AutoCloner

Multiple sequence alignment - TraesCS4A01G155300

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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	TraesCS4A01G155300	chr4A	100.000	2201	0	0	1	2201	310757216	310755016	0.000000e+00	4065
1	TraesCS4A01G155300	chr2A	96.328	2206	76	4	1	2201	726901128	726903333	0.000000e+00	3620
2	TraesCS4A01G155300	chr2A	94.651	2206	111	6	1	2201	335800747	335802950	0.000000e+00	3413
3	TraesCS4A01G155300	chr3D	95.964	2205	85	4	1	2201	589258201	589260405	0.000000e+00	3576
4	TraesCS4A01G155300	chr3B	95.966	2206	84	4	1	2201	201569460	201571665	0.000000e+00	3576
5	TraesCS4A01G155300	chr3B	95.828	2205	86	5	1	2201	201544844	201542642	0.000000e+00	3557
6	TraesCS4A01G155300	chr3B	95.618	1666	69	3	1	1663	757831130	757832794	0.000000e+00	2669
7	TraesCS4A01G155300	chr3B	94.033	486	28	1	1717	2201	757833037	757833522	0.000000e+00	736
8	TraesCS4A01G155300	chr3B	94.311	334	16	2	1512	1842	733064810	733064477	1.950000e-140	508
9	TraesCS4A01G155300	chr7B	95.918	2205	86	3	1	2201	662732240	662730036	0.000000e+00	3570
10	TraesCS4A01G155300	chr7A	95.782	2205	89	4	1	2201	258305487	258307691	0.000000e+00	3554
11	TraesCS4A01G155300	chr6B	95.784	2206	88	4	1	2201	450085129	450082924	0.000000e+00	3554

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	TraesCS4A01G155300	chr4A	310755016	310757216	2200	True	4065.0	4065	100.0000	1	2201	1	chr4A.!!$R1	2200
1	TraesCS4A01G155300	chr2A	726901128	726903333	2205	False	3620.0	3620	96.3280	1	2201	1	chr2A.!!$F2	2200
2	TraesCS4A01G155300	chr2A	335800747	335802950	2203	False	3413.0	3413	94.6510	1	2201	1	chr2A.!!$F1	2200
3	TraesCS4A01G155300	chr3D	589258201	589260405	2204	False	3576.0	3576	95.9640	1	2201	1	chr3D.!!$F1	2200
4	TraesCS4A01G155300	chr3B	201569460	201571665	2205	False	3576.0	3576	95.9660	1	2201	1	chr3B.!!$F1	2200
5	TraesCS4A01G155300	chr3B	201542642	201544844	2202	True	3557.0	3557	95.8280	1	2201	1	chr3B.!!$R1	2200
6	TraesCS4A01G155300	chr3B	757831130	757833522	2392	False	1702.5	2669	94.8255	1	2201	2	chr3B.!!$F2	2200
7	TraesCS4A01G155300	chr7B	662730036	662732240	2204	True	3570.0	3570	95.9180	1	2201	1	chr7B.!!$R1	2200
8	TraesCS4A01G155300	chr7A	258305487	258307691	2204	False	3554.0	3554	95.7820	1	2201	1	chr7A.!!$F1	2200
9	TraesCS4A01G155300	chr6B	450082924	450085129	2205	True	3554.0	3554	95.7840	1	2201	1	chr6B.!!$R1	2200

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
298	299	0.97504	CTCTGAGCTACAGGCCCAGT	60.975	60.0	0.0	0.15	45.32	4.0	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1567	1571	0.036671	AAAAGGTAACGGAGGCGAGG	60.037	55.0	0.0	0.0	46.39	4.63	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
153	154	9.095065	CATACCTAAGTTCAATAGCTTTACGTT	57.905	33.333	0.00	0.00	0.00	3.99
205	206	3.069005	AGGGGGAAAGTAAAGACCCTTT	58.931	45.455	0.00	0.00	45.95	3.11
252	253	1.595357	GATTCGAACCCCCGACACT	59.405	57.895	0.00	0.00	38.39	3.55
298	299	0.975040	CTCTGAGCTACAGGCCCAGT	60.975	60.000	0.00	0.15	45.32	4.00
450	451	6.204108	TGAGGTTTTGAATAAGACGACCTTTC	59.796	38.462	0.00	0.00	36.25	2.62
569	570	2.960104	GCAGGACCTCCCCTACAGTATT	60.960	54.545	0.00	0.00	34.07	1.89
650	651	4.021016	GCCTAGGACACCAGAATATCGAAT	60.021	45.833	14.75	0.00	0.00	3.34
660	661	6.367149	CACCAGAATATCGAATCATGAACGAT	59.633	38.462	29.53	29.53	46.07	3.73
681	682	8.037382	ACGATGAAAGGCATGAGATAAATATG	57.963	34.615	0.00	0.00	37.34	1.78
760	761	4.045334	CCCTCCCTCTCTATCTATCCAAGT	59.955	50.000	0.00	0.00	0.00	3.16
831	834	7.855375	AGAGTTGAACAATGAAGATAGATGGA	58.145	34.615	0.00	0.00	0.00	3.41
840	843	6.753913	ATGAAGATAGATGGAAAGTGCCTA	57.246	37.500	0.00	0.00	0.00	3.93
841	844	6.166984	TGAAGATAGATGGAAAGTGCCTAG	57.833	41.667	0.00	0.00	0.00	3.02
900	903	2.344025	GTTCGTTCGTTAGGATGCCTT	58.656	47.619	0.00	0.00	34.61	4.35
954	957	3.446516	ACCTATTTAAACGGCTCGTCTCT	59.553	43.478	5.50	0.00	39.99	3.10
987	990	8.651389	CCTTATCCTATTTCCATACTTCTGTCA	58.349	37.037	0.00	0.00	0.00	3.58
1028	1031	2.412037	GAACCCGTCGTTGTCTCGGT	62.412	60.000	0.00	0.00	42.30	4.69
1036	1039	3.508762	GTCGTTGTCTCGGTTGTGATAT	58.491	45.455	0.00	0.00	0.00	1.63
1038	1041	3.191791	TCGTTGTCTCGGTTGTGATATCA	59.808	43.478	0.00	0.00	0.00	2.15
1066	1069	0.705253	AGGGAAGTCGGAGGAGAGAA	59.295	55.000	0.00	0.00	0.00	2.87
1124	1127	0.749649	AGCAGTTATCCTCTCCGCAG	59.250	55.000	0.00	0.00	0.00	5.18
1202	1205	0.179936	CCGGTCCTCTCGTACTAGGT	59.820	60.000	0.00	0.00	34.30	3.08
1234	1237	2.025981	TCAATGCTCTAATGCCCACACT	60.026	45.455	0.00	0.00	0.00	3.55
1411	1414	3.515562	AGATCAGCCTGTTATCCCTAGG	58.484	50.000	0.06	0.06	34.67	3.02
1420	1424	5.339778	GCCTGTTATCCCTAGGGTAACTTTT	60.340	44.000	31.65	15.56	35.17	2.27
1453	1457	2.847234	ACCCTTCCACTCGGCACA	60.847	61.111	0.00	0.00	0.00	4.57
1457	1461	1.668294	CTTCCACTCGGCACAGTCT	59.332	57.895	0.00	0.00	0.00	3.24
1477	1481	3.260884	TCTGATCACTAAGGCCGACTTTT	59.739	43.478	0.00	0.00	40.64	2.27
1484	1488	2.640316	AAGGCCGACTTTTGTCTCTT	57.360	45.000	0.00	0.00	46.76	2.85
1567	1571	0.538746	TTGGCCCGAGGAAACCTTTC	60.539	55.000	0.00	0.00	31.76	2.62
1598	1602	2.040679	GTTACCTTTTGGGAGGCCTACA	59.959	50.000	19.26	11.77	46.08	2.74
1614	1618	3.453353	GCCTACACCCCATAGAAACTGTA	59.547	47.826	0.00	0.00	0.00	2.74
1615	1619	4.682589	GCCTACACCCCATAGAAACTGTAC	60.683	50.000	0.00	0.00	0.00	2.90
1638	1643	2.526873	AGACTGTCCTTGGCCCGT	60.527	61.111	0.00	0.00	0.00	5.28
1741	1935	1.596934	CCTTCCACCTAAGCTGCGA	59.403	57.895	0.00	0.00	0.00	5.10
1766	1960	3.804490	GCCCAAAGCCAATCCCAA	58.196	55.556	0.00	0.00	34.35	4.12
1813	2007	0.036952	CTGTCCAGGTGCAGGTAGTG	60.037	60.000	0.00	0.00	0.00	2.74
1814	2008	0.762842	TGTCCAGGTGCAGGTAGTGT	60.763	55.000	0.00	0.00	0.00	3.55
1815	2009	0.037232	GTCCAGGTGCAGGTAGTGTC	60.037	60.000	0.00	0.00	0.00	3.67
1824	2018	2.637382	TGCAGGTAGTGTCCATCTTCAA	59.363	45.455	0.00	0.00	0.00	2.69
1842	2036	8.944029	CATCTTCAAAGACATGTCTATTTCACT	58.056	33.333	28.10	8.46	39.39	3.41
1954	2148	0.466543	TAGTTATGGCCGCCGTTCAT	59.533	50.000	10.04	0.00	0.00	2.57
1968	2162	2.287274	TTCATCGGGGCTTCGGTCA	61.287	57.895	1.61	0.00	0.00	4.02
1969	2163	1.622607	TTCATCGGGGCTTCGGTCAT	61.623	55.000	1.61	0.00	0.00	3.06
2058	2252	2.288579	ACATGGTCTTACGACTTTGCGA	60.289	45.455	0.00	0.00	40.10	5.10
2088	2282	2.054232	TTTTGGTAAACAGTCGCCCA	57.946	45.000	0.00	0.00	0.00	5.36
2089	2283	2.279935	TTTGGTAAACAGTCGCCCAT	57.720	45.000	0.00	0.00	0.00	4.00
2173	2368	3.019799	TGCCGAGTTCCTTAGAGAGAT	57.980	47.619	0.00	0.00	0.00	2.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	2.711547	ACTCCTAAGGGTCAAAGCAAGT	59.288	45.455	0.00	0.00	0.00	3.16
153	154	3.961480	AAATCATGATCGGGATAGCGA	57.039	42.857	9.06	0.00	0.00	4.93
514	515	5.220931	GCTCGATGCCAGAATGATAAAAAGT	60.221	40.000	0.00	0.00	39.69	2.66
569	570	3.553508	GGTTAAACTCTACTGCGGTGACA	60.554	47.826	8.92	0.00	0.00	3.58
650	651	3.608796	TCATGCCTTTCATCGTTCATGA	58.391	40.909	0.00	0.00	39.99	3.07
660	661	5.477984	GCCCATATTTATCTCATGCCTTTCA	59.522	40.000	0.00	0.00	0.00	2.69
681	682	3.021695	GGGGTTTCACAATTACTAGCCC	58.978	50.000	0.00	0.00	36.30	5.19
760	761	2.574006	AAAGCTCTGCACTTCCATCA	57.426	45.000	0.00	0.00	0.00	3.07
831	834	4.832248	TGATCAAATCGACTAGGCACTTT	58.168	39.130	0.00	0.00	41.75	2.66
840	843	0.537188	ACGGCCTGATCAAATCGACT	59.463	50.000	15.12	0.00	0.00	4.18
841	844	0.652592	CACGGCCTGATCAAATCGAC	59.347	55.000	15.12	0.00	0.00	4.20
900	903	5.451937	GGAAGTGCAGTGATGTATGTAGCTA	60.452	44.000	0.00	0.00	0.00	3.32
954	957	4.485875	TGGAAATAGGATAAGGTAGCGGA	58.514	43.478	0.00	0.00	0.00	5.54
1019	1022	4.142160	CCTCTGATATCACAACCGAGACAA	60.142	45.833	16.56	0.00	0.00	3.18
1028	1031	4.140924	TCCCTAGAGCCTCTGATATCACAA	60.141	45.833	3.98	0.00	0.00	3.33
1036	1039	1.408961	CGACTTCCCTAGAGCCTCTGA	60.409	57.143	3.98	0.00	0.00	3.27
1038	1041	0.106419	CCGACTTCCCTAGAGCCTCT	60.106	60.000	0.00	0.00	0.00	3.69
1066	1069	2.078452	CCCACCCCAAGATGAGTGT	58.922	57.895	0.00	0.00	0.00	3.55
1202	1205	6.586344	CATTAGAGCATTGAGAGGACCTTTA	58.414	40.000	0.00	0.00	0.00	1.85
1234	1237	2.693591	GAGACAGTTCGGTCCATATCCA	59.306	50.000	0.02	0.00	38.59	3.41
1366	1369	0.243907	CAAGAGTCCACATCGACGGT	59.756	55.000	0.00	0.00	37.85	4.83
1411	1414	3.928375	TCGCTCAACGGATAAAAGTTACC	59.072	43.478	0.00	0.00	43.89	2.85
1420	1424	1.430632	GGTCGTCGCTCAACGGATA	59.569	57.895	3.79	0.00	42.80	2.59
1453	1457	1.751924	GTCGGCCTTAGTGATCAGACT	59.248	52.381	0.00	0.00	0.00	3.24
1457	1461	3.244422	ACAAAAGTCGGCCTTAGTGATCA	60.244	43.478	0.00	0.00	31.48	2.92
1477	1481	0.250597	TCACCCGTCGAGAAGAGACA	60.251	55.000	0.00	0.00	38.46	3.41
1484	1488	1.863662	GCAAGACTCACCCGTCGAGA	61.864	60.000	0.00	0.00	38.90	4.04
1546	1550	0.114364	AAGGTTTCCTCGGGCCAAAT	59.886	50.000	4.39	0.00	30.89	2.32
1548	1552	0.538746	GAAAGGTTTCCTCGGGCCAA	60.539	55.000	4.39	0.00	30.89	4.52
1567	1571	0.036671	AAAAGGTAACGGAGGCGAGG	60.037	55.000	0.00	0.00	46.39	4.63
1569	1573	0.320946	CCAAAAGGTAACGGAGGCGA	60.321	55.000	0.00	0.00	46.39	5.54
1598	1602	3.263425	CAGGTGTACAGTTTCTATGGGGT	59.737	47.826	0.00	0.00	0.00	4.95
1614	1618	1.051812	CCAAGGACAGTCTCAGGTGT	58.948	55.000	0.00	0.00	0.00	4.16
1615	1619	0.321122	GCCAAGGACAGTCTCAGGTG	60.321	60.000	0.00	0.00	0.00	4.00
1638	1643	0.320374	CTAACCTTGCGTCAGACCCA	59.680	55.000	0.00	0.00	0.00	4.51
1648	1653	2.159028	AGAGCTCGGATTCTAACCTTGC	60.159	50.000	8.37	0.00	0.00	4.01
1766	1960	4.536489	ACCCTATGAAGCTTTACTGTTCCT	59.464	41.667	0.00	0.00	0.00	3.36
1813	2007	7.856145	AATAGACATGTCTTTGAAGATGGAC	57.144	36.000	32.14	0.00	40.93	4.02
1814	2008	8.102676	TGAAATAGACATGTCTTTGAAGATGGA	58.897	33.333	32.14	11.61	40.93	3.41
1815	2009	8.180267	GTGAAATAGACATGTCTTTGAAGATGG	58.820	37.037	32.14	0.00	40.93	3.51
1824	2018	5.046014	AGGCTCAGTGAAATAGACATGTCTT	60.046	40.000	32.14	15.84	40.93	3.01
1954	2148	3.833645	CGATGACCGAAGCCCCGA	61.834	66.667	0.00	0.00	41.76	5.14
1968	2162	0.467384	CTGATGACAGGGAAGCCGAT	59.533	55.000	0.00	0.00	40.14	4.18
1969	2163	1.900351	CTGATGACAGGGAAGCCGA	59.100	57.895	0.00	0.00	40.14	5.54
2058	2252	5.479027	ACTGTTTACCAAAAACACAGGTCTT	59.521	36.000	0.00	0.00	35.45	3.01
2173	2368	2.577059	CTAGGGGCGCGAGACAAA	59.423	61.111	12.10	0.00	45.40	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.