AutoCloner

Multiple sequence alignment - TraesCS2D01G247900

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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	TraesCS2D01G247900	chr2D	100.000	2342	0	0	1	2342	291773506	291775847	0.000000e+00	4325.0
1	TraesCS2D01G247900	chr5A	96.191	2363	68	11	1	2342	16544441	16546802	0.000000e+00	3845.0
2	TraesCS2D01G247900	chr5A	96.182	2357	68	7	1	2342	420185589	420187938	0.000000e+00	3834.0
3	TraesCS2D01G247900	chr5A	88.618	246	27	1	2043	2288	327918944	327918700	4.890000e-77	298.0
4	TraesCS2D01G247900	chr7B	96.190	2362	68	8	2	2342	716784495	716786855	0.000000e+00	3843.0
5	TraesCS2D01G247900	chr7B	96.107	2363	70	8	1	2342	742948851	742946490	0.000000e+00	3834.0
6	TraesCS2D01G247900	chr7A	96.149	2363	69	8	1	2342	60168880	60166519	0.000000e+00	3840.0
7	TraesCS2D01G247900	chr7A	96.022	2363	72	8	1	2342	60084823	60087184	0.000000e+00	3823.0
8	TraesCS2D01G247900	chr1B	95.538	2353	83	12	1	2342	583561662	583559321	0.000000e+00	3744.0
9	TraesCS2D01G247900	chr1D	95.180	2365	84	12	1	2342	275778815	275781172	0.000000e+00	3709.0
10	TraesCS2D01G247900	chr6B	94.245	2363	100	17	1	2342	388287150	388284803	0.000000e+00	3578.0
11	TraesCS2D01G247900	chr3B	98.148	54	0	1	2290	2342	108133566	108133619	2.480000e-15	93.5

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	TraesCS2D01G247900	chr2D	291773506	291775847	2341	False	4325	4325	100.000	1	2342	1	chr2D.!!$F1	2341
1	TraesCS2D01G247900	chr5A	16544441	16546802	2361	False	3845	3845	96.191	1	2342	1	chr5A.!!$F1	2341
2	TraesCS2D01G247900	chr5A	420185589	420187938	2349	False	3834	3834	96.182	1	2342	1	chr5A.!!$F2	2341
3	TraesCS2D01G247900	chr7B	716784495	716786855	2360	False	3843	3843	96.190	2	2342	1	chr7B.!!$F1	2340
4	TraesCS2D01G247900	chr7B	742946490	742948851	2361	True	3834	3834	96.107	1	2342	1	chr7B.!!$R1	2341
5	TraesCS2D01G247900	chr7A	60166519	60168880	2361	True	3840	3840	96.149	1	2342	1	chr7A.!!$R1	2341
6	TraesCS2D01G247900	chr7A	60084823	60087184	2361	False	3823	3823	96.022	1	2342	1	chr7A.!!$F1	2341
7	TraesCS2D01G247900	chr1B	583559321	583561662	2341	True	3744	3744	95.538	1	2342	1	chr1B.!!$R1	2341
8	TraesCS2D01G247900	chr1D	275778815	275781172	2357	False	3709	3709	95.180	1	2342	1	chr1D.!!$F1	2341
9	TraesCS2D01G247900	chr6B	388284803	388287150	2347	True	3578	3578	94.245	1	2342	1	chr6B.!!$R1	2341

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
372	373	0.322975	AGACCTTGATGCTGCGACTT	59.677	50.0	0.0	0.0	0.0	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2122	2141	0.751643	CAAGTAAATCCCCGGCCCAG	60.752	60.0	0.0	0.0	0.0	4.45	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
40	41	7.654022	GGGATGTTTTCTATTTACATTCCCA	57.346	36.000	0.00	0.00	40.58	4.37
63	64	4.846779	CTCTTAGAGAGAGCCGCTAAAT	57.153	45.455	2.53	0.00	45.07	1.40
74	75	1.878102	GCCGCTAAATGATCGGACCAT	60.878	52.381	3.91	0.00	45.53	3.55
76	77	3.861840	CCGCTAAATGATCGGACCATAT	58.138	45.455	0.00	0.00	45.53	1.78
93	94	1.617322	TATAGGTGCAGGTAGCTCGG	58.383	55.000	0.00	0.00	45.94	4.63
96	97	2.423898	GGTGCAGGTAGCTCGGCTA	61.424	63.158	5.92	1.99	45.94	3.93
97	98	1.742768	GTGCAGGTAGCTCGGCTAT	59.257	57.895	8.54	0.00	43.30	2.97
104	105	1.962100	GGTAGCTCGGCTATGTTACCT	59.038	52.381	8.54	0.00	43.30	3.08
168	169	4.949238	CCACCAATGTGATCTCCATTACAA	59.051	41.667	9.80	0.00	45.76	2.41
179	180	8.902806	GTGATCTCCATTACAAATGGACAAATA	58.097	33.333	15.70	2.59	42.81	1.40
207	208	5.487433	TGGAAACAGAGATCTTTTATCGCA	58.513	37.500	0.00	0.00	35.01	5.10
217	218	8.637986	AGAGATCTTTTATCGCAGAATTAGACT	58.362	33.333	0.00	0.00	43.58	3.24
220	221	9.685828	GATCTTTTATCGCAGAATTAGACTAGT	57.314	33.333	0.00	0.00	43.58	2.57
245	246	1.668419	ATGTTGGCTTATCCGTCAGC	58.332	50.000	0.00	0.00	37.80	4.26
246	247	0.613260	TGTTGGCTTATCCGTCAGCT	59.387	50.000	0.00	0.00	37.80	4.24
253	254	3.751401	TATCCGTCAGCTGCGTCGC	62.751	63.158	22.70	11.10	0.00	5.19
320	321	7.952074	AGTTCAAAACTGGAATTGGCACAATAG	60.952	37.037	0.00	0.00	42.25	1.73
372	373	0.322975	AGACCTTGATGCTGCGACTT	59.677	50.000	0.00	0.00	0.00	3.01
379	380	1.412343	TGATGCTGCGACTTAGGCATA	59.588	47.619	0.00	0.00	44.06	3.14
492	493	2.146342	CTGTCAACGGCTTCTGTGATT	58.854	47.619	0.00	0.00	0.00	2.57
629	630	6.207417	TGGAACCAGATGCTTCTTTAAAAGAG	59.793	38.462	0.00	0.00	39.03	2.85
656	657	6.149633	CACTTTGCCTTACCTGTGAATTAAC	58.850	40.000	0.00	0.00	0.00	2.01
789	790	0.881118	CCATGCGTAAACCAAGCTGT	59.119	50.000	0.00	0.00	32.19	4.40
790	791	1.401409	CCATGCGTAAACCAAGCTGTG	60.401	52.381	0.00	0.00	32.19	3.66
791	792	1.535028	CATGCGTAAACCAAGCTGTGA	59.465	47.619	0.00	0.00	32.19	3.58
792	793	1.225855	TGCGTAAACCAAGCTGTGAG	58.774	50.000	0.00	0.00	32.19	3.51
793	794	1.202592	TGCGTAAACCAAGCTGTGAGA	60.203	47.619	0.00	0.00	32.19	3.27
794	795	1.461127	GCGTAAACCAAGCTGTGAGAG	59.539	52.381	0.00	0.00	0.00	3.20
795	796	2.755650	CGTAAACCAAGCTGTGAGAGT	58.244	47.619	0.00	0.00	0.00	3.24
898	913	8.734763	ACCTATACCTATACCTATACCTGATGG	58.265	40.741	0.00	0.00	39.83	3.51
1047	1062	7.395190	TCGAATCATCAACAAGAAATCCAAT	57.605	32.000	0.00	0.00	0.00	3.16
1127	1142	6.067217	AGAAGGTGCTAAATCAATAGGTGT	57.933	37.500	0.00	0.00	0.00	4.16
1128	1143	6.485171	AGAAGGTGCTAAATCAATAGGTGTT	58.515	36.000	0.00	0.00	0.00	3.32
1315	1330	3.287867	TGGCCTTTCTGATCTCATTCC	57.712	47.619	3.32	0.00	0.00	3.01
1406	1421	6.654793	AAAGTCAATATCTCGTTCTCTTGC	57.345	37.500	0.00	0.00	0.00	4.01
1576	1592	5.188555	GCCTTACTTTACTAACAGGTAGGGT	59.811	44.000	0.00	0.00	33.85	4.34
1579	1595	3.905591	ACTTTACTAACAGGTAGGGTGCA	59.094	43.478	0.00	0.00	33.68	4.57
1612	1628	1.663173	TTTTTGCTGCTTACCCGCC	59.337	52.632	0.00	0.00	0.00	6.13
1777	1793	1.545428	GCCACCTCATGTGTCTTTCCA	60.545	52.381	0.00	0.00	43.85	3.53
1781	1797	4.082571	CCACCTCATGTGTCTTTCCATTTC	60.083	45.833	0.00	0.00	43.85	2.17
1822	1840	3.944087	AGCTTCGTTAGAGAAAGCCATT	58.056	40.909	2.91	0.00	0.00	3.16
1848	1866	4.473196	TGAACTACAAAGCATGGGATCCTA	59.527	41.667	12.58	5.82	0.00	2.94
1853	1871	4.019174	ACAAAGCATGGGATCCTAAACAG	58.981	43.478	12.58	0.00	0.00	3.16
2064	2083	2.565391	TCAGGTAAGGCACTCGATCAAA	59.435	45.455	0.00	0.00	38.49	2.69
2086	2105	5.161943	AGCCTATACATCCGGGAATTTAC	57.838	43.478	0.00	0.00	0.00	2.01
2122	2141	2.064014	GACTTGCTTTGCTGCATTTCC	58.936	47.619	1.84	0.00	42.96	3.13
2133	2152	3.738481	CATTTCCTGGGCCGGGGA	61.738	66.667	31.01	21.72	0.00	4.81
2149	2168	3.767131	CCGGGGATTTACTTGATTTTGGT	59.233	43.478	0.00	0.00	0.00	3.67
2182	2201	5.455326	GGCCATATGATCTACTTTCTGGTGT	60.455	44.000	3.65	0.00	0.00	4.16
2187	2206	3.576982	TGATCTACTTTCTGGTGTCGGTT	59.423	43.478	0.00	0.00	0.00	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	75	1.617322	CCGAGCTACCTGCACCTATA	58.383	55.000	0.00	0.00	45.94	1.31
76	77	2.423898	GCCGAGCTACCTGCACCTA	61.424	63.158	0.00	0.00	45.94	3.08
93	94	6.072728	TGTGTTTCAATCACAGGTAACATAGC	60.073	38.462	0.00	0.00	40.26	2.97
96	97	6.707440	TTGTGTTTCAATCACAGGTAACAT	57.293	33.333	1.65	0.00	44.71	2.71
97	98	5.449862	GCTTGTGTTTCAATCACAGGTAACA	60.450	40.000	11.24	0.00	44.71	2.41
104	105	3.286353	TCCAGCTTGTGTTTCAATCACA	58.714	40.909	0.00	0.00	42.84	3.58
168	169	7.961351	TCTGTTTCCAAACATATTTGTCCATT	58.039	30.769	5.35	0.00	46.71	3.16
179	180	8.454106	CGATAAAAGATCTCTGTTTCCAAACAT	58.546	33.333	5.35	0.00	46.71	2.71
217	218	8.205512	TGACGGATAAGCCAACATTAATAACTA	58.794	33.333	0.00	0.00	35.94	2.24
220	221	6.017440	GCTGACGGATAAGCCAACATTAATAA	60.017	38.462	0.00	0.00	35.94	1.40
227	228	0.613260	AGCTGACGGATAAGCCAACA	59.387	50.000	0.00	0.00	40.42	3.33
372	373	4.653801	TGCACCTCTATTGAGTTATGCCTA	59.346	41.667	16.72	3.56	39.22	3.93
379	380	2.307098	AGCCTTGCACCTCTATTGAGTT	59.693	45.455	3.47	0.00	38.61	3.01
492	493	5.809001	AGAAATTCTGTCTAGTGGCATTCA	58.191	37.500	0.00	0.00	0.00	2.57
526	527	9.429359	CAGGATTAATAGTACTTAGAATGGCTG	57.571	37.037	0.00	0.00	0.00	4.85
563	564	4.399219	AGCCACCTTTTTCTAAGAAGGAC	58.601	43.478	16.55	7.39	44.15	3.85
629	630	1.537202	CACAGGTAAGGCAAAGTGCTC	59.463	52.381	0.00	0.00	44.28	4.26
678	679	3.922171	AAGCCTTCTTCCTACATCTGG	57.078	47.619	0.00	0.00	0.00	3.86
766	767	0.109319	CTTGGTTTACGCATGGCACC	60.109	55.000	0.00	0.00	0.00	5.01
789	790	0.472925	TGTGGCTGGGGTAACTCTCA	60.473	55.000	0.00	0.00	38.64	3.27
790	791	0.690762	TTGTGGCTGGGGTAACTCTC	59.309	55.000	0.00	0.00	38.64	3.20
791	792	0.693049	CTTGTGGCTGGGGTAACTCT	59.307	55.000	0.00	0.00	38.64	3.24
792	793	0.322546	CCTTGTGGCTGGGGTAACTC	60.323	60.000	0.00	0.00	37.88	3.01
793	794	1.767692	CCTTGTGGCTGGGGTAACT	59.232	57.895	0.00	0.00	0.00	2.24
794	795	1.304134	CCCTTGTGGCTGGGGTAAC	60.304	63.158	0.00	0.00	39.76	2.50
795	796	3.176297	CCCTTGTGGCTGGGGTAA	58.824	61.111	0.00	0.00	39.76	2.85
860	864	3.639264	AGGTATAGGTAGGGGGTCCATA	58.361	50.000	0.00	0.00	34.83	2.74
862	866	1.945786	AGGTATAGGTAGGGGGTCCA	58.054	55.000	0.00	0.00	34.83	4.02
898	913	8.330302	CAAGAAAATGAGTTGTGGATTGAAAAC	58.670	33.333	0.00	0.00	0.00	2.43
1047	1062	4.333372	ACGTTTTTCCTTCGCTGTTCTTTA	59.667	37.500	0.00	0.00	0.00	1.85
1127	1142	2.205022	AGCAATTGTAGCAGCTCCAA	57.795	45.000	2.44	2.44	30.05	3.53
1128	1143	2.205022	AAGCAATTGTAGCAGCTCCA	57.795	45.000	7.40	0.00	36.07	3.86
1315	1330	5.627172	TGACTTTTTATGCGATCGGAAAAG	58.373	37.500	22.75	22.75	40.99	2.27
1406	1421	9.678941	CACATCATCCAATTCATGATTTAAGAG	57.321	33.333	0.00	0.03	38.67	2.85
1612	1628	9.788960	GAAAGGGCAAGTAAATAATCTAAACAG	57.211	33.333	0.00	0.00	0.00	3.16
1777	1793	6.530019	AATGCCGAATTAAAGACCTGAAAT	57.470	33.333	0.00	0.00	0.00	2.17
1781	1797	4.576463	AGCTAATGCCGAATTAAAGACCTG	59.424	41.667	0.00	0.00	40.80	4.00
1822	1840	2.037902	TCCCATGCTTTGTAGTTCACGA	59.962	45.455	0.00	0.00	0.00	4.35
1848	1866	1.400494	ACGCTTTCTTTCGTGCTGTTT	59.600	42.857	0.00	0.00	37.55	2.83
1853	1871	2.985139	AGTAGTACGCTTTCTTTCGTGC	59.015	45.455	0.00	0.00	40.66	5.34
2064	2083	4.019591	GGTAAATTCCCGGATGTATAGGCT	60.020	45.833	0.73	0.00	0.00	4.58
2086	2105	2.256117	AGTCGTCTTTGGTTTGGAGG	57.744	50.000	0.00	0.00	0.00	4.30
2122	2141	0.751643	CAAGTAAATCCCCGGCCCAG	60.752	60.000	0.00	0.00	0.00	4.45
2133	2152	9.546428	CCTTTCTTTCACCAAAATCAAGTAAAT	57.454	29.630	0.00	0.00	0.00	1.40
2149	2168	7.141758	AGTAGATCATATGGCCTTTCTTTCA	57.858	36.000	3.32	0.00	0.00	2.69
2182	2201	3.596214	GCTATCTTTGTGAAGGAACCGA	58.404	45.455	0.00	0.00	33.56	4.69
2187	2206	2.562296	AGGGGCTATCTTTGTGAAGGA	58.438	47.619	0.00	0.00	33.56	3.36
2234	2259	6.479884	AGCTTCAGAACTCTTGTATTCCAAT	58.520	36.000	0.00	0.00	31.20	3.16
2235	2260	5.869579	AGCTTCAGAACTCTTGTATTCCAA	58.130	37.500	0.00	0.00	0.00	3.53

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.