AutoCloner

Multiple sequence alignment - TraesCS4A01G155000

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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	TraesCS4A01G155000	chr4A	100.000	2199	0	0	1	2199	310743452	310741254	0.000000e+00	4061
1	TraesCS4A01G155000	chr3B	95.565	2232	63	8	1	2199	101916060	101913832	0.000000e+00	3541
2	TraesCS4A01G155000	chr3D	95.553	2226	69	6	1	2199	589272076	589274298	0.000000e+00	3535
3	TraesCS4A01G155000	chrUn	95.508	2226	69	6	1	2199	216513725	216515946	0.000000e+00	3528
4	TraesCS4A01G155000	chrUn	95.508	2226	69	6	1	2199	286269658	286267437	0.000000e+00	3528
5	TraesCS4A01G155000	chrUn	94.603	1019	34	5	1201	2199	421835931	421834914	0.000000e+00	1557
6	TraesCS4A01G155000	chr5D	95.422	2228	71	5	1	2199	503223100	503220875	0.000000e+00	3520
7	TraesCS4A01G155000	chr5D	95.241	1912	62	5	315	2199	446178864	446176955	0.000000e+00	3000
8	TraesCS4A01G155000	chr1D	95.238	2226	77	5	1	2199	254393232	254395455	0.000000e+00	3496
9	TraesCS4A01G155000	chr3A	95.103	2226	78	7	1	2199	594894747	594896968	0.000000e+00	3478
10	TraesCS4A01G155000	chr3A	94.971	2227	68	13	1	2199	164859181	164861391	0.000000e+00	3452
11	TraesCS4A01G155000	chr3A	96.398	1749	48	3	1	1737	66012741	66014486	0.000000e+00	2867
12	TraesCS4A01G155000	chr6D	95.496	2065	64	5	1	2038	168262550	168260488	0.000000e+00	3271
13	TraesCS4A01G155000	chr5A	95.908	1906	58	4	1	1889	510135612	510137514	0.000000e+00	3070
14	TraesCS4A01G155000	chr5A	91.832	453	22	4	1762	2199	164645963	164646415	3.100000e-173	617
15	TraesCS4A01G155000	chr2D	94.838	1511	47	6	718	2199	272789806	272791314	0.000000e+00	2329
16	TraesCS4A01G155000	chr2D	97.308	260	4	2	1942	2199	272567910	272567652	2.590000e-119	438
17	TraesCS4A01G155000	chr6A	96.307	1408	49	2	1	1408	215597781	215599185	0.000000e+00	2309
18	TraesCS4A01G155000	chr6A	92.366	524	20	4	1696	2199	567833816	567833293	0.000000e+00	728
19	TraesCS4A01G155000	chr7A	95.583	1132	42	5	1	1127	60222604	60221476	0.000000e+00	1807

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	TraesCS4A01G155000	chr4A	310741254	310743452	2198	True	4061	4061	100.000	1	2199	1	chr4A.!!$R1	2198
1	TraesCS4A01G155000	chr3B	101913832	101916060	2228	True	3541	3541	95.565	1	2199	1	chr3B.!!$R1	2198
2	TraesCS4A01G155000	chr3D	589272076	589274298	2222	False	3535	3535	95.553	1	2199	1	chr3D.!!$F1	2198
3	TraesCS4A01G155000	chrUn	216513725	216515946	2221	False	3528	3528	95.508	1	2199	1	chrUn.!!$F1	2198
4	TraesCS4A01G155000	chrUn	286267437	286269658	2221	True	3528	3528	95.508	1	2199	1	chrUn.!!$R1	2198
5	TraesCS4A01G155000	chrUn	421834914	421835931	1017	True	1557	1557	94.603	1201	2199	1	chrUn.!!$R2	998
6	TraesCS4A01G155000	chr5D	503220875	503223100	2225	True	3520	3520	95.422	1	2199	1	chr5D.!!$R2	2198
7	TraesCS4A01G155000	chr5D	446176955	446178864	1909	True	3000	3000	95.241	315	2199	1	chr5D.!!$R1	1884
8	TraesCS4A01G155000	chr1D	254393232	254395455	2223	False	3496	3496	95.238	1	2199	1	chr1D.!!$F1	2198
9	TraesCS4A01G155000	chr3A	594894747	594896968	2221	False	3478	3478	95.103	1	2199	1	chr3A.!!$F3	2198
10	TraesCS4A01G155000	chr3A	164859181	164861391	2210	False	3452	3452	94.971	1	2199	1	chr3A.!!$F2	2198
11	TraesCS4A01G155000	chr3A	66012741	66014486	1745	False	2867	2867	96.398	1	1737	1	chr3A.!!$F1	1736
12	TraesCS4A01G155000	chr6D	168260488	168262550	2062	True	3271	3271	95.496	1	2038	1	chr6D.!!$R1	2037
13	TraesCS4A01G155000	chr5A	510135612	510137514	1902	False	3070	3070	95.908	1	1889	1	chr5A.!!$F2	1888
14	TraesCS4A01G155000	chr2D	272789806	272791314	1508	False	2329	2329	94.838	718	2199	1	chr2D.!!$F1	1481
15	TraesCS4A01G155000	chr6A	215597781	215599185	1404	False	2309	2309	96.307	1	1408	1	chr6A.!!$F1	1407
16	TraesCS4A01G155000	chr6A	567833293	567833816	523	True	728	728	92.366	1696	2199	1	chr6A.!!$R1	503
17	TraesCS4A01G155000	chr7A	60221476	60222604	1128	True	1807	1807	95.583	1	1127	1	chr7A.!!$R1	1126

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
842	843	2.791501	ATACCGAACCACACCGTGCC	62.792	60.0	0.0	0.0	31.34	5.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1668	1685	3.081061	TGCGCTCAAAGGATACAAACAT	58.919	40.909	9.73	0.0	41.41	2.71	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
27	28	3.829886	TTCTCATCAAACGAATGGCAC	57.170	42.857	0.00	0.00	0.00	5.01
95	96	8.814038	AATCTCCTTGCTATTACTCAAACAAT	57.186	30.769	0.00	0.00	0.00	2.71
127	128	6.881065	ACTTATGCTTGCATATTCGTCCATAT	59.119	34.615	14.94	0.00	0.00	1.78
130	131	4.002982	GCTTGCATATTCGTCCATATGGA	58.997	43.478	20.98	20.98	43.08	3.41
256	257	9.745323	GAACTTTTGCTTGCATTGTATTATTTC	57.255	29.630	0.00	0.00	0.00	2.17
257	258	9.492973	AACTTTTGCTTGCATTGTATTATTTCT	57.507	25.926	0.00	0.00	0.00	2.52
345	346	4.343814	GCTCTCTCTTTAGCCCTATGTCTT	59.656	45.833	0.00	0.00	32.40	3.01
438	439	3.825328	AGCAGGCCTATATTTCTTGGTG	58.175	45.455	3.98	0.00	0.00	4.17
525	526	5.261209	TGACTGGACAAAACCAAGAAATG	57.739	39.130	0.00	0.00	39.59	2.32
539	540	3.737559	AGAAATGACCCCTTATGTGCA	57.262	42.857	0.00	0.00	0.00	4.57
579	580	7.457535	TCCCCTTTAAGATCAAACAATTCCATT	59.542	33.333	0.00	0.00	0.00	3.16
611	612	7.150640	AGTATGACTGTATGTGTGATAGCATG	58.849	38.462	0.00	0.00	0.00	4.06
647	648	6.324770	GGAATATCAATGAACCCCATTCTTGT	59.675	38.462	0.00	0.00	43.27	3.16
665	666	4.473196	TCTTGTAATTGCTCAGGATACCCA	59.527	41.667	0.00	0.00	33.88	4.51
675	676	4.698575	CTCAGGATACCCACTTTTAGCTC	58.301	47.826	0.00	0.00	33.88	4.09
676	677	3.132289	TCAGGATACCCACTTTTAGCTCG	59.868	47.826	0.00	0.00	33.88	5.03
716	717	6.726764	AGTTCAAGATCCCTCTTACTAACTGT	59.273	38.462	0.00	0.00	39.78	3.55
783	784	5.993441	GGCGCTAGGGTTATGAACTTATAAA	59.007	40.000	7.64	0.00	0.00	1.40
834	835	3.606687	AGTTCATTCCATACCGAACCAC	58.393	45.455	0.00	0.00	38.80	4.16
842	843	2.791501	ATACCGAACCACACCGTGCC	62.792	60.000	0.00	0.00	31.34	5.01
843	844	4.920112	CCGAACCACACCGTGCCA	62.920	66.667	0.00	0.00	31.34	4.92
927	928	7.512992	AGAAATCCCTACATCCTTACATTCTG	58.487	38.462	0.00	0.00	0.00	3.02
938	939	9.533831	ACATCCTTACATTCTGTTTAGGATTTT	57.466	29.630	15.42	7.75	42.74	1.82
1121	1134	4.105486	TCGAAGCTATTTGATGTCTGACG	58.895	43.478	2.98	0.00	0.00	4.35
1257	1270	3.629398	GCCTTGATGGTGAAATGGTAGAG	59.371	47.826	0.00	0.00	38.35	2.43
1277	1290	2.229062	AGACGCGAGACTCAAAATCTCA	59.771	45.455	15.93	0.00	42.39	3.27
1396	1409	1.686052	CTGGCGCTCTCCTCTATCTTT	59.314	52.381	7.64	0.00	0.00	2.52
1440	1453	7.289317	TCCCTGAGAAAAGTAGACAGTAAAAGA	59.711	37.037	0.00	0.00	0.00	2.52
1668	1685	2.224161	CCCCTTTTTGTTTGCGAATCCA	60.224	45.455	0.00	0.00	0.00	3.41
1793	1820	4.379499	GGATTTGGTTCTCTCGCGAAAATT	60.379	41.667	11.33	0.00	0.00	1.82
1822	1849	4.259356	TGCAGAGATGAGAACCATGAAAG	58.741	43.478	0.00	0.00	35.17	2.62
1824	1851	4.624843	GCAGAGATGAGAACCATGAAAGGA	60.625	45.833	0.00	0.00	35.17	3.36
1831	1858	6.131972	TGAGAACCATGAAAGGAAAGATCT	57.868	37.500	0.00	0.00	0.00	2.75
1832	1859	6.546484	TGAGAACCATGAAAGGAAAGATCTT	58.454	36.000	0.88	0.88	0.00	2.40
1852	1879	9.354673	AGATCTTGAATAAGAAAACAGAAACCA	57.645	29.630	0.00	0.00	45.47	3.67
1858	1885	8.923270	TGAATAAGAAAACAGAAACCAAGGAAT	58.077	29.630	0.00	0.00	0.00	3.01
1913	1940	5.296780	TCTCGTCTTTTGTCATTCTTTGCTT	59.703	36.000	0.00	0.00	0.00	3.91
2117	2161	7.068839	GTGAATTAGAGAATAGACAGAGGTCCA	59.931	40.741	0.00	0.00	45.48	4.02
2156	2200	2.877154	TCTCCTTTCAGGGCCTATCT	57.123	50.000	5.28	0.00	35.59	1.98
2193	2237	4.762289	ACCTCTTGGTCCTGAATATCAC	57.238	45.455	0.00	0.00	44.78	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	4.769345	AGCTAGGATTTCCAGAAGAAGG	57.231	45.455	0.00	0.00	38.89	3.46
95	96	7.134163	CGAATATGCAAGCATAAGTTTCATGA	58.866	34.615	17.63	0.00	41.53	3.07
345	346	2.702748	GGAAGGCCTCCTAGGGATAAA	58.297	52.381	5.23	0.00	41.61	1.40
438	439	6.334102	ACGATCATAAGGAGTCCTATTGAC	57.666	41.667	20.65	14.92	44.82	3.18
512	513	5.843969	ACATAAGGGGTCATTTCTTGGTTTT	59.156	36.000	0.00	0.00	0.00	2.43
525	526	7.817418	TCTATAATTTTGCACATAAGGGGTC	57.183	36.000	0.00	0.00	0.00	4.46
579	580	7.610865	TCACACATACAGTCATACTCAATTCA	58.389	34.615	0.00	0.00	0.00	2.57
611	612	9.654663	GGTTCATTGATATTCCTGGTATAGTAC	57.345	37.037	0.00	0.00	0.00	2.73
647	648	5.450818	AAAGTGGGTATCCTGAGCAATTA	57.549	39.130	0.00	0.00	0.00	1.40
665	666	7.407393	AGAAATAGACCTACGAGCTAAAAGT	57.593	36.000	0.00	0.00	0.00	2.66
783	784	3.319122	TGATGATCGAGTCGATTCCATGT	59.681	43.478	27.65	9.35	47.00	3.21
834	835	5.527214	TCTCATAATAAGAATTGGCACGGTG	59.473	40.000	3.15	3.15	0.00	4.94
842	843	8.930846	ATGACCCCTTCTCATAATAAGAATTG	57.069	34.615	0.00	0.00	32.56	2.32
843	844	9.579932	GAATGACCCCTTCTCATAATAAGAATT	57.420	33.333	0.00	0.00	32.56	2.17
893	894	7.746703	AGGATGTAGGGATTTCTATGTAAACC	58.253	38.462	0.00	0.00	0.00	3.27
927	928	8.584063	TTACACCCATTCCTAAAATCCTAAAC	57.416	34.615	0.00	0.00	0.00	2.01
937	938	5.036916	AGGTCTGATTACACCCATTCCTAA	58.963	41.667	0.00	0.00	0.00	2.69
938	939	4.408921	CAGGTCTGATTACACCCATTCCTA	59.591	45.833	0.00	0.00	0.00	2.94
945	946	2.789409	AAGCAGGTCTGATTACACCC	57.211	50.000	0.00	0.00	37.44	4.61
1008	1009	5.684704	TCTCGATTCAATAGAAGCCCAAAT	58.315	37.500	0.00	0.00	36.84	2.32
1121	1134	1.469940	CGATCGGTCATATAGGCCTGC	60.470	57.143	17.99	0.00	40.99	4.85
1257	1270	2.596452	TGAGATTTTGAGTCTCGCGTC	58.404	47.619	5.77	0.00	43.95	5.19
1494	1507	8.058847	ACCATCTGCTTTGGGTTCTTTATTATA	58.941	33.333	5.37	0.00	38.64	0.98
1621	1638	5.462530	TCATAGTCACTTTTTCCTGTCGA	57.537	39.130	0.00	0.00	0.00	4.20
1668	1685	3.081061	TGCGCTCAAAGGATACAAACAT	58.919	40.909	9.73	0.00	41.41	2.71
1831	1858	8.299990	TCCTTGGTTTCTGTTTTCTTATTCAA	57.700	30.769	0.00	0.00	0.00	2.69
1832	1859	7.889873	TCCTTGGTTTCTGTTTTCTTATTCA	57.110	32.000	0.00	0.00	0.00	2.57
1852	1879	5.073144	TCACTCTTGTGGTTTCCTATTCCTT	59.927	40.000	0.00	0.00	43.94	3.36
1858	1885	4.654262	AGTCTTCACTCTTGTGGTTTCCTA	59.346	41.667	0.00	0.00	43.94	2.94
2156	2200	5.046304	CCAAGAGGTACTGGATTCTCTTTCA	60.046	44.000	6.98	0.00	42.56	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.