AutoCloner

Multiple sequence alignment - TraesCS5B01G424800

Loading Multiple Alignment...

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	TraesCS5B01G424800	chr5B	100.000	2485	0	0	1	2485	600727083	600729567	0.000000e+00	4590
1	TraesCS5B01G424800	chr5A	93.563	2501	138	13	1	2485	608949370	608951863	0.000000e+00	3705
2	TraesCS5B01G424800	chr5D	95.137	1460	65	3	314	1770	488203202	488204658	0.000000e+00	2298
3	TraesCS5B01G424800	chr5D	92.127	597	37	5	1766	2355	488205713	488206306	0.000000e+00	833
4	TraesCS5B01G424800	chr5D	94.286	140	8	0	2346	2485	488214901	488215040	5.380000e-52	215
5	TraesCS5B01G424800	chr5D	94.737	133	6	1	1	132	488203072	488203204	3.240000e-49	206
6	TraesCS5B01G424800	chr1A	79.545	1672	265	46	427	2047	42670184	42671829	0.000000e+00	1122
7	TraesCS5B01G424800	chr1A	80.846	1300	201	30	784	2041	42685951	42687244	0.000000e+00	977
8	TraesCS5B01G424800	chr1A	80.460	1305	209	25	784	2047	42721114	42722413	0.000000e+00	955
9	TraesCS5B01G424800	chr1A	77.108	249	45	6	427	665	42692914	42693160	1.550000e-27	134
10	TraesCS5B01G424800	chr1B	79.487	1677	257	55	427	2048	63201664	63203308	0.000000e+00	1110
11	TraesCS5B01G424800	chr1B	78.756	1318	192	54	427	1694	63888743	63890022	0.000000e+00	802
12	TraesCS5B01G424800	chr1D	79.378	1673	265	51	427	2047	43305634	43307278	0.000000e+00	1105
13	TraesCS5B01G424800	chr1D	80.847	1039	152	25	686	1694	44628959	44629980	0.000000e+00	773

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	TraesCS5B01G424800	chr5B	600727083	600729567	2484	False	4590.000000	4590	100.000000	1	2485	1	chr5B.!!$F1	2484
1	TraesCS5B01G424800	chr5A	608949370	608951863	2493	False	3705.000000	3705	93.563000	1	2485	1	chr5A.!!$F1	2484
2	TraesCS5B01G424800	chr5D	488203072	488206306	3234	False	1112.333333	2298	94.000333	1	2355	3	chr5D.!!$F2	2354
3	TraesCS5B01G424800	chr1A	42670184	42671829	1645	False	1122.000000	1122	79.545000	427	2047	1	chr1A.!!$F1	1620
4	TraesCS5B01G424800	chr1A	42685951	42687244	1293	False	977.000000	977	80.846000	784	2041	1	chr1A.!!$F2	1257
5	TraesCS5B01G424800	chr1A	42721114	42722413	1299	False	955.000000	955	80.460000	784	2047	1	chr1A.!!$F4	1263
6	TraesCS5B01G424800	chr1B	63201664	63203308	1644	False	1110.000000	1110	79.487000	427	2048	1	chr1B.!!$F1	1621
7	TraesCS5B01G424800	chr1B	63888743	63890022	1279	False	802.000000	802	78.756000	427	1694	1	chr1B.!!$F2	1267
8	TraesCS5B01G424800	chr1D	43305634	43307278	1644	False	1105.000000	1105	79.378000	427	2047	1	chr1D.!!$F1	1620
9	TraesCS5B01G424800	chr1D	44628959	44629980	1021	False	773.000000	773	80.847000	686	1694	1	chr1D.!!$F2	1008

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
391	395	0.539986	ACGACCCGGTGCATATTTCT	59.46	50.0	0.0	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2357	3506	0.523966	CGCGAGGATCCCATCTAGTC	59.476	60.0	8.55	0.0	0.0	2.59	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
69	70	5.190726	TGGTCATGAAAGGTATATGTGGTGA	59.809	40.000	0.00	0.00	0.00	4.02
128	130	8.523464	CGTTGAGTTTAGTTCAATTCAAAAGTG	58.477	33.333	0.00	0.00	36.96	3.16
172	174	7.905604	TCTTGTCACATAATTTGTAGGTCTG	57.094	36.000	0.00	0.00	36.57	3.51
203	205	9.445786	TTTTCAAAATGTAAATCGAGAACACTC	57.554	29.630	0.00	0.00	0.00	3.51
212	214	9.268268	TGTAAATCGAGAACACTCTTACATTTT	57.732	29.630	0.00	0.00	30.88	1.82
213	215	9.742552	GTAAATCGAGAACACTCTTACATTTTC	57.257	33.333	0.00	0.00	29.54	2.29
214	216	6.969828	ATCGAGAACACTCTTACATTTTCC	57.030	37.500	0.00	0.00	29.54	3.13
263	267	4.580868	TGCTTTATGTAACATGGTTCCGA	58.419	39.130	0.00	0.00	0.00	4.55
287	291	3.289836	CAATGTGTGGGGCATCATCTAA	58.710	45.455	0.00	0.00	0.00	2.10
293	297	5.309282	TGTGTGGGGCATCATCTAATATACA	59.691	40.000	0.00	0.00	0.00	2.29
297	301	6.372659	GTGGGGCATCATCTAATATACACAAG	59.627	42.308	0.00	0.00	0.00	3.16
339	343	5.527951	TGGTTCTTCAAATACACACAATGC	58.472	37.500	0.00	0.00	0.00	3.56
356	360	2.535012	TGCACGTGTCCAATGTCTTA	57.465	45.000	18.38	0.00	0.00	2.10
376	380	9.836076	TGTCTTACATAGTGCAATATATACGAC	57.164	33.333	17.31	17.31	0.00	4.34
378	382	8.464404	TCTTACATAGTGCAATATATACGACCC	58.536	37.037	6.32	0.00	0.00	4.46
391	395	0.539986	ACGACCCGGTGCATATTTCT	59.460	50.000	0.00	0.00	0.00	2.52
760	789	9.190858	GCAGTGTTCTATCTTCAAGATATACAG	57.809	37.037	16.96	10.92	36.67	2.74
780	809	4.164221	ACAGCTAATGTATGGTGTAGCCTT	59.836	41.667	0.00	0.00	41.60	4.35
843	872	9.463902	ACGGTACTATAGCTTCAAGATATACAT	57.536	33.333	0.00	0.00	28.68	2.29
969	1007	3.243704	TGCACCATTCTAACAACAAAGGC	60.244	43.478	0.00	0.00	0.00	4.35
1024	1073	3.485877	GGCGAAACTCATGTGCTTATGTC	60.486	47.826	0.00	0.00	0.00	3.06
1096	1145	1.293924	CCGACAGGACATGATCAAGC	58.706	55.000	0.00	0.00	41.02	4.01
1110	1159	2.358737	AAGCAGTGCGGCCAGTAC	60.359	61.111	10.00	5.58	35.57	2.73
1146	1195	3.882131	GCCAAAGCTAGACCCATCA	57.118	52.632	0.00	0.00	35.50	3.07
1318	1367	9.485206	GCGGAAGTAAGTGAAATATATTAAGGA	57.515	33.333	0.00	0.00	0.00	3.36
1371	1420	9.206870	TGCAGTTTTGATATCAAATTTTCTTCC	57.793	29.630	27.11	16.27	44.30	3.46
1490	1542	1.393603	CTCCTCTGGCGTAGTGATGA	58.606	55.000	0.00	0.00	0.00	2.92
1707	1772	9.958180	TCTTTTGGTTCTATTTATGACTCATGA	57.042	29.630	1.42	0.00	0.00	3.07
1735	1800	6.937465	GGTGAAGGGATCAAGGATATTAGAAC	59.063	42.308	0.00	0.00	40.50	3.01
1745	1810	8.292444	TCAAGGATATTAGAACAAATTGGTGG	57.708	34.615	0.00	0.00	0.00	4.61
1747	1812	8.531146	CAAGGATATTAGAACAAATTGGTGGTT	58.469	33.333	0.00	0.00	0.00	3.67
1798	2922	5.327737	ACCTCCAAAGTTAATGGGTGTAA	57.672	39.130	0.00	0.00	38.54	2.41
1853	2985	7.432148	TTGTAACCTGAATTCCTAGCTGATA	57.568	36.000	2.27	0.00	0.00	2.15
1864	2996	3.132289	TCCTAGCTGATACAAAACTCCGG	59.868	47.826	0.00	0.00	0.00	5.14
1960	3100	4.157105	AGTTGTATTAATCCGCCCACAAAC	59.843	41.667	0.00	0.00	0.00	2.93
1965	3105	0.893727	AATCCGCCCACAAACCTGAC	60.894	55.000	0.00	0.00	0.00	3.51
1980	3120	6.321181	ACAAACCTGACATAGTTCAATTGTGT	59.679	34.615	5.13	1.61	31.13	3.72
2030	3170	6.157904	TGCAATTTCTGTGTTGTCCATTATG	58.842	36.000	0.00	0.00	0.00	1.90
2213	3360	2.399916	AACTCGACTAGCGACTAGGT	57.600	50.000	15.28	0.79	45.59	3.08
2236	3383	5.127031	GTCTAGCCTTGAGACTCTCATTCTT	59.873	44.000	9.63	0.32	40.39	2.52
2294	3441	5.163131	ACCACTTAAGGTTCCTTTTAGCTCA	60.163	40.000	9.46	0.00	39.34	4.26
2297	3444	7.039714	CCACTTAAGGTTCCTTTTAGCTCATTT	60.040	37.037	9.46	0.00	0.00	2.32
2298	3445	8.360390	CACTTAAGGTTCCTTTTAGCTCATTTT	58.640	33.333	9.46	0.00	0.00	1.82
2299	3446	8.924303	ACTTAAGGTTCCTTTTAGCTCATTTTT	58.076	29.630	9.46	0.00	0.00	1.94
2300	3447	9.196552	CTTAAGGTTCCTTTTAGCTCATTTTTG	57.803	33.333	9.46	0.00	0.00	2.44
2304	3451	8.700973	AGGTTCCTTTTAGCTCATTTTTGTTTA	58.299	29.630	0.00	0.00	0.00	2.01
2339	3488	2.571212	TCGCTTGGACTTGTTGATGTT	58.429	42.857	0.00	0.00	0.00	2.71
2342	3491	3.632189	GCTTGGACTTGTTGATGTTCAC	58.368	45.455	0.00	0.00	0.00	3.18
2343	3492	3.066621	GCTTGGACTTGTTGATGTTCACA	59.933	43.478	0.00	0.00	0.00	3.58
2363	3512	5.130705	ACATAGACCCATGTGAGACTAGA	57.869	43.478	0.00	0.00	37.74	2.43
2375	3524	1.816224	GAGACTAGATGGGATCCTCGC	59.184	57.143	12.58	0.80	0.00	5.03
2401	3550	9.168451	CGTAGGACTTCTCTATGATGTGTATAT	57.832	37.037	0.00	0.00	33.86	0.86
2405	3554	9.800433	GGACTTCTCTATGATGTGTATATCATG	57.200	37.037	12.58	0.00	45.00	3.07
2447	3596	4.724279	AGTCCTTGTCCAAAAGGTATGT	57.276	40.909	3.06	0.00	45.94	2.29
2481	3630	3.058570	GCATTGATGGTGTTACGTCACAA	60.059	43.478	3.73	0.00	39.76	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	4.681025	CCTTTCATGACCACACAAAATTCG	59.319	41.667	0.00	0.00	0.00	3.34
69	70	9.841295	TTAACTATATATTTTTCTCCCAGCGTT	57.159	29.630	0.00	0.00	0.00	4.84
100	101	4.768145	TGAATTGAACTAAACTCAACGCG	58.232	39.130	3.53	3.53	35.70	6.01
149	151	7.905604	TCAGACCTACAAATTATGTGACAAG	57.094	36.000	0.00	0.00	43.77	3.16
212	214	8.361889	GCTTAAAACAACTAAAACTAATGGGGA	58.638	33.333	0.00	0.00	0.00	4.81
213	215	8.145122	TGCTTAAAACAACTAAAACTAATGGGG	58.855	33.333	0.00	0.00	0.00	4.96
214	216	8.974408	GTGCTTAAAACAACTAAAACTAATGGG	58.026	33.333	0.00	0.00	0.00	4.00
274	278	6.476378	ACTTGTGTATATTAGATGATGCCCC	58.524	40.000	0.00	0.00	0.00	5.80
287	291	4.742743	GCCGGCTTTCCTACTTGTGTATAT	60.743	45.833	22.15	0.00	0.00	0.86
293	297	1.375523	CGCCGGCTTTCCTACTTGT	60.376	57.895	26.68	0.00	0.00	3.16
297	301	1.092348	AAAATCGCCGGCTTTCCTAC	58.908	50.000	26.68	0.00	0.00	3.18
304	308	0.893727	AAGAACCAAAATCGCCGGCT	60.894	50.000	26.68	2.78	0.00	5.52
339	343	5.062183	CACTATGTAAGACATTGGACACGTG	59.938	44.000	15.48	15.48	39.88	4.49
356	360	5.393787	CCGGGTCGTATATATTGCACTATGT	60.394	44.000	6.82	2.96	0.00	2.29
376	380	4.260620	CGTTCTTTAGAAATATGCACCGGG	60.261	45.833	6.32	0.00	35.58	5.73
378	382	5.712217	TCGTTCTTTAGAAATATGCACCG	57.288	39.130	0.00	0.00	35.58	4.94
391	395	5.100259	GCTACAGTACTGCATCGTTCTTTA	58.900	41.667	22.90	2.83	0.00	1.85
580	599	7.120138	TGCATGCATCAGTTGTATATATCTTGG	59.880	37.037	18.46	0.00	0.00	3.61
651	680	8.749354	TGTGTATACCTCGAAGATATGCAATAT	58.251	33.333	0.00	0.00	43.59	1.28
760	789	4.275936	CCAAAGGCTACACCATACATTAGC	59.724	45.833	0.00	0.00	43.14	3.09
780	809	6.581171	TGTGTACATTAATTGCACATCCAA	57.419	33.333	0.00	0.00	34.17	3.53
872	908	9.787435	TGTTAGCTATGGTTTGGTTTATATAGG	57.213	33.333	0.00	0.00	0.00	2.57
969	1007	1.234821	TGCTACACCGCCTTCTTTTG	58.765	50.000	0.00	0.00	0.00	2.44
1024	1073	0.873054	GCAATGGCGAGGATGATGAG	59.127	55.000	0.00	0.00	0.00	2.90
1056	1105	0.107508	CACCCTCACATTCATCGGCT	60.108	55.000	0.00	0.00	0.00	5.52
1096	1145	3.112075	CGTGTACTGGCCGCACTG	61.112	66.667	14.56	7.21	0.00	3.66
1110	1159	1.798735	CTCTGCTGGCCATTTCGTG	59.201	57.895	5.51	0.00	0.00	4.35
1146	1195	1.226267	CACAGCACAACACGCGTTT	60.226	52.632	10.22	0.00	31.13	3.60
1318	1367	4.526970	AGAAATGCCCATCATCGTAACTT	58.473	39.130	0.00	0.00	33.40	2.66
1371	1420	8.568732	AACTAATAACAAAACCGTGTGAATTG	57.431	30.769	0.00	0.00	0.00	2.32
1415	1464	5.362556	AACATGTGATTACAAGAGCACAC	57.637	39.130	0.00	0.00	43.17	3.82
1490	1542	3.228453	TCTCCTCCCGCGACTAAAATAT	58.772	45.455	8.23	0.00	0.00	1.28
1525	1577	2.637382	TGAGGCCAGACACATGAAAGTA	59.363	45.455	5.01	0.00	0.00	2.24
1707	1772	2.044793	TCCTTGATCCCTTCACCAGT	57.955	50.000	0.00	0.00	32.84	4.00
1735	1800	7.690224	CGTTGTTTCTTTAAAACCACCAATTTG	59.310	33.333	0.00	0.00	0.00	2.32
1745	1810	8.964150	AGCATATGAACGTTGTTTCTTTAAAAC	58.036	29.630	5.00	0.00	0.00	2.43
1747	1812	9.176181	GAAGCATATGAACGTTGTTTCTTTAAA	57.824	29.630	5.00	0.00	30.70	1.52
1754	1819	6.430000	AGGTAAGAAGCATATGAACGTTGTTT	59.570	34.615	5.00	0.00	0.00	2.83
1853	2985	9.418045	CAAATTAATTTGTATCCGGAGTTTTGT	57.582	29.630	26.14	0.00	41.58	2.83
1904	3040	3.942115	GCCACTTATCTTTGTCTTCCCTC	59.058	47.826	0.00	0.00	0.00	4.30
1913	3049	9.113838	ACTAACTGAATATGCCACTTATCTTTG	57.886	33.333	0.00	0.00	0.00	2.77
2213	3360	4.865905	AGAATGAGAGTCTCAAGGCTAGA	58.134	43.478	26.06	0.78	44.04	2.43
2236	3383	4.022589	AGTCAAAATAGTTCACTCGTCGGA	60.023	41.667	0.00	0.00	0.00	4.55
2297	3444	6.474102	GCGAATGAAAGTCCAAGTTAAACAAA	59.526	34.615	0.00	0.00	0.00	2.83
2298	3445	5.974751	GCGAATGAAAGTCCAAGTTAAACAA	59.025	36.000	0.00	0.00	0.00	2.83
2299	3446	5.298276	AGCGAATGAAAGTCCAAGTTAAACA	59.702	36.000	0.00	0.00	0.00	2.83
2300	3447	5.758924	AGCGAATGAAAGTCCAAGTTAAAC	58.241	37.500	0.00	0.00	0.00	2.01
2304	3451	3.004734	CCAAGCGAATGAAAGTCCAAGTT	59.995	43.478	0.00	0.00	0.00	2.66
2320	3469	2.290367	TGAACATCAACAAGTCCAAGCG	59.710	45.455	0.00	0.00	0.00	4.68
2342	3491	5.047448	CCATCTAGTCTCACATGGGTCTATG	60.047	48.000	0.00	0.00	33.37	2.23
2343	3492	5.083122	CCATCTAGTCTCACATGGGTCTAT	58.917	45.833	0.00	0.00	33.37	1.98
2355	3504	1.816224	GCGAGGATCCCATCTAGTCTC	59.184	57.143	8.55	0.00	0.00	3.36
2357	3506	0.523966	CGCGAGGATCCCATCTAGTC	59.476	60.000	8.55	0.00	0.00	2.59
2375	3524	5.759506	ACACATCATAGAGAAGTCCTACG	57.240	43.478	0.00	0.00	0.00	3.51
2401	3550	6.018469	AGATCCTTGTTTTCCAAATCCATGA	58.982	36.000	0.00	0.00	31.20	3.07
2405	3554	6.095580	GGACTAGATCCTTGTTTTCCAAATCC	59.904	42.308	0.00	0.00	45.22	3.01
2447	3596	1.811965	CATCAATGCCCAAGAACGACA	59.188	47.619	0.00	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.