AutoCloner

Multiple sequence alignment - TraesCS2B01G130800

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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	TraesCS2B01G130800	chr2B	100.000	2306	0	0	1	2306	97952576	97950271	0.000000e+00	4259.0
1	TraesCS2B01G130800	chr2B	97.596	915	19	2	422	1333	790271129	790272043	0.000000e+00	1565.0
2	TraesCS2B01G130800	chr2B	97.590	913	20	1	422	1332	781200325	781199413	0.000000e+00	1563.0
3	TraesCS2B01G130800	chr2D	97.590	913	20	2	422	1332	60591029	60590117	0.000000e+00	1563.0
4	TraesCS2B01G130800	chr2D	96.436	477	14	2	1831	2306	62401420	62400946	0.000000e+00	784.0
5	TraesCS2B01G130800	chr2D	87.223	587	52	15	1592	2156	473089527	473090112	0.000000e+00	647.0
6	TraesCS2B01G130800	chr2D	85.167	209	19	5	1332	1540	473088597	473088793	1.080000e-48	204.0
7	TraesCS2B01G130800	chr2D	93.701	127	7	1	2181	2306	473090096	473090222	3.020000e-44	189.0
8	TraesCS2B01G130800	chr2D	100.000	34	0	0	234	267	62401511	62401478	1.910000e-06	63.9
9	TraesCS2B01G130800	chr3A	97.146	911	24	2	422	1330	652644810	652645720	0.000000e+00	1537.0
10	TraesCS2B01G130800	chr3A	94.286	105	3	2	135	236	600913797	600913901	8.530000e-35	158.0
11	TraesCS2B01G130800	chr7D	97.348	905	19	4	430	1332	77417275	77418176	0.000000e+00	1533.0
12	TraesCS2B01G130800	chr1B	96.831	915	26	2	422	1334	679360574	679359661	0.000000e+00	1526.0
13	TraesCS2B01G130800	chr1B	96.076	892	27	5	422	1311	596256685	596257570	0.000000e+00	1447.0
14	TraesCS2B01G130800	chr3B	96.718	914	27	2	422	1332	133436244	133437157	0.000000e+00	1519.0
15	TraesCS2B01G130800	chr3B	97.561	123	3	0	113	235	75980663	75980785	6.450000e-51	211.0
16	TraesCS2B01G130800	chr3B	93.056	72	5	0	24	95	75980534	75980605	3.130000e-19	106.0
17	TraesCS2B01G130800	chrUn	95.724	912	36	2	422	1331	11115513	11116423	0.000000e+00	1465.0
18	TraesCS2B01G130800	chr2A	97.276	771	15	4	1538	2306	63357712	63356946	0.000000e+00	1303.0
19	TraesCS2B01G130800	chr2A	97.608	209	5	0	1332	1540	63358724	63358516	2.180000e-95	359.0
20	TraesCS2B01G130800	chr2A	86.813	273	30	5	1886	2156	614574402	614574670	1.340000e-77	300.0
21	TraesCS2B01G130800	chr2A	94.059	101	5	1	234	333	63359269	63359169	3.970000e-33	152.0
22	TraesCS2B01G130800	chr6D	94.697	132	5	1	103	234	467538020	467538149	1.080000e-48	204.0
23	TraesCS2B01G130800	chr4B	93.636	110	5	1	113	222	424721165	424721272	1.830000e-36	163.0
24	TraesCS2B01G130800	chr7A	93.056	72	5	0	24	95	360083358	360083287	3.130000e-19	106.0
25	TraesCS2B01G130800	chr6A	93.333	45	2	1	1943	1987	609026027	609026070	5.320000e-07	65.8

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	TraesCS2B01G130800	chr2B	97950271	97952576	2305	True	4259.000000	4259	100.000000	1	2306	1	chr2B.!!$R1	2305
1	TraesCS2B01G130800	chr2B	790271129	790272043	914	False	1565.000000	1565	97.596000	422	1333	1	chr2B.!!$F1	911
2	TraesCS2B01G130800	chr2B	781199413	781200325	912	True	1563.000000	1563	97.590000	422	1332	1	chr2B.!!$R2	910
3	TraesCS2B01G130800	chr2D	60590117	60591029	912	True	1563.000000	1563	97.590000	422	1332	1	chr2D.!!$R1	910
4	TraesCS2B01G130800	chr2D	62400946	62401511	565	True	423.950000	784	98.218000	234	2306	2	chr2D.!!$R2	2072
5	TraesCS2B01G130800	chr2D	473088597	473090222	1625	False	346.666667	647	88.697000	1332	2306	3	chr2D.!!$F1	974
6	TraesCS2B01G130800	chr3A	652644810	652645720	910	False	1537.000000	1537	97.146000	422	1330	1	chr3A.!!$F2	908
7	TraesCS2B01G130800	chr7D	77417275	77418176	901	False	1533.000000	1533	97.348000	430	1332	1	chr7D.!!$F1	902
8	TraesCS2B01G130800	chr1B	679359661	679360574	913	True	1526.000000	1526	96.831000	422	1334	1	chr1B.!!$R1	912
9	TraesCS2B01G130800	chr1B	596256685	596257570	885	False	1447.000000	1447	96.076000	422	1311	1	chr1B.!!$F1	889
10	TraesCS2B01G130800	chr3B	133436244	133437157	913	False	1519.000000	1519	96.718000	422	1332	1	chr3B.!!$F1	910
11	TraesCS2B01G130800	chrUn	11115513	11116423	910	False	1465.000000	1465	95.724000	422	1331	1	chrUn.!!$F1	909
12	TraesCS2B01G130800	chr2A	63356946	63359269	2323	True	604.666667	1303	96.314333	234	2306	3	chr2A.!!$R1	2072

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	0.107945	GTGCCCCTGTTTTTGTGCAA	60.108	50.0	0.0	0.0	0.0	4.08	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1477	3537	0.033504	GTCGAGGGCACTTCAGTTGA	59.966	55.0	0.0	0.0	0.0	3.18	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
24	25	5.473796	TTTAATTAGGTTAAGCGCTTCCG	57.526	39.130	28.82	0.00	33.99	4.30
25	26	2.973694	ATTAGGTTAAGCGCTTCCGA	57.026	45.000	28.82	16.22	36.29	4.55
26	27	2.973694	TTAGGTTAAGCGCTTCCGAT	57.026	45.000	28.82	14.11	36.29	4.18
27	28	4.595762	ATTAGGTTAAGCGCTTCCGATA	57.404	40.909	28.82	13.05	36.29	2.92
28	29	2.973694	AGGTTAAGCGCTTCCGATAA	57.026	45.000	28.82	12.44	36.29	1.75
29	30	3.255969	AGGTTAAGCGCTTCCGATAAA	57.744	42.857	28.82	11.62	36.29	1.40
30	31	3.805207	AGGTTAAGCGCTTCCGATAAAT	58.195	40.909	28.82	0.87	36.29	1.40
31	32	4.196971	AGGTTAAGCGCTTCCGATAAATT	58.803	39.130	28.82	0.00	36.29	1.82
32	33	4.035208	AGGTTAAGCGCTTCCGATAAATTG	59.965	41.667	28.82	0.00	36.29	2.32
33	34	4.201881	GGTTAAGCGCTTCCGATAAATTGT	60.202	41.667	28.82	0.00	36.29	2.71
34	35	3.405170	AAGCGCTTCCGATAAATTGTG	57.595	42.857	18.98	0.00	36.29	3.33
35	36	2.356135	AGCGCTTCCGATAAATTGTGT	58.644	42.857	2.64	0.00	36.29	3.72
36	37	2.747446	AGCGCTTCCGATAAATTGTGTT	59.253	40.909	2.64	0.00	36.29	3.32
37	38	3.936453	AGCGCTTCCGATAAATTGTGTTA	59.064	39.130	2.64	0.00	36.29	2.41
38	39	4.574828	AGCGCTTCCGATAAATTGTGTTAT	59.425	37.500	2.64	0.00	36.29	1.89
39	40	4.904154	GCGCTTCCGATAAATTGTGTTATC	59.096	41.667	0.00	0.00	37.20	1.75
40	41	5.277345	GCGCTTCCGATAAATTGTGTTATCT	60.277	40.000	0.00	0.00	38.03	1.98
41	42	6.715464	CGCTTCCGATAAATTGTGTTATCTT	58.285	36.000	4.06	0.00	38.03	2.40
42	43	6.846283	CGCTTCCGATAAATTGTGTTATCTTC	59.154	38.462	4.06	0.00	38.03	2.87
43	44	7.465379	CGCTTCCGATAAATTGTGTTATCTTCA	60.465	37.037	4.06	0.00	38.03	3.02
44	45	8.181573	GCTTCCGATAAATTGTGTTATCTTCAA	58.818	33.333	4.06	0.00	38.03	2.69
45	46	9.708222	CTTCCGATAAATTGTGTTATCTTCAAG	57.292	33.333	4.06	0.00	38.03	3.02
46	47	8.208718	TCCGATAAATTGTGTTATCTTCAAGG	57.791	34.615	4.06	0.00	38.03	3.61
47	48	8.044309	TCCGATAAATTGTGTTATCTTCAAGGA	58.956	33.333	4.06	0.93	38.03	3.36
48	49	8.338259	CCGATAAATTGTGTTATCTTCAAGGAG	58.662	37.037	4.06	0.00	38.03	3.69

Showing 1 to 25 of 251 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	6.149142	TCGGAAGCGCTTAACCTAATTAAAAA	59.851	34.615	25.11	0.00	32.26	1.94
1	2	5.642919	TCGGAAGCGCTTAACCTAATTAAAA	59.357	36.000	25.11	0.00	32.26	1.52
2	3	5.177326	TCGGAAGCGCTTAACCTAATTAAA	58.823	37.500	25.11	0.00	32.26	1.52
3	4	4.757594	TCGGAAGCGCTTAACCTAATTAA	58.242	39.130	25.11	0.00	0.00	1.40
4	5	4.389890	TCGGAAGCGCTTAACCTAATTA	57.610	40.909	25.11	1.63	0.00	1.40
5	6	3.255969	TCGGAAGCGCTTAACCTAATT	57.744	42.857	25.11	0.00	0.00	1.40
6	7	2.973694	TCGGAAGCGCTTAACCTAAT	57.026	45.000	25.11	0.00	0.00	1.73
7	8	2.973694	ATCGGAAGCGCTTAACCTAA	57.026	45.000	25.11	11.91	0.00	2.69
8	9	4.389890	TTTATCGGAAGCGCTTAACCTA	57.610	40.909	25.11	13.57	0.00	3.08
9	10	2.973694	TTATCGGAAGCGCTTAACCT	57.026	45.000	25.11	11.11	0.00	3.50
10	11	4.201881	ACAATTTATCGGAAGCGCTTAACC	60.202	41.667	25.11	19.87	0.00	2.85
11	12	4.728608	CACAATTTATCGGAAGCGCTTAAC	59.271	41.667	25.11	17.93	0.00	2.01
12	13	4.393680	ACACAATTTATCGGAAGCGCTTAA	59.606	37.500	25.11	13.15	0.00	1.85
13	14	3.936453	ACACAATTTATCGGAAGCGCTTA	59.064	39.130	25.11	8.33	0.00	3.09
14	15	2.747446	ACACAATTTATCGGAAGCGCTT	59.253	40.909	25.35	25.35	0.00	4.68
15	16	2.356135	ACACAATTTATCGGAAGCGCT	58.644	42.857	2.64	2.64	0.00	5.92
16	17	2.825086	ACACAATTTATCGGAAGCGC	57.175	45.000	0.00	0.00	0.00	5.92
17	18	6.287107	AGATAACACAATTTATCGGAAGCG	57.713	37.500	0.00	0.00	41.53	4.68
18	19	7.693952	TGAAGATAACACAATTTATCGGAAGC	58.306	34.615	0.00	0.00	41.53	3.86
19	20	9.708222	CTTGAAGATAACACAATTTATCGGAAG	57.292	33.333	0.00	0.00	41.53	3.46
20	21	8.673711	CCTTGAAGATAACACAATTTATCGGAA	58.326	33.333	0.00	0.00	41.53	4.30
21	22	8.044309	TCCTTGAAGATAACACAATTTATCGGA	58.956	33.333	0.00	0.00	41.53	4.55
22	23	8.208718	TCCTTGAAGATAACACAATTTATCGG	57.791	34.615	0.00	0.00	41.53	4.18
23	24	9.098355	TCTCCTTGAAGATAACACAATTTATCG	57.902	33.333	0.00	0.00	41.53	2.92
41	42	9.174166	GCCAAGTAAACTATTTAATCTCCTTGA	57.826	33.333	0.00	0.00	31.31	3.02

Showing 1 to 25 of 263 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.