AutoCloner

Multiple sequence alignment - TraesCS6D01G402900

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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	TraesCS6D01G402900	chr6D	100.000	3188	0	0	1	3188	471072667	471069480	0.000000e+00	5888
1	TraesCS6D01G402900	chr6D	89.691	97	8	2	2728	2822	63328288	63328192	4.320000e-24	122
2	TraesCS6D01G402900	chr6A	90.909	2981	197	25	1	2926	615891386	615888425	0.000000e+00	3936
3	TraesCS6D01G402900	chr6A	93.511	262	15	2	2929	3188	615888366	615888105	3.860000e-104	388
4	TraesCS6D01G402900	chr6B	93.476	2575	131	17	12	2566	719507594	719510151	0.000000e+00	3790
5	TraesCS6D01G402900	chr6B	94.074	270	16	0	2658	2927	719515597	719515866	8.230000e-111	411
6	TraesCS6D01G402900	chr6B	91.954	261	11	5	2929	3188	719510638	719510889	1.090000e-94	357
7	TraesCS6D01G402900	chr6B	90.458	262	17	3	2929	3188	719515923	719516178	3.940000e-89	339
8	TraesCS6D01G402900	chr6B	94.702	151	8	0	2512	2662	719515373	719515523	5.320000e-58	235
9	TraesCS6D01G402900	chr6B	94.737	114	6	0	2814	2927	719510467	719510580	9.090000e-41	178
10	TraesCS6D01G402900	chr3D	80.313	447	74	9	3	444	583321663	583322100	3.070000e-85	326
11	TraesCS6D01G402900	chr3D	94.253	87	4	1	2731	2817	508471382	508471297	7.180000e-27	132
12	TraesCS6D01G402900	chr5D	80.815	417	69	10	8	419	332073251	332072841	1.850000e-82	316
13	TraesCS6D01G402900	chr2B	79.393	461	73	14	1	457	87518970	87518528	4.000000e-79	305
14	TraesCS6D01G402900	chr3A	79.295	454	79	11	1	448	644817061	644817505	1.440000e-78	303
15	TraesCS6D01G402900	chr1D	78.373	467	91	8	9	469	449970574	449971036	8.650000e-76	294
16	TraesCS6D01G402900	chr2D	78.214	459	94	4	10	467	608485152	608484699	4.020000e-74	289
17	TraesCS6D01G402900	chr5A	77.551	490	92	14	8	491	569527698	569527221	2.420000e-71	279
18	TraesCS6D01G402900	chr5A	93.023	86	6	0	2731	2816	624795595	624795510	3.340000e-25	126
19	TraesCS6D01G402900	chr7D	93.258	89	6	0	2730	2818	557386817	557386905	7.180000e-27	132
20	TraesCS6D01G402900	chr1B	96.250	80	3	0	2736	2815	554241277	554241198	7.180000e-27	132
21	TraesCS6D01G402900	chr4B	93.976	83	5	0	2731	2813	650697295	650697377	3.340000e-25	126
22	TraesCS6D01G402900	chr1A	93.023	86	6	0	2731	2816	42512548	42512633	3.340000e-25	126

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	TraesCS6D01G402900	chr6D	471069480	471072667	3187	True	5888.000000	5888	100.000	1	3188	1	chr6D.!!$R2	3187
1	TraesCS6D01G402900	chr6A	615888105	615891386	3281	True	2162.000000	3936	92.210	1	3188	2	chr6A.!!$R1	3187
2	TraesCS6D01G402900	chr6B	719507594	719510889	3295	False	1441.666667	3790	93.389	12	3188	3	chr6B.!!$F1	3176
3	TraesCS6D01G402900	chr6B	719515373	719516178	805	False	328.333333	411	93.078	2512	3188	3	chr6B.!!$F2	676

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
388	390	0.324614	TAGGTGGTCTACGGACGTGA	59.675	55.000	7.73	0.56	42.97	4.35	F
808	824	1.003233	AAAGCTCGAGTCTTGGGCC	60.003	57.895	15.13	0.00	0.00	5.80	F
1661	1681	1.098050	GCTTGCAATGGTTCCTCGAT	58.902	50.000	0.00	0.00	0.00	3.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1342	1359	1.210478	CTGGATCCCATTTCTGGACGT	59.790	52.381	9.90	46.37	4.34	R
1830	1850	1.359459	GACCAGCGCTTAGGTTTCCG	61.359	60.000	19.44	38.50	4.30	R
3157	3420	0.173708	GATGTGAGACCCAGACGTCC	59.826	60.000	13.01	32.91	4.79	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
26	27	4.290722	ACTCCTTGAAGATGGAATGAGGTT	59.709	41.667	0.00	0.00	31.23	3.50
68	69	2.317609	ACGGTGCGTCTCATGTTGC	61.318	57.895	0.00	0.00	33.69	4.17
69	70	2.029288	CGGTGCGTCTCATGTTGCT	61.029	57.895	0.00	0.00	0.00	3.91
70	71	1.499056	GGTGCGTCTCATGTTGCTG	59.501	57.895	0.00	0.00	0.00	4.41
115	116	2.752144	GCAGATCTTGCGAGATTTGG	57.248	50.000	27.39	16.99	42.66	3.28
183	184	0.966179	TGCGGTCATGTGTCTACAGT	59.034	50.000	0.00	0.00	40.79	3.55
195	196	3.515901	GTGTCTACAGTTTGGATCCTCCT	59.484	47.826	14.23	2.89	37.46	3.69
233	235	2.442212	TGGCGACGATTGTTGTTCTA	57.558	45.000	0.00	0.00	0.00	2.10
247	249	0.458716	GTTCTAGTGCGCTGGTCCTC	60.459	60.000	10.80	0.00	0.00	3.71
261	263	0.548510	GTCCTCTGGGGCTTTAGCAT	59.451	55.000	3.88	0.00	44.36	3.79
264	266	1.144503	CCTCTGGGGCTTTAGCATGAT	59.855	52.381	0.00	0.00	44.36	2.45
275	277	4.384056	CTTTAGCATGATGACTTCCCGAT	58.616	43.478	0.00	0.00	0.00	4.18
285	287	5.833667	TGATGACTTCCCGATTGTCTACTAT	59.166	40.000	0.00	0.00	0.00	2.12
294	296	6.381994	TCCCGATTGTCTACTATAACAAGGTT	59.618	38.462	0.00	0.00	38.66	3.50
302	304	3.089284	ACTATAACAAGGTTTGCCTGGC	58.911	45.455	12.87	12.87	46.33	4.85
304	306	1.616159	TAACAAGGTTTGCCTGGCTC	58.384	50.000	21.03	10.08	46.33	4.70
309	311	3.365265	GTTTGCCTGGCTCCGGTG	61.365	66.667	21.03	0.00	0.00	4.94
315	317	2.427245	CCTGGCTCCGGTGAGGTAG	61.427	68.421	7.92	0.00	41.99	3.18
352	354	1.741401	CACATTCGGCTCGCTCCAA	60.741	57.895	0.00	0.00	0.00	3.53
388	390	0.324614	TAGGTGGTCTACGGACGTGA	59.675	55.000	7.73	0.56	42.97	4.35
425	427	7.473411	CGTTACTTTTCGTGTTCTTTATACTGC	59.527	37.037	0.00	0.00	0.00	4.40
503	505	7.913674	TTGGAAACTTGCTAAACATTTTGTT	57.086	28.000	0.00	0.00	43.41	2.83
513	515	8.094798	TGCTAAACATTTTGTTCCACTACTAG	57.905	34.615	0.00	0.00	40.14	2.57
537	539	4.272504	CACTGTTTGTACTTACTGGGTGTG	59.727	45.833	0.00	0.00	0.00	3.82
588	590	2.951642	TGCTTGTTGAGAAAAGACAGGG	59.048	45.455	0.00	0.00	0.00	4.45
804	820	1.355066	GCCGGAAAGCTCGAGTCTTG	61.355	60.000	15.13	7.18	0.00	3.02
808	824	1.003233	AAAGCTCGAGTCTTGGGCC	60.003	57.895	15.13	0.00	0.00	5.80
887	903	1.550976	CCAGCCTAGGTCGTTTCTTCT	59.449	52.381	11.31	0.00	0.00	2.85
898	915	4.253685	GTCGTTTCTTCTTCATCCATCCA	58.746	43.478	0.00	0.00	0.00	3.41
931	948	1.826024	CGATTGGCCTCTAGCTGGT	59.174	57.895	3.32	0.00	43.05	4.00
957	974	2.168326	TCTCGCTGTGAATTTCTGCA	57.832	45.000	11.54	0.00	0.00	4.41
1342	1359	4.478371	CCCTCTGCATCGCTGGCA	62.478	66.667	0.00	0.00	39.32	4.92
1455	1472	2.184322	GCGATCGAGGGTGCAGAA	59.816	61.111	21.57	0.00	0.00	3.02
1464	1481	1.673665	GGGTGCAGAAGAGGCTGTG	60.674	63.158	0.00	0.00	38.17	3.66
1467	1484	2.749441	GCAGAAGAGGCTGTGGGC	60.749	66.667	0.00	0.00	38.17	5.36
1590	1607	2.606826	GGACCCAAGAGACCCCGT	60.607	66.667	0.00	0.00	0.00	5.28
1661	1681	1.098050	GCTTGCAATGGTTCCTCGAT	58.902	50.000	0.00	0.00	0.00	3.59
1732	1752	4.342665	GGAAATCCGGTGAGAGAACTATCT	59.657	45.833	0.00	0.00	39.10	1.98
1830	1850	3.548770	TGCTGACAATGGAGATGGAATC	58.451	45.455	0.00	0.00	46.04	2.52
1918	1938	1.889829	ACGGTGAACAGAGAGAAGAGG	59.110	52.381	0.00	0.00	0.00	3.69
1944	1967	4.840716	AGAAACAGAGCAATCCAGAGAT	57.159	40.909	0.00	0.00	0.00	2.75
1980	2006	0.235926	GCAACGAGCTCAAGTCCAAC	59.764	55.000	15.40	0.00	41.15	3.77
1984	2010	1.301716	GAGCTCAAGTCCAACGGCA	60.302	57.895	9.40	0.00	0.00	5.69
2102	2128	1.064952	CAAGAAGTTCAAACCGGCGTT	59.935	47.619	6.01	0.00	0.00	4.84
2151	2177	3.392616	AGATGTTGTGTTCCTCCAGTTCT	59.607	43.478	0.00	0.00	0.00	3.01
2259	2297	7.939588	TCAGATGCGTGTCCTAGCTATATATAT	59.060	37.037	0.00	0.00	0.00	0.86
2260	2298	9.220767	CAGATGCGTGTCCTAGCTATATATATA	57.779	37.037	0.00	2.49	0.00	0.86
2578	2645	2.690497	TGTCCTCTTTATCTGCCTCTCG	59.310	50.000	0.00	0.00	0.00	4.04
2647	2756	3.131223	TGACTCCTAGCAGCAACTATGTC	59.869	47.826	0.00	0.00	0.00	3.06
2648	2757	2.099921	ACTCCTAGCAGCAACTATGTCG	59.900	50.000	0.00	0.00	0.00	4.35
2745	2933	5.875359	CCTGTTCATTACTCCCTCTGTAAAC	59.125	44.000	0.00	0.00	34.20	2.01
2927	3133	5.478679	AGATAAATACTCTGTAGCGGCAGAT	59.521	40.000	12.41	7.04	43.61	2.90
2937	3199	1.675641	GCGGCAGATGGTTGAAGGT	60.676	57.895	0.00	0.00	0.00	3.50
2985	3248	1.755783	GGCAAAGATGAGGGCCTGG	60.756	63.158	12.95	0.00	43.09	4.45
3070	3333	2.654863	CCAATAACACCCCCTGATGAC	58.345	52.381	0.00	0.00	0.00	3.06
3157	3420	1.672881	GGCGGAGACCATTTCTGAATG	59.327	52.381	0.00	0.00	41.87	2.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
7	8	4.880696	GGAGAACCTCATTCCATCTTCAAG	59.119	45.833	0.00	0.00	38.16	3.02
8	9	4.324563	GGGAGAACCTCATTCCATCTTCAA	60.325	45.833	0.00	0.00	38.16	2.69
10	11	3.434310	GGGGAGAACCTCATTCCATCTTC	60.434	52.174	0.00	0.00	38.16	2.87
50	51	2.317609	GCAACATGAGACGCACCGT	61.318	57.895	0.00	0.00	45.10	4.83
68	69	2.336478	ACCTCGACACGCTCTCCAG	61.336	63.158	0.00	0.00	0.00	3.86
69	70	2.282251	ACCTCGACACGCTCTCCA	60.282	61.111	0.00	0.00	0.00	3.86
70	71	2.179517	CACCTCGACACGCTCTCC	59.820	66.667	0.00	0.00	0.00	3.71
104	105	2.684001	AATACCGACCAAATCTCGCA	57.316	45.000	0.00	0.00	0.00	5.10
107	108	6.248631	CGAAGAAAAATACCGACCAAATCTC	58.751	40.000	0.00	0.00	0.00	2.75
113	114	3.068560	CACCGAAGAAAAATACCGACCA	58.931	45.455	0.00	0.00	0.00	4.02
115	116	3.328505	TCCACCGAAGAAAAATACCGAC	58.671	45.455	0.00	0.00	0.00	4.79
195	196	5.052481	CGCCATGAAGAGAAATGTAGATCA	58.948	41.667	0.00	0.00	0.00	2.92
233	235	3.699894	CCAGAGGACCAGCGCACT	61.700	66.667	11.47	0.00	0.00	4.40
247	249	1.952296	GTCATCATGCTAAAGCCCCAG	59.048	52.381	0.00	0.00	41.18	4.45
254	256	3.904800	TCGGGAAGTCATCATGCTAAA	57.095	42.857	0.00	0.00	0.00	1.85
261	263	4.023980	AGTAGACAATCGGGAAGTCATCA	58.976	43.478	0.00	0.00	34.80	3.07
264	266	6.604396	TGTTATAGTAGACAATCGGGAAGTCA	59.396	38.462	0.00	0.00	34.80	3.41
294	296	4.020617	CTCACCGGAGCCAGGCAA	62.021	66.667	15.80	0.00	33.67	4.52
299	301	2.363795	CCTACCTCACCGGAGCCA	60.364	66.667	9.46	0.00	39.96	4.75
302	304	2.444140	CCCCCTACCTCACCGGAG	60.444	72.222	9.46	0.00	41.02	4.63
309	311	2.857744	CGTCATCGCCCCCTACCTC	61.858	68.421	0.00	0.00	0.00	3.85
335	337	1.091771	CATTGGAGCGAGCCGAATGT	61.092	55.000	10.58	0.00	0.00	2.71
341	343	2.796651	CAAGCATTGGAGCGAGCC	59.203	61.111	0.00	0.00	43.94	4.70
352	354	1.065701	CCTAGCGACGACTACAAGCAT	59.934	52.381	0.00	0.00	0.00	3.79
388	390	5.401079	CACGAAAAGTAACGGAAATTGCATT	59.599	36.000	0.00	0.00	0.00	3.56
501	503	4.377897	ACAAACAGTGCTAGTAGTGGAAC	58.622	43.478	18.45	0.00	0.00	3.62
503	505	4.831155	AGTACAAACAGTGCTAGTAGTGGA	59.169	41.667	18.45	0.00	41.71	4.02
513	515	3.250040	CACCCAGTAAGTACAAACAGTGC	59.750	47.826	0.00	0.00	0.00	4.40
588	590	8.057536	TCTCTGTCTCTCTCCAGTTTATTAAC	57.942	38.462	0.00	0.00	34.36	2.01
794	810	4.821589	GCCGGCCCAAGACTCGAG	62.822	72.222	18.11	11.84	0.00	4.04
822	838	3.654143	TCAGAGGGGACGGACGGA	61.654	66.667	0.00	0.00	0.00	4.69
830	846	3.453717	CTCAATCAATCAGTCAGAGGGGA	59.546	47.826	0.00	0.00	0.00	4.81
868	884	3.254892	GAAGAAGAAACGACCTAGGCTG	58.745	50.000	9.30	3.68	0.00	4.85
887	903	0.535780	GCGCTGGATGGATGGATGAA	60.536	55.000	0.00	0.00	0.00	2.57
931	948	5.578336	CAGAAATTCACAGCGAGATTCACTA	59.422	40.000	0.00	0.00	0.00	2.74
1342	1359	1.210478	CTGGATCCCATTTCTGGACGT	59.790	52.381	9.90	0.00	46.37	4.34
1449	1466	2.752358	CCCACAGCCTCTTCTGCA	59.248	61.111	0.00	0.00	37.59	4.41
1467	1484	2.124983	CTGGGAGTGGCATCACCG	60.125	66.667	0.00	0.00	44.64	4.94
1475	1492	4.864334	GATGCGGCCTGGGAGTGG	62.864	72.222	0.00	0.00	0.00	4.00
1590	1607	1.562008	TCTTTCCCATCGGCAATACCA	59.438	47.619	0.00	0.00	39.03	3.25
1596	1613	1.227102	CCCATCTTTCCCATCGGCA	59.773	57.895	0.00	0.00	0.00	5.69
1661	1681	2.591429	CCTCAGTTGGCGTGTGCA	60.591	61.111	0.00	0.00	45.35	4.57
1732	1752	3.967987	GGAGCCCTAATCTTGGAAGAGTA	59.032	47.826	0.00	0.00	38.66	2.59
1811	1831	3.136763	CCGATTCCATCTCCATTGTCAG	58.863	50.000	0.00	0.00	0.00	3.51
1813	1833	3.475566	TCCGATTCCATCTCCATTGTC	57.524	47.619	0.00	0.00	0.00	3.18
1815	1835	3.316308	GGTTTCCGATTCCATCTCCATTG	59.684	47.826	0.00	0.00	0.00	2.82
1830	1850	1.359459	GACCAGCGCTTAGGTTTCCG	61.359	60.000	19.44	0.00	38.50	4.30
1918	1938	6.820656	TCTCTGGATTGCTCTGTTTCTTTATC	59.179	38.462	0.00	0.00	0.00	1.75
1965	1991	2.383527	GCCGTTGGACTTGAGCTCG	61.384	63.158	9.64	0.00	0.00	5.03
1980	2006	1.961277	AGGTCGCTTTTCTGTGCCG	60.961	57.895	0.00	0.00	0.00	5.69
1984	2010	1.947456	GAAACCAGGTCGCTTTTCTGT	59.053	47.619	0.00	0.00	0.00	3.41
2052	2078	1.590147	GGACGTGATCTTGGTCGGT	59.410	57.895	0.00	0.00	0.00	4.69
2102	2128	3.268965	GAGGAGCAGTGCGACGACA	62.269	63.158	10.00	0.00	0.00	4.35
2151	2177	2.669569	GCAGAGGTTTCAGCCGCA	60.670	61.111	0.00	0.00	30.25	5.69
2259	2297	8.109705	ACATACAAAATCTCACAACAAGCATA	57.890	30.769	0.00	0.00	0.00	3.14
2260	2298	6.985117	ACATACAAAATCTCACAACAAGCAT	58.015	32.000	0.00	0.00	0.00	3.79
2647	2756	6.201517	CAATTTTGCTATAACAGGTGGATCG	58.798	40.000	0.00	0.00	0.00	3.69
2809	3012	6.139671	AGATCAGGACCATTACATGTACTCT	58.860	40.000	4.68	0.00	0.00	3.24
2937	3199	4.215399	CAGAATTTCAGAAGTTGCGGGTAA	59.785	41.667	0.00	0.00	0.00	2.85
3157	3420	0.173708	GATGTGAGACCCAGACGTCC	59.826	60.000	13.01	0.00	32.91	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.