AutoCloner

Multiple sequence alignment - TraesCS1A01G376200

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	TraesCS1A01G376200	chr1A	100.000	2288	0	0	1	2288	550447986	550445699	0.000000e+00	4226
1	TraesCS1A01G376200	chr1A	94.030	67	4	0	1500	1566	550446441	550446375	4.020000e-18	102
2	TraesCS1A01G376200	chr1A	94.030	67	4	0	1546	1612	550446487	550446421	4.020000e-18	102
3	TraesCS1A01G376200	chr2D	94.314	1319	71	3	1	1318	480564150	480562835	0.000000e+00	2017
4	TraesCS1A01G376200	chr3A	93.992	1315	78	1	1	1315	435815340	435816653	0.000000e+00	1989
5	TraesCS1A01G376200	chrUn	93.263	1321	86	2	1	1320	200754915	200756233	0.000000e+00	1943
6	TraesCS1A01G376200	chrUn	93.025	1319	89	2	1	1318	200673339	200672023	0.000000e+00	1923
7	TraesCS1A01G376200	chrUn	93.025	1319	89	2	1	1318	200779850	200781166	0.000000e+00	1923
8	TraesCS1A01G376200	chr6A	93.511	1310	79	6	1	1307	532535781	532534475	0.000000e+00	1943
9	TraesCS1A01G376200	chr6B	93.090	1317	88	2	1	1316	8638756	8640070	0.000000e+00	1925
10	TraesCS1A01G376200	chr6B	93.030	1320	89	2	1	1319	8650926	8652243	0.000000e+00	1925
11	TraesCS1A01G376200	chr6B	92.955	1320	90	2	1	1319	8710380	8711697	0.000000e+00	1919
12	TraesCS1A01G376200	chr1B	87.029	956	69	26	1362	2288	628055043	628054114	0.000000e+00	1027
13	TraesCS1A01G376200	chr1D	92.308	598	36	6	1701	2288	457976574	457975977	0.000000e+00	841
14	TraesCS1A01G376200	chr1D	92.083	240	9	3	1454	1683	457977164	457976925	1.690000e-86	329
15	TraesCS1A01G376200	chr2B	83.607	244	22	12	2050	2278	23110294	23110054	1.780000e-51	213
16	TraesCS1A01G376200	chr2B	80.451	266	40	7	1632	1897	23110708	23110455	2.320000e-45	193
17	TraesCS1A01G376200	chr2B	83.920	199	22	6	2097	2288	360971682	360971877	5.020000e-42	182
18	TraesCS1A01G376200	chr2A	83.920	199	22	6	2097	2288	387646776	387646581	5.020000e-42	182

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	TraesCS1A01G376200	chr1A	550445699	550447986	2287	True	1476.666667	4226	96.0200	1	2288	3	chr1A.!!$R1	2287
1	TraesCS1A01G376200	chr2D	480562835	480564150	1315	True	2017.000000	2017	94.3140	1	1318	1	chr2D.!!$R1	1317
2	TraesCS1A01G376200	chr3A	435815340	435816653	1313	False	1989.000000	1989	93.9920	1	1315	1	chr3A.!!$F1	1314
3	TraesCS1A01G376200	chrUn	200754915	200756233	1318	False	1943.000000	1943	93.2630	1	1320	1	chrUn.!!$F1	1319
4	TraesCS1A01G376200	chrUn	200672023	200673339	1316	True	1923.000000	1923	93.0250	1	1318	1	chrUn.!!$R1	1317
5	TraesCS1A01G376200	chrUn	200779850	200781166	1316	False	1923.000000	1923	93.0250	1	1318	1	chrUn.!!$F2	1317
6	TraesCS1A01G376200	chr6A	532534475	532535781	1306	True	1943.000000	1943	93.5110	1	1307	1	chr6A.!!$R1	1306
7	TraesCS1A01G376200	chr6B	8638756	8640070	1314	False	1925.000000	1925	93.0900	1	1316	1	chr6B.!!$F1	1315
8	TraesCS1A01G376200	chr6B	8650926	8652243	1317	False	1925.000000	1925	93.0300	1	1319	1	chr6B.!!$F2	1318
9	TraesCS1A01G376200	chr6B	8710380	8711697	1317	False	1919.000000	1919	92.9550	1	1319	1	chr6B.!!$F3	1318
10	TraesCS1A01G376200	chr1B	628054114	628055043	929	True	1027.000000	1027	87.0290	1362	2288	1	chr1B.!!$R1	926
11	TraesCS1A01G376200	chr1D	457975977	457977164	1187	True	585.000000	841	92.1955	1454	2288	2	chr1D.!!$R1	834
12	TraesCS1A01G376200	chr2B	23110054	23110708	654	True	203.000000	213	82.0290	1632	2278	2	chr2B.!!$R1	646

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
466	468	0.03601	ATGGGCAAGAGGACACGAAG	60.036	55.0	0.0	0.0	0.0	3.79	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1351	1357	0.036875	GACAAGAAGGAGGGGTGGTG	59.963	60.0	0.0	0.0	0.0	4.17	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
115	116	7.169158	TGAAGATTTGGTGAGACAAACTTTT	57.831	32.000	0.00	0.00	42.51	2.27
124	125	4.270808	GTGAGACAAACTTTTTGGCCAATG	59.729	41.667	21.26	15.88	0.00	2.82
135	136	1.454847	GGCCAATGGATGCCCGTAA	60.455	57.895	2.05	0.00	41.97	3.18
187	188	6.542005	ACAATATGTCGGACTTTATTGCATGA	59.458	34.615	26.45	2.85	0.00	3.07
195	197	7.118390	GTCGGACTTTATTGCATGAAGCTATAT	59.882	37.037	0.00	0.00	45.94	0.86
253	255	2.353109	GGAGGAATGGAAAAAGCAGCAC	60.353	50.000	0.00	0.00	0.00	4.40
256	258	1.269448	GAATGGAAAAAGCAGCACGGA	59.731	47.619	0.00	0.00	0.00	4.69
408	410	1.777030	CGCGTTACACTGGCCAACAA	61.777	55.000	7.01	0.00	0.00	2.83
437	439	2.530460	AACTCAGCCAATATGCCCAA	57.470	45.000	0.00	0.00	0.00	4.12
442	444	0.754472	AGCCAATATGCCCAACATGC	59.246	50.000	0.00	0.00	40.06	4.06
466	468	0.036010	ATGGGCAAGAGGACACGAAG	60.036	55.000	0.00	0.00	0.00	3.79
481	483	6.480320	AGGACACGAAGCATGTATTATTTCTC	59.520	38.462	0.00	0.00	0.00	2.87
487	489	6.238456	CGAAGCATGTATTATTTCTCTGCCAA	60.238	38.462	0.00	0.00	0.00	4.52
505	507	3.678529	GCCAAAAGGCAAAAGAAGTGTGA	60.679	43.478	0.84	0.00	34.62	3.58
518	520	5.779241	AGAAGTGTGAGAATATTTGGGGA	57.221	39.130	0.00	0.00	0.00	4.81
531	533	2.435372	TTGGGGATGTATGAAGTGGC	57.565	50.000	0.00	0.00	0.00	5.01
598	602	6.994496	TGAATTCTTACTCCTTATGCCTGATG	59.006	38.462	7.05	0.00	0.00	3.07
624	628	0.559205	TACCTATCTTGGGCTCCCGA	59.441	55.000	0.00	0.00	39.42	5.14
644	648	3.279434	GAAATGCAGGGGAACTAATCGT	58.721	45.455	0.00	0.00	0.00	3.73
739	743	0.403271	CTCCATGGGGATTAGGGCTG	59.597	60.000	5.34	0.00	43.91	4.85
814	818	3.785859	GGCGCAGACCTCCCATGA	61.786	66.667	10.83	0.00	0.00	3.07
896	900	3.494048	GGGGCTGTTATCAGAGATGACAG	60.494	52.174	20.92	20.92	43.76	3.51
923	927	9.275572	AGGAAATTTCATAGTAGGTGGTAACTA	57.724	33.333	19.49	0.00	32.98	2.24
933	937	9.710818	ATAGTAGGTGGTAACTAGAAGATTCAA	57.289	33.333	0.00	0.00	32.01	2.69
946	950	6.161855	AGAAGATTCAATACTGTGCGGATA	57.838	37.500	0.00	0.00	0.00	2.59
975	979	0.888619	CGGAGGTGTTAGCACTCAGA	59.111	55.000	9.71	0.00	44.65	3.27
990	994	6.296026	AGCACTCAGATTTGGTTTACTGTTA	58.704	36.000	0.00	0.00	0.00	2.41
1136	1142	2.971330	TGGGCTGTGATTTTCCACAAAT	59.029	40.909	0.00	0.00	45.27	2.32
1183	1189	4.258702	ACGAACAAAGTAGCTCATGAGT	57.741	40.909	23.38	12.80	0.00	3.41
1237	1243	3.328931	GGATTGGATAGAGAAGCCCATGA	59.671	47.826	0.00	0.00	0.00	3.07
1362	1368	1.491668	AAAAACAACACCACCCCTCC	58.508	50.000	0.00	0.00	0.00	4.30
1363	1369	0.634465	AAAACAACACCACCCCTCCT	59.366	50.000	0.00	0.00	0.00	3.69
1364	1370	0.634465	AAACAACACCACCCCTCCTT	59.366	50.000	0.00	0.00	0.00	3.36
1365	1371	0.185175	AACAACACCACCCCTCCTTC	59.815	55.000	0.00	0.00	0.00	3.46
1366	1372	0.697854	ACAACACCACCCCTCCTTCT	60.698	55.000	0.00	0.00	0.00	2.85
1382	1388	5.110814	TCCTTCTTGTCTGTCAAAAGGAA	57.889	39.130	18.60	7.63	39.34	3.36
1383	1389	5.505780	TCCTTCTTGTCTGTCAAAAGGAAA	58.494	37.500	18.60	7.04	39.34	3.13
1384	1390	5.949354	TCCTTCTTGTCTGTCAAAAGGAAAA	59.051	36.000	18.60	6.61	39.34	2.29
1385	1391	6.435904	TCCTTCTTGTCTGTCAAAAGGAAAAA	59.564	34.615	18.60	6.39	39.34	1.94
1415	1421	2.859422	CCCCTCCCCTCGCCTATA	59.141	66.667	0.00	0.00	0.00	1.31
1420	1426	1.686741	CCTCCCCTCGCCTATATCTCC	60.687	61.905	0.00	0.00	0.00	3.71
1421	1427	0.335361	TCCCCTCGCCTATATCTCCC	59.665	60.000	0.00	0.00	0.00	4.30
1425	1431	1.096416	CTCGCCTATATCTCCCGACC	58.904	60.000	0.00	0.00	0.00	4.79
1426	1432	0.697079	TCGCCTATATCTCCCGACCT	59.303	55.000	0.00	0.00	0.00	3.85
1427	1433	1.096416	CGCCTATATCTCCCGACCTC	58.904	60.000	0.00	0.00	0.00	3.85
1428	1434	1.096416	GCCTATATCTCCCGACCTCG	58.904	60.000	0.00	0.00	39.44	4.63
1429	1435	1.096416	CCTATATCTCCCGACCTCGC	58.904	60.000	0.00	0.00	38.18	5.03
1430	1436	1.096416	CTATATCTCCCGACCTCGCC	58.904	60.000	0.00	0.00	38.18	5.54
1432	1438	3.687509	TATATCTCCCGACCTCGCCCC	62.688	61.905	0.00	0.00	38.18	5.80
1705	2072	2.040359	CCTCCCCCTCCCTCCTTC	60.040	72.222	0.00	0.00	0.00	3.46
1706	2073	2.040359	CTCCCCCTCCCTCCTTCC	60.040	72.222	0.00	0.00	0.00	3.46
1728	2098	1.206371	CCCTAGGGTTTCGTTGTCGAT	59.794	52.381	20.88	0.00	45.65	3.59
1969	2340	0.823356	TGGAGTTTGGACAGGCTTGC	60.823	55.000	0.00	0.00	0.00	4.01
2093	2508	4.712337	TGTAGTTTTTGCCTTTTTGGGAGA	59.288	37.500	0.00	0.00	37.50	3.71
2095	2510	3.774766	AGTTTTTGCCTTTTTGGGAGACT	59.225	39.130	0.00	0.00	37.50	3.24
2116	2532	6.495872	AGACTTATCCGGGCACTACATATTTA	59.504	38.462	0.00	0.00	0.00	1.40
2134	2550	9.407380	ACATATTTATTGTGATTGAGCTAACCA	57.593	29.630	0.00	0.00	0.00	3.67
2140	2559	5.426689	TGTGATTGAGCTAACCATCTTCT	57.573	39.130	0.00	0.00	0.00	2.85
2141	2560	5.809001	TGTGATTGAGCTAACCATCTTCTT	58.191	37.500	0.00	0.00	0.00	2.52
2209	2632	4.813161	CGAGATAATGGTGAGTTCATTGCT	59.187	41.667	0.00	0.00	36.40	3.91
2239	2666	6.826668	TGTTAAGCAGCTAGGCAATCTTATA	58.173	36.000	0.00	0.00	35.83	0.98
2278	2706	2.884827	GCATTGGTCTCATGCCTTTTC	58.115	47.619	0.00	0.00	35.44	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
124	125	1.540580	GCTAGGACTTTACGGGCATCC	60.541	57.143	0.00	0.00	0.00	3.51
135	136	1.249407	GATCGGGATCGCTAGGACTT	58.751	55.000	8.28	0.00	36.13	3.01
253	255	5.428253	TCTGAGTATTCCAATTTCCTTCCG	58.572	41.667	0.00	0.00	0.00	4.30
256	258	5.595952	GCCATCTGAGTATTCCAATTTCCTT	59.404	40.000	0.00	0.00	0.00	3.36
309	311	6.316390	ACAAGCTAATTTTCAGATCTTACCCG	59.684	38.462	0.00	0.00	0.00	5.28
375	377	1.233285	AACGCGACACGGTAGAGTCT	61.233	55.000	15.93	0.00	42.60	3.24
408	410	8.143835	GGCATATTGGCTGAGTTTTTATATGTT	58.856	33.333	0.00	0.00	40.14	2.71
437	439	0.040058	TCTTGCCCATCCAAGCATGT	59.960	50.000	0.00	0.00	41.47	3.21
442	444	0.329261	TGTCCTCTTGCCCATCCAAG	59.671	55.000	0.00	0.00	42.73	3.61
466	468	6.698766	CCTTTTGGCAGAGAAATAATACATGC	59.301	38.462	0.00	0.00	0.00	4.06
487	489	5.859205	ATTCTCACACTTCTTTTGCCTTT	57.141	34.783	0.00	0.00	0.00	3.11
505	507	7.006509	CCACTTCATACATCCCCAAATATTCT	58.993	38.462	0.00	0.00	0.00	2.40
551	555	2.232298	GACTTCCTCTCCTGCACGGG	62.232	65.000	2.86	0.00	0.00	5.28
566	570	7.554476	GCATAAGGAGTAAGAATTCAAGGACTT	59.446	37.037	8.44	7.27	0.00	3.01
598	602	5.249420	GGAGCCCAAGATAGGTAATTCATC	58.751	45.833	0.00	0.00	0.00	2.92
624	628	3.366052	ACGATTAGTTCCCCTGCATTT	57.634	42.857	0.00	0.00	0.00	2.32
644	648	6.714810	CCACCATAAATACCAAGCAGCTATAA	59.285	38.462	0.00	0.00	0.00	0.98
739	743	7.010091	GTGGGCATTTACATAATTTGCTGTTAC	59.990	37.037	0.00	0.00	0.00	2.50
814	818	6.650390	GCATCCACATTCAATTTAACAAACCT	59.350	34.615	0.00	0.00	0.00	3.50
876	880	4.501229	CCTCTGTCATCTCTGATAACAGCC	60.501	50.000	6.09	0.00	43.17	4.85
896	900	8.265764	AGTTACCACCTACTATGAAATTTCCTC	58.734	37.037	15.48	0.00	0.00	3.71
923	927	4.471904	TCCGCACAGTATTGAATCTTCT	57.528	40.909	0.00	0.00	0.00	2.85
933	937	3.288092	TGTCAGAGTATCCGCACAGTAT	58.712	45.455	0.00	0.00	33.66	2.12
946	950	1.115930	AACACCTCCGCTGTCAGAGT	61.116	55.000	3.32	0.00	0.00	3.24
962	966	6.204688	CAGTAAACCAAATCTGAGTGCTAACA	59.795	38.462	0.00	0.00	0.00	2.41
1118	1124	4.874970	ACTGATTTGTGGAAAATCACAGC	58.125	39.130	8.95	0.00	46.61	4.40
1205	1211	6.352016	TCTCTATCCAATCCTTAGTCATGC	57.648	41.667	0.00	0.00	0.00	4.06
1214	1220	3.066208	TGGGCTTCTCTATCCAATCCT	57.934	47.619	0.00	0.00	0.00	3.24
1343	1349	1.007842	AGGAGGGGTGGTGTTGTTTTT	59.992	47.619	0.00	0.00	0.00	1.94
1344	1350	0.634465	AGGAGGGGTGGTGTTGTTTT	59.366	50.000	0.00	0.00	0.00	2.43
1345	1351	0.634465	AAGGAGGGGTGGTGTTGTTT	59.366	50.000	0.00	0.00	0.00	2.83
1346	1352	0.185175	GAAGGAGGGGTGGTGTTGTT	59.815	55.000	0.00	0.00	0.00	2.83
1347	1353	0.697854	AGAAGGAGGGGTGGTGTTGT	60.698	55.000	0.00	0.00	0.00	3.32
1348	1354	0.478507	AAGAAGGAGGGGTGGTGTTG	59.521	55.000	0.00	0.00	0.00	3.33
1349	1355	0.478507	CAAGAAGGAGGGGTGGTGTT	59.521	55.000	0.00	0.00	0.00	3.32
1350	1356	0.697854	ACAAGAAGGAGGGGTGGTGT	60.698	55.000	0.00	0.00	0.00	4.16
1351	1357	0.036875	GACAAGAAGGAGGGGTGGTG	59.963	60.000	0.00	0.00	0.00	4.17
1352	1358	0.104409	AGACAAGAAGGAGGGGTGGT	60.104	55.000	0.00	0.00	0.00	4.16
1353	1359	0.326264	CAGACAAGAAGGAGGGGTGG	59.674	60.000	0.00	0.00	0.00	4.61
1354	1360	1.002544	GACAGACAAGAAGGAGGGGTG	59.997	57.143	0.00	0.00	0.00	4.61
1355	1361	1.353091	GACAGACAAGAAGGAGGGGT	58.647	55.000	0.00	0.00	0.00	4.95
1356	1362	1.352083	TGACAGACAAGAAGGAGGGG	58.648	55.000	0.00	0.00	0.00	4.79
1357	1363	3.492102	TTTGACAGACAAGAAGGAGGG	57.508	47.619	0.00	0.00	39.77	4.30
1358	1364	3.817647	CCTTTTGACAGACAAGAAGGAGG	59.182	47.826	15.09	4.75	42.40	4.30
1359	1365	4.708177	TCCTTTTGACAGACAAGAAGGAG	58.292	43.478	17.11	2.49	42.87	3.69
1360	1366	4.771114	TCCTTTTGACAGACAAGAAGGA	57.229	40.909	17.11	17.11	43.95	3.36
1361	1367	5.835113	TTTCCTTTTGACAGACAAGAAGG	57.165	39.130	14.51	14.51	41.88	3.46
1385	1391	1.895231	GAGGGGGCGTGTCGTTTTT	60.895	57.895	0.00	0.00	0.00	1.94
1386	1392	2.281276	GAGGGGGCGTGTCGTTTT	60.281	61.111	0.00	0.00	0.00	2.43
1411	1417	1.096416	GGCGAGGTCGGGAGATATAG	58.904	60.000	0.89	0.00	43.27	1.31
1742	2112	0.317269	CCAATTATTCGCCGCAGCAG	60.317	55.000	0.00	0.00	39.83	4.24
1746	2116	0.393132	TCCACCAATTATTCGCCGCA	60.393	50.000	0.00	0.00	0.00	5.69
1752	2122	4.918810	AGCCGAAATCCACCAATTATTC	57.081	40.909	0.00	0.00	0.00	1.75
2093	2508	5.562298	AAATATGTAGTGCCCGGATAAGT	57.438	39.130	0.73	0.00	0.00	2.24
2095	2510	7.389330	CACAATAAATATGTAGTGCCCGGATAA	59.611	37.037	0.73	0.00	0.00	1.75
2116	2532	6.421485	AGAAGATGGTTAGCTCAATCACAAT	58.579	36.000	0.00	0.00	27.35	2.71
2167	2590	3.009115	CCCAAGCCTTCCCCTCGA	61.009	66.667	0.00	0.00	0.00	4.04
2239	2666	8.148999	ACCAATGCCAAAATAAATTGCAAATTT	58.851	25.926	1.71	2.15	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.