AutoCloner

Multiple sequence alignment - TraesCS4D01G302400

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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	TraesCS4D01G302400	chr4D	100.000	2264	0	0	1	2264	470196636	470194373	0.000000e+00	4181
1	TraesCS4D01G302400	chr4D	88.571	245	24	3	2022	2264	470194335	470194577	6.120000e-76	294
2	TraesCS4D01G302400	chr4D	81.868	364	46	20	1911	2264	470194341	470194694	2.850000e-74	289
3	TraesCS4D01G302400	chr4D	96.429	84	2	1	2182	2264	450523022	450522939	1.090000e-28	137
4	TraesCS4D01G302400	chr2D	96.059	2157	79	6	1	2155	619853633	619855785	0.000000e+00	3507
5	TraesCS4D01G302400	chr7D	95.406	2155	91	8	1	2152	528561189	528563338	0.000000e+00	3424
6	TraesCS4D01G302400	chr7D	93.781	2219	127	10	1	2217	131689396	131691605	0.000000e+00	3323
7	TraesCS4D01G302400	chr3D	96.886	1991	52	5	1	1990	446922426	446924407	0.000000e+00	3325
8	TraesCS4D01G302400	chrUn	94.194	2170	116	10	1	2166	10399175	10401338	0.000000e+00	3301
9	TraesCS4D01G302400	chr4B	92.067	2269	145	26	1	2264	551060039	551062277	0.000000e+00	3160
10	TraesCS4D01G302400	chr6B	93.110	2148	134	14	1	2143	181111562	181109424	0.000000e+00	3134
11	TraesCS4D01G302400	chr6B	79.475	419	66	20	1795	2203	679253390	679253798	1.710000e-71	279
12	TraesCS4D01G302400	chr5B	93.110	2148	133	14	1	2143	506965545	506967682	0.000000e+00	3133
13	TraesCS4D01G302400	chr2B	92.175	2211	157	16	1	2203	549352847	549355049	0.000000e+00	3110
14	TraesCS4D01G302400	chr2A	83.190	232	26	12	2037	2264	14627532	14627310	1.370000e-47	200

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	TraesCS4D01G302400	chr4D	470194373	470196636	2263	True	4181	4181	100.000	1	2264	1	chr4D.!!$R2	2263
1	TraesCS4D01G302400	chr2D	619853633	619855785	2152	False	3507	3507	96.059	1	2155	1	chr2D.!!$F1	2154
2	TraesCS4D01G302400	chr7D	528561189	528563338	2149	False	3424	3424	95.406	1	2152	1	chr7D.!!$F2	2151
3	TraesCS4D01G302400	chr7D	131689396	131691605	2209	False	3323	3323	93.781	1	2217	1	chr7D.!!$F1	2216
4	TraesCS4D01G302400	chr3D	446922426	446924407	1981	False	3325	3325	96.886	1	1990	1	chr3D.!!$F1	1989
5	TraesCS4D01G302400	chrUn	10399175	10401338	2163	False	3301	3301	94.194	1	2166	1	chrUn.!!$F1	2165
6	TraesCS4D01G302400	chr4B	551060039	551062277	2238	False	3160	3160	92.067	1	2264	1	chr4B.!!$F1	2263
7	TraesCS4D01G302400	chr6B	181109424	181111562	2138	True	3134	3134	93.110	1	2143	1	chr6B.!!$R1	2142
8	TraesCS4D01G302400	chr5B	506965545	506967682	2137	False	3133	3133	93.110	1	2143	1	chr5B.!!$F1	2142
9	TraesCS4D01G302400	chr2B	549352847	549355049	2202	False	3110	3110	92.175	1	2203	1	chr2B.!!$F1	2202

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
420	421	0.037303	CCTTGATGCCTCACAGTGGT	59.963	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2221	2238	0.909623	GTGGCAGTAGGGTGGTGTAT	59.09	55.0	0.0	0.0	0.0	2.29	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
420	421	0.037303	CCTTGATGCCTCACAGTGGT	59.963	55.000	0.00	0.00	0.00	4.16
468	469	1.221840	GATCCCGCACTCATGGTGT	59.778	57.895	13.59	2.11	46.86	4.16
502	503	7.164803	GGAAGAAGAAGAAAGAAGAGATTCCA	58.835	38.462	0.00	0.00	33.23	3.53
568	569	3.364460	TGGTAGTGGTCATTTCATGGG	57.636	47.619	0.00	0.00	0.00	4.00
584	585	2.359975	GGGCCACCGGAGAACAAG	60.360	66.667	9.46	0.00	0.00	3.16
603	604	4.873817	CAAGAATTGTGGAGAATGCAACA	58.126	39.130	0.00	0.00	39.09	3.33
826	827	2.349755	CCGTGGATCCGGTGGTTT	59.650	61.111	7.39	0.00	43.07	3.27
964	965	5.301551	TGCCTCTTTACATGTCAATGTGTTT	59.698	36.000	0.00	0.00	46.66	2.83
1042	1044	4.927782	GGCCACCGTGTGCTCACA	62.928	66.667	18.23	0.00	44.02	3.58
1353	1355	3.525537	TCTATGCAAGTACTTCAGCTGC	58.474	45.455	9.47	12.98	0.00	5.25
1651	1654	1.674057	CTTCGCTTGGGTGGACTCT	59.326	57.895	0.00	0.00	0.00	3.24
1809	1813	4.840772	GTCGTGAATGAATTCAGTTTGTCG	59.159	41.667	14.54	13.42	46.44	4.35
1858	1862	7.094508	TCTTATTGAAAAACTGTTGTGCTGA	57.905	32.000	0.00	0.00	0.00	4.26
1860	1864	5.581126	ATTGAAAAACTGTTGTGCTGAGA	57.419	34.783	0.00	0.00	0.00	3.27
2043	2056	1.373435	CAAACCCTACCGCCACAGA	59.627	57.895	0.00	0.00	0.00	3.41
2044	2057	0.673644	CAAACCCTACCGCCACAGAG	60.674	60.000	0.00	0.00	0.00	3.35
2049	2062	4.082523	TACCGCCACAGAGCCTGC	62.083	66.667	2.50	0.00	34.37	4.85
2077	2090	0.105862	TGCTATACCCTACCGCCAGT	60.106	55.000	0.00	0.00	0.00	4.00
2110	2125	4.820173	GGTAGGGTGGTGTATATTTTCTGC	59.180	45.833	0.00	0.00	0.00	4.26
2158	2175	1.071814	GGTTGACCTACCGCCACAA	59.928	57.895	0.00	0.00	0.00	3.33
2174	2191	1.752694	CAACCAATGGCGGTAGGGG	60.753	63.158	0.00	0.00	38.76	4.79
2175	2192	2.235761	AACCAATGGCGGTAGGGGT	61.236	57.895	0.00	0.00	38.76	4.95
2176	2193	2.124320	CCAATGGCGGTAGGGGTG	60.124	66.667	0.00	0.00	0.00	4.61
2178	2195	1.001393	CAATGGCGGTAGGGGTGTT	60.001	57.895	0.00	0.00	0.00	3.32
2211	2228	3.712881	GCGCTGGCGTTTCTCGTT	61.713	61.111	16.21	0.00	42.09	3.85
2218	2235	2.798283	CTGGCGTTTCTCGTTACAGAAA	59.202	45.455	6.09	6.09	39.59	2.52
2219	2236	3.196463	TGGCGTTTCTCGTTACAGAAAA	58.804	40.909	10.04	0.00	42.68	2.29
2221	2238	4.989797	TGGCGTTTCTCGTTACAGAAAATA	59.010	37.500	10.04	0.00	42.68	1.40
2223	2240	6.812656	TGGCGTTTCTCGTTACAGAAAATATA	59.187	34.615	10.04	0.00	42.68	0.86
2224	2241	7.115553	GGCGTTTCTCGTTACAGAAAATATAC	58.884	38.462	10.04	1.44	42.68	1.47
2225	2242	7.201461	GGCGTTTCTCGTTACAGAAAATATACA	60.201	37.037	10.04	0.00	42.68	2.29
2228	2245	8.928733	GTTTCTCGTTACAGAAAATATACACCA	58.071	33.333	10.04	0.00	42.68	4.17
2235	2252	6.886178	ACAGAAAATATACACCACCCTACT	57.114	37.500	0.00	0.00	0.00	2.57
2240	2257	0.909623	ATACACCACCCTACTGCCAC	59.090	55.000	0.00	0.00	0.00	5.01
2242	2259	3.319198	ACCACCCTACTGCCACGG	61.319	66.667	0.00	0.00	0.00	4.94
2243	2260	3.319198	CCACCCTACTGCCACGGT	61.319	66.667	0.00	0.00	0.00	4.83
2244	2261	2.264794	CACCCTACTGCCACGGTC	59.735	66.667	0.00	0.00	0.00	4.79
2245	2262	3.379445	ACCCTACTGCCACGGTCG	61.379	66.667	0.00	0.00	0.00	4.79
2259	2276	3.142838	GTCGCTGGCGGTAGGGTA	61.143	66.667	14.94	0.00	40.25	3.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
420	421	1.555075	GTCTGGCCCAACATACTCAGA	59.445	52.381	0.00	0.00	0.00	3.27
468	469	6.264528	TCTTTCTTCTTCTTCCCCTCATAGA	58.735	40.000	0.00	0.00	0.00	1.98
502	503	4.281435	CAGCTAGATCATCCATGTCACTCT	59.719	45.833	0.00	0.00	0.00	3.24
568	569	0.322546	ATTCTTGTTCTCCGGTGGCC	60.323	55.000	0.00	0.00	0.00	5.36
584	585	4.445385	GTGTTGTTGCATTCTCCACAATTC	59.555	41.667	2.94	0.00	0.00	2.17
603	604	2.168936	TCCTAACGTTGTGTCCTGTGTT	59.831	45.455	11.99	0.00	0.00	3.32
826	827	1.259609	ATCAACCCGACGTGTCCTAA	58.740	50.000	0.00	0.00	0.00	2.69
993	994	0.179020	CGGATGAAGCCATGCCCTAA	60.179	55.000	0.00	0.00	37.79	2.69
996	997	2.908940	CCGGATGAAGCCATGCCC	60.909	66.667	0.00	0.00	37.79	5.36
1042	1044	3.067180	CACTTGTGTGGCATGTCTTCTTT	59.933	43.478	0.00	0.00	40.33	2.52
1182	1184	5.199982	TGGGGCAAACAAAATATCTCCTA	57.800	39.130	0.00	0.00	0.00	2.94
1353	1355	6.688637	TCTTTTGGCACTTCATGATCTATG	57.311	37.500	0.00	0.00	38.17	2.23
1592	1594	2.247358	GCCATTTCCCCTTCTTGTCAA	58.753	47.619	0.00	0.00	0.00	3.18
1641	1644	2.677037	CGGTTACATGAAGAGTCCACCC	60.677	54.545	0.00	0.00	0.00	4.61
1651	1654	2.026729	TGGCTTCATCCGGTTACATGAA	60.027	45.455	13.82	13.82	36.80	2.57
1809	1813	9.661187	GAATCATGACAAATCACAGAATATGAC	57.339	33.333	0.00	0.00	37.79	3.06
1858	1862	6.498538	TCTGTTCTATCCCTCTTCTCTTTCT	58.501	40.000	0.00	0.00	0.00	2.52
1860	1864	6.498651	TGTTCTGTTCTATCCCTCTTCTCTTT	59.501	38.462	0.00	0.00	0.00	2.52
1979	1990	7.201461	GGCGTTTCTCGTTACAGAAAATATACA	60.201	37.037	10.04	0.00	42.68	2.29
2049	2062	1.972978	GGGTATAGCAGCCTACCGG	59.027	63.158	0.00	0.00	41.95	5.28
2062	2075	1.047034	GGTCACTGGCGGTAGGGTAT	61.047	60.000	0.00	0.00	0.00	2.73
2094	2107	5.483811	TCTCGTTGCAGAAAATATACACCA	58.516	37.500	0.00	0.00	0.00	4.17
2097	2110	6.530567	CGTTTCTCGTTGCAGAAAATATACA	58.469	36.000	0.86	0.00	42.68	2.29
2110	2125	2.170985	CGCTGGCGTTTCTCGTTG	59.829	61.111	6.83	0.00	42.13	4.10
2158	2175	2.612746	ACCCCTACCGCCATTGGT	60.613	61.111	4.26	0.00	46.26	3.67
2174	2191	4.338710	TGGCGGTAGGGGCAACAC	62.339	66.667	0.00	0.00	39.78	3.32
2175	2192	4.028490	CTGGCGGTAGGGGCAACA	62.028	66.667	0.00	0.00	42.34	3.33
2176	2193	4.796495	CCTGGCGGTAGGGGCAAC	62.796	72.222	0.00	0.00	42.34	4.17
2211	2228	7.634210	GCAGTAGGGTGGTGTATATTTTCTGTA	60.634	40.741	0.00	0.00	0.00	2.74
2218	2235	3.135895	GTGGCAGTAGGGTGGTGTATATT	59.864	47.826	0.00	0.00	0.00	1.28
2219	2236	2.704065	GTGGCAGTAGGGTGGTGTATAT	59.296	50.000	0.00	0.00	0.00	0.86
2221	2238	0.909623	GTGGCAGTAGGGTGGTGTAT	59.090	55.000	0.00	0.00	0.00	2.29
2223	2240	2.879233	CGTGGCAGTAGGGTGGTGT	61.879	63.158	0.00	0.00	0.00	4.16
2224	2241	2.047274	CGTGGCAGTAGGGTGGTG	60.047	66.667	0.00	0.00	0.00	4.17
2225	2242	3.319198	CCGTGGCAGTAGGGTGGT	61.319	66.667	0.00	0.00	0.00	4.16
2228	2245	3.379445	CGACCGTGGCAGTAGGGT	61.379	66.667	8.22	4.18	41.22	4.34
2242	2259	3.142838	TACCCTACCGCCAGCGAC	61.143	66.667	14.67	0.00	42.83	5.19
2243	2260	3.142838	GTACCCTACCGCCAGCGA	61.143	66.667	14.67	0.00	42.83	4.93
2244	2261	3.426117	CTGTACCCTACCGCCAGCG	62.426	68.421	4.75	4.75	39.44	5.18
2245	2262	2.499685	CTGTACCCTACCGCCAGC	59.500	66.667	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.