AutoCloner

Multiple sequence alignment - TraesCS2B01G282100

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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	TraesCS2B01G282100	chr2B	100.000	2588	0	0	1	2588	390805834	390803247	0.000000e+00	4780.0
1	TraesCS2B01G282100	chr2B	97.219	827	23	0	1761	2587	629164726	629165552	0.000000e+00	1400.0
2	TraesCS2B01G282100	chr2B	96.864	829	26	0	1760	2588	87757974	87757146	0.000000e+00	1387.0
3	TraesCS2B01G282100	chr2B	95.349	43	0	2	26	67	390805308	390805349	1.660000e-07	67.6
4	TraesCS2B01G282100	chr2B	93.478	46	1	2	483	527	390805765	390805809	1.660000e-07	67.6
5	TraesCS2B01G282100	chr2D	95.455	1738	41	8	56	1766	322858553	322856827	0.000000e+00	2737.0
6	TraesCS2B01G282100	chr2D	95.349	43	0	2	26	67	322858092	322858133	1.660000e-07	67.6
7	TraesCS2B01G282100	chr2A	94.830	1644	47	6	58	1677	408086917	408088546	0.000000e+00	2531.0
8	TraesCS2B01G282100	chr2A	96.860	828	25	1	1761	2588	89173516	89174342	0.000000e+00	1384.0
9	TraesCS2B01G282100	chr2A	97.297	37	0	1	26	61	408087386	408087350	7.730000e-06	62.1
10	TraesCS2B01G282100	chr7B	97.587	829	19	1	1760	2588	729022806	729023633	0.000000e+00	1419.0
11	TraesCS2B01G282100	chr3B	97.226	829	23	0	1760	2588	161679393	161678565	0.000000e+00	1404.0
12	TraesCS2B01G282100	chr3B	97.105	829	23	1	1760	2588	727124635	727123808	0.000000e+00	1397.0
13	TraesCS2B01G282100	chr3B	96.864	829	26	0	1760	2588	772415379	772414551	0.000000e+00	1387.0
14	TraesCS2B01G282100	chr1B	97.226	829	23	0	1760	2588	92335849	92336677	0.000000e+00	1404.0
15	TraesCS2B01G282100	chr7A	96.743	829	27	0	1760	2588	11062110	11062938	0.000000e+00	1382.0

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	TraesCS2B01G282100	chr2B	390803247	390805834	2587	True	4780	4780	100.000	1	2588	1	chr2B.!!$R2	2587
1	TraesCS2B01G282100	chr2B	629164726	629165552	826	False	1400	1400	97.219	1761	2587	1	chr2B.!!$F1	826
2	TraesCS2B01G282100	chr2B	87757146	87757974	828	True	1387	1387	96.864	1760	2588	1	chr2B.!!$R1	828
3	TraesCS2B01G282100	chr2D	322856827	322858553	1726	True	2737	2737	95.455	56	1766	1	chr2D.!!$R1	1710
4	TraesCS2B01G282100	chr2A	408086917	408088546	1629	False	2531	2531	94.830	58	1677	1	chr2A.!!$F2	1619
5	TraesCS2B01G282100	chr2A	89173516	89174342	826	False	1384	1384	96.860	1761	2588	1	chr2A.!!$F1	827
6	TraesCS2B01G282100	chr7B	729022806	729023633	827	False	1419	1419	97.587	1760	2588	1	chr7B.!!$F1	828
7	TraesCS2B01G282100	chr3B	161678565	161679393	828	True	1404	1404	97.226	1760	2588	1	chr3B.!!$R1	828
8	TraesCS2B01G282100	chr3B	727123808	727124635	827	True	1397	1397	97.105	1760	2588	1	chr3B.!!$R2	828
9	TraesCS2B01G282100	chr3B	772414551	772415379	828	True	1387	1387	96.864	1760	2588	1	chr3B.!!$R3	828
10	TraesCS2B01G282100	chr1B	92335849	92336677	828	False	1404	1404	97.226	1760	2588	1	chr1B.!!$F1	828
11	TraesCS2B01G282100	chr7A	11062110	11062938	828	False	1382	1382	96.743	1760	2588	1	chr7A.!!$F1	828

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
21	22	0.032615	CCACCTGCTCCTACTCCTCT	60.033	60.0	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1702	1733	1.39739	GCCCTGCCCCTTTCATCATG	61.397	60.0	0.0	0.0	0.0	3.07	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
17	18	3.635510	CCCCACCTGCTCCTACTC	58.364	66.667	0.00	0.00	0.00	2.59
18	19	2.066999	CCCCACCTGCTCCTACTCC	61.067	68.421	0.00	0.00	0.00	3.85
19	20	1.002274	CCCACCTGCTCCTACTCCT	59.998	63.158	0.00	0.00	0.00	3.69
20	21	1.045911	CCCACCTGCTCCTACTCCTC	61.046	65.000	0.00	0.00	0.00	3.71
21	22	0.032615	CCACCTGCTCCTACTCCTCT	60.033	60.000	0.00	0.00	0.00	3.69
22	23	1.621072	CCACCTGCTCCTACTCCTCTT	60.621	57.143	0.00	0.00	0.00	2.85
23	24	1.480137	CACCTGCTCCTACTCCTCTTG	59.520	57.143	0.00	0.00	0.00	3.02
24	25	1.118838	CCTGCTCCTACTCCTCTTGG	58.881	60.000	0.00	0.00	0.00	3.61
25	26	1.621072	CCTGCTCCTACTCCTCTTGGT	60.621	57.143	0.00	0.00	34.23	3.67
26	27	1.754226	CTGCTCCTACTCCTCTTGGTC	59.246	57.143	0.00	0.00	34.23	4.02
27	28	1.116308	GCTCCTACTCCTCTTGGTCC	58.884	60.000	0.00	0.00	34.23	4.46
28	29	1.619977	GCTCCTACTCCTCTTGGTCCA	60.620	57.143	0.00	0.00	34.23	4.02
29	30	2.383855	CTCCTACTCCTCTTGGTCCAG	58.616	57.143	0.00	0.00	34.23	3.86
30	31	0.827368	CCTACTCCTCTTGGTCCAGC	59.173	60.000	0.00	0.00	34.23	4.85
31	32	1.561643	CTACTCCTCTTGGTCCAGCA	58.438	55.000	0.00	0.00	34.23	4.41
32	33	1.205893	CTACTCCTCTTGGTCCAGCAC	59.794	57.143	0.00	0.00	34.23	4.40
41	42	2.854522	GGTCCAGCACCATGTACAC	58.145	57.895	0.00	0.00	45.98	2.90
42	43	0.676782	GGTCCAGCACCATGTACACC	60.677	60.000	0.00	0.00	45.98	4.16
43	44	1.019278	GTCCAGCACCATGTACACCG	61.019	60.000	0.00	0.00	0.00	4.94
44	45	2.398554	CCAGCACCATGTACACCGC	61.399	63.158	0.00	0.00	0.00	5.68
45	46	1.375908	CAGCACCATGTACACCGCT	60.376	57.895	0.00	0.61	0.00	5.52
46	47	1.375908	AGCACCATGTACACCGCTG	60.376	57.895	0.00	0.00	0.00	5.18
47	48	1.375396	GCACCATGTACACCGCTGA	60.375	57.895	0.00	0.00	0.00	4.26
48	49	1.635663	GCACCATGTACACCGCTGAC	61.636	60.000	0.00	0.00	0.00	3.51
49	50	0.320334	CACCATGTACACCGCTGACA	60.320	55.000	0.00	0.00	0.00	3.58
50	51	0.320421	ACCATGTACACCGCTGACAC	60.320	55.000	0.00	0.00	0.00	3.67
51	52	1.351430	CCATGTACACCGCTGACACG	61.351	60.000	0.00	0.00	0.00	4.49
52	53	0.666274	CATGTACACCGCTGACACGT	60.666	55.000	0.00	0.00	0.00	4.49
53	54	0.388134	ATGTACACCGCTGACACGTC	60.388	55.000	0.00	0.00	0.00	4.34
54	55	1.731969	GTACACCGCTGACACGTCC	60.732	63.158	0.00	0.00	0.00	4.79
230	231	1.800315	CTACTTCGGTGACACGGCG	60.800	63.158	4.80	4.80	0.00	6.46
367	368	3.399181	GGTGATCACCGAGGGGCA	61.399	66.667	28.52	0.00	42.29	5.36
664	665	2.421424	CCTAGAACAAGTCTGCCATTGC	59.579	50.000	0.00	0.00	37.12	3.56
730	743	3.381949	CCGGTTTTAGGATCAGTCGATC	58.618	50.000	0.00	0.00	46.34	3.69
744	763	1.819288	GTCGATCTGGGAGAGAACACA	59.181	52.381	0.00	0.00	33.12	3.72
958	989	3.319122	ACAACTTGTCATTTCAGCTTCCC	59.681	43.478	0.00	0.00	0.00	3.97
1580	1611	3.060020	GACGCCGACGAATCCCTCA	62.060	63.158	0.00	0.00	43.93	3.86
1589	1620	2.869192	GACGAATCCCTCATTTCTGAGC	59.131	50.000	0.00	0.00	46.39	4.26
1702	1733	1.552226	CATGCATGCATGTTCGGTTC	58.448	50.000	40.30	9.65	46.20	3.62
1796	1827	1.136828	TATTTAGGACTGCCGGCCAT	58.863	50.000	26.77	12.48	39.96	4.40
1956	1987	4.876107	ACCTATGCAATGTCGGTCTTTAAG	59.124	41.667	0.00	0.00	0.00	1.85
1965	1997	7.012421	GCAATGTCGGTCTTTAAGATTCCTAAT	59.988	37.037	0.00	0.00	0.00	1.73
1966	1998	8.893727	CAATGTCGGTCTTTAAGATTCCTAATT	58.106	33.333	0.00	0.00	0.00	1.40
1967	1999	9.462606	AATGTCGGTCTTTAAGATTCCTAATTT	57.537	29.630	0.00	0.00	0.00	1.82
1968	2000	8.857694	TGTCGGTCTTTAAGATTCCTAATTTT	57.142	30.769	0.00	0.00	0.00	1.82
1969	2001	9.292195	TGTCGGTCTTTAAGATTCCTAATTTTT	57.708	29.630	0.00	0.00	0.00	1.94
2229	2263	3.689649	GTGACTTGTTGAACACTGACCTT	59.310	43.478	0.00	0.00	0.00	3.50
2253	2287	2.649742	AGGGATCTTCCTTCACCTGA	57.350	50.000	0.00	0.00	36.57	3.86
2351	2385	1.595382	GGGAGGACGCATGGATTCG	60.595	63.158	0.00	0.00	0.00	3.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.066999	GGAGTAGGAGCAGGTGGGG	61.067	68.421	0.00	0.00	0.00	4.96
1	2	1.002274	AGGAGTAGGAGCAGGTGGG	59.998	63.158	0.00	0.00	0.00	4.61
2	3	0.032615	AGAGGAGTAGGAGCAGGTGG	60.033	60.000	0.00	0.00	0.00	4.61
3	4	1.480137	CAAGAGGAGTAGGAGCAGGTG	59.520	57.143	0.00	0.00	0.00	4.00
4	5	1.621072	CCAAGAGGAGTAGGAGCAGGT	60.621	57.143	0.00	0.00	36.89	4.00
5	6	1.118838	CCAAGAGGAGTAGGAGCAGG	58.881	60.000	0.00	0.00	36.89	4.85
6	7	1.754226	GACCAAGAGGAGTAGGAGCAG	59.246	57.143	0.00	0.00	38.69	4.24
7	8	1.619977	GGACCAAGAGGAGTAGGAGCA	60.620	57.143	0.00	0.00	38.69	4.26
8	9	1.116308	GGACCAAGAGGAGTAGGAGC	58.884	60.000	0.00	0.00	38.69	4.70
9	10	2.383855	CTGGACCAAGAGGAGTAGGAG	58.616	57.143	0.00	0.00	38.69	3.69
10	11	1.619977	GCTGGACCAAGAGGAGTAGGA	60.620	57.143	0.00	0.00	38.69	2.94
11	12	0.827368	GCTGGACCAAGAGGAGTAGG	59.173	60.000	0.00	0.00	38.69	3.18
12	13	1.205893	GTGCTGGACCAAGAGGAGTAG	59.794	57.143	0.00	0.00	38.69	2.57
13	14	1.267121	GTGCTGGACCAAGAGGAGTA	58.733	55.000	0.00	0.00	38.69	2.59
14	15	1.484444	GGTGCTGGACCAAGAGGAGT	61.484	60.000	13.96	0.00	45.34	3.85
15	16	1.298014	GGTGCTGGACCAAGAGGAG	59.702	63.158	13.96	0.00	45.34	3.69
16	17	3.483587	GGTGCTGGACCAAGAGGA	58.516	61.111	13.96	0.00	45.34	3.71
23	24	0.676782	GGTGTACATGGTGCTGGACC	60.677	60.000	11.87	11.87	46.37	4.46
24	25	1.019278	CGGTGTACATGGTGCTGGAC	61.019	60.000	0.00	0.00	0.00	4.02
25	26	1.295101	CGGTGTACATGGTGCTGGA	59.705	57.895	0.00	0.00	0.00	3.86
26	27	2.398554	GCGGTGTACATGGTGCTGG	61.399	63.158	0.00	0.00	0.00	4.85
27	28	1.375908	AGCGGTGTACATGGTGCTG	60.376	57.895	11.64	0.13	0.00	4.41
28	29	1.375908	CAGCGGTGTACATGGTGCT	60.376	57.895	14.61	11.30	0.00	4.40
29	30	1.375396	TCAGCGGTGTACATGGTGC	60.375	57.895	15.22	12.38	0.00	5.01
30	31	0.320334	TGTCAGCGGTGTACATGGTG	60.320	55.000	15.22	18.71	0.00	4.17
31	32	0.320421	GTGTCAGCGGTGTACATGGT	60.320	55.000	15.22	0.00	0.00	3.55
32	33	1.351430	CGTGTCAGCGGTGTACATGG	61.351	60.000	21.43	14.10	0.00	3.66
33	34	0.666274	ACGTGTCAGCGGTGTACATG	60.666	55.000	24.67	24.67	36.44	3.21
34	35	0.388134	GACGTGTCAGCGGTGTACAT	60.388	55.000	15.22	3.78	35.98	2.29
35	36	1.008194	GACGTGTCAGCGGTGTACA	60.008	57.895	15.22	14.14	35.98	2.90
36	37	1.731969	GGACGTGTCAGCGGTGTAC	60.732	63.158	15.22	13.57	35.98	2.90
37	38	1.859427	GAGGACGTGTCAGCGGTGTA	61.859	60.000	15.22	2.24	35.98	2.90
38	39	3.208884	GAGGACGTGTCAGCGGTGT	62.209	63.158	15.22	0.00	35.98	4.16
39	40	2.430921	GAGGACGTGTCAGCGGTG	60.431	66.667	8.67	8.67	35.98	4.94
40	41	4.039357	CGAGGACGTGTCAGCGGT	62.039	66.667	0.00	0.00	35.98	5.68
51	52	4.415332	TTGAGCGACGGCGAGGAC	62.415	66.667	18.90	1.71	46.35	3.85
52	53	4.415332	GTTGAGCGACGGCGAGGA	62.415	66.667	18.90	0.00	46.35	3.71
53	54	4.421479	AGTTGAGCGACGGCGAGG	62.421	66.667	18.90	5.63	46.35	4.63
54	55	2.876645	GAGTTGAGCGACGGCGAG	60.877	66.667	18.90	8.50	46.35	5.03
206	207	0.541063	TGTCACCGAAGTAGCTCCCA	60.541	55.000	0.00	0.00	0.00	4.37
230	231	1.030488	TCAGGAGGTCGTCGATCACC	61.030	60.000	13.50	13.50	0.00	4.02
367	368	3.066198	GGGTGCTCCCGTTGTACT	58.934	61.111	8.37	0.00	44.74	2.73
467	468	4.673298	CACAGCACGTGCCCGGTA	62.673	66.667	35.51	0.00	43.38	4.02
480	481	4.135153	CTCGGCCGTCCTCCACAG	62.135	72.222	27.15	8.60	0.00	3.66
604	605	1.303561	GACATGTTCCTGCTGCCCA	60.304	57.895	0.00	0.00	0.00	5.36
637	638	4.041567	TGGCAGACTTGTTCTAGGAATCAA	59.958	41.667	0.00	0.00	31.12	2.57
664	665	0.462047	GTGGGAGATACAAGTGGCGG	60.462	60.000	0.00	0.00	0.00	6.13
696	709	0.601841	AAACCGGCAAGACCAGTACG	60.602	55.000	0.00	0.00	39.03	3.67
705	718	2.678336	GACTGATCCTAAAACCGGCAAG	59.322	50.000	0.00	0.00	0.00	4.01
730	743	1.081892	CGCATTGTGTTCTCTCCCAG	58.918	55.000	0.00	0.00	0.00	4.45
744	763	0.953471	TGAAAGCTACGCACCGCATT	60.953	50.000	0.00	0.00	0.00	3.56
1341	1372	2.099831	GTGCTCCCGTCGTACTCG	59.900	66.667	0.00	0.00	38.55	4.18
1379	1410	2.196382	CTCCTTCTTGGACGCGTCGA	62.196	60.000	30.99	26.08	40.56	4.20
1589	1620	5.277154	CGTCCATTAGTATTTTTAGCGTGGG	60.277	44.000	0.00	0.00	0.00	4.61
1702	1733	1.397390	GCCCTGCCCCTTTCATCATG	61.397	60.000	0.00	0.00	0.00	3.07
1968	2000	5.107683	CGCGTCAATAATTCCTTTGCAAAAA	60.108	36.000	13.84	6.04	0.00	1.94
1969	2001	4.384247	CGCGTCAATAATTCCTTTGCAAAA	59.616	37.500	13.84	0.00	0.00	2.44
2009	2043	2.044793	TTGGTTGTCCTCATCTCCCT	57.955	50.000	0.00	0.00	34.23	4.20
2205	2239	3.006940	GTCAGTGTTCAACAAGTCACCA	58.993	45.455	0.00	0.00	0.00	4.17
2253	2287	3.013921	CACACCCGCCATAATACTTTGT	58.986	45.455	0.00	0.00	0.00	2.83
2351	2385	6.710611	ACAATTTTACGGTTTGCACAATTTC	58.289	32.000	0.00	0.00	0.00	2.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.