AutoCloner

Multiple sequence alignment - TraesCS1D01G140200

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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	TraesCS1D01G140200	chr1D	100.000	3464	0	0	1	3464	193357046	193360509	0.000000e+00	6397
1	TraesCS1D01G140200	chr1B	97.307	2636	57	6	833	3464	267965522	267968147	0.000000e+00	4462
2	TraesCS1D01G140200	chr1A	96.696	2603	65	9	877	3464	239099883	239102479	0.000000e+00	4311
3	TraesCS1D01G140200	chr1A	85.762	892	70	18	1	838	239098981	239099869	0.000000e+00	891
4	TraesCS1D01G140200	chr4D	87.500	512	59	5	1	510	316766084	316765576	1.390000e-163	586
5	TraesCS1D01G140200	chr3D	87.135	513	61	5	1	511	389595033	389595542	8.340000e-161	577
6	TraesCS1D01G140200	chr3D	87.041	517	56	10	1	511	124300558	124301069	1.080000e-159	573
7	TraesCS1D01G140200	chr3D	86.745	513	62	6	1	511	292867616	292867108	1.800000e-157	566
8	TraesCS1D01G140200	chr5D	86.965	514	60	5	2	511	170977044	170976534	3.880000e-159	571
9	TraesCS1D01G140200	chr4A	86.940	513	62	5	1	511	589926019	589925510	3.880000e-159	571
10	TraesCS1D01G140200	chr4A	86.940	513	62	5	1	511	589933867	589933358	3.880000e-159	571
11	TraesCS1D01G140200	chr4A	86.745	513	63	5	1	511	589953333	589952824	1.800000e-157	566
12	TraesCS1D01G140200	chr4B	80.075	266	28	5	519	762	439314812	439314550	1.280000e-39	174
13	TraesCS1D01G140200	chr7D	87.640	89	11	0	597	685	4410770	4410858	1.700000e-18	104
14	TraesCS1D01G140200	chr7D	86.517	89	12	0	597	685	4410976	4411064	7.910000e-17	99

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	TraesCS1D01G140200	chr1D	193357046	193360509	3463	False	6397	6397	100.000	1	3464	1	chr1D.!!$F1	3463
1	TraesCS1D01G140200	chr1B	267965522	267968147	2625	False	4462	4462	97.307	833	3464	1	chr1B.!!$F1	2631
2	TraesCS1D01G140200	chr1A	239098981	239102479	3498	False	2601	4311	91.229	1	3464	2	chr1A.!!$F1	3463
3	TraesCS1D01G140200	chr4D	316765576	316766084	508	True	586	586	87.500	1	510	1	chr4D.!!$R1	509
4	TraesCS1D01G140200	chr3D	389595033	389595542	509	False	577	577	87.135	1	511	1	chr3D.!!$F2	510
5	TraesCS1D01G140200	chr3D	124300558	124301069	511	False	573	573	87.041	1	511	1	chr3D.!!$F1	510
6	TraesCS1D01G140200	chr3D	292867108	292867616	508	True	566	566	86.745	1	511	1	chr3D.!!$R1	510
7	TraesCS1D01G140200	chr5D	170976534	170977044	510	True	571	571	86.965	2	511	1	chr5D.!!$R1	509
8	TraesCS1D01G140200	chr4A	589925510	589926019	509	True	571	571	86.940	1	511	1	chr4A.!!$R1	510
9	TraesCS1D01G140200	chr4A	589933358	589933867	509	True	571	571	86.940	1	511	1	chr4A.!!$R2	510
10	TraesCS1D01G140200	chr4A	589952824	589953333	509	True	566	566	86.745	1	511	1	chr4A.!!$R3	510

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
733	788	0.535335	TCGACCCACTGGCTGTAATC	59.465	55.0	0.0	0.0	33.59	1.75	F
1386	1466	1.067295	ACCTTGTCTCCTGGAATGCA	58.933	50.0	0.0	0.0	0.00	3.96	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1653	1733	1.192146	AGCCACGCTCCTGAAGGTAA	61.192	55.0	0.00	0.0	30.62	2.85	R
3186	3274	0.734889	CTCCGGATGTTTGGCATGAC	59.265	55.0	3.57	0.0	38.06	3.06	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
47	48	9.869757	GCTTGGTAGTTAATGGACAATAATTTT	57.130	29.630	0.00	0.00	0.00	1.82
130	132	5.048782	TGTTTATGGTGCACTCTTTGATCAC	60.049	40.000	17.98	3.32	0.00	3.06
175	177	6.331042	TCCCTCACTCCTTTGATCATATCATT	59.669	38.462	0.00	0.00	39.39	2.57
200	202	7.889873	TTGGTCCTGAAAAGAAAGATTGTTA	57.110	32.000	0.00	0.00	0.00	2.41
201	203	7.272037	TGGTCCTGAAAAGAAAGATTGTTAC	57.728	36.000	0.00	0.00	0.00	2.50
203	205	6.264518	GGTCCTGAAAAGAAAGATTGTTACCA	59.735	38.462	0.00	0.00	0.00	3.25
207	209	6.512297	TGAAAAGAAAGATTGTTACCAAGCC	58.488	36.000	0.00	0.00	37.70	4.35
404	406	7.079451	ACTTGGAGAGTTGAAAGATAAAGGA	57.921	36.000	0.00	0.00	33.92	3.36
511	541	7.984617	TCGTGATCAATTGTTGGATCTATTGTA	59.015	33.333	5.13	0.00	40.41	2.41
521	551	2.430382	ATCTATTGTACGGCGGGGCG	62.430	60.000	13.24	13.33	0.00	6.13
522	552	4.224274	TATTGTACGGCGGGGCGG	62.224	66.667	18.86	5.46	35.02	6.13
533	563	4.241555	GGGGCGGAGATCATGCGT	62.242	66.667	0.00	0.00	45.78	5.24
575	605	1.007118	TGGTGGTGGCTCTAGATGAGA	59.993	52.381	0.00	0.00	45.39	3.27
591	621	2.724454	TGAGAGTCGGTAGGGAGAAAG	58.276	52.381	0.00	0.00	0.00	2.62
598	628	3.090037	TCGGTAGGGAGAAAGTGAAGAG	58.910	50.000	0.00	0.00	0.00	2.85
622	677	0.808125	TGCTGAGAGAGAAGAGCGAC	59.192	55.000	0.00	0.00	33.97	5.19
635	690	5.516090	AGAAGAGCGACGAGATAGATTTTC	58.484	41.667	0.00	0.00	0.00	2.29
648	703	9.743057	CGAGATAGATTTTCTAGAGACAAACAT	57.257	33.333	0.00	0.00	31.67	2.71
654	709	8.811017	AGATTTTCTAGAGACAAACATCTGAGA	58.189	33.333	0.00	0.00	0.00	3.27
662	717	7.555087	AGAGACAAACATCTGAGAAGATAAGG	58.445	38.462	0.00	0.00	0.00	2.69
677	732	5.862924	AGATAAGGTTCAACAACGATGTG	57.137	39.130	0.00	0.00	40.46	3.21
686	741	8.586550	GGTTCAACAACGATGTGTGAATCACA	62.587	42.308	12.63	12.63	45.61	3.58
725	780	4.082523	ATGCGGTCGACCCACTGG	62.083	66.667	28.52	15.13	37.80	4.00
733	788	0.535335	TCGACCCACTGGCTGTAATC	59.465	55.000	0.00	0.00	33.59	1.75
759	814	3.623510	CGACTGATAGGAAAGCTTTTCCC	59.376	47.826	14.05	10.94	39.39	3.97
798	854	2.240921	TGGACGAATGGATGATGGGAAA	59.759	45.455	0.00	0.00	0.00	3.13
799	855	2.880890	GGACGAATGGATGATGGGAAAG	59.119	50.000	0.00	0.00	0.00	2.62
815	872	8.377034	TGATGGGAAAGAAATGAAACATGAAAT	58.623	29.630	0.00	0.00	0.00	2.17
820	877	9.044150	GGAAAGAAATGAAACATGAAATTGTGA	57.956	29.630	0.00	0.00	0.00	3.58
824	881	9.865321	AGAAATGAAACATGAAATTGTGATAGG	57.135	29.630	0.00	0.00	0.00	2.57
830	887	9.342308	GAAACATGAAATTGTGATAGGGATAGA	57.658	33.333	0.00	0.00	0.00	1.98
896	970	7.889589	AACATTTTATACTTGCTGAAAAGCC	57.110	32.000	0.00	0.00	0.00	4.35
970	1044	1.735973	GGCTCAATCAATTCCCGCC	59.264	57.895	0.00	0.00	0.00	6.13
1293	1373	3.341857	GACATCTATGTCGCGAACTCT	57.658	47.619	12.06	0.00	46.46	3.24
1386	1466	1.067295	ACCTTGTCTCCTGGAATGCA	58.933	50.000	0.00	0.00	0.00	3.96
1485	1565	1.147824	CTCCTGGAGCGCCATGATT	59.852	57.895	10.50	0.00	44.91	2.57
1582	1662	4.511454	GCAATGGTGTTAGAGCGAATGATA	59.489	41.667	0.00	0.00	0.00	2.15
1653	1733	1.153086	GGGAAGGCAGATGCATCGT	60.153	57.895	20.67	6.92	44.36	3.73
1762	1842	1.228124	CTTGAGGTGTTTCGGGCCA	60.228	57.895	4.39	0.00	0.00	5.36
1797	1877	4.067896	GCACCGATGTTCTGATATGGAAT	58.932	43.478	0.00	0.00	0.00	3.01
2432	2512	7.147949	GGAGATGAAAATGAAGGATGATGTTGT	60.148	37.037	0.00	0.00	0.00	3.32
2510	2590	4.389374	TCAAAAGTAAGTTCTCCTGCAGG	58.611	43.478	27.87	27.87	0.00	4.85
2590	2670	5.830991	TGGTTACTTATGCAGACTTGGTTTT	59.169	36.000	0.00	0.00	0.00	2.43
2728	2808	5.750547	AGAAGAAGTATGACGTGTGCATATG	59.249	40.000	0.00	0.46	31.54	1.78
2780	2860	0.110056	GTGCATTCTGTTGCTGGACG	60.110	55.000	0.00	0.00	43.18	4.79
2883	2970	2.893489	GGGCAAGAACATTCCAAAGACT	59.107	45.455	0.00	0.00	0.00	3.24
2905	2992	5.163269	ACTGCTGACTATTTATGCCAGATGA	60.163	40.000	0.00	0.00	0.00	2.92
3076	3163	0.521735	CTGAGCTTTGCCCGTTAACC	59.478	55.000	0.00	0.00	0.00	2.85
3208	3296	1.315257	ATGCCAAACATCCGGAGCAC	61.315	55.000	15.18	0.00	31.52	4.40
3351	3439	5.818136	AAATAACATGACCTGTGAATCCG	57.182	39.130	0.00	0.00	38.39	4.18
3358	3447	1.886542	GACCTGTGAATCCGCCTTTTT	59.113	47.619	0.00	0.00	0.00	1.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	69	7.596494	CACAATCAATCTTTGTGTGGTAATCT	58.404	34.615	8.08	0.00	45.60	2.40
130	132	4.878397	GGGATTGACACAATCCTAACTCAG	59.122	45.833	29.81	0.00	44.35	3.35
175	177	6.790232	ACAATCTTTCTTTTCAGGACCAAA	57.210	33.333	0.00	0.00	0.00	3.28
200	202	5.279506	CCATCGATATGTTACTAGGCTTGGT	60.280	44.000	0.00	0.00	0.00	3.67
201	203	5.171476	CCATCGATATGTTACTAGGCTTGG	58.829	45.833	0.00	0.00	0.00	3.61
203	205	6.420913	AACCATCGATATGTTACTAGGCTT	57.579	37.500	9.95	0.00	0.00	4.35
323	325	3.323691	TCCAACACAGATTCTCGGAGAAA	59.676	43.478	23.06	8.22	37.82	2.52
393	395	9.700831	ACTACATTAGGCAAATCCTTTATCTTT	57.299	29.630	0.00	0.00	44.75	2.52
418	421	8.306761	ACACAAAAGATATCCCTTTGAATGAAC	58.693	33.333	24.37	0.00	36.57	3.18
420	423	7.451255	ACACACAAAAGATATCCCTTTGAATGA	59.549	33.333	24.37	0.00	36.57	2.57
421	424	7.543172	CACACACAAAAGATATCCCTTTGAATG	59.457	37.037	24.37	21.92	36.57	2.67
472	502	7.864108	AATTGATCACGAAGGTCAATTGATA	57.136	32.000	23.18	0.00	45.64	2.15
553	583	2.437281	CTCATCTAGAGCCACCACCATT	59.563	50.000	0.00	0.00	37.59	3.16
575	605	2.599408	TCACTTTCTCCCTACCGACT	57.401	50.000	0.00	0.00	0.00	4.18
581	611	2.567615	GCCACTCTTCACTTTCTCCCTA	59.432	50.000	0.00	0.00	0.00	3.53
591	621	0.319728	TCTCAGCAGCCACTCTTCAC	59.680	55.000	0.00	0.00	0.00	3.18
598	628	0.894141	TCTTCTCTCTCAGCAGCCAC	59.106	55.000	0.00	0.00	0.00	5.01
622	677	9.743057	ATGTTTGTCTCTAGAAAATCTATCTCG	57.257	33.333	0.00	0.00	0.00	4.04
635	690	9.734620	CTTATCTTCTCAGATGTTTGTCTCTAG	57.265	37.037	0.00	0.00	40.28	2.43
648	703	5.926542	CGTTGTTGAACCTTATCTTCTCAGA	59.073	40.000	0.00	0.00	0.00	3.27
651	706	6.369065	ACATCGTTGTTGAACCTTATCTTCTC	59.631	38.462	0.00	0.00	29.55	2.87
654	709	5.763204	ACACATCGTTGTTGAACCTTATCTT	59.237	36.000	0.00	0.00	32.34	2.40
662	717	4.843147	TGATTCACACATCGTTGTTGAAC	58.157	39.130	18.11	14.41	36.56	3.18
677	732	0.095245	CGCGTGTCCATGTGATTCAC	59.905	55.000	9.93	9.93	34.56	3.18
686	741	3.971453	CTGCTCGACGCGTGTCCAT	62.971	63.158	20.70	0.00	42.37	3.41
687	742	4.700365	CTGCTCGACGCGTGTCCA	62.700	66.667	20.70	13.89	42.37	4.02
733	788	1.137872	AGCTTTCCTATCAGTCGGCTG	59.862	52.381	11.77	11.77	43.87	4.85
740	795	7.056635	TGATAAGGGAAAAGCTTTCCTATCAG	58.943	38.462	17.36	0.00	39.99	2.90
744	799	7.518188	CCTATGATAAGGGAAAAGCTTTCCTA	58.482	38.462	17.36	5.08	39.99	2.94
759	814	4.503296	CGTCCAACCTTCCCCTATGATAAG	60.503	50.000	0.00	0.00	0.00	1.73
773	829	2.421952	CCATCATCCATTCGTCCAACCT	60.422	50.000	0.00	0.00	0.00	3.50
775	831	1.949525	CCCATCATCCATTCGTCCAAC	59.050	52.381	0.00	0.00	0.00	3.77
798	854	9.865321	CCTATCACAATTTCATGTTTCATTTCT	57.135	29.630	0.00	0.00	0.00	2.52
799	855	9.090692	CCCTATCACAATTTCATGTTTCATTTC	57.909	33.333	0.00	0.00	0.00	2.17
887	961	1.004185	CATGCGAGATCGGCTTTTCAG	60.004	52.381	12.10	0.00	40.23	3.02
888	962	1.009078	CATGCGAGATCGGCTTTTCA	58.991	50.000	12.10	0.00	40.23	2.69
889	963	1.009829	ACATGCGAGATCGGCTTTTC	58.990	50.000	12.10	0.00	40.23	2.29
890	964	0.729116	CACATGCGAGATCGGCTTTT	59.271	50.000	12.10	0.00	40.23	2.27
896	970	1.926561	TTTCCTCACATGCGAGATCG	58.073	50.000	12.38	0.00	43.27	3.69
970	1044	1.519719	CGGAAGGAGGAGAGCAAGG	59.480	63.158	0.00	0.00	0.00	3.61
1290	1370	1.532090	GCGTACATGTGGACGAGAGAG	60.532	57.143	22.07	0.00	41.60	3.20
1293	1373	1.135939	CGCGTACATGTGGACGAGA	59.864	57.895	22.07	0.00	40.71	4.04
1344	1424	1.627424	CCGCGGTATTTCGTCGAAC	59.373	57.895	19.50	0.00	33.87	3.95
1582	1662	2.574006	AGCACACTGACCATTGTGAT	57.426	45.000	20.05	13.34	42.42	3.06
1653	1733	1.192146	AGCCACGCTCCTGAAGGTAA	61.192	55.000	0.00	0.00	30.62	2.85
1762	1842	2.034687	GGTGCTGGTCACTGGCAT	59.965	61.111	0.00	0.00	44.98	4.40
1797	1877	1.608055	CAAGTCCACCAATCACAGCA	58.392	50.000	0.00	0.00	0.00	4.41
2510	2590	5.758784	TCAGACAAGATGCATGATCAGAATC	59.241	40.000	2.46	4.38	32.86	2.52
2527	2607	4.996793	TGAATTTCCCCTGATTCAGACAA	58.003	39.130	15.36	2.03	37.35	3.18
2590	2670	5.702670	TGTTTGGCAGTCAAATTTTCAACAA	59.297	32.000	2.88	0.00	45.79	2.83
2728	2808	3.126686	GCAGCTCAAAGAATCTCAAGACC	59.873	47.826	0.00	0.00	0.00	3.85
2780	2860	5.877012	TGAAGATGTTTACTCTCTGATTGCC	59.123	40.000	0.00	0.00	0.00	4.52
2883	2970	5.294734	TCATCTGGCATAAATAGTCAGCA	57.705	39.130	0.00	0.00	0.00	4.41
2905	2992	2.760650	TCTCTACGACATGGTTCAGCAT	59.239	45.455	0.00	0.00	0.00	3.79
3076	3163	4.294232	CGCTATACACAACCAGAGATCTG	58.706	47.826	0.00	2.72	43.40	2.90
3149	3237	5.869649	AAGCAACACTAATTTTGGGAACT	57.130	34.783	0.00	0.00	0.00	3.01
3186	3274	0.734889	CTCCGGATGTTTGGCATGAC	59.265	55.000	3.57	0.00	38.06	3.06
3351	3439	2.371841	AGAAAATGTGGGGGAAAAAGGC	59.628	45.455	0.00	0.00	0.00	4.35
3358	3447	3.628832	AAAAGGAGAAAATGTGGGGGA	57.371	42.857	0.00	0.00	0.00	4.81

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.