AutoCloner

Multiple sequence alignment - TraesCS1D01G161100

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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	TraesCS1D01G161100	chr1D	100.000	2112	0	0	684	2795	227867064	227869175	0.000000e+00	3901.0
1	TraesCS1D01G161100	chr1D	95.085	1241	55	3	692	1931	208239550	208238315	0.000000e+00	1949.0
2	TraesCS1D01G161100	chr1D	94.952	733	30	5	1927	2658	208202666	208201940	0.000000e+00	1142.0
3	TraesCS1D01G161100	chr1D	100.000	349	0	0	1	349	227866381	227866729	0.000000e+00	645.0
4	TraesCS1D01G161100	chr1D	95.442	351	11	3	1	349	208239954	208239607	3.150000e-154	555.0
5	TraesCS1D01G161100	chr1D	98.077	104	2	0	2652	2755	208201912	208201809	6.150000e-42	182.0
6	TraesCS1D01G161100	chr1B	95.648	1976	78	4	686	2658	327487031	327489001	0.000000e+00	3166.0
7	TraesCS1D01G161100	chr1B	93.182	352	17	5	1	348	327486372	327486720	6.910000e-141	510.0
8	TraesCS1D01G161100	chr1B	94.231	104	5	1	2652	2755	327489029	327489131	1.040000e-34	158.0
9	TraesCS1D01G161100	chr1A	95.179	1701	73	5	693	2392	295465819	295467511	0.000000e+00	2678.0
10	TraesCS1D01G161100	chr1A	94.571	350	11	6	1	347	295465129	295465473	4.100000e-148	534.0
11	TraesCS1D01G161100	chr1A	94.834	271	14	0	2383	2653	295517172	295517442	9.250000e-115	424.0
12	TraesCS1D01G161100	chr1A	95.327	107	5	0	2652	2758	295517475	295517581	1.330000e-38	171.0
13	TraesCS1D01G161100	chr5D	85.911	1959	243	20	714	2659	552444459	552442521	0.000000e+00	2058.0
14	TraesCS1D01G161100	chr5D	85.928	334	33	9	1	328	552445010	552444685	7.410000e-91	344.0
15	TraesCS1D01G161100	chr5D	78.125	512	98	12	1803	2308	543503005	543502502	2.090000e-81	313.0
16	TraesCS1D01G161100	chr5D	96.078	102	4	0	2655	2756	552442488	552442387	1.720000e-37	167.0
17	TraesCS1D01G161100	chr5D	71.991	432	103	14	1010	1435	552422797	552422378	8.180000e-21	111.0
18	TraesCS1D01G161100	chr5D	77.941	136	24	5	980	1113	543503744	543503613	2.310000e-11	80.5
19	TraesCS1D01G161100	chr5B	79.059	425	84	5	1803	2224	685322355	685321933	1.270000e-73	287.0
20	TraesCS1D01G161100	chr5B	77.974	227	40	6	983	1208	685323103	685322886	1.750000e-27	134.0
21	TraesCS1D01G161100	chr5B	77.974	227	40	6	983	1208	685503740	685503957	1.750000e-27	134.0
22	TraesCS1D01G161100	chr4A	79.290	169	34	1	1041	1208	616897491	616897323	1.760000e-22	117.0

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	TraesCS1D01G161100	chr1D	227866381	227869175	2794	False	2273.000000	3901	100.000000	1	2795	2	chr1D.!!$F1	2794
1	TraesCS1D01G161100	chr1D	208238315	208239954	1639	True	1252.000000	1949	95.263500	1	1931	2	chr1D.!!$R2	1930
2	TraesCS1D01G161100	chr1D	208201809	208202666	857	True	662.000000	1142	96.514500	1927	2755	2	chr1D.!!$R1	828
3	TraesCS1D01G161100	chr1B	327486372	327489131	2759	False	1278.000000	3166	94.353667	1	2755	3	chr1B.!!$F1	2754
4	TraesCS1D01G161100	chr1A	295465129	295467511	2382	False	1606.000000	2678	94.875000	1	2392	2	chr1A.!!$F1	2391
5	TraesCS1D01G161100	chr5D	552442387	552445010	2623	True	856.333333	2058	89.305667	1	2756	3	chr5D.!!$R3	2755
6	TraesCS1D01G161100	chr5B	685321933	685323103	1170	True	210.500000	287	78.516500	983	2224	2	chr5B.!!$R1	1241

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
886	907	4.137116	ACTCAGCTACAAGTCAACAACA	57.863	40.909	0.00	0.0	0.0	3.33	F
1738	1795	0.031178	GGCATGCATCGAATCAACCC	59.969	55.000	21.36	0.0	0.0	4.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1755	1812	2.085320	TGGAGTAGAGTGAGTCTTCGC	58.915	52.381	0.0	0.0	36.64	4.70	R
2679	2780	3.947196	CCAAACTATGGTTGATGCTGCTA	59.053	43.478	0.0	0.0	44.85	3.49	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
98	101	9.630098	GCAAAATATATTCACATCCATTAGGTG	57.370	33.333	0.00	0.00	41.29	4.00
157	162	8.959705	ACTAGTATGGTTTTTAGGAGTATTGC	57.040	34.615	0.00	0.00	0.00	3.56
878	899	7.769044	TCTTAAAAAGACAACTCAGCTACAAGT	59.231	33.333	0.00	0.00	31.20	3.16
886	907	4.137116	ACTCAGCTACAAGTCAACAACA	57.863	40.909	0.00	0.00	0.00	3.33
971	992	4.500477	GCCACATTTATTTGCTTCATCGAC	59.500	41.667	0.00	0.00	0.00	4.20
1039	1060	1.221840	CTAGCGGCACCATCCTTGT	59.778	57.895	1.45	0.00	0.00	3.16
1076	1097	1.408969	GAGATCTTCCTCCGCTTCCT	58.591	55.000	0.00	0.00	0.00	3.36
1127	1148	2.999355	CCTCACTTGCAAGTAAGCTCTC	59.001	50.000	30.67	0.00	37.08	3.20
1273	1294	2.742053	CCTGTATCACACTTTGTTCCCG	59.258	50.000	0.00	0.00	0.00	5.14
1286	1307	2.884980	TTCCCGCCACAACATCCGA	61.885	57.895	0.00	0.00	0.00	4.55
1323	1344	0.824109	ATGGCTGGATCGAGTCGAAA	59.176	50.000	20.74	7.51	39.99	3.46
1368	1389	4.235079	TGGTCATGTTCTATTTGGGGAG	57.765	45.455	0.00	0.00	0.00	4.30
1436	1457	2.665000	CTGGACGGAGGTGCACAT	59.335	61.111	20.43	12.71	39.79	3.21
1477	1498	1.213537	GACAACCGTGTAGCCGCTA	59.786	57.895	0.00	0.00	38.41	4.26
1500	1521	1.331756	CTTTGTGCTATGACCGGATGC	59.668	52.381	9.46	5.16	0.00	3.91
1530	1551	0.039618	AATGTCATGAGGGCCCGTTT	59.960	50.000	18.44	0.00	0.00	3.60
1539	1560	2.908428	GGCCCGTTTCGGTTGGTT	60.908	61.111	7.40	0.00	46.80	3.67
1736	1793	1.672363	TGAGGCATGCATCGAATCAAC	59.328	47.619	25.58	2.19	0.00	3.18
1737	1794	1.002033	GAGGCATGCATCGAATCAACC	60.002	52.381	21.36	0.00	0.00	3.77
1738	1795	0.031178	GGCATGCATCGAATCAACCC	59.969	55.000	21.36	0.00	0.00	4.11
1739	1796	0.031178	GCATGCATCGAATCAACCCC	59.969	55.000	14.21	0.00	0.00	4.95
1740	1797	0.670162	CATGCATCGAATCAACCCCC	59.330	55.000	0.00	0.00	0.00	5.40
1773	1830	3.004171	TCAGCGAAGACTCACTCTACTC	58.996	50.000	0.00	0.00	0.00	2.59
1896	1953	1.475280	TGTCGGTGCCACTATACTCAC	59.525	52.381	0.00	0.00	0.00	3.51
1921	1978	0.761323	TGGAGGACGACAGTTTGGGA	60.761	55.000	0.00	0.00	0.00	4.37
2011	2069	2.364002	TGGACTCAACGAACAGTCATCA	59.636	45.455	12.30	2.67	40.85	3.07
2051	2109	2.481449	CCGTTCGAAATCCCGAGAGAAT	60.481	50.000	0.00	0.00	39.90	2.40
2080	2138	1.302907	AATTGGATCTGTGGAGGGCT	58.697	50.000	0.00	0.00	0.00	5.19
2087	2145	1.195115	TCTGTGGAGGGCTGTGATAC	58.805	55.000	0.00	0.00	0.00	2.24
2399	2458	5.488645	TTGCATATTAGCATGGCATATCG	57.511	39.130	0.00	0.00	45.19	2.92
2679	2780	8.429641	TCTTGTAATGAACCTCTAGTTTCTTGT	58.570	33.333	0.00	0.00	39.40	3.16
2762	2863	4.481930	TTTTATGGTGACTCGCTTGTTG	57.518	40.909	0.00	0.00	0.00	3.33
2763	2864	2.093306	TATGGTGACTCGCTTGTTGG	57.907	50.000	0.00	0.00	0.00	3.77
2764	2865	0.606401	ATGGTGACTCGCTTGTTGGG	60.606	55.000	0.00	0.00	0.00	4.12
2765	2866	1.966451	GGTGACTCGCTTGTTGGGG	60.966	63.158	0.00	0.00	0.00	4.96
2766	2867	1.070786	GTGACTCGCTTGTTGGGGA	59.929	57.895	0.00	0.00	0.00	4.81
2767	2868	0.534203	GTGACTCGCTTGTTGGGGAA	60.534	55.000	0.00	0.00	0.00	3.97
2768	2869	0.534203	TGACTCGCTTGTTGGGGAAC	60.534	55.000	0.00	0.00	0.00	3.62
2769	2870	1.566018	GACTCGCTTGTTGGGGAACG	61.566	60.000	0.00	0.00	0.00	3.95
2770	2871	1.597027	CTCGCTTGTTGGGGAACGT	60.597	57.895	0.00	0.00	0.00	3.99
2771	2872	0.320073	CTCGCTTGTTGGGGAACGTA	60.320	55.000	0.00	0.00	0.00	3.57
2772	2873	0.320073	TCGCTTGTTGGGGAACGTAG	60.320	55.000	0.00	0.00	0.00	3.51
2774	2875	1.337074	CGCTTGTTGGGGAACGTAGTA	60.337	52.381	0.00	0.00	45.00	1.82
2775	2876	2.675889	CGCTTGTTGGGGAACGTAGTAT	60.676	50.000	0.00	0.00	45.00	2.12
2776	2877	3.340928	GCTTGTTGGGGAACGTAGTATT	58.659	45.455	0.00	0.00	45.00	1.89
2777	2878	3.754850	GCTTGTTGGGGAACGTAGTATTT	59.245	43.478	0.00	0.00	45.00	1.40
2778	2879	4.142752	GCTTGTTGGGGAACGTAGTATTTC	60.143	45.833	0.00	0.00	45.00	2.17
2779	2880	4.620589	TGTTGGGGAACGTAGTATTTCA	57.379	40.909	0.00	0.00	45.00	2.69
2780	2881	4.970711	TGTTGGGGAACGTAGTATTTCAA	58.029	39.130	0.00	0.00	45.00	2.69
2781	2882	5.374921	TGTTGGGGAACGTAGTATTTCAAA	58.625	37.500	0.00	0.00	45.00	2.69
2782	2883	5.826737	TGTTGGGGAACGTAGTATTTCAAAA	59.173	36.000	0.00	0.00	45.00	2.44
2783	2884	6.320672	TGTTGGGGAACGTAGTATTTCAAAAA	59.679	34.615	0.00	0.00	45.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
64	67	8.268738	GGATGTGAATATATTTTGCTTTTTCGC	58.731	33.333	0.00	0.00	0.00	4.70
98	101	6.943718	TCAACAATAAAATATATCCGGTCCCC	59.056	38.462	0.00	0.00	0.00	4.81
99	102	7.989416	TCAACAATAAAATATATCCGGTCCC	57.011	36.000	0.00	0.00	0.00	4.46
157	162	7.959651	GCTACACAACATCAAAATGTCTTAGAG	59.040	37.037	0.00	0.00	45.48	2.43
295	303	9.565090	ACGAGAATACCCTTTTAAGTAACTTTT	57.435	29.630	0.00	0.00	0.00	2.27
683	693	5.010213	GCCTCTCTCCGTCTTATTCAACTAT	59.990	44.000	0.00	0.00	0.00	2.12
684	694	4.338682	GCCTCTCTCCGTCTTATTCAACTA	59.661	45.833	0.00	0.00	0.00	2.24
763	784	7.279313	CCATATTCAAAATGAAAAGGCTCTTGG	59.721	37.037	0.00	0.00	40.12	3.61
878	899	1.398692	GGGGTTGCTCTTGTTGTTGA	58.601	50.000	0.00	0.00	0.00	3.18
886	907	2.960688	GCGAGAGGGGGTTGCTCTT	61.961	63.158	0.00	0.00	0.00	2.85
971	992	1.183030	GGTTTCGGGTGGGGGAAAAG	61.183	60.000	0.00	0.00	34.26	2.27
1127	1148	1.738099	CTGGTGAGAAGGCCGAACG	60.738	63.158	0.00	0.00	0.00	3.95
1273	1294	0.729116	CATGAGTCGGATGTTGTGGC	59.271	55.000	0.00	0.00	0.00	5.01
1286	1307	3.813240	GCCATCCTTGGATATGCATGAGT	60.813	47.826	10.16	0.00	46.92	3.41
1307	1328	3.902150	TCATATTTCGACTCGATCCAGC	58.098	45.455	1.07	0.00	35.23	4.85
1323	1344	4.019411	TGTCGGCAATCCCATACATCATAT	60.019	41.667	0.00	0.00	0.00	1.78
1368	1389	1.035932	TCGTGGATCTCCGACCCTTC	61.036	60.000	3.64	0.00	39.43	3.46
1436	1457	3.626222	GGCCACCATGTATCTTTTGGGTA	60.626	47.826	0.00	0.00	34.72	3.69
1500	1521	1.745115	ATGACATTGGCGGTGGTCG	60.745	57.895	0.00	0.00	42.76	4.79
1530	1551	2.351706	AGTAGGCAAAAACCAACCGA	57.648	45.000	0.00	0.00	0.00	4.69
1539	1560	4.042311	TCTCCCACATACAAGTAGGCAAAA	59.958	41.667	0.00	0.00	0.00	2.44
1755	1812	2.085320	TGGAGTAGAGTGAGTCTTCGC	58.915	52.381	0.00	0.00	36.64	4.70
1896	1953	3.723235	CTGTCGTCCTCCATGGCCG	62.723	68.421	6.96	6.73	38.75	6.13
1921	1978	5.590259	GGGTTAATCTATCATGTGTGCAAGT	59.410	40.000	0.00	0.00	0.00	3.16
2011	2069	2.751816	CGGGGAGAAGGTTTTTGAGGTT	60.752	50.000	0.00	0.00	0.00	3.50
2051	2109	6.679542	TCCACAGATCCAATTAGTCTAGGTA	58.320	40.000	0.00	0.00	0.00	3.08
2080	2138	8.038944	GTCTATAGTCACAAAAAGGGTATCACA	58.961	37.037	0.00	0.00	0.00	3.58
2087	2145	5.648092	CCAAGGTCTATAGTCACAAAAAGGG	59.352	44.000	0.00	0.00	0.00	3.95
2233	2291	5.886609	TGATCCCAAACCACATAAGAAAGA	58.113	37.500	0.00	0.00	0.00	2.52
2418	2477	4.021544	TCGCCCTTTCTGCAAACATATTTT	60.022	37.500	0.00	0.00	0.00	1.82
2576	2635	4.598036	ACCCCAAGAGAATTGATCACAT	57.402	40.909	0.00	0.00	0.00	3.21
2679	2780	3.947196	CCAAACTATGGTTGATGCTGCTA	59.053	43.478	0.00	0.00	44.85	3.49
2756	2857	4.998672	TGAAATACTACGTTCCCCAACAAG	59.001	41.667	0.00	0.00	32.14	3.16
2757	2858	4.970711	TGAAATACTACGTTCCCCAACAA	58.029	39.130	0.00	0.00	32.14	2.83
2758	2859	4.620589	TGAAATACTACGTTCCCCAACA	57.379	40.909	0.00	0.00	32.14	3.33
2759	2860	5.945466	TTTGAAATACTACGTTCCCCAAC	57.055	39.130	0.00	0.00	0.00	3.77
2760	2861	6.956202	TTTTTGAAATACTACGTTCCCCAA	57.044	33.333	0.00	0.00	0.00	4.12

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.