AutoCloner

Multiple sequence alignment - TraesCS3B01G335100

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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	TraesCS3B01G335100	chr3B	100.000	4124	0	0	1	4124	541208135	541204012	0.000000e+00	7616.0
1	TraesCS3B01G335100	chr3B	100.000	1431	0	0	4352	5782	541203784	541202354	0.000000e+00	2643.0
2	TraesCS3B01G335100	chr3B	82.948	563	73	10	34	594	489361807	489361266	2.420000e-133	486.0
3	TraesCS3B01G335100	chr3B	87.847	288	35	0	5495	5782	295370049	295369762	7.180000e-89	339.0
4	TraesCS3B01G335100	chr3D	94.026	3783	129	40	393	4124	415165186	415161450	0.000000e+00	5644.0
5	TraesCS3B01G335100	chr3D	91.022	724	50	8	4352	5063	415161410	415160690	0.000000e+00	963.0
6	TraesCS3B01G335100	chr3D	92.513	374	17	4	1	372	415165539	415165175	5.130000e-145	525.0
7	TraesCS3B01G335100	chr3D	88.116	345	35	5	28	372	375211237	375210899	6.980000e-109	405.0
8	TraesCS3B01G335100	chr3A	95.192	2496	84	10	1638	4124	535191526	535193994	0.000000e+00	3912.0
9	TraesCS3B01G335100	chr3A	88.828	1280	53	38	393	1637	535190261	535191485	0.000000e+00	1489.0
10	TraesCS3B01G335100	chr3A	91.760	716	57	2	4352	5066	535194034	535194748	0.000000e+00	994.0
11	TraesCS3B01G335100	chr3A	94.415	376	17	2	1	372	535189897	535190272	5.020000e-160	575.0
12	TraesCS3B01G335100	chr3A	88.427	337	33	5	34	370	498247061	498246731	9.020000e-108	401.0
13	TraesCS3B01G335100	chrUn	93.154	409	26	2	5078	5486	119407212	119407618	2.980000e-167	599.0
14	TraesCS3B01G335100	chrUn	93.333	330	20	2	5078	5407	119412267	119412594	2.420000e-133	486.0
15	TraesCS3B01G335100	chr7D	92.118	406	29	3	5081	5486	625154988	625154586	2.340000e-158	569.0
16	TraesCS3B01G335100	chr7D	86.804	341	37	6	32	372	175919417	175919085	1.970000e-99	374.0
17	TraesCS3B01G335100	chr7A	89.976	409	40	1	5078	5486	19188546	19188139	1.430000e-145	527.0
18	TraesCS3B01G335100	chr4D	93.617	329	18	3	5078	5406	493791616	493791941	6.730000e-134	488.0
19	TraesCS3B01G335100	chr4D	93.561	264	15	2	5078	5341	493780285	493780546	5.430000e-105	392.0
20	TraesCS3B01G335100	chr4D	91.034	145	6	6	633	777	416451343	416451480	7.650000e-44	189.0
21	TraesCS3B01G335100	chr5D	92.424	330	20	3	5078	5406	341309539	341309864	3.160000e-127	466.0
22	TraesCS3B01G335100	chr5D	81.395	344	47	9	32	372	458925969	458926298	1.240000e-66	265.0
23	TraesCS3B01G335100	chr5D	87.500	192	22	2	394	584	458926288	458926478	2.710000e-53	220.0
24	TraesCS3B01G335100	chr2A	82.440	541	71	12	32	571	706751372	706750855	8.830000e-123	451.0
25	TraesCS3B01G335100	chr5A	92.079	303	20	4	5106	5406	524744659	524744359	1.930000e-114	424.0
26	TraesCS3B01G335100	chr5A	93.750	272	15	2	5081	5352	672595534	672595265	1.940000e-109	407.0
27	TraesCS3B01G335100	chr5A	83.430	344	48	6	32	372	577963581	577963918	1.560000e-80	311.0
28	TraesCS3B01G335100	chr5A	94.030	201	12	0	5286	5486	672600357	672600157	7.280000e-79	305.0
29	TraesCS3B01G335100	chr7B	86.804	341	36	7	32	372	141799005	141798674	7.080000e-99	372.0
30	TraesCS3B01G335100	chr7B	87.500	296	37	0	5487	5782	529479902	529479607	5.550000e-90	342.0
31	TraesCS3B01G335100	chr7B	86.301	292	38	2	5492	5782	675479030	675478740	3.360000e-82	316.0
32	TraesCS3B01G335100	chr6B	88.276	290	33	1	5492	5781	93180538	93180826	4.290000e-91	346.0
33	TraesCS3B01G335100	chr6B	100.000	29	0	0	32	60	643844128	643844156	3.000000e-03	54.7
34	TraesCS3B01G335100	chr4B	86.379	301	41	0	5482	5782	307032093	307031793	4.320000e-86	329.0
35	TraesCS3B01G335100	chr4B	86.916	214	21	5	393	601	513100773	513100984	3.480000e-57	233.0
36	TraesCS3B01G335100	chr4B	94.483	145	8	0	633	777	513101057	513101201	2.100000e-54	224.0
37	TraesCS3B01G335100	chr1B	86.869	297	36	3	5487	5782	440162309	440162015	4.320000e-86	329.0
38	TraesCS3B01G335100	chr1B	86.275	204	25	3	393	594	429583897	429583695	9.750000e-53	219.0
39	TraesCS3B01G335100	chr5B	85.522	297	43	0	5486	5782	618624522	618624226	1.560000e-80	311.0
40	TraesCS3B01G335100	chr5B	81.686	344	46	10	32	372	562979095	562979424	2.660000e-68	270.0
41	TraesCS3B01G335100	chr5B	84.615	117	16	2	395	511	157594712	157594598	1.320000e-21	115.0
42	TraesCS3B01G335100	chr2B	85.666	293	39	3	5492	5782	213001954	213001663	7.280000e-79	305.0
43	TraesCS3B01G335100	chr2B	85.862	290	38	3	5492	5780	431613656	431613943	7.280000e-79	305.0
44	TraesCS3B01G335100	chr2B	96.970	33	1	0	32	64	437091717	437091749	8.090000e-04	56.5
45	TraesCS3B01G335100	chr1A	81.473	421	32	19	393	777	508197945	508197535	2.620000e-78	303.0
46	TraesCS3B01G335100	chr1D	86.932	176	21	2	393	567	317427229	317427055	4.570000e-46	196.0
47	TraesCS3B01G335100	chr4A	90.345	145	6	3	633	777	47627007	47626871	3.560000e-42	183.0

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	TraesCS3B01G335100	chr3B	541202354	541208135	5781	True	5129.500000	7616	100.000000	1	5782	2	chr3B.!!$R3	5781
1	TraesCS3B01G335100	chr3B	489361266	489361807	541	True	486.000000	486	82.948000	34	594	1	chr3B.!!$R2	560
2	TraesCS3B01G335100	chr3D	415160690	415165539	4849	True	2377.333333	5644	92.520333	1	5063	3	chr3D.!!$R2	5062
3	TraesCS3B01G335100	chr3A	535189897	535194748	4851	False	1742.500000	3912	92.548750	1	5066	4	chr3A.!!$F1	5065
4	TraesCS3B01G335100	chr5D	458925969	458926478	509	False	242.500000	265	84.447500	32	584	2	chr5D.!!$F2	552
5	TraesCS3B01G335100	chr2A	706750855	706751372	517	True	451.000000	451	82.440000	32	571	1	chr2A.!!$R1	539

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	Hairpin	End Stability	Orientation
660	713	0.029567	CCTGGACGTCTAGCGATGAC	59.970	60.0	22.41	44.77	3.06	F
1093	1191	0.033504	TCTCTCCGGCTGTGTGTTTC	59.966	55.0	0.00	0.00	2.78	F
1545	1653	0.391130	GGGATGCTACGTGCTGTCAA	60.391	55.0	0.00	43.37	3.18	F
3092	3246	0.466124	AGGGAAGCATCGCCTAACTC	59.534	55.0	2.02	39.23	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1905	2053	1.283793	CACAAAGCCAGCCTTCACG	59.716	57.895	31.99	4.35	R
2409	2560	2.887152	AGCTGGTCAGGTCATTGAAAAC	59.113	45.455	33.18	2.43	R
3240	3394	2.215196	TCTAAACAAGAACGTGGGCAC	58.785	47.619	0.00	5.01	R
5090	5259	0.319900	TGTCCGCTTCTGCTTCAGTC	60.320	55.000	36.97	3.51	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
66	70	1.747444	ACAGGGTGGTCCATCTTCTT	58.253	50.000	1.17	0.00	38.24	2.52
67	71	1.630878	ACAGGGTGGTCCATCTTCTTC	59.369	52.381	1.17	0.00	38.24	2.87
68	72	1.912043	CAGGGTGGTCCATCTTCTTCT	59.088	52.381	1.17	0.00	38.24	2.85
109	113	9.368674	TGACATGCCAACATTCTAATTAATTTG	57.631	29.630	5.91	4.59	32.87	2.32
257	266	0.863144	TTTGTTAAGAGTGGCGTCGC	59.137	50.000	9.22	9.22	0.00	5.19
323	332	8.865978	CATTATTTTGTCATTGATCAGGTGTTG	58.134	33.333	0.00	0.00	0.00	3.33
360	385	7.656412	AGCAAAATAATGTGTATGTGTTCACA	58.344	30.769	8.09	8.09	46.23	3.58
361	386	7.809331	AGCAAAATAATGTGTATGTGTTCACAG	59.191	33.333	11.24	0.00	45.56	3.66
362	387	7.062138	GCAAAATAATGTGTATGTGTTCACAGG	59.938	37.037	11.24	0.00	45.56	4.00
363	388	7.994425	AAATAATGTGTATGTGTTCACAGGA	57.006	32.000	11.24	0.00	45.56	3.86
364	389	6.985188	ATAATGTGTATGTGTTCACAGGAC	57.015	37.500	11.24	11.34	45.56	3.85
365	390	4.623932	ATGTGTATGTGTTCACAGGACT	57.376	40.909	11.24	0.00	45.56	3.85
367	392	3.133901	TGTGTATGTGTTCACAGGACTGT	59.866	43.478	11.24	0.00	46.17	3.55
428	453	0.750850	TACTGGATAGCAAGTCCGGC	59.249	55.000	0.00	0.00	44.42	6.13
452	477	6.255020	GCTGTTTAGCTAACGCAATAGACTTA	59.745	38.462	5.45	0.00	46.57	2.24
467	492	3.436243	AGACTTAGACTCTTCCACCTGG	58.564	50.000	0.00	0.00	0.00	4.45
481	506	3.202818	TCCACCTGGTTGATGCAATAGAT	59.797	43.478	0.00	0.00	36.34	1.98
660	713	0.029567	CCTGGACGTCTAGCGATGAC	59.970	60.000	22.41	0.00	44.77	3.06
667	720	0.592754	GTCTAGCGATGACGAGGCAC	60.593	60.000	0.00	0.00	42.66	5.01
795	860	1.990160	TTTGTTGGGCTGAGACGGGT	61.990	55.000	0.00	0.00	0.00	5.28
841	910	3.565764	TTCTCAGGCCCATCTGTAATG	57.434	47.619	0.00	0.00	36.25	1.90
842	911	1.770658	TCTCAGGCCCATCTGTAATGG	59.229	52.381	0.00	0.00	38.88	3.16
843	912	1.492176	CTCAGGCCCATCTGTAATGGT	59.508	52.381	0.00	0.00	37.48	3.55
844	913	2.705658	CTCAGGCCCATCTGTAATGGTA	59.294	50.000	0.00	0.00	37.48	3.25
846	915	3.072915	TCAGGCCCATCTGTAATGGTATG	59.927	47.826	0.00	0.17	37.48	2.39

Showing 1 to 25 of 589 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
66	70	6.314018	GCATGTCATATTTGTTGTCGAAAGA	58.686	36.000	0.00	0.00	38.16	2.52
67	71	5.512788	GGCATGTCATATTTGTTGTCGAAAG	59.487	40.000	0.00	0.00	0.00	2.62
68	72	5.048434	TGGCATGTCATATTTGTTGTCGAAA	60.048	36.000	0.00	0.00	0.00	3.46
222	230	6.638873	TCTTAACAAATTAACAATGCCACACG	59.361	34.615	0.00	0.00	0.00	4.49
257	266	4.621886	GCCACTCTTAACAAGTTACTCGAG	59.378	45.833	11.84	11.84	0.00	4.04
259	268	4.304110	TGCCACTCTTAACAAGTTACTCG	58.696	43.478	0.00	0.00	0.00	4.18
323	332	8.893727	ACACATTATTTTGCTATCCAGTACTTC	58.106	33.333	0.00	0.00	0.00	3.01
379	404	9.313118	GAACACACAGTCCTTTTATTTCAAATT	57.687	29.630	0.00	0.00	0.00	1.82
380	405	8.474025	TGAACACACAGTCCTTTTATTTCAAAT	58.526	29.630	0.00	0.00	0.00	2.32
381	406	7.831753	TGAACACACAGTCCTTTTATTTCAAA	58.168	30.769	0.00	0.00	0.00	2.69
382	407	7.397892	TGAACACACAGTCCTTTTATTTCAA	57.602	32.000	0.00	0.00	0.00	2.69
383	408	7.068103	ACATGAACACACAGTCCTTTTATTTCA	59.932	33.333	0.00	0.00	0.00	2.69
384	409	7.425606	ACATGAACACACAGTCCTTTTATTTC	58.574	34.615	0.00	0.00	0.00	2.17
385	410	7.346751	ACATGAACACACAGTCCTTTTATTT	57.653	32.000	0.00	0.00	0.00	1.40
386	411	6.959639	ACATGAACACACAGTCCTTTTATT	57.040	33.333	0.00	0.00	0.00	1.40
387	412	7.173218	CAGTACATGAACACACAGTCCTTTTAT	59.827	37.037	0.00	0.00	0.00	1.40
388	413	6.481976	CAGTACATGAACACACAGTCCTTTTA	59.518	38.462	0.00	0.00	0.00	1.52
389	414	5.296780	CAGTACATGAACACACAGTCCTTTT	59.703	40.000	0.00	0.00	0.00	2.27
390	415	4.816385	CAGTACATGAACACACAGTCCTTT	59.184	41.667	0.00	0.00	0.00	3.11
391	416	4.380531	CAGTACATGAACACACAGTCCTT	58.619	43.478	0.00	0.00	0.00	3.36
428	453	6.648725	AAGTCTATTGCGTTAGCTAAACAG	57.351	37.500	7.99	4.22	45.42	3.16
452	477	2.103153	TCAACCAGGTGGAAGAGTCT	57.897	50.000	2.10	0.00	38.94	3.24
467	492	6.141462	GCTCTTTGCTATCTATTGCATCAAC	58.859	40.000	0.05	0.00	38.26	3.18
481	506	2.566833	TCAGGCTTTGCTCTTTGCTA	57.433	45.000	0.00	0.00	43.37	3.49
552	578	0.967380	AAGCCTTGAGCCCGATTTGG	60.967	55.000	0.00	0.00	45.47	3.28

Showing 1 to 25 of 598 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.