AutoCloner

Multiple sequence alignment - TraesCS7D01G305400

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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	TraesCS7D01G305400	chr7D	100.000	4126	0	0	1	4126	386843614	386847739	0.000000e+00	7620.0
1	TraesCS7D01G305400	chr7D	74.008	731	169	16	106	825	490443608	490444328	1.130000e-70	278.0
2	TraesCS7D01G305400	chr7B	89.160	3238	189	67	923	4124	382130443	382133554	0.000000e+00	3886.0
3	TraesCS7D01G305400	chr7B	96.970	33	1	0	3452	3484	730395439	730395407	5.760000e-04	56.5
4	TraesCS7D01G305400	chr7A	92.756	2333	111	26	839	3133	436881173	436883485	0.000000e+00	3319.0
5	TraesCS7D01G305400	chr7A	91.194	670	42	9	3281	3946	436883571	436884227	0.000000e+00	894.0
6	TraesCS7D01G305400	chr7A	91.083	157	0	4	3970	4126	436884219	436884361	2.520000e-47	200.0
7	TraesCS7D01G305400	chr1A	81.795	769	135	5	1	766	520175890	520175124	1.250000e-179	640.0
8	TraesCS7D01G305400	chr3D	83.578	682	108	4	6	685	554147277	554146598	1.620000e-178	636.0
9	TraesCS7D01G305400	chr3D	94.444	36	2	0	727	762	403675284	403675319	5.760000e-04	56.5
10	TraesCS7D01G305400	chr1D	84.683	568	85	2	1	566	423828118	423827551	2.150000e-157	566.0
11	TraesCS7D01G305400	chr4A	71.510	702	174	15	8	703	26424138	26423457	9.180000e-37	165.0
12	TraesCS7D01G305400	chr2D	71.408	703	173	25	6	694	252616084	252616772	4.270000e-35	159.0
13	TraesCS7D01G305400	chr3A	72.995	374	80	19	222	584	36555384	36555021	1.210000e-20	111.0
14	TraesCS7D01G305400	chr3A	94.444	36	2	0	727	762	525627500	525627535	5.760000e-04	56.5
15	TraesCS7D01G305400	chr3A	100.000	28	0	0	3454	3481	431818513	431818540	7.000000e-03	52.8
16	TraesCS7D01G305400	chr6D	74.057	212	55	0	29	240	246935293	246935504	2.040000e-13	87.9
17	TraesCS7D01G305400	chr6D	73.659	205	54	0	36	240	246932033	246932237	3.420000e-11	80.5
18	TraesCS7D01G305400	chr6D	83.582	67	11	0	29	95	246935944	246935878	3.440000e-06	63.9
19	TraesCS7D01G305400	chr5D	73.364	214	52	5	29	240	305725426	305725216	1.590000e-09	75.0
20	TraesCS7D01G305400	chr6A	93.478	46	1	2	415	459	611322443	611322399	2.660000e-07	67.6
21	TraesCS7D01G305400	chr3B	94.872	39	2	0	728	766	457204878	457204840	1.240000e-05	62.1
22	TraesCS7D01G305400	chr4D	100.000	31	0	0	3454	3484	113929715	113929685	1.600000e-04	58.4
23	TraesCS7D01G305400	chr1B	100.000	29	0	0	3454	3482	173123443	173123471	2.000000e-03	54.7

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	TraesCS7D01G305400	chr7D	386843614	386847739	4125	False	7620	7620	100.000000	1	4126	1	chr7D.!!$F1	4125
1	TraesCS7D01G305400	chr7D	490443608	490444328	720	False	278	278	74.008000	106	825	1	chr7D.!!$F2	719
2	TraesCS7D01G305400	chr7B	382130443	382133554	3111	False	3886	3886	89.160000	923	4124	1	chr7B.!!$F1	3201
3	TraesCS7D01G305400	chr7A	436881173	436884361	3188	False	1471	3319	91.677667	839	4126	3	chr7A.!!$F1	3287
4	TraesCS7D01G305400	chr1A	520175124	520175890	766	True	640	640	81.795000	1	766	1	chr1A.!!$R1	765
5	TraesCS7D01G305400	chr3D	554146598	554147277	679	True	636	636	83.578000	6	685	1	chr3D.!!$R1	679
6	TraesCS7D01G305400	chr1D	423827551	423828118	567	True	566	566	84.683000	1	566	1	chr1D.!!$R1	565

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	End Stability	Orientation
790	792	0.378257	CACAGTGACACGCTTTGCTT	59.622	50.000	3.91	F
917	919	1.029947	CCCAGCCCACATAAACGGTC	61.030	60.000	4.79	F
1682	1725	1.546773	GGGCATGTTGTGTTAGGTCCA	60.547	52.381	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2119	2168	0.458669	GAGCATCAAACTGCATGGGG	59.541	55.000	44.77	4.96	R
2120	2169	1.471119	AGAGCATCAAACTGCATGGG	58.529	50.000	44.77	4.00	R
3361	3429	1.672356	ATGTCTCCGCCAACACAGC	60.672	57.895	0.00	4.40	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
20	21	2.143122	CTGCGCCACTAAAACTTCTGA	58.857	47.619	4.18	0.00	0.00	3.27
54	55	4.907269	TCAGATGCTCACATAATCCCCTTA	59.093	41.667	0.00	0.00	36.35	2.69
55	56	5.369404	TCAGATGCTCACATAATCCCCTTAA	59.631	40.000	0.00	0.00	36.35	1.85
62	63	7.035612	GCTCACATAATCCCCTTAAAAACTTG	58.964	38.462	0.00	0.00	0.00	3.16
68	69	9.771534	CATAATCCCCTTAAAAACTTGAAACAA	57.228	29.630	0.00	0.00	0.00	2.83
74	75	7.768582	CCCCTTAAAAACTTGAAACAAGACATT	59.231	33.333	16.65	10.41	0.00	2.71
158	160	4.996793	TGGTTTTCTCAATCCATCCTTGA	58.003	39.130	0.00	0.00	28.23	3.02
172	174	6.385443	TCCATCCTTGAACTCTACTCCATAT	58.615	40.000	0.00	0.00	0.00	1.78
220	222	5.317808	TCCATTTTTCGAAGAACCCACATA	58.682	37.500	2.87	0.00	45.90	2.29
230	232	5.376625	GAAGAACCCACATAAGATGGCATA	58.623	41.667	0.00	0.00	35.74	3.14
275	277	9.995003	AAAGTTTCATTAGGAACATGCAATAAA	57.005	25.926	0.00	0.00	34.56	1.40
276	278	8.986477	AGTTTCATTAGGAACATGCAATAAAC	57.014	30.769	0.00	0.00	34.56	2.01
287	289	7.870445	GGAACATGCAATAAACCTTTTACTTCA	59.130	33.333	0.00	0.00	0.00	3.02
311	313	9.163894	TCATCTCTTATATTTTCTGGACATCCT	57.836	33.333	0.00	0.00	36.82	3.24
324	326	5.046304	TCTGGACATCCTTTACTGAAGAAGG	60.046	44.000	0.00	0.00	43.04	3.46
335	337	9.508642	CCTTTACTGAAGAAGGTAGAAGATTTT	57.491	33.333	0.00	0.00	38.07	1.82
365	367	7.220030	AGTTTATACATTGTCTAGATGCCTGG	58.780	38.462	0.00	0.00	0.00	4.45
394	396	7.833285	ATGTGGTTAACAACTGATTTACCTT	57.167	32.000	14.21	0.00	43.61	3.50
403	405	6.016555	ACAACTGATTTACCTTATTTGCCCT	58.983	36.000	0.00	0.00	0.00	5.19
432	434	3.260632	ACTTGCCTTGAAAAACAACAGGT	59.739	39.130	0.00	0.00	34.56	4.00
464	466	4.719040	CGAATAACAAGTGGTTTACAGGC	58.281	43.478	0.00	0.00	40.96	4.85
533	535	6.579292	CGTCTATAGATTTTAAGAGGCACGAG	59.421	42.308	5.57	0.00	0.00	4.18
547	549	3.073735	CGAGAGGCCCTCTGCTGT	61.074	66.667	20.40	0.00	41.35	4.40
565	567	4.716784	TGCTGTTATCAGGAAGAGGTACAT	59.283	41.667	3.05	0.00	38.99	2.29
567	569	5.163405	GCTGTTATCAGGAAGAGGTACATGA	60.163	44.000	0.00	0.00	41.57	3.07

Showing 1 to 25 of 336 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	6.072112	TGTTGATTCAGAAGTTTTAGTGGC	57.928	37.500	0.00	0.00	0.00	5.01
20	21	7.818997	ATGTGAGCATCTGAATATGTTGATT	57.181	32.000	0.00	0.00	34.92	2.57
86	87	3.505680	TCAAGTCTGTTGCACAAGTTGTT	59.494	39.130	5.57	0.00	0.00	2.83
107	108	2.152016	GCTGGTAAGGAAGTGTTGGTC	58.848	52.381	0.00	0.00	0.00	4.02
355	357	2.442878	ACCACATATTGCCAGGCATCTA	59.557	45.455	17.09	10.83	38.76	1.98
365	367	9.072294	GTAAATCAGTTGTTAACCACATATTGC	57.928	33.333	11.97	2.56	34.43	3.56
394	396	2.513753	CAAGTGGTGACAGGGCAAATA	58.486	47.619	0.00	0.00	44.46	1.40
403	405	2.136298	TTTCAAGGCAAGTGGTGACA	57.864	45.000	0.00	0.00	37.96	3.58
432	434	4.154015	CCACTTGTTATTCGCAGATGACAA	59.846	41.667	6.51	6.51	35.04	3.18
477	479	1.354368	CATGAGTGGGGTAAAGGTGGT	59.646	52.381	0.00	0.00	0.00	4.16
533	535	0.833287	TGATAACAGCAGAGGGCCTC	59.167	55.000	26.42	26.42	46.50	4.70
547	549	7.255625	CGATCTTCATGTACCTCTTCCTGATAA	60.256	40.741	0.00	0.00	0.00	1.75
584	586	1.351017	ACACCATCCCGTGAAATCAGT	59.649	47.619	0.00	0.00	37.20	3.41
586	588	1.349357	TCACACCATCCCGTGAAATCA	59.651	47.619	0.00	0.00	39.14	2.57
587	589	2.107950	TCACACCATCCCGTGAAATC	57.892	50.000	0.00	0.00	39.14	2.17
591	593	1.339631	GGAATTCACACCATCCCGTGA	60.340	52.381	7.93	0.00	40.30	4.35
620	622	7.461749	AGTTCTCAGTTTTATTCAATGGGAGA	58.538	34.615	0.00	0.00	0.00	3.71
621	623	7.693969	AGTTCTCAGTTTTATTCAATGGGAG	57.306	36.000	0.00	0.00	0.00	4.30
623	625	9.626045	GTAAAGTTCTCAGTTTTATTCAATGGG	57.374	33.333	0.00	0.00	0.00	4.00
633	635	7.338449	TGGTAAAGCAGTAAAGTTCTCAGTTTT	59.662	33.333	0.00	0.00	0.00	2.43
634	636	6.826741	TGGTAAAGCAGTAAAGTTCTCAGTTT	59.173	34.615	0.00	0.00	0.00	2.66
635	637	6.354130	TGGTAAAGCAGTAAAGTTCTCAGTT	58.646	36.000	0.00	0.00	0.00	3.16
636	638	5.925509	TGGTAAAGCAGTAAAGTTCTCAGT	58.074	37.500	0.00	0.00	0.00	3.41
637	639	6.861065	TTGGTAAAGCAGTAAAGTTCTCAG	57.139	37.500	0.00	0.00	0.00	3.35
638	640	6.826741	AGTTTGGTAAAGCAGTAAAGTTCTCA	59.173	34.615	0.00	0.00	0.00	3.27

Showing 1 to 25 of 275 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.