AutoCloner

Multiple sequence alignment - TraesCS6B01G018000

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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	TraesCS6B01G018000	chr6B	100.000	4007	0	0	1	4007	11410227	11406221	0.000000e+00	7400.0
1	TraesCS6B01G018000	chr6B	88.777	1595	138	12	175	1730	11515353	11513761	0.000000e+00	1916.0
2	TraesCS6B01G018000	chr6B	87.713	1172	95	20	2397	3550	11512743	11511603	0.000000e+00	1321.0
3	TraesCS6B01G018000	chr6B	98.292	527	8	1	2463	2989	31996567	31997092	0.000000e+00	922.0
4	TraesCS6B01G018000	chr6B	89.823	226	16	5	3785	4007	11341041	11340820	2.360000e-72	283.0
5	TraesCS6B01G018000	chr6B	89.823	226	16	5	3785	4007	11357170	11356949	2.360000e-72	283.0
6	TraesCS6B01G018000	chr6B	88.546	227	17	7	3785	4007	11380343	11380122	2.370000e-67	267.0
7	TraesCS6B01G018000	chr6B	88.957	163	18	0	2235	2397	11512955	11512793	6.790000e-48	202.0
8	TraesCS6B01G018000	chr6D	93.626	2275	86	15	1	2239	6110790	6108539	0.000000e+00	3343.0
9	TraesCS6B01G018000	chr6D	94.295	1788	68	7	2235	4007	6108502	6106734	0.000000e+00	2706.0
10	TraesCS6B01G018000	chr6D	86.552	2268	223	36	26	2241	6250224	6247987	0.000000e+00	2423.0
11	TraesCS6B01G018000	chr6D	89.140	1197	100	20	2397	3580	6247704	6246525	0.000000e+00	1463.0
12	TraesCS6B01G018000	chr6D	88.957	163	18	0	2235	2397	6247916	6247754	6.790000e-48	202.0
13	TraesCS6B01G018000	chr6D	78.689	244	47	3	1441	1684	12643005	12642767	1.490000e-34	158.0
14	TraesCS6B01G018000	chr6D	89.109	101	9	2	3688	3786	6246535	6246435	1.510000e-24	124.0
15	TraesCS6B01G018000	chr6A	92.619	2276	122	12	1	2239	5468332	5466066	0.000000e+00	3230.0
16	TraesCS6B01G018000	chr6A	90.211	2278	106	32	1	2239	5494640	5492441	0.000000e+00	2863.0
17	TraesCS6B01G018000	chr6A	94.482	1486	67	4	2235	3707	5466029	5464546	0.000000e+00	2276.0
18	TraesCS6B01G018000	chr6A	88.115	1767	126	32	4	1726	5544342	5542616	0.000000e+00	2023.0
19	TraesCS6B01G018000	chr6A	93.460	948	46	3	2567	3502	5492129	5491186	0.000000e+00	1393.0
20	TraesCS6B01G018000	chr6A	89.194	1055	86	13	2447	3482	5542148	5541103	0.000000e+00	1291.0
21	TraesCS6B01G018000	chr6A	90.643	513	43	3	3499	4007	5489425	5488914	0.000000e+00	676.0
22	TraesCS6B01G018000	chr6A	90.287	453	39	4	1775	2224	5542602	5542152	4.460000e-164	588.0
23	TraesCS6B01G018000	chr6A	95.730	281	12	0	2235	2515	5492404	5492124	1.700000e-123	453.0
24	TraesCS6B01G018000	chr6A	90.879	307	25	2	3704	4007	5445293	5444987	3.730000e-110	409.0
25	TraesCS6B01G018000	chr6A	77.007	274	55	6	1441	1711	13983797	13983529	2.490000e-32	150.0
26	TraesCS6B01G018000	chr6A	89.899	99	8	2	3687	3784	5541054	5540957	4.200000e-25	126.0
27	TraesCS6B01G018000	chr3B	88.202	178	11	7	3835	4004	508219893	508219718	1.890000e-48	204.0
28	TraesCS6B01G018000	chr2A	87.845	181	12	7	3835	4007	27534162	27533984	1.890000e-48	204.0
29	TraesCS6B01G018000	chr1D	86.224	196	17	7	3817	4004	30289121	30289314	1.890000e-48	204.0
30	TraesCS6B01G018000	chrUn	81.818	132	24	0	1441	1572	410434832	410434963	1.180000e-20	111.0
31	TraesCS6B01G018000	chrUn	81.818	132	24	0	1441	1572	451882298	451882429	1.180000e-20	111.0
32	TraesCS6B01G018000	chr7D	94.737	38	2	0	482	519	42685800	42685837	4.320000e-05	60.2
33	TraesCS6B01G018000	chr7B	94.444	36	2	0	482	517	725520332	725520367	5.590000e-04	56.5
34	TraesCS6B01G018000	chr4B	96.970	33	1	0	482	514	3866742	3866774	5.590000e-04	56.5

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	TraesCS6B01G018000	chr6B	11406221	11410227	4006	True	7400.000000	7400	100.000000	1	4007	1	chr6B.!!$R4	4006
1	TraesCS6B01G018000	chr6B	11511603	11515353	3750	True	1146.333333	1916	88.482333	175	3550	3	chr6B.!!$R5	3375
2	TraesCS6B01G018000	chr6B	31996567	31997092	525	False	922.000000	922	98.292000	2463	2989	1	chr6B.!!$F1	526
3	TraesCS6B01G018000	chr6D	6106734	6110790	4056	True	3024.500000	3343	93.960500	1	4007	2	chr6D.!!$R2	4006
4	TraesCS6B01G018000	chr6D	6246435	6250224	3789	True	1053.000000	2423	88.439500	26	3786	4	chr6D.!!$R3	3760
5	TraesCS6B01G018000	chr6A	5464546	5468332	3786	True	2753.000000	3230	93.550500	1	3707	2	chr6A.!!$R3	3706
6	TraesCS6B01G018000	chr6A	5488914	5494640	5726	True	1346.250000	2863	92.511000	1	4007	4	chr6A.!!$R4	4006
7	TraesCS6B01G018000	chr6A	5540957	5544342	3385	True	1007.000000	2023	89.373750	4	3784	4	chr6A.!!$R5	3780

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
425	437	2.129823	TTGAGGTATAGCGCGCTAAC	57.870	50.0	40.9	33.87	31.73	2.34	F
1887	2215	0.741915	TTTCACCCGAAACTGTTGGC	59.258	50.0	0.0	0.00	36.19	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1941	2269	0.343372	ATTAGGGTGGCAGAGGGAGA	59.657	55.000	0.0	0.0	0.0	3.71	R
3753	6064	1.525077	GCACAACCTTCGACCACCA	60.525	57.895	0.0	0.0	0.0	4.17	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
75	76	6.085416	ACATTTTGACCCTTTAATTACCCCA	58.915	36.000	0.00	0.00	0.00	4.96
294	300	7.935520	ACATGCATATGTACCTCTCTATATCG	58.064	38.462	0.00	0.00	45.45	2.92
336	342	9.608617	GATATTGTGATTCTATGAATGCTTGTG	57.391	33.333	0.00	0.00	0.00	3.33
342	348	6.207221	TGATTCTATGAATGCTTGTGTGTTGT	59.793	34.615	0.00	0.00	0.00	3.32
425	437	2.129823	TTGAGGTATAGCGCGCTAAC	57.870	50.000	40.90	33.87	31.73	2.34
625	637	4.963318	TTAGCATGGATAGTCAAGGGAG	57.037	45.455	0.00	0.00	0.00	4.30
649	662	8.843885	AGTTTTTAGGGTGAACTTAGTATGAC	57.156	34.615	0.00	0.00	29.81	3.06
656	669	5.655532	GGGTGAACTTAGTATGACAGACCTA	59.344	44.000	0.00	0.00	0.00	3.08
675	688	9.301153	CAGACCTAAAATAAATAAAGCGCATTT	57.699	29.630	11.47	9.88	34.72	2.32
692	714	7.412853	AGCGCATTTTTGTGATATCTTTCTAG	58.587	34.615	11.47	0.00	0.00	2.43
923	951	4.602340	ATGGTACCCTAGTAATCAAGCG	57.398	45.455	10.07	0.00	0.00	4.68
944	973	5.127031	AGCGCCCATTTATTGATGTTTTACT	59.873	36.000	2.29	0.00	0.00	2.24
1124	1153	6.183360	GGAGCAAGAGATATTAACCAAACCAC	60.183	42.308	0.00	0.00	0.00	4.16
1258	1290	5.940192	TGGCATCGACATAAATGGTTATC	57.060	39.130	0.00	0.00	0.00	1.75
1356	1388	7.384387	GGTTATCCTCACGGTAATTCTAATGAC	59.616	40.741	0.00	0.00	0.00	3.06
1387	1419	2.634600	GTAATGGTAATGGTGGTCGCA	58.365	47.619	0.00	0.00	0.00	5.10
1388	1420	2.208132	AATGGTAATGGTGGTCGCAA	57.792	45.000	0.00	0.00	0.00	4.85
1574	1678	2.488545	GAGATGGTGTAGTGACAGACGT	59.511	50.000	0.00	0.00	35.82	4.34
1577	1681	2.235891	TGGTGTAGTGACAGACGTGAT	58.764	47.619	0.00	0.00	35.82	3.06
1580	1684	3.119459	GGTGTAGTGACAGACGTGATGAT	60.119	47.826	0.00	0.00	35.82	2.45
1617	1721	8.832735	ACTATGGAGGAATTAGAAAACCTTACA	58.167	33.333	0.00	0.00	32.53	2.41
1635	1739	3.207474	ACAAAGCACTAGGTACGTACG	57.793	47.619	18.98	15.01	0.00	3.67
1677	1781	5.177327	GCATGGATGTTTTCGTTTCATTGTT	59.823	36.000	0.00	0.00	0.00	2.83
1683	1787	7.011016	GGATGTTTTCGTTTCATTGTTCCTTTT	59.989	33.333	0.00	0.00	0.00	2.27
1726	1830	1.332144	CCCTTGCACCCCATTCCATG	61.332	60.000	0.00	0.00	0.00	3.66
1812	2140	4.840271	CCCCATCTTACCGTTTAGTTTCT	58.160	43.478	0.00	0.00	0.00	2.52
1834	2162	4.838904	AGGGGAGTAACATAAAGACCAC	57.161	45.455	0.00	0.00	0.00	4.16
1849	2177	2.909006	AGACCACTCACATCCATGTTCT	59.091	45.455	0.00	0.00	39.39	3.01
1887	2215	0.741915	TTTCACCCGAAACTGTTGGC	59.258	50.000	0.00	0.00	36.19	4.52
1941	2269	3.434167	GCCACCCTCATGATCACTGTTAT	60.434	47.826	0.00	0.00	0.00	1.89
1981	2309	3.303049	TCTGAGCTCATCATCCTTGCTA	58.697	45.455	18.63	0.00	37.28	3.49
1987	2316	2.171237	CTCATCATCCTTGCTACCACCA	59.829	50.000	0.00	0.00	0.00	4.17
2052	2383	1.334869	GTGTGTGTCTTTCCTTGGCAG	59.665	52.381	0.00	0.00	0.00	4.85
2160	2492	5.804639	ACAACTATGCAGGTAGTCAAATGA	58.195	37.500	0.54	0.00	33.92	2.57
2301	2712	1.790387	GTCCGTGTGCAGCAGATTC	59.210	57.895	0.00	0.00	0.00	2.52
2303	2714	1.376424	CCGTGTGCAGCAGATTCCT	60.376	57.895	0.00	0.00	0.00	3.36
2452	2913	3.257375	GCTCCAAATAACGGAAAAAGGGT	59.743	43.478	0.00	0.00	30.33	4.34
2526	2988	6.114187	TCTGCTCCTTAATCTGAAACTTGA	57.886	37.500	0.00	0.00	0.00	3.02
2574	3093	3.386768	TTCAGTGTGTAGCCTGAACTC	57.613	47.619	0.00	0.00	41.47	3.01
2852	3378	4.330250	AGTCCAAACATGAAGATGGTGAG	58.670	43.478	0.00	0.00	33.39	3.51
3171	3712	4.993584	ACAACACTCTCTTATCTTGCACAG	59.006	41.667	0.00	0.00	0.00	3.66
3331	3872	0.317160	TGCAACACCCGTGAGAGTAG	59.683	55.000	0.96	0.00	0.00	2.57
3609	5918	0.970937	TACCGGAAGCTGAGGAGTGG	60.971	60.000	9.46	0.00	0.00	4.00
3621	5930	1.342174	GAGGAGTGGTGTACCGACAAA	59.658	52.381	0.00	0.00	37.31	2.83
3674	5983	6.768381	GGGAGAATTCTAAAAGTCATACAGGG	59.232	42.308	8.25	0.00	31.94	4.45
3698	6007	8.358895	GGGAACTACACCTAGAATATTGTCTAC	58.641	40.741	0.00	0.00	0.00	2.59
3780	6091	2.811431	TCGAAGGTTGTGCATTTAGTGG	59.189	45.455	0.00	0.00	0.00	4.00
3808	6119	2.697431	TGGTTATTTCAGTTGCGCAC	57.303	45.000	11.12	5.61	0.00	5.34
3915	6229	2.953821	CGCACAAAGGGCACGATT	59.046	55.556	0.00	0.00	0.00	3.34
3925	6239	0.383949	GGGCACGATTGTTGTGTGTT	59.616	50.000	0.00	0.00	39.53	3.32
3928	6242	1.064803	GCACGATTGTTGTGTGTTCCA	59.935	47.619	0.00	0.00	39.53	3.53
3963	6278	3.037833	CAGCTGCACGACTTCGCA	61.038	61.111	0.00	0.00	44.43	5.10
3964	6279	2.047844	AGCTGCACGACTTCGCAT	60.048	55.556	1.02	0.00	44.43	4.73
4004	6319	2.700773	GGGGTTGTTGCGAGCATCC	61.701	63.158	0.00	0.16	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	7.817478	GGGTAATTAAAGGGTCAAAATGTTCTG	59.183	37.037	0.00	0.00	0.00	3.02
75	76	8.833231	AGATAATTTAGCTTGCGTATACACAT	57.167	30.769	3.32	0.00	0.00	3.21
329	335	4.717233	ATCTTTCAACAACACACAAGCA	57.283	36.364	0.00	0.00	0.00	3.91
336	342	9.959749	TGGATAACTAAAATCTTTCAACAACAC	57.040	29.630	0.00	0.00	0.00	3.32
342	348	8.801299	TGCACATGGATAACTAAAATCTTTCAA	58.199	29.630	0.00	0.00	0.00	2.69
400	412	2.599848	GCGCGCTATACCTCAATTTGTG	60.600	50.000	26.67	0.00	0.00	3.33
425	437	5.762218	AGCCATTTAGCACTATTTAGCTCAG	59.238	40.000	0.00	0.00	42.05	3.35
606	618	2.769209	ACTCCCTTGACTATCCATGCT	58.231	47.619	0.00	0.00	0.00	3.79
625	637	8.611654	TGTCATACTAAGTTCACCCTAAAAAC	57.388	34.615	0.00	0.00	0.00	2.43
649	662	8.856490	AATGCGCTTTATTTATTTTAGGTCTG	57.144	30.769	9.73	0.00	0.00	3.51
731	757	7.994425	TTCTCTTATATTGTTTGGCTTGTCA	57.006	32.000	0.00	0.00	0.00	3.58
736	762	9.657419	CCAAAAATTCTCTTATATTGTTTGGCT	57.343	29.630	0.00	0.00	36.95	4.75
787	813	3.636679	AGATGGCTACTGACTTGAGCTA	58.363	45.455	0.00	0.00	36.43	3.32
1124	1153	2.436646	CACCACCGCTTAGCCAGG	60.437	66.667	0.00	0.41	0.00	4.45
1258	1290	6.368243	GCACTGAGAGTACCATAATGATGATG	59.632	42.308	0.00	0.00	34.73	3.07
1387	1419	6.245408	TGCTTCCACTTGTTATAACTCCATT	58.755	36.000	16.33	0.00	0.00	3.16
1388	1420	5.815581	TGCTTCCACTTGTTATAACTCCAT	58.184	37.500	16.33	0.00	0.00	3.41
1435	1509	1.417517	AGCATCTCCACGCATTCCATA	59.582	47.619	0.00	0.00	0.00	2.74
1471	1548	1.737355	TTTTGAGGCTGCACTGCACC	61.737	55.000	0.00	7.04	33.79	5.01
1556	1633	2.235891	TCACGTCTGTCACTACACCAT	58.764	47.619	0.00	0.00	0.00	3.55
1574	1678	4.503123	CCATAGTTAGCCCACGAATCATCA	60.503	45.833	0.00	0.00	0.00	3.07
1577	1681	3.035363	TCCATAGTTAGCCCACGAATCA	58.965	45.455	0.00	0.00	0.00	2.57
1580	1684	1.760613	CCTCCATAGTTAGCCCACGAA	59.239	52.381	0.00	0.00	0.00	3.85
1617	1721	2.162681	ACCGTACGTACCTAGTGCTTT	58.837	47.619	19.67	0.00	0.00	3.51
1635	1739	5.474532	TCCATGCATGCAAATATAGAGAACC	59.525	40.000	26.68	0.00	0.00	3.62
1677	1781	9.913310	AGGAAAAATGGTGAAATTTTAAAAGGA	57.087	25.926	6.79	0.00	38.49	3.36
1683	1787	8.151596	GGGTACAGGAAAAATGGTGAAATTTTA	58.848	33.333	0.00	0.00	38.49	1.52
1726	1830	9.914131	AAAGGCTCTATACAAAAGATTTTTGTC	57.086	29.630	19.63	7.71	42.10	3.18
1812	2140	5.596763	AGTGGTCTTTATGTTACTCCCCTA	58.403	41.667	0.00	0.00	0.00	3.53
1834	2162	7.485913	CCGAATTAAAAAGAACATGGATGTGAG	59.514	37.037	0.00	0.00	41.61	3.51
1849	2177	6.370166	GGTGAAAATGCATCCCGAATTAAAAA	59.630	34.615	0.00	0.00	0.00	1.94
1887	2215	1.478105	GGCCCTTGTGAAGCAATTAGG	59.522	52.381	0.00	0.00	36.36	2.69
1941	2269	0.343372	ATTAGGGTGGCAGAGGGAGA	59.657	55.000	0.00	0.00	0.00	3.71
1987	2316	3.785859	ATCACAGCGACGGGGCAT	61.786	61.111	0.00	0.00	34.64	4.40
2230	2564	6.211587	ACATGTATTTGTAGTGCGTACCTA	57.788	37.500	0.00	0.00	0.00	3.08
2274	2685	1.529438	CTGCACACGGACGTTGTAAAT	59.471	47.619	0.00	0.00	0.00	1.40
2380	2791	7.112122	TCATGCTTGGAGAACAGTAAATGTAT	58.888	34.615	0.00	0.00	43.00	2.29
2452	2913	1.804151	GTTGTTCAGCGGTGCTCAATA	59.196	47.619	20.36	4.29	36.40	1.90
2574	3093	0.731417	CGAGCCCTGCATTCTGAAAG	59.269	55.000	0.00	0.00	0.00	2.62
2782	3308	4.154942	ACTCTTGGTGCAATCAATTTCCT	58.845	39.130	4.50	0.00	0.00	3.36
2852	3378	3.273434	TGCATCTTTGTCCATCACTAGC	58.727	45.455	0.00	0.00	0.00	3.42
3036	3563	9.423061	GAACCAAGATACTACAATTGCAAAATT	57.577	29.630	1.71	0.00	0.00	1.82
3149	3690	5.233225	TCTGTGCAAGATAAGAGAGTGTTG	58.767	41.667	0.00	0.00	0.00	3.33
3235	3776	3.055385	TCGCCTAAACCTATGTTGCTTCT	60.055	43.478	0.00	0.00	34.13	2.85
3331	3872	2.224784	AGGACGAACGGTTGCATTTTAC	59.775	45.455	0.00	0.00	0.00	2.01
3578	5887	6.056884	TCAGCTTCCGGTAAACTAAGAAAAA	58.943	36.000	0.00	0.00	0.00	1.94
3628	5937	7.726291	TCTCCCTGTTATACCATTTGTTTTGAA	59.274	33.333	0.00	0.00	0.00	2.69
3634	5943	7.643123	AGAATTCTCCCTGTTATACCATTTGT	58.357	34.615	0.88	0.00	0.00	2.83
3635	5944	9.627123	TTAGAATTCTCCCTGTTATACCATTTG	57.373	33.333	12.24	0.00	0.00	2.32
3674	5983	8.619546	ACGTAGACAATATTCTAGGTGTAGTTC	58.380	37.037	8.35	0.00	42.72	3.01
3698	6007	4.380841	TTTACACTATGAGGGCAGTACG	57.619	45.455	0.00	0.00	0.00	3.67
3753	6064	1.525077	GCACAACCTTCGACCACCA	60.525	57.895	0.00	0.00	0.00	4.17
3780	6091	7.462724	GCGCAACTGAAATAACCAACAATAATC	60.463	37.037	0.30	0.00	0.00	1.75
3833	6144	8.311836	TCTGAAGAAAAACTAACACCTATCGAT	58.688	33.333	2.16	2.16	0.00	3.59
3891	6205	1.103987	TGCCCTTTGTGCGCTAACAA	61.104	50.000	9.73	9.33	38.26	2.83
3903	6217	1.066908	CACACAACAATCGTGCCCTTT	59.933	47.619	0.00	0.00	37.93	3.11
3925	6239	4.037222	TGGCTCCTAACTATTCACATGGA	58.963	43.478	0.00	0.00	0.00	3.41
3928	6242	3.713764	AGCTGGCTCCTAACTATTCACAT	59.286	43.478	0.00	0.00	0.00	3.21
3977	6292	2.282887	AACAACCCCATCGTGCCC	60.283	61.111	0.00	0.00	0.00	5.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.