AutoCloner

Multiple sequence alignment - TraesCS3A01G507900

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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	TraesCS3A01G507900	chr3A	100.000	5107	0	0	1	5107	729181542	729186648	0.000000e+00	9431.0
1	TraesCS3A01G507900	chr3A	94.361	2979	91	32	837	3785	729578945	729576014	0.000000e+00	4499.0
2	TraesCS3A01G507900	chr3A	95.720	1285	42	6	3824	5103	729576008	729574732	0.000000e+00	2056.0
3	TraesCS3A01G507900	chr3A	99.507	1015	5	0	2661	3675	729353231	729354245	0.000000e+00	1847.0
4	TraesCS3A01G507900	chr3A	85.278	557	58	14	3996	4541	599421758	599421215	2.080000e-153	553.0
5	TraesCS3A01G507900	chr3A	77.590	473	64	23	4674	5107	585433461	585432992	1.100000e-61	248.0
6	TraesCS3A01G507900	chr3A	93.913	115	7	0	3671	3785	729356330	729356444	1.890000e-39	174.0
7	TraesCS3A01G507900	chr3A	86.992	123	15	1	4542	4664	369461372	369461251	2.480000e-28	137.0
8	TraesCS3A01G507900	chr3A	86.869	99	12	1	4543	4641	585433561	585433464	5.410000e-20	110.0
9	TraesCS3A01G507900	chr3B	91.780	3017	139	43	816	3785	807078706	807081660	0.000000e+00	4096.0
10	TraesCS3A01G507900	chr3B	96.023	855	28	5	4070	4918	807081973	807082827	0.000000e+00	1386.0
11	TraesCS3A01G507900	chr3B	94.332	247	8	4	3828	4072	807081656	807081898	1.740000e-99	374.0
12	TraesCS3A01G507900	chr3B	97.409	193	5	0	4915	5107	807116032	807116224	3.810000e-86	329.0
13	TraesCS3A01G507900	chr3B	75.610	410	60	18	847	1234	807187209	807186818	3.160000e-37	167.0
14	TraesCS3A01G507900	chr3B	89.011	91	3	3	2314	2397	257512492	257512402	6.990000e-19	106.0
15	TraesCS3A01G507900	chr3D	95.756	919	32	3	2874	3785	599165150	599166068	0.000000e+00	1474.0
16	TraesCS3A01G507900	chr3D	86.966	890	71	23	1446	2318	599164254	599165115	0.000000e+00	959.0
17	TraesCS3A01G507900	chr3D	91.956	547	29	5	824	1369	599163690	599164222	0.000000e+00	752.0
18	TraesCS3A01G507900	chr3D	80.717	809	86	22	7	776	599162897	599163674	2.670000e-157	566.0
19	TraesCS3A01G507900	chr3D	76.923	455	61	18	4674	5103	444536065	444535630	8.610000e-53	219.0
20	TraesCS3A01G507900	chr3D	100.000	28	0	0	1713	1740	599164552	599164579	9.000000e-03	52.8
21	TraesCS3A01G507900	chr5B	82.679	560	68	17	3994	4541	494900795	494900253	2.150000e-128	470.0
22	TraesCS3A01G507900	chr5B	82.129	526	57	13	4042	4534	11149115	11148594	2.840000e-112	416.0
23	TraesCS3A01G507900	chr4A	81.400	500	55	17	4046	4535	662585172	662585643	1.740000e-99	374.0
24	TraesCS3A01G507900	chr4A	76.396	555	101	18	4540	5082	491722979	491723515	6.520000e-69	272.0
25	TraesCS3A01G507900	chr4A	82.743	226	29	8	4882	5103	156619906	156619687	5.220000e-45	193.0
26	TraesCS3A01G507900	chr2D	77.913	575	93	23	4542	5103	12983256	12983809	1.370000e-85	327.0
27	TraesCS3A01G507900	chr2D	76.938	529	73	29	4584	5103	13071769	13072257	6.560000e-64	255.0
28	TraesCS3A01G507900	chr4D	76.271	531	91	28	4584	5102	318239625	318240132	3.050000e-62	250.0
29	TraesCS3A01G507900	chr4D	88.889	90	8	2	2306	2393	43548860	43548949	5.410000e-20	110.0
30	TraesCS3A01G507900	chr2A	83.264	239	30	4	4868	5103	15126457	15126688	1.440000e-50	211.0
31	TraesCS3A01G507900	chr2A	83.333	180	17	9	4007	4180	578905602	578905774	2.460000e-33	154.0
32	TraesCS3A01G507900	chr5D	79.720	286	40	12	4830	5103	381147931	381147652	1.880000e-44	191.0
33	TraesCS3A01G507900	chr5D	97.143	70	0	2	2317	2384	546839010	546838941	3.230000e-22	117.0
34	TraesCS3A01G507900	chr1A	92.405	79	4	2	2313	2390	24740562	24740639	1.500000e-20	111.0
35	TraesCS3A01G507900	chr1A	91.463	82	4	3	2311	2390	24610948	24611028	5.410000e-20	110.0
36	TraesCS3A01G507900	chr1A	90.361	83	5	3	2310	2390	24591517	24591598	6.990000e-19	106.0
37	TraesCS3A01G507900	chr2B	88.764	89	6	4	2305	2390	168852032	168851945	6.990000e-19	106.0
38	TraesCS3A01G507900	chr7D	79.675	123	22	3	4543	4664	524553858	524553978	9.110000e-13	86.1

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	TraesCS3A01G507900	chr3A	729181542	729186648	5106	False	9431.00	9431	100.0000	1	5107	1	chr3A.!!$F1	5106
1	TraesCS3A01G507900	chr3A	729574732	729578945	4213	True	3277.50	4499	95.0405	837	5103	2	chr3A.!!$R4	4266
2	TraesCS3A01G507900	chr3A	729353231	729356444	3213	False	1010.50	1847	96.7100	2661	3785	2	chr3A.!!$F2	1124
3	TraesCS3A01G507900	chr3A	599421215	599421758	543	True	553.00	553	85.2780	3996	4541	1	chr3A.!!$R2	545
4	TraesCS3A01G507900	chr3B	807078706	807082827	4121	False	1952.00	4096	94.0450	816	4918	3	chr3B.!!$F2	4102
5	TraesCS3A01G507900	chr3D	599162897	599166068	3171	False	760.76	1474	91.0790	7	3785	5	chr3D.!!$F1	3778
6	TraesCS3A01G507900	chr5B	494900253	494900795	542	True	470.00	470	82.6790	3994	4541	1	chr5B.!!$R2	547
7	TraesCS3A01G507900	chr5B	11148594	11149115	521	True	416.00	416	82.1290	4042	4534	1	chr5B.!!$R1	492
8	TraesCS3A01G507900	chr4A	491722979	491723515	536	False	272.00	272	76.3960	4540	5082	1	chr4A.!!$F1	542
9	TraesCS3A01G507900	chr2D	12983256	12983809	553	False	327.00	327	77.9130	4542	5103	1	chr2D.!!$F1	561
10	TraesCS3A01G507900	chr4D	318239625	318240132	507	False	250.00	250	76.2710	4584	5102	1	chr4D.!!$F2	518

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
408	433	0.245539	CTGCTCAAAACATGCCCAGG	59.754	55.000	0.00	0.00	0.0	4.45	F
544	569	0.598158	TTAAACGGCGTCTGAAGCGT	60.598	50.000	15.17	8.09	35.0	5.07	F
817	855	2.334977	TCTCTGTTGAAAGGTAGCCCA	58.665	47.619	0.00	0.00	0.0	5.36	F
1685	1778	1.211949	TCAAAAGCTAATCCCCCTCGG	59.788	52.381	0.00	0.00	0.0	4.63	F
3573	3742	3.603158	TGAAGCTATCACGCCAAGTTA	57.397	42.857	0.00	0.00	31.5	2.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1664	1756	2.158608	CCGAGGGGGATTAGCTTTTGAT	60.159	50.000	0.00	0.00	38.47	2.57	R
1685	1778	4.507879	GGCAACATGGCAATGAGC	57.492	55.556	8.45	11.15	43.14	4.26	R
2567	2723	5.726980	ATTTTCTGCCTCAAACTTGCATA	57.273	34.783	0.00	0.00	33.97	3.14	R
3620	3789	1.420138	TCTTCTTCCTCACCAACACCC	59.580	52.381	0.00	0.00	0.00	4.61	R
4807	7187	0.107165	GGCGCAGAGGGGATTTAGTT	60.107	55.000	10.83	0.00	0.00	2.24	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
130	135	4.664150	AAGTCCGCAGATTTTGGAAAAA	57.336	36.364	0.00	0.00	32.60	1.94
182	187	8.254178	TGTGGATTTGAAAAATATTCATGCAC	57.746	30.769	8.54	8.54	33.36	4.57
233	238	9.921637	TGTATTTGAATAAAGTTCATTGGGTTC	57.078	29.630	0.00	0.00	0.00	3.62
315	340	6.596309	AAAGCAGATAAAGGGAAGAAAAGG	57.404	37.500	0.00	0.00	0.00	3.11
319	344	6.435591	AGCAGATAAAGGGAAGAAAAGGAAAG	59.564	38.462	0.00	0.00	0.00	2.62
325	350	4.878968	AGGGAAGAAAAGGAAAGACCAAA	58.121	39.130	0.00	0.00	42.04	3.28
330	355	6.876789	GGAAGAAAAGGAAAGACCAAACAAAA	59.123	34.615	0.00	0.00	42.04	2.44
365	390	7.843490	AAAAACTAAAAGAGCAGGGAAAAAC	57.157	32.000	0.00	0.00	0.00	2.43
403	428	2.719426	AGAAGCTGCTCAAAACATGC	57.281	45.000	1.00	0.00	0.00	4.06
408	433	0.245539	CTGCTCAAAACATGCCCAGG	59.754	55.000	0.00	0.00	0.00	4.45
418	443	1.379576	ATGCCCAGGAAGCTTCTGC	60.380	57.895	25.05	20.74	40.05	4.26
421	446	1.003355	CCCAGGAAGCTTCTGCGAA	60.003	57.895	25.05	0.00	45.42	4.70
427	452	0.799393	GAAGCTTCTGCGAACTTCCC	59.201	55.000	19.44	0.00	45.42	3.97
434	459	1.133915	TCTGCGAACTTCCCAAAACCT	60.134	47.619	0.00	0.00	0.00	3.50
435	460	1.001378	CTGCGAACTTCCCAAAACCTG	60.001	52.381	0.00	0.00	0.00	4.00
436	461	1.314730	GCGAACTTCCCAAAACCTGA	58.685	50.000	0.00	0.00	0.00	3.86
439	464	3.702330	CGAACTTCCCAAAACCTGAAAC	58.298	45.455	0.00	0.00	0.00	2.78
458	483	3.056328	GGAGCTTCCCGTTGGTGC	61.056	66.667	0.00	0.00	34.20	5.01
464	489	1.094785	CTTCCCGTTGGTGCCTTATG	58.905	55.000	0.00	0.00	0.00	1.90
475	500	1.883084	GCCTTATGCAGACCGTCCG	60.883	63.158	0.00	0.00	40.77	4.79
490	515	5.047943	AGACCGTCCGATAAAGATTCTATGG	60.048	44.000	0.00	0.00	0.00	2.74
520	545	1.015109	TGTGCGGCTTGTACGAAAAA	58.985	45.000	0.00	0.00	35.72	1.94
531	556	5.108518	GCTTGTACGAAAAAGCCTTTAAACG	60.109	40.000	4.68	0.00	42.40	3.60
544	569	0.598158	TTAAACGGCGTCTGAAGCGT	60.598	50.000	15.17	8.09	35.00	5.07
554	579	2.854777	CGTCTGAAGCGTCAAATAGGAG	59.145	50.000	3.39	0.00	31.88	3.69

Showing 1 to 25 of 88 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	8.173542	ACAATTTTCCTAGTTCGTGGTAATTT	57.826	30.769	0.00	0.00	0.00	1.82
1	2	7.754851	ACAATTTTCCTAGTTCGTGGTAATT	57.245	32.000	0.00	0.00	0.00	1.40
2	3	7.446013	TGAACAATTTTCCTAGTTCGTGGTAAT	59.554	33.333	0.00	0.00	42.35	1.89
5	6	5.127491	TGAACAATTTTCCTAGTTCGTGGT	58.873	37.500	0.00	0.00	42.35	4.16
9	10	8.970691	AATTCATGAACAATTTTCCTAGTTCG	57.029	30.769	11.07	0.00	42.35	3.95
78	79	9.685828	CAAAAACGATGAACTATTCCCTTTTTA	57.314	29.630	0.00	0.00	0.00	1.52
81	82	7.519032	TCAAAAACGATGAACTATTCCCTTT	57.481	32.000	0.00	0.00	0.00	3.11
82	83	7.519032	TTCAAAAACGATGAACTATTCCCTT	57.481	32.000	0.00	0.00	32.10	3.95
84	85	8.582433	TTTTTCAAAAACGATGAACTATTCCC	57.418	30.769	0.00	0.00	36.57	3.97
160	165	9.153721	TCAAGTGCATGAATATTTTTCAAATCC	57.846	29.630	0.00	0.00	31.55	3.01
285	290	7.690256	TCTTCCCTTTATCTGCTTTTTCTAGT	58.310	34.615	0.00	0.00	0.00	2.57
286	291	8.567285	TTCTTCCCTTTATCTGCTTTTTCTAG	57.433	34.615	0.00	0.00	0.00	2.43
287	292	8.934023	TTTCTTCCCTTTATCTGCTTTTTCTA	57.066	30.769	0.00	0.00	0.00	2.10
288	293	7.839680	TTTCTTCCCTTTATCTGCTTTTTCT	57.160	32.000	0.00	0.00	0.00	2.52
289	294	7.600375	CCTTTTCTTCCCTTTATCTGCTTTTTC	59.400	37.037	0.00	0.00	0.00	2.29
292	297	6.314917	TCCTTTTCTTCCCTTTATCTGCTTT	58.685	36.000	0.00	0.00	0.00	3.51
296	301	7.094162	GGTCTTTCCTTTTCTTCCCTTTATCTG	60.094	40.741	0.00	0.00	0.00	2.90
298	303	6.719829	TGGTCTTTCCTTTTCTTCCCTTTATC	59.280	38.462	0.00	0.00	37.07	1.75
299	304	6.620429	TGGTCTTTCCTTTTCTTCCCTTTAT	58.380	36.000	0.00	0.00	37.07	1.40
300	305	6.020881	TGGTCTTTCCTTTTCTTCCCTTTA	57.979	37.500	0.00	0.00	37.07	1.85
304	309	4.404394	TGTTTGGTCTTTCCTTTTCTTCCC	59.596	41.667	0.00	0.00	37.07	3.97
305	310	5.592104	TGTTTGGTCTTTCCTTTTCTTCC	57.408	39.130	0.00	0.00	37.07	3.46
344	369	5.531122	GGTTTTTCCCTGCTCTTTTAGTT	57.469	39.130	0.00	0.00	0.00	2.24
383	408	2.489329	GGCATGTTTTGAGCAGCTTCTA	59.511	45.455	0.00	0.00	0.00	2.10
403	428	1.003355	TTCGCAGAAGCTTCCTGGG	60.003	57.895	22.81	23.68	45.90	4.45

Showing 1 to 25 of 111 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.