AutoCloner

Multiple sequence alignment - TraesCS2D01G282200

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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	TraesCS2D01G282200	chr2D	100.000	2340	0	0	1	2340	355291628	355293967	0.000000e+00	4322.0
1	TraesCS2D01G282200	chr2B	97.433	857	18	4	442	1295	422966188	422967043	0.000000e+00	1458.0
2	TraesCS2D01G282200	chr2B	96.210	686	20	3	1659	2340	422967321	422968004	0.000000e+00	1118.0
3	TraesCS2D01G282200	chr2B	97.635	296	3	3	1325	1616	422967040	422967335	2.680000e-139	505.0
4	TraesCS2D01G282200	chr2A	93.234	606	25	5	650	1253	475528051	475528642	0.000000e+00	878.0
5	TraesCS2D01G282200	chr2A	84.812	586	53	19	1675	2243	475528941	475529507	7.300000e-155	556.0
6	TraesCS2D01G282200	chr2A	93.056	216	12	3	442	655	475523197	475523411	1.750000e-81	313.0
7	TraesCS2D01G282200	chr2A	93.000	200	14	0	1	200	475522213	475522412	2.270000e-75	292.0
8	TraesCS2D01G282200	chr2A	81.053	95	11	2	1251	1338	617636118	617636024	4.170000e-08	69.4
9	TraesCS2D01G282200	chr2A	80.233	86	10	2	1251	1329	38968501	38968416	9.030000e-05	58.4
10	TraesCS2D01G282200	chr3A	82.843	204	18	14	1	201	686731157	686731346	1.440000e-37	167.0
11	TraesCS2D01G282200	chr5B	84.713	157	18	4	13	166	540321212	540321059	4.030000e-33	152.0
12	TraesCS2D01G282200	chr5B	86.111	72	3	2	1262	1327	269975169	269975239	1.160000e-08	71.3
13	TraesCS2D01G282200	chr5B	91.304	46	4	0	1616	1661	429187837	429187792	1.940000e-06	63.9
14	TraesCS2D01G282200	chr5B	100.000	34	0	0	1	34	658229147	658229180	1.940000e-06	63.9
15	TraesCS2D01G282200	chr7D	80.833	120	17	5	1031	1147	128912440	128912556	3.200000e-14	89.8
16	TraesCS2D01G282200	chr7B	80.833	120	17	5	1031	1147	90189637	90189753	3.200000e-14	89.8
17	TraesCS2D01G282200	chr7B	95.455	44	2	0	1262	1305	436752481	436752438	1.160000e-08	71.3
18	TraesCS2D01G282200	chr7A	80.833	120	17	5	1031	1147	128826546	128826662	3.200000e-14	89.8
19	TraesCS2D01G282200	chr1A	78.295	129	14	8	78	199	481925769	481925890	1.160000e-08	71.3
20	TraesCS2D01G282200	chr6A	87.097	62	7	1	1251	1312	488070348	488070288	4.170000e-08	69.4
21	TraesCS2D01G282200	chr4B	97.368	38	1	0	1268	1305	526729039	526729076	5.400000e-07	65.8
22	TraesCS2D01G282200	chr5D	100.000	34	0	0	1	34	521904950	521904983	1.940000e-06	63.9
23	TraesCS2D01G282200	chr3D	94.737	38	2	0	1269	1306	326117325	326117288	2.510000e-05	60.2
24	TraesCS2D01G282200	chr6D	96.970	33	1	0	1260	1292	470915951	470915919	3.250000e-04	56.5
25	TraesCS2D01G282200	chr3B	81.081	74	11	3	96	169	787664391	787664321	3.250000e-04	56.5
26	TraesCS2D01G282200	chr1D	90.698	43	3	1	1620	1661	112631654	112631612	3.250000e-04	56.5

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	TraesCS2D01G282200	chr2D	355291628	355293967	2339	False	4322.0	4322	100.000000	1	2340	1	chr2D.!!$F1	2339
1	TraesCS2D01G282200	chr2B	422966188	422968004	1816	False	1027.0	1458	97.092667	442	2340	3	chr2B.!!$F1	1898
2	TraesCS2D01G282200	chr2A	475528051	475529507	1456	False	717.0	878	89.023000	650	2243	2	chr2A.!!$F2	1593
3	TraesCS2D01G282200	chr2A	475522213	475523411	1198	False	302.5	313	93.028000	1	655	2	chr2A.!!$F1	654

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
862	1438	1.484065	CCAGCCTAGATTCCCTAGCCT	60.484	57.143	0.0	0.0	42.79	4.58	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2203	2829	2.7364	GCATGATGCACTTAAGTTGCCC	60.736	50.0	13.36	14.75	44.26	5.36	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
114	115	2.038659	CATGTGGTGGTGGGTCTTTTT	58.961	47.619	0.00	0.00	0.00	1.94
137	138	5.813080	TCATGCATTTCTCTCATGTTGAG	57.187	39.130	0.00	10.69	45.59	3.02
167	168	8.248945	GGCTTTATTCCATCCATAATTGATGAG	58.751	37.037	5.95	0.00	41.72	2.90
265	266	9.809395	TCTCTTATGTATATATAGGATTCGGGG	57.191	37.037	2.44	0.00	0.00	5.73
290	291	7.868415	GGCAACTTCGTTAATCTCTATATCAGT	59.132	37.037	0.00	0.00	0.00	3.41
313	314	4.034858	TCGACTAAGTGCTCATAGGTAACG	59.965	45.833	3.41	0.00	46.39	3.18
318	319	8.097078	ACTAAGTGCTCATAGGTAACGTATAG	57.903	38.462	3.41	0.00	46.39	1.31
345	346	4.453819	GCATGTATTTATGGAGAGGAGTGC	59.546	45.833	0.00	0.00	0.00	4.40
395	397	5.404366	TCTTTTTACGACGAATCAACCTGAG	59.596	40.000	0.00	0.00	0.00	3.35
398	400	3.928727	ACGACGAATCAACCTGAGTTA	57.071	42.857	0.00	0.00	33.27	2.24
410	413	7.311092	TCAACCTGAGTTAGATGGTTAGAAA	57.689	36.000	0.00	0.00	40.39	2.52
451	1025	7.202016	TCTTCTAACTTAACAAATGCACTGG	57.798	36.000	0.00	0.00	0.00	4.00
454	1028	3.896648	ACTTAACAAATGCACTGGTCG	57.103	42.857	0.00	0.00	0.00	4.79
586	1161	2.280119	TGTCAGTCGCAGCACACC	60.280	61.111	0.00	0.00	0.00	4.16
631	1206	2.433145	ATGTCTGTCTGCGCGGTG	60.433	61.111	17.37	8.14	0.00	4.94
862	1438	1.484065	CCAGCCTAGATTCCCTAGCCT	60.484	57.143	0.00	0.00	42.79	4.58
1068	1645	4.918201	CGGCGGGGGATCTGCTTC	62.918	72.222	0.00	0.00	46.69	3.86
1161	1738	1.137086	CTCGTCATCAACCCCTTCGAT	59.863	52.381	0.00	0.00	0.00	3.59
1296	1873	8.828688	AAAAGCGTTTAGATCACTTAAGTAGT	57.171	30.769	8.04	0.00	37.68	2.73
1323	1900	9.883142	GATCTAAATATATTTCTGGACAGAGGG	57.117	37.037	13.95	0.00	38.88	4.30
1358	1935	7.957484	CGAATTAGGCCAATGTTTCGAATATAG	59.043	37.037	5.01	0.00	29.64	1.31
1359	1936	8.691661	AATTAGGCCAATGTTTCGAATATAGT	57.308	30.769	5.01	0.00	0.00	2.12
1360	1937	9.787435	AATTAGGCCAATGTTTCGAATATAGTA	57.213	29.630	5.01	0.00	0.00	1.82
1362	1939	9.787435	TTAGGCCAATGTTTCGAATATAGTATT	57.213	29.630	5.01	0.00	0.00	1.89
1363	1940	8.691661	AGGCCAATGTTTCGAATATAGTATTT	57.308	30.769	5.01	0.00	0.00	1.40
1553	2169	4.262292	CCAGCTGTAACCACACTACAGTAA	60.262	45.833	13.81	0.00	45.36	2.24
1616	2232	6.619801	CTACAGTTGTAGCTTTTGTTCCTT	57.380	37.500	6.38	0.00	41.15	3.36
1617	2233	5.914898	ACAGTTGTAGCTTTTGTTCCTTT	57.085	34.783	0.00	0.00	0.00	3.11
1618	2234	5.891451	ACAGTTGTAGCTTTTGTTCCTTTC	58.109	37.500	0.00	0.00	0.00	2.62
1619	2235	5.652452	ACAGTTGTAGCTTTTGTTCCTTTCT	59.348	36.000	0.00	0.00	0.00	2.52
1620	2236	6.152831	ACAGTTGTAGCTTTTGTTCCTTTCTT	59.847	34.615	0.00	0.00	0.00	2.52
1621	2237	7.035612	CAGTTGTAGCTTTTGTTCCTTTCTTT	58.964	34.615	0.00	0.00	0.00	2.52
1622	2238	7.545615	CAGTTGTAGCTTTTGTTCCTTTCTTTT	59.454	33.333	0.00	0.00	0.00	2.27
1623	2239	8.094548	AGTTGTAGCTTTTGTTCCTTTCTTTTT	58.905	29.630	0.00	0.00	0.00	1.94
1640	2256	3.390175	TTTTTGAAAGTCACTGGGGGA	57.610	42.857	0.00	0.00	0.00	4.81
1641	2257	2.656947	TTTGAAAGTCACTGGGGGAG	57.343	50.000	0.00	0.00	0.00	4.30
1642	2258	0.771127	TTGAAAGTCACTGGGGGAGG	59.229	55.000	0.00	0.00	0.00	4.30
1643	2259	0.104672	TGAAAGTCACTGGGGGAGGA	60.105	55.000	0.00	0.00	0.00	3.71
1644	2260	0.615850	GAAAGTCACTGGGGGAGGAG	59.384	60.000	0.00	0.00	0.00	3.69
1645	2261	0.104409	AAAGTCACTGGGGGAGGAGT	60.104	55.000	0.00	0.00	0.00	3.85
1646	2262	0.545548	AAGTCACTGGGGGAGGAGTC	60.546	60.000	0.00	0.00	0.00	3.36
1647	2263	1.990614	GTCACTGGGGGAGGAGTCC	60.991	68.421	0.00	0.00	43.05	3.85
1659	2275	4.876752	GAGTCCCTCCACCTGAGT	57.123	61.111	0.00	0.00	39.65	3.41
1661	2277	1.770294	GAGTCCCTCCACCTGAGTAG	58.230	60.000	0.00	0.00	39.65	2.57
1682	2298	9.202273	GAGTAGCTTTTGTTCCTATGATATCAG	57.798	37.037	11.78	0.00	0.00	2.90
1742	2360	5.780793	ACTGTGTTACCTAGGATCAGTCTTT	59.219	40.000	17.98	0.00	30.43	2.52
1761	2379	6.208797	AGTCTTTTAAGAGTTTATGGCAACCC	59.791	38.462	0.00	0.00	35.18	4.11
1845	2468	1.200252	AGGATCGATATCAGGCGTTCG	59.800	52.381	0.00	0.00	33.41	3.95
2203	2829	4.869861	TCATATCCATAATGATGAACCGCG	59.130	41.667	0.00	0.00	34.73	6.46
2253	2883	8.475639	GTCAACAGGAGGAGATTATACTACAAA	58.524	37.037	0.00	0.00	0.00	2.83
2254	2884	8.475639	TCAACAGGAGGAGATTATACTACAAAC	58.524	37.037	0.00	0.00	0.00	2.93
2258	2888	6.490721	AGGAGGAGATTATACTACAAACCGAG	59.509	42.308	0.00	0.00	0.00	4.63

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
137	138	2.452600	TGGATGGAATAAAGCCCACC	57.547	50.000	0.00	0.00	34.92	4.61
239	240	9.809395	CCCCGAATCCTATATATACATAAGAGA	57.191	37.037	0.00	0.00	0.00	3.10
290	291	4.034858	CGTTACCTATGAGCACTTAGTCGA	59.965	45.833	3.92	0.00	0.00	4.20
313	314	6.811665	TCTCCATAAATACATGCACGCTATAC	59.188	38.462	0.00	0.00	0.00	1.47
318	319	3.187227	CCTCTCCATAAATACATGCACGC	59.813	47.826	0.00	0.00	0.00	5.34
320	321	5.468072	CACTCCTCTCCATAAATACATGCAC	59.532	44.000	0.00	0.00	0.00	4.57
345	346	9.692749	ATATTAGAAACACACTATACATGGACG	57.307	33.333	0.00	0.00	0.00	4.79
372	373	5.176958	ACTCAGGTTGATTCGTCGTAAAAAG	59.823	40.000	0.00	0.00	0.00	2.27
379	381	4.092771	TCTAACTCAGGTTGATTCGTCG	57.907	45.455	0.00	0.00	36.92	5.12
386	388	6.928348	TTCTAACCATCTAACTCAGGTTGA	57.072	37.500	5.98	0.00	43.71	3.18
429	432	6.293190	CGACCAGTGCATTTGTTAAGTTAGAA	60.293	38.462	0.00	0.00	0.00	2.10
433	436	3.880490	TCGACCAGTGCATTTGTTAAGTT	59.120	39.130	0.00	0.00	0.00	2.66
438	441	2.254546	TCTCGACCAGTGCATTTGTT	57.745	45.000	0.00	0.00	0.00	2.83
441	444	1.148310	CGTTCTCGACCAGTGCATTT	58.852	50.000	0.00	0.00	39.71	2.32
442	445	0.033504	ACGTTCTCGACCAGTGCATT	59.966	50.000	0.00	0.00	40.62	3.56
482	1056	1.102978	ATTTGGCTTATCCGTGGTGC	58.897	50.000	0.00	0.00	37.80	5.01
916	1493	4.189188	CAGCAGCGCTTCATGGCC	62.189	66.667	7.50	0.00	36.40	5.36
1161	1738	1.896660	GAAGCGTTGGAAGGTGCCA	60.897	57.895	0.00	0.00	35.78	4.92
1188	1765	1.896339	GCACAAGCACATACGTCGCA	61.896	55.000	0.00	0.00	41.58	5.10
1297	1874	9.883142	CCCTCTGTCCAGAAATATATTTAGATC	57.117	37.037	10.68	0.00	36.94	2.75
1298	1875	9.621239	TCCCTCTGTCCAGAAATATATTTAGAT	57.379	33.333	10.68	0.00	36.94	1.98
1299	1876	9.094578	CTCCCTCTGTCCAGAAATATATTTAGA	57.905	37.037	10.68	8.01	36.94	2.10
1300	1877	8.875168	ACTCCCTCTGTCCAGAAATATATTTAG	58.125	37.037	10.68	6.87	36.94	1.85
1301	1878	8.798975	ACTCCCTCTGTCCAGAAATATATTTA	57.201	34.615	10.68	0.00	36.94	1.40
1302	1879	7.698163	ACTCCCTCTGTCCAGAAATATATTT	57.302	36.000	10.51	10.51	36.94	1.40
1303	1880	7.789831	TGTACTCCCTCTGTCCAGAAATATATT	59.210	37.037	0.00	0.00	36.94	1.28
1304	1881	7.306013	TGTACTCCCTCTGTCCAGAAATATAT	58.694	38.462	0.00	0.00	36.94	0.86
1305	1882	6.679542	TGTACTCCCTCTGTCCAGAAATATA	58.320	40.000	0.00	0.00	36.94	0.86
1306	1883	5.529289	TGTACTCCCTCTGTCCAGAAATAT	58.471	41.667	0.00	0.00	36.94	1.28
1307	1884	4.942944	TGTACTCCCTCTGTCCAGAAATA	58.057	43.478	0.00	0.00	36.94	1.40
1308	1885	3.791320	TGTACTCCCTCTGTCCAGAAAT	58.209	45.455	0.00	0.00	36.94	2.17
1309	1886	3.254093	TGTACTCCCTCTGTCCAGAAA	57.746	47.619	0.00	0.00	36.94	2.52
1310	1887	2.992847	TGTACTCCCTCTGTCCAGAA	57.007	50.000	0.00	0.00	36.94	3.02
1311	1888	2.992847	TTGTACTCCCTCTGTCCAGA	57.007	50.000	0.00	0.00	35.85	3.86
1312	1889	2.099921	CGATTGTACTCCCTCTGTCCAG	59.900	54.545	0.00	0.00	0.00	3.86
1313	1890	2.100197	CGATTGTACTCCCTCTGTCCA	58.900	52.381	0.00	0.00	0.00	4.02
1314	1891	2.376109	TCGATTGTACTCCCTCTGTCC	58.624	52.381	0.00	0.00	0.00	4.02
1315	1892	4.657436	ATTCGATTGTACTCCCTCTGTC	57.343	45.455	0.00	0.00	0.00	3.51
1316	1893	5.069251	CCTAATTCGATTGTACTCCCTCTGT	59.931	44.000	0.00	0.00	0.00	3.41
1317	1894	5.533482	CCTAATTCGATTGTACTCCCTCTG	58.467	45.833	0.00	0.00	0.00	3.35
1318	1895	4.039366	GCCTAATTCGATTGTACTCCCTCT	59.961	45.833	0.00	0.00	0.00	3.69
1319	1896	4.308265	GCCTAATTCGATTGTACTCCCTC	58.692	47.826	0.00	0.00	0.00	4.30
1320	1897	3.071167	GGCCTAATTCGATTGTACTCCCT	59.929	47.826	0.00	0.00	0.00	4.20
1321	1898	3.181458	TGGCCTAATTCGATTGTACTCCC	60.181	47.826	3.32	0.00	0.00	4.30
1322	1899	4.067972	TGGCCTAATTCGATTGTACTCC	57.932	45.455	3.32	0.00	0.00	3.85
1323	1900	5.527582	ACATTGGCCTAATTCGATTGTACTC	59.472	40.000	3.32	0.00	0.00	2.59
1553	2169	4.873746	ACTGTAGTGTGCAGTAGAACAT	57.126	40.909	0.00	0.00	44.41	2.71
1620	2236	3.295973	CTCCCCCAGTGACTTTCAAAAA	58.704	45.455	0.00	0.00	0.00	1.94
1621	2237	2.424234	CCTCCCCCAGTGACTTTCAAAA	60.424	50.000	0.00	0.00	0.00	2.44
1622	2238	1.144913	CCTCCCCCAGTGACTTTCAAA	59.855	52.381	0.00	0.00	0.00	2.69
1623	2239	0.771127	CCTCCCCCAGTGACTTTCAA	59.229	55.000	0.00	0.00	0.00	2.69
1624	2240	0.104672	TCCTCCCCCAGTGACTTTCA	60.105	55.000	0.00	0.00	0.00	2.69
1625	2241	0.615850	CTCCTCCCCCAGTGACTTTC	59.384	60.000	0.00	0.00	0.00	2.62
1626	2242	0.104409	ACTCCTCCCCCAGTGACTTT	60.104	55.000	0.00	0.00	0.00	2.66
1627	2243	0.545548	GACTCCTCCCCCAGTGACTT	60.546	60.000	0.00	0.00	0.00	3.01
1628	2244	1.079438	GACTCCTCCCCCAGTGACT	59.921	63.158	0.00	0.00	0.00	3.41
1629	2245	1.990614	GGACTCCTCCCCCAGTGAC	60.991	68.421	0.00	0.00	0.00	3.67
1630	2246	2.450243	GGACTCCTCCCCCAGTGA	59.550	66.667	0.00	0.00	0.00	3.41
1649	2265	3.496160	GGAACAAAAGCTACTCAGGTGGA	60.496	47.826	0.00	0.00	31.35	4.02
1650	2266	2.814336	GGAACAAAAGCTACTCAGGTGG	59.186	50.000	0.00	0.00	31.35	4.61
1651	2267	3.744660	AGGAACAAAAGCTACTCAGGTG	58.255	45.455	0.00	0.00	31.35	4.00
1652	2268	5.248477	TCATAGGAACAAAAGCTACTCAGGT	59.752	40.000	0.00	0.00	0.00	4.00
1653	2269	5.734720	TCATAGGAACAAAAGCTACTCAGG	58.265	41.667	0.00	0.00	0.00	3.86
1654	2270	9.202273	GATATCATAGGAACAAAAGCTACTCAG	57.798	37.037	0.00	0.00	0.00	3.35
1655	2271	8.704668	TGATATCATAGGAACAAAAGCTACTCA	58.295	33.333	0.00	0.00	0.00	3.41
1656	2272	9.202273	CTGATATCATAGGAACAAAAGCTACTC	57.798	37.037	5.72	0.00	0.00	2.59
1657	2273	8.709308	ACTGATATCATAGGAACAAAAGCTACT	58.291	33.333	5.72	0.00	0.00	2.57
1658	2274	8.768955	CACTGATATCATAGGAACAAAAGCTAC	58.231	37.037	5.72	0.00	0.00	3.58
1659	2275	7.933577	CCACTGATATCATAGGAACAAAAGCTA	59.066	37.037	15.19	0.00	0.00	3.32
1660	2276	6.769822	CCACTGATATCATAGGAACAAAAGCT	59.230	38.462	15.19	0.00	0.00	3.74
1661	2277	6.767902	TCCACTGATATCATAGGAACAAAAGC	59.232	38.462	18.83	0.00	0.00	3.51
1682	2298	6.477360	GCAGCTCTTACTTAATTCTAGTCCAC	59.523	42.308	0.00	0.00	0.00	4.02
1742	2360	5.253330	CAGAGGGTTGCCATAAACTCTTAA	58.747	41.667	0.00	0.00	41.04	1.85
1761	2379	8.364142	TCTCTAGAAGAAGAAAAAGAACCAGAG	58.636	37.037	0.00	0.00	0.00	3.35
1845	2468	5.985781	TCAGAAGCAACAAAACGATAGAAC	58.014	37.500	0.00	0.00	41.38	3.01
1881	2504	5.381174	AGAAATAACCAACTTTAACGGGC	57.619	39.130	0.00	0.00	0.00	6.13
1962	2586	8.067189	GGCAAAACATAGTTTTGTAAATTGGTG	58.933	33.333	26.55	7.78	40.47	4.17
2203	2829	2.736400	GCATGATGCACTTAAGTTGCCC	60.736	50.000	13.36	14.75	44.26	5.36
2253	2883	6.401047	TTGCAGTTTATATACTAGCTCGGT	57.599	37.500	14.06	0.00	0.00	4.69
2254	2884	5.346281	GCTTGCAGTTTATATACTAGCTCGG	59.654	44.000	14.06	0.00	28.99	4.63
2258	2888	7.439655	AGTTCAGCTTGCAGTTTATATACTAGC	59.560	37.037	7.94	7.94	30.76	3.42

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.