AutoCloner

Multiple sequence alignment - TraesCS3D01G336200

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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	TraesCS3D01G336200	chr3D	100.000	2308	0	0	1	2308	447988567	447990874	0.000000e+00	4263.0
1	TraesCS3D01G336200	chr3D	100.000	2005	0	0	2652	4656	447991218	447993222	0.000000e+00	3703.0
2	TraesCS3D01G336200	chr3D	92.949	936	61	2	930	1860	206467204	206466269	0.000000e+00	1358.0
3	TraesCS3D01G336200	chr3A	97.147	2313	51	5	1	2308	589392114	589394416	0.000000e+00	3892.0
4	TraesCS3D01G336200	chr3A	91.161	2059	96	32	2652	4656	589394622	589396648	0.000000e+00	2715.0
5	TraesCS3D01G336200	chr3B	97.588	1617	38	1	692	2308	587565690	587567305	0.000000e+00	2769.0
6	TraesCS3D01G336200	chr3B	87.592	1765	86	48	2965	4656	587567714	587569418	0.000000e+00	1923.0
7	TraesCS3D01G336200	chr3B	92.308	676	30	7	1	667	587564681	587565343	0.000000e+00	941.0
8	TraesCS3D01G336200	chr3B	93.458	214	8	3	2698	2911	587567508	587567715	3.500000e-81	313.0
9	TraesCS3D01G336200	chr1A	88.824	859	83	5	930	1787	193040815	193041661	0.000000e+00	1042.0
10	TraesCS3D01G336200	chr1A	78.215	1244	243	20	1076	2305	496046234	496045005	0.000000e+00	771.0
11	TraesCS3D01G336200	chr1A	82.517	572	92	7	3037	3604	496044270	496043703	3.240000e-136	496.0
12	TraesCS3D01G336200	chr1D	78.198	1243	245	17	1076	2305	399190925	399189696	0.000000e+00	771.0
13	TraesCS3D01G336200	chr1D	83.392	572	87	7	3037	3604	399188907	399188340	1.480000e-144	523.0
14	TraesCS3D01G336200	chr1D	80.000	185	32	5	1511	1693	399044424	399044243	1.050000e-26	132.0
15	TraesCS3D01G336200	chr1B	82.867	572	90	7	3037	3604	535384850	535384283	1.490000e-139	507.0
16	TraesCS3D01G336200	chr1B	80.174	575	100	11	3037	3604	535143911	535143344	7.210000e-113	418.0
17	TraesCS3D01G336200	chr4A	80.000	220	37	6	3309	3526	60926384	60926170	6.240000e-34	156.0
18	TraesCS3D01G336200	chr5D	87.719	57	4	3	3313	3368	432041665	432041611	3.890000e-06	63.9
19	TraesCS3D01G336200	chr5B	87.719	57	4	3	3313	3368	523908273	523908327	3.890000e-06	63.9
20	TraesCS3D01G336200	chr5B	87.719	57	4	3	3313	3368	523908401	523908455	3.890000e-06	63.9

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	TraesCS3D01G336200	chr3D	447988567	447993222	4655	False	3983.0	4263	100.0000	1	4656	2	chr3D.!!$F1	4655
1	TraesCS3D01G336200	chr3D	206466269	206467204	935	True	1358.0	1358	92.9490	930	1860	1	chr3D.!!$R1	930
2	TraesCS3D01G336200	chr3A	589392114	589396648	4534	False	3303.5	3892	94.1540	1	4656	2	chr3A.!!$F1	4655
3	TraesCS3D01G336200	chr3B	587564681	587569418	4737	False	1486.5	2769	92.7365	1	4656	4	chr3B.!!$F1	4655
4	TraesCS3D01G336200	chr1A	193040815	193041661	846	False	1042.0	1042	88.8240	930	1787	1	chr1A.!!$F1	857
5	TraesCS3D01G336200	chr1A	496043703	496046234	2531	True	633.5	771	80.3660	1076	3604	2	chr1A.!!$R1	2528
6	TraesCS3D01G336200	chr1D	399188340	399190925	2585	True	647.0	771	80.7950	1076	3604	2	chr1D.!!$R2	2528
7	TraesCS3D01G336200	chr1B	535384283	535384850	567	True	507.0	507	82.8670	3037	3604	1	chr1B.!!$R2	567
8	TraesCS3D01G336200	chr1B	535143344	535143911	567	True	418.0	418	80.1740	3037	3604	1	chr1B.!!$R1	567

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	Hairpin	End Stability	Orientation
393	394	1.144913	CCCCAGAACCCTCAAGAACAA	59.855	52.381	0.00	2.83	F
1086	1434	1.656095	GAAAGTGCCGATCTCAACTCG	59.344	52.381	35.92	4.18	F
1938	2290	1.840635	GCAGACACCCCTAAGGAAGAT	59.159	52.381	39.89	2.40	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1938	2290	3.258372	CCTCCTGAACACTACTGCTGTAA	59.742	47.826	4.91	0.00	2.41	R
3049	3816	0.954449	CCAGTGCAGCTCTTCCAGTG	60.954	60.000	0.00	0.00	3.66	R
3911	4692	0.102844	CAGGGCAACACAAACACCAG	59.897	55.000	0.00	39.74	4.00	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
61	62	4.651778	TGAGAACCAATAAGAACCACCAG	58.348	43.478	0.00	0.00	0.00	4.00
232	233	5.720162	TCTCTCCTGGATCATTCTATTGGA	58.280	41.667	0.00	0.00	0.00	3.53
276	277	3.745975	CGATTGCACCAGTTTCTGTTCTA	59.254	43.478	0.00	0.00	0.00	2.10
280	281	4.713553	TGCACCAGTTTCTGTTCTAATCA	58.286	39.130	0.00	0.00	0.00	2.57
283	284	6.265196	TGCACCAGTTTCTGTTCTAATCATTT	59.735	34.615	0.00	0.00	0.00	2.32
382	383	1.478105	CTTAAATGCTGCCCCAGAACC	59.522	52.381	0.00	0.00	32.44	3.62
393	394	1.144913	CCCCAGAACCCTCAAGAACAA	59.855	52.381	0.00	0.00	0.00	2.83
430	431	9.640963	GACGAGGTATACTATTGCTTATTTGAT	57.359	33.333	2.25	0.00	0.00	2.57
440	450	7.883311	ACTATTGCTTATTTGATAGCCGGTATT	59.117	33.333	1.90	0.00	0.00	1.89
441	451	9.378551	CTATTGCTTATTTGATAGCCGGTATTA	57.621	33.333	1.90	0.00	0.00	0.98
472	482	5.163343	GGTCTGTCAAAGCCCTGTATATGTA	60.163	44.000	0.00	0.00	0.00	2.29
547	557	7.382218	GGGATATTGATTTTAAAGCCATGAACG	59.618	37.037	0.00	0.00	0.00	3.95
584	594	6.801539	ATGCAACCCATATACTGTTAATCG	57.198	37.500	0.00	0.00	30.69	3.34
799	1131	8.630037	AGTATATTTAGGTGCAAAGTTTATGCC	58.370	33.333	0.00	0.00	43.16	4.40
954	1286	2.677337	GTGAAGAGCTGATGAGAAAGCC	59.323	50.000	0.00	0.00	40.42	4.35
1086	1434	1.656095	GAAAGTGCCGATCTCAACTCG	59.344	52.381	0.00	0.00	35.92	4.18
1467	1815	5.628797	ACAACACTTTTGATGGGGAAATT	57.371	34.783	0.00	0.00	29.82	1.82
1938	2290	1.840635	GCAGACACCCCTAAGGAAGAT	59.159	52.381	0.00	0.00	39.89	2.40
2688	3040	7.282585	TGCTAGTTAATATGCTGAATCCTTGT	58.717	34.615	0.00	0.00	0.00	3.16
2772	3126	9.753674	TCCTCCAATTTCTGTAAATAAACTGAT	57.246	29.630	0.00	0.00	34.12	2.90
3049	3816	2.306847	TGACTTTCAGGGAACAAAGCC	58.693	47.619	0.00	0.00	33.57	4.35
3199	3966	2.232452	CCTTCTGTCACAGAACCTCGAT	59.768	50.000	16.67	0.00	44.27	3.59
3211	3978	2.491621	CTCGATGGCTGCGTCTCA	59.508	61.111	0.00	0.00	0.00	3.27
3220	3987	1.581954	CTGCGTCTCAGAGTTCGGT	59.418	57.895	15.46	0.00	45.72	4.69
3367	4134	1.586154	AAATGCTGACCGGAAAGGCG	61.586	55.000	9.46	0.00	46.52	5.52
3370	4137	4.394712	CTGACCGGAAAGGCGCCT	62.395	66.667	27.08	27.08	46.52	5.52
3737	4510	6.049790	GCTAAGCTAGGTTGCATAGTTACTT	58.950	40.000	17.34	0.00	36.82	2.24
3738	4511	6.201234	GCTAAGCTAGGTTGCATAGTTACTTC	59.799	42.308	17.34	0.00	36.82	3.01
3739	4512	5.941555	AGCTAGGTTGCATAGTTACTTCT	57.058	39.130	0.00	0.00	34.99	2.85
3740	4513	6.301169	AGCTAGGTTGCATAGTTACTTCTT	57.699	37.500	0.00	0.00	34.99	2.52
3741	4514	7.419711	AGCTAGGTTGCATAGTTACTTCTTA	57.580	36.000	0.00	0.00	34.99	2.10
3742	4515	7.266400	AGCTAGGTTGCATAGTTACTTCTTAC	58.734	38.462	0.00	0.00	34.99	2.34
3877	4658	2.325761	CGTTTTCGGAGTAGTGACTGG	58.674	52.381	0.00	0.00	35.45	4.00
3878	4659	2.288030	CGTTTTCGGAGTAGTGACTGGT	60.288	50.000	0.00	0.00	35.45	4.00
3879	4660	3.057734	GTTTTCGGAGTAGTGACTGGTG	58.942	50.000	0.00	0.00	35.45	4.17
3880	4661	2.281539	TTCGGAGTAGTGACTGGTGA	57.718	50.000	0.00	0.00	35.45	4.02
3906	4687	5.421693	GCTACTGATCTGGATATCTGATGGT	59.578	44.000	13.65	13.35	34.74	3.55
3911	4692	5.186603	TGATCTGGATATCTGATGGTACTGC	59.813	44.000	13.65	2.65	34.74	4.40
3933	4723	1.336755	GGTGTTTGTGTTGCCCTGTAG	59.663	52.381	0.00	0.00	0.00	2.74
3944	4734	1.948721	GCCCTGTAGTTTGGCATGCC	61.949	60.000	30.54	30.54	44.70	4.40
3945	4735	0.323725	CCCTGTAGTTTGGCATGCCT	60.324	55.000	35.53	19.28	36.94	4.75
3984	4774	7.284034	AGTGTGATTAATGGGATTCATTGAGTC	59.716	37.037	0.00	0.73	45.00	3.36
3988	4778	6.866010	TTAATGGGATTCATTGAGTCGATG	57.134	37.500	13.52	13.52	45.00	3.84
3991	4781	4.588899	TGGGATTCATTGAGTCGATGTTT	58.411	39.130	18.13	8.46	0.00	2.83
4012	4802	0.884704	CCCCTGTTTGTCACCTGTCG	60.885	60.000	0.00	0.00	0.00	4.35
4015	4805	1.270839	CCTGTTTGTCACCTGTCGGAT	60.271	52.381	0.00	0.00	0.00	4.18
4035	4825	4.389687	GGATTTTCTAGTTTGGCGTTCGTA	59.610	41.667	0.00	0.00	0.00	3.43
4055	4845	4.091365	CGTAGAAGATTTGATTCGTGTGCA	59.909	41.667	0.00	0.00	0.00	4.57
4080	4870	1.081175	GCTGGCTGCCTTCGTTTTC	60.081	57.895	21.03	0.00	35.15	2.29
4089	4882	0.512952	CCTTCGTTTTCAGTCAGGCG	59.487	55.000	0.00	0.00	0.00	5.52
4243	5076	1.586564	GAGGACACCGCGATCTTCG	60.587	63.158	8.23	0.00	43.89	3.79
4354	5191	1.532316	ACTCTTGGGTTCGGTCGGA	60.532	57.895	0.00	0.00	0.00	4.55
4417	5255	0.177836	GCTCTTCTCTTCTCCCCAGC	59.822	60.000	0.00	0.00	0.00	4.85
4418	5256	0.459489	CTCTTCTCTTCTCCCCAGCG	59.541	60.000	0.00	0.00	0.00	5.18
4419	5257	1.153469	CTTCTCTTCTCCCCAGCGC	60.153	63.158	0.00	0.00	0.00	5.92
4420	5258	2.897641	CTTCTCTTCTCCCCAGCGCG	62.898	65.000	0.00	0.00	0.00	6.86
4540	5403	3.646162	TCTCGGCCAGATAATAACATGGT	59.354	43.478	2.24	0.00	35.17	3.55

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
308	309	7.333528	TCATTAGGCATAACCAGAAATTGTC	57.666	36.000	0.00	0.00	43.14	3.18
382	383	4.935205	TCCAACACGATATTGTTCTTGAGG	59.065	41.667	10.24	1.47	37.62	3.86
430	431	5.180271	CAGACCAAACTTTAATACCGGCTA	58.820	41.667	0.00	0.00	0.00	3.93
440	450	4.911514	GGCTTTGACAGACCAAACTTTA	57.088	40.909	0.00	0.00	33.07	1.85
441	451	3.801114	GGCTTTGACAGACCAAACTTT	57.199	42.857	0.00	0.00	33.07	2.66
472	482	7.004555	TCATCGGCCAGATAACAAATAGTAT	57.995	36.000	2.24	0.00	37.52	2.12
547	557	1.097232	TTGCATACTGGCATCTGCAC	58.903	50.000	15.53	0.00	43.74	4.57
584	594	8.770438	AGTGAGATACTGAAAATGTTCTCTTC	57.230	34.615	0.00	0.00	38.49	2.87
689	1021	9.004231	AGTATGGAAGGACTAATAGTGGATTTT	57.996	33.333	0.00	0.00	0.00	1.82
954	1286	4.264460	AGCTTTCAACTCTGTACTCCAG	57.736	45.455	0.00	0.00	42.97	3.86
1086	1434	1.163554	CAAGAAGAGCCTGCTTGTCC	58.836	55.000	12.48	0.00	41.06	4.02
1467	1815	5.954752	AGTGAGATTCTGTACTCTCAATGGA	59.045	40.000	12.63	0.00	46.89	3.41
1938	2290	3.258372	CCTCCTGAACACTACTGCTGTAA	59.742	47.826	4.91	0.00	0.00	2.41
2688	3040	8.695456	AGAAATTTTAGAGAAAAGGACAAAGCA	58.305	29.630	0.00	0.00	37.94	3.91
2962	3510	7.016153	TGGACACTAAATCTTATCAACCACT	57.984	36.000	0.00	0.00	0.00	4.00
2963	3511	7.201732	CCATGGACACTAAATCTTATCAACCAC	60.202	40.741	5.56	0.00	0.00	4.16
3025	3694	3.374042	TTGTTCCCTGAAAGTCAACCA	57.626	42.857	0.00	0.00	0.00	3.67
3049	3816	0.954449	CCAGTGCAGCTCTTCCAGTG	60.954	60.000	0.00	0.00	0.00	3.66
3199	3966	1.290324	GAACTCTGAGACGCAGCCA	59.710	57.895	12.44	0.00	44.52	4.75
3211	3978	3.288308	CTGCGCCAGACCGAACTCT	62.288	63.158	4.18	0.00	32.44	3.24
3220	3987	2.125391	GTCATGAGCTGCGCCAGA	60.125	61.111	4.18	0.00	32.44	3.86
3652	4419	3.644966	TTTTTATCTCCACGCCCTCAT	57.355	42.857	0.00	0.00	0.00	2.90
3741	4514	9.587772	CGCTCAAAGCTATATATATAACCAAGT	57.412	33.333	4.06	0.00	39.60	3.16
3742	4515	9.803315	TCGCTCAAAGCTATATATATAACCAAG	57.197	33.333	4.06	0.00	39.60	3.61
3754	4527	6.201044	GCTATCAACTTTCGCTCAAAGCTATA	59.799	38.462	5.21	1.83	45.00	1.31
3874	4655	1.411977	CCAGATCAGTAGCCTCACCAG	59.588	57.143	0.00	0.00	0.00	4.00
3875	4656	1.007118	TCCAGATCAGTAGCCTCACCA	59.993	52.381	0.00	0.00	0.00	4.17
3876	4657	1.781786	TCCAGATCAGTAGCCTCACC	58.218	55.000	0.00	0.00	0.00	4.02
3877	4658	5.016173	AGATATCCAGATCAGTAGCCTCAC	58.984	45.833	0.00	0.00	0.00	3.51
3878	4659	5.015515	CAGATATCCAGATCAGTAGCCTCA	58.984	45.833	0.00	0.00	0.00	3.86
3879	4660	5.260424	TCAGATATCCAGATCAGTAGCCTC	58.740	45.833	0.00	0.00	0.00	4.70
3880	4661	5.268131	TCAGATATCCAGATCAGTAGCCT	57.732	43.478	0.00	0.00	0.00	4.58
3906	4687	1.403679	GCAACACAAACACCAGCAGTA	59.596	47.619	0.00	0.00	0.00	2.74
3911	4692	0.102844	CAGGGCAACACAAACACCAG	59.897	55.000	0.00	0.00	39.74	4.00
3984	4774	1.539827	GACAAACAGGGGGAAACATCG	59.460	52.381	0.00	0.00	0.00	3.84
3988	4778	1.037493	GGTGACAAACAGGGGGAAAC	58.963	55.000	0.00	0.00	0.00	2.78
3991	4781	0.991355	ACAGGTGACAAACAGGGGGA	60.991	55.000	0.00	0.00	0.00	4.81
4012	4802	3.187842	ACGAACGCCAAACTAGAAAATCC	59.812	43.478	0.00	0.00	0.00	3.01
4015	4805	4.619973	TCTACGAACGCCAAACTAGAAAA	58.380	39.130	0.00	0.00	0.00	2.29
4035	4825	3.120060	GCTGCACACGAATCAAATCTTCT	60.120	43.478	0.00	0.00	0.00	2.85
4066	4856	0.944386	TGACTGAAAACGAAGGCAGC	59.056	50.000	0.00	0.00	31.74	5.25
4067	4857	2.957576	CTGACTGAAAACGAAGGCAG	57.042	50.000	0.00	0.00	42.93	4.85
4068	4858	1.593196	CCTGACTGAAAACGAAGGCA	58.407	50.000	0.00	0.00	0.00	4.75
4069	4859	0.238553	GCCTGACTGAAAACGAAGGC	59.761	55.000	0.00	0.00	43.05	4.35
4080	4870	3.414700	GTCGTTGCCGCCTGACTG	61.415	66.667	0.00	0.00	0.00	3.51
4540	5403	2.355412	GGCGATCATCCATCATCATCCA	60.355	50.000	0.00	0.00	0.00	3.41
4575	5442	2.272146	CAACAGGACATCCCCGGG	59.728	66.667	15.80	15.80	36.42	5.73
4583	5450	1.234821	GTGAAATCGCCAACAGGACA	58.765	50.000	0.00	0.00	0.00	4.02

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.