AutoCloner

Multiple sequence alignment - TraesCS1B01G211500

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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	TraesCS1B01G211500	chr1B	100.000	2288	0	0	1	2288	385028458	385030745	0.000000e+00	4226
1	TraesCS1B01G211500	chr1B	89.670	1607	141	13	138	1728	192469991	192468394	0.000000e+00	2025
2	TraesCS1B01G211500	chr3A	90.604	1607	134	8	138	1728	418765543	418763938	0.000000e+00	2115
3	TraesCS1B01G211500	chr4D	90.236	1608	138	9	138	1729	421048519	421046915	0.000000e+00	2082
4	TraesCS1B01G211500	chr4D	90.044	1607	137	9	138	1728	116524440	116522841	0.000000e+00	2060
5	TraesCS1B01G211500	chr4D	89.833	1613	136	12	140	1732	493970990	493969386	0.000000e+00	2045
6	TraesCS1B01G211500	chr4D	92.427	581	30	5	138	705	508924828	508925407	0.000000e+00	817
7	TraesCS1B01G211500	chr7D	89.801	1608	147	7	138	1730	432740426	432738821	0.000000e+00	2045
8	TraesCS1B01G211500	chr5A	89.689	1610	145	10	138	1730	604231943	604230338	0.000000e+00	2034
9	TraesCS1B01G211500	chr5A	85.924	341	44	4	1938	2276	433202779	433203117	6.010000e-96	361
10	TraesCS1B01G211500	chr5A	83.706	313	49	2	1938	2249	520149551	520149862	6.180000e-76	294
11	TraesCS1B01G211500	chr5A	93.902	82	5	0	2	83	533981427	533981346	8.580000e-25	124
12	TraesCS1B01G211500	chr2B	89.621	1609	144	12	143	1733	713704617	713703014	0.000000e+00	2025
13	TraesCS1B01G211500	chr2B	89.732	1529	135	8	216	1728	495053922	495055444	0.000000e+00	1934
14	TraesCS1B01G211500	chr2B	85.276	326	42	5	1926	2249	90999801	91000122	4.710000e-87	331
15	TraesCS1B01G211500	chr2B	84.012	344	55	0	1939	2282	542351629	542351972	4.710000e-87	331
16	TraesCS1B01G211500	chr2B	83.714	350	57	0	1939	2288	663916258	663915909	4.710000e-87	331
17	TraesCS1B01G211500	chr2A	89.448	1611	145	13	137	1728	456462400	456460796	0.000000e+00	2010
18	TraesCS1B01G211500	chr2A	84.928	345	51	1	1936	2279	693375564	693375908	4.680000e-92	348
19	TraesCS1B01G211500	chr2A	84.211	342	54	0	1938	2279	597862799	597862458	1.310000e-87	333
20	TraesCS1B01G211500	chr2A	84.118	340	50	4	1938	2276	7309747	7310083	2.190000e-85	326
21	TraesCS1B01G211500	chr4B	89.321	1620	140	19	138	1733	551730224	551731834	0.000000e+00	2002
22	TraesCS1B01G211500	chr4B	89.129	1619	145	17	138	1733	551784832	551786442	0.000000e+00	1986
23	TraesCS1B01G211500	chr6D	89.337	1613	141	18	138	1728	450906076	450907679	0.000000e+00	1997
24	TraesCS1B01G211500	chr7B	89.198	1620	127	19	138	1731	679357757	679359354	0.000000e+00	1978
25	TraesCS1B01G211500	chr5D	87.800	1623	133	26	138	1730	492732680	492731093	0.000000e+00	1840
26	TraesCS1B01G211500	chr6B	90.520	654	44	8	138	775	649827930	649827279	0.000000e+00	848
27	TraesCS1B01G211500	chr6B	84.726	347	47	6	1938	2281	177834482	177834139	2.180000e-90	342
28	TraesCS1B01G211500	chr3D	93.496	369	24	0	141	509	575955936	575955568	1.190000e-152	549
29	TraesCS1B01G211500	chr3D	77.211	294	51	14	1940	2225	41695222	41695507	8.460000e-35	158
30	TraesCS1B01G211500	chr6A	85.965	342	48	0	1938	2279	616904098	616904439	1.290000e-97	366
31	TraesCS1B01G211500	chr6A	84.071	339	53	1	1938	2276	23757231	23757568	2.190000e-85	326
32	TraesCS1B01G211500	chr6A	80.523	344	58	8	1939	2279	533990659	533990322	2.920000e-64	255
33	TraesCS1B01G211500	chr6A	93.671	79	5	0	1829	1907	445267477	445267555	3.990000e-23	119
34	TraesCS1B01G211500	chr4A	85.987	314	40	4	1938	2249	741785895	741786206	1.310000e-87	333
35	TraesCS1B01G211500	chr4A	85.000	320	48	0	1939	2258	693233800	693233481	2.190000e-85	326
36	TraesCS1B01G211500	chr4A	83.824	340	54	1	1939	2278	693294471	693294809	2.840000e-84	322
37	TraesCS1B01G211500	chr2D	84.071	339	52	2	1941	2279	633506052	633506388	2.190000e-85	326
38	TraesCS1B01G211500	chr2D	87.952	249	27	2	1939	2187	112276861	112277106	8.000000e-75	291
39	TraesCS1B01G211500	chr5B	82.997	347	56	2	1937	2281	493588811	493588466	6.140000e-81	311
40	TraesCS1B01G211500	chr5B	83.136	338	56	1	1939	2276	690067364	690067700	7.940000e-80	307
41	TraesCS1B01G211500	chr5B	82.436	353	57	5	1938	2288	17599175	17598826	1.030000e-78	303
42	TraesCS1B01G211500	chr1A	83.596	317	44	7	1938	2249	39615945	39616258	8.000000e-75	291
43	TraesCS1B01G211500	chr1A	78.912	294	56	6	1938	2228	554232246	554232536	6.450000e-46	195

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	TraesCS1B01G211500	chr1B	385028458	385030745	2287	False	4226	4226	100.000	1	2288	1	chr1B.!!$F1	2287
1	TraesCS1B01G211500	chr1B	192468394	192469991	1597	True	2025	2025	89.670	138	1728	1	chr1B.!!$R1	1590
2	TraesCS1B01G211500	chr3A	418763938	418765543	1605	True	2115	2115	90.604	138	1728	1	chr3A.!!$R1	1590
3	TraesCS1B01G211500	chr4D	421046915	421048519	1604	True	2082	2082	90.236	138	1729	1	chr4D.!!$R2	1591
4	TraesCS1B01G211500	chr4D	116522841	116524440	1599	True	2060	2060	90.044	138	1728	1	chr4D.!!$R1	1590
5	TraesCS1B01G211500	chr4D	493969386	493970990	1604	True	2045	2045	89.833	140	1732	1	chr4D.!!$R3	1592
6	TraesCS1B01G211500	chr4D	508924828	508925407	579	False	817	817	92.427	138	705	1	chr4D.!!$F1	567
7	TraesCS1B01G211500	chr7D	432738821	432740426	1605	True	2045	2045	89.801	138	1730	1	chr7D.!!$R1	1592
8	TraesCS1B01G211500	chr5A	604230338	604231943	1605	True	2034	2034	89.689	138	1730	1	chr5A.!!$R2	1592
9	TraesCS1B01G211500	chr2B	713703014	713704617	1603	True	2025	2025	89.621	143	1733	1	chr2B.!!$R2	1590
10	TraesCS1B01G211500	chr2B	495053922	495055444	1522	False	1934	1934	89.732	216	1728	1	chr2B.!!$F2	1512
11	TraesCS1B01G211500	chr2A	456460796	456462400	1604	True	2010	2010	89.448	137	1728	1	chr2A.!!$R1	1591
12	TraesCS1B01G211500	chr4B	551730224	551731834	1610	False	2002	2002	89.321	138	1733	1	chr4B.!!$F1	1595
13	TraesCS1B01G211500	chr4B	551784832	551786442	1610	False	1986	1986	89.129	138	1733	1	chr4B.!!$F2	1595
14	TraesCS1B01G211500	chr6D	450906076	450907679	1603	False	1997	1997	89.337	138	1728	1	chr6D.!!$F1	1590
15	TraesCS1B01G211500	chr7B	679357757	679359354	1597	False	1978	1978	89.198	138	1731	1	chr7B.!!$F1	1593
16	TraesCS1B01G211500	chr5D	492731093	492732680	1587	True	1840	1840	87.800	138	1730	1	chr5D.!!$R1	1592
17	TraesCS1B01G211500	chr6B	649827279	649827930	651	True	848	848	90.520	138	775	1	chr6B.!!$R2	637

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
29	30	0.033503	CCCACCTCGCCCCTTTTAAT	60.034	55.0	0.0	0.0	0.0	1.4	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2011	2086	0.039165	GGCTCCGGACTTTTTGCTTG	60.039	55.0	0.0	0.0	0.0	4.01	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
20	21	2.037144	TCTAATTAGTCCCACCTCGCC	58.963	52.381	12.19	0.00	0.00	5.54
21	22	1.070289	CTAATTAGTCCCACCTCGCCC	59.930	57.143	4.18	0.00	0.00	6.13
22	23	1.632965	AATTAGTCCCACCTCGCCCC	61.633	60.000	0.00	0.00	0.00	5.80
23	24	2.547123	ATTAGTCCCACCTCGCCCCT	62.547	60.000	0.00	0.00	0.00	4.79
24	25	2.758852	TTAGTCCCACCTCGCCCCTT	62.759	60.000	0.00	0.00	0.00	3.95
25	26	2.758852	TAGTCCCACCTCGCCCCTTT	62.759	60.000	0.00	0.00	0.00	3.11
26	27	2.856988	TCCCACCTCGCCCCTTTT	60.857	61.111	0.00	0.00	0.00	2.27
27	28	1.539372	TCCCACCTCGCCCCTTTTA	60.539	57.895	0.00	0.00	0.00	1.52
28	29	1.135068	TCCCACCTCGCCCCTTTTAA	61.135	55.000	0.00	0.00	0.00	1.52
29	30	0.033503	CCCACCTCGCCCCTTTTAAT	60.034	55.000	0.00	0.00	0.00	1.40
30	31	1.618616	CCCACCTCGCCCCTTTTAATT	60.619	52.381	0.00	0.00	0.00	1.40
31	32	2.357361	CCCACCTCGCCCCTTTTAATTA	60.357	50.000	0.00	0.00	0.00	1.40
32	33	3.358118	CCACCTCGCCCCTTTTAATTAA	58.642	45.455	0.00	0.00	0.00	1.40
33	34	3.764972	CCACCTCGCCCCTTTTAATTAAA	59.235	43.478	6.54	6.54	0.00	1.52
34	35	4.404394	CCACCTCGCCCCTTTTAATTAAAT	59.596	41.667	11.33	0.00	0.00	1.40
35	36	5.105106	CCACCTCGCCCCTTTTAATTAAATT	60.105	40.000	11.33	0.00	0.00	1.82
36	37	6.403049	CACCTCGCCCCTTTTAATTAAATTT	58.597	36.000	11.33	0.00	0.00	1.82
37	38	6.533723	CACCTCGCCCCTTTTAATTAAATTTC	59.466	38.462	11.33	0.33	0.00	2.17
38	39	6.211785	ACCTCGCCCCTTTTAATTAAATTTCA	59.788	34.615	11.33	0.00	0.00	2.69
39	40	6.533723	CCTCGCCCCTTTTAATTAAATTTCAC	59.466	38.462	11.33	2.05	0.00	3.18
40	41	6.399743	TCGCCCCTTTTAATTAAATTTCACC	58.600	36.000	11.33	0.00	0.00	4.02
41	42	6.014499	TCGCCCCTTTTAATTAAATTTCACCA	60.014	34.615	11.33	0.00	0.00	4.17
42	43	6.651225	CGCCCCTTTTAATTAAATTTCACCAA	59.349	34.615	11.33	0.00	0.00	3.67
43	44	7.335673	CGCCCCTTTTAATTAAATTTCACCAAT	59.664	33.333	11.33	0.00	0.00	3.16
44	45	9.019656	GCCCCTTTTAATTAAATTTCACCAATT	57.980	29.630	11.33	0.00	36.57	2.32

Showing 1 to 25 of 511 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	2.037144	GGCGAGGTGGGACTAATTAGA	58.963	52.381	19.38	0.00	0.00	2.10
1	2	1.070289	GGGCGAGGTGGGACTAATTAG	59.930	57.143	11.05	11.05	0.00	1.73
2	3	1.125633	GGGCGAGGTGGGACTAATTA	58.874	55.000	0.00	0.00	0.00	1.40
3	4	1.632965	GGGGCGAGGTGGGACTAATT	61.633	60.000	0.00	0.00	0.00	1.40
4	5	2.070650	GGGGCGAGGTGGGACTAAT	61.071	63.158	0.00	0.00	0.00	1.73
5	6	2.686106	GGGGCGAGGTGGGACTAA	60.686	66.667	0.00	0.00	0.00	2.24
6	7	2.758852	AAAGGGGCGAGGTGGGACTA	62.759	60.000	0.00	0.00	0.00	2.59
7	8	4.658786	AAGGGGCGAGGTGGGACT	62.659	66.667	0.00	0.00	0.00	3.85
8	9	1.844544	TAAAAGGGGCGAGGTGGGAC	61.845	60.000	0.00	0.00	0.00	4.46
9	10	1.135068	TTAAAAGGGGCGAGGTGGGA	61.135	55.000	0.00	0.00	0.00	4.37
10	11	0.033503	ATTAAAAGGGGCGAGGTGGG	60.034	55.000	0.00	0.00	0.00	4.61
11	12	1.847328	AATTAAAAGGGGCGAGGTGG	58.153	50.000	0.00	0.00	0.00	4.61
12	13	5.592104	ATTTAATTAAAAGGGGCGAGGTG	57.408	39.130	14.35	0.00	0.00	4.00
13	14	6.211785	TGAAATTTAATTAAAAGGGGCGAGGT	59.788	34.615	14.35	0.00	0.00	3.85
14	15	6.533723	GTGAAATTTAATTAAAAGGGGCGAGG	59.466	38.462	14.35	0.00	0.00	4.63
15	16	6.533723	GGTGAAATTTAATTAAAAGGGGCGAG	59.466	38.462	14.35	0.00	0.00	5.03
16	17	6.014499	TGGTGAAATTTAATTAAAAGGGGCGA	60.014	34.615	14.35	1.47	0.00	5.54
17	18	6.166982	TGGTGAAATTTAATTAAAAGGGGCG	58.833	36.000	14.35	0.00	0.00	6.13
18	19	7.987750	TTGGTGAAATTTAATTAAAAGGGGC	57.012	32.000	14.35	5.87	0.00	5.80
34	35	9.739276	CTCATAGGCCTATATAAATTGGTGAAA	57.261	33.333	25.00	0.00	31.32	2.69
35	36	8.890472	ACTCATAGGCCTATATAAATTGGTGAA	58.110	33.333	25.00	0.00	31.32	3.18
36	37	8.449423	ACTCATAGGCCTATATAAATTGGTGA	57.551	34.615	25.00	14.06	31.32	4.02
37	38	8.950210	CAACTCATAGGCCTATATAAATTGGTG	58.050	37.037	25.00	10.42	31.32	4.17
38	39	8.669571	ACAACTCATAGGCCTATATAAATTGGT	58.330	33.333	25.00	12.48	31.32	3.67
47	48	9.471702	GTAGGTTATACAACTCATAGGCCTATA	57.528	37.037	25.00	8.28	34.88	1.31

Showing 1 to 25 of 517 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.