AutoCloner

Multiple sequence alignment - TraesCS1A01G166700

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	TraesCS1A01G166700	chr1A	100.000	2232	0	0	561	2792	299540153	299542384	0.000000e+00	4122.0
1	TraesCS1A01G166700	chr1A	95.440	614	28	0	561	1174	97423713	97423100	0.000000e+00	979.0
2	TraesCS1A01G166700	chr1A	100.000	226	0	0	1	226	299539593	299539818	4.300000e-113	418.0
3	TraesCS1A01G166700	chr1A	95.197	229	8	1	1	226	97423955	97423727	2.640000e-95	359.0
4	TraesCS1A01G166700	chr1A	96.396	111	4	0	2682	2792	97423109	97422999	1.710000e-42	183.0
5	TraesCS1A01G166700	chr1A	96.703	91	3	0	1	91	97421473	97421563	4.820000e-33	152.0
6	TraesCS1A01G166700	chr1A	95.604	91	4	0	1	91	299543899	299543809	2.240000e-31	147.0
7	TraesCS1A01G166700	chr2A	98.082	2190	40	2	603	2792	102023725	102021538	0.000000e+00	3810.0
8	TraesCS1A01G166700	chr2A	96.491	228	5	2	1	226	102024315	102024089	9.440000e-100	374.0
9	TraesCS1A01G166700	chr2A	96.774	62	1	1	561	621	102023735	102023674	4.920000e-18	102.0
10	TraesCS1A01G166700	chr1D	96.751	1693	54	1	585	2277	50967458	50969149	0.000000e+00	2820.0
11	TraesCS1A01G166700	chr1D	96.286	1050	39	0	1158	2207	51002253	51003302	0.000000e+00	1724.0
12	TraesCS1A01G166700	chr1D	94.850	602	30	1	561	1162	51000313	51000913	0.000000e+00	939.0
13	TraesCS1A01G166700	chr1D	98.635	293	4	0	2500	2792	50969151	50969443	1.150000e-143	520.0
14	TraesCS1A01G166700	chr1D	96.903	226	4	3	1	226	50966979	50967201	2.630000e-100	375.0
15	TraesCS1A01G166700	chr1D	95.794	214	8	1	3	216	51000099	51000311	7.400000e-91	344.0
16	TraesCS1A01G166700	chr1D	98.901	91	1	0	1	91	50970972	50970882	2.230000e-36	163.0
17	TraesCS1A01G166700	chr1D	94.231	52	3	0	570	621	50967476	50967527	2.310000e-11	80.5
18	TraesCS1A01G166700	chr3B	93.638	1336	79	4	835	2165	448751272	448752606	0.000000e+00	1991.0
19	TraesCS1A01G166700	chr3B	87.591	137	11	2	627	763	448751135	448751265	1.340000e-33	154.0
20	TraesCS1A01G166700	chr3B	95.556	90	1	2	4	91	448752943	448752855	1.040000e-29	141.0
21	TraesCS1A01G166700	chr3B	100.000	29	0	0	594	622	448751135	448751163	1.000000e-03	54.7
22	TraesCS1A01G166700	chr7A	81.991	211	13	12	27	226	533036357	533036553	3.720000e-34	156.0
23	TraesCS1A01G166700	chr7A	94.253	87	4	1	1	87	533037397	533037312	6.270000e-27	132.0
24	TraesCS1A01G166700	chr6D	71.074	363	92	12	2240	2593	452314711	452314353	2.980000e-10	76.8
25	TraesCS1A01G166700	chr5B	93.617	47	3	0	2555	2601	260237153	260237107	1.390000e-08	71.3
26	TraesCS1A01G166700	chr2B	93.617	47	3	0	2543	2589	697521724	697521770	1.390000e-08	71.3
27	TraesCS1A01G166700	chr2B	70.811	370	93	14	2240	2599	801009564	801009200	1.390000e-08	71.3
28	TraesCS1A01G166700	chr7D	91.489	47	4	0	2543	2589	552506640	552506686	6.460000e-07	65.8

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	TraesCS1A01G166700	chr1A	299539593	299542384	2791	False	2270.000000	4122	100.000000	1	2792	2	chr1A.!!$F2	2791
1	TraesCS1A01G166700	chr1A	97422999	97423955	956	True	507.000000	979	95.677667	1	2792	3	chr1A.!!$R2	2791
2	TraesCS1A01G166700	chr2A	102021538	102024315	2777	True	1428.666667	3810	97.115667	1	2792	3	chr2A.!!$R1	2791
3	TraesCS1A01G166700	chr1D	51000099	51003302	3203	False	1002.333333	1724	95.643333	3	2207	3	chr1D.!!$F2	2204
4	TraesCS1A01G166700	chr1D	50966979	50969443	2464	False	948.875000	2820	96.630000	1	2792	4	chr1D.!!$F1	2791
5	TraesCS1A01G166700	chr3B	448751135	448752606	1471	False	733.233333	1991	93.743000	594	2165	3	chr3B.!!$F1	1571

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
129	130	1.544825	CGAGCACCCCCTTTCTCTCA	61.545	60.0	0.0	0.0	0.0	3.27	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1820	3445	2.065899	TGTGCACTTTGCCCTTACTT	57.934	45.0	19.41	0.0	44.23	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
129	130	1.544825	CGAGCACCCCCTTTCTCTCA	61.545	60.000	0.00	0.00	0.00	3.27
158	162	2.045047	TCTCTCTCAGATTTCCCCACCT	59.955	50.000	0.00	0.00	0.00	4.00
624	900	3.299190	GCCCCGATCTCTCCCGAG	61.299	72.222	0.00	0.00	38.67	4.63
625	901	2.598985	CCCCGATCTCTCCCGAGG	60.599	72.222	0.00	0.00	37.86	4.63
626	902	2.516405	CCCGATCTCTCCCGAGGA	59.484	66.667	0.00	0.00	37.86	3.71
851	1127	2.649034	GACGCGAGGTTGAGGACA	59.351	61.111	15.93	0.00	0.00	4.02
1022	1303	4.508551	TGGATCCAGCAGATTGTATTGT	57.491	40.909	11.44	0.00	34.42	2.71
1143	1424	6.128336	CCTTGAGCTTACAGAGAATTCAACAG	60.128	42.308	8.44	1.24	0.00	3.16
1457	3082	2.362077	GTGACTTTGTGCCACCAGATTT	59.638	45.455	0.00	0.00	0.00	2.17
1470	3095	4.581824	CCACCAGATTTTTCATCGGATGAT	59.418	41.667	20.53	6.52	39.39	2.45
1605	3230	6.189859	ACCTGAAGGCAATTATGAAGATGAA	58.810	36.000	0.00	0.00	39.32	2.57
1614	3239	7.201145	GCAATTATGAAGATGAATCAAGTGCT	58.799	34.615	0.00	0.00	0.00	4.40
1789	3414	6.206634	TCGTTATGCACTGAAGGAAAGAAAAT	59.793	34.615	0.00	0.00	0.00	1.82
1820	3445	7.079451	AGTTCTTAAAAGATGAGGGAGTCAA	57.921	36.000	0.00	0.00	39.19	3.18
1915	3540	6.170506	AGTTGGCAGATTACTTCATTTACGA	58.829	36.000	0.00	0.00	0.00	3.43
1966	3591	8.577048	AGATAGTGCACTAGTTACAAGTAGAA	57.423	34.615	29.05	5.71	35.85	2.10
1969	3594	5.539193	AGTGCACTAGTTACAAGTAGAAGGT	59.461	40.000	20.16	0.00	35.85	3.50
2036	3661	6.211184	TGGTCAATCCAGCAATTAAAGTCAAT	59.789	34.615	0.00	0.00	41.93	2.57
2137	3762	1.334243	CGGCTAAAGAGGGAGAGTACG	59.666	57.143	0.00	0.00	0.00	3.67
2197	3822	1.348064	CCCTGGGACTACTTGTGTGA	58.652	55.000	7.01	0.00	0.00	3.58
2239	3864	3.222603	GAAGAACCAACATTCCACCACT	58.777	45.455	0.00	0.00	0.00	4.00
2348	3974	5.467035	AGAGCAGGAGAGATATTAAGTGC	57.533	43.478	0.00	0.00	0.00	4.40
2478	4104	2.814805	AAGTTGGAGATGGTGATGGG	57.185	50.000	0.00	0.00	0.00	4.00
2492	4118	5.594777	TGGTGATGGGTGGGTTATAATTTT	58.405	37.500	0.00	0.00	0.00	1.82
2519	4145	7.493320	TGATCAGCAAAAAGGAATATTGAATGC	59.507	33.333	0.00	0.00	0.00	3.56

Showing 1 to 25 of 27 entries

Previous1 2Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
129	130	5.243730	GGGAAATCTGAGAGAGAGATCGAAT	59.756	44.000	0.00	32.80	3.34
621	897	4.803426	GTGGCGCTGGTCTCCTCG	62.803	72.222	7.64	0.00	4.63
622	898	4.459089	GGTGGCGCTGGTCTCCTC	62.459	72.222	7.64	0.00	3.71
775	1051	3.242641	CGATACTTCACCGTCGAGATCAA	60.243	47.826	0.00	36.25	2.57
851	1127	6.483640	GGAATATTGCTCACCTAATTCTTCGT	59.516	38.462	0.00	0.00	3.85
1022	1303	4.502259	CCCCATTGAAATGAAAACGGACAA	60.502	41.667	4.58	38.70	3.18
1143	1424	5.049474	TGTGACATAATGCTCACTCAAACAC	60.049	40.000	3.56	38.12	3.32
1406	3031	4.811024	CGGAGCTGCTTTCTACATCAATTA	59.189	41.667	2.53	0.00	1.40
1470	3095	4.321718	GCTTAATAGCATCTGCCTCATCA	58.678	43.478	0.00	46.95	3.07
1605	3230	4.564782	TTCATCCTCTTCAGCACTTGAT	57.435	40.909	0.00	35.27	2.57
1614	3239	6.239148	CCTCGTCATAAGATTCATCCTCTTCA	60.239	42.308	0.00	34.81	3.02
1820	3445	2.065899	TGTGCACTTTGCCCTTACTT	57.934	45.000	19.41	44.23	2.24
1915	3540	4.081697	CCTTTTTGGACAAGTGTGTTCCTT	60.082	41.667	0.00	38.41	3.36
1966	3591	4.706962	ACTCTCAAACTTTTCTGCAAACCT	59.293	37.500	0.00	0.00	3.50
1969	3594	6.686630	TCAAACTCTCAAACTTTTCTGCAAA	58.313	32.000	0.00	0.00	3.68
2137	3762	3.320826	AGTTGGTAATCAAACACTTGGCC	59.679	43.478	0.00	37.08	5.36
2197	3822	4.410099	TCAAAATCTGGGTGAAGCTTGAT	58.590	39.130	2.10	0.00	2.57
2239	3864	5.599732	ACAAGCATCAAAGCACACATAAAA	58.400	33.333	0.00	36.85	1.52
2348	3974	3.270027	TGATTTGCATCTCTACCAACGG	58.730	45.455	0.00	0.00	4.44
2478	4104	8.770438	TTTGCTGATCAAAAATTATAACCCAC	57.230	30.769	0.00	41.36	4.61
2492	4118	9.373603	CATTCAATATTCCTTTTTGCTGATCAA	57.626	29.630	0.00	0.00	2.57
2519	4145	1.302832	GGAGCCCAGTGGTGAACAG	60.303	63.158	8.74	0.00	3.16
2741	4367	1.440618	TCCTAACCTGAACCAAGCCA	58.559	50.000	0.00	0.00	4.75

Showing 1 to 23 of 23 entries

Previous1Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.