AutoCloner

Multiple sequence alignment - TraesCS4D01G236300

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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	TraesCS4D01G236300	chr4D	100.000	2201	0	0	1	2201	398284612	398286812	0.000000e+00	4065.0
1	TraesCS4D01G236300	chr1D	97.350	1170	30	1	1	1170	423893232	423894400	0.000000e+00	1988.0
2	TraesCS4D01G236300	chr1D	98.261	460	8	0	1167	1626	445569422	445569881	0.000000e+00	806.0
3	TraesCS4D01G236300	chr1D	96.937	457	13	1	1167	1623	369901800	369902255	0.000000e+00	765.0
4	TraesCS4D01G236300	chr2D	96.681	1175	33	3	1	1170	644388704	644389877	0.000000e+00	1949.0
5	TraesCS4D01G236300	chr2A	96.658	1167	37	2	1	1167	706884642	706885806	0.000000e+00	1938.0
6	TraesCS4D01G236300	chr2A	100.000	38	0	0	2164	2201	758405906	758405943	1.090000e-08	71.3
7	TraesCS4D01G236300	chr3D	96.072	1171	44	2	1	1170	5431576	5430407	0.000000e+00	1906.0
8	TraesCS4D01G236300	chr3D	96.072	1171	42	2	1	1170	121530605	121531772	0.000000e+00	1905.0
9	TraesCS4D01G236300	chr7D	95.901	1171	38	2	1	1170	621162221	621163382	0.000000e+00	1888.0
10	TraesCS4D01G236300	chr7D	98.684	456	6	0	1167	1622	621163577	621164032	0.000000e+00	809.0
11	TraesCS4D01G236300	chr7D	98.043	460	7	2	1167	1625	474490191	474489733	0.000000e+00	798.0
12	TraesCS4D01G236300	chr3B	95.726	1170	48	2	1	1170	97752987	97751820	0.000000e+00	1882.0
13	TraesCS4D01G236300	chr3B	91.525	59	5	0	2143	2201	752208230	752208288	5.040000e-12	82.4
14	TraesCS4D01G236300	chr7A	95.474	1171	50	3	1	1170	86218459	86217291	0.000000e+00	1866.0
15	TraesCS4D01G236300	chr7A	92.045	88	7	0	1957	2044	165901722	165901809	8.250000e-25	124.0
16	TraesCS4D01G236300	chr7A	81.818	110	8	6	2103	2201	734694517	734694625	5.040000e-12	82.4
17	TraesCS4D01G236300	chr7B	95.389	1171	52	2	1	1170	457414190	457415359	0.000000e+00	1862.0
18	TraesCS4D01G236300	chr7B	96.753	462	14	1	1167	1627	457415554	457416015	0.000000e+00	769.0
19	TraesCS4D01G236300	chr7B	96.711	456	15	0	1167	1622	494220284	494219829	0.000000e+00	760.0
20	TraesCS4D01G236300	chr6D	98.026	456	9	0	1167	1622	446603384	446602929	0.000000e+00	793.0
21	TraesCS4D01G236300	chr6D	88.308	402	43	2	1623	2024	4056787	4057184	1.530000e-131	479.0
22	TraesCS4D01G236300	chr2B	97.368	456	12	0	1167	1622	643126383	643126838	0.000000e+00	776.0
23	TraesCS4D01G236300	chr6B	96.544	463	15	1	1165	1627	567282352	567282813	0.000000e+00	765.0
24	TraesCS4D01G236300	chr1A	88.266	571	62	4	1633	2201	410447556	410446989	0.000000e+00	678.0
25	TraesCS4D01G236300	chr4A	87.707	423	47	5	1623	2044	75922617	75922199	2.540000e-134	488.0
26	TraesCS4D01G236300	chr4A	91.525	59	5	0	2143	2201	75922216	75922158	5.040000e-12	82.4
27	TraesCS4D01G236300	chr4A	91.525	59	5	0	2143	2201	713105548	713105606	5.040000e-12	82.4
28	TraesCS4D01G236300	chr5A	85.816	423	55	5	1623	2044	455272689	455273107	5.580000e-121	444.0
29	TraesCS4D01G236300	chr5A	89.130	92	6	2	1957	2044	698460425	698460334	6.420000e-21	111.0
30	TraesCS4D01G236300	chr5A	91.525	59	5	0	2143	2201	698460351	698460293	5.040000e-12	82.4
31	TraesCS4D01G236300	chr3A	84.634	423	62	3	1623	2044	646537280	646536860	3.380000e-113	418.0
32	TraesCS4D01G236300	chr3A	91.525	59	5	0	2143	2201	646471422	646471364	5.040000e-12	82.4
33	TraesCS4D01G236300	chr3A	91.525	59	5	0	2143	2201	646536877	646536819	5.040000e-12	82.4

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	TraesCS4D01G236300	chr4D	398284612	398286812	2200	False	4065.0	4065	100.0000	1	2201	1	chr4D.!!$F1	2200
1	TraesCS4D01G236300	chr1D	423893232	423894400	1168	False	1988.0	1988	97.3500	1	1170	1	chr1D.!!$F2	1169
2	TraesCS4D01G236300	chr2D	644388704	644389877	1173	False	1949.0	1949	96.6810	1	1170	1	chr2D.!!$F1	1169
3	TraesCS4D01G236300	chr2A	706884642	706885806	1164	False	1938.0	1938	96.6580	1	1167	1	chr2A.!!$F1	1166
4	TraesCS4D01G236300	chr3D	5430407	5431576	1169	True	1906.0	1906	96.0720	1	1170	1	chr3D.!!$R1	1169
5	TraesCS4D01G236300	chr3D	121530605	121531772	1167	False	1905.0	1905	96.0720	1	1170	1	chr3D.!!$F1	1169
6	TraesCS4D01G236300	chr7D	621162221	621164032	1811	False	1348.5	1888	97.2925	1	1622	2	chr7D.!!$F1	1621
7	TraesCS4D01G236300	chr3B	97751820	97752987	1167	True	1882.0	1882	95.7260	1	1170	1	chr3B.!!$R1	1169
8	TraesCS4D01G236300	chr7A	86217291	86218459	1168	True	1866.0	1866	95.4740	1	1170	1	chr7A.!!$R1	1169
9	TraesCS4D01G236300	chr7B	457414190	457416015	1825	False	1315.5	1862	96.0710	1	1627	2	chr7B.!!$F1	1626
10	TraesCS4D01G236300	chr1A	410446989	410447556	567	True	678.0	678	88.2660	1633	2201	1	chr1A.!!$R1	568

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
977	982	0.456221	GAGGAAGATCCGAAGACGCA	59.544	55.0	0.0	0.0	42.75	5.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1814	2024	0.738412	CCGCCGGTCATCTTTACGTT	60.738	55.0	1.9	0.0	0.0	3.99	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
41	42	1.368268	TTGGGATTGGGGGATAGGGC	61.368	60.000	0.00	0.00	0.00	5.19
219	220	1.668101	CTGGCAGGTAGGACGGACTC	61.668	65.000	6.61	0.00	0.00	3.36
611	612	1.382695	CCCGAGGAAGAAGGCCCTA	60.383	63.158	0.00	0.00	31.84	3.53
730	733	1.283905	GGGTAAATAGTGGTGGGCAGT	59.716	52.381	0.00	0.00	0.00	4.40
966	971	2.722201	GCCCACCGTCGAGGAAGAT	61.722	63.158	6.70	0.00	45.00	2.40
977	982	0.456221	GAGGAAGATCCGAAGACGCA	59.544	55.000	0.00	0.00	42.75	5.24
979	984	2.293677	GAGGAAGATCCGAAGACGCATA	59.706	50.000	0.00	0.00	42.75	3.14
1236	1444	1.495878	TCGAGCGTACTATCGAGTCC	58.504	55.000	13.34	0.00	42.61	3.85
1336	1545	7.836842	TGATGCTCTGTTTATACTCTGTTGTA	58.163	34.615	0.00	0.00	0.00	2.41
1429	1638	3.380142	CTTGCATACAACCAAACACCAC	58.620	45.455	0.00	0.00	0.00	4.16
1622	1831	4.293648	GGCAACCAAACACGCCCC	62.294	66.667	0.00	0.00	38.67	5.80
1627	1836	0.536460	AACCAAACACGCCCCTAGTG	60.536	55.000	0.00	0.00	44.57	2.74
1628	1837	1.373435	CCAAACACGCCCCTAGTGA	59.627	57.895	3.20	0.00	41.83	3.41
1629	1838	0.953960	CCAAACACGCCCCTAGTGAC	60.954	60.000	3.20	0.00	41.83	3.67
1630	1839	0.953960	CAAACACGCCCCTAGTGACC	60.954	60.000	3.20	0.00	41.83	4.02
1631	1840	2.120737	AAACACGCCCCTAGTGACCC	62.121	60.000	3.20	0.00	41.83	4.46
1649	1858	3.991051	CCCACGCTGGACACGAGT	61.991	66.667	5.71	0.00	40.96	4.18
1653	1862	2.202623	CGCTGGACACGAGTAGGC	60.203	66.667	0.00	0.00	0.00	3.93
1657	1866	2.227089	CTGGACACGAGTAGGCCCAC	62.227	65.000	0.00	0.00	0.00	4.61
1664	1873	0.465705	CGAGTAGGCCCACACATCAT	59.534	55.000	3.54	0.00	0.00	2.45
1665	1874	1.539065	CGAGTAGGCCCACACATCATC	60.539	57.143	3.54	0.00	0.00	2.92
1706	1916	0.826715	CTTCTTCCCGCATCCTCTCA	59.173	55.000	0.00	0.00	0.00	3.27
1719	1929	2.111384	TCCTCTCATTTCTTCCCCTCG	58.889	52.381	0.00	0.00	0.00	4.63
1735	1945	1.082690	CTCGCAGCCTTCTTTCTTCC	58.917	55.000	0.00	0.00	0.00	3.46
1736	1946	0.687354	TCGCAGCCTTCTTTCTTCCT	59.313	50.000	0.00	0.00	0.00	3.36
1740	1950	0.687354	AGCCTTCTTTCTTCCTCGCA	59.313	50.000	0.00	0.00	0.00	5.10
1746	1956	3.040147	TCTTTCTTCCTCGCAACGAAT	57.960	42.857	0.00	0.00	34.74	3.34
1749	1959	1.710013	TCTTCCTCGCAACGAATGAC	58.290	50.000	0.00	0.00	34.74	3.06
1761	1971	4.435518	GCAACGAATGACGAAGCTTTGATA	60.436	41.667	20.86	8.71	45.77	2.15
1765	1975	6.478588	ACGAATGACGAAGCTTTGATATTTC	58.521	36.000	20.86	14.41	45.77	2.17
1783	1993	1.673337	CTGCTACCAGCTGCTTGCA	60.673	57.895	15.72	15.72	45.94	4.08
1787	1997	2.786539	CTACCAGCTGCTTGCACCGA	62.787	60.000	8.66	0.00	45.94	4.69
1804	2014	2.009774	CCGATGCTTCAAACTACAGGG	58.990	52.381	0.08	0.00	0.00	4.45
1810	2020	0.688487	TTCAAACTACAGGGGTCGGG	59.312	55.000	0.00	0.00	0.00	5.14
1812	2022	1.159184	AAACTACAGGGGTCGGGGA	59.841	57.895	0.00	0.00	0.00	4.81
1813	2023	0.474273	AAACTACAGGGGTCGGGGAA	60.474	55.000	0.00	0.00	0.00	3.97
1814	2024	0.474273	AACTACAGGGGTCGGGGAAA	60.474	55.000	0.00	0.00	0.00	3.13
1830	2040	2.417586	GGGAAAACGTAAAGATGACCGG	59.582	50.000	0.00	0.00	0.00	5.28
1861	2071	3.660501	ACTGCTGTCGTCATCAAACTA	57.339	42.857	0.00	0.00	0.00	2.24
1867	2077	3.054166	TGTCGTCATCAAACTACAACGG	58.946	45.455	0.00	0.00	0.00	4.44
1901	2111	0.671781	GAGAGCGAACATGCCACAGT	60.672	55.000	0.00	0.00	34.65	3.55
1903	2113	0.110056	GAGCGAACATGCCACAGTTG	60.110	55.000	0.00	0.00	34.65	3.16
1910	2120	0.961857	CATGCCACAGTTGCCTGCTA	60.962	55.000	0.00	0.00	42.81	3.49
1934	2144	1.519013	GCCGGAACCGCGTGTATAA	60.519	57.895	5.05	0.00	38.24	0.98
1936	2146	1.357907	CCGGAACCGCGTGTATAAAA	58.642	50.000	4.92	0.00	38.24	1.52
1937	2147	1.325338	CCGGAACCGCGTGTATAAAAG	59.675	52.381	4.92	0.00	38.24	2.27
1938	2148	1.994779	CGGAACCGCGTGTATAAAAGT	59.005	47.619	4.92	0.00	0.00	2.66
1939	2149	2.222640	CGGAACCGCGTGTATAAAAGTG	60.223	50.000	4.92	0.00	0.00	3.16
1941	2151	3.187022	GGAACCGCGTGTATAAAAGTGTT	59.813	43.478	4.92	0.00	0.00	3.32
1942	2152	3.799137	ACCGCGTGTATAAAAGTGTTG	57.201	42.857	4.92	0.00	0.00	3.33
1943	2153	2.096119	ACCGCGTGTATAAAAGTGTTGC	60.096	45.455	4.92	0.00	0.00	4.17
1944	2154	2.501881	CGCGTGTATAAAAGTGTTGCC	58.498	47.619	0.00	0.00	0.00	4.52
1945	2155	2.096169	CGCGTGTATAAAAGTGTTGCCA	60.096	45.455	0.00	0.00	0.00	4.92
1947	2157	3.817238	CGTGTATAAAAGTGTTGCCACC	58.183	45.455	0.00	0.00	42.88	4.61
1948	2158	3.665848	CGTGTATAAAAGTGTTGCCACCG	60.666	47.826	0.00	0.00	42.88	4.94
2005	2215	5.003804	GGCTTCAACCACAGATAGAAAAGA	58.996	41.667	0.00	0.00	0.00	2.52
2051	2261	6.998968	AAAAAGTTGCAACCATTTGATTGA	57.001	29.167	25.62	0.00	34.24	2.57
2054	2264	6.607735	AAGTTGCAACCATTTGATTGAAAG	57.392	33.333	25.62	0.00	34.24	2.62
2071	2281	4.922206	TGAAAGGCTTCAATCATAGGTGT	58.078	39.130	0.00	0.00	38.65	4.16
2085	2295	6.109156	TCATAGGTGTAGAAAGCTTCAACA	57.891	37.500	0.00	1.64	32.13	3.33
2086	2296	6.711277	TCATAGGTGTAGAAAGCTTCAACAT	58.289	36.000	0.00	0.00	32.13	2.71
2098	2309	4.764336	CAACATGGCACCGCGCAG	62.764	66.667	8.75	0.00	45.17	5.18

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
23	24	1.778383	GCCCTATCCCCCAATCCCA	60.778	63.158	0.00	0.00	0.00	4.37
41	42	1.497716	GTACCCCCTTTCCCCCTATTG	59.502	57.143	0.00	0.00	0.00	1.90
203	204	2.799371	CGAGTCCGTCCTACCTGC	59.201	66.667	0.00	0.00	0.00	4.85
611	612	0.849094	TCCCTTGGGGTATTGGCTGT	60.849	55.000	5.78	0.00	44.74	4.40
966	971	0.174845	CACCCTTATGCGTCTTCGGA	59.825	55.000	0.00	0.00	42.23	4.55
977	982	2.001361	CTCGTCGTCGCCACCCTTAT	62.001	60.000	0.00	0.00	36.96	1.73
979	984	4.052229	CTCGTCGTCGCCACCCTT	62.052	66.667	0.00	0.00	36.96	3.95
1236	1444	7.665471	CATAAACCATAAACATGTTCAAAGCG	58.335	34.615	12.39	0.51	0.00	4.68
1336	1545	1.066215	TCGGCAGCACACATCATAAGT	60.066	47.619	0.00	0.00	0.00	2.24
1429	1638	0.250553	TAGTCCACAAACCCAAGGCG	60.251	55.000	0.00	0.00	0.00	5.52
1631	1840	4.742201	CTCGTGTCCAGCGTGGGG	62.742	72.222	4.52	0.00	38.32	4.96
1635	1844	2.991076	GCCTACTCGTGTCCAGCGT	61.991	63.158	0.00	0.00	0.00	5.07
1646	1855	1.765314	AGATGATGTGTGGGCCTACTC	59.235	52.381	21.02	17.29	0.00	2.59
1649	1858	3.737559	AAAAGATGATGTGTGGGCCTA	57.262	42.857	4.53	0.00	0.00	3.93
1679	1888	3.433740	GGATGCGGGAAGAAGATAAGGTT	60.434	47.826	0.00	0.00	0.00	3.50
1706	1916	1.077429	GGCTGCGAGGGGAAGAAAT	60.077	57.895	0.00	0.00	0.00	2.17
1719	1929	1.082690	CGAGGAAGAAAGAAGGCTGC	58.917	55.000	0.00	0.00	0.00	5.25
1735	1945	0.246912	GCTTCGTCATTCGTTGCGAG	60.247	55.000	0.00	0.00	37.14	5.03
1736	1946	0.666274	AGCTTCGTCATTCGTTGCGA	60.666	50.000	0.00	0.00	40.85	5.10
1740	1950	6.422776	AATATCAAAGCTTCGTCATTCGTT	57.577	33.333	0.00	0.00	40.80	3.85
1746	1956	4.937620	AGCAGAAATATCAAAGCTTCGTCA	59.062	37.500	0.00	0.00	29.72	4.35
1749	1959	5.294306	TGGTAGCAGAAATATCAAAGCTTCG	59.706	40.000	0.00	0.00	34.03	3.79
1761	1971	2.089980	CAAGCAGCTGGTAGCAGAAAT	58.910	47.619	25.66	7.47	45.56	2.17
1765	1975	1.673337	TGCAAGCAGCTGGTAGCAG	60.673	57.895	20.51	17.67	45.56	4.24
1783	1993	2.615493	CCCTGTAGTTTGAAGCATCGGT	60.615	50.000	0.00	0.00	0.00	4.69
1787	1997	2.615493	CGACCCCTGTAGTTTGAAGCAT	60.615	50.000	0.00	0.00	0.00	3.79
1798	2008	1.829523	CGTTTTCCCCGACCCCTGTA	61.830	60.000	0.00	0.00	0.00	2.74
1799	2009	2.841317	GTTTTCCCCGACCCCTGT	59.159	61.111	0.00	0.00	0.00	4.00
1804	2014	2.168326	TCTTTACGTTTTCCCCGACC	57.832	50.000	0.00	0.00	0.00	4.79
1810	2020	2.159612	GCCGGTCATCTTTACGTTTTCC	60.160	50.000	1.90	0.00	0.00	3.13
1812	2022	1.461897	CGCCGGTCATCTTTACGTTTT	59.538	47.619	1.90	0.00	0.00	2.43
1813	2023	1.073177	CGCCGGTCATCTTTACGTTT	58.927	50.000	1.90	0.00	0.00	3.60
1814	2024	0.738412	CCGCCGGTCATCTTTACGTT	60.738	55.000	1.90	0.00	0.00	3.99
1830	2040	3.730761	CAGCAGTTCCAGCACCGC	61.731	66.667	0.00	0.00	0.00	5.68
1839	2049	2.802816	AGTTTGATGACGACAGCAGTTC	59.197	45.455	5.90	1.80	43.27	3.01
1845	2055	3.121279	CCGTTGTAGTTTGATGACGACAG	59.879	47.826	0.00	0.00	36.69	3.51
1939	2149	3.907894	TTTTTAGATCACGGTGGCAAC	57.092	42.857	8.50	0.00	0.00	4.17
1970	2180	2.217429	TTGAAGCCTTTTTCAACCGC	57.783	45.000	0.00	0.00	40.95	5.68
1978	2188	4.985538	TCTATCTGTGGTTGAAGCCTTTT	58.014	39.130	0.00	0.00	0.00	2.27
1982	2192	5.003804	TCTTTTCTATCTGTGGTTGAAGCC	58.996	41.667	0.00	0.00	0.00	4.35
1993	2203	6.259608	AGTGCCGATTGAATCTTTTCTATCTG	59.740	38.462	3.43	4.02	40.07	2.90
2030	2240	6.038492	CCTTTCAATCAAATGGTTGCAACTTT	59.962	34.615	27.64	18.40	34.50	2.66
2031	2241	5.528320	CCTTTCAATCAAATGGTTGCAACTT	59.472	36.000	27.64	13.47	34.50	2.66
2032	2242	5.058490	CCTTTCAATCAAATGGTTGCAACT	58.942	37.500	27.64	7.56	34.50	3.16
2033	2243	4.319694	GCCTTTCAATCAAATGGTTGCAAC	60.320	41.667	21.59	21.59	34.50	4.17
2049	2259	4.922206	ACACCTATGATTGAAGCCTTTCA	58.078	39.130	0.00	0.00	41.44	2.69
2051	2261	6.313519	TCTACACCTATGATTGAAGCCTTT	57.686	37.500	0.00	0.00	0.00	3.11
2054	2264	5.008118	GCTTTCTACACCTATGATTGAAGCC	59.992	44.000	0.00	0.00	0.00	4.35
2063	2273	6.183360	CCATGTTGAAGCTTTCTACACCTATG	60.183	42.308	0.00	3.39	45.40	2.23
2064	2274	5.882557	CCATGTTGAAGCTTTCTACACCTAT	59.117	40.000	0.00	0.00	45.40	2.57
2071	2281	2.819608	GGTGCCATGTTGAAGCTTTCTA	59.180	45.455	0.00	0.00	0.00	2.10
2109	2320	5.596836	AAGCTTTTCTGTCAATGGTTGAA	57.403	34.783	0.00	0.00	42.15	2.69
2161	2372	2.618709	GCCGGCAGTAGCAAAATCTAAT	59.381	45.455	24.80	0.00	44.61	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.