AutoCloner

Multiple sequence alignment - TraesCS2B01G134200

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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	TraesCS2B01G134200	chr2B	100.000	5957	0	0	1	5957	100339647	100333691	0.000000e+00	11001.0
1	TraesCS2B01G134200	chr2B	99.074	108	1	0	4179	4286	100335415	100335308	1.690000e-45	195.0
2	TraesCS2B01G134200	chr2B	99.074	108	1	0	4233	4340	100335469	100335362	1.690000e-45	195.0
3	TraesCS2B01G134200	chr2B	98.148	54	1	0	4179	4232	100335361	100335308	1.770000e-15	95.3
4	TraesCS2B01G134200	chr2B	98.148	54	1	0	4287	4340	100335469	100335416	1.770000e-15	95.3
5	TraesCS2B01G134200	chr2A	95.385	3770	132	16	493	4225	65670255	65666491	0.000000e+00	5960.0
6	TraesCS2B01G134200	chr2A	96.310	786	23	3	4292	5075	65666532	65665751	0.000000e+00	1286.0
7	TraesCS2B01G134200	chr2A	91.000	400	30	5	5077	5475	65665709	65665315	8.790000e-148	534.0
8	TraesCS2B01G134200	chr2A	93.521	355	21	1	1	355	65670612	65670260	1.470000e-145	527.0
9	TraesCS2B01G134200	chr2A	90.842	273	20	5	5555	5823	65665294	65665023	1.580000e-95	361.0
10	TraesCS2B01G134200	chr2A	98.000	150	1	2	352	499	377320063	377320212	5.920000e-65	259.0
11	TraesCS2B01G134200	chr2A	84.942	259	33	6	998	1254	43143386	43143640	2.130000e-64	257.0
12	TraesCS2B01G134200	chr2A	92.647	136	6	4	752	883	65670139	65670004	6.090000e-45	193.0
13	TraesCS2B01G134200	chr2A	89.423	104	10	1	5468	5570	361381616	361381719	4.850000e-26	130.0
14	TraesCS2B01G134200	chr2A	89.024	82	8	1	5877	5957	65664552	65664471	3.800000e-17	100.0
15	TraesCS2B01G134200	chr2D	96.198	2367	78	9	493	2851	64187489	64185127	0.000000e+00	3862.0
16	TraesCS2B01G134200	chr2D	95.745	1269	44	5	2972	4230	64185118	64183850	0.000000e+00	2036.0
17	TraesCS2B01G134200	chr2D	88.158	1216	86	36	4292	5469	64183896	64182701	0.000000e+00	1395.0
18	TraesCS2B01G134200	chr2D	95.775	355	13	1	1	355	64187846	64187494	6.700000e-159	571.0
19	TraesCS2B01G134200	chr2D	92.697	178	10	2	5647	5823	64182466	64182291	2.760000e-63	254.0
20	TraesCS2B01G134200	chr2D	89.630	135	11	2	752	883	64187373	64187239	1.030000e-37	169.0
21	TraesCS2B01G134200	chr2D	90.000	100	10	0	5464	5563	117843131	117843032	4.850000e-26	130.0
22	TraesCS2B01G134200	chr2D	93.827	81	5	0	5877	5957	64182080	64182000	8.110000e-24	122.0
23	TraesCS2B01G134200	chr2D	96.923	65	2	0	5815	5879	64182266	64182202	6.310000e-20	110.0
24	TraesCS2B01G134200	chr5D	81.795	390	47	13	4831	5200	262397798	262397413	7.500000e-79	305.0
25	TraesCS2B01G134200	chr5A	98.000	150	1	2	352	499	6212906	6212757	5.920000e-65	259.0
26	TraesCS2B01G134200	chr5A	98.000	150	1	2	352	499	299774100	299774249	5.920000e-65	259.0
27	TraesCS2B01G134200	chr5A	95.506	89	4	0	5468	5556	218994215	218994303	6.220000e-30	143.0
28	TraesCS2B01G134200	chr4B	98.639	147	1	1	352	497	413735070	413734924	5.920000e-65	259.0
29	TraesCS2B01G134200	chr4B	94.382	89	5	0	5469	5557	668489827	668489915	2.900000e-28	137.0
30	TraesCS2B01G134200	chr4B	83.133	83	12	2	3212	3293	146558509	146558428	2.300000e-09	75.0
31	TraesCS2B01G134200	chr1B	97.386	153	2	2	352	502	234818448	234818600	5.920000e-65	259.0
32	TraesCS2B01G134200	chr7B	99.291	141	1	0	352	492	52907091	52907231	7.660000e-64	255.0
33	TraesCS2B01G134200	chr7B	93.407	91	6	0	5468	5558	639796286	639796196	1.040000e-27	135.0
34	TraesCS2B01G134200	chr7A	96.774	155	2	3	352	504	404121676	404121523	7.660000e-64	255.0
35	TraesCS2B01G134200	chr7A	87.634	186	20	3	4831	5015	104530948	104530765	4.680000e-51	213.0
36	TraesCS2B01G134200	chr7A	86.667	75	6	4	3212	3284	32300595	32300523	4.950000e-11	80.5
37	TraesCS2B01G134200	chr3A	96.774	155	1	3	352	506	90137416	90137266	7.660000e-64	255.0
38	TraesCS2B01G134200	chr3A	90.000	100	8	2	5456	5555	99426282	99426185	1.740000e-25	128.0
39	TraesCS2B01G134200	chr1A	96.774	155	1	3	352	506	155847062	155846912	7.660000e-64	255.0
40	TraesCS2B01G134200	chr6B	96.512	86	3	0	5470	5555	705518148	705518233	6.220000e-30	143.0
41	TraesCS2B01G134200	chr7D	96.471	85	3	0	5471	5555	4511732	4511648	2.240000e-29	141.0
42	TraesCS2B01G134200	chr7D	89.333	75	4	4	3212	3284	31996313	31996241	2.290000e-14	91.6
43	TraesCS2B01G134200	chr6D	95.349	86	4	0	5470	5555	47081293	47081378	2.900000e-28	137.0
44	TraesCS2B01G134200	chrUn	88.000	75	5	4	3212	3284	366954127	366954055	1.060000e-12	86.1
45	TraesCS2B01G134200	chrUn	88.000	75	5	4	3212	3284	366956098	366956026	1.060000e-12	86.1
46	TraesCS2B01G134200	chrUn	88.000	75	5	4	3212	3284	444590120	444590192	1.060000e-12	86.1
47	TraesCS2B01G134200	chr4A	88.000	75	5	4	3212	3284	694667077	694667149	1.060000e-12	86.1

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	TraesCS2B01G134200	chr2B	100333691	100339647	5956	True	11001.000000	11001	100.000000	1	5957	1	chr2B.!!$R1	5956
1	TraesCS2B01G134200	chr2A	65664471	65670612	6141	True	1280.142857	5960	92.675571	1	5957	7	chr2A.!!$R1	5956
2	TraesCS2B01G134200	chr2D	64182000	64187846	5846	True	1064.875000	3862	93.619125	1	5957	8	chr2D.!!$R2	5956

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
464	465	0.037303	ACCTCATGGTCACAAGGCAG	59.963	55.000	0.00	44.78	4.85	F
477	478	0.111253	AAGGCAGCAGCTTTACCACT	59.889	50.000	0.00	38.40	4.00	F
588	589	0.397941	ATGGACCATATGAGGGCACG	59.602	55.000	4.75	38.98	5.34	F
2383	2399	1.403679	GGATGAGACCTCACGACTCAG	59.596	57.143	1.31	43.11	3.35	F
4107	4151	0.378257	CTGCAATGGGAACGAATCGG	59.622	55.000	7.80	0.00	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability	Orientation
2017	2028	0.808755	GTACCATGAACTTTGCGGGG	59.191	55.000	0.00	0.00	5.73	R
2473	2489	1.798813	GGCATAACCGAGGAAATAGCG	59.201	52.381	0.00	0.00	4.26	R
2542	2558	5.376625	TCAGGTATGCAGTTCAAAGAAGTT	58.623	37.500	0.00	0.00	2.66	R
4195	4239	0.036577	CTTGCTAGCAGGCTGTCACT	60.037	55.000	18.45	7.36	3.41	R
5674	5862	0.322816	GCAGGCCCAATCACTCAAGA	60.323	55.000	0.00	0.00	3.02	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
143	144	6.071616	TGAGAACCTTAATATTTTGCACCACC	60.072	38.462	0.00	0.00	0.00	4.61
200	201	0.177604	CAAGCAGAGGGCCTCTACTG	59.822	60.000	32.12	24.80	46.50	2.74
208	209	1.134037	AGGGCCTCTACTGTCTACTCG	60.134	57.143	0.00	0.00	0.00	4.18
228	229	3.952323	TCGGGAAGAGTATGTAAGAGTGG	59.048	47.826	0.00	0.00	0.00	4.00
232	233	4.442192	GGAAGAGTATGTAAGAGTGGCAGG	60.442	50.000	0.00	0.00	0.00	4.85
311	312	7.653767	AATCGTTAAACAGCCAGCTATATAC	57.346	36.000	0.00	0.00	0.00	1.47
312	313	6.151663	TCGTTAAACAGCCAGCTATATACA	57.848	37.500	0.00	0.00	0.00	2.29
355	356	6.065976	TGTGGAATGTCTACAAATGAGGAT	57.934	37.500	0.00	0.00	34.87	3.24
356	357	6.115446	TGTGGAATGTCTACAAATGAGGATC	58.885	40.000	0.00	0.00	34.87	3.36
359	360	5.762218	GGAATGTCTACAAATGAGGATCCAG	59.238	44.000	15.82	0.00	0.00	3.86
360	361	4.760530	TGTCTACAAATGAGGATCCAGG	57.239	45.455	15.82	0.00	0.00	4.45
361	362	3.455910	TGTCTACAAATGAGGATCCAGGG	59.544	47.826	15.82	0.00	0.00	4.45
362	363	3.711704	GTCTACAAATGAGGATCCAGGGA	59.288	47.826	15.82	0.00	0.00	4.20
363	364	4.164221	GTCTACAAATGAGGATCCAGGGAA	59.836	45.833	15.82	0.00	0.00	3.97
365	366	2.243221	ACAAATGAGGATCCAGGGAAGG	59.757	50.000	15.82	0.00	0.00	3.46
366	367	1.527457	AATGAGGATCCAGGGAAGGG	58.473	55.000	15.82	0.00	0.00	3.95
367	368	0.348370	ATGAGGATCCAGGGAAGGGT	59.652	55.000	15.82	0.00	0.00	4.34
368	369	0.326618	TGAGGATCCAGGGAAGGGTC	60.327	60.000	15.82	0.00	38.11	4.46
370	371	3.231298	GATCCAGGGAAGGGTCCG	58.769	66.667	0.00	0.00	46.04	4.79
371	372	1.382695	GATCCAGGGAAGGGTCCGA	60.383	63.158	0.00	0.00	46.04	4.55
372	373	1.687297	GATCCAGGGAAGGGTCCGAC	61.687	65.000	0.00	0.00	46.04	4.79
373	374	3.400054	CCAGGGAAGGGTCCGACC	61.400	72.222	9.30	9.30	46.04	4.79
374	375	2.606519	CAGGGAAGGGTCCGACCA	60.607	66.667	19.43	0.00	46.04	4.02
375	376	2.606826	AGGGAAGGGTCCGACCAC	60.607	66.667	19.43	8.70	46.04	4.16
376	377	2.606826	GGGAAGGGTCCGACCACT	60.607	66.667	19.43	10.80	46.04	4.00

Showing 1 to 25 of 317 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	1.962807	CCTTTTCAGGTGCACATGGAA	59.037	47.619	29.24	25.23	35.06	3.53
101	102	5.351465	GGTTCTCATAATCGTGAGCAGAAAA	59.649	40.000	0.00	0.00	44.15	2.29
143	144	5.431765	ACTTGTTACCAGATCTATGCAAGG	58.568	41.667	19.41	9.96	37.12	3.61
192	193	3.118334	TCTTCCCGAGTAGACAGTAGAGG	60.118	52.174	0.00	0.00	0.00	3.69
208	209	3.451178	TGCCACTCTTACATACTCTTCCC	59.549	47.826	0.00	0.00	0.00	3.97
228	229	0.326264	ACTGGATTGACTGACCCTGC	59.674	55.000	0.00	0.00	0.00	4.85
232	233	2.234908	AGTAGCACTGGATTGACTGACC	59.765	50.000	0.00	0.00	0.00	4.02
282	283	4.083484	AGCTGGCTGTTTAACGATTAACAC	60.083	41.667	0.00	0.00	0.00	3.32
311	312	6.032094	CACATAAATGCAAAGCTCTAACCTG	58.968	40.000	0.00	0.00	0.00	4.00
312	313	5.126061	CCACATAAATGCAAAGCTCTAACCT	59.874	40.000	0.00	0.00	0.00	3.50
355	356	2.284405	GTCGGACCCTTCCCTGGA	60.284	66.667	0.00	0.00	38.99	3.86
356	357	3.400054	GGTCGGACCCTTCCCTGG	61.400	72.222	16.55	0.00	38.99	4.45
359	360	1.775934	AAAGTGGTCGGACCCTTCCC	61.776	60.000	23.81	7.17	38.99	3.97
360	361	0.605589	CAAAGTGGTCGGACCCTTCC	60.606	60.000	23.81	9.51	37.50	3.46
361	362	0.605589	CCAAAGTGGTCGGACCCTTC	60.606	60.000	23.81	13.97	37.50	3.46
362	363	1.454539	CCAAAGTGGTCGGACCCTT	59.545	57.895	23.81	21.08	37.50	3.95
363	364	2.526046	CCCAAAGTGGTCGGACCCT	61.526	63.158	23.81	16.82	37.50	4.34
365	366	1.302271	GACCCAAAGTGGTCGGACC	60.302	63.158	20.36	20.36	44.98	4.46
366	367	4.373771	GACCCAAAGTGGTCGGAC	57.626	61.111	0.00	0.00	44.98	4.79
371	372	3.131755	GCGTACTATAGACCCAAAGTGGT	59.868	47.826	6.78	0.00	42.79	4.16
372	373	3.131577	TGCGTACTATAGACCCAAAGTGG	59.868	47.826	6.78	0.00	37.25	4.00
373	374	4.360563	CTGCGTACTATAGACCCAAAGTG	58.639	47.826	6.78	0.00	0.00	3.16
374	375	3.181478	GCTGCGTACTATAGACCCAAAGT	60.181	47.826	6.78	0.00	0.00	2.66
375	376	3.381949	GCTGCGTACTATAGACCCAAAG	58.618	50.000	6.78	0.00	0.00	2.77
376	377	2.101917	GGCTGCGTACTATAGACCCAAA	59.898	50.000	6.78	0.00	0.00	3.28

Showing 1 to 25 of 310 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.