AutoCloner

Multiple sequence alignment - TraesCS1A01G364800

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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	TraesCS1A01G364800	chr1A	100.000	4472	0	0	1	4472	544388416	544392887	0.000000e+00	8259.0
1	TraesCS1A01G364800	chr1A	96.581	117	4	0	2844	2960	376145834	376145950	1.270000e-45	195.0
2	TraesCS1A01G364800	chr1A	96.703	91	3	0	294	384	551465799	551465709	7.750000e-33	152.0
3	TraesCS1A01G364800	chr1A	81.437	167	29	2	1839	2004	544487895	544488060	7.800000e-28	135.0
4	TraesCS1A01G364800	chr1A	91.954	87	5	2	1083	1168	544487077	544487162	2.180000e-23	121.0
5	TraesCS1A01G364800	chr1A	100.000	31	0	0	3077	3107	502805192	502805162	1.740000e-04	58.4
6	TraesCS1A01G364800	chr1B	88.226	2497	140	70	379	2812	614499311	614501716	0.000000e+00	2841.0
7	TraesCS1A01G364800	chr1B	84.424	886	72	21	3605	4472	614502271	614503108	0.000000e+00	811.0
8	TraesCS1A01G364800	chr1B	86.376	734	67	11	3742	4472	614507495	614508198	0.000000e+00	771.0
9	TraesCS1A01G364800	chr1B	85.566	769	55	31	2985	3740	614506660	614507385	0.000000e+00	754.0
10	TraesCS1A01G364800	chr1B	86.257	553	39	17	2989	3538	614501728	614502246	2.330000e-157	566.0
11	TraesCS1A01G364800	chr1B	93.431	137	9	0	2640	2776	614505636	614505772	2.110000e-48	204.0
12	TraesCS1A01G364800	chr1B	89.630	135	11	2	168	302	614499127	614499258	7.690000e-38	169.0
13	TraesCS1A01G364800	chr1B	94.000	100	4	2	293	390	686756519	686756420	2.790000e-32	150.0
14	TraesCS1A01G364800	chr1B	90.654	107	8	2	281	386	503353001	503352896	1.680000e-29	141.0
15	TraesCS1A01G364800	chr1B	78.140	215	45	2	1839	2052	614943484	614943697	7.800000e-28	135.0
16	TraesCS1A01G364800	chr1B	92.857	84	5	1	1085	1168	614942675	614942757	2.180000e-23	121.0
17	TraesCS1A01G364800	chr1B	94.737	38	0	1	3077	3112	547523424	547523387	1.740000e-04	58.4
18	TraesCS1A01G364800	chr1D	89.437	2272	109	43	585	2814	448786373	448788555	0.000000e+00	2745.0
19	TraesCS1A01G364800	chr1D	85.724	1548	122	45	2962	4472	448788554	448790039	0.000000e+00	1543.0
20	TraesCS1A01G364800	chr1D	89.866	1194	53	27	585	1747	448754235	448755391	0.000000e+00	1472.0
21	TraesCS1A01G364800	chr1D	92.748	524	36	2	3951	4472	448792352	448792875	0.000000e+00	756.0
22	TraesCS1A01G364800	chr1D	94.828	290	13	2	4185	4472	448755389	448755678	6.820000e-123	451.0
23	TraesCS1A01G364800	chr1D	78.241	216	45	2	1838	2052	449282698	449282912	2.170000e-28	137.0
24	TraesCS1A01G364800	chr1D	94.048	84	4	1	1085	1168	449281872	449281954	4.700000e-25	126.0
25	TraesCS1A01G364800	chr1D	100.000	31	0	0	3077	3107	407160379	407160349	1.740000e-04	58.4
26	TraesCS1A01G364800	chr3D	97.414	116	2	1	2850	2965	433565992	433566106	3.530000e-46	196.0
27	TraesCS1A01G364800	chr3D	90.385	52	4	1	4211	4261	532172001	532172052	2.890000e-07	67.6
28	TraesCS1A01G364800	chr4A	97.321	112	3	0	2849	2960	528813883	528813994	1.640000e-44	191.0
29	TraesCS1A01G364800	chr4A	93.496	123	7	1	2850	2972	281354303	281354424	9.880000e-42	182.0
30	TraesCS1A01G364800	chr4A	95.238	42	2	0	1965	2006	538840138	538840097	2.890000e-07	67.6
31	TraesCS1A01G364800	chr5D	98.148	108	2	0	2853	2960	424123549	424123656	5.910000e-44	189.0
32	TraesCS1A01G364800	chr5D	92.913	127	7	2	2840	2965	560426070	560426195	2.750000e-42	183.0
33	TraesCS1A01G364800	chr5A	89.404	151	10	6	2849	2995	69844898	69844750	7.640000e-43	185.0
34	TraesCS1A01G364800	chr6D	92.366	131	6	4	2832	2959	468641022	468640893	2.750000e-42	183.0
35	TraesCS1A01G364800	chr7D	91.603	131	7	4	2832	2959	414289181	414289310	1.280000e-40	178.0
36	TraesCS1A01G364800	chr7D	89.091	55	5	1	4211	4264	46993653	46993599	2.890000e-07	67.6
37	TraesCS1A01G364800	chr7D	94.444	36	2	0	1966	2001	513312802	513312837	6.250000e-04	56.5
38	TraesCS1A01G364800	chr7D	86.275	51	7	0	1966	2016	515220643	515220593	6.250000e-04	56.5
39	TraesCS1A01G364800	chr7D	86.275	51	7	0	1966	2016	515236849	515236799	6.250000e-04	56.5
40	TraesCS1A01G364800	chr4D	94.495	109	4	2	280	387	478669028	478668921	2.770000e-37	167.0
41	TraesCS1A01G364800	chr5B	97.778	90	2	0	289	378	600647492	600647581	5.990000e-34	156.0
42	TraesCS1A01G364800	chr2A	97.753	89	2	0	292	380	196345032	196345120	2.150000e-33	154.0
43	TraesCS1A01G364800	chr7A	95.699	93	4	0	293	385	705090326	705090234	2.790000e-32	150.0
44	TraesCS1A01G364800	chr7A	90.385	52	4	1	4211	4261	200512562	200512511	2.890000e-07	67.6
45	TraesCS1A01G364800	chr3B	92.233	103	8	0	284	386	549759058	549759160	3.600000e-31	147.0
46	TraesCS1A01G364800	chr2D	93.000	100	7	0	289	388	270480956	270480857	3.600000e-31	147.0
47	TraesCS1A01G364800	chr2D	84.507	71	9	2	4220	4289	207252557	207252488	8.030000e-08	69.4

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	TraesCS1A01G364800	chr1A	544388416	544392887	4471	False	8259.000000	8259	100.000000	1	4472	1	chr1A.!!$F2	4471
1	TraesCS1A01G364800	chr1B	614499127	614508198	9071	False	873.714286	2841	87.701429	168	4472	7	chr1B.!!$F1	4304
2	TraesCS1A01G364800	chr1D	448786373	448792875	6502	False	1681.333333	2745	89.303000	585	4472	3	chr1D.!!$F2	3887
3	TraesCS1A01G364800	chr1D	448754235	448755678	1443	False	961.500000	1472	92.347000	585	4472	2	chr1D.!!$F1	3887

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
164	165	0.307760	CGGCATTTCGGTTGATAGGC	59.692	55.0	0.00	0.00	33.02	3.93	F
1399	1456	0.108804	GCTCAAGCTGCTGGTACGTA	60.109	55.0	1.35	0.00	38.21	3.57	F
1788	1857	0.248134	CGACGACCTGAATCTCGGTC	60.248	60.0	10.75	10.75	44.88	4.79	F
2402	2529	0.039798	ACGCTTCATTTGCAGCACAG	60.040	50.0	0.00	0.00	33.92	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1769	1838	0.248134	GACCGAGATTCAGGTCGTCG	60.248	60.0	13.25	0.82	46.08	5.12	R
2267	2375	0.393077	ATTCTTCGTATCCCGGCCTG	59.607	55.0	0.00	0.00	37.11	4.85	R
2943	3076	0.744414	TACGTACTCCCTCCGTTCCG	60.744	60.0	0.00	0.00	36.12	4.30	R
3825	3989	1.455383	CCACCCTTGCGCAAAGAAGT	61.455	55.0	25.01	15.27	38.24	3.01	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
35	36	8.032952	AGGTGCGTAAAATACTTAGTTTAACC	57.967	34.615	0.00	2.43	30.36	2.85
36	37	7.119699	AGGTGCGTAAAATACTTAGTTTAACCC	59.880	37.037	0.00	0.00	30.45	4.11
37	38	7.094848	GGTGCGTAAAATACTTAGTTTAACCCA	60.095	37.037	0.00	0.00	29.11	4.51
38	39	8.288913	GTGCGTAAAATACTTAGTTTAACCCAA	58.711	33.333	0.00	0.00	29.11	4.12
39	40	8.505625	TGCGTAAAATACTTAGTTTAACCCAAG	58.494	33.333	0.00	5.76	29.11	3.61
40	41	8.720562	GCGTAAAATACTTAGTTTAACCCAAGA	58.279	33.333	12.17	0.38	29.11	3.02
46	47	9.730705	AATACTTAGTTTAACCCAAGACTTACC	57.269	33.333	12.17	0.00	0.00	2.85
47	48	6.537355	ACTTAGTTTAACCCAAGACTTACCC	58.463	40.000	12.17	0.00	0.00	3.69
48	49	4.377762	AGTTTAACCCAAGACTTACCCC	57.622	45.455	0.00	0.00	0.00	4.95
49	50	3.723154	AGTTTAACCCAAGACTTACCCCA	59.277	43.478	0.00	0.00	0.00	4.96
50	51	4.168479	AGTTTAACCCAAGACTTACCCCAA	59.832	41.667	0.00	0.00	0.00	4.12
51	52	2.971901	AACCCAAGACTTACCCCAAG	57.028	50.000	0.00	0.00	40.38	3.61
52	53	2.127651	ACCCAAGACTTACCCCAAGA	57.872	50.000	0.00	0.00	37.71	3.02
53	54	1.985895	ACCCAAGACTTACCCCAAGAG	59.014	52.381	0.00	0.00	37.71	2.85
54	55	1.340114	CCCAAGACTTACCCCAAGAGC	60.340	57.143	0.00	0.00	37.71	4.09
55	56	1.351017	CCAAGACTTACCCCAAGAGCA	59.649	52.381	0.00	0.00	37.71	4.26
56	57	2.224769	CCAAGACTTACCCCAAGAGCAA	60.225	50.000	0.00	0.00	37.71	3.91
57	58	2.814336	CAAGACTTACCCCAAGAGCAAC	59.186	50.000	0.00	0.00	37.71	4.17
58	59	2.054799	AGACTTACCCCAAGAGCAACA	58.945	47.619	0.00	0.00	37.71	3.33
59	60	2.441750	AGACTTACCCCAAGAGCAACAA	59.558	45.455	0.00	0.00	37.71	2.83
60	61	2.814336	GACTTACCCCAAGAGCAACAAG	59.186	50.000	0.00	0.00	37.71	3.16
61	62	2.174854	ACTTACCCCAAGAGCAACAAGT	59.825	45.455	0.00	0.00	37.71	3.16
62	63	2.270352	TACCCCAAGAGCAACAAGTG	57.730	50.000	0.00	0.00	0.00	3.16
63	64	0.468029	ACCCCAAGAGCAACAAGTGG	60.468	55.000	0.00	0.00	0.00	4.00
64	65	0.468029	CCCCAAGAGCAACAAGTGGT	60.468	55.000	0.00	0.00	41.89	4.16

Showing 1 to 25 of 396 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	8.506437	GGTTAAACTAAGTATTTTACGCACCTT	58.494	33.333	0.00	0.00	0.00	3.50
11	12	7.094848	TGGGTTAAACTAAGTATTTTACGCACC	60.095	37.037	0.00	0.00	36.92	5.01
12	13	7.805700	TGGGTTAAACTAAGTATTTTACGCAC	58.194	34.615	0.00	0.00	36.92	5.34
13	14	7.976135	TGGGTTAAACTAAGTATTTTACGCA	57.024	32.000	0.00	3.29	38.42	5.24
14	15	8.720562	TCTTGGGTTAAACTAAGTATTTTACGC	58.279	33.333	15.36	0.00	34.19	4.42
20	21	9.730705	GGTAAGTCTTGGGTTAAACTAAGTATT	57.269	33.333	15.36	13.13	0.00	1.89
21	22	8.324306	GGGTAAGTCTTGGGTTAAACTAAGTAT	58.676	37.037	15.36	6.64	0.00	2.12
22	23	7.256655	GGGGTAAGTCTTGGGTTAAACTAAGTA	60.257	40.741	15.36	0.00	0.00	2.24
23	24	6.466326	GGGGTAAGTCTTGGGTTAAACTAAGT	60.466	42.308	15.36	0.59	0.00	2.24
24	25	5.942236	GGGGTAAGTCTTGGGTTAAACTAAG	59.058	44.000	10.21	10.21	0.00	2.18
25	26	5.372066	TGGGGTAAGTCTTGGGTTAAACTAA	59.628	40.000	0.00	0.00	0.00	2.24
26	27	4.912744	TGGGGTAAGTCTTGGGTTAAACTA	59.087	41.667	0.00	0.00	0.00	2.24
27	28	3.723154	TGGGGTAAGTCTTGGGTTAAACT	59.277	43.478	0.00	0.00	0.00	2.66
28	29	4.103013	TGGGGTAAGTCTTGGGTTAAAC	57.897	45.455	0.00	0.00	0.00	2.01
29	30	4.416179	TCTTGGGGTAAGTCTTGGGTTAAA	59.584	41.667	0.00	0.00	37.65	1.52
30	31	3.982052	TCTTGGGGTAAGTCTTGGGTTAA	59.018	43.478	0.00	0.00	37.65	2.01
31	32	3.585732	CTCTTGGGGTAAGTCTTGGGTTA	59.414	47.826	0.00	0.00	37.65	2.85
32	33	2.375509	CTCTTGGGGTAAGTCTTGGGTT	59.624	50.000	0.00	0.00	37.65	4.11
33	34	1.985895	CTCTTGGGGTAAGTCTTGGGT	59.014	52.381	0.00	0.00	37.65	4.51
34	35	1.340114	GCTCTTGGGGTAAGTCTTGGG	60.340	57.143	0.00	0.00	37.65	4.12
35	36	1.351017	TGCTCTTGGGGTAAGTCTTGG	59.649	52.381	0.00	0.00	37.65	3.61
36	37	2.814336	GTTGCTCTTGGGGTAAGTCTTG	59.186	50.000	0.00	0.00	37.65	3.02
37	38	2.441750	TGTTGCTCTTGGGGTAAGTCTT	59.558	45.455	0.00	0.00	37.65	3.01
38	39	2.054799	TGTTGCTCTTGGGGTAAGTCT	58.945	47.619	0.00	0.00	37.65	3.24
39	40	2.561478	TGTTGCTCTTGGGGTAAGTC	57.439	50.000	0.00	0.00	37.65	3.01

Showing 1 to 25 of 407 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.