AutoCloner

Multiple sequence alignment - TraesCS2A01G354600

Loading Multiple Alignment...

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	TraesCS2A01G354600	chr2A	100.000	2318	0	0	1	2318	595979657	595981974	0.00000	4281.0
1	TraesCS2A01G354600	chr1D	91.841	1336	96	3	1	1332	279118449	279119775	0.00000	1851.0
2	TraesCS2A01G354600	chr5A	88.938	1347	143	3	1	1342	469654491	469655836	0.00000	1657.0
3	TraesCS2A01G354600	chr5A	81.009	1348	251	3	1	1344	609281982	609280636	0.00000	1066.0
4	TraesCS2A01G354600	chr2D	86.813	1365	168	8	1	1360	473429685	473431042	0.00000	1513.0
5	TraesCS2A01G354600	chr2D	89.247	1023	35	14	1343	2313	454805603	454804604	0.00000	1210.0
6	TraesCS2A01G354600	chr6B	82.815	1350	227	2	1	1345	583458950	583457601	0.00000	1203.0
7	TraesCS2A01G354600	chr4A	82.815	1350	226	3	1	1345	665828915	665830263	0.00000	1203.0
8	TraesCS2A01G354600	chr5B	82.866	1354	216	15	1	1344	505773918	505772571	0.00000	1201.0
9	TraesCS2A01G354600	chr5B	81.879	1352	229	14	1	1342	382368100	382366755	0.00000	1125.0
10	TraesCS2A01G354600	chr2B	90.538	930	36	12	1343	2238	534398849	534397938	0.00000	1182.0
11	TraesCS2A01G354600	chr2B	100.000	31	0	0	2288	2318	534397945	534397915	0.00009	58.4
12	TraesCS2A01G354600	chr1A	82.470	1352	228	8	1	1346	15525978	15524630	0.00000	1175.0
13	TraesCS2A01G354600	chr3A	80.417	1343	254	8	12	1348	15482050	15480711	0.00000	1014.0

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	TraesCS2A01G354600	chr2A	595979657	595981974	2317	False	4281.0	4281	100.000	1	2318	1	chr2A.!!$F1	2317
1	TraesCS2A01G354600	chr1D	279118449	279119775	1326	False	1851.0	1851	91.841	1	1332	1	chr1D.!!$F1	1331
2	TraesCS2A01G354600	chr5A	469654491	469655836	1345	False	1657.0	1657	88.938	1	1342	1	chr5A.!!$F1	1341
3	TraesCS2A01G354600	chr5A	609280636	609281982	1346	True	1066.0	1066	81.009	1	1344	1	chr5A.!!$R1	1343
4	TraesCS2A01G354600	chr2D	473429685	473431042	1357	False	1513.0	1513	86.813	1	1360	1	chr2D.!!$F1	1359
5	TraesCS2A01G354600	chr2D	454804604	454805603	999	True	1210.0	1210	89.247	1343	2313	1	chr2D.!!$R1	970
6	TraesCS2A01G354600	chr6B	583457601	583458950	1349	True	1203.0	1203	82.815	1	1345	1	chr6B.!!$R1	1344
7	TraesCS2A01G354600	chr4A	665828915	665830263	1348	False	1203.0	1203	82.815	1	1345	1	chr4A.!!$F1	1344
8	TraesCS2A01G354600	chr5B	505772571	505773918	1347	True	1201.0	1201	82.866	1	1344	1	chr5B.!!$R2	1343
9	TraesCS2A01G354600	chr5B	382366755	382368100	1345	True	1125.0	1125	81.879	1	1342	1	chr5B.!!$R1	1341
10	TraesCS2A01G354600	chr2B	534397915	534398849	934	True	620.2	1182	95.269	1343	2318	2	chr2B.!!$R1	975
11	TraesCS2A01G354600	chr1A	15524630	15525978	1348	True	1175.0	1175	82.470	1	1346	1	chr1A.!!$R1	1345
12	TraesCS2A01G354600	chr3A	15480711	15482050	1339	True	1014.0	1014	80.417	12	1348	1	chr3A.!!$R1	1336

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
949	957	0.323302	TGTCATCTTTGCGGCCTACA	59.677	50.0	0.0	0.0	0.0	2.74	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2049	2107	0.035915	AGGCGGAGGAAAAAGAGAGC	60.036	55.0	0.0	0.0	0.0	4.09	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
57	58	6.014327	AGAAATTGCAGATACAATTGGGTTGT	60.014	34.615	10.83	0.00	46.80	3.32
92	93	3.200605	TGACTCTGGTGCATGGAATATGT	59.799	43.478	0.00	0.00	0.00	2.29
102	103	4.136796	GCATGGAATATGTAGAGGTTGCA	58.863	43.478	0.00	0.00	0.00	4.08
124	125	7.011994	TGCAACAATATTTCTGGGATATGGAT	58.988	34.615	0.00	0.00	0.00	3.41
226	228	6.598753	TTGTTCACAGTTAAGAGTGCTTAC	57.401	37.500	3.01	2.83	36.37	2.34
284	286	0.464373	CGCATCAAGTACCAGCCCAT	60.464	55.000	0.00	0.00	0.00	4.00
324	326	1.302511	GGCGAGTTTGGGAAGCTCA	60.303	57.895	0.00	0.00	0.00	4.26
329	331	2.587522	GAGTTTGGGAAGCTCAGGTTT	58.412	47.619	0.00	0.00	0.00	3.27
407	409	5.484173	TTCTTGCAAGAAATATAGGCACG	57.516	39.130	34.01	2.89	41.75	5.34
527	529	1.344438	TGCGTTCAGTGTGGAATCTCT	59.656	47.619	0.00	0.00	0.00	3.10
604	606	4.745649	TGAATTGCAATGATGAAATGCGA	58.254	34.783	13.82	0.00	42.91	5.10
635	639	7.665559	GCACCATAATGTTAATCTGGAGGATTA	59.334	37.037	0.00	0.00	43.59	1.75
715	723	7.012044	ACGACTACCTTCAAAATTATATGCACC	59.988	37.037	0.00	0.00	0.00	5.01
760	768	6.012337	ACTCTACAGAGGAGATCATCAAGA	57.988	41.667	10.86	0.00	46.13	3.02
770	778	4.040706	GGAGATCATCAAGAGGAAGATGCT	59.959	45.833	0.00	0.00	41.02	3.79
788	796	5.890985	AGATGCTAGTGTAGTGTGAAGATCT	59.109	40.000	0.00	0.00	0.00	2.75
864	872	1.058695	CAAGTTGCGTTATCGGTCGAC	59.941	52.381	7.13	7.13	37.56	4.20
942	950	3.261580	TGATGGTAGTGTCATCTTTGCG	58.738	45.455	0.00	0.00	41.01	4.85
949	957	0.323302	TGTCATCTTTGCGGCCTACA	59.677	50.000	0.00	0.00	0.00	2.74
950	958	1.065491	TGTCATCTTTGCGGCCTACAT	60.065	47.619	0.00	0.00	0.00	2.29
984	992	1.016627	GCAATGATGCGTTAGAGGCA	58.983	50.000	0.00	0.00	43.83	4.75
1031	1039	4.439305	TGGCATTAGCAATTCAACACTC	57.561	40.909	0.00	0.00	44.61	3.51
1044	1052	8.897752	GCAATTCAACACTCTAATCTTCCTATT	58.102	33.333	0.00	0.00	0.00	1.73
1115	1123	0.673985	CTCTCCCGTTCGGCATATGA	59.326	55.000	6.97	0.00	0.00	2.15
1166	1174	8.826765	TCTTATGGGTGAAAGAGAGTTTATTCT	58.173	33.333	0.00	0.00	0.00	2.40
1210	1218	6.041637	ACATAATAGGGTAGCAGATCGTTTGA	59.958	38.462	0.00	0.00	0.00	2.69
1273	1281	1.839894	CAGGGCCCTCCTTGTATCC	59.160	63.158	25.77	0.00	45.47	2.59
1387	1395	4.362279	AGAAACAGCTTAAACGTACGTCA	58.638	39.130	23.05	10.06	0.00	4.35
1663	1687	0.034767	CCTTGCCCATCTGCTTCAGA	60.035	55.000	0.00	0.00	44.99	3.27
1677	1701	0.392595	TTCAGATGCTCCAGCTGCAG	60.393	55.000	10.11	10.11	45.97	4.41
1886	1914	2.027192	GGAGTTGATCAACCCAGCACTA	60.027	50.000	30.34	0.00	42.06	2.74
1914	1942	5.908341	AGAAAACGAAACCAGGCAAAATAA	58.092	33.333	0.00	0.00	0.00	1.40
1915	1943	6.521162	AGAAAACGAAACCAGGCAAAATAAT	58.479	32.000	0.00	0.00	0.00	1.28
1917	1945	8.145122	AGAAAACGAAACCAGGCAAAATAATAA	58.855	29.630	0.00	0.00	0.00	1.40
1920	1948	9.930693	AAACGAAACCAGGCAAAATAATAATAA	57.069	25.926	0.00	0.00	0.00	1.40
1921	1949	8.920509	ACGAAACCAGGCAAAATAATAATAAC	57.079	30.769	0.00	0.00	0.00	1.89
1922	1950	7.698970	ACGAAACCAGGCAAAATAATAATAACG	59.301	33.333	0.00	0.00	0.00	3.18
2049	2107	2.939103	GTGGAACCCATTCAATCTCTCG	59.061	50.000	0.00	0.00	35.28	4.04
2056	2114	3.181467	CCCATTCAATCTCTCGCTCTCTT	60.181	47.826	0.00	0.00	0.00	2.85
2057	2115	4.440880	CCATTCAATCTCTCGCTCTCTTT	58.559	43.478	0.00	0.00	0.00	2.52
2058	2116	4.874966	CCATTCAATCTCTCGCTCTCTTTT	59.125	41.667	0.00	0.00	0.00	2.27
2059	2117	5.353678	CCATTCAATCTCTCGCTCTCTTTTT	59.646	40.000	0.00	0.00	0.00	1.94
2060	2118	6.456718	CCATTCAATCTCTCGCTCTCTTTTTC	60.457	42.308	0.00	0.00	0.00	2.29
2065	2123	1.202582	TCTCGCTCTCTTTTTCCTCCG	59.797	52.381	0.00	0.00	0.00	4.63
2066	2124	0.389948	TCGCTCTCTTTTTCCTCCGC	60.390	55.000	0.00	0.00	0.00	5.54
2134	2211	4.394712	GCTGAGGTGACGGGGTGG	62.395	72.222	0.00	0.00	0.00	4.61
2135	2212	2.603473	CTGAGGTGACGGGGTGGA	60.603	66.667	0.00	0.00	0.00	4.02
2136	2213	1.990060	CTGAGGTGACGGGGTGGAT	60.990	63.158	0.00	0.00	0.00	3.41
2137	2214	2.244117	CTGAGGTGACGGGGTGGATG	62.244	65.000	0.00	0.00	0.00	3.51
2138	2215	2.203938	AGGTGACGGGGTGGATGT	60.204	61.111	0.00	0.00	0.00	3.06
2139	2216	2.046314	GGTGACGGGGTGGATGTG	60.046	66.667	0.00	0.00	0.00	3.21
2140	2217	2.747686	GTGACGGGGTGGATGTGT	59.252	61.111	0.00	0.00	0.00	3.72
2141	2218	1.671054	GTGACGGGGTGGATGTGTG	60.671	63.158	0.00	0.00	0.00	3.82
2142	2219	2.144078	TGACGGGGTGGATGTGTGT	61.144	57.895	0.00	0.00	0.00	3.72
2143	2220	1.671054	GACGGGGTGGATGTGTGTG	60.671	63.158	0.00	0.00	0.00	3.82
2144	2221	2.359850	CGGGGTGGATGTGTGTGG	60.360	66.667	0.00	0.00	0.00	4.17
2145	2222	2.676471	GGGGTGGATGTGTGTGGC	60.676	66.667	0.00	0.00	0.00	5.01
2146	2223	2.436109	GGGTGGATGTGTGTGGCT	59.564	61.111	0.00	0.00	0.00	4.75
2147	2224	1.675641	GGGTGGATGTGTGTGGCTC	60.676	63.158	0.00	0.00	0.00	4.70
2148	2225	2.034879	GGTGGATGTGTGTGGCTCG	61.035	63.158	0.00	0.00	0.00	5.03
2149	2226	1.301716	GTGGATGTGTGTGGCTCGT	60.302	57.895	0.00	0.00	0.00	4.18
2150	2227	1.301637	TGGATGTGTGTGGCTCGTG	60.302	57.895	0.00	0.00	0.00	4.35
2191	2268	2.223665	GCCACCTGCAGATTATTCAAGC	60.224	50.000	17.39	0.87	40.77	4.01
2207	2284	6.846325	ATTCAAGCGTTTATTCTAGGTAGC	57.154	37.500	0.00	0.00	0.00	3.58
2221	2298	1.063266	AGGTAGCAGGAGAGGAGAAGG	60.063	57.143	0.00	0.00	0.00	3.46
2279	2366	7.070322	TGTCATGTCCTAATTCAGAGATGATCA	59.930	37.037	15.98	0.00	42.58	2.92
2284	2371	7.098477	GTCCTAATTCAGAGATGATCATGGAG	58.902	42.308	14.30	0.33	0.00	3.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	2.568956	CCAGAGTCATCCAGAAAGTCCA	59.431	50.000	0.00	0.00	0.00	4.02
92	93	5.652014	CCCAGAAATATTGTTGCAACCTCTA	59.348	40.000	26.14	14.76	0.00	2.43
124	125	4.862574	CGGATCTTCATAATTTCGCGGATA	59.137	41.667	6.13	0.00	0.00	2.59
226	228	5.543507	ATTGGTTCTCTACTGCTAGATGG	57.456	43.478	0.00	0.00	0.00	3.51
237	239	3.282021	GCATCTGCCAATTGGTTCTCTA	58.718	45.455	25.19	6.47	37.57	2.43
284	286	4.408821	GATGGGCCTGTGTCCGCA	62.409	66.667	4.53	0.00	40.01	5.69
324	326	3.685139	TTCTCATCTTGAGCGAAACCT	57.315	42.857	0.00	0.00	43.95	3.50
329	331	4.060900	GCCATAATTCTCATCTTGAGCGA	58.939	43.478	0.00	0.00	43.95	4.93
527	529	1.648504	CGCAGCAGTTGATGATCAGA	58.351	50.000	0.09	0.00	32.25	3.27
604	606	5.824624	CCAGATTAACATTATGGTGCAGTCT	59.175	40.000	0.00	0.00	0.00	3.24
635	639	1.136305	CATGTCCGACCGTAACATCCT	59.864	52.381	0.00	0.00	31.43	3.24
639	643	1.079681	GCCATGTCCGACCGTAACA	60.080	57.895	0.00	0.00	0.00	2.41
704	712	4.458989	CCAAATGTAGCGGGTGCATATAAT	59.541	41.667	11.09	0.00	46.23	1.28
715	723	3.179443	TCTTCTAGCCAAATGTAGCGG	57.821	47.619	0.00	0.00	0.00	5.52
760	768	4.344978	TCACACTACACTAGCATCTTCCT	58.655	43.478	0.00	0.00	0.00	3.36
770	778	5.321927	TGACCAGATCTTCACACTACACTA	58.678	41.667	0.00	0.00	0.00	2.74
835	843	2.359850	CGCAACTTGGCCAGCCTA	60.360	61.111	5.11	0.80	36.94	3.93
848	856	1.514657	CCGTCGACCGATAACGCAA	60.515	57.895	10.58	0.00	39.56	4.85
864	872	1.426041	CCGTAGATGAAAACGCCCCG	61.426	60.000	0.00	0.00	37.78	5.73
942	950	5.640732	CAGTTGAAAATACACATGTAGGCC	58.359	41.667	0.00	0.00	33.52	5.19
949	957	7.821595	CATCATTGCAGTTGAAAATACACAT	57.178	32.000	5.63	0.00	0.00	3.21
978	986	3.641434	ATTGCATGTAGTTCTGCCTCT	57.359	42.857	0.00	0.00	37.59	3.69
1044	1052	6.220726	TGTGAAGAGTCGGATTGAATGATA	57.779	37.500	0.00	0.00	0.00	2.15
1048	1056	3.866651	CCTGTGAAGAGTCGGATTGAAT	58.133	45.455	0.00	0.00	0.00	2.57
1115	1123	6.108687	TGACGAATCTCAGCAACTAAATGAT	58.891	36.000	0.00	0.00	0.00	2.45
1210	1218	6.424509	GTGCTCTCTGTACGACTATACATAGT	59.575	42.308	1.48	1.48	45.73	2.12
1273	1281	1.321474	TCAAGTGGCAAAAGCTCCTG	58.679	50.000	0.00	0.00	0.00	3.86
1387	1395	4.891727	GCCGGTGCCATCGACGAT	62.892	66.667	4.05	4.05	0.00	3.73
1548	1572	2.047655	GGGCCACGATGAACGACA	60.048	61.111	4.39	0.00	45.77	4.35
1583	1607	2.664851	CTGCACGGCGTTCAAGGA	60.665	61.111	11.19	0.00	0.00	3.36
1638	1662	0.253044	GCAGATGGGCAAGGTACAGA	59.747	55.000	0.00	0.00	0.00	3.41
1886	1914	2.572290	CCTGGTTTCGTTTTCTCACCT	58.428	47.619	0.00	0.00	0.00	4.00
1922	1950	7.745972	TCATATCAAGTACGTACGATCCATAC	58.254	38.462	24.41	13.29	0.00	2.39
2039	2097	4.221703	AGGAAAAAGAGAGCGAGAGATTGA	59.778	41.667	0.00	0.00	0.00	2.57
2040	2098	4.502962	AGGAAAAAGAGAGCGAGAGATTG	58.497	43.478	0.00	0.00	0.00	2.67
2042	2100	3.132111	GGAGGAAAAAGAGAGCGAGAGAT	59.868	47.826	0.00	0.00	0.00	2.75
2043	2101	2.494073	GGAGGAAAAAGAGAGCGAGAGA	59.506	50.000	0.00	0.00	0.00	3.10
2045	2103	1.202582	CGGAGGAAAAAGAGAGCGAGA	59.797	52.381	0.00	0.00	0.00	4.04
2046	2104	1.634702	CGGAGGAAAAAGAGAGCGAG	58.365	55.000	0.00	0.00	0.00	5.03
2047	2105	0.389948	GCGGAGGAAAAAGAGAGCGA	60.390	55.000	0.00	0.00	0.00	4.93
2048	2106	1.362406	GGCGGAGGAAAAAGAGAGCG	61.362	60.000	0.00	0.00	0.00	5.03
2049	2107	0.035915	AGGCGGAGGAAAAAGAGAGC	60.036	55.000	0.00	0.00	0.00	4.09
2056	2114	1.537889	TGGGAGAGGCGGAGGAAAA	60.538	57.895	0.00	0.00	0.00	2.29
2057	2115	2.121832	TGGGAGAGGCGGAGGAAA	59.878	61.111	0.00	0.00	0.00	3.13
2058	2116	2.683933	GTGGGAGAGGCGGAGGAA	60.684	66.667	0.00	0.00	0.00	3.36
2081	2139	0.037232	CAGAGTTCGGTCCTGTTCCC	60.037	60.000	0.00	0.00	0.00	3.97
2088	2146	3.403276	CGAAGACAGAGTTCGGTCC	57.597	57.895	8.48	0.00	42.47	4.46
2134	2211	0.391661	ATCCACGAGCCACACACATC	60.392	55.000	0.00	0.00	0.00	3.06
2135	2212	0.674581	CATCCACGAGCCACACACAT	60.675	55.000	0.00	0.00	0.00	3.21
2136	2213	1.301637	CATCCACGAGCCACACACA	60.302	57.895	0.00	0.00	0.00	3.72
2137	2214	2.034879	CCATCCACGAGCCACACAC	61.035	63.158	0.00	0.00	0.00	3.82
2138	2215	1.552799	ATCCATCCACGAGCCACACA	61.553	55.000	0.00	0.00	0.00	3.72
2139	2216	0.811616	GATCCATCCACGAGCCACAC	60.812	60.000	0.00	0.00	0.00	3.82
2140	2217	1.264045	TGATCCATCCACGAGCCACA	61.264	55.000	0.00	0.00	0.00	4.17
2141	2218	0.811616	GTGATCCATCCACGAGCCAC	60.812	60.000	0.00	0.00	0.00	5.01
2142	2219	1.522092	GTGATCCATCCACGAGCCA	59.478	57.895	0.00	0.00	0.00	4.75
2143	2220	4.445699	GTGATCCATCCACGAGCC	57.554	61.111	0.00	0.00	0.00	4.70
2148	2225	1.429148	GCGGTTCGTGATCCATCCAC	61.429	60.000	0.00	0.00	0.00	4.02
2149	2226	1.153449	GCGGTTCGTGATCCATCCA	60.153	57.895	0.00	0.00	0.00	3.41
2150	2227	2.237751	CGCGGTTCGTGATCCATCC	61.238	63.158	0.00	0.00	39.94	3.51
2191	2268	5.278561	CCTCTCCTGCTACCTAGAATAAACG	60.279	48.000	0.00	0.00	0.00	3.60
2207	2284	1.422531	CCATCCCTTCTCCTCTCCTG	58.577	60.000	0.00	0.00	0.00	3.86
2221	2298	4.442192	GGAGCTATTCATCGATACCCATCC	60.442	50.000	0.00	0.00	0.00	3.51
2279	2366	1.145738	ACAAGTTCAACCAGGCTCCAT	59.854	47.619	0.00	0.00	0.00	3.41
2284	2371	0.385390	CCACACAAGTTCAACCAGGC	59.615	55.000	0.00	0.00	0.00	4.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.