AutoCloner

Multiple sequence alignment - TraesCS2A01G312700

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	TraesCS2A01G312700	chr2A	100.000	5026	0	0	1	5026	537399885	537404910	0.000000e+00	9282.0
1	TraesCS2A01G312700	chr2D	94.949	3425	124	22	942	4341	400051049	400054449	0.000000e+00	5321.0
2	TraesCS2A01G312700	chr2D	87.342	553	29	9	4501	5026	400054449	400054987	3.350000e-166	595.0
3	TraesCS2A01G312700	chr2D	96.721	122	4	0	784	905	400050923	400051044	2.370000e-48	204.0
4	TraesCS2A01G312700	chr2B	95.381	1797	71	5	1127	2919	474403840	474405628	0.000000e+00	2848.0
5	TraesCS2A01G312700	chr2B	94.479	1431	49	19	2918	4337	474405752	474407163	0.000000e+00	2178.0
6	TraesCS2A01G312700	chr2B	88.361	421	11	6	4644	5026	474443402	474443822	5.890000e-129	472.0
7	TraesCS2A01G312700	chr2B	93.793	290	13	3	825	1109	474403209	474403498	1.000000e-116	431.0
8	TraesCS2A01G312700	chr2B	92.169	166	10	1	4340	4505	800062976	800062814	1.090000e-56	231.0
9	TraesCS2A01G312700	chr7B	96.361	742	26	1	1	741	104082024	104081283	0.000000e+00	1219.0
10	TraesCS2A01G312700	chr7B	85.124	121	17	1	624	743	630132796	630132916	6.830000e-24	122.0
11	TraesCS2A01G312700	chrUn	89.267	587	40	9	161	742	31685756	31685188	0.000000e+00	713.0
12	TraesCS2A01G312700	chrUn	91.111	45	1	3	2905	2946	1995154	1995110	1.950000e-04	58.4
13	TraesCS2A01G312700	chr1B	88.567	586	54	10	161	742	248260381	248260957	0.000000e+00	699.0
14	TraesCS2A01G312700	chr1B	93.168	161	9	1	1	161	248260188	248260346	8.410000e-58	235.0
15	TraesCS2A01G312700	chr3D	89.400	500	47	6	245	742	498094435	498093940	4.270000e-175	625.0
16	TraesCS2A01G312700	chr3D	90.286	175	12	3	4334	4507	571465533	571465363	1.820000e-54	224.0
17	TraesCS2A01G312700	chr3D	90.286	175	12	3	4334	4507	579494787	579494957	1.820000e-54	224.0
18	TraesCS2A01G312700	chr3D	83.871	124	19	1	624	746	98598451	98598328	3.180000e-22	117.0
19	TraesCS2A01G312700	chr7D	84.138	580	62	13	173	741	460521221	460521781	7.410000e-148	534.0
20	TraesCS2A01G312700	chr7D	97.222	36	1	0	126	161	401092284	401092319	1.510000e-05	62.1
21	TraesCS2A01G312700	chr6D	92.216	167	10	1	4336	4502	229430889	229431052	3.030000e-57	233.0
22	TraesCS2A01G312700	chr4B	92.169	166	10	1	4337	4502	535345159	535344997	1.090000e-56	231.0
23	TraesCS2A01G312700	chr4A	91.716	169	11	1	4338	4506	669197976	669198141	1.090000e-56	231.0
24	TraesCS2A01G312700	chr6B	90.286	175	12	3	4334	4507	130112762	130112592	1.820000e-54	224.0
25	TraesCS2A01G312700	chr6B	89.583	48	3	2	2899	2945	135488330	135488376	5.430000e-05	60.2
26	TraesCS2A01G312700	chr3A	90.286	175	12	3	4334	4507	568001365	568001195	1.820000e-54	224.0
27	TraesCS2A01G312700	chr3B	89.071	183	15	3	4335	4516	243784042	243784220	6.550000e-54	222.0
28	TraesCS2A01G312700	chr3B	95.000	40	2	0	2902	2941	239920877	239920838	4.200000e-06	63.9
29	TraesCS2A01G312700	chr6A	85.833	120	16	1	624	742	495110612	495110731	5.280000e-25	126.0
30	TraesCS2A01G312700	chr6A	84.615	65	9	1	507	570	560376422	560376358	4.200000e-06	63.9
31	TraesCS2A01G312700	chr6A	84.375	64	10	0	507	570	560425916	560425853	4.200000e-06	63.9
32	TraesCS2A01G312700	chr6A	84.375	64	10	0	507	570	560438279	560438216	4.200000e-06	63.9
33	TraesCS2A01G312700	chr1A	85.965	114	15	1	631	743	101327583	101327470	2.460000e-23	121.0
34	TraesCS2A01G312700	chr1A	97.297	37	1	0	2902	2938	367025162	367025126	4.200000e-06	63.9
35	TraesCS2A01G312700	chr1A	83.582	67	10	1	509	574	128043211	128043277	1.510000e-05	62.1
36	TraesCS2A01G312700	chr1D	83.621	116	19	0	507	622	487204248	487204363	5.320000e-20	110.0
37	TraesCS2A01G312700	chr4D	97.368	38	1	0	2902	2939	408572549	408572512	1.170000e-06	65.8
38	TraesCS2A01G312700	chr5D	91.304	46	3	1	2895	2940	47855906	47855862	1.510000e-05	62.1
39	TraesCS2A01G312700	chr7A	89.583	48	3	2	2902	2948	591163650	591163604	5.430000e-05	60.2

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	TraesCS2A01G312700	chr2A	537399885	537404910	5025	False	9282	9282	100.0000	1	5026	1	chr2A.!!$F1	5025
1	TraesCS2A01G312700	chr2D	400050923	400054987	4064	False	2040	5321	93.0040	784	5026	3	chr2D.!!$F1	4242
2	TraesCS2A01G312700	chr2B	474403209	474407163	3954	False	1819	2848	94.5510	825	4337	3	chr2B.!!$F2	3512
3	TraesCS2A01G312700	chr7B	104081283	104082024	741	True	1219	1219	96.3610	1	741	1	chr7B.!!$R1	740
4	TraesCS2A01G312700	chrUn	31685188	31685756	568	True	713	713	89.2670	161	742	1	chrUn.!!$R2	581
5	TraesCS2A01G312700	chr1B	248260188	248260957	769	False	467	699	90.8675	1	742	2	chr1B.!!$F1	741
6	TraesCS2A01G312700	chr7D	460521221	460521781	560	False	534	534	84.1380	173	741	1	chr7D.!!$F2	568

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
764	814	0.321671	ATGAGTGCTTGCGTGGTACT	59.678	50.0	0.00	0.0	32.67	2.73	F
769	819	0.462937	TGCTTGCGTGGTACTGTGTT	60.463	50.0	0.00	0.0	0.00	3.32	F
1528	1917	0.704076	TTGGGGAGTCAAATCAGGGG	59.296	55.0	0.00	0.0	0.00	4.79	F
2712	3114	2.234908	GTGGAGCAGTACTGAGGATGTT	59.765	50.0	27.08	0.0	0.00	2.71	F
3741	4271	2.169769	CCCAAGGAAGATTACTACGCCA	59.830	50.0	0.00	0.0	0.00	5.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1989	2390	0.678048	GTCCCATCAGGCAGTCCAAC	60.678	60.000	0.0	0.0	34.51	3.77	R
2039	2440	1.072331	GGCTCAGGAAGTTGAACAGGA	59.928	52.381	0.0	0.0	0.00	3.86	R
3087	3615	2.582636	AGGAATGTTGCCCATCTTACCT	59.417	45.455	0.0	0.0	31.75	3.08	R
3788	4318	0.394899	CCTCTTTGCCACCATCCTCC	60.395	60.000	0.0	0.0	0.00	4.30	R
4883	5448	0.038744	CTGGGATGCTGGTGGAGTTT	59.961	55.000	0.0	0.0	0.00	2.66	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
152	153	3.709587	ACTCCCTCCGTCTCAAGATAAA	58.290	45.455	0.00	0.00	0.00	1.40
266	309	4.082841	ACACATCTTCACAAAATATGCGCA	60.083	37.500	14.96	14.96	0.00	6.09
286	329	3.062909	GCAGGGAACAAAAACGGAAAAAC	59.937	43.478	0.00	0.00	0.00	2.43
567	617	6.806668	TGAAGTGGGTTCATATGTATCTGA	57.193	37.500	1.90	0.00	40.45	3.27
571	621	7.200434	AGTGGGTTCATATGTATCTGAGTTT	57.800	36.000	1.90	0.00	0.00	2.66
673	723	7.116805	GTCTTGAATCATTTCTTCGGCATTTTT	59.883	33.333	0.00	0.00	32.78	1.94
686	736	9.921637	TCTTCGGCATTTTTATGTCTTATTTTT	57.078	25.926	0.00	0.00	0.00	1.94
747	797	6.718389	CGTGCACGCATACTAGTATATATG	57.282	41.667	28.16	13.26	32.83	1.78
748	798	6.483687	CGTGCACGCATACTAGTATATATGA	58.516	40.000	28.16	2.62	31.54	2.15
749	799	6.629252	CGTGCACGCATACTAGTATATATGAG	59.371	42.308	28.16	9.86	35.46	2.90
750	800	7.473366	GTGCACGCATACTAGTATATATGAGT	58.527	38.462	15.03	10.47	40.92	3.41
752	802	7.900299	CACGCATACTAGTATATATGAGTGC	57.100	40.000	20.20	15.29	45.85	4.40
753	803	7.698628	CACGCATACTAGTATATATGAGTGCT	58.301	38.462	20.20	6.97	45.85	4.40
754	804	8.184848	CACGCATACTAGTATATATGAGTGCTT	58.815	37.037	20.20	9.55	45.85	3.91
755	805	8.184848	ACGCATACTAGTATATATGAGTGCTTG	58.815	37.037	15.03	5.02	39.43	4.01
756	806	7.166638	CGCATACTAGTATATATGAGTGCTTGC	59.833	40.741	15.03	10.02	31.54	4.01
757	807	7.166638	GCATACTAGTATATATGAGTGCTTGCG	59.833	40.741	15.03	0.00	31.54	4.85
758	808	6.576662	ACTAGTATATATGAGTGCTTGCGT	57.423	37.500	0.00	0.00	0.00	5.24
759	809	6.382608	ACTAGTATATATGAGTGCTTGCGTG	58.617	40.000	0.00	0.00	0.00	5.34
760	810	4.560128	AGTATATATGAGTGCTTGCGTGG	58.440	43.478	0.00	0.00	0.00	4.94
761	811	2.979814	TATATGAGTGCTTGCGTGGT	57.020	45.000	0.00	0.00	0.00	4.16
762	812	2.979814	ATATGAGTGCTTGCGTGGTA	57.020	45.000	0.00	0.00	0.00	3.25
763	813	2.004583	TATGAGTGCTTGCGTGGTAC	57.995	50.000	0.00	0.00	0.00	3.34
764	814	0.321671	ATGAGTGCTTGCGTGGTACT	59.678	50.000	0.00	0.00	32.67	2.73
765	815	0.599991	TGAGTGCTTGCGTGGTACTG	60.600	55.000	0.00	0.00	30.31	2.74

Showing 1 to 25 of 186 entries

Previous1 2 3 4 5…8Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
152	153	3.182887	ACTCCCTCTGTCTTGAGTCAT	57.817	47.619	0.00	0.00	32.85	3.06
266	309	4.538746	TGTTTTTCCGTTTTTGTTCCCT	57.461	36.364	0.00	0.00	0.00	4.20
286	329	4.085107	GCGGCGGCAAAATAAAAAGATATG	60.085	41.667	9.78	0.00	39.62	1.78
322	365	3.527533	ACGCTATTTCGAAGCACCAATA	58.472	40.909	8.23	0.00	40.08	1.90
701	751	1.330521	CAATGCGCGCCTTTACACTAT	59.669	47.619	30.77	9.00	0.00	2.12
742	792	2.979814	ACCACGCAAGCACTCATATA	57.020	45.000	0.00	0.00	45.62	0.86
743	793	2.168521	AGTACCACGCAAGCACTCATAT	59.831	45.455	0.00	0.00	45.62	1.78
744	794	1.548719	AGTACCACGCAAGCACTCATA	59.451	47.619	0.00	0.00	45.62	2.15
745	795	0.321671	AGTACCACGCAAGCACTCAT	59.678	50.000	0.00	0.00	45.62	2.90
746	796	0.599991	CAGTACCACGCAAGCACTCA	60.600	55.000	0.00	0.00	45.62	3.41
747	797	0.600255	ACAGTACCACGCAAGCACTC	60.600	55.000	0.00	0.00	45.62	3.51
748	798	0.880278	CACAGTACCACGCAAGCACT	60.880	55.000	0.00	0.00	45.62	4.40
749	799	1.157870	ACACAGTACCACGCAAGCAC	61.158	55.000	0.00	0.00	45.62	4.40
750	800	0.462937	AACACAGTACCACGCAAGCA	60.463	50.000	0.00	0.00	45.62	3.91
751	801	1.504359	TAACACAGTACCACGCAAGC	58.496	50.000	0.00	0.00	45.62	4.01
753	803	6.615264	TTATTTTAACACAGTACCACGCAA	57.385	33.333	0.00	0.00	0.00	4.85
754	804	6.804770	ATTATTTTAACACAGTACCACGCA	57.195	33.333	0.00	0.00	0.00	5.24
755	805	7.741198	TGTATTATTTTAACACAGTACCACGC	58.259	34.615	0.00	0.00	0.00	5.34
756	806	7.901377	GCTGTATTATTTTAACACAGTACCACG	59.099	37.037	7.34	0.00	39.03	4.94
757	807	8.943002	AGCTGTATTATTTTAACACAGTACCAC	58.057	33.333	7.34	0.00	39.03	4.16
758	808	8.941977	CAGCTGTATTATTTTAACACAGTACCA	58.058	33.333	5.25	0.00	39.03	3.25
759	809	9.158233	TCAGCTGTATTATTTTAACACAGTACC	57.842	33.333	14.67	0.00	39.03	3.34
760	810	9.968743	GTCAGCTGTATTATTTTAACACAGTAC	57.031	33.333	14.67	0.00	39.03	2.73
761	811	9.938280	AGTCAGCTGTATTATTTTAACACAGTA	57.062	29.630	14.67	0.00	39.03	2.74
762	812	8.848474	AGTCAGCTGTATTATTTTAACACAGT	57.152	30.769	14.67	0.00	39.03	3.55

Showing 1 to 25 of 165 entries

Previous1 2 3 4 5 6 7Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.