AutoCloner

Multiple sequence alignment - TraesCS6B01G104400

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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	TraesCS6B01G104400	chr6B	100.000	4729	0	0	1	4729	83866045	83870773	0.000000e+00	8733
1	TraesCS6B01G104400	chr3B	96.426	4728	165	4	1	4726	817686344	817691069	0.000000e+00	7792
2	TraesCS6B01G104400	chr3B	96.449	3971	140	1	756	4726	817710255	817714224	0.000000e+00	6551
3	TraesCS6B01G104400	chr3B	96.308	3304	119	2	761	4061	745188	748491	0.000000e+00	5422
4	TraesCS6B01G104400	chr7B	96.173	4730	180	1	1	4729	695576178	695571449	0.000000e+00	7731
5	TraesCS6B01G104400	chr6A	95.921	4732	187	5	1	4729	307922647	307917919	0.000000e+00	7664
6	TraesCS6B01G104400	chr7A	95.918	4728	190	3	1	4726	395513524	395518250	0.000000e+00	7659
7	TraesCS6B01G104400	chr7A	91.445	1426	93	19	3224	4632	298784564	298785977	0.000000e+00	1930
8	TraesCS6B01G104400	chr7A	84.106	302	42	6	4427	4726	29872060	29872357	2.150000e-73	287
9	TraesCS6B01G104400	chr5A	95.792	4729	166	6	1	4726	213046758	213051456	0.000000e+00	7600
10	TraesCS6B01G104400	chr5A	96.409	3954	142	0	776	4729	631069218	631065265	0.000000e+00	6516
11	TraesCS6B01G104400	chr1A	95.356	4737	181	16	1	4726	236391029	236395737	0.000000e+00	7492
12	TraesCS6B01G104400	chr2A	95.624	1394	56	5	1	1392	290318352	290319742	0.000000e+00	2231
13	TraesCS6B01G104400	chr4A	89.507	934	71	18	3716	4632	658679800	658678877	0.000000e+00	1157
14	TraesCS6B01G104400	chr3A	90.421	783	68	7	1	778	290710198	290709418	0.000000e+00	1024
15	TraesCS6B01G104400	chr3A	87.801	705	69	14	1	699	157346598	157347291	0.000000e+00	809
16	TraesCS6B01G104400	chr3A	91.267	584	44	6	1	581	496383872	496384451	0.000000e+00	789

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	TraesCS6B01G104400	chr6B	83866045	83870773	4728	False	8733	8733	100.000	1	4729	1	chr6B.!!$F1	4728
1	TraesCS6B01G104400	chr3B	817686344	817691069	4725	False	7792	7792	96.426	1	4726	1	chr3B.!!$F2	4725
2	TraesCS6B01G104400	chr3B	817710255	817714224	3969	False	6551	6551	96.449	756	4726	1	chr3B.!!$F3	3970
3	TraesCS6B01G104400	chr3B	745188	748491	3303	False	5422	5422	96.308	761	4061	1	chr3B.!!$F1	3300
4	TraesCS6B01G104400	chr7B	695571449	695576178	4729	True	7731	7731	96.173	1	4729	1	chr7B.!!$R1	4728
5	TraesCS6B01G104400	chr6A	307917919	307922647	4728	True	7664	7664	95.921	1	4729	1	chr6A.!!$R1	4728
6	TraesCS6B01G104400	chr7A	395513524	395518250	4726	False	7659	7659	95.918	1	4726	1	chr7A.!!$F3	4725
7	TraesCS6B01G104400	chr7A	298784564	298785977	1413	False	1930	1930	91.445	3224	4632	1	chr7A.!!$F2	1408
8	TraesCS6B01G104400	chr5A	213046758	213051456	4698	False	7600	7600	95.792	1	4726	1	chr5A.!!$F1	4725
9	TraesCS6B01G104400	chr5A	631065265	631069218	3953	True	6516	6516	96.409	776	4729	1	chr5A.!!$R1	3953
10	TraesCS6B01G104400	chr1A	236391029	236395737	4708	False	7492	7492	95.356	1	4726	1	chr1A.!!$F1	4725
11	TraesCS6B01G104400	chr2A	290318352	290319742	1390	False	2231	2231	95.624	1	1392	1	chr2A.!!$F1	1391
12	TraesCS6B01G104400	chr4A	658678877	658679800	923	True	1157	1157	89.507	3716	4632	1	chr4A.!!$R1	916
13	TraesCS6B01G104400	chr3A	290709418	290710198	780	True	1024	1024	90.421	1	778	1	chr3A.!!$R1	777
14	TraesCS6B01G104400	chr3A	157346598	157347291	693	False	809	809	87.801	1	699	1	chr3A.!!$F1	698
15	TraesCS6B01G104400	chr3A	496383872	496384451	579	False	789	789	91.267	1	581	1	chr3A.!!$F2	580

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	Hairpin	End Stability	Orientation
847	855	0.969409	ACCCCTAACTTCGTCGGGAG	60.969	60.0	39.08	4.30	F
1288	1305	0.035630	GAGCTGATGGAACTGGTGCT	60.036	55.0	0.00	4.40	F
2508	2527	0.307760	CGCACCAACTCCAACAAGTC	59.692	55.0	0.00	3.01	F
3171	3190	0.987294	CTCTCCCTCTGCTCCCAAAA	59.013	55.0	0.00	2.44	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2041	2058	0.693049	AAGGGTCAAGCGATTGGTCT	59.307	50.000	14.27	5.95	0.00	3.85	R
2828	2847	1.335182	ACTGCCTGATACTGTCGATCG	59.665	52.381	9.36	9.36	0.00	3.69	R
3559	3606	1.270274	CACAAGGCATAGCAAGCACAA	59.730	47.619	0.00	0.00	0.00	3.33	R
4673	4738	1.218316	GGTCACTAGCAACCTCCCG	59.782	63.158	6.84	0.00	32.54	5.14	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
617	625	1.984570	CGCACCCTTCTCTCCCTCA	60.985	63.158	0.00	0.00	0.00	3.86
642	650	2.693017	GCCCCTCTCTCCTCTCCA	59.307	66.667	0.00	0.00	0.00	3.86
804	812	4.697756	CTCGCCCGCAACCCTCAA	62.698	66.667	0.00	0.00	0.00	3.02
807	815	4.660938	GCCCGCAACCCTCAACCT	62.661	66.667	0.00	0.00	0.00	3.50
847	855	0.969409	ACCCCTAACTTCGTCGGGAG	60.969	60.000	0.00	0.00	39.08	4.30
858	866	2.125147	TCGGGAGCTGCCAAATCG	60.125	61.111	25.24	9.80	38.95	3.34
1004	1021	0.673985	GATGGGACGACGATGATGGA	59.326	55.000	0.00	0.00	0.00	3.41
1025	1042	3.606204	AGGGGCAAACCTCCATGT	58.394	55.556	0.00	0.00	36.95	3.21
1178	1195	3.311110	GACCCACTCGGCTGTCCA	61.311	66.667	0.00	0.00	33.26	4.02
1190	1207	1.904852	GCTGTCCATGCGTGTGTCAG	61.905	60.000	4.96	10.70	0.00	3.51
1245	1262	0.179004	ACTTTGTTCGTCCATGGCCA	60.179	50.000	8.56	8.56	0.00	5.36
1259	1276	3.275338	GCCAGCCAGTAGATGCGC	61.275	66.667	0.00	0.00	0.00	6.09
1288	1305	0.035630	GAGCTGATGGAACTGGTGCT	60.036	55.000	0.00	0.00	0.00	4.40
1354	1371	6.881570	TCTTTGATCAGATGATGCTTAGACA	58.118	36.000	0.00	0.00	34.37	3.41
1479	1496	7.180408	ACTCTTGTATGTCAATACCAGGTAGTT	59.820	37.037	5.31	0.00	38.33	2.24
1524	1541	7.381766	TGATTAGATGCAATATGGTGTATGC	57.618	36.000	0.00	0.00	39.22	3.14
1533	1550	5.504665	GCAATATGGTGTATGCTCAACTCAC	60.505	44.000	0.00	0.00	35.93	3.51
1945	1962	2.224821	CCATCAAGGGCCTGCTCTA	58.775	57.895	6.92	0.00	0.00	2.43
1985	2002	2.870119	CGGTACCACCACGTTCCCA	61.870	63.158	13.54	0.00	38.47	4.37
2032	2049	2.509916	CCATGCCTCCTCTGCTCC	59.490	66.667	0.00	0.00	0.00	4.70
2053	2070	1.078143	GGGCTCAGACCAATCGCTT	60.078	57.895	0.00	0.00	0.00	4.68
2074	2091	1.969862	CCCTTCAGGTACGGACGTT	59.030	57.895	1.57	0.00	28.33	3.99
2114	2132	0.395586	TGTGAGTGCCAACTTGCCTT	60.396	50.000	0.00	0.00	36.52	4.35
2121	2139	0.678950	GCCAACTTGCCTTTTGCCTA	59.321	50.000	0.00	0.00	40.16	3.93
2352	2371	4.094294	TGTTGCCTTAATACAATCTGCGTC	59.906	41.667	0.00	0.00	0.00	5.19
2508	2527	0.307760	CGCACCAACTCCAACAAGTC	59.692	55.000	0.00	0.00	0.00	3.01
2511	2530	2.287788	GCACCAACTCCAACAAGTCATG	60.288	50.000	0.00	0.00	0.00	3.07
2615	2634	6.121776	ACAACCTGATCAATGTACAACCTA	57.878	37.500	0.00	0.00	0.00	3.08
2626	2645	8.121305	TCAATGTACAACCTATTTGCTTGAAT	57.879	30.769	0.00	0.00	39.01	2.57
2709	2728	5.878332	TCTAAAACTACCGTCGTGTGATA	57.122	39.130	0.00	0.00	0.00	2.15
2725	2744	3.709141	TGTGATAATGCAGGTGCCTAGTA	59.291	43.478	0.00	0.00	41.18	1.82
2793	2812	4.850680	AGTTTGTCACCTTGTTTCCACTA	58.149	39.130	0.00	0.00	0.00	2.74
2828	2847	3.652274	TGTTTGCTGCTTATGCTTTTCC	58.348	40.909	0.00	0.00	40.48	3.13
2906	2925	9.304731	CAAATCCATGATTTTGTTATGTACTGG	57.695	33.333	0.00	0.00	39.82	4.00
2914	2933	5.940192	TTTGTTATGTACTGGTTGCTCAG	57.060	39.130	0.00	0.00	40.40	3.35
2950	2969	6.802608	AGTTAACCTTTCTTGTTAAGGCAAC	58.197	36.000	0.88	0.00	44.91	4.17
3171	3190	0.987294	CTCTCCCTCTGCTCCCAAAA	59.013	55.000	0.00	0.00	0.00	2.44
3298	3317	1.407656	CGGATTGCCTAGTGCCCCTA	61.408	60.000	1.42	0.00	40.16	3.53
3411	3458	2.507102	CGTCGATGAAGCGGCAGT	60.507	61.111	1.45	0.00	35.20	4.40
3549	3596	1.303236	CCTGTTTCATGGCCGTGGA	60.303	57.895	24.78	14.45	0.00	4.02
3559	3606	4.787551	TCATGGCCGTGGATTATTTAGTT	58.212	39.130	24.78	0.00	0.00	2.24
3908	3970	1.628846	CTTAGTTGGGTAGGTGCTGGT	59.371	52.381	0.00	0.00	0.00	4.00
3963	4025	5.451242	GGACTTGCACTAAATGGACACAAAA	60.451	40.000	0.00	0.00	0.00	2.44
4017	4080	7.816640	TCTAACTGGAAACAATTTCTGTATGC	58.183	34.615	1.62	0.00	42.06	3.14
4019	4082	7.759489	AACTGGAAACAATTTCTGTATGCTA	57.241	32.000	1.62	0.00	42.06	3.49
4062	4125	9.029368	TGATAGCTGATCTGTAGCAAATATAGT	57.971	33.333	0.00	0.00	43.53	2.12
4146	4209	2.284417	GTGCGAAGACGTGAAGAAAAGT	59.716	45.455	0.00	0.00	41.98	2.66
4235	4299	7.533083	AGCTGGTATACCTAGGTTGTAATAGA	58.467	38.462	22.11	0.00	36.82	1.98
4697	4762	3.477530	GAGGTTGCTAGTGACCAAAACT	58.522	45.455	15.96	3.71	38.42	2.66

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
335	340	9.636965	GTCAGCAAATTTGAATTTAGTTTTCAC	57.363	29.630	22.31	0.00	36.52	3.18
474	480	5.065988	GGACCAATCAAAACGCAGTATACAT	59.934	40.000	5.50	0.00	45.00	2.29
563	571	3.771160	GTGGGTGAGACGGGCGAT	61.771	66.667	0.00	0.00	0.00	4.58
617	625	1.979693	GAGAGAGGGGCGTCAGTGT	60.980	63.158	0.00	0.00	0.00	3.55
642	650	5.839606	TGGATTCAGATCAGATCAGAGTGAT	59.160	40.000	13.14	1.13	35.39	3.06
772	780	2.178890	CGAGTACTAGAGGGCGCGT	61.179	63.158	8.43	0.00	0.00	6.01
804	812	1.683441	CCGAAACCCTAGCCAAGGT	59.317	57.895	2.24	0.00	44.90	3.50
807	815	1.002624	CAGCCGAAACCCTAGCCAA	60.003	57.895	0.00	0.00	0.00	4.52
1025	1042	4.308458	CTTGGTGGCGACCCGTCA	62.308	66.667	16.02	0.00	42.34	4.35
1178	1195	2.738521	GGTCGCTGACACACGCAT	60.739	61.111	10.14	0.00	33.68	4.73
1190	1207	1.439644	CTCAAGAGCTAGGGGTCGC	59.560	63.158	0.00	0.00	43.89	5.19
1245	1262	2.503061	CCAGCGCATCTACTGGCT	59.497	61.111	11.47	0.00	46.50	4.75
1259	1276	5.757320	CAGTTCCATCAGCTCTTAATACCAG	59.243	44.000	0.00	0.00	0.00	4.00
1288	1305	3.069079	AGCTGTACTACTCACTTCCGA	57.931	47.619	0.00	0.00	0.00	4.55
1354	1371	3.615155	GGCAGAAGCTACAATCTTCCTT	58.385	45.455	0.00	0.00	40.48	3.36
1479	1496	7.956328	ATCATAGGACACTAGTCTGTAACAA	57.044	36.000	0.00	0.00	44.36	2.83
1945	1962	2.977808	TGGTCAAGGAAGAAGAGGAGT	58.022	47.619	0.00	0.00	0.00	3.85
2032	2049	2.190578	GATTGGTCTGAGCCCGGG	59.809	66.667	19.09	19.09	0.00	5.73
2041	2058	0.693049	AAGGGTCAAGCGATTGGTCT	59.307	50.000	14.27	5.95	0.00	3.85
2069	2086	6.922407	GGGTTGAGATAATAGTAGGAAACGTC	59.078	42.308	0.00	0.00	0.00	4.34
2074	2091	7.130099	TCACAGGGTTGAGATAATAGTAGGAA	58.870	38.462	0.00	0.00	0.00	3.36
2114	2132	3.118038	AGTCAACACTCTTGGTAGGCAAA	60.118	43.478	0.00	0.00	0.00	3.68
2121	2139	3.316308	GCAATTCAGTCAACACTCTTGGT	59.684	43.478	0.00	0.00	0.00	3.67
2352	2371	6.382282	TCTCCATATGGATACCAGCTAATGAG	59.618	42.308	24.73	8.08	44.46	2.90
2540	2559	4.095036	GTGCAAGAAGGCATTTACTAGGTC	59.905	45.833	0.00	0.00	46.92	3.85
2654	2673	2.038952	ACTGTTCCATGCAGTCTTAGCA	59.961	45.455	0.00	0.00	42.90	3.49
2700	2719	1.368641	GCACCTGCATTATCACACGA	58.631	50.000	0.00	0.00	41.59	4.35
2709	2728	3.652057	AACATACTAGGCACCTGCATT	57.348	42.857	0.00	0.00	44.36	3.56
2793	2812	4.498009	GCAGCAAACAATATCCTGCGTATT	60.498	41.667	0.00	0.00	39.39	1.89
2828	2847	1.335182	ACTGCCTGATACTGTCGATCG	59.665	52.381	9.36	9.36	0.00	3.69
2938	2957	3.219281	GTTCTCAGGGTTGCCTTAACAA	58.781	45.455	0.00	0.00	41.18	2.83
2950	2969	1.605710	CACAAGCAAGTGTTCTCAGGG	59.394	52.381	0.81	0.00	34.83	4.45
2998	3017	7.305813	TGGGTAACAGTACATCTTTACTTGA	57.694	36.000	0.00	0.00	39.74	3.02
3004	3023	5.250774	AGACCATGGGTAACAGTACATCTTT	59.749	40.000	18.09	0.00	35.25	2.52
3256	3275	7.067859	TCCGGTAGCAATGTCATATATAGGTAC	59.932	40.741	0.00	0.00	0.00	3.34
3298	3317	3.778265	ACAAGTTTAGCCCACCATGAAT	58.222	40.909	0.00	0.00	0.00	2.57
3549	3596	6.980397	GGCATAGCAAGCACAAACTAAATAAT	59.020	34.615	0.00	0.00	0.00	1.28
3559	3606	1.270274	CACAAGGCATAGCAAGCACAA	59.730	47.619	0.00	0.00	0.00	3.33
3646	3693	6.183347	ACCTTAGCAGAATAAGCAGAACAAT	58.817	36.000	0.00	0.00	32.42	2.71
3908	3970	5.991933	TGCATATAAACTTTTGCTCCCAA	57.008	34.783	0.00	0.00	36.10	4.12
3963	4025	9.628500	AAGTTCACTTAATACTCAACTCCTTTT	57.372	29.630	0.00	0.00	33.79	2.27
4062	4125	4.877251	ACCAAGTAAAGAAGTTACGCACAA	59.123	37.500	0.00	0.00	45.84	3.33
4146	4209	2.428960	TAGCACTTCACGGCTTCGCA	62.429	55.000	0.00	0.00	41.41	5.10
4498	4562	8.355913	CCCAATATTTCAGCCTTTTTATCTCTC	58.644	37.037	0.00	0.00	0.00	3.20
4575	4640	2.643551	CCTAGCCCAACAATTCGACAT	58.356	47.619	0.00	0.00	0.00	3.06
4673	4738	1.218316	GGTCACTAGCAACCTCCCG	59.782	63.158	6.84	0.00	32.54	5.14
4697	4762	7.369551	ACGACCAAAATATTCCTACTATGGA	57.630	36.000	0.00	0.00	0.00	3.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.