AutoCloner

Multiple sequence alignment - TraesCS3D01G454500

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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	TraesCS3D01G454500	chr3D	100.000	4772	0	0	1	4772	561011824	561016595	0.000000e+00	8813
1	TraesCS3D01G454500	chr2D	96.044	4778	152	15	1	4772	534496897	534501643	0.000000e+00	7742
2	TraesCS3D01G454500	chr1D	95.568	4783	158	20	1	4772	78402243	78397504	0.000000e+00	7609
3	TraesCS3D01G454500	chr5B	85.822	2659	295	60	446	3065	522093133	522090518	0.000000e+00	2747
4	TraesCS3D01G454500	chr5B	84.012	1720	223	39	3092	4772	522090386	522088680	0.000000e+00	1605
5	TraesCS3D01G454500	chr5B	86.818	440	39	8	1	422	522093566	522093128	1.550000e-129	473
6	TraesCS3D01G454500	chr2A	86.111	1980	186	49	6	1919	718349641	718351597	0.000000e+00	2050
7	TraesCS3D01G454500	chr2A	84.921	1711	215	28	3092	4772	718352845	718354542	0.000000e+00	1690
8	TraesCS3D01G454500	chr2A	86.498	1148	120	29	1961	3096	718351606	718352730	0.000000e+00	1229
9	TraesCS3D01G454500	chr4A	81.395	258	43	5	4220	4475	544597695	544597949	6.260000e-49	206
10	TraesCS3D01G454500	chr6A	79.688	256	49	3	4221	4475	42687641	42687388	1.050000e-41	182
11	TraesCS3D01G454500	chr6A	78.988	257	51	3	4223	4478	42641018	42640764	6.350000e-39	172
12	TraesCS3D01G454500	chr6A	78.346	254	52	3	4223	4475	42353672	42353421	1.370000e-35	161
13	TraesCS3D01G454500	chr6A	78.346	254	46	6	4223	4475	42608315	42608070	6.390000e-34	156

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	TraesCS3D01G454500	chr3D	561011824	561016595	4771	False	8813.000000	8813	100.000000	1	4772	1	chr3D.!!$F1	4771
1	TraesCS3D01G454500	chr2D	534496897	534501643	4746	False	7742.000000	7742	96.044000	1	4772	1	chr2D.!!$F1	4771
2	TraesCS3D01G454500	chr1D	78397504	78402243	4739	True	7609.000000	7609	95.568000	1	4772	1	chr1D.!!$R1	4771
3	TraesCS3D01G454500	chr5B	522088680	522093566	4886	True	1608.333333	2747	85.550667	1	4772	3	chr5B.!!$R1	4771
4	TraesCS3D01G454500	chr2A	718349641	718354542	4901	False	1656.333333	2050	85.843333	6	4772	3	chr2A.!!$F1	4766

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	Hairpin	End Stability	Orientation
757	816	0.319083	TTCGTTATGCCACACGTCCT	59.681	50.000	0.00	37.66	3.85	F
2306	2400	0.030504	CAGCTGAGAGATGCGTCGAT	59.969	55.000	8.42	0.00	3.59	F
2844	2938	1.541588	GTGGTTTCACTGATTGCCCTC	59.458	52.381	0.00	40.58	4.30	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
2679	2773	0.323360	GTCAACTGCATAAGGCCCCA	60.323	55.0	43.89	4.96	R
3395	3623	0.250124	ACCACGGATCAGTTGCGAAA	60.250	50.0	42.53	3.46	R
4620	4876	0.180406	AGAGCACACCGACCACTTTT	59.820	50.0	0.00	2.27	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
31	32	4.531351	CCACCCGGGTTTGGATTT	57.469	55.556	27.83	0.00	34.46	2.17
100	101	4.113815	CCCCAGATCCAGGCGCAA	62.114	66.667	10.83	0.00	0.00	4.85
250	281	0.607489	CACAAGGCCTAGCTGCAGTT	60.607	55.000	16.64	12.62	0.00	3.16
252	283	0.607489	CAAGGCCTAGCTGCAGTTGT	60.607	55.000	16.64	2.99	0.00	3.32
321	352	8.512138	GTTGATGGTTGTGTTAGCTAAGTAATT	58.488	33.333	6.38	0.00	0.00	1.40
325	356	6.999272	TGGTTGTGTTAGCTAAGTAATTTCCA	59.001	34.615	6.38	7.40	0.00	3.53
358	411	5.646692	AGGGCACTCCTTTATTAATAGCA	57.353	39.130	0.00	0.00	45.47	3.49
493	547	9.765795	ACTATGTAATGCTTTATCAGACCTTAC	57.234	33.333	0.00	0.00	0.00	2.34
504	559	2.758979	TCAGACCTTACTTAAGCTCCCG	59.241	50.000	1.29	0.00	32.02	5.14
757	816	0.319083	TTCGTTATGCCACACGTCCT	59.681	50.000	0.00	0.00	37.66	3.85
834	894	3.312697	GGGCAGAACCGTCATTTCTATTC	59.687	47.826	0.00	0.00	40.62	1.75
876	936	2.434331	CGGTTCCACCCACACCAT	59.566	61.111	0.00	0.00	33.75	3.55
1055	1119	8.988064	TCTACAGCTCTTTTGTATCTAGTTTG	57.012	34.615	0.00	0.00	31.17	2.93
1094	1175	2.257207	TCTGAATCTTGTCCGGGTCTT	58.743	47.619	0.00	0.00	0.00	3.01
1136	1219	4.277174	CAGGATGATAGTAGTTCGCAGTCT	59.723	45.833	0.00	0.00	39.69	3.24
1508	1591	2.905736	CAAGGTTTTTGGGATCCCATGT	59.094	45.455	34.21	12.22	46.64	3.21
1576	1659	8.579006	TGAAGCTGTTCATTTCATAAAGACAAT	58.421	29.630	0.00	0.00	37.79	2.71
1604	1689	1.135939	GGATAAAACCGGCGTGCAC	59.864	57.895	6.82	6.82	0.00	4.57
1956	2042	3.755378	AGCGCAACTTTTCTGAATGAGAT	59.245	39.130	11.47	0.00	0.00	2.75
2073	2159	4.217334	TGATCTCGGCATTTTAAACAAGCA	59.783	37.500	0.00	0.00	0.00	3.91
2121	2207	2.632996	ACTTCGACCCAGAGTCATTTCA	59.367	45.455	0.00	0.00	46.69	2.69
2306	2400	0.030504	CAGCTGAGAGATGCGTCGAT	59.969	55.000	8.42	0.00	0.00	3.59
2425	2519	4.263506	ACCTTCAATTCACAACTCCCCTAG	60.264	45.833	0.00	0.00	0.00	3.02
2679	2773	6.918892	TGATTATAAAACAGCAGTACGCAT	57.081	33.333	11.30	0.00	46.13	4.73
2740	2834	2.430332	AGCAGGCTTTGTTACAAGCAAA	59.570	40.909	16.66	0.01	43.49	3.68
2775	2869	7.013750	TGCAACTGGATATGTACAAGTTTTCAA	59.986	33.333	0.00	0.00	0.00	2.69
2844	2938	1.541588	GTGGTTTCACTGATTGCCCTC	59.458	52.381	0.00	0.00	40.58	4.30
2878	2972	9.936759	TCGTCATAAAATCCTATGCATGTTATA	57.063	29.630	10.16	0.00	30.61	0.98
3125	3352	3.710165	TGCTGATCTCAGATCACTCCATT	59.290	43.478	13.76	0.00	46.59	3.16
3395	3623	4.134563	GGAAATACATATTCCAGCACGGT	58.865	43.478	0.56	0.00	44.70	4.83
3570	3801	1.168714	AGAGTTGCGCTCATTTTCCC	58.831	50.000	9.73	0.00	46.47	3.97
3811	4048	4.015084	CAGTCTGATCAGGAAGCCAATTT	58.985	43.478	22.42	0.00	0.00	1.82
4237	4479	0.036022	ACTCAGTTCTTCCTGCCTGC	59.964	55.000	0.00	0.00	32.32	4.85
4301	4543	3.265791	GTCAAGGAAGCTCCATGTACTG	58.734	50.000	5.21	0.00	39.61	2.74
4539	4781	1.133025	GCTACATGGCAGCACGAAATT	59.867	47.619	14.69	0.00	38.93	1.82
4620	4876	6.856135	TTCGCTATCTTACGAACAGAGATA	57.144	37.500	0.00	0.00	42.85	1.98
4629	4885	7.088905	TCTTACGAACAGAGATAAAAGTGGTC	58.911	38.462	0.00	0.00	0.00	4.02
4685	4941	2.242196	CCAGAAGCTCAAAATCCCCCTA	59.758	50.000	0.00	0.00	0.00	3.53
4757	5017	4.987408	TTTCCATTGTAGTCGATACGGA	57.013	40.909	0.00	0.00	37.17	4.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
250	281	1.001974	ACTGCAGCCATAAGAACGACA	59.998	47.619	15.27	0.00	0.00	4.35
252	283	1.275010	TCACTGCAGCCATAAGAACGA	59.725	47.619	15.27	0.00	0.00	3.85
321	352	4.827789	AGTGCCCTAGAATACCTATGGAA	58.172	43.478	0.00	0.00	35.79	3.53
325	356	4.768807	AGGAGTGCCCTAGAATACCTAT	57.231	45.455	0.00	0.00	45.48	2.57
510	566	7.716799	ACAATCTGAACCCAGCAAAATAATA	57.283	32.000	0.00	0.00	40.20	0.98
757	816	3.909662	GGGGAGACGCGTGTACTA	58.090	61.111	20.70	0.00	0.00	1.82
834	894	4.122776	GGATAGGGATATAATGCGTGCTG	58.877	47.826	0.00	0.00	0.00	4.41
876	936	3.718434	AGAAATGGGCAGGATATGAGTGA	59.282	43.478	0.00	0.00	0.00	3.41
1031	1092	8.988064	TCAAACTAGATACAAAAGAGCTGTAG	57.012	34.615	0.00	0.00	32.96	2.74
1033	1094	9.593134	CTATCAAACTAGATACAAAAGAGCTGT	57.407	33.333	0.00	0.00	0.00	4.40
1034	1095	9.809096	TCTATCAAACTAGATACAAAAGAGCTG	57.191	33.333	0.00	0.00	0.00	4.24
1055	1119	6.291648	TCAGATCCAGGCATACAATCTATC	57.708	41.667	0.00	0.00	0.00	2.08
1508	1591	0.813610	CTTTCACACTGCGGTGACCA	60.814	55.000	31.98	11.89	46.76	4.02
1576	1659	4.095185	CGCCGGTTTTATCCATTTGAAGTA	59.905	41.667	1.90	0.00	0.00	2.24
1619	1704	3.071786	TCGCGCAACAGAAAATTTTCA	57.928	38.095	28.00	5.82	39.61	2.69
1956	2042	3.410508	TGACATAACTTGCTGTGCATCA	58.589	40.909	0.00	0.00	38.76	3.07
2073	2159	4.736611	ATCCTTGGGAGCACATTATGAT	57.263	40.909	0.00	0.00	34.05	2.45
2121	2207	7.350744	TCAGCAGCCATAATCAACATTTTAT	57.649	32.000	0.00	0.00	0.00	1.40
2249	2340	0.673985	GGGGGCCGATTAGCATTTTC	59.326	55.000	0.00	0.00	0.00	2.29
2306	2400	2.585876	TGCCGTATGTAGCAGACCA	58.414	52.632	0.00	0.00	33.08	4.02
2425	2519	3.651480	GACCAGCGTCGCAATGTGC	62.651	63.158	21.09	0.00	40.69	4.57
2679	2773	0.323360	GTCAACTGCATAAGGCCCCA	60.323	55.000	0.00	0.00	43.89	4.96
2775	2869	5.930135	AGACACTGAGTTGATTACTTGGTT	58.070	37.500	0.00	0.00	37.17	3.67
2844	2938	3.134804	AGGATTTTATGACGACCTGAGGG	59.865	47.826	2.38	0.00	38.88	4.30
2878	2972	6.258727	CGAGAGATAACACAGGCATAAAATGT	59.741	38.462	0.00	0.00	0.00	2.71
3100	3327	4.121317	GGAGTGATCTGAGATCAGCAAAG	58.879	47.826	24.38	0.00	43.46	2.77
3395	3623	0.250124	ACCACGGATCAGTTGCGAAA	60.250	50.000	0.00	0.00	42.53	3.46
3811	4048	1.595311	ATTCATGTAGGGGCACTCCA	58.405	50.000	0.00	0.00	37.22	3.86
3956	4193	7.002250	TGGTCTTTAATGGAAAATTGCATGA	57.998	32.000	0.00	0.00	39.28	3.07
4253	4495	3.779738	TGTCCCACATGATCACTATCCAA	59.220	43.478	0.00	0.00	0.00	3.53
4301	4543	3.866582	CCCCTGATGAGCGGGTCC	61.867	72.222	4.54	0.00	41.87	4.46
4330	4572	1.849219	GCTTATCTCTCGTTGCGTCAG	59.151	52.381	0.00	0.00	0.00	3.51
4571	4827	9.444600	AAAATGGATCAGAAAAATGGAAAGATG	57.555	29.630	0.00	0.00	0.00	2.90
4581	4837	8.055279	AGATAGCGAAAAATGGATCAGAAAAA	57.945	30.769	0.00	0.00	0.00	1.94
4620	4876	0.180406	AGAGCACACCGACCACTTTT	59.820	50.000	0.00	0.00	0.00	2.27
4629	4885	5.171476	CCTAATTATATGGAGAGCACACCG	58.829	45.833	0.00	0.00	0.00	4.94
4742	5002	2.292569	GCTGGATCCGTATCGACTACAA	59.707	50.000	7.39	0.00	32.44	2.41

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.