AutoCloner

Multiple sequence alignment - TraesCS2D01G239600

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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	TraesCS2D01G239600	chr2D	100.000	6613	0	0	1	6613	255622894	255616282	0.000000e+00	12213.0
1	TraesCS2D01G239600	chr2D	95.322	171	6	1	5896	6064	396613963	396613793	3.040000e-68	270.0
2	TraesCS2D01G239600	chr2D	92.308	52	3	1	4959	5010	119281357	119281307	9.200000e-09	73.1
3	TraesCS2D01G239600	chr2A	97.032	5087	87	18	836	5916	236834247	236839275	0.000000e+00	8499.0
4	TraesCS2D01G239600	chr2A	97.143	245	6	1	6249	6492	236841202	236841446	4.770000e-111	412.0
5	TraesCS2D01G239600	chr2A	96.759	216	7	0	6038	6253	236839320	236839535	1.750000e-95	361.0
6	TraesCS2D01G239600	chr2A	90.833	120	10	1	6495	6613	236841666	236841785	6.860000e-35	159.0
7	TraesCS2D01G239600	chr2A	95.349	86	4	0	6528	6613	236841806	236841891	3.220000e-28	137.0
8	TraesCS2D01G239600	chr2A	94.737	57	2	1	4961	5017	40430385	40430330	3.290000e-13	87.9
9	TraesCS2D01G239600	chr2B	95.306	2791	77	23	836	3592	280483054	280485824	0.000000e+00	4379.0
10	TraesCS2D01G239600	chr2B	97.004	701	19	1	4056	4756	280493557	280494255	0.000000e+00	1177.0
11	TraesCS2D01G239600	chr2B	91.446	643	24	10	5262	5899	280495794	280496410	0.000000e+00	854.0
12	TraesCS2D01G239600	chr2B	85.041	849	96	19	1	832	616478177	616477343	0.000000e+00	835.0
13	TraesCS2D01G239600	chr2B	93.359	512	17	10	3576	4073	280492692	280493200	0.000000e+00	741.0
14	TraesCS2D01G239600	chr2B	90.811	555	41	7	6057	6605	280496410	280496960	0.000000e+00	734.0
15	TraesCS2D01G239600	chr2B	91.093	494	33	8	6118	6605	280497080	280497568	0.000000e+00	658.0
16	TraesCS2D01G239600	chr2B	96.736	337	11	0	4929	5265	280495377	280495713	4.480000e-156	562.0
17	TraesCS2D01G239600	chr2B	96.708	243	5	2	4739	4981	280495130	280495369	1.030000e-107	401.0
18	TraesCS2D01G239600	chr2B	90.625	288	20	4	6118	6402	280497682	280497965	6.260000e-100	375.0
19	TraesCS2D01G239600	chr2B	95.420	131	5	1	6476	6605	280497967	280498097	2.420000e-49	207.0
20	TraesCS2D01G239600	chr4D	86.068	847	93	17	3	832	296675998	296676836	0.000000e+00	887.0
21	TraesCS2D01G239600	chr4D	83.590	195	28	4	3918	4110	294346465	294346273	5.270000e-41	180.0
22	TraesCS2D01G239600	chr4D	80.882	204	34	4	3912	4110	402546679	402546476	8.880000e-34	156.0
23	TraesCS2D01G239600	chr1D	85.280	856	95	16	1	832	24943611	24942763	0.000000e+00	854.0
24	TraesCS2D01G239600	chr3B	84.870	846	102	18	7	832	419795128	419795967	0.000000e+00	830.0
25	TraesCS2D01G239600	chr3B	75.000	552	90	28	306	829	247501042	247500511	1.870000e-50	211.0
26	TraesCS2D01G239600	chr5B	84.778	854	90	16	2	832	58187653	58186817	0.000000e+00	821.0
27	TraesCS2D01G239600	chr5B	78.721	860	142	29	3	835	254263306	254262461	2.710000e-148	536.0
28	TraesCS2D01G239600	chr5B	94.828	174	7	1	5887	6058	575061331	575061158	3.040000e-68	270.0
29	TraesCS2D01G239600	chr5B	91.753	194	13	2	5894	6085	427931368	427931176	3.930000e-67	267.0
30	TraesCS2D01G239600	chr5B	82.667	225	25	10	3901	4112	485912058	485912281	3.150000e-43	187.0
31	TraesCS2D01G239600	chr5B	80.292	137	25	2	693	829	485627348	485627482	1.170000e-17	102.0
32	TraesCS2D01G239600	chr1B	84.579	843	108	11	6	832	497330138	497329302	0.000000e+00	817.0
33	TraesCS2D01G239600	chr1B	74.552	782	120	49	95	827	346416269	346415518	1.090000e-67	268.0
34	TraesCS2D01G239600	chr1B	90.476	63	4	2	4949	5010	57536881	57536942	1.530000e-11	82.4
35	TraesCS2D01G239600	chr1A	83.867	843	117	13	1	829	34193593	34192756	0.000000e+00	785.0
36	TraesCS2D01G239600	chr1A	95.833	168	5	1	5892	6057	132544054	132544221	3.040000e-68	270.0
37	TraesCS2D01G239600	chr7B	83.937	828	107	10	1	803	229213927	229214753	0.000000e+00	769.0
38	TraesCS2D01G239600	chr5D	83.429	869	97	24	2	831	447102249	447101389	0.000000e+00	763.0
39	TraesCS2D01G239600	chr4B	83.294	850	117	14	1	832	418758655	418757813	0.000000e+00	760.0
40	TraesCS2D01G239600	chr4B	92.973	185	9	3	5896	6078	113961281	113961099	3.930000e-67	267.0
41	TraesCS2D01G239600	chr4B	84.153	183	26	3	3929	4110	362144214	362144034	2.450000e-39	174.0
42	TraesCS2D01G239600	chr4B	80.769	208	33	6	3912	4114	565735392	565735187	8.880000e-34	156.0
43	TraesCS2D01G239600	chr4B	94.737	57	2	1	4961	5017	104337366	104337421	3.290000e-13	87.9
44	TraesCS2D01G239600	chr7A	82.331	815	109	15	29	822	114090412	114089612	0.000000e+00	675.0
45	TraesCS2D01G239600	chr7A	76.712	511	84	26	346	827	260263787	260264291	1.100000e-62	252.0
46	TraesCS2D01G239600	chr6D	95.906	171	5	1	5896	6064	406391359	406391529	6.530000e-70	276.0
47	TraesCS2D01G239600	chr6D	93.820	178	8	2	5896	6070	392896975	392897152	1.410000e-66	265.0
48	TraesCS2D01G239600	chr6D	91.228	57	3	2	4954	5010	262513949	262513895	7.110000e-10	76.8
49	TraesCS2D01G239600	chr7D	94.857	175	7	1	5893	6065	500255330	500255156	8.450000e-69	272.0
50	TraesCS2D01G239600	chr7D	80.882	204	35	3	3911	4110	71339574	71339777	2.470000e-34	158.0
51	TraesCS2D01G239600	chr7D	94.737	57	2	1	4961	5017	553426331	553426386	3.290000e-13	87.9
52	TraesCS2D01G239600	chr3A	94.798	173	6	2	5895	6065	585605803	585605632	3.930000e-67	267.0
53	TraesCS2D01G239600	chr3A	94.737	57	2	1	4961	5017	113364102	113364047	3.290000e-13	87.9
54	TraesCS2D01G239600	chr3A	94.737	57	2	1	4961	5017	714035475	714035420	3.290000e-13	87.9
55	TraesCS2D01G239600	chr4A	81.159	207	33	5	3910	4110	179057200	179057406	1.910000e-35	161.0
56	TraesCS2D01G239600	chr4A	94.737	57	2	1	4961	5017	211051169	211051114	3.290000e-13	87.9
57	TraesCS2D01G239600	chr4A	90.476	63	4	2	4949	5010	617962610	617962671	1.530000e-11	82.4
58	TraesCS2D01G239600	chr6A	94.737	57	2	1	4961	5017	588944625	588944570	3.290000e-13	87.9

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	TraesCS2D01G239600	chr2D	255616282	255622894	6612	True	12213.000000	12213	100.000000	1	6613	1	chr2D.!!$R2	6612
1	TraesCS2D01G239600	chr2A	236834247	236841891	7644	False	1913.600000	8499	95.423200	836	6613	5	chr2A.!!$F1	5777
2	TraesCS2D01G239600	chr2B	280483054	280485824	2770	False	4379.000000	4379	95.306000	836	3592	1	chr2B.!!$F1	2756
3	TraesCS2D01G239600	chr2B	616477343	616478177	834	True	835.000000	835	85.041000	1	832	1	chr2B.!!$R1	831
4	TraesCS2D01G239600	chr2B	280492692	280498097	5405	False	634.333333	1177	93.689111	3576	6605	9	chr2B.!!$F2	3029
5	TraesCS2D01G239600	chr4D	296675998	296676836	838	False	887.000000	887	86.068000	3	832	1	chr4D.!!$F1	829
6	TraesCS2D01G239600	chr1D	24942763	24943611	848	True	854.000000	854	85.280000	1	832	1	chr1D.!!$R1	831
7	TraesCS2D01G239600	chr3B	419795128	419795967	839	False	830.000000	830	84.870000	7	832	1	chr3B.!!$F1	825
8	TraesCS2D01G239600	chr3B	247500511	247501042	531	True	211.000000	211	75.000000	306	829	1	chr3B.!!$R1	523
9	TraesCS2D01G239600	chr5B	58186817	58187653	836	True	821.000000	821	84.778000	2	832	1	chr5B.!!$R1	830
10	TraesCS2D01G239600	chr5B	254262461	254263306	845	True	536.000000	536	78.721000	3	835	1	chr5B.!!$R2	832
11	TraesCS2D01G239600	chr1B	497329302	497330138	836	True	817.000000	817	84.579000	6	832	1	chr1B.!!$R2	826
12	TraesCS2D01G239600	chr1B	346415518	346416269	751	True	268.000000	268	74.552000	95	827	1	chr1B.!!$R1	732
13	TraesCS2D01G239600	chr1A	34192756	34193593	837	True	785.000000	785	83.867000	1	829	1	chr1A.!!$R1	828
14	TraesCS2D01G239600	chr7B	229213927	229214753	826	False	769.000000	769	83.937000	1	803	1	chr7B.!!$F1	802
15	TraesCS2D01G239600	chr5D	447101389	447102249	860	True	763.000000	763	83.429000	2	831	1	chr5D.!!$R1	829
16	TraesCS2D01G239600	chr4B	418757813	418758655	842	True	760.000000	760	83.294000	1	832	1	chr4B.!!$R3	831
17	TraesCS2D01G239600	chr7A	114089612	114090412	800	True	675.000000	675	82.331000	29	822	1	chr7A.!!$R1	793
18	TraesCS2D01G239600	chr7A	260263787	260264291	504	False	252.000000	252	76.712000	346	827	1	chr7A.!!$F1	481

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	End Stability	Orientation
483	509	0.529833	CTCTGCTTCCTCTGCTTCGA	59.470	55.000	0.00	3.71	F
1248	1424	0.323302	TATTGTTGCGCTCAGGTGGA	59.677	50.000	9.73	4.02	F
1628	1806	3.296322	TGGAAGGCTTTTATTGCAACG	57.704	42.857	0.00	4.10	F
3431	3627	3.211045	GCTTTCTTTGTCCACCAGTGTA	58.789	45.455	0.00	2.90	F
4681	5269	0.908198	GATCCAGCCTCTCTTGTGGT	59.092	55.000	0.00	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1775	1962	0.109132	GCCTTTGTAGCATGTGTGGC	60.109	55.000	0.00	0.00	0.00	5.01	R
2883	3079	5.238432	ACTTCAATTAGACGCAAATGACACA	59.762	36.000	0.00	0.00	0.00	3.72	R
3598	3795	6.183360	ACACTTTCCAAGTTTGACTAATGTGG	60.183	38.462	15.87	0.00	40.46	4.17	R
5325	6948	2.232452	CCCTCCGAGTATATCTTGCCAG	59.768	54.545	0.00	0.00	0.00	4.85	R
5779	7408	0.105964	TCCTAGCTAGAGGCAGGTGG	60.106	60.000	22.70	2.85	44.79	4.61	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
18	19	3.775065	CGTCGAGGATGATGCGTAT	57.225	52.632	0.00	0.00	0.00	3.06
63	64	1.138247	GTACTGGACGCCGACGAAT	59.862	57.895	0.00	0.00	43.93	3.34
157	158	4.430765	CCGTCGGCGTTGCTAGGT	62.431	66.667	9.28	0.00	36.15	3.08
282	284	1.323271	ATCATCCCTGTGCGAGACGT	61.323	55.000	0.00	0.00	0.00	4.34
362	388	2.528127	TGTCCCGGGCCTTCTTGA	60.528	61.111	18.49	0.00	0.00	3.02
483	509	0.529833	CTCTGCTTCCTCTGCTTCGA	59.470	55.000	0.00	0.00	0.00	3.71
673	793	3.733960	GACCCACGCGCCTTTTCC	61.734	66.667	5.73	0.00	0.00	3.13
758	893	3.437741	ACCGGCGAAAAACGAGATTTTAT	59.562	39.130	9.30	0.00	45.77	1.40
771	906	3.537580	AGATTTTATGGGCGCGACTAAA	58.462	40.909	13.91	7.17	0.00	1.85
782	917	2.411806	GCGCGACTAAACCGATTTTCAA	60.412	45.455	12.10	0.00	0.00	2.69
879	1025	2.124570	GCATGTCGGTGGCCAGAT	60.125	61.111	5.11	0.00	0.00	2.90
955	1101	2.564553	GATTCTCCTCACGCACCGCT	62.565	60.000	0.00	0.00	0.00	5.52
956	1102	2.172483	ATTCTCCTCACGCACCGCTT	62.172	55.000	0.00	0.00	0.00	4.68
958	1104	3.288308	CTCCTCACGCACCGCTTCT	62.288	63.158	0.00	0.00	0.00	2.85
1120	1284	2.437359	CCTTCTCCAAGGCCGCTG	60.437	66.667	0.00	0.00	43.14	5.18
1121	1285	3.130160	CTTCTCCAAGGCCGCTGC	61.130	66.667	0.00	0.00	0.00	5.25
1248	1424	0.323302	TATTGTTGCGCTCAGGTGGA	59.677	50.000	9.73	0.00	0.00	4.02
1383	1559	6.852853	CGTAGATTTGCAACATGGAATATGTC	59.147	38.462	0.00	0.00	0.00	3.06
1494	1672	7.648510	CCTACAGTATTTTCGTTCATAGGACTC	59.351	40.741	0.00	0.00	30.23	3.36
1628	1806	3.296322	TGGAAGGCTTTTATTGCAACG	57.704	42.857	0.00	0.00	0.00	4.10
1667	1854	5.287674	AGATGTGTGGATGTATGGAGAAG	57.712	43.478	0.00	0.00	0.00	2.85
1691	1878	7.349598	AGTGGAAGGATTATATTGCAAAGTCT	58.650	34.615	1.71	0.00	0.00	3.24
1692	1879	7.284034	AGTGGAAGGATTATATTGCAAAGTCTG	59.716	37.037	1.71	0.00	0.00	3.51
1767	1954	5.231265	TCATCGCTACTTAGTGTGTACTG	57.769	43.478	0.00	0.00	37.78	2.74
1775	1962	5.584253	ACTTAGTGTGTACTGCCTATCTG	57.416	43.478	0.00	0.00	37.78	2.90

Showing 1 to 25 of 136 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
87	88	1.535202	TTTTCACATGGCCACCCCC	60.535	57.895	8.16	0.00	0.00	5.40
102	103	3.039252	TCAACCCCAACATCACCTTTT	57.961	42.857	0.00	0.00	0.00	2.27
282	284	2.048222	CGGCGGAACAAGCAGAGA	60.048	61.111	0.00	0.00	36.08	3.10
362	388	2.665185	GCGGAACAGGCTCAACGT	60.665	61.111	0.00	0.00	0.00	3.99
483	509	4.284550	ATGCCAACGCCACCCAGT	62.285	61.111	0.00	0.00	0.00	4.00
686	806	2.045045	CGAATGCAAGCCCTGGGA	60.045	61.111	19.27	0.00	0.00	4.37
698	832	3.564027	GCGAACCCGAGCCGAATG	61.564	66.667	0.00	0.00	38.22	2.67
758	893	2.510064	AATCGGTTTAGTCGCGCCCA	62.510	55.000	0.00	0.00	0.00	5.36
771	906	2.686816	CCGGCGCTTGAAAATCGGT	61.687	57.895	7.64	0.00	35.73	4.69
806	949	3.579302	CCCCAACAGGCACCCTCA	61.579	66.667	0.00	0.00	0.00	3.86
832	978	2.740440	CCGCGTGTGTGTATGCCA	60.740	61.111	4.92	0.00	0.00	4.92
834	980	4.160635	GCCCGCGTGTGTGTATGC	62.161	66.667	4.92	0.00	0.00	3.14
879	1025	0.042581	TCCAGCCACAGAGATACCCA	59.957	55.000	0.00	0.00	0.00	4.51
1248	1424	1.410517	CCGCCAGATCACACTATGAGT	59.589	52.381	0.00	0.00	41.91	3.41
1383	1559	3.748083	AGCACACATATCAAGCCTATGG	58.252	45.455	0.00	0.00	32.06	2.74
1494	1672	3.628032	TCGAGTGTTGCTAGGTAGATCAG	59.372	47.826	0.00	0.00	0.00	2.90
1561	1739	6.488006	AGTGCACATCTTTGTAGATCAAAAGT	59.512	34.615	21.04	0.00	44.08	2.66
1628	1806	5.527582	ACACATCTTTACAGACTTGTTGGAC	59.472	40.000	0.00	0.00	38.76	4.02
1667	1854	7.283127	TCAGACTTTGCAATATAATCCTTCCAC	59.717	37.037	0.00	0.00	0.00	4.02
1691	1878	6.540551	TGTATAAGTCAGCAACAAACTTGTCA	59.459	34.615	0.00	0.00	41.31	3.58
1692	1879	6.954944	TGTATAAGTCAGCAACAAACTTGTC	58.045	36.000	0.00	0.00	41.31	3.18
1730	1917	7.896811	AGTAGCGATGAATATCACTAAATGGA	58.103	34.615	0.00	0.00	31.66	3.41
1767	1954	0.465097	AGCATGTGTGGCAGATAGGC	60.465	55.000	9.92	9.92	44.50	3.93
1775	1962	0.109132	GCCTTTGTAGCATGTGTGGC	60.109	55.000	0.00	0.00	0.00	5.01
2163	2356	8.575589	TCTTATTGCAGCAGAAATACAGAAAAA	58.424	29.630	0.00	0.00	0.00	1.94

Showing 1 to 25 of 122 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.