AutoCloner

Multiple sequence alignment - TraesCS6A01G096400

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	TraesCS6A01G096400	chr6A	100.000	2126	0	0	1	2126	63611706	63609581	0.000000e+00	3927.0
1	TraesCS6A01G096400	chr6A	84.358	179	21	6	2	177	63638677	63638503	3.630000e-38	169.0
2	TraesCS6A01G096400	chr6D	89.612	2243	86	78	4	2122	52725852	52723633	0.000000e+00	2715.0
3	TraesCS6A01G096400	chr6B	94.041	1225	34	19	929	2123	119849749	119848534	0.000000e+00	1821.0
4	TraesCS6A01G096400	chr6B	83.072	957	58	51	2	888	119850762	119849840	0.000000e+00	774.0
5	TraesCS6A01G096400	chr7B	85.463	227	16	5	1351	1577	547711306	547711515	9.880000e-54	220.0
6	TraesCS6A01G096400	chr7D	88.889	135	4	4	1989	2112	37275867	37276001	2.820000e-34	156.0
7	TraesCS6A01G096400	chr7D	88.298	94	5	1	1345	1438	420082363	420082450	8.020000e-20	108.0
8	TraesCS6A01G096400	chr5D	88.889	135	4	4	1989	2112	297792759	297792625	2.820000e-34	156.0
9	TraesCS6A01G096400	chr5D	88.889	135	4	4	1989	2112	384073755	384073889	2.820000e-34	156.0
10	TraesCS6A01G096400	chr5D	98.039	51	1	0	1072	1122	285247438	285247488	2.910000e-14	89.8
11	TraesCS6A01G096400	chr5D	90.000	50	5	0	1077	1126	113391895	113391846	4.900000e-07	65.8
12	TraesCS6A01G096400	chr3D	88.889	135	4	4	1989	2112	70729664	70729798	2.820000e-34	156.0
13	TraesCS6A01G096400	chr3D	88.148	135	5	4	1989	2112	443945626	443945760	1.310000e-32	150.0
14	TraesCS6A01G096400	chr3D	98.182	55	1	0	1072	1126	252334799	252334853	1.740000e-16	97.1
15	TraesCS6A01G096400	chr2D	88.889	135	4	4	1989	2112	106236306	106236172	2.820000e-34	156.0
16	TraesCS6A01G096400	chr2D	88.889	135	4	4	1989	2112	422777646	422777512	2.820000e-34	156.0
17	TraesCS6A01G096400	chr1D	85.621	153	13	2	1333	1485	413940935	413941078	3.650000e-33	152.0
18	TraesCS6A01G096400	chr3A	87.879	132	7	5	1354	1485	531906055	531905933	1.700000e-31	147.0
19	TraesCS6A01G096400	chr3A	98.182	55	1	0	1072	1126	332220139	332220085	1.740000e-16	97.1
20	TraesCS6A01G096400	chr1A	85.816	141	11	3	1345	1485	467151152	467151283	7.910000e-30	141.0
21	TraesCS6A01G096400	chr4A	89.412	85	3	1	1354	1438	613673563	613673485	3.730000e-18	102.0
22	TraesCS6A01G096400	chr3B	98.182	55	1	0	1072	1126	313808032	313808086	1.740000e-16	97.1
23	TraesCS6A01G096400	chr5B	98.039	51	1	0	1072	1122	322858711	322858761	2.910000e-14	89.8
24	TraesCS6A01G096400	chr5A	98.039	51	1	0	1072	1122	377119607	377119657	2.910000e-14	89.8
25	TraesCS6A01G096400	chr2B	100.000	36	0	0	1370	1405	34588163	34588128	1.360000e-07	67.6

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	TraesCS6A01G096400	chr6A	63609581	63611706	2125	True	3927.0	3927	100.0000	1	2126	1	chr6A.!!$R1	2125
1	TraesCS6A01G096400	chr6D	52723633	52725852	2219	True	2715.0	2715	89.6120	4	2122	1	chr6D.!!$R1	2118
2	TraesCS6A01G096400	chr6B	119848534	119850762	2228	True	1297.5	1821	88.5565	2	2123	2	chr6B.!!$R1	2121

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
825	925	0.041833	TTCCTCCTCCTCCACTCCAG	59.958	60.0	0.0	0.0	0.0	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1823	2028	0.030603	GGGGGAGGATCTGAAGAGGT	60.031	60.0	0.0	0.0	33.73	3.85	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
47	49	4.384208	CCCACGAATCAAAAGAGGTCCTAT	60.384	45.833	0.00	0.00	0.00	2.57
48	50	5.163343	CCCACGAATCAAAAGAGGTCCTATA	60.163	44.000	0.00	0.00	0.00	1.31
49	51	5.986135	CCACGAATCAAAAGAGGTCCTATAG	59.014	44.000	0.00	0.00	0.00	1.31
50	52	6.407074	CCACGAATCAAAAGAGGTCCTATAGT	60.407	42.308	0.00	0.00	0.00	2.12
51	53	6.697892	CACGAATCAAAAGAGGTCCTATAGTC	59.302	42.308	0.00	0.00	0.00	2.59
52	54	6.183360	ACGAATCAAAAGAGGTCCTATAGTCC	60.183	42.308	0.00	1.31	0.00	3.85
53	55	5.793030	ATCAAAAGAGGTCCTATAGTCCG	57.207	43.478	0.00	0.00	0.00	4.79
54	56	4.607239	TCAAAAGAGGTCCTATAGTCCGT	58.393	43.478	0.00	0.00	0.00	4.69
55	57	5.759059	TCAAAAGAGGTCCTATAGTCCGTA	58.241	41.667	0.00	0.00	0.00	4.02
88	90	1.800655	CGAGGCTCGTGAGATTTGGAG	60.801	57.143	27.92	0.00	40.84	3.86
143	149	1.257936	CGTGATTCAAATCGTAGCCCG	59.742	52.381	0.00	0.00	38.26	6.13
144	150	1.003866	GTGATTCAAATCGTAGCCCGC	60.004	52.381	0.00	0.00	38.26	6.13
145	151	0.586802	GATTCAAATCGTAGCCCGCC	59.413	55.000	0.00	0.00	36.19	6.13
298	310	3.130340	AGACTCAGATTCTCTCCGCTTTC	59.870	47.826	0.00	0.00	0.00	2.62
299	311	2.828520	ACTCAGATTCTCTCCGCTTTCA	59.171	45.455	0.00	0.00	0.00	2.69
329	341	2.847234	CCGGGCCAGGGTAGCATA	60.847	66.667	15.20	0.00	0.00	3.14
349	366	2.415697	ATTTTCACTTTTCACCGCCG	57.584	45.000	0.00	0.00	0.00	6.46
442	477	2.548295	GGCCTCCTCTCTAGACGCG	61.548	68.421	3.53	3.53	0.00	6.01
515	552	0.463654	AGCCAAGTGAAGTGAACGCA	60.464	50.000	0.00	0.00	0.00	5.24
670	741	2.045242	CTCTGCTGTGCTGCCCAT	60.045	61.111	0.00	0.00	0.00	4.00
726	824	0.611200	ATCACATTCCCGTTCGTCCA	59.389	50.000	0.00	0.00	0.00	4.02
728	826	0.601576	CACATTCCCGTTCGTCCACA	60.602	55.000	0.00	0.00	0.00	4.17
825	925	0.041833	TTCCTCCTCCTCCACTCCAG	59.958	60.000	0.00	0.00	0.00	3.86
858	968	1.447945	CAGCGAGAGAGACAGAGTCA	58.552	55.000	0.00	0.00	34.60	3.41
869	979	4.162320	AGAGACAGAGTCAGTCTAGAGAGG	59.838	50.000	17.27	0.00	45.79	3.69
872	982	3.589735	ACAGAGTCAGTCTAGAGAGGGAA	59.410	47.826	0.00	0.00	32.51	3.97
873	983	4.199310	CAGAGTCAGTCTAGAGAGGGAAG	58.801	52.174	0.00	0.00	32.51	3.46
874	984	4.080582	CAGAGTCAGTCTAGAGAGGGAAGA	60.081	50.000	0.00	0.00	32.51	2.87
875	985	4.164221	AGAGTCAGTCTAGAGAGGGAAGAG	59.836	50.000	0.00	0.00	31.71	2.85
876	986	4.108570	AGTCAGTCTAGAGAGGGAAGAGA	58.891	47.826	0.00	0.00	0.00	3.10
879	989	3.632145	CAGTCTAGAGAGGGAAGAGAAGC	59.368	52.174	0.00	0.00	0.00	3.86
880	990	3.268334	AGTCTAGAGAGGGAAGAGAAGCA	59.732	47.826	0.00	0.00	0.00	3.91
881	991	3.632145	GTCTAGAGAGGGAAGAGAAGCAG	59.368	52.174	0.00	0.00	0.00	4.24
894	1065	2.232298	GAAGCAGGGAGAGGTCGGTG	62.232	65.000	0.00	0.00	0.00	4.94
933	1108	2.287849	GCTTGGTTGGTTGCTTCTCTTC	60.288	50.000	0.00	0.00	0.00	2.87
1139	1314	1.760613	CTCATAAACTACTCGCCCCCA	59.239	52.381	0.00	0.00	0.00	4.96
1140	1315	2.368875	CTCATAAACTACTCGCCCCCAT	59.631	50.000	0.00	0.00	0.00	4.00
1141	1316	3.576982	CTCATAAACTACTCGCCCCCATA	59.423	47.826	0.00	0.00	0.00	2.74
1247	1434	3.786586	GTCGTCGTCGTCGCCTCT	61.787	66.667	7.01	0.00	38.33	3.69
1248	1435	3.485431	TCGTCGTCGTCGCCTCTC	61.485	66.667	7.01	0.00	38.33	3.20
1249	1436	3.488978	CGTCGTCGTCGCCTCTCT	61.489	66.667	0.00	0.00	36.96	3.10
1250	1437	2.163390	CGTCGTCGTCGCCTCTCTA	61.163	63.158	0.00	0.00	36.96	2.43
1251	1438	1.637402	GTCGTCGTCGCCTCTCTAG	59.363	63.158	0.00	0.00	36.96	2.43
1252	1439	0.805322	GTCGTCGTCGCCTCTCTAGA	60.805	60.000	0.00	0.00	36.96	2.43
1253	1440	0.528033	TCGTCGTCGCCTCTCTAGAG	60.528	60.000	13.98	13.98	37.59	2.43
1323	1510	3.525268	ACAACAACAAAGGAAAGCAGG	57.475	42.857	0.00	0.00	0.00	4.85
1346	1537	4.065281	CCTGCCTGCTTGCTTGGC	62.065	66.667	17.89	17.89	46.26	4.52
1786	1991	3.646715	CCACCACCACCGACCCAT	61.647	66.667	0.00	0.00	0.00	4.00
1918	2125	4.144681	GCACAAGAGCGAGCGCAG	62.145	66.667	17.68	3.93	44.88	5.18
1970	2180	6.547880	TGCTTCTGGTGTTTCAGGTTAATTAA	59.452	34.615	0.00	0.00	35.58	1.40
1971	2181	6.861572	GCTTCTGGTGTTTCAGGTTAATTAAC	59.138	38.462	18.30	18.30	35.58	2.01
2011	2226	0.594602	GTGGAGTTTTTACCGCACCC	59.405	55.000	0.00	0.00	36.77	4.61
2123	2338	3.472263	CATGCATGCATCACCATCG	57.528	52.632	30.07	13.50	33.90	3.84
2124	2339	0.948678	CATGCATGCATCACCATCGA	59.051	50.000	30.07	0.00	33.90	3.59
2125	2340	1.539827	CATGCATGCATCACCATCGAT	59.460	47.619	30.07	3.48	33.90	3.59

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	8.306313	GGAACCTGGAAAATTTGTAGGAATAT	57.694	34.615	17.65	5.67	32.86	1.28
1	2	7.712204	GGAACCTGGAAAATTTGTAGGAATA	57.288	36.000	17.65	0.00	32.86	1.75
2	3	6.605471	GGAACCTGGAAAATTTGTAGGAAT	57.395	37.500	17.65	9.18	32.86	3.01
21	22	3.146847	ACCTCTTTTGATTCGTGGGAAC	58.853	45.455	0.00	0.00	34.37	3.62
94	99	0.542232	AGTCTAGCAACGGACCAGGT	60.542	55.000	0.00	0.00	33.39	4.00
228	240	0.906756	CCTCTGTCTGGGCTCCAAGA	60.907	60.000	0.00	0.00	30.80	3.02
319	331	7.309805	GGTGAAAAGTGAAAATTATGCTACCCT	60.310	37.037	0.00	0.00	0.00	4.34
329	341	2.544903	CCGGCGGTGAAAAGTGAAAATT	60.545	45.455	19.97	0.00	0.00	1.82
442	477	3.044305	GTGTGCTGACTGGCGGAC	61.044	66.667	0.00	0.00	34.52	4.79
574	630	0.755686	GAGTGGATCCGAGGCTGAAT	59.244	55.000	7.39	0.00	0.00	2.57
627	683	0.674581	TGCAGGAATGGCTGAACGAG	60.675	55.000	0.00	0.00	0.00	4.18
628	684	0.035152	ATGCAGGAATGGCTGAACGA	60.035	50.000	0.00	0.00	0.00	3.85
631	687	1.324740	GGCATGCAGGAATGGCTGAA	61.325	55.000	21.36	0.00	46.63	3.02
667	738	2.350522	GAATGGGAATCCGATCGATGG	58.649	52.381	18.66	0.00	35.24	3.51
669	740	1.279271	GGGAATGGGAATCCGATCGAT	59.721	52.381	18.66	0.00	37.87	3.59
670	741	0.685097	GGGAATGGGAATCCGATCGA	59.315	55.000	18.66	2.91	37.87	3.59
710	808	0.601841	GTGTGGACGAACGGGAATGT	60.602	55.000	0.00	0.00	0.00	2.71
858	968	3.268334	TGCTTCTCTTCCCTCTCTAGACT	59.732	47.826	0.00	0.00	0.00	3.24
869	979	0.829990	CCTCTCCCTGCTTCTCTTCC	59.170	60.000	0.00	0.00	0.00	3.46
872	982	0.682855	CGACCTCTCCCTGCTTCTCT	60.683	60.000	0.00	0.00	0.00	3.10
873	983	1.671901	CCGACCTCTCCCTGCTTCTC	61.672	65.000	0.00	0.00	0.00	2.87
874	984	1.684049	CCGACCTCTCCCTGCTTCT	60.684	63.158	0.00	0.00	0.00	2.85
875	985	1.985116	ACCGACCTCTCCCTGCTTC	60.985	63.158	0.00	0.00	0.00	3.86
876	986	2.120718	ACCGACCTCTCCCTGCTT	59.879	61.111	0.00	0.00	0.00	3.91
879	989	0.972983	ATGACACCGACCTCTCCCTG	60.973	60.000	0.00	0.00	0.00	4.45
880	990	0.684805	GATGACACCGACCTCTCCCT	60.685	60.000	0.00	0.00	0.00	4.20
881	991	1.677637	GGATGACACCGACCTCTCCC	61.678	65.000	0.00	0.00	0.00	4.30
894	1065	1.510480	GCTAGGCGGCAATGGATGAC	61.510	60.000	13.08	0.00	0.00	3.06
933	1108	4.426313	GGGTTGCCTCCGGGAAGG	62.426	72.222	0.00	2.45	42.97	3.46
1139	1314	1.710709	AGAGGAGGGGGAGGGCTAT	60.711	63.158	0.00	0.00	0.00	2.97
1140	1315	2.288847	AGAGGAGGGGGAGGGCTA	60.289	66.667	0.00	0.00	0.00	3.93
1141	1316	3.773154	GAGAGGAGGGGGAGGGCT	61.773	72.222	0.00	0.00	0.00	5.19
1245	1432	4.340097	CGGACTGACTCTAGACTCTAGAGA	59.660	50.000	35.23	20.63	42.68	3.10
1247	1434	4.025360	ACGGACTGACTCTAGACTCTAGA	58.975	47.826	14.05	14.05	0.00	2.43
1248	1435	4.395959	ACGGACTGACTCTAGACTCTAG	57.604	50.000	6.74	6.74	0.00	2.43
1249	1436	4.202141	GCTACGGACTGACTCTAGACTCTA	60.202	50.000	0.00	0.00	0.00	2.43
1250	1437	3.431207	GCTACGGACTGACTCTAGACTCT	60.431	52.174	0.00	0.00	0.00	3.24
1251	1438	2.867975	GCTACGGACTGACTCTAGACTC	59.132	54.545	0.00	0.00	0.00	3.36
1252	1439	2.502538	AGCTACGGACTGACTCTAGACT	59.497	50.000	0.00	0.00	0.00	3.24
1253	1440	2.610374	CAGCTACGGACTGACTCTAGAC	59.390	54.545	0.00	0.00	37.32	2.59
1323	1510	3.060615	CAAGCAGGCAGGCACTCC	61.061	66.667	0.00	0.00	34.60	3.85
1785	1990	3.458163	TCGAAGCCGCCGAGGAAT	61.458	61.111	0.91	0.00	45.00	3.01
1786	1991	4.430765	GTCGAAGCCGCCGAGGAA	62.431	66.667	0.91	0.00	45.00	3.36
1812	2017	1.062880	CTGAAGAGGTAGTCGTCGAGC	59.937	57.143	0.00	0.00	36.52	5.03
1813	2018	2.619147	TCTGAAGAGGTAGTCGTCGAG	58.381	52.381	0.00	0.00	36.52	4.04
1818	2023	2.882137	GGAGGATCTGAAGAGGTAGTCG	59.118	54.545	0.00	0.00	33.73	4.18
1823	2028	0.030603	GGGGGAGGATCTGAAGAGGT	60.031	60.000	0.00	0.00	33.73	3.85
1892	2097	2.952245	CTCTTGTGCTGCTGCCAC	59.048	61.111	13.47	11.36	38.71	5.01
1939	2149	2.158623	TGAAACACCAGAAGCATCAGGT	60.159	45.455	0.00	0.00	45.55	4.00
1970	2180	3.418995	TGCTCTCCGAGTTTGTAGTAGT	58.581	45.455	0.00	0.00	31.39	2.73
1971	2181	3.440872	ACTGCTCTCCGAGTTTGTAGTAG	59.559	47.826	0.00	0.00	31.39	2.57
1991	2206	1.601166	GGTGCGGTAAAAACTCCACT	58.399	50.000	0.00	0.00	0.00	4.00

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.