AutoCloner

Multiple sequence alignment - TraesCS3B01G397600

Loading Multiple Alignment...

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	TraesCS3B01G397600	chr3B	100.000	5774	0	0	1	5774	627911988	627906215	0.000000e+00	10663.0
1	TraesCS3B01G397600	chr3A	93.538	3064	161	20	2390	5431	614762571	614759523	0.000000e+00	4527.0
2	TraesCS3B01G397600	chr3A	85.915	1569	88	56	575	2062	614764233	614762717	0.000000e+00	1550.0
3	TraesCS3B01G397600	chr3A	92.593	243	18	0	5532	5774	614759227	614758985	3.310000e-92	350.0
4	TraesCS3B01G397600	chr3A	88.768	276	22	8	37	304	614771293	614771019	4.310000e-86	329.0
5	TraesCS3B01G397600	chr3D	94.263	2876	127	19	2585	5431	472404827	472401961	0.000000e+00	4362.0
6	TraesCS3B01G397600	chr3D	86.224	1401	70	37	434	1764	472406974	472405627	0.000000e+00	1404.0
7	TraesCS3B01G397600	chr3D	92.787	305	20	2	1	304	472407906	472407603	1.910000e-119	440.0
8	TraesCS3B01G397600	chr3D	89.180	305	20	7	1764	2062	472405441	472405144	9.140000e-98	368.0
9	TraesCS3B01G397600	chr3D	86.431	339	28	10	5446	5774	472401861	472401531	7.120000e-94	355.0
10	TraesCS3B01G397600	chr3D	84.906	106	15	1	2163	2267	583290883	583290778	7.910000e-19	106.0
11	TraesCS3B01G397600	chr6A	84.049	163	22	1	2076	2238	101760761	101760603	2.790000e-33	154.0
12	TraesCS3B01G397600	chr5B	81.283	187	25	7	2079	2259	472674721	472674539	6.030000e-30	143.0
13	TraesCS3B01G397600	chr5B	87.912	91	11	0	2172	2262	266982238	266982148	2.200000e-19	108.0
14	TraesCS3B01G397600	chr2A	91.753	97	8	0	2079	2175	656365296	656365200	1.010000e-27	135.0
15	TraesCS3B01G397600	chr2A	87.000	100	11	2	2172	2270	25326867	25326769	1.700000e-20	111.0
16	TraesCS3B01G397600	chr1B	91.753	97	8	0	2079	2175	643155993	643156089	1.010000e-27	135.0
17	TraesCS3B01G397600	chr1A	91.753	97	8	0	2079	2175	435066021	435066117	1.010000e-27	135.0
18	TraesCS3B01G397600	chr1A	90.196	102	9	1	2076	2176	574192145	574192246	1.310000e-26	132.0
19	TraesCS3B01G397600	chr7B	91.667	96	8	0	2080	2175	48123741	48123646	3.630000e-27	134.0
20	TraesCS3B01G397600	chr7B	82.105	95	17	0	2162	2256	310555489	310555583	1.330000e-11	82.4
21	TraesCS3B01G397600	chr7A	90.909	99	9	0	2077	2175	593450831	593450733	3.630000e-27	134.0
22	TraesCS3B01G397600	chr7A	89.773	88	9	0	2172	2259	276146116	276146029	4.730000e-21	113.0
23	TraesCS3B01G397600	chr4D	90.000	100	10	0	2076	2175	36413365	36413266	4.700000e-26	130.0
24	TraesCS3B01G397600	chrUn	87.912	91	11	0	2172	2262	66416496	66416406	2.200000e-19	108.0
25	TraesCS3B01G397600	chr5A	89.412	85	9	0	2172	2256	603991071	603991155	2.200000e-19	108.0
26	TraesCS3B01G397600	chr2D	87.368	95	10	2	2172	2265	344031542	344031449	2.200000e-19	108.0
27	TraesCS3B01G397600	chr5D	82.243	107	18	1	2162	2267	504792253	504792359	2.220000e-14	91.6
28	TraesCS3B01G397600	chr5D	80.734	109	16	4	2148	2254	113384613	113384718	4.800000e-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	TraesCS3B01G397600	chr3B	627906215	627911988	5773	True	10663.000000	10663	100.000	1	5774	1	chr3B.!!$R1	5773
1	TraesCS3B01G397600	chr3A	614758985	614764233	5248	True	2142.333333	4527	90.682	575	5774	3	chr3A.!!$R2	5199
2	TraesCS3B01G397600	chr3D	472401531	472407906	6375	True	1385.800000	4362	89.777	1	5774	5	chr3D.!!$R2	5773

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
969	1540	0.034616	ATCAGGCTCCTATTCGCAGC	59.965	55.000	0.00	0.00	5.25	F
2338	3201	0.107897	CACACATACAAGCCCCGCTA	60.108	55.000	0.00	38.25	4.26	F
2360	3223	0.033504	AACGCACGGCATAGGATAGG	59.966	55.000	0.00	0.00	2.57	F
3316	4189	0.248621	GCGATATGGTTGCAGTTGCC	60.249	55.000	1.06	41.18	4.52	F
4173	5046	1.004440	GCGACTTCAAGGAGGCTGT	60.004	57.895	0.00	0.00	4.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	End Stability	Orientation
2341	3204	0.033504	CCTATCCTATGCCGTGCGTT	59.966	55.0	0.00	4.84	R
4212	5085	0.315251	TCGCGGAAGGATAGCTCATG	59.685	55.0	6.13	3.07	R
4216	5089	1.381928	TTCGTCGCGGAAGGATAGCT	61.382	55.0	6.13	3.32	R
4395	5268	0.036010	AAACATCACTCTGGAGGGCG	60.036	55.0	2.58	6.13	R
5620	6719	0.250209	AGTGGTGCAGCAGAAGTGAG	60.250	55.0	20.85	3.51	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	2.031157	CCAAGGTTCGTGCTACAAAAGG	60.031	50.000	0.00	0.00	0.00	3.11
34	35	3.756933	AGGTTCGTGCTACAAAAGGTA	57.243	42.857	0.00	0.00	0.00	3.08
56	57	9.017509	AGGTATAAATTGCATCTTGATATGGTG	57.982	33.333	0.00	0.00	0.00	4.17
57	58	7.756722	GGTATAAATTGCATCTTGATATGGTGC	59.243	37.037	0.00	0.00	36.39	5.01
73	74	1.891919	TGCTGACGCACCAAGGTTC	60.892	57.895	0.00	0.00	42.25	3.62
77	78	2.699954	CTGACGCACCAAGGTTCTAAT	58.300	47.619	0.00	0.00	0.00	1.73
78	79	3.074412	CTGACGCACCAAGGTTCTAATT	58.926	45.455	0.00	0.00	0.00	1.40
105	106	5.781210	TGGTTATTTGACATGCAGAACAA	57.219	34.783	0.00	0.00	0.00	2.83
136	137	1.843851	CTCCCCAAGTGTAAGGGCATA	59.156	52.381	0.00	0.00	44.06	3.14
170	171	7.246674	TGACAAGACGAAATTATCTTATGCC	57.753	36.000	0.00	0.00	33.35	4.40
279	281	9.588096	ACTCCTAAATTTTTGTAGGATGAGTTT	57.412	29.630	7.69	0.00	43.88	2.66
281	283	9.581289	TCCTAAATTTTTGTAGGATGAGTTTGA	57.419	29.630	3.69	0.00	40.80	2.69
328	381	7.423199	ACAATTCTATCTATTGCATGCACTTG	58.577	34.615	22.58	16.48	36.65	3.16
343	396	7.392113	TGCATGCACTTGATATCAATATCATCA	59.608	33.333	18.46	15.23	45.99	3.07
428	481	9.783256	AACGCTAATGGTCAAATATAACTTTTC	57.217	29.630	0.00	0.00	0.00	2.29
429	482	8.952278	ACGCTAATGGTCAAATATAACTTTTCA	58.048	29.630	0.00	0.00	0.00	2.69
430	483	9.781834	CGCTAATGGTCAAATATAACTTTTCAA	57.218	29.630	0.00	0.00	0.00	2.69
473	981	6.463995	ACATCAGTTTAAACTTTTGGAGCA	57.536	33.333	18.25	0.00	37.08	4.26
475	983	6.980397	ACATCAGTTTAAACTTTTGGAGCAAG	59.020	34.615	18.25	3.66	37.08	4.01
481	989	9.922264	AGTTTAAACTTTTGGAGCAAGTGGCTG	62.922	40.741	15.22	0.00	45.49	4.85
493	1001	3.395639	CAAGTGGCTGCAACATGAATTT	58.604	40.909	10.27	0.00	0.00	1.82
506	1014	6.417635	GCAACATGAATTTTGTATGGTATCCG	59.582	38.462	0.00	0.00	0.00	4.18
509	1017	6.017109	ACATGAATTTTGTATGGTATCCGAGC	60.017	38.462	0.00	0.00	0.00	5.03
516	1024	6.474140	TTGTATGGTATCCGAGCTAAGAAA	57.526	37.500	0.00	0.00	0.00	2.52
526	1034	5.411781	TCCGAGCTAAGAAATCTTGAGTTC	58.588	41.667	5.93	3.01	37.40	3.01

Showing 1 to 25 of 365 entries

Previous1 2 3 4 5…15Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
12	13	2.616842	ACCTTTTGTAGCACGAACCTTG	59.383	45.455	0.00	0.00	0.00	3.61
32	33	8.517878	AGCACCATATCAAGATGCAATTTATAC	58.482	33.333	0.00	0.00	38.79	1.47
34	35	7.231925	TCAGCACCATATCAAGATGCAATTTAT	59.768	33.333	0.00	0.00	38.79	1.40
56	57	0.320421	TAGAACCTTGGTGCGTCAGC	60.320	55.000	0.00	2.68	45.41	4.26
57	58	2.163818	TTAGAACCTTGGTGCGTCAG	57.836	50.000	0.00	0.00	0.00	3.51
78	79	9.183368	TGTTCTGCATGTCAAATAACCATATTA	57.817	29.630	0.00	0.00	31.44	0.98
95	96	4.712476	AGTTCTGTCTTCTTGTTCTGCAT	58.288	39.130	0.00	0.00	0.00	3.96
105	106	2.370189	CACTTGGGGAGTTCTGTCTTCT	59.630	50.000	0.00	0.00	36.10	2.85
136	137	1.133598	TCGTCTTGTCAACGACAGTGT	59.866	47.619	0.00	0.00	43.69	3.55
142	143	8.592155	CATAAGATAATTTCGTCTTGTCAACGA	58.408	33.333	9.43	0.00	46.54	3.85
170	171	0.734309	TGCTCTAAATGGCATGCACG	59.266	50.000	21.36	0.46	33.23	5.34
251	253	9.588096	ACTCATCCTACAAAAATTTAGGAGTTT	57.412	29.630	11.97	0.00	45.68	2.66
380	433	7.415206	GCGTTTTCAACTCCAAATGTATAGGAT	60.415	37.037	0.00	0.00	0.00	3.24
381	434	6.128117	GCGTTTTCAACTCCAAATGTATAGGA	60.128	38.462	0.00	0.00	0.00	2.94
383	436	6.842163	AGCGTTTTCAACTCCAAATGTATAG	58.158	36.000	0.00	0.00	0.00	1.31
384	437	6.811253	AGCGTTTTCAACTCCAAATGTATA	57.189	33.333	0.00	0.00	0.00	1.47
385	438	5.705609	AGCGTTTTCAACTCCAAATGTAT	57.294	34.783	0.00	0.00	0.00	2.29
386	439	6.621316	TTAGCGTTTTCAACTCCAAATGTA	57.379	33.333	0.00	0.00	0.00	2.29
387	440	5.508200	TTAGCGTTTTCAACTCCAAATGT	57.492	34.783	0.00	0.00	0.00	2.71
388	441	5.345741	CCATTAGCGTTTTCAACTCCAAATG	59.654	40.000	0.00	0.00	0.00	2.32
392	445	3.482436	ACCATTAGCGTTTTCAACTCCA	58.518	40.909	0.00	0.00	0.00	3.86
393	446	3.500680	TGACCATTAGCGTTTTCAACTCC	59.499	43.478	0.00	0.00	0.00	3.85
428	481	7.144722	TGTAAAGAGGCAGACAATATGTTTG	57.855	36.000	0.00	0.00	35.78	2.93
429	482	7.611467	TGATGTAAAGAGGCAGACAATATGTTT	59.389	33.333	0.00	0.00	0.00	2.83
430	483	7.112122	TGATGTAAAGAGGCAGACAATATGTT	58.888	34.615	0.00	0.00	0.00	2.71

Showing 1 to 25 of 345 entries

Previous1 2 3 4 5…14Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.