AutoCloner

Multiple sequence alignment - TraesCS3A01G520300

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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	TraesCS3A01G520300	chr3A	100.000	4767	0	0	1	4767	737383015	737378249	0.000000e+00	8804.0
1	TraesCS3A01G520300	chr3B	88.772	2004	194	21	209	2189	814158018	814156023	0.000000e+00	2425.0
2	TraesCS3A01G520300	chr3B	86.767	1194	149	7	998	2189	815043499	815042313	0.000000e+00	1321.0
3	TraesCS3A01G520300	chr3B	88.402	1095	125	2	998	2091	814747739	814746646	0.000000e+00	1317.0
4	TraesCS3A01G520300	chr3B	86.195	1188	157	6	995	2181	814895873	814894692	0.000000e+00	1279.0
5	TraesCS3A01G520300	chr3B	86.995	1138	139	7	995	2129	814659161	814658030	0.000000e+00	1273.0
6	TraesCS3A01G520300	chr3B	85.642	1184	163	7	999	2181	814575190	814574013	0.000000e+00	1238.0
7	TraesCS3A01G520300	chr3B	85.852	933	83	27	3361	4292	814844785	814843901	0.000000e+00	946.0
8	TraesCS3A01G520300	chr3B	87.857	700	76	8	3289	3979	815037654	815036955	0.000000e+00	813.0
9	TraesCS3A01G520300	chr3B	87.372	681	74	6	3289	3969	814573271	814572603	0.000000e+00	771.0
10	TraesCS3A01G520300	chr3B	86.147	693	74	12	3289	3979	814745721	814745049	0.000000e+00	728.0
11	TraesCS3A01G520300	chr3B	85.484	682	75	11	3298	3979	814154012	814153355	0.000000e+00	689.0
12	TraesCS3A01G520300	chr3B	85.239	691	78	12	3289	3979	814893629	814892963	0.000000e+00	689.0
13	TraesCS3A01G520300	chr3B	84.370	691	83	13	3289	3979	814654867	814654202	0.000000e+00	654.0
14	TraesCS3A01G520300	chr3B	88.415	164	15	4	4568	4730	814843645	814843485	1.350000e-45	195.0
15	TraesCS3A01G520300	chr3B	86.782	174	22	1	4118	4291	814572484	814572312	4.870000e-45	193.0
16	TraesCS3A01G520300	chr3B	92.593	108	7	1	4183	4290	814503992	814503886	2.300000e-33	154.0
17	TraesCS3A01G520300	chr3B	86.331	139	17	2	4118	4255	814800587	814800450	2.970000e-32	150.0
18	TraesCS3A01G520300	chr3B	83.660	153	20	5	4118	4268	814654060	814653911	6.430000e-29	139.0
19	TraesCS3A01G520300	chr3B	80.137	146	13	5	4626	4767	814503337	814503204	1.410000e-15	95.3
20	TraesCS3A01G520300	chr5D	87.172	1411	164	10	995	2391	41143145	41141738	0.000000e+00	1587.0
21	TraesCS3A01G520300	chr5D	90.244	1066	78	15	3116	4179	41141074	41140033	0.000000e+00	1369.0
22	TraesCS3A01G520300	chr5D	88.112	429	33	10	2463	2880	41141514	41141093	1.190000e-135	494.0
23	TraesCS3A01G520300	chr5D	87.075	147	13	2	4626	4767	41139309	41139164	1.370000e-35	161.0
24	TraesCS3A01G520300	chr5D	93.578	109	4	2	4183	4291	41139964	41139859	4.940000e-35	159.0
25	TraesCS3A01G520300	chr5D	74.550	389	39	42	369	734	41143799	41143448	1.080000e-21	115.0
26	TraesCS3A01G520300	chr5D	84.615	104	8	6	2364	2460	41141737	41141635	3.930000e-16	97.1
27	TraesCS3A01G520300	chr5D	95.455	44	2	0	2687	2730	41141693	41141650	2.380000e-08	71.3
28	TraesCS3A01G520300	chr5B	86.719	1408	172	10	995	2391	35257804	35256401	0.000000e+00	1550.0
29	TraesCS3A01G520300	chr5B	89.493	1066	85	16	3116	4179	35255737	35254697	0.000000e+00	1323.0
30	TraesCS3A01G520300	chr5B	99.548	221	1	0	2895	3115	292191583	292191803	2.070000e-108	403.0
31	TraesCS3A01G520300	chr5B	99.548	221	1	0	2895	3115	352993146	352993366	2.070000e-108	403.0
32	TraesCS3A01G520300	chr5B	94.495	109	3	2	4183	4291	35254628	35254523	1.060000e-36	165.0
33	TraesCS3A01G520300	chr5B	83.803	142	17	3	4626	4767	35252293	35252158	3.870000e-26	130.0
34	TraesCS3A01G520300	chr5B	84.615	104	8	6	2364	2460	35256400	35256298	3.930000e-16	97.1
35	TraesCS3A01G520300	chr5B	95.652	46	2	0	2687	2732	35256356	35256311	1.840000e-09	75.0
36	TraesCS3A01G520300	chrUn	86.917	1200	140	10	995	2189	46233160	46234347	0.000000e+00	1330.0
37	TraesCS3A01G520300	chrUn	85.735	694	69	15	3286	3976	46236587	46237253	0.000000e+00	706.0
38	TraesCS3A01G520300	chr3D	88.608	474	42	4	3289	3762	606481274	606480813	2.490000e-157	566.0
39	TraesCS3A01G520300	chr6B	99.115	226	1	1	2895	3119	46958935	46959160	5.740000e-109	405.0
40	TraesCS3A01G520300	chr6B	99.550	222	1	0	2895	3116	96639047	96638826	5.740000e-109	405.0
41	TraesCS3A01G520300	chr6B	98.261	230	2	1	2895	3122	689168755	689168984	7.430000e-108	401.0
42	TraesCS3A01G520300	chr2B	99.550	222	1	0	2895	3116	38277086	38276865	5.740000e-109	405.0
43	TraesCS3A01G520300	chr2B	99.550	222	1	0	2895	3116	631870689	631870468	5.740000e-109	405.0
44	TraesCS3A01G520300	chr6A	99.548	221	1	0	2895	3115	222648694	222648474	2.070000e-108	403.0
45	TraesCS3A01G520300	chr1B	99.548	221	1	0	2895	3115	151843167	151842947	2.070000e-108	403.0

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	TraesCS3A01G520300	chr3A	737378249	737383015	4766	True	8804.000000	8804	100.000000	1	4767	1	chr3A.!!$R1	4766
1	TraesCS3A01G520300	chr3B	814153355	814158018	4663	True	1557.000000	2425	87.128000	209	3979	2	chr3B.!!$R4	3770
2	TraesCS3A01G520300	chr3B	815042313	815043499	1186	True	1321.000000	1321	86.767000	998	2189	1	chr3B.!!$R3	1191
3	TraesCS3A01G520300	chr3B	814745049	814747739	2690	True	1022.500000	1317	87.274500	998	3979	2	chr3B.!!$R8	2981
4	TraesCS3A01G520300	chr3B	814892963	814895873	2910	True	984.000000	1279	85.717000	995	3979	2	chr3B.!!$R10	2984
5	TraesCS3A01G520300	chr3B	815036955	815037654	699	True	813.000000	813	87.857000	3289	3979	1	chr3B.!!$R2	690
6	TraesCS3A01G520300	chr3B	814572312	814575190	2878	True	734.000000	1238	86.598667	999	4291	3	chr3B.!!$R6	3292
7	TraesCS3A01G520300	chr3B	814653911	814659161	5250	True	688.666667	1273	85.008333	995	4268	3	chr3B.!!$R7	3273
8	TraesCS3A01G520300	chr3B	814843485	814844785	1300	True	570.500000	946	87.133500	3361	4730	2	chr3B.!!$R9	1369
9	TraesCS3A01G520300	chr5D	41139164	41143799	4635	True	506.675000	1587	87.600125	369	4767	8	chr5D.!!$R1	4398
10	TraesCS3A01G520300	chr5B	35252158	35257804	5646	True	556.683333	1550	89.129500	995	4767	6	chr5B.!!$R1	3772
11	TraesCS3A01G520300	chrUn	46233160	46237253	4093	False	1018.000000	1330	86.326000	995	3976	2	chrUn.!!$F1	2981

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
337	344	0.035439	GCTCCCCAAAACCAGATCGA	60.035	55.0	0.0	0.0	0.00	3.59	F
815	875	0.111446	TTTGGTCGCCATTGAAGGGA	59.889	50.0	0.0	0.0	31.53	4.20	F
1362	1485	0.115152	TCAGAGCTGAGGTGGAGGAA	59.885	55.0	0.0	0.0	34.14	3.36	F
3023	6849	0.179037	TGCTATCCATGTGCCAGAGC	60.179	55.0	0.0	0.0	40.48	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2283	2420	0.255890	CAACCGGATGATGGGGAAGT	59.744	55.0	9.46	0.0	0.0	3.01	R
2738	3488	0.106708	ATGTGCTGACCAGTGAACGT	59.893	50.0	0.00	0.0	0.0	3.99	R
3072	6898	0.036294	GCCTTTAGTCCCAAGCGAGT	60.036	55.0	0.00	0.0	0.0	4.18	R
4645	10866	2.094390	CCATGGTGCAAGGAGAATGTTG	60.094	50.0	2.57	0.0	0.0	3.33	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
17	18	4.863707	ATCCCACTGCGTGCTATG	57.136	55.556	3.56	0.00	31.34	2.23
18	19	1.907739	ATCCCACTGCGTGCTATGT	59.092	52.632	3.56	0.00	31.34	2.29
19	20	1.119684	ATCCCACTGCGTGCTATGTA	58.880	50.000	3.56	0.00	31.34	2.29
20	21	0.459899	TCCCACTGCGTGCTATGTAG	59.540	55.000	3.56	0.00	31.34	2.74
21	22	0.175760	CCCACTGCGTGCTATGTAGT	59.824	55.000	3.56	0.00	29.93	2.73
22	23	1.407618	CCCACTGCGTGCTATGTAGTA	59.592	52.381	3.56	0.00	28.85	1.82
23	24	2.543861	CCCACTGCGTGCTATGTAGTAG	60.544	54.545	3.56	0.00	28.85	2.57
24	25	2.099263	CCACTGCGTGCTATGTAGTAGT	59.901	50.000	3.56	0.00	28.85	2.73
25	26	3.314357	CCACTGCGTGCTATGTAGTAGTA	59.686	47.826	3.56	0.00	28.85	1.82
26	27	4.023107	CCACTGCGTGCTATGTAGTAGTAT	60.023	45.833	3.56	0.00	28.85	2.12
27	28	5.507482	CCACTGCGTGCTATGTAGTAGTATT	60.507	44.000	3.56	0.00	28.85	1.89
28	29	6.293790	CCACTGCGTGCTATGTAGTAGTATTA	60.294	42.308	3.56	0.00	28.85	0.98
29	30	7.136772	CACTGCGTGCTATGTAGTAGTATTAA	58.863	38.462	0.00	0.00	28.85	1.40
30	31	7.808381	CACTGCGTGCTATGTAGTAGTATTAAT	59.192	37.037	0.00	0.00	28.85	1.40
31	32	8.358148	ACTGCGTGCTATGTAGTAGTATTAATT	58.642	33.333	0.00	0.00	28.09	1.40
32	33	9.193133	CTGCGTGCTATGTAGTAGTATTAATTT	57.807	33.333	0.00	0.00	32.72	1.82
33	34	8.974408	TGCGTGCTATGTAGTAGTATTAATTTG	58.026	33.333	0.00	0.00	32.72	2.32
34	35	9.188588	GCGTGCTATGTAGTAGTATTAATTTGA	57.811	33.333	0.00	0.00	32.72	2.69
42	43	9.263446	TGTAGTAGTATTAATTTGACTCCAGGT	57.737	33.333	0.00	0.00	0.00	4.00
43	44	9.530633	GTAGTAGTATTAATTTGACTCCAGGTG	57.469	37.037	0.00	0.00	0.00	4.00
44	45	7.048512	AGTAGTATTAATTTGACTCCAGGTGC	58.951	38.462	0.00	0.00	0.00	5.01
45	46	5.815581	AGTATTAATTTGACTCCAGGTGCA	58.184	37.500	0.00	0.00	0.00	4.57
46	47	5.648092	AGTATTAATTTGACTCCAGGTGCAC	59.352	40.000	8.80	8.80	0.00	4.57
47	48	1.620822	AATTTGACTCCAGGTGCACC	58.379	50.000	29.22	29.22	0.00	5.01
49	50	0.550914	TTTGACTCCAGGTGCACCTT	59.449	50.000	36.06	21.95	46.09	3.50

Showing 1 to 25 of 446 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	8.744008	AATTAATACTACTACATAGCACGCAG	57.256	34.615	0.00	0.00	33.73	5.18
8	9	9.188588	TCAAATTAATACTACTACATAGCACGC	57.811	33.333	0.00	0.00	33.73	5.34
16	17	9.263446	ACCTGGAGTCAAATTAATACTACTACA	57.737	33.333	0.00	8.05	0.00	2.74
17	18	9.530633	CACCTGGAGTCAAATTAATACTACTAC	57.469	37.037	0.00	1.40	0.00	2.73
18	19	8.202137	GCACCTGGAGTCAAATTAATACTACTA	58.798	37.037	0.00	0.00	0.00	1.82
19	20	7.048512	GCACCTGGAGTCAAATTAATACTACT	58.951	38.462	0.00	0.00	0.00	2.57
20	21	6.821665	TGCACCTGGAGTCAAATTAATACTAC	59.178	38.462	0.00	0.00	0.00	2.73
21	22	6.821665	GTGCACCTGGAGTCAAATTAATACTA	59.178	38.462	5.22	0.00	0.00	1.82
22	23	5.648092	GTGCACCTGGAGTCAAATTAATACT	59.352	40.000	5.22	0.00	0.00	2.12
23	24	5.163652	GGTGCACCTGGAGTCAAATTAATAC	60.164	44.000	29.12	0.00	0.00	1.89
24	25	4.947388	GGTGCACCTGGAGTCAAATTAATA	59.053	41.667	29.12	0.00	0.00	0.98
25	26	3.763897	GGTGCACCTGGAGTCAAATTAAT	59.236	43.478	29.12	0.00	0.00	1.40
26	27	3.153919	GGTGCACCTGGAGTCAAATTAA	58.846	45.455	29.12	0.00	0.00	1.40
27	28	2.375174	AGGTGCACCTGGAGTCAAATTA	59.625	45.455	37.39	0.00	46.55	1.40
28	29	1.145738	AGGTGCACCTGGAGTCAAATT	59.854	47.619	37.39	8.97	46.55	1.82
29	30	0.773644	AGGTGCACCTGGAGTCAAAT	59.226	50.000	37.39	9.56	46.55	2.32
30	31	2.230664	AGGTGCACCTGGAGTCAAA	58.769	52.632	37.39	0.00	46.55	2.69
31	32	3.986054	AGGTGCACCTGGAGTCAA	58.014	55.556	37.39	0.00	46.55	3.18
40	41	2.574018	GGCCCTTCAAAGGTGCACC	61.574	63.158	29.22	29.22	44.98	5.01
41	42	1.809567	CTGGCCCTTCAAAGGTGCAC	61.810	60.000	8.80	8.80	44.98	4.57
42	43	1.531365	CTGGCCCTTCAAAGGTGCA	60.531	57.895	18.07	0.00	44.98	4.57
43	44	2.935740	GCTGGCCCTTCAAAGGTGC	61.936	63.158	0.00	10.04	44.98	5.01
44	45	2.278330	GGCTGGCCCTTCAAAGGTG	61.278	63.158	0.00	1.27	44.98	4.00
45	46	2.118294	GGCTGGCCCTTCAAAGGT	59.882	61.111	0.00	0.00	44.98	3.50
55	56	2.806009	TTGCAAAAGTGGGCTGGCC	61.806	57.895	14.23	14.23	0.00	5.36

Showing 1 to 25 of 454 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.