AutoCloner

Multiple sequence alignment - TraesCS3D01G100800

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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	TraesCS3D01G100800	chr3D	100.000	5286	0	0	1	5286	53462134	53467419	0.000000e+00	9762
1	TraesCS3D01G100800	chr3D	97.041	169	5	0	2688	2856	379483466	379483298	8.660000e-73	285
2	TraesCS3D01G100800	chr3D	97.576	165	4	0	2687	2851	302228235	302228071	3.120000e-72	283
3	TraesCS3D01G100800	chr3A	94.364	2360	107	18	347	2687	64778457	64780809	0.000000e+00	3598
4	TraesCS3D01G100800	chr3A	95.739	1596	55	11	2851	4438	64780811	64782401	0.000000e+00	2558
5	TraesCS3D01G100800	chr3A	93.000	200	11	3	5090	5286	64782925	64783124	6.700000e-74	289
6	TraesCS3D01G100800	chr3A	88.584	219	11	7	4480	4685	64782453	64782670	2.440000e-63	254
7	TraesCS3D01G100800	chr3A	97.468	79	1	1	4438	4516	64782376	64782453	3.320000e-27	134
8	TraesCS3D01G100800	chr3B	92.788	2468	113	19	2850	5286	83883681	83886114	0.000000e+00	3511
9	TraesCS3D01G100800	chr3B	93.747	2159	124	7	539	2689	83881527	83883682	0.000000e+00	3229
10	TraesCS3D01G100800	chr3B	84.180	689	70	18	1120	1798	82453070	82452411	2.690000e-177	632
11	TraesCS3D01G100800	chr3B	83.167	600	71	12	1792	2389	82447174	82446603	6.070000e-144	521
12	TraesCS3D01G100800	chr3B	97.531	81	2	0	7	87	83843580	83843660	7.140000e-29	139
13	TraesCS3D01G100800	chr2D	98.830	171	2	0	2682	2852	351055240	351055410	6.650000e-79	305
14	TraesCS3D01G100800	chr2D	98.214	168	3	0	2688	2855	78903197	78903364	1.440000e-75	294
15	TraesCS3D01G100800	chr2D	97.590	166	4	0	2686	2851	587279416	587279251	8.660000e-73	285
16	TraesCS3D01G100800	chr1D	98.780	164	2	0	2688	2851	396035330	396035493	5.180000e-75	292
17	TraesCS3D01G100800	chr1D	85.475	179	15	5	4516	4685	421882427	421882251	5.440000e-40	176
18	TraesCS3D01G100800	chr7B	97.633	169	4	0	2688	2856	664801022	664800854	1.860000e-74	291
19	TraesCS3D01G100800	chr4D	97.605	167	4	0	2685	2851	293550124	293550290	2.410000e-73	287
20	TraesCS3D01G100800	chrUn	97.590	166	3	1	2687	2852	99637990	99638154	3.120000e-72	283
21	TraesCS3D01G100800	chr1B	86.592	179	13	5	4516	4685	570842207	570842031	2.510000e-43	187
22	TraesCS3D01G100800	chr6A	89.655	145	15	0	207	351	380160061	380160205	9.040000e-43	185
23	TraesCS3D01G100800	chr4A	88.667	150	15	2	207	356	284949735	284949882	1.170000e-41	182
24	TraesCS3D01G100800	chr1A	85.475	179	15	6	4516	4685	517896090	517895914	5.440000e-40	176
25	TraesCS3D01G100800	chr7D	88.194	144	16	1	207	350	199822998	199822856	2.530000e-38	171
26	TraesCS3D01G100800	chr2A	96.610	59	2	0	289	347	760912699	760912757	1.210000e-16	99

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	TraesCS3D01G100800	chr3D	53462134	53467419	5285	False	9762.0	9762	100.0000	1	5286	1	chr3D.!!$F1	5285
1	TraesCS3D01G100800	chr3A	64778457	64783124	4667	False	1366.6	3598	93.8310	347	5286	5	chr3A.!!$F1	4939
2	TraesCS3D01G100800	chr3B	83881527	83886114	4587	False	3370.0	3511	93.2675	539	5286	2	chr3B.!!$F2	4747
3	TraesCS3D01G100800	chr3B	82452411	82453070	659	True	632.0	632	84.1800	1120	1798	1	chr3B.!!$R2	678
4	TraesCS3D01G100800	chr3B	82446603	82447174	571	True	521.0	521	83.1670	1792	2389	1	chr3B.!!$R1	597

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
169	170	0.032952	TAAGGCCGCGCTTGGTATAG	59.967	55.0	5.56	0.0	0.00	1.31	F
421	422	0.036875	CACCTGGTTCTGGGAAGGTC	59.963	60.0	0.00	0.0	41.14	3.85	F
1936	1965	0.539051	AAGACAGAGGCGAAGGATGG	59.461	55.0	0.00	0.0	0.00	3.51	F
2699	2732	0.412640	ACCCTTCTACTCCCTCCGTT	59.587	55.0	0.00	0.0	0.00	4.44	F
3959	4008	0.616111	GCCAGTCCCAGAGAAGAGGA	60.616	60.0	0.00	0.0	0.00	3.71	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1877	1906	0.323725	TCCTCAATCCTGCTTTGGCC	60.324	55.000	0.0	0.0	37.74	5.36	R
2297	2326	0.606096	TGCATTCGAGGAAGACCGAA	59.394	50.000	0.0	0.0	46.72	4.30	R
2907	2941	1.123077	TGGGATCTTGAGGTGGATCG	58.877	55.000	0.0	0.0	39.19	3.69	R
4170	4219	0.323816	CCTCTCTTTCCCTTTGCCCC	60.324	60.000	0.0	0.0	0.00	5.80	R
5041	5146	1.200020	CCTGTCGGCATTTCCAACTTC	59.800	52.381	0.0	0.0	34.01	3.01	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
18	19	2.784547	CAATGATTGGCTCGGCTCA	58.215	52.632	0.00	0.00	0.00	4.26
19	20	1.315690	CAATGATTGGCTCGGCTCAT	58.684	50.000	0.00	0.00	0.00	2.90
20	21	1.679680	CAATGATTGGCTCGGCTCATT	59.320	47.619	0.00	3.23	38.52	2.57
21	22	1.315690	ATGATTGGCTCGGCTCATTG	58.684	50.000	0.00	0.00	0.00	2.82
22	23	1.358046	GATTGGCTCGGCTCATTGC	59.642	57.895	0.00	0.00	41.94	3.56
32	33	3.025866	GCTCATTGCCAAAAGAGCG	57.974	52.632	16.19	0.00	44.48	5.03
33	34	0.242017	GCTCATTGCCAAAAGAGCGT	59.758	50.000	16.19	0.00	44.48	5.07
34	35	1.973138	CTCATTGCCAAAAGAGCGTG	58.027	50.000	0.00	0.00	0.00	5.34
35	36	1.536766	CTCATTGCCAAAAGAGCGTGA	59.463	47.619	0.00	0.00	0.00	4.35
36	37	1.536766	TCATTGCCAAAAGAGCGTGAG	59.463	47.619	0.00	0.00	0.00	3.51
37	38	0.883833	ATTGCCAAAAGAGCGTGAGG	59.116	50.000	0.00	0.00	0.00	3.86
39	40	1.165907	TGCCAAAAGAGCGTGAGGTG	61.166	55.000	0.00	0.00	45.11	4.00
40	41	0.884704	GCCAAAAGAGCGTGAGGTGA	60.885	55.000	0.00	0.00	45.11	4.02
41	42	1.593196	CCAAAAGAGCGTGAGGTGAA	58.407	50.000	0.00	0.00	45.11	3.18
42	43	1.532868	CCAAAAGAGCGTGAGGTGAAG	59.467	52.381	0.00	0.00	45.11	3.02
43	44	1.069636	CAAAAGAGCGTGAGGTGAAGC	60.070	52.381	0.00	0.00	45.11	3.86
44	45	0.946221	AAAGAGCGTGAGGTGAAGCG	60.946	55.000	0.00	0.00	45.11	4.68
45	46	1.806461	AAGAGCGTGAGGTGAAGCGA	61.806	55.000	0.00	0.00	45.11	4.93
46	47	1.803519	GAGCGTGAGGTGAAGCGAG	60.804	63.158	0.00	0.00	45.11	5.03
47	48	3.482783	GCGTGAGGTGAAGCGAGC	61.483	66.667	0.00	0.00	0.00	5.03
48	49	2.811317	CGTGAGGTGAAGCGAGCC	60.811	66.667	0.00	0.00	0.00	4.70
49	50	2.811317	GTGAGGTGAAGCGAGCCG	60.811	66.667	0.00	0.00	0.00	5.52
50	51	2.989253	TGAGGTGAAGCGAGCCGA	60.989	61.111	0.00	0.00	0.00	5.54
51	52	2.261671	GAGGTGAAGCGAGCCGAA	59.738	61.111	0.00	0.00	0.00	4.30
52	53	2.048127	AGGTGAAGCGAGCCGAAC	60.048	61.111	0.00	0.00	0.00	3.95

Showing 1 to 25 of 397 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	1.315690	ATGAGCCGAGCCAATCATTG	58.684	50.000	0.00	0.00	0.00	2.82
1	2	1.679680	CAATGAGCCGAGCCAATCATT	59.320	47.619	6.22	6.22	41.77	2.57
2	3	1.315690	CAATGAGCCGAGCCAATCAT	58.684	50.000	0.00	0.00	33.91	2.45
3	4	1.378882	GCAATGAGCCGAGCCAATCA	61.379	55.000	0.00	0.00	37.23	2.57
4	5	1.358046	GCAATGAGCCGAGCCAATC	59.642	57.895	0.00	0.00	37.23	2.67
5	6	3.518003	GCAATGAGCCGAGCCAAT	58.482	55.556	0.00	0.00	37.23	3.16
15	16	1.536766	TCACGCTCTTTTGGCAATGAG	59.463	47.619	19.79	19.79	37.28	2.90
16	17	1.536766	CTCACGCTCTTTTGGCAATGA	59.463	47.619	0.00	1.91	0.00	2.57
17	18	1.401931	CCTCACGCTCTTTTGGCAATG	60.402	52.381	0.00	0.00	0.00	2.82
18	19	0.883833	CCTCACGCTCTTTTGGCAAT	59.116	50.000	0.00	0.00	0.00	3.56
19	20	0.465460	ACCTCACGCTCTTTTGGCAA	60.465	50.000	0.00	0.00	0.00	4.52
20	21	1.148273	ACCTCACGCTCTTTTGGCA	59.852	52.632	0.00	0.00	0.00	4.92
21	22	0.884704	TCACCTCACGCTCTTTTGGC	60.885	55.000	0.00	0.00	0.00	4.52
22	23	1.532868	CTTCACCTCACGCTCTTTTGG	59.467	52.381	0.00	0.00	0.00	3.28
23	24	1.069636	GCTTCACCTCACGCTCTTTTG	60.070	52.381	0.00	0.00	0.00	2.44
24	25	1.230324	GCTTCACCTCACGCTCTTTT	58.770	50.000	0.00	0.00	0.00	2.27
25	26	0.946221	CGCTTCACCTCACGCTCTTT	60.946	55.000	0.00	0.00	0.00	2.52
26	27	1.373497	CGCTTCACCTCACGCTCTT	60.373	57.895	0.00	0.00	0.00	2.85
27	28	2.206515	CTCGCTTCACCTCACGCTCT	62.207	60.000	0.00	0.00	0.00	4.09
28	29	1.803519	CTCGCTTCACCTCACGCTC	60.804	63.158	0.00	0.00	0.00	5.03
29	30	2.259818	CTCGCTTCACCTCACGCT	59.740	61.111	0.00	0.00	0.00	5.07
30	31	3.482783	GCTCGCTTCACCTCACGC	61.483	66.667	0.00	0.00	0.00	5.34
31	32	2.811317	GGCTCGCTTCACCTCACG	60.811	66.667	0.00	0.00	0.00	4.35
32	33	2.765250	TTCGGCTCGCTTCACCTCAC	62.765	60.000	0.00	0.00	0.00	3.51
33	34	2.570284	TTCGGCTCGCTTCACCTCA	61.570	57.895	0.00	0.00	0.00	3.86

Showing 1 to 25 of 447 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.