AutoCloner

Multiple sequence alignment - TraesCS7D01G109300

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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	TraesCS7D01G109300	chr7D	100.000	2312	0	0	1	2312	65760945	65763256	0.000000e+00	4270
1	TraesCS7D01G109300	chr7D	89.100	633	58	9	1	625	397552655	397552026	0.000000e+00	776
2	TraesCS7D01G109300	chr7D	96.296	216	5	1	2100	2312	577328767	577328982	3.650000e-93	351
3	TraesCS7D01G109300	chr7D	95.775	213	6	1	2103	2312	71524519	71524307	7.910000e-90	340
4	TraesCS7D01G109300	chr7D	94.931	217	7	2	2099	2312	544151489	544151704	1.020000e-88	337
5	TraesCS7D01G109300	chr7D	81.890	254	37	8	999	1246	66484783	66485033	3.010000e-49	206
6	TraesCS7D01G109300	chr7D	79.842	253	44	5	999	1246	68924160	68923910	6.560000e-41	178
7	TraesCS7D01G109300	chr7D	78.824	255	43	9	999	1246	66513514	66513764	6.610000e-36	161
8	TraesCS7D01G109300	chr7D	78.656	253	47	5	999	1246	68914052	68913802	6.610000e-36	161
9	TraesCS7D01G109300	chr7B	87.544	851	46	22	755	1579	7440958	7441774	0.000000e+00	929
10	TraesCS7D01G109300	chr7B	80.469	256	40	7	999	1246	10174932	10174679	1.090000e-43	187
11	TraesCS7D01G109300	chr7B	88.571	105	11	1	1999	2102	606375831	606375935	2.410000e-25	126
12	TraesCS7D01G109300	chr2D	90.348	632	50	8	1	625	489573707	489573080	0.000000e+00	819
13	TraesCS7D01G109300	chr2D	89.573	633	52	13	1	624	113479225	113478598	0.000000e+00	791
14	TraesCS7D01G109300	chr5D	89.873	632	48	14	1	625	454030131	454029509	0.000000e+00	798
15	TraesCS7D01G109300	chr5D	88.994	636	49	19	1	625	544788181	544788806	0.000000e+00	767
16	TraesCS7D01G109300	chr5D	95.327	214	6	2	2103	2312	233272253	233272466	1.020000e-88	337
17	TraesCS7D01G109300	chr1D	89.715	632	52	11	1	625	58616968	58617593	0.000000e+00	795
18	TraesCS7D01G109300	chr1D	81.028	253	41	5	999	1246	486922473	486922723	6.520000e-46	195
19	TraesCS7D01G109300	chr3D	89.666	629	54	9	1	624	475866688	475867310	0.000000e+00	791
20	TraesCS7D01G109300	chr3D	93.939	231	10	2	2085	2312	21765878	21766107	1.700000e-91	346
21	TraesCS7D01G109300	chr3D	95.794	214	6	1	2102	2312	584377907	584378120	2.200000e-90	342
22	TraesCS7D01G109300	chr3D	94.954	218	7	2	2098	2312	147499866	147500082	2.850000e-89	339
23	TraesCS7D01G109300	chr6D	89.399	632	49	17	1	624	59176400	59177021	0.000000e+00	780
24	TraesCS7D01G109300	chr6D	95.775	213	6	1	2103	2312	221065229	221065441	7.910000e-90	340
25	TraesCS7D01G109300	chr6A	89.206	630	53	11	1	623	456772359	456772980	0.000000e+00	773
26	TraesCS7D01G109300	chr6A	87.255	102	9	2	2002	2102	100310633	100310535	1.880000e-21	113
27	TraesCS7D01G109300	chr7A	89.895	475	17	18	991	1445	70107591	70108054	1.190000e-162	582
28	TraesCS7D01G109300	chr7A	87.575	499	43	10	1439	1933	70111035	70111518	5.580000e-156	560
29	TraesCS7D01G109300	chr7A	81.818	253	39	5	999	1246	74610774	74610524	3.010000e-49	206
30	TraesCS7D01G109300	chr7A	82.394	142	21	4	1074	1213	71110325	71110464	1.120000e-23	121
31	TraesCS7D01G109300	chr2B	95.794	214	6	1	2102	2312	669559852	669560065	2.200000e-90	342
32	TraesCS7D01G109300	chr2B	90.476	105	9	1	1999	2102	660155291	660155395	1.110000e-28	137
33	TraesCS7D01G109300	chr2B	90.196	102	9	1	2002	2102	762098039	762097938	5.180000e-27	132
34	TraesCS7D01G109300	chr4A	91.346	104	8	1	2000	2102	688045923	688046026	8.610000e-30	141
35	TraesCS7D01G109300	chr6B	89.216	102	10	1	2002	2102	75530996	75531097	2.410000e-25	126
36	TraesCS7D01G109300	chr6B	89.216	102	10	1	2002	2102	400299022	400299123	2.410000e-25	126
37	TraesCS7D01G109300	chr4B	89.216	102	10	1	2002	2102	77005989	77006090	2.410000e-25	126
38	TraesCS7D01G109300	chr2A	89.247	93	9	1	2011	2102	11013563	11013471	5.220000e-22	115

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	TraesCS7D01G109300	chr7D	65760945	65763256	2311	False	4270	4270	100.000	1	2312	1	chr7D.!!$F1	2311
1	TraesCS7D01G109300	chr7D	397552026	397552655	629	True	776	776	89.100	1	625	1	chr7D.!!$R4	624
2	TraesCS7D01G109300	chr7B	7440958	7441774	816	False	929	929	87.544	755	1579	1	chr7B.!!$F1	824
3	TraesCS7D01G109300	chr2D	489573080	489573707	627	True	819	819	90.348	1	625	1	chr2D.!!$R2	624
4	TraesCS7D01G109300	chr2D	113478598	113479225	627	True	791	791	89.573	1	624	1	chr2D.!!$R1	623
5	TraesCS7D01G109300	chr5D	454029509	454030131	622	True	798	798	89.873	1	625	1	chr5D.!!$R1	624
6	TraesCS7D01G109300	chr5D	544788181	544788806	625	False	767	767	88.994	1	625	1	chr5D.!!$F2	624
7	TraesCS7D01G109300	chr1D	58616968	58617593	625	False	795	795	89.715	1	625	1	chr1D.!!$F1	624
8	TraesCS7D01G109300	chr3D	475866688	475867310	622	False	791	791	89.666	1	624	1	chr3D.!!$F3	623
9	TraesCS7D01G109300	chr6D	59176400	59177021	621	False	780	780	89.399	1	624	1	chr6D.!!$F1	623
10	TraesCS7D01G109300	chr6A	456772359	456772980	621	False	773	773	89.206	1	623	1	chr6A.!!$F1	622
11	TraesCS7D01G109300	chr7A	70107591	70111518	3927	False	571	582	88.735	991	1933	2	chr7A.!!$F2	942

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
674	709	0.037046	GGCTTGTTTGGGCCATGAAG	60.037	55.0	7.26	11.05	46.84	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1971	5046	0.0293	CCTGTGCAGTGTTCAAACGG	59.971	55.0	0.0	0.0	0.0	4.44	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

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
179	202	0.591170	CAAAAGGTACGGGTGTGCTG	59.409	55.000	0.00	0.00	0.00	4.41
441	475	1.813859	TCGACGCGAGGAATCCAAT	59.186	52.632	15.93	0.00	0.00	3.16
443	477	0.527600	CGACGCGAGGAATCCAATGA	60.528	55.000	15.93	0.00	0.00	2.57
480	514	0.462225	TTGGACGCACGGTTTGAGAA	60.462	50.000	0.00	0.00	0.00	2.87
541	576	3.188159	ACTTTCAGGTTGCGACAAGTA	57.812	42.857	6.39	0.00	0.00	2.24
543	578	2.163818	TTCAGGTTGCGACAAGTAGG	57.836	50.000	6.39	0.00	0.00	3.18
555	590	0.461870	CAAGTAGGGCGCTGCATGTA	60.462	55.000	20.46	0.00	0.00	2.29
567	602	2.549926	CTGCATGTACGCCACTTATCA	58.450	47.619	0.00	0.00	0.00	2.15
591	626	7.333423	TCACAACTAGGGAAATTAAAGTGATCG	59.667	37.037	0.00	0.00	0.00	3.69
625	660	9.099454	GAATACTTCTCAATTAGTGATTTCGGT	57.901	33.333	0.00	0.00	35.07	4.69
626	661	9.449719	AATACTTCTCAATTAGTGATTTCGGTT	57.550	29.630	0.00	0.00	35.07	4.44
627	662	7.745620	ACTTCTCAATTAGTGATTTCGGTTT	57.254	32.000	0.00	0.00	35.07	3.27
628	663	7.807680	ACTTCTCAATTAGTGATTTCGGTTTC	58.192	34.615	0.00	0.00	35.07	2.78
629	664	6.737254	TCTCAATTAGTGATTTCGGTTTCC	57.263	37.500	0.00	0.00	35.07	3.13
630	665	5.350365	TCTCAATTAGTGATTTCGGTTTCCG	59.650	40.000	1.45	1.45	41.44	4.30
631	666	5.121768	CTCAATTAGTGATTTCGGTTTCCGT	59.878	40.000	8.03	0.00	41.09	4.69
632	667	6.311935	CTCAATTAGTGATTTCGGTTTCCGTA	59.688	38.462	8.03	0.00	41.09	4.02
633	668	7.011109	CTCAATTAGTGATTTCGGTTTCCGTAT	59.989	37.037	8.03	3.69	41.09	3.06
637	672	3.063045	GTGATTTCGGTTTCCGTATGGAC	59.937	47.826	2.15	0.00	46.45	4.02
638	673	2.097680	TTTCGGTTTCCGTATGGACC	57.902	50.000	2.15	2.23	46.45	4.46
639	674	0.975135	TTCGGTTTCCGTATGGACCA	59.025	50.000	2.15	0.00	46.45	4.02
640	675	0.247185	TCGGTTTCCGTATGGACCAC	59.753	55.000	2.15	3.55	46.45	4.16
641	676	0.037139	CGGTTTCCGTATGGACCACA	60.037	55.000	2.15	0.00	46.45	4.17
642	677	1.445871	GGTTTCCGTATGGACCACAC	58.554	55.000	2.15	0.00	46.45	3.82
643	678	1.270947	GGTTTCCGTATGGACCACACA	60.271	52.381	2.15	0.00	46.45	3.72

Showing 1 to 25 of 371 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
88	100	0.321671	TTCCCTTTCTGAGAGGCACG	59.678	55.000	8.69	0.00	32.74	5.34
89	101	2.568623	TTTCCCTTTCTGAGAGGCAC	57.431	50.000	8.69	0.00	32.74	5.01
163	186	1.370064	GACAGCACACCCGTACCTT	59.630	57.895	0.00	0.00	0.00	3.50
167	190	2.137425	CTCGTGACAGCACACCCGTA	62.137	60.000	0.00	0.00	45.41	4.02
179	202	2.126424	GGCCGTGACTCTCGTGAC	60.126	66.667	0.00	0.00	0.00	3.67
398	432	7.052873	AGATCTTCAAAACTAGATCCCATGTG	58.947	38.462	0.00	0.00	38.24	3.21
441	475	2.672961	ATCTCGAACCGCTTTCATCA	57.327	45.000	0.00	0.00	33.24	3.07
443	477	2.420022	CCAAATCTCGAACCGCTTTCAT	59.580	45.455	0.00	0.00	33.24	2.57
555	590	2.093658	CCCTAGTTGTGATAAGTGGCGT	60.094	50.000	0.00	0.00	0.00	5.68
567	602	7.166167	ACGATCACTTTAATTTCCCTAGTTGT	58.834	34.615	0.00	0.00	0.00	3.32
606	641	6.737254	GGAAACCGAAATCACTAATTGAGA	57.263	37.500	0.00	0.00	37.77	3.27
625	660	1.416772	TGTGTGTGGTCCATACGGAAA	59.583	47.619	13.48	0.00	45.20	3.13
626	661	1.049402	TGTGTGTGGTCCATACGGAA	58.951	50.000	13.48	0.00	45.20	4.30
627	662	1.049402	TTGTGTGTGGTCCATACGGA	58.951	50.000	13.48	0.37	37.96	4.69
628	663	2.006888	GATTGTGTGTGGTCCATACGG	58.993	52.381	13.48	0.00	37.96	4.02
629	664	2.694213	TGATTGTGTGTGGTCCATACG	58.306	47.619	13.48	0.00	37.96	3.06
630	665	5.219633	GTTTTGATTGTGTGTGGTCCATAC	58.780	41.667	11.68	11.68	35.86	2.39
631	666	4.023622	CGTTTTGATTGTGTGTGGTCCATA	60.024	41.667	0.00	0.00	0.00	2.74
632	667	3.243367	CGTTTTGATTGTGTGTGGTCCAT	60.243	43.478	0.00	0.00	0.00	3.41
633	668	2.098280	CGTTTTGATTGTGTGTGGTCCA	59.902	45.455	0.00	0.00	0.00	4.02
634	669	2.542824	CCGTTTTGATTGTGTGTGGTCC	60.543	50.000	0.00	0.00	0.00	4.46
635	670	2.542824	CCCGTTTTGATTGTGTGTGGTC	60.543	50.000	0.00	0.00	0.00	4.02
636	671	1.407258	CCCGTTTTGATTGTGTGTGGT	59.593	47.619	0.00	0.00	0.00	4.16
637	672	1.867698	GCCCGTTTTGATTGTGTGTGG	60.868	52.381	0.00	0.00	0.00	4.17
638	673	1.066908	AGCCCGTTTTGATTGTGTGTG	59.933	47.619	0.00	0.00	0.00	3.82

Showing 1 to 25 of 347 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.