AutoCloner

Multiple sequence alignment - TraesCS7D01G324800

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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	TraesCS7D01G324800	chr7D	100.000	3662	0	0	1	3662	414494039	414490378	0.000000e+00	6763
1	TraesCS7D01G324800	chr7D	85.424	590	76	6	1	586	577180895	577181478	4.040000e-169	604
2	TraesCS7D01G324800	chr7A	91.582	1675	89	22	341	1998	476940741	476939102	0.000000e+00	2265
3	TraesCS7D01G324800	chr7A	93.497	815	29	11	2527	3323	476938233	476937425	0.000000e+00	1190
4	TraesCS7D01G324800	chr7A	83.386	319	37	11	2197	2511	476938729	476938423	7.740000e-72	281
5	TraesCS7D01G324800	chr7A	86.310	168	17	3	2021	2188	476939005	476938844	1.040000e-40	178
6	TraesCS7D01G324800	chr7A	86.420	162	19	2	3411	3570	476937338	476937178	1.350000e-39	174
7	TraesCS7D01G324800	chr7B	94.049	773	40	4	1236	2006	428928053	428927285	0.000000e+00	1168
8	TraesCS7D01G324800	chr7B	90.741	648	28	16	2527	3172	428926538	428925921	0.000000e+00	835
9	TraesCS7D01G324800	chr7B	93.011	558	8	8	699	1250	428928606	428928074	0.000000e+00	785
10	TraesCS7D01G324800	chr7B	82.294	497	57	19	2009	2500	428927210	428926740	5.700000e-108	401
11	TraesCS7D01G324800	chr7B	89.286	224	13	9	3349	3563	428922712	428922491	1.680000e-68	270
12	TraesCS7D01G324800	chr7B	84.348	115	8	5	3558	3662	428922126	428922012	1.800000e-18	104
13	TraesCS7D01G324800	chr5D	85.692	643	77	11	1	636	458001155	458000521	0.000000e+00	664
14	TraesCS7D01G324800	chr5D	88.288	555	52	8	1	548	497817668	497817120	0.000000e+00	652
15	TraesCS7D01G324800	chr2D	89.808	520	44	6	1	516	587269652	587269138	0.000000e+00	658
16	TraesCS7D01G324800	chr2D	86.102	590	71	7	1	585	479318648	479318065	3.100000e-175	625
17	TraesCS7D01G324800	chr2D	80.000	185	31	5	3354	3533	566268422	566268239	8.250000e-27	132
18	TraesCS7D01G324800	chr6A	89.205	528	47	6	1	523	115035552	115035030	0.000000e+00	651
19	TraesCS7D01G324800	chr6A	88.065	553	56	8	1	548	444709056	444708509	0.000000e+00	647
20	TraesCS7D01G324800	chr3B	89.251	521	45	7	1	516	182466681	182467195	3.080000e-180	641
21	TraesCS7D01G324800	chr5A	86.102	590	68	8	4	585	615294448	615293865	1.120000e-174	623
22	TraesCS7D01G324800	chr6B	83.158	190	25	5	3364	3549	694255289	694255475	2.260000e-37	167
23	TraesCS7D01G324800	chr6B	80.100	201	34	5	3338	3533	81010772	81010573	1.060000e-30	145
24	TraesCS7D01G324800	chr4B	80.000	235	33	9	3338	3565	101712692	101712919	1.050000e-35	161
25	TraesCS7D01G324800	chr2B	80.203	197	30	7	3379	3570	597000073	596999881	4.930000e-29	139
26	TraesCS7D01G324800	chr2B	78.818	203	35	6	3338	3533	465132922	465133123	2.970000e-26	130
27	TraesCS7D01G324800	chr1B	80.105	191	20	8	3353	3539	667386760	667386584	3.840000e-25	126

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	TraesCS7D01G324800	chr7D	414490378	414494039	3661	True	6763.000000	6763	100.000000	1	3662	1	chr7D.!!$R1	3661
1	TraesCS7D01G324800	chr7D	577180895	577181478	583	False	604.000000	604	85.424000	1	586	1	chr7D.!!$F1	585
2	TraesCS7D01G324800	chr7A	476937178	476940741	3563	True	817.600000	2265	88.239000	341	3570	5	chr7A.!!$R1	3229
3	TraesCS7D01G324800	chr7B	428922012	428928606	6594	True	593.833333	1168	88.954833	699	3662	6	chr7B.!!$R1	2963
4	TraesCS7D01G324800	chr5D	458000521	458001155	634	True	664.000000	664	85.692000	1	636	1	chr5D.!!$R1	635
5	TraesCS7D01G324800	chr5D	497817120	497817668	548	True	652.000000	652	88.288000	1	548	1	chr5D.!!$R2	547
6	TraesCS7D01G324800	chr2D	587269138	587269652	514	True	658.000000	658	89.808000	1	516	1	chr2D.!!$R3	515
7	TraesCS7D01G324800	chr2D	479318065	479318648	583	True	625.000000	625	86.102000	1	585	1	chr2D.!!$R1	584
8	TraesCS7D01G324800	chr6A	115035030	115035552	522	True	651.000000	651	89.205000	1	523	1	chr6A.!!$R1	522
9	TraesCS7D01G324800	chr6A	444708509	444709056	547	True	647.000000	647	88.065000	1	548	1	chr6A.!!$R2	547
10	TraesCS7D01G324800	chr3B	182466681	182467195	514	False	641.000000	641	89.251000	1	516	1	chr3B.!!$F1	515
11	TraesCS7D01G324800	chr5A	615293865	615294448	583	True	623.000000	623	86.102000	4	585	1	chr5A.!!$R1	581

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	Hairpin	End Stability	Orientation
588	606	0.179192	TTCGTATTCGTGTCCGTCCG	60.179	55.0	38.33	4.79	F
1246	1272	0.326332	GTACTGCTAACCCCCTCCCT	60.326	60.0	0.00	4.20	F
2416	2666	0.396811	ACTGAAACCCCTGTTCCGAG	59.603	55.0	32.15	4.63	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2525	2954	0.250467	TCTCAGGAGCTGCCAAACAC	60.250	55.0	0.00	0.00	40.02	3.32	R
2556	2985	0.317269	CCGCTCTGCAACAAACACAG	60.317	55.0	0.00	0.00	0.00	3.66	R
3590	7447	0.320073	CAAACAAGGTGGCTGGCATG	60.320	55.0	7.33	4.37	0.00	4.06	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
39	41	3.141398	GTCAGCACCATCTCAAACTCAA	58.859	45.455	0.00	0.00	0.00	3.02
96	100	4.837972	AGAAGCAACTAGAAAGGATGTCC	58.162	43.478	0.00	0.00	0.00	4.02
200	206	5.824624	GGAGGTGATGACATATTGTGTGATT	59.175	40.000	0.00	0.00	42.36	2.57
384	396	7.711772	AGCTGAAAGAAGATCTGATTGAGTATG	59.288	37.037	0.00	0.00	34.07	2.39
385	397	7.710044	GCTGAAAGAAGATCTGATTGAGTATGA	59.290	37.037	0.00	0.00	34.07	2.15
386	398	9.767228	CTGAAAGAAGATCTGATTGAGTATGAT	57.233	33.333	0.00	0.00	34.07	2.45
404	416	2.983192	TGATCAGTGGGTGGTTAAAGGA	59.017	45.455	0.00	0.00	0.00	3.36
420	432	3.312736	AAGGAGACAACAATGTTGGGT	57.687	42.857	27.15	15.26	40.74	4.51
483	498	2.864343	GCGGCTATTTGAACGTCTGTAT	59.136	45.455	0.00	0.00	0.00	2.29
496	511	2.279741	GTCTGTATCCTTTGCATGCGA	58.720	47.619	14.09	8.74	0.00	5.10
523	538	7.961325	ATTTGATTGTGCGGACTTTAAAAAT	57.039	28.000	8.99	5.69	0.00	1.82
534	551	9.424319	TGCGGACTTTAAAAATATATGCAAAAA	57.576	25.926	0.00	0.00	0.00	1.94
567	585	3.789756	CGCTAATAACGTTGATGTCGTCT	59.210	43.478	11.99	0.00	40.69	4.18
576	594	4.682860	ACGTTGATGTCGTCTTTTCGTATT	59.317	37.500	0.00	0.00	36.85	1.89
586	604	3.058651	GTCTTTTCGTATTCGTGTCCGTC	59.941	47.826	0.00	0.00	38.33	4.79
587	605	1.981254	TTTCGTATTCGTGTCCGTCC	58.019	50.000	0.00	0.00	38.33	4.79
588	606	0.179192	TTCGTATTCGTGTCCGTCCG	60.179	55.000	0.00	0.00	38.33	4.79
589	607	1.135315	CGTATTCGTGTCCGTCCGT	59.865	57.895	0.00	0.00	35.01	4.69
590	608	1.129879	CGTATTCGTGTCCGTCCGTG	61.130	60.000	0.00	0.00	35.01	4.94
592	610	0.959867	TATTCGTGTCCGTCCGTGGA	60.960	55.000	0.00	0.00	35.04	4.02
598	616	2.987547	TCCGTCCGTGGACTGGTC	60.988	66.667	21.18	0.00	42.54	4.02
599	617	2.989824	CCGTCCGTGGACTGGTCT	60.990	66.667	16.51	0.00	42.54	3.85
605	623	0.393077	CCGTGGACTGGTCTTCTGTT	59.607	55.000	0.67	0.00	0.00	3.16
606	624	1.202651	CCGTGGACTGGTCTTCTGTTT	60.203	52.381	0.67	0.00	0.00	2.83
612	630	3.576648	GACTGGTCTTCTGTTTACGGAG	58.423	50.000	0.00	0.00	32.05	4.63

Showing 1 to 25 of 137 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	0.764890	TGGTGCTGACAAAGGTAGCT	59.235	50.000	0.00	0.00	38.25	3.32
96	100	2.089980	CAGAACTCCAAATGCCCTCTG	58.910	52.381	0.00	0.00	0.00	3.35
200	206	3.115554	CTCGACGATCATGTTGTGCATA	58.884	45.455	0.00	0.00	35.74	3.14
384	396	3.263425	TCTCCTTTAACCACCCACTGATC	59.737	47.826	0.00	0.00	0.00	2.92
385	397	3.009143	GTCTCCTTTAACCACCCACTGAT	59.991	47.826	0.00	0.00	0.00	2.90
386	398	2.370849	GTCTCCTTTAACCACCCACTGA	59.629	50.000	0.00	0.00	0.00	3.41
404	416	2.106566	TGCAACCCAACATTGTTGTCT	58.893	42.857	24.01	9.03	42.91	3.41
483	498	3.342719	TCAAATAGTCGCATGCAAAGGA	58.657	40.909	19.57	3.42	0.00	3.36
496	511	6.811253	TTAAAGTCCGCACAATCAAATAGT	57.189	33.333	0.00	0.00	0.00	2.12
534	551	3.181487	ACGTTATTAGCGTACATCCGGTT	60.181	43.478	0.00	0.00	41.06	4.44
545	562	3.789756	AGACGACATCAACGTTATTAGCG	59.210	43.478	0.00	5.50	43.97	4.26
548	565	6.363088	ACGAAAAGACGACATCAACGTTATTA	59.637	34.615	0.00	0.00	43.97	0.98
553	570	2.466846	ACGAAAAGACGACATCAACGT	58.533	42.857	0.00	0.00	46.58	3.99
567	585	2.327568	GGACGGACACGAATACGAAAA	58.672	47.619	2.34	0.00	44.60	2.29
586	604	0.393077	AACAGAAGACCAGTCCACGG	59.607	55.000	0.00	0.00	0.00	4.94
587	605	2.240493	AAACAGAAGACCAGTCCACG	57.760	50.000	0.00	0.00	0.00	4.94
588	606	3.057734	CGTAAACAGAAGACCAGTCCAC	58.942	50.000	0.00	0.00	0.00	4.02
589	607	2.036733	CCGTAAACAGAAGACCAGTCCA	59.963	50.000	0.00	0.00	0.00	4.02
590	608	2.298163	TCCGTAAACAGAAGACCAGTCC	59.702	50.000	0.00	0.00	0.00	3.85
592	610	2.299297	CCTCCGTAAACAGAAGACCAGT	59.701	50.000	0.00	0.00	0.00	4.00
593	611	2.353803	CCCTCCGTAAACAGAAGACCAG	60.354	54.545	0.00	0.00	0.00	4.00
595	613	1.897802	TCCCTCCGTAAACAGAAGACC	59.102	52.381	0.00	0.00	0.00	3.85
596	614	3.522553	CATCCCTCCGTAAACAGAAGAC	58.477	50.000	0.00	0.00	0.00	3.01
597	615	2.500098	CCATCCCTCCGTAAACAGAAGA	59.500	50.000	0.00	0.00	0.00	2.87
598	616	2.420129	CCCATCCCTCCGTAAACAGAAG	60.420	54.545	0.00	0.00	0.00	2.85

Showing 1 to 25 of 148 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.