGGAGGGAGTATATACA	59.361	50.000	15.18	0.00	0.00	2.29
42	43	3.340814	TCGGACGGAGGGAGTATATAC	57.659	52.381	4.60	4.60	0.00	1.47
43	44	4.371624	TTTCGGACGGAGGGAGTATATA	57.628	45.455	0.00	0.00	0.00	0.86
44	45	2.965671	TTCGGACGGAGGGAGTATAT	57.034	50.000	0.00	0.00	0.00	0.86
45	46	2.734755	TTTCGGACGGAGGGAGTATA	57.265	50.000	0.00	0.00	0.00	1.47
46	47	1.856629	TTTTCGGACGGAGGGAGTAT	58.143	50.000	0.00	0.00	0.00	2.12
47	48	1.856629	ATTTTCGGACGGAGGGAGTA	58.143	50.000	0.00	0.00	0.00	2.59
48	49	1.479730	GTATTTTCGGACGGAGGGAGT	59.520	52.381	0.00	0.00	0.00	3.85
49	50	1.755380	AGTATTTTCGGACGGAGGGAG	59.245	52.381	0.00	0.00	0.00	4.30
50	51	1.856629	AGTATTTTCGGACGGAGGGA	58.143	50.000	0.00	0.00	0.00	4.20
51	52	2.685850	AAGTATTTTCGGACGGAGGG	57.314	50.000	0.00	0.00	0.00	4.30
52	53	3.867493	GGTTAAGTATTTTCGGACGGAGG	59.133	47.826	0.00	0.00	0.00	4.30
53	54	3.867493	GGGTTAAGTATTTTCGGACGGAG	59.133	47.826	0.00	0.00	0.00	4.63
54	55	3.260380	TGGGTTAAGTATTTTCGGACGGA	59.740	43.478	0.00	0.00	0.00	4.69
55	56	3.598299	TGGGTTAAGTATTTTCGGACGG	58.402	45.455	0.00	0.00	0.00	4.79
56	57	4.248058	ACTGGGTTAAGTATTTTCGGACG	58.752	43.478	0.00	0.00	0.00	4.79
57	58	7.854557	AATACTGGGTTAAGTATTTTCGGAC	57.145	36.000	4.20	0.00	46.44	4.79
263	264	8.712363	TCTAATAGCTAAGAAATATTTGCAGCG	58.288	33.333	5.17	0.00	34.02	5.18
382	383	3.014304	ACTATCTTCTGCTGGTACCGA	57.986	47.619	7.57	0.00	0.00	4.69
425	426	0.229753	GAACGAACAGTGTGAGTGCG	59.770	55.000	0.00	0.00	43.60	5.34
725	726	9.734984	TTTCCTTCGAAAGTTCTTTATTATCCT	57.265	29.630	0.00	0.00	32.96	3.24
820	821	7.993183	AGAGAACACTTCTTTTCACAGGATTTA	59.007	33.333	0.00	0.00	40.87	1.40
1118	1119	5.144100	TCCTATTTTTCCAAGTGAAAGCCA	58.856	37.500	0.00	0.00	43.57	4.75
1839	1841	1.640917	TACCTTTCGAGACCAAGCCT	58.359	50.000	0.00	0.00	0.00	4.58
1910	1912	1.720781	AAGCAAGGTTCAAAGCCCAT	58.279	45.000	0.00	0.00	0.00	4.00
2343	2345	1.614996	TCCAAAGAATCAAAGCGCCA	58.385	45.000	2.29	0.00	0.00	5.69
2377	2379	7.016760	GGAAGGCCTCCTAAAAAGATCTACTAT	59.983	40.741	5.23	0.00	41.61	2.12
2436	2438	3.581755	GTGAACAGCTAACCATCGTACA	58.418	45.455	0.00	0.00	0.00	2.90
2515	2517	2.425578	TAAGATTGCGTGTCGTGTCA	57.574	45.000	0.00	0.00	0.00	3.58
2538	2540	5.880332	GTCAAAGATGAAGGCCATACTGTAA	59.120	40.000	5.01	0.00	37.30	2.41
2611	2613	1.134788	GTTGTAGGTGGATGGACCTCG	60.135	57.143	0.00	0.00	43.33	4.63
2619	2621	6.592870	GGAGCTTTATTAGTTGTAGGTGGAT	58.407	40.000	0.00	0.00	0.00	3.41
3015	3017	6.494835	GGTGGATAAATTCAATAATGAGGGCT	59.505	38.462	0.00	0.00	36.78	5.19
3038	3040	2.890311	TGAATTTGGTTGCATCGAAGGT	59.110	40.909	0.00	0.00	0.00	3.50
3100	3102	3.055819	CCAGCCTACGGATAATACATGCT	60.056	47.826	0.00	0.00	0.00	3.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.