AutoCloner

Multiple sequence alignment - TraesCS1B01G196900

Loading Multiple Alignment...

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	TraesCS1B01G196900	chr1B	100.000	3449	0	0	1	3449	354236033	354232585	0.000000e+00	6370.0
1	TraesCS1B01G196900	chr1B	86.301	292	30	9	2524	2808	442965884	442966172	3.340000e-80	309.0
2	TraesCS1B01G196900	chr1B	83.756	197	32	0	1435	1631	354240235	354240039	1.630000e-43	187.0
3	TraesCS1B01G196900	chr1A	92.768	1037	54	15	608	1638	342393646	342392625	0.000000e+00	1480.0
4	TraesCS1B01G196900	chr1A	97.112	831	23	1	1746	2575	342392628	342391798	0.000000e+00	1400.0
5	TraesCS1B01G196900	chr1A	96.707	668	18	3	2783	3449	342391766	342391102	0.000000e+00	1109.0
6	TraesCS1B01G196900	chr1A	95.525	581	15	5	26	603	342394860	342394288	0.000000e+00	918.0
7	TraesCS1B01G196900	chr1A	91.506	259	19	2	345	603	342394273	342394018	1.520000e-93	353.0
8	TraesCS1B01G196900	chr1A	83.000	300	37	10	2524	2818	216420022	216420312	3.410000e-65	259.0
9	TraesCS1B01G196900	chr1A	84.772	197	30	0	1435	1631	342434643	342434447	7.550000e-47	198.0
10	TraesCS1B01G196900	chr1A	82.845	239	20	10	345	570	342394003	342393773	9.770000e-46	195.0
11	TraesCS1B01G196900	chr1D	92.678	1038	53	13	608	1638	258575504	258576525	0.000000e+00	1474.0
12	TraesCS1B01G196900	chr1D	95.017	883	26	8	1746	2627	258576522	258577387	0.000000e+00	1371.0
13	TraesCS1B01G196900	chr1D	96.707	668	18	3	2783	3449	258577381	258578045	0.000000e+00	1109.0
14	TraesCS1B01G196900	chr1D	96.220	582	19	2	1	582	258574817	258575395	0.000000e+00	950.0
15	TraesCS1B01G196900	chr1D	83.249	197	33	0	1435	1631	258553659	258553855	7.600000e-42	182.0
16	TraesCS1B01G196900	chr5A	97.222	180	3	2	2622	2799	35197112	35196933	1.560000e-78	303.0
17	TraesCS1B01G196900	chr5A	94.030	201	11	1	2617	2817	582916447	582916646	1.560000e-78	303.0
18	TraesCS1B01G196900	chr5A	86.891	267	24	11	2570	2831	8807686	8807946	4.360000e-74	289.0
19	TraesCS1B01G196900	chr7B	95.187	187	7	2	2622	2807	739630271	739630086	9.360000e-76	294.0
20	TraesCS1B01G196900	chr7B	89.427	227	20	3	2616	2838	636433793	636433567	2.030000e-72	283.0
21	TraesCS1B01G196900	chr7B	86.335	161	17	5	2573	2730	378407028	378407186	1.650000e-38	171.0
22	TraesCS1B01G196900	chr7B	84.091	88	12	2	2523	2610	436087762	436087677	2.210000e-12	84.2
23	TraesCS1B01G196900	chr7B	84.211	95	6	7	2585	2672	565435162	565435254	2.210000e-12	84.2
24	TraesCS1B01G196900	chr6A	93.846	195	9	3	2594	2788	596588475	596588284	1.210000e-74	291.0
25	TraesCS1B01G196900	chr6B	88.261	230	22	5	2573	2799	716638146	716638373	1.580000e-68	270.0
26	TraesCS1B01G196900	chr6B	84.242	165	18	4	2573	2730	719967614	719967451	1.660000e-33	154.0
27	TraesCS1B01G196900	chr2B	84.064	251	33	7	2570	2816	385568926	385568679	5.750000e-58	235.0
28	TraesCS1B01G196900	chr2B	89.011	91	8	2	2524	2613	209085342	209085253	1.010000e-20	111.0
29	TraesCS1B01G196900	chr3A	79.399	233	40	7	2570	2799	501866740	501866513	1.280000e-34	158.0
30	TraesCS1B01G196900	chr3A	77.828	221	41	7	2570	2787	501882594	501882379	2.790000e-26	130.0
31	TraesCS1B01G196900	chr3A	93.976	83	3	2	2523	2604	79398349	79398430	1.300000e-24	124.0
32	TraesCS1B01G196900	chr5D	91.111	90	7	1	2524	2613	265961975	265961887	1.680000e-23	121.0
33	TraesCS1B01G196900	chr5B	90.110	91	7	2	2524	2613	299602372	299602283	2.170000e-22	117.0
34	TraesCS1B01G196900	chr4B	91.892	74	3	3	2524	2595	173038561	173038489	2.190000e-17	100.0

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	TraesCS1B01G196900	chr1B	354232585	354236033	3448	True	6370.000000	6370	100.000000	1	3449	1	chr1B.!!$R1	3448
1	TraesCS1B01G196900	chr1A	342391102	342394860	3758	True	909.166667	1480	92.743833	26	3449	6	chr1A.!!$R2	3423
2	TraesCS1B01G196900	chr1D	258574817	258578045	3228	False	1226.000000	1474	95.155500	1	3449	4	chr1D.!!$F2	3448

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
892	1532	0.253044	CTGCCACTAGCTTAGCCCAA	59.747	55.0	0.0	0.0	44.23	4.12	F
1683	2330	0.034896	TCTGAAACTGAAGACCCCGC	59.965	55.0	0.0	0.0	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1698	2345	0.098376	AGTCGTTAGTGTCGCCGATC	59.902	55.0	0.00	0.00	0.00	3.69	R
3218	3869	0.471191	AATGCGGGAGATGATCAGCA	59.529	50.0	14.38	10.56	43.87	4.41	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
37	38	4.518249	AGATTCTAGTAAAGCAACCAGGC	58.482	43.478	0.00	0.00	0.00	4.85
40	41	0.978151	TAGTAAAGCAACCAGGCGGA	59.022	50.000	2.43	0.00	39.27	5.54
114	115	2.936498	ACACACCGAACTTCTGAAACAG	59.064	45.455	0.00	0.00	0.00	3.16
138	139	6.396450	GGTCTTTACCTACCAAGAACACTAG	58.604	44.000	0.00	0.00	43.08	2.57
357	359	0.980423	AAACTGAGGCAGGAGAGACC	59.020	55.000	0.00	0.00	35.51	3.85
380	382	7.162082	ACCAGAATAGAGTTTTGGTGAAGTAG	58.838	38.462	2.61	0.00	40.47	2.57
434	436	2.477825	GACATCATCTCCCATGTCACG	58.522	52.381	7.09	0.00	45.64	4.35
587	857	8.208575	TGGTTATAGCCCAAACCTAAAAATTT	57.791	30.769	2.81	0.00	44.55	1.82
603	873	2.780149	ATTTCTTGGACGCGCGCAAC	62.780	55.000	32.58	22.79	0.00	4.17
619	1258	1.474077	GCAACCTTTCGGAGCATGATT	59.526	47.619	0.00	0.00	35.78	2.57
624	1263	3.191371	ACCTTTCGGAGCATGATTGAAAC	59.809	43.478	0.00	0.00	0.00	2.78
634	1273	7.573843	CGGAGCATGATTGAAACTCTACTTTTT	60.574	37.037	0.00	0.00	0.00	1.94
646	1285	6.441088	ACTCTACTTTTTGGATTCCTCTGT	57.559	37.500	3.95	0.00	0.00	3.41
665	1304	6.094603	CCTCTGTTTCTCCTCCAACATTATTG	59.905	42.308	0.00	0.00	32.50	1.90
673	1312	3.257873	CCTCCAACATTATTGTGTGCCAA	59.742	43.478	0.00	0.00	35.83	4.52
676	1315	4.586421	TCCAACATTATTGTGTGCCAAGAA	59.414	37.500	0.00	0.00	38.53	2.52
683	1322	2.869233	TGTGTGCCAAGAAAAAGCTC	57.131	45.000	0.00	0.00	0.00	4.09
746	1385	1.273327	CCTGGAGTGAAAATTGGTGGC	59.727	52.381	0.00	0.00	0.00	5.01
832	1472	2.204074	TGCCCTGGCCTCCACTAA	60.204	61.111	3.32	0.00	41.09	2.24
840	1480	1.746991	GCCTCCACTAAGTGCTGCC	60.747	63.158	0.00	0.00	31.34	4.85
841	1481	1.679311	CCTCCACTAAGTGCTGCCA	59.321	57.895	0.00	0.00	31.34	4.92
892	1532	0.253044	CTGCCACTAGCTTAGCCCAA	59.747	55.000	0.00	0.00	44.23	4.12
928	1568	0.978146	TAAGCTGTCCTCCTCCTGCC	60.978	60.000	0.00	0.00	0.00	4.85
1011	1655	4.809496	CCTCCAATGGCGGCTGCT	62.809	66.667	18.85	0.00	42.25	4.24
1029	1673	1.608590	GCTGCTGCTTCAACAGGTAAA	59.391	47.619	8.53	0.00	38.16	2.01

Showing 1 to 25 of 269 entries

Previous1 2 3 4 5…11Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	1.002624	CCTCCGCCTGGTTGCTTTA	60.003	57.895	0.00	0.00	36.30	1.85
37	38	2.883828	AAGGTGCACCACTCCTCCG	61.884	63.158	36.39	0.00	41.51	4.63
40	41	1.451936	GTCAAGGTGCACCACTCCT	59.548	57.895	36.39	14.05	44.30	3.69
138	139	2.514824	GATGGCCTTCTGGGTCGC	60.515	66.667	11.34	0.00	44.07	5.19
357	359	9.360093	CTACTACTTCACCAAAACTCTATTCTG	57.640	37.037	0.00	0.00	0.00	3.02
434	436	3.713288	TGTACGCACATCTTACATAGGC	58.287	45.455	0.00	0.00	0.00	3.93
572	842	5.176774	GCGTCCAAGAAATTTTTAGGTTTGG	59.823	40.000	0.00	1.48	35.95	3.28
604	874	4.394300	AGAGTTTCAATCATGCTCCGAAAG	59.606	41.667	0.00	0.00	0.00	2.62
619	1258	7.445402	CAGAGGAATCCAAAAAGTAGAGTTTCA	59.555	37.037	0.61	0.00	0.00	2.69
624	1263	7.663493	AGAAACAGAGGAATCCAAAAAGTAGAG	59.337	37.037	0.61	0.00	0.00	2.43
634	1273	2.840651	GGAGGAGAAACAGAGGAATCCA	59.159	50.000	0.61	0.00	0.00	3.41
646	1285	5.048083	GCACACAATAATGTTGGAGGAGAAA	60.048	40.000	0.00	0.00	37.82	2.52
665	1304	2.869233	TGAGCTTTTTCTTGGCACAC	57.131	45.000	0.00	0.00	39.29	3.82
673	1312	8.572185	GGAGTAATTTTCTCTTGAGCTTTTTCT	58.428	33.333	3.47	0.00	33.06	2.52
676	1315	9.004717	GTAGGAGTAATTTTCTCTTGAGCTTTT	57.995	33.333	3.47	0.00	33.06	2.27
683	1322	7.386851	TGACAGGTAGGAGTAATTTTCTCTTG	58.613	38.462	3.47	0.00	33.06	3.02
796	1436	0.811281	ACGGCCTACCAACGTAGTAC	59.189	55.000	0.00	0.00	45.00	2.73
797	1437	0.810648	CACGGCCTACCAACGTAGTA	59.189	55.000	0.00	0.00	45.00	1.82
799	1439	1.808390	GCACGGCCTACCAACGTAG	60.808	63.158	0.00	0.00	41.55	3.51
800	1440	2.262292	GCACGGCCTACCAACGTA	59.738	61.111	0.00	0.00	39.02	3.57
801	1441	4.692475	GGCACGGCCTACCAACGT	62.692	66.667	0.00	0.00	46.69	3.99
840	1480	4.741676	GGTGACACTTTGCTGAAAGAAATG	59.258	41.667	5.39	0.00	41.12	2.32
841	1481	4.498009	CGGTGACACTTTGCTGAAAGAAAT	60.498	41.667	5.39	0.00	41.12	2.17
892	1532	3.011257	AGCTTAATGTGTTGGGTGGGTAT	59.989	43.478	0.00	0.00	0.00	2.73
928	1568	1.285641	GATGTGTGGCGTTGTTGGG	59.714	57.895	0.00	0.00	0.00	4.12

Showing 1 to 25 of 271 entries

Previous1 2 3 4 5…11Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.