AutoCloner

Multiple sequence alignment - TraesCS1D01G315000

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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	TraesCS1D01G315000	chr1D	100.000	2180	0	0	485	2664	410472779	410470600	0.000000e+00	4026
1	TraesCS1D01G315000	chr1D	97.848	883	7	8	863	1741	410483031	410482157	0.000000e+00	1515
2	TraesCS1D01G315000	chr1D	87.597	1032	91	20	726	1741	410491377	410490367	0.000000e+00	1162
3	TraesCS1D01G315000	chr1D	100.000	244	0	0	1	244	410473263	410473020	4.040000e-123	451
4	TraesCS1D01G315000	chr1D	100.000	244	0	0	1	244	410483915	410483672	4.040000e-123	451
5	TraesCS1D01G315000	chr1D	100.000	219	0	0	485	703	410483260	410483042	3.190000e-109	405
6	TraesCS1D01G315000	chr1B	92.683	1517	61	16	727	2219	553025525	553024035	0.000000e+00	2141
7	TraesCS1D01G315000	chr1B	87.826	1035	90	21	730	1741	553136453	553135432	0.000000e+00	1181
8	TraesCS1D01G315000	chr1B	93.792	451	24	4	2217	2664	553023971	553023522	0.000000e+00	675
9	TraesCS1D01G315000	chr1B	80.101	397	41	17	1853	2219	341209213	341209601	7.310000e-66	261
10	TraesCS1D01G315000	chr1A	91.698	1060	44	16	727	1772	506309137	506308108	0.000000e+00	1430
11	TraesCS1D01G315000	chr1A	87.838	1036	92	19	727	1741	506493939	506492917	0.000000e+00	1184
12	TraesCS1D01G315000	chr1A	87.500	1040	87	20	726	1741	506474460	506473440	0.000000e+00	1160
13	TraesCS1D01G315000	chr1A	87.314	1009	98	20	726	1716	506489607	506488611	0.000000e+00	1127
14	TraesCS1D01G315000	chr1A	94.228	589	23	8	1192	1772	506288731	506288146	0.000000e+00	889
15	TraesCS1D01G315000	chr1A	89.296	710	52	14	1047	1741	506481145	506480445	0.000000e+00	869
16	TraesCS1D01G315000	chr1A	91.983	474	14	3	727	1195	506294537	506294083	0.000000e+00	643
17	TraesCS1D01G315000	chr1A	90.323	155	11	2	2510	2664	506287952	506287802	1.620000e-47	200
18	TraesCS1D01G315000	chr1A	90.323	155	11	2	2510	2664	506307914	506307764	1.620000e-47	200
19	TraesCS1D01G315000	chrUn	100.000	244	0	0	1	244	445057937	445057694	4.040000e-123	451
20	TraesCS1D01G315000	chrUn	77.778	396	51	22	1852	2219	259645361	259645747	2.690000e-50	209
21	TraesCS1D01G315000	chr2D	93.388	242	16	0	3	244	32773080	32773321	2.520000e-95	359
22	TraesCS1D01G315000	chr2D	79.293	396	48	20	1852	2219	628812291	628812680	2.050000e-61	246
23	TraesCS1D01G315000	chr3D	92.975	242	17	0	3	244	309692175	309691934	1.170000e-93	353
24	TraesCS1D01G315000	chr3D	80.556	396	41	14	1853	2219	141341903	141341515	3.380000e-69	272
25	TraesCS1D01G315000	chr3D	79.851	402	45	15	1847	2219	120722752	120723146	7.310000e-66	261
26	TraesCS1D01G315000	chr7A	90.535	243	14	6	3	244	162874441	162874675	1.990000e-81	313
27	TraesCS1D01G315000	chr7A	86.831	243	29	3	3	244	28172662	28172902	4.370000e-68	268
28	TraesCS1D01G315000	chr7A	78.392	398	48	21	1851	2217	619562907	619562517	9.600000e-55	224
29	TraesCS1D01G315000	chr6D	80.051	396	43	14	1853	2219	6891519	6891131	7.310000e-66	261
30	TraesCS1D01G315000	chr7D	79.597	397	47	20	1851	2219	150630	150240	1.220000e-63	254
31	TraesCS1D01G315000	chr7D	79.345	397	48	20	1851	2219	264965223	264964833	5.690000e-62	248
32	TraesCS1D01G315000	chr7D	79.093	397	49	20	1851	2219	264960583	264960193	2.650000e-60	243
33	TraesCS1D01G315000	chr6A	79.093	397	49	20	1851	2219	391448617	391448227	2.650000e-60	243
34	TraesCS1D01G315000	chr6A	78.841	397	46	14	1851	2217	270784117	270783729	1.590000e-57	233
35	TraesCS1D01G315000	chr6A	77.273	242	50	4	3	239	382506792	382507033	1.290000e-28	137
36	TraesCS1D01G315000	chr4A	79.255	376	42	16	1874	2219	52646625	52646994	2.060000e-56	230
37	TraesCS1D01G315000	chr5A	78.338	397	48	16	1851	2217	44929253	44928865	3.450000e-54	222
38	TraesCS1D01G315000	chr5A	78.086	397	49	14	1851	2217	119077254	119076866	1.610000e-52	217
39	TraesCS1D01G315000	chr3B	79.204	226	29	9	24	244	7331359	7331571	9.940000e-30	141
40	TraesCS1D01G315000	chr6B	81.955	133	22	2	7	137	416605795	416605663	7.800000e-21	111

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	TraesCS1D01G315000	chr1D	410470600	410473263	2663	True	2238.500000	4026	100.000000	1	2664	2	chr1D.!!$R2	2663
1	TraesCS1D01G315000	chr1D	410490367	410491377	1010	True	1162.000000	1162	87.597000	726	1741	1	chr1D.!!$R1	1015
2	TraesCS1D01G315000	chr1D	410482157	410483915	1758	True	790.333333	1515	99.282667	1	1741	3	chr1D.!!$R3	1740
3	TraesCS1D01G315000	chr1B	553023522	553025525	2003	True	1408.000000	2141	93.237500	727	2664	2	chr1B.!!$R2	1937
4	TraesCS1D01G315000	chr1B	553135432	553136453	1021	True	1181.000000	1181	87.826000	730	1741	1	chr1B.!!$R1	1011
5	TraesCS1D01G315000	chr1A	506473440	506474460	1020	True	1160.000000	1160	87.500000	726	1741	1	chr1A.!!$R2	1015
6	TraesCS1D01G315000	chr1A	506488611	506493939	5328	True	1155.500000	1184	87.576000	726	1741	2	chr1A.!!$R6	1015
7	TraesCS1D01G315000	chr1A	506480445	506481145	700	True	869.000000	869	89.296000	1047	1741	1	chr1A.!!$R3	694
8	TraesCS1D01G315000	chr1A	506307764	506309137	1373	True	815.000000	1430	91.010500	727	2664	2	chr1A.!!$R5	1937
9	TraesCS1D01G315000	chr1A	506287802	506288731	929	True	544.500000	889	92.275500	1192	2664	2	chr1A.!!$R4	1472

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
709	881	0.034896	CACCAACTACTCGCTGGGTT	59.965	55.0	0.0	0.0	32.98	4.11	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1671	1896	0.17576	AAGAGAATCCGCAGCGCTAA	59.824	50.0	10.99	0.0	33.66	3.09	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
703	875	1.369625	CCATTCCACCAACTACTCGC	58.630	55.000	0.00	0.00	0.00	5.03
704	876	1.066143	CCATTCCACCAACTACTCGCT	60.066	52.381	0.00	0.00	0.00	4.93
705	877	2.002586	CATTCCACCAACTACTCGCTG	58.997	52.381	0.00	0.00	0.00	5.18
706	878	0.320374	TTCCACCAACTACTCGCTGG	59.680	55.000	0.00	0.00	34.93	4.85
707	879	1.079127	CCACCAACTACTCGCTGGG	60.079	63.158	0.00	0.00	32.98	4.45
708	880	1.671742	CACCAACTACTCGCTGGGT	59.328	57.895	0.00	0.00	32.98	4.51
709	881	0.034896	CACCAACTACTCGCTGGGTT	59.965	55.000	0.00	0.00	32.98	4.11
710	882	0.320697	ACCAACTACTCGCTGGGTTC	59.679	55.000	0.00	0.00	32.98	3.62
711	883	0.320374	CCAACTACTCGCTGGGTTCA	59.680	55.000	0.00	0.00	0.00	3.18
712	884	1.429463	CAACTACTCGCTGGGTTCAC	58.571	55.000	0.00	0.00	0.00	3.18
713	885	1.000955	CAACTACTCGCTGGGTTCACT	59.999	52.381	0.00	0.00	0.00	3.41
714	886	2.211250	ACTACTCGCTGGGTTCACTA	57.789	50.000	0.00	0.00	0.00	2.74
715	887	2.736347	ACTACTCGCTGGGTTCACTAT	58.264	47.619	0.00	0.00	0.00	2.12
716	888	3.097614	ACTACTCGCTGGGTTCACTATT	58.902	45.455	0.00	0.00	0.00	1.73
717	889	2.386661	ACTCGCTGGGTTCACTATTG	57.613	50.000	0.00	0.00	0.00	1.90
718	890	1.066143	ACTCGCTGGGTTCACTATTGG	60.066	52.381	0.00	0.00	0.00	3.16
719	891	0.251916	TCGCTGGGTTCACTATTGGG	59.748	55.000	0.00	0.00	0.00	4.12
720	892	0.035439	CGCTGGGTTCACTATTGGGT	60.035	55.000	0.00	0.00	0.00	4.51
721	893	1.463674	GCTGGGTTCACTATTGGGTG	58.536	55.000	0.00	0.00	38.44	4.61
722	894	1.004277	GCTGGGTTCACTATTGGGTGA	59.996	52.381	0.00	0.00	43.41	4.02
723	895	2.941415	GCTGGGTTCACTATTGGGTGAG	60.941	54.545	0.00	0.00	45.29	3.51
724	896	2.571653	CTGGGTTCACTATTGGGTGAGA	59.428	50.000	0.00	0.00	45.29	3.27
758	930	2.420043	GCGAGTTATGGCGCCCTA	59.580	61.111	26.77	16.85	46.93	3.53
764	938	0.754472	GTTATGGCGCCCTAGGTGTA	59.246	55.000	26.77	1.65	35.34	2.90
1671	1896	6.350277	CCCTTCGTCAACATCTAAGACTACTT	60.350	42.308	0.00	0.00	39.81	2.24
1751	1984	5.351233	TGTAGCCACGTTTATGTCAAAAG	57.649	39.130	0.00	0.00	0.00	2.27
1752	1985	5.057819	TGTAGCCACGTTTATGTCAAAAGA	58.942	37.500	0.00	0.00	0.00	2.52
1753	1986	5.527951	TGTAGCCACGTTTATGTCAAAAGAA	59.472	36.000	0.00	0.00	0.00	2.52
1955	2798	6.548622	CCATGTTGAAGGACCAATCTCATAAT	59.451	38.462	0.00	0.00	0.00	1.28
1996	2839	8.567948	CATACTGAAACACTTACCAAAATCTGT	58.432	33.333	0.00	0.00	0.00	3.41
2000	2843	8.006298	TGAAACACTTACCAAAATCTGTCAAT	57.994	30.769	0.00	0.00	0.00	2.57
2033	2876	1.672356	AGAATGCGGACAGTGTGGC	60.672	57.895	0.00	4.55	0.00	5.01
2253	3867	4.102210	TGGTGCTTCCAAATTCCAAATTGA	59.898	37.500	0.00	0.00	44.12	2.57
2307	3921	5.845953	CACGAATAATAGCTATTTGTTGGCG	59.154	40.000	23.47	18.52	41.07	5.69
2365	3984	2.159254	GGTTACATCATGCGGCATGTTT	60.159	45.455	34.49	23.43	41.98	2.83
2387	4006	0.527113	TCATGGCTTGTTTGCGATGG	59.473	50.000	10.56	0.00	45.15	3.51
2388	4007	1.079875	CATGGCTTGTTTGCGATGGC	61.080	55.000	0.00	0.00	42.68	4.40
2402	4021	1.772836	GATGGCCATCTTTGGAAGCT	58.227	50.000	34.20	2.13	46.92	3.74
2418	4037	3.119708	GGAAGCTCCTAATGTTTGCACTG	60.120	47.826	0.00	0.00	32.53	3.66
2426	4045	5.412594	TCCTAATGTTTGCACTGATCAAGTC	59.587	40.000	0.00	0.00	36.83	3.01
2449	4069	0.737219	GCATGCTACTGCTCCCTTTG	59.263	55.000	11.37	0.00	39.12	2.77
2451	4071	1.741706	CATGCTACTGCTCCCTTTGTG	59.258	52.381	0.00	0.00	40.48	3.33
2471	4091	7.615582	TTGTGGTCAAATCATTAGCTCTAAG	57.384	36.000	0.00	0.00	0.00	2.18
2472	4092	5.586243	TGTGGTCAAATCATTAGCTCTAAGC	59.414	40.000	0.00	0.00	42.84	3.09
2485	4106	2.546162	GCTCTAAGCTACCGGGATTCAC	60.546	54.545	6.32	0.00	38.45	3.18
2515	4136	8.723942	TGCTCTTTTATCTTATGGAGTTTCTC	57.276	34.615	0.00	0.00	0.00	2.87
2596	4330	6.096001	GCTGATAAAGAAACATCCAGGTTCAT	59.904	38.462	0.00	0.00	46.70	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
703	875	2.571653	TCTCACCCAATAGTGAACCCAG	59.428	50.000	0.00	0.00	45.77	4.45
704	876	2.571653	CTCTCACCCAATAGTGAACCCA	59.428	50.000	0.00	0.00	45.77	4.51
705	877	2.681097	GCTCTCACCCAATAGTGAACCC	60.681	54.545	0.00	0.00	45.77	4.11
706	878	2.027192	TGCTCTCACCCAATAGTGAACC	60.027	50.000	0.00	0.00	45.77	3.62
707	879	3.003480	GTGCTCTCACCCAATAGTGAAC	58.997	50.000	0.00	0.00	45.77	3.18
708	880	2.906389	AGTGCTCTCACCCAATAGTGAA	59.094	45.455	0.00	0.00	45.77	3.18
709	881	2.540383	AGTGCTCTCACCCAATAGTGA	58.460	47.619	0.00	0.00	44.16	3.41
710	882	3.340814	AAGTGCTCTCACCCAATAGTG	57.659	47.619	0.00	0.00	44.16	2.74
711	883	4.373156	AAAAGTGCTCTCACCCAATAGT	57.627	40.909	0.00	0.00	44.16	2.12
712	884	4.082571	CCAAAAAGTGCTCTCACCCAATAG	60.083	45.833	0.00	0.00	44.16	1.73
713	885	3.826157	CCAAAAAGTGCTCTCACCCAATA	59.174	43.478	0.00	0.00	44.16	1.90
714	886	2.629617	CCAAAAAGTGCTCTCACCCAAT	59.370	45.455	0.00	0.00	44.16	3.16
715	887	2.031120	CCAAAAAGTGCTCTCACCCAA	58.969	47.619	0.00	0.00	44.16	4.12
716	888	1.691196	CCAAAAAGTGCTCTCACCCA	58.309	50.000	0.00	0.00	44.16	4.51
717	889	0.315251	GCCAAAAAGTGCTCTCACCC	59.685	55.000	0.00	0.00	44.16	4.61
718	890	0.040067	CGCCAAAAAGTGCTCTCACC	60.040	55.000	0.00	0.00	44.16	4.02
719	891	0.944386	TCGCCAAAAAGTGCTCTCAC	59.056	50.000	0.00	0.00	43.44	3.51
720	892	1.202639	TCTCGCCAAAAAGTGCTCTCA	60.203	47.619	0.00	0.00	0.00	3.27
721	893	1.462670	CTCTCGCCAAAAAGTGCTCTC	59.537	52.381	0.00	0.00	0.00	3.20
722	894	1.517242	CTCTCGCCAAAAAGTGCTCT	58.483	50.000	0.00	0.00	0.00	4.09
723	895	0.110010	GCTCTCGCCAAAAAGTGCTC	60.110	55.000	0.00	0.00	0.00	4.26
724	896	1.845809	CGCTCTCGCCAAAAAGTGCT	61.846	55.000	0.00	0.00	31.54	4.40
755	927	1.741706	ACATCGACGTGTACACCTAGG	59.258	52.381	20.11	7.41	0.00	3.02
757	929	2.417586	CTCACATCGACGTGTACACCTA	59.582	50.000	20.11	3.74	38.12	3.08
758	930	1.199327	CTCACATCGACGTGTACACCT	59.801	52.381	20.11	8.88	38.12	4.00
764	938	2.261671	GGGCTCACATCGACGTGT	59.738	61.111	11.85	0.00	38.12	4.49
1671	1896	0.175760	AAGAGAATCCGCAGCGCTAA	59.824	50.000	10.99	0.00	33.66	3.09
1751	1984	1.851658	ACGTGGCTGCAACATTTTTC	58.148	45.000	8.09	0.00	0.00	2.29
1752	1985	1.932511	CAACGTGGCTGCAACATTTTT	59.067	42.857	8.09	0.00	0.00	1.94
1753	1986	1.569708	CAACGTGGCTGCAACATTTT	58.430	45.000	8.09	0.00	0.00	1.82
1788	2021	5.748402	TGAGATTTACAGATTGCCATCACT	58.252	37.500	0.01	0.00	0.00	3.41
1860	2699	8.504812	AAGTTGTTTGAGTGGCATTTATTTTT	57.495	26.923	0.00	0.00	0.00	1.94
1861	2700	8.504812	AAAGTTGTTTGAGTGGCATTTATTTT	57.495	26.923	0.00	0.00	0.00	1.82
1865	2704	6.214191	TGAAAGTTGTTTGAGTGGCATTTA	57.786	33.333	0.00	0.00	0.00	1.40
1868	2707	4.160252	ACTTGAAAGTTGTTTGAGTGGCAT	59.840	37.500	0.00	0.00	35.21	4.40
1869	2708	3.509575	ACTTGAAAGTTGTTTGAGTGGCA	59.490	39.130	0.00	0.00	35.21	4.92
1870	2709	4.110036	ACTTGAAAGTTGTTTGAGTGGC	57.890	40.909	0.00	0.00	35.21	5.01
1912	2755	5.509498	ACATGGCATAGACAATGTACCTTT	58.491	37.500	0.00	0.00	37.93	3.11
1919	2762	4.641541	TCCTTCAACATGGCATAGACAATG	59.358	41.667	0.00	0.00	38.74	2.82
1925	2768	3.003394	TGGTCCTTCAACATGGCATAG	57.997	47.619	0.00	0.00	0.00	2.23
2000	2843	9.168451	TGTCCGCATTCTGTTTTATATAGAAAA	57.832	29.630	1.14	1.14	37.50	2.29
2007	2850	5.121611	CACACTGTCCGCATTCTGTTTTATA	59.878	40.000	0.00	0.00	0.00	0.98
2033	2876	2.543848	TGCTCAAACTGCAACTTCGTAG	59.456	45.455	0.00	0.00	37.51	3.51
2047	2890	5.945191	TCAGAATATGTTGGTGATGCTCAAA	59.055	36.000	0.00	0.00	0.00	2.69
2061	2904	7.448161	TGTTCCATCAACAACTTCAGAATATGT	59.552	33.333	0.00	0.00	42.35	2.29
2109	2959	1.741327	GATGGCCACCATGGTGATGC	61.741	60.000	40.60	33.90	45.26	3.91
2253	3867	8.950210	GTATTAGGTTGCATCAACATAGCATAT	58.050	33.333	11.22	2.90	45.11	1.78
2298	3912	1.899534	GGTAGGGCACGCCAACAAA	60.900	57.895	10.83	0.00	37.98	2.83
2307	3921	0.392998	CACAGATGGTGGTAGGGCAC	60.393	60.000	0.00	0.00	44.04	5.01
2365	3984	1.028130	TCGCAAACAAGCCATGACAA	58.972	45.000	0.00	0.00	0.00	3.18
2402	4021	5.316167	ACTTGATCAGTGCAAACATTAGGA	58.684	37.500	0.00	0.00	32.83	2.94
2418	4037	0.875908	TAGCATGCGCGGACTTGATC	60.876	55.000	13.01	0.00	45.49	2.92
2449	4069	6.054035	GCTTAGAGCTAATGATTTGACCAC	57.946	41.667	0.00	0.00	38.45	4.16
2471	4091	2.607187	CATATCGTGAATCCCGGTAGC	58.393	52.381	0.00	0.00	0.00	3.58
2472	4092	2.231478	AGCATATCGTGAATCCCGGTAG	59.769	50.000	0.00	0.00	0.00	3.18
2473	4093	2.230508	GAGCATATCGTGAATCCCGGTA	59.769	50.000	0.00	0.00	0.00	4.02
2474	4094	1.000955	GAGCATATCGTGAATCCCGGT	59.999	52.381	0.00	0.00	0.00	5.28
2485	4106	8.994429	ACTCCATAAGATAAAAGAGCATATCG	57.006	34.615	0.00	0.00	34.45	2.92
2515	4136	6.040391	TCCAACTCCAAAAACATAACTGGAAG	59.960	38.462	0.00	0.00	37.51	3.46

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.