AutoCloner

Multiple sequence alignment - TraesCS6D01G248900

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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	TraesCS6D01G248900	chr6D	100.000	2545	0	0	1	2545	352358485	352355941	0.000000e+00	4700
1	TraesCS6D01G248900	chr6D	83.466	629	93	10	1920	2542	352154081	352153458	2.200000e-160	575
2	TraesCS6D01G248900	chr6A	90.068	2628	141	45	1	2545	490492586	490495176	0.000000e+00	3297
3	TraesCS6D01G248900	chr6A	83.412	633	94	10	1916	2542	490836347	490836974	6.110000e-161	577
4	TraesCS6D01G248900	chr6B	94.142	1690	53	18	886	2545	526718536	526720209	0.000000e+00	2531
5	TraesCS6D01G248900	chr6B	89.569	882	56	20	1	874	526717636	526718489	0.000000e+00	1086
6	TraesCS6D01G248900	chr6B	84.194	620	90	7	1927	2542	526736600	526737215	1.690000e-166	595
7	TraesCS6D01G248900	chr2A	86.667	1080	96	27	1492	2545	763369790	763368733	0.000000e+00	1153
8	TraesCS6D01G248900	chr2B	85.714	1064	101	28	1510	2545	797627803	797626763	0.000000e+00	1075
9	TraesCS6D01G248900	chrUn	86.415	714	82	11	1841	2544	84014912	84015620	0.000000e+00	767
10	TraesCS6D01G248900	chr7D	86.115	713	86	9	1841	2544	59732200	59732908	0.000000e+00	756

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	TraesCS6D01G248900	chr6D	352355941	352358485	2544	True	4700.0	4700	100.0000	1	2545	1	chr6D.!!$R2	2544
1	TraesCS6D01G248900	chr6D	352153458	352154081	623	True	575.0	575	83.4660	1920	2542	1	chr6D.!!$R1	622
2	TraesCS6D01G248900	chr6A	490492586	490495176	2590	False	3297.0	3297	90.0680	1	2545	1	chr6A.!!$F1	2544
3	TraesCS6D01G248900	chr6A	490836347	490836974	627	False	577.0	577	83.4120	1916	2542	1	chr6A.!!$F2	626
4	TraesCS6D01G248900	chr6B	526717636	526720209	2573	False	1808.5	2531	91.8555	1	2545	2	chr6B.!!$F2	2544
5	TraesCS6D01G248900	chr6B	526736600	526737215	615	False	595.0	595	84.1940	1927	2542	1	chr6B.!!$F1	615
6	TraesCS6D01G248900	chr2A	763368733	763369790	1057	True	1153.0	1153	86.6670	1492	2545	1	chr2A.!!$R1	1053
7	TraesCS6D01G248900	chr2B	797626763	797627803	1040	True	1075.0	1075	85.7140	1510	2545	1	chr2B.!!$R1	1035
8	TraesCS6D01G248900	chrUn	84014912	84015620	708	False	767.0	767	86.4150	1841	2544	1	chrUn.!!$F1	703
9	TraesCS6D01G248900	chr7D	59732200	59732908	708	False	756.0	756	86.1150	1841	2544	1	chr7D.!!$F1	703

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
470	509	1.064825	AGGGTTGGGACGTTTCAGAT	58.935	50.0	0.0	0.0	0.0	2.9	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1763	1895	1.585521	GGTCGTAGTCATCCACGCG	60.586	63.158	3.53	3.53	38.05	6.01	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
123	130	6.981708	GCATATGCTTGAATGTTACACAAAC	58.018	36.000	20.64	0.00	37.01	2.93
124	131	6.585702	GCATATGCTTGAATGTTACACAAACA	59.414	34.615	20.64	0.00	44.24	2.83
258	296	9.466497	TGCCAGAATAAAGAACTTTCATTAGAT	57.534	29.630	2.99	0.00	34.23	1.98
288	326	4.336433	ACTGTTAATGCCGAAATGGATCAG	59.664	41.667	0.00	0.00	42.00	2.90
294	332	6.906157	AATGCCGAAATGGATCAGAATTAT	57.094	33.333	0.00	0.00	42.00	1.28
296	334	8.408043	AATGCCGAAATGGATCAGAATTATTA	57.592	30.769	0.00	0.00	42.00	0.98
298	336	8.408043	TGCCGAAATGGATCAGAATTATTAAT	57.592	30.769	0.00	0.00	42.00	1.40
299	337	8.298854	TGCCGAAATGGATCAGAATTATTAATG	58.701	33.333	0.00	0.00	42.00	1.90
300	338	8.514594	GCCGAAATGGATCAGAATTATTAATGA	58.485	33.333	0.00	0.00	42.00	2.57
366	405	8.270799	CCCAGACAACGTATAATAAATTACACG	58.729	37.037	10.98	10.98	45.59	4.49
392	431	1.210931	CAGTTCAAGCCATGGTGCG	59.789	57.895	14.67	1.63	36.02	5.34
403	442	2.159254	GCCATGGTGCGTCATGTTTATT	60.159	45.455	14.67	0.00	42.02	1.40
421	460	8.092521	TGTTTATTGGCAAAAATACACATTGG	57.907	30.769	3.01	0.00	31.17	3.16
470	509	1.064825	AGGGTTGGGACGTTTCAGAT	58.935	50.000	0.00	0.00	0.00	2.90
473	512	2.228103	GGGTTGGGACGTTTCAGATTTC	59.772	50.000	0.00	0.00	0.00	2.17
489	528	1.203237	TTTCTCTCCCATGGCGATGA	58.797	50.000	10.66	0.00	0.00	2.92
503	542	1.789464	GCGATGACAGCTCCGAAATAG	59.211	52.381	0.00	0.00	0.00	1.73
516	555	4.766375	TCCGAAATAGTCAGACAAATCCC	58.234	43.478	2.66	0.00	0.00	3.85
520	559	4.946160	AATAGTCAGACAAATCCCCCAA	57.054	40.909	2.66	0.00	0.00	4.12
522	561	3.833559	AGTCAGACAAATCCCCCAATT	57.166	42.857	2.66	0.00	0.00	2.32
539	578	1.213296	ATTACCCCAGAAGCATCGGT	58.787	50.000	0.00	0.00	0.00	4.69
554	593	3.279116	GGTGACGCAGCAAGCACA	61.279	61.111	10.39	0.00	46.13	4.57
565	604	1.946768	AGCAAGCACAACGTGTAATGT	59.053	42.857	0.00	0.00	38.00	2.71
572	614	5.390885	AAGCACAACGTGTAATGTGATCATC	60.391	40.000	19.56	4.00	44.63	2.92
575	617	5.185454	ACAACGTGTAATGTGATCATCCAT	58.815	37.500	0.00	0.00	35.29	3.41
576	618	5.647658	ACAACGTGTAATGTGATCATCCATT	59.352	36.000	14.06	14.06	35.29	3.16
590	632	9.643693	GTGATCATCCATTCAAATAAAACAAGT	57.356	29.630	0.00	0.00	0.00	3.16
598	640	9.626045	CCATTCAAATAAAACAAGTCTTCCTAC	57.374	33.333	0.00	0.00	0.00	3.18
607	649	8.706322	AAAACAAGTCTTCCTACATACCAATT	57.294	30.769	0.00	0.00	0.00	2.32
615	657	5.499004	TCCTACATACCAATTGATAGCCC	57.501	43.478	7.12	0.00	0.00	5.19
616	658	4.910913	TCCTACATACCAATTGATAGCCCA	59.089	41.667	7.12	0.00	0.00	5.36
696	738	2.301738	GGACCTGGGGAGTGGAAGG	61.302	68.421	0.00	0.00	35.82	3.46
703	745	2.726351	GGGAGTGGAAGGCGAGGAG	61.726	68.421	0.00	0.00	0.00	3.69
739	781	4.747529	GGTACGACCCACACGGCC	62.748	72.222	0.00	0.00	33.26	6.13
807	850	2.687566	GACGGGGGTGGATCCACT	60.688	66.667	37.26	22.00	45.52	4.00
841	884	2.257371	CGGTTTCGTCGGAGCAGA	59.743	61.111	0.00	0.00	0.00	4.26
842	885	1.801913	CGGTTTCGTCGGAGCAGAG	60.802	63.158	0.00	0.00	0.00	3.35
843	886	1.585006	GGTTTCGTCGGAGCAGAGA	59.415	57.895	0.00	0.00	0.00	3.10
878	954	4.760047	CTTGGAGGGTGGCGACGG	62.760	72.222	0.00	0.00	0.00	4.79
947	1025	3.195698	CGCCGAAGCCCAGTTAGC	61.196	66.667	0.00	0.00	34.57	3.09
1048	1154	3.556306	CGAGGTGGTGGTGGTGGT	61.556	66.667	0.00	0.00	0.00	4.16
1092	1198	4.147449	CTGATCTGGGCGACGGCA	62.147	66.667	23.66	8.43	42.47	5.69
1501	1611	8.344831	TCTATGTATGCACTGCAAATCATAAAC	58.655	33.333	8.03	0.00	43.62	2.01
1577	1689	6.308766	GCGTTTGAATTTGCTATCACTGAATT	59.691	34.615	0.00	0.00	0.00	2.17
1587	1699	5.587443	TGCTATCACTGAATTCTGTTGATGG	59.413	40.000	24.13	22.89	0.00	3.51
1663	1780	8.422577	ACTGCTCTAAAAGGTATTTTTGGAAT	57.577	30.769	1.21	0.00	43.08	3.01
1683	1800	8.801882	TGGAATAAGTGTCAAAGTTTATAGGG	57.198	34.615	0.00	0.00	0.00	3.53
1812	1944	3.045601	ACACGCATCTAGAAGCTTTGT	57.954	42.857	17.18	15.82	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
121	128	5.257082	ACTTCAAACCGCAAAGTAATGTT	57.743	34.783	0.00	0.00	31.68	2.71
122	129	4.911514	ACTTCAAACCGCAAAGTAATGT	57.088	36.364	0.00	0.00	31.68	2.71
123	130	5.048991	ACCTACTTCAAACCGCAAAGTAATG	60.049	40.000	0.00	0.00	35.64	1.90
124	131	5.067954	ACCTACTTCAAACCGCAAAGTAAT	58.932	37.500	0.00	0.00	35.64	1.89
125	132	4.453751	ACCTACTTCAAACCGCAAAGTAA	58.546	39.130	0.00	0.00	35.64	2.24
126	133	4.060205	GACCTACTTCAAACCGCAAAGTA	58.940	43.478	0.00	0.00	35.08	2.24
184	191	3.266510	TGGATCCGGATCTTTCACTTG	57.733	47.619	36.72	0.00	37.92	3.16
230	268	9.565213	CTAATGAAAGTTCTTTATTCTGGCAAG	57.435	33.333	0.00	0.00	0.00	4.01
258	296	5.670149	TTTCGGCATTAACAGTTTCGTAA	57.330	34.783	0.00	0.00	0.00	3.18
270	308	8.408043	AATAATTCTGATCCATTTCGGCATTA	57.592	30.769	0.00	0.00	29.00	1.90
294	332	8.857694	AGAACTCTTCCGGTTTATTTCATTAA	57.142	30.769	0.00	0.00	0.00	1.40
296	334	7.761038	AAGAACTCTTCCGGTTTATTTCATT	57.239	32.000	0.00	0.00	0.00	2.57
298	336	6.796705	GAAGAACTCTTCCGGTTTATTTCA	57.203	37.500	0.00	0.00	44.93	2.69
315	353	4.495422	TGCATACTTCGAAGAGGAAGAAC	58.505	43.478	31.08	11.81	44.93	3.01
366	405	3.568538	CATGGCTTGAACTGCTAACAAC	58.431	45.455	0.00	0.00	0.00	3.32
369	408	2.095059	CACCATGGCTTGAACTGCTAAC	60.095	50.000	13.04	0.00	0.00	2.34
392	431	8.304202	TGTGTATTTTTGCCAATAAACATGAC	57.696	30.769	0.00	0.00	33.58	3.06
403	442	4.776837	AGGATCCAATGTGTATTTTTGCCA	59.223	37.500	15.82	0.00	0.00	4.92
421	460	1.475682	CCTTTGCTTTGCCAGAGGATC	59.524	52.381	0.00	0.00	38.93	3.36
454	493	4.065789	AGAGAAATCTGAAACGTCCCAAC	58.934	43.478	0.00	0.00	0.00	3.77
457	496	3.263261	GGAGAGAAATCTGAAACGTCCC	58.737	50.000	0.00	0.00	0.00	4.46
458	497	3.263261	GGGAGAGAAATCTGAAACGTCC	58.737	50.000	0.00	0.00	0.00	4.79
470	509	1.134401	GTCATCGCCATGGGAGAGAAA	60.134	52.381	15.13	0.00	34.53	2.52
473	512	0.249784	CTGTCATCGCCATGGGAGAG	60.250	60.000	15.13	6.19	34.53	3.20
489	528	2.826128	TGTCTGACTATTTCGGAGCTGT	59.174	45.455	9.51	0.00	40.55	4.40
503	542	3.699538	GGTAATTGGGGGATTTGTCTGAC	59.300	47.826	0.00	0.00	0.00	3.51
516	555	2.310538	GATGCTTCTGGGGTAATTGGG	58.689	52.381	0.00	0.00	0.00	4.12
520	559	1.134098	CACCGATGCTTCTGGGGTAAT	60.134	52.381	12.62	0.00	0.00	1.89
522	561	0.616395	TCACCGATGCTTCTGGGGTA	60.616	55.000	10.82	0.00	0.00	3.69
539	578	2.715005	GTTGTGCTTGCTGCGTCA	59.285	55.556	0.00	0.00	46.63	4.35
554	593	5.879777	TGAATGGATGATCACATTACACGTT	59.120	36.000	10.59	0.00	37.43	3.99
565	604	9.859427	GACTTGTTTTATTTGAATGGATGATCA	57.141	29.630	0.00	0.00	0.00	2.92
572	614	9.626045	GTAGGAAGACTTGTTTTATTTGAATGG	57.374	33.333	0.00	0.00	0.00	3.16
590	632	6.239887	GGGCTATCAATTGGTATGTAGGAAGA	60.240	42.308	5.42	0.00	0.00	2.87
598	640	7.111247	TCTTTTTGGGCTATCAATTGGTATG	57.889	36.000	5.42	0.00	0.00	2.39
607	649	5.600484	TGTTCCTTTTCTTTTTGGGCTATCA	59.400	36.000	0.00	0.00	0.00	2.15
615	657	7.115378	CAGATCGGAATGTTCCTTTTCTTTTTG	59.885	37.037	9.90	0.00	45.33	2.44
616	658	7.014230	TCAGATCGGAATGTTCCTTTTCTTTTT	59.986	33.333	9.90	0.00	45.33	1.94
696	738	1.446966	GTGAGAACCAGCTCCTCGC	60.447	63.158	0.00	0.00	39.57	5.03
841	884	4.988716	TCCGCGTCACCACCCTCT	62.989	66.667	4.92	0.00	0.00	3.69
842	885	3.524648	TTTCCGCGTCACCACCCTC	62.525	63.158	4.92	0.00	0.00	4.30
843	886	3.552384	TTTCCGCGTCACCACCCT	61.552	61.111	4.92	0.00	0.00	4.34
947	1025	1.535860	GCAGCGAGAGAGAAAGGCTAG	60.536	57.143	0.00	0.00	31.72	3.42
1036	1142	3.174987	CCTCCACCACCACCACCA	61.175	66.667	0.00	0.00	0.00	4.17
1045	1151	2.669133	CCTTCGCCATCCTCCACCA	61.669	63.158	0.00	0.00	0.00	4.17
1046	1152	2.190578	CCTTCGCCATCCTCCACC	59.809	66.667	0.00	0.00	0.00	4.61
1047	1153	2.514824	GCCTTCGCCATCCTCCAC	60.515	66.667	0.00	0.00	0.00	4.02
1326	1432	2.506472	CTAGGCGCCTTCCTTCCC	59.494	66.667	37.74	0.00	37.66	3.97
1399	1505	5.593968	TGCCGTATACATTACAATCGACTT	58.406	37.500	3.32	0.00	0.00	3.01
1501	1611	3.763097	TTCTTATGGCTTCGCAACATG	57.237	42.857	0.00	0.00	0.00	3.21
1663	1780	7.747690	TGGAACCCTATAAACTTTGACACTTA	58.252	34.615	0.00	0.00	0.00	2.24
1683	1800	1.726853	ATGCGTGCTAGTTCTGGAAC	58.273	50.000	5.43	5.43	41.45	3.62
1729	1850	4.549458	ACAATAATTATCAGCCGCAATGC	58.451	39.130	0.00	0.00	0.00	3.56
1763	1895	1.585521	GGTCGTAGTCATCCACGCG	60.586	63.158	3.53	3.53	38.05	6.01
1812	1944	4.483950	TCTCCACCAAAAGAGAGAGAGAA	58.516	43.478	0.00	0.00	34.23	2.87

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.