AutoCloner

Multiple sequence alignment - TraesCS7A01G137600

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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	TraesCS7A01G137600	chr7A	100.000	2519	0	0	1	2519	90228013	90225495	0.000000e+00	4652.0
1	TraesCS7A01G137600	chr7D	93.082	1113	60	3	928	2040	88879753	88878658	0.000000e+00	1613.0
2	TraesCS7A01G137600	chr7D	93.505	739	48	0	1	739	506893419	506892681	0.000000e+00	1099.0
3	TraesCS7A01G137600	chr7D	96.868	479	12	1	2043	2518	88878604	88878126	0.000000e+00	798.0
4	TraesCS7A01G137600	chr7D	89.934	457	42	4	2048	2501	88183881	88183426	1.000000e-163	586.0
5	TraesCS7A01G137600	chr7D	90.576	191	18	0	2315	2505	88319353	88319163	1.160000e-63	254.0
6	TraesCS7A01G137600	chr7D	76.104	385	71	18	2048	2423	88457061	88457433	5.540000e-42	182.0
7	TraesCS7A01G137600	chr7D	78.302	106	19	3	1732	1836	88339441	88339339	5.820000e-07	65.8
8	TraesCS7A01G137600	chr7B	92.315	1119	78	3	929	2045	39172572	39171460	0.000000e+00	1583.0
9	TraesCS7A01G137600	chr7B	91.075	930	56	4	1	929	56450499	56449596	0.000000e+00	1232.0
10	TraesCS7A01G137600	chr7B	95.359	474	22	0	2046	2519	39171409	39170936	0.000000e+00	754.0
11	TraesCS7A01G137600	chr7B	89.588	461	41	6	2048	2504	37845555	37845098	1.680000e-161	579.0
12	TraesCS7A01G137600	chr7B	83.105	438	66	6	2048	2483	38443165	38442734	2.350000e-105	392.0
13	TraesCS7A01G137600	chr7B	91.146	192	17	0	2314	2505	38374190	38373999	6.910000e-66	261.0
14	TraesCS7A01G137600	chr7B	85.185	243	34	2	2051	2291	38374427	38374185	5.380000e-62	248.0
15	TraesCS7A01G137600	chr1D	92.565	928	59	2	1	928	40317922	40317005	0.000000e+00	1323.0
16	TraesCS7A01G137600	chr1D	93.579	732	47	0	1	732	40236863	40236132	0.000000e+00	1092.0
17	TraesCS7A01G137600	chr4B	91.622	931	68	7	1	928	97875110	97874187	0.000000e+00	1279.0
18	TraesCS7A01G137600	chr4B	91.006	934	72	10	1	928	97786540	97785613	0.000000e+00	1249.0
19	TraesCS7A01G137600	chr3B	91.738	932	45	12	1	929	826277837	826278739	0.000000e+00	1266.0
20	TraesCS7A01G137600	chr3D	88.267	929	51	22	1	928	18363376	18362505	0.000000e+00	1059.0
21	TraesCS7A01G137600	chr4A	92.308	338	22	2	1	335	542557250	542556914	6.300000e-131	477.0
22	TraesCS7A01G137600	chr4A	87.108	287	17	8	642	928	542556885	542556619	8.750000e-80	307.0
23	TraesCS7A01G137600	chr4A	89.730	185	18	1	260	444	542557066	542556883	4.190000e-58	235.0
24	TraesCS7A01G137600	chr2B	96.429	84	3	0	845	928	322644316	322644399	3.380000e-29	139.0
25	TraesCS7A01G137600	chr2B	94.048	84	5	0	845	928	322463308	322463225	7.310000e-26	128.0

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	TraesCS7A01G137600	chr7A	90225495	90228013	2518	True	4652.000000	4652	100.000000	1	2519	1	chr7A.!!$R1	2518
1	TraesCS7A01G137600	chr7D	88878126	88879753	1627	True	1205.500000	1613	94.975000	928	2518	2	chr7D.!!$R5	1590
2	TraesCS7A01G137600	chr7D	506892681	506893419	738	True	1099.000000	1099	93.505000	1	739	1	chr7D.!!$R4	738
3	TraesCS7A01G137600	chr7B	56449596	56450499	903	True	1232.000000	1232	91.075000	1	929	1	chr7B.!!$R3	928
4	TraesCS7A01G137600	chr7B	39170936	39172572	1636	True	1168.500000	1583	93.837000	929	2519	2	chr7B.!!$R5	1590
5	TraesCS7A01G137600	chr1D	40317005	40317922	917	True	1323.000000	1323	92.565000	1	928	1	chr1D.!!$R2	927
6	TraesCS7A01G137600	chr1D	40236132	40236863	731	True	1092.000000	1092	93.579000	1	732	1	chr1D.!!$R1	731
7	TraesCS7A01G137600	chr4B	97874187	97875110	923	True	1279.000000	1279	91.622000	1	928	1	chr4B.!!$R2	927
8	TraesCS7A01G137600	chr4B	97785613	97786540	927	True	1249.000000	1249	91.006000	1	928	1	chr4B.!!$R1	927
9	TraesCS7A01G137600	chr3B	826277837	826278739	902	False	1266.000000	1266	91.738000	1	929	1	chr3B.!!$F1	928
10	TraesCS7A01G137600	chr3D	18362505	18363376	871	True	1059.000000	1059	88.267000	1	928	1	chr3D.!!$R1	927
11	TraesCS7A01G137600	chr4A	542556619	542557250	631	True	339.666667	477	89.715333	1	928	3	chr4A.!!$R1	927

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
729	735	0.179145	CGTCTGGGTATTCTTCGCGT	60.179	55.0	5.77	0.0	0.0	6.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2128	2226	0.179161	GCGTGACGATGCACTCTAGT	60.179	55.0	10.1	0.0	36.65	2.57	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
68	70	1.270465	CCTCAAAGCCTTTTTGCCCAG	60.270	52.381	0.00	0.00	0.00	4.45
195	198	6.040616	ACGAGTAAGGGGATTGTAGAAGTATG	59.959	42.308	0.00	0.00	0.00	2.39
253	256	5.793817	TGTTCAGACTTGTATATGTGCAGT	58.206	37.500	0.00	0.00	0.00	4.40
367	370	8.474025	AGACCTATCACTGAACTATTGAGAAAG	58.526	37.037	0.00	0.00	0.00	2.62
455	458	1.269174	TGGATTGTGTTGGCATGTTCG	59.731	47.619	0.00	0.00	0.00	3.95
480	483	1.089920	CTCGGTTGCTTCTTCCATGG	58.910	55.000	4.97	4.97	0.00	3.66
499	505	5.449588	CCATGGGAGAAAAGATGTTTGATCG	60.450	44.000	2.85	0.00	0.00	3.69
510	516	6.618287	AGATGTTTGATCGAGTTCAACAAA	57.382	33.333	0.95	0.00	35.42	2.83
544	550	7.591006	CCATGAGAAAAATGGAAACTTGATG	57.409	36.000	0.00	0.00	46.44	3.07
566	572	3.149196	GAGTTCCAAAGCAACCTGATGA	58.851	45.455	0.00	0.00	0.00	2.92
572	578	2.134789	AAGCAACCTGATGATGGACC	57.865	50.000	0.00	0.00	0.00	4.46
611	617	7.944061	AGTGTTTTCATTCATGTGAAAGATGA	58.056	30.769	10.36	0.00	45.77	2.92
674	680	4.021925	GAGCAGGGCGTCCACCTT	62.022	66.667	9.71	0.00	35.78	3.50
720	726	3.849951	CTGGCGCCGTCTGGGTAT	61.850	66.667	23.90	0.00	38.44	2.73
729	735	0.179145	CGTCTGGGTATTCTTCGCGT	60.179	55.000	5.77	0.00	0.00	6.01
756	783	1.671379	GTCTCCTCGCGCCCTTTTT	60.671	57.895	0.00	0.00	0.00	1.94
765	792	2.035783	GCCCTTTTTCCCCTCGCT	59.964	61.111	0.00	0.00	0.00	4.93
792	819	4.060038	CGGTTCGTAGTGGGCCGT	62.060	66.667	0.00	0.00	37.87	5.68
794	821	1.140375	GGTTCGTAGTGGGCCGTAG	59.860	63.158	0.00	0.00	0.00	3.51
840	867	3.248495	TGAGCAAATCAGAGAGAGCTG	57.752	47.619	0.00	0.00	37.24	4.24
841	868	2.093606	TGAGCAAATCAGAGAGAGCTGG	60.094	50.000	0.00	0.00	36.55	4.85
842	869	2.168106	GAGCAAATCAGAGAGAGCTGGA	59.832	50.000	0.00	0.00	36.55	3.86
843	870	2.570752	AGCAAATCAGAGAGAGCTGGAA	59.429	45.455	0.00	0.00	36.55	3.53
1086	1124	3.267860	CTCTTGCTGATCGCCGCC	61.268	66.667	7.00	0.00	38.05	6.13
1114	1152	3.760035	CCTCGTCCCTGACCACCG	61.760	72.222	0.00	0.00	0.00	4.94
1116	1154	2.203523	TCGTCCCTGACCACCGAA	60.204	61.111	0.00	0.00	0.00	4.30
1125	1163	2.027625	GACCACCGAAGCCGAAGTG	61.028	63.158	0.00	0.00	38.22	3.16
1126	1164	3.423154	CCACCGAAGCCGAAGTGC	61.423	66.667	0.00	0.00	38.22	4.40
1288	1326	3.689002	CTCCCCGCCTTCTTCTGCC	62.689	68.421	0.00	0.00	0.00	4.85
1518	1556	2.095750	CGAATCCGACGGAGAGTGA	58.904	57.895	22.99	0.00	38.22	3.41
1644	1682	2.222027	CAGGATAAGAAATCGGTGGCC	58.778	52.381	0.00	0.00	0.00	5.36
1668	1706	2.250190	GTGTACAAACACGGCGCC	59.750	61.111	19.07	19.07	46.11	6.53
1678	1716	4.444838	ACGGCGCCGCAGTTGATA	62.445	61.111	46.22	0.00	44.19	2.15
1686	1724	0.600255	CCGCAGTTGATATCCGGACC	60.600	60.000	6.12	0.00	41.34	4.46
1753	1800	3.737172	GCGCATCACCACCACCAC	61.737	66.667	0.30	0.00	0.00	4.16
1754	1801	3.055719	CGCATCACCACCACCACC	61.056	66.667	0.00	0.00	0.00	4.61
1781	1828	3.607741	CTTCTCCTCGTACTACTGGTGA	58.392	50.000	0.00	0.00	0.00	4.02
1782	1829	3.928005	TCTCCTCGTACTACTGGTGAT	57.072	47.619	0.00	0.00	0.00	3.06
1839	1886	7.136822	TGTCCAATTAGCACATACTCCTTAT	57.863	36.000	0.00	0.00	0.00	1.73
1841	1888	7.715249	TGTCCAATTAGCACATACTCCTTATTC	59.285	37.037	0.00	0.00	0.00	1.75
1871	1918	3.113745	CGCCAGGCATGAATCCAC	58.886	61.111	13.30	0.00	0.00	4.02
1881	1928	2.680805	GCATGAATCCACCGGAAGAGAA	60.681	50.000	9.46	0.00	34.34	2.87
1882	1929	3.201290	CATGAATCCACCGGAAGAGAAG	58.799	50.000	9.46	0.00	34.34	2.85
1891	1938	1.153469	GGAAGAGAAGGCGGCAGAG	60.153	63.158	13.08	0.00	0.00	3.35
1956	2003	3.045634	TGTCTGGGAAGAAGAGGAAACA	58.954	45.455	0.00	0.00	0.00	2.83
1985	2032	3.767278	ACCGCTATTGTAGAAGACGAAC	58.233	45.455	0.00	0.00	0.00	3.95
1993	2040	1.126296	GTAGAAGACGAACTTTGCCGC	59.874	52.381	0.00	0.00	39.13	6.53
1996	2043	0.531974	AAGACGAACTTTGCCGCTCA	60.532	50.000	0.00	0.00	34.94	4.26
1997	2044	0.946221	AGACGAACTTTGCCGCTCAG	60.946	55.000	0.00	0.00	0.00	3.35
2041	2088	2.438434	CCACCGGGATTGTCTGGC	60.438	66.667	6.32	0.00	36.66	4.85
2077	2175	2.740055	CCACAGCACTCGCCTGTC	60.740	66.667	0.00	0.00	39.83	3.51
2128	2226	1.183549	GGAAGGTCTCGCAGAAGGTA	58.816	55.000	0.00	0.00	34.09	3.08
2505	2606	3.423154	CGGTGAAGCGGGCAACTC	61.423	66.667	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
68	70	4.703897	TGGTCATATTGGCTTAGCTACAC	58.296	43.478	3.59	0.00	0.00	2.90
195	198	6.969828	ACCAAATTTCTCGATAGTTCAGTC	57.030	37.500	0.00	0.00	37.40	3.51
367	370	7.923344	AGTCTGCACATAGTCAGATTTACATAC	59.077	37.037	0.00	0.00	40.89	2.39
438	441	1.269448	GGACGAACATGCCAACACAAT	59.731	47.619	0.00	0.00	0.00	2.71
439	442	0.665835	GGACGAACATGCCAACACAA	59.334	50.000	0.00	0.00	0.00	3.33
455	458	2.003301	GAAGAAGCAACCGAGATGGAC	58.997	52.381	0.00	0.00	42.00	4.02
480	483	6.147821	TGAACTCGATCAAACATCTTTTCTCC	59.852	38.462	0.00	0.00	0.00	3.71
499	505	6.377327	TGGAAGAATCAGTTTGTTGAACTC	57.623	37.500	0.00	0.00	45.40	3.01
510	516	6.950041	TCCATTTTTCTCATGGAAGAATCAGT	59.050	34.615	0.00	0.00	46.06	3.41
544	550	1.981256	TCAGGTTGCTTTGGAACTCC	58.019	50.000	2.34	0.00	0.00	3.85
566	572	3.769844	ACTACAACTGATCGAAGGTCCAT	59.230	43.478	0.00	0.00	0.00	3.41
572	578	6.525121	TGAAAACACTACAACTGATCGAAG	57.475	37.500	0.00	0.00	0.00	3.79
611	617	4.832266	CCTAATACTCTGCTCCTCTCATGT	59.168	45.833	0.00	0.00	0.00	3.21
674	680	3.280634	GAGATCGCCGGAGCTCGA	61.281	66.667	5.05	4.62	44.84	4.04
720	726	3.454375	AGACAGAAAAAGACGCGAAGAA	58.546	40.909	15.93	0.00	0.00	2.52
729	735	1.935300	GCGCGAGGAGACAGAAAAAGA	60.935	52.381	12.10	0.00	0.00	2.52
765	792	2.203972	CTACGAACCGAGGGACGCAA	62.204	60.000	9.30	0.25	41.07	4.85
792	819	1.602323	CAAAACCAGCGGCCCACTA	60.602	57.895	0.00	0.00	0.00	2.74
794	821	3.989787	CCAAAACCAGCGGCCCAC	61.990	66.667	0.00	0.00	0.00	4.61
804	831	1.200948	GCTCAGATCAGCACCAAAACC	59.799	52.381	0.00	0.00	39.43	3.27
837	864	2.866085	ATCAGACGGCAGCTTCCAGC	62.866	60.000	2.54	0.00	42.84	4.85
838	865	1.088340	CATCAGACGGCAGCTTCCAG	61.088	60.000	2.54	0.00	0.00	3.86
839	866	1.078918	CATCAGACGGCAGCTTCCA	60.079	57.895	2.54	0.00	0.00	3.53
840	867	1.817099	CCATCAGACGGCAGCTTCC	60.817	63.158	0.00	0.00	0.00	3.46
841	868	0.674895	AACCATCAGACGGCAGCTTC	60.675	55.000	0.00	0.00	0.00	3.86
842	869	0.957395	CAACCATCAGACGGCAGCTT	60.957	55.000	0.00	0.00	0.00	3.74
843	870	1.376424	CAACCATCAGACGGCAGCT	60.376	57.895	0.00	0.00	0.00	4.24
1086	1124	2.876645	GACGAGGTGAAGCGCTCG	60.877	66.667	12.06	12.16	40.89	5.03
1114	1152	3.435186	GGCCTGCACTTCGGCTTC	61.435	66.667	13.78	0.00	45.57	3.86
1274	1312	1.743252	GTCTGGCAGAAGAAGGCGG	60.743	63.158	20.62	0.00	39.11	6.13
1277	1315	3.882025	GCGTCTGGCAGAAGAAGG	58.118	61.111	30.39	13.84	42.87	3.46
1288	1326	1.153939	CGAAGTGGGAGAGCGTCTG	60.154	63.158	0.00	0.00	0.00	3.51
1410	1448	1.929836	CTTCGGAGCGAGAAGAAATGG	59.070	52.381	11.64	0.00	45.78	3.16
1518	1556	4.163458	GTCAGGAAGAAAAACCCCCTTTTT	59.837	41.667	0.00	0.00	43.50	1.94
1668	1706	0.389391	AGGTCCGGATATCAACTGCG	59.611	55.000	7.81	0.00	0.00	5.18
1746	1793	3.637273	GAAGGCGGAGGTGGTGGT	61.637	66.667	0.00	0.00	0.00	4.16
1747	1794	3.316573	GAGAAGGCGGAGGTGGTGG	62.317	68.421	0.00	0.00	0.00	4.61
1748	1795	2.266055	GAGAAGGCGGAGGTGGTG	59.734	66.667	0.00	0.00	0.00	4.17
1749	1796	3.003763	GGAGAAGGCGGAGGTGGT	61.004	66.667	0.00	0.00	0.00	4.16
1750	1797	2.685380	AGGAGAAGGCGGAGGTGG	60.685	66.667	0.00	0.00	0.00	4.61
1751	1798	2.896443	GAGGAGAAGGCGGAGGTG	59.104	66.667	0.00	0.00	0.00	4.00
1752	1799	2.207501	TACGAGGAGAAGGCGGAGGT	62.208	60.000	0.00	0.00	0.00	3.85
1753	1800	1.453379	TACGAGGAGAAGGCGGAGG	60.453	63.158	0.00	0.00	0.00	4.30
1754	1801	0.748729	AGTACGAGGAGAAGGCGGAG	60.749	60.000	0.00	0.00	0.00	4.63
1781	1828	0.749091	GGGGGCGCGTTTACCTTTAT	60.749	55.000	8.43	0.00	0.00	1.40
1782	1829	1.377072	GGGGGCGCGTTTACCTTTA	60.377	57.895	8.43	0.00	0.00	1.85
1839	1886	0.821301	TGGCGCATGAACCACAAGAA	60.821	50.000	10.83	0.00	0.00	2.52
1841	1888	1.210931	CTGGCGCATGAACCACAAG	59.789	57.895	10.83	0.00	0.00	3.16
1864	1911	1.744114	GCCTTCTCTTCCGGTGGATTC	60.744	57.143	0.00	0.00	0.00	2.52
1865	1912	0.253327	GCCTTCTCTTCCGGTGGATT	59.747	55.000	0.00	0.00	0.00	3.01
1871	1918	4.082523	TGCCGCCTTCTCTTCCGG	62.083	66.667	0.00	0.00	43.38	5.14
1891	1938	0.666577	CCGTGTTCACCTTCTCGGTC	60.667	60.000	0.00	0.00	44.93	4.79
1896	1943	1.371558	GGCTCCGTGTTCACCTTCT	59.628	57.895	0.00	0.00	0.00	2.85
1929	1976	1.291877	CTTCTTCCCAGACAACGGCG	61.292	60.000	4.80	4.80	0.00	6.46
1942	1989	1.985895	TCCCCCTGTTTCCTCTTCTTC	59.014	52.381	0.00	0.00	0.00	2.87
1956	2003	0.263765	TACAATAGCGGTCTCCCCCT	59.736	55.000	0.00	0.00	0.00	4.79
1971	2018	2.798283	CGGCAAAGTTCGTCTTCTACAA	59.202	45.455	0.00	0.00	35.02	2.41
2128	2226	0.179161	GCGTGACGATGCACTCTAGT	60.179	55.000	10.10	0.00	36.65	2.57
2405	2506	1.673665	GTCCAGCTGCTCCAACAGG	60.674	63.158	8.66	0.00	38.16	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.