AutoCloner

Multiple sequence alignment - TraesCS7D01G083100

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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	TraesCS7D01G083100	chr7D	100.000	5321	0	0	1	5321	49877061	49871741	0.000000e+00	9827.0
1	TraesCS7D01G083100	chr7D	92.308	455	29	2	1	449	463977224	463976770	4.490000e-180	641.0
2	TraesCS7D01G083100	chr4A	94.477	4545	182	34	786	5271	664481567	664477033	0.000000e+00	6938.0
3	TraesCS7D01G083100	chr4A	98.182	55	0	1	5268	5321	664453622	664453568	1.580000e-15	95.3
4	TraesCS7D01G083100	chr4A	100.000	43	0	0	789	831	704149954	704149912	4.420000e-11	80.5
5	TraesCS7D01G083100	chr7A	95.707	4239	150	16	786	5006	52965669	52961445	0.000000e+00	6791.0
6	TraesCS7D01G083100	chr7A	94.737	209	11	0	5005	5213	52961405	52961197	5.140000e-85	326.0
7	TraesCS7D01G083100	chr7A	92.035	113	5	3	5211	5321	52960950	52960840	7.140000e-34	156.0
8	TraesCS7D01G083100	chr7A	80.208	96	18	1	628	723	231588069	231587975	2.660000e-08	71.3
9	TraesCS7D01G083100	chr5D	94.855	447	22	1	1	447	60521933	60522378	0.000000e+00	697.0
10	TraesCS7D01G083100	chr6D	93.274	446	28	1	1	446	448956913	448957356	0.000000e+00	656.0
11	TraesCS7D01G083100	chr6D	92.601	446	32	1	1	446	80673306	80673750	1.620000e-179	640.0
12	TraesCS7D01G083100	chr4D	92.494	453	33	1	1	452	496005981	496005529	0.000000e+00	647.0
13	TraesCS7D01G083100	chr3B	92.222	450	33	2	1	450	141753561	141753114	2.090000e-178	636.0
14	TraesCS7D01G083100	chr3B	97.674	43	1	0	789	831	72720897	72720855	2.060000e-09	75.0
15	TraesCS7D01G083100	chr3D	92.088	455	28	4	1	449	448311135	448311587	7.520000e-178	634.0
16	TraesCS7D01G083100	chr7B	92.000	450	35	1	1	450	415416775	415416327	9.730000e-177	630.0
17	TraesCS7D01G083100	chr5A	92.018	451	31	3	1	449	607299455	607299008	3.500000e-176	628.0
18	TraesCS7D01G083100	chr5A	80.800	125	14	8	5103	5226	210535690	210535575	7.340000e-14	89.8
19	TraesCS7D01G083100	chr5A	81.319	91	14	3	633	721	41357976	41357887	2.660000e-08	71.3
20	TraesCS7D01G083100	chr2B	82.090	134	11	9	5110	5241	588520410	588520288	9.430000e-18	102.0
21	TraesCS7D01G083100	chr2B	100.000	43	0	0	789	831	632254786	632254828	4.420000e-11	80.5
22	TraesCS7D01G083100	chr1A	81.890	127	11	6	5102	5226	293712672	293712556	4.390000e-16	97.1
23	TraesCS7D01G083100	chr1D	81.102	127	12	6	5102	5226	226450037	226449921	2.040000e-14	91.6
24	TraesCS7D01G083100	chr4B	100.000	43	0	0	789	831	16879330	16879288	4.420000e-11	80.5
25	TraesCS7D01G083100	chr2D	100.000	43	0	0	789	831	24574781	24574823	4.420000e-11	80.5
26	TraesCS7D01G083100	chr2D	97.727	44	1	0	788	831	593363728	593363771	5.710000e-10	76.8
27	TraesCS7D01G083100	chr5B	97.674	43	1	0	789	831	120303639	120303681	2.060000e-09	75.0
28	TraesCS7D01G083100	chr5B	82.667	75	8	2	589	663	146280127	146280196	1.600000e-05	62.1
29	TraesCS7D01G083100	chr6A	84.416	77	9	3	5148	5224	511613191	511613118	7.390000e-09	73.1
30	TraesCS7D01G083100	chr3A	79.817	109	14	7	5109	5213	649031828	649031724	7.390000e-09	73.1
31	TraesCS7D01G083100	chr3A	79.412	102	19	2	5125	5224	698838277	698838378	2.660000e-08	71.3
32	TraesCS7D01G083100	chr1B	94.737	38	1	1	5249	5285	503354234	503354271	2.070000e-04	58.4

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	TraesCS7D01G083100	chr7D	49871741	49877061	5320	True	9827.000000	9827	100.000000	1	5321	1	chr7D.!!$R1	5320
1	TraesCS7D01G083100	chr4A	664477033	664481567	4534	True	6938.000000	6938	94.477000	786	5271	1	chr4A.!!$R2	4485
2	TraesCS7D01G083100	chr7A	52960840	52965669	4829	True	2424.333333	6791	94.159667	786	5321	3	chr7A.!!$R2	4535

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
118	119	0.034896	TTCGTCCCTGGAAGAACTGC	59.965	55.0	10.01	0.00	37.61	4.40	F
196	197	0.036010	ATCCAGTCCAGAAACGCCAG	60.036	55.0	0.00	0.00	0.00	4.85	F
328	329	0.037139	TAGCTGGCTCGGCGTTTTAA	60.037	50.0	6.85	0.00	41.21	1.52	F
558	559	0.098200	GAGGAATAAACAACGCCGGC	59.902	55.0	19.07	19.07	0.00	6.13	F
1857	1882	0.106318	ATGGGAAGGCAAGGCAGATC	60.106	55.0	0.00	0.00	0.00	2.75	F
2413	2438	0.829333	GCTGCAGGGAATGAGAGAGA	59.171	55.0	17.12	0.00	0.00	3.10	F
3586	3611	1.093972	TGATGGGCTTTGCACGTATG	58.906	50.0	0.00	0.00	32.76	2.39	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1437	1462	1.002430	TGATATGATGCTTCCCGGCTC	59.998	52.381	0.00	0.00	0.00	4.70	R
1454	1479	1.267574	ATCTGCCACCACCTCGTGAT	61.268	55.000	0.00	0.00	35.23	3.06	R
1689	1714	1.342174	GTCTCCGTAGTGTGGTGGAAA	59.658	52.381	0.00	0.00	0.00	3.13	R
2414	2439	1.173913	GGCCAATGGAGTACAACCAC	58.826	55.000	2.05	2.53	40.36	4.16	R
3586	3611	2.444351	GCACTCGCATAATGCTGAAAC	58.556	47.619	0.00	0.00	42.25	2.78	R
3961	3986	1.278985	TGAAGGCTCACATCCATCGTT	59.721	47.619	0.00	0.00	0.00	3.85	R
5000	5031	0.401738	CCAAGAGAAACCTGGGCTCA	59.598	55.000	13.50	0.00	0.00	4.26	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
18	19	2.772739	CTCAAGCAACTCGGGGATG	58.227	57.895	0.00	0.00	0.00	3.51
19	20	1.372087	CTCAAGCAACTCGGGGATGC	61.372	60.000	1.29	1.29	40.34	3.91
21	22	2.586792	AGCAACTCGGGGATGCTC	59.413	61.111	6.83	0.00	46.98	4.26
22	23	2.514824	GCAACTCGGGGATGCTCC	60.515	66.667	2.48	0.00	37.12	4.70
30	31	3.059287	GGGGATGCTCCGATCTACT	57.941	57.895	0.00	0.00	37.43	2.57
31	32	0.892063	GGGGATGCTCCGATCTACTC	59.108	60.000	0.00	0.00	37.43	2.59
33	34	1.240256	GGATGCTCCGATCTACTCGT	58.760	55.000	0.00	0.00	46.18	4.18
34	35	1.609555	GGATGCTCCGATCTACTCGTT	59.390	52.381	0.00	0.00	46.18	3.85
35	36	2.034812	GGATGCTCCGATCTACTCGTTT	59.965	50.000	0.00	0.00	46.18	3.60
36	37	3.491104	GGATGCTCCGATCTACTCGTTTT	60.491	47.826	0.00	0.00	46.18	2.43
37	38	2.876091	TGCTCCGATCTACTCGTTTTG	58.124	47.619	0.00	0.00	46.18	2.44
38	39	2.490509	TGCTCCGATCTACTCGTTTTGA	59.509	45.455	0.00	0.00	46.18	2.69
39	40	3.130516	TGCTCCGATCTACTCGTTTTGAT	59.869	43.478	0.00	0.00	46.18	2.57
40	41	3.487574	GCTCCGATCTACTCGTTTTGATG	59.512	47.826	0.00	0.00	46.18	3.07
41	42	4.733815	GCTCCGATCTACTCGTTTTGATGA	60.734	45.833	0.00	0.00	46.18	2.92
42	43	5.515797	TCCGATCTACTCGTTTTGATGAT	57.484	39.130	0.00	0.00	46.18	2.45
43	44	5.520632	TCCGATCTACTCGTTTTGATGATC	58.479	41.667	0.00	0.00	46.18	2.92
44	45	5.067283	TCCGATCTACTCGTTTTGATGATCA	59.933	40.000	0.00	0.00	46.18	2.92
45	46	5.748630	CCGATCTACTCGTTTTGATGATCAA	59.251	40.000	3.29	3.29	46.18	2.57
46	47	6.255670	CCGATCTACTCGTTTTGATGATCAAA	59.744	38.462	16.04	16.04	46.18	2.69
47	48	7.201522	CCGATCTACTCGTTTTGATGATCAAAA	60.202	37.037	24.82	24.82	46.20	2.44
60	61	8.687292	TTGATGATCAAAATAGAAGATCTGGG	57.313	34.615	5.21	0.00	39.07	4.45
61	62	7.229308	TGATGATCAAAATAGAAGATCTGGGG	58.771	38.462	0.00	0.00	39.07	4.96
62	63	5.945310	TGATCAAAATAGAAGATCTGGGGG	58.055	41.667	0.00	0.00	39.07	5.40
63	64	5.671735	TGATCAAAATAGAAGATCTGGGGGA	59.328	40.000	0.00	0.00	39.07	4.81

Showing 1 to 25 of 523 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	1.372087	GCATCCCCGAGTTGCTTGAG	61.372	60.000	0.00	0.00	38.05	3.02
19	20	8.155352	TTGATCATCAAAACGAGTAGATCGGAG	61.155	40.741	0.00	0.00	43.83	4.63
20	21	6.405397	TTGATCATCAAAACGAGTAGATCGGA	60.405	38.462	0.00	0.00	43.83	4.55
21	22	5.748630	TTGATCATCAAAACGAGTAGATCGG	59.251	40.000	0.00	0.00	43.83	4.18
22	23	6.812481	TTGATCATCAAAACGAGTAGATCG	57.188	37.500	0.00	0.00	44.51	3.69
34	35	9.128404	CCCAGATCTTCTATTTTGATCATCAAA	57.872	33.333	8.85	8.85	43.84	2.69
35	36	7.722728	CCCCAGATCTTCTATTTTGATCATCAA	59.277	37.037	0.00	0.00	39.07	2.57
36	37	7.229308	CCCCAGATCTTCTATTTTGATCATCA	58.771	38.462	0.00	0.00	39.07	3.07
37	38	6.658391	CCCCCAGATCTTCTATTTTGATCATC	59.342	42.308	0.00	0.00	39.07	2.92
38	39	6.333702	TCCCCCAGATCTTCTATTTTGATCAT	59.666	38.462	0.00	0.00	39.07	2.45
39	40	5.671735	TCCCCCAGATCTTCTATTTTGATCA	59.328	40.000	0.00	0.00	39.07	2.92
40	41	6.043706	TCTCCCCCAGATCTTCTATTTTGATC	59.956	42.308	0.00	0.00	37.46	2.92
41	42	5.913534	TCTCCCCCAGATCTTCTATTTTGAT	59.086	40.000	0.00	0.00	0.00	2.57
42	43	5.288687	TCTCCCCCAGATCTTCTATTTTGA	58.711	41.667	0.00	0.00	0.00	2.69
43	44	5.636903	TCTCCCCCAGATCTTCTATTTTG	57.363	43.478	0.00	0.00	0.00	2.44
44	45	6.855375	AATCTCCCCCAGATCTTCTATTTT	57.145	37.500	0.00	0.00	41.47	1.82
45	46	6.411320	CCAAATCTCCCCCAGATCTTCTATTT	60.411	42.308	0.00	0.00	41.47	1.40
46	47	5.074239	CCAAATCTCCCCCAGATCTTCTATT	59.926	44.000	0.00	0.00	41.47	1.73
47	48	4.600983	CCAAATCTCCCCCAGATCTTCTAT	59.399	45.833	0.00	0.00	41.47	1.98
48	49	3.976654	CCAAATCTCCCCCAGATCTTCTA	59.023	47.826	0.00	0.00	41.47	2.10
49	50	2.782341	CCAAATCTCCCCCAGATCTTCT	59.218	50.000	0.00	0.00	41.47	2.85
50	51	2.511637	ACCAAATCTCCCCCAGATCTTC	59.488	50.000	0.00	0.00	41.47	2.87
51	52	2.243221	CACCAAATCTCCCCCAGATCTT	59.757	50.000	0.00	0.00	41.47	2.40
52	53	1.849039	CACCAAATCTCCCCCAGATCT	59.151	52.381	0.00	0.00	41.47	2.75
53	54	1.846439	TCACCAAATCTCCCCCAGATC	59.154	52.381	0.00	0.00	41.47	2.75

Showing 1 to 25 of 510 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.