AutoCloner

Multiple sequence alignment - TraesCS7D01G491800

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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	TraesCS7D01G491800	chr7D	100.000	2237	0	0	1	2237	600863742	600865978	0.000000e+00	4132.0
1	TraesCS7D01G491800	chr7B	95.118	1270	40	5	1	1253	680073701	680074965	0.000000e+00	1982.0
2	TraesCS7D01G491800	chr7B	94.265	1081	33	14	1	1058	707879509	707880583	0.000000e+00	1626.0
3	TraesCS7D01G491800	chr7B	92.197	833	40	7	1347	2155	680074968	680075799	0.000000e+00	1155.0
4	TraesCS7D01G491800	chr7B	92.661	654	28	5	1400	2037	707881132	707881781	0.000000e+00	924.0
5	TraesCS7D01G491800	chr7B	90.229	481	32	2	1690	2155	707883196	707883676	4.080000e-172	614.0
6	TraesCS7D01G491800	chr7B	95.789	190	7	1	1051	1239	707880730	707880919	2.790000e-79	305.0
7	TraesCS7D01G491800	chr6D	87.529	1275	92	36	498	1734	459552023	459550778	0.000000e+00	1411.0
8	TraesCS7D01G491800	chr6D	88.571	840	72	9	414	1241	471112251	471113078	0.000000e+00	998.0
9	TraesCS7D01G491800	chr6D	86.559	930	94	15	355	1273	471277083	471276174	0.000000e+00	996.0
10	TraesCS7D01G491800	chr6D	86.928	153	16	4	76	225	471103970	471104121	3.820000e-38	169.0
11	TraesCS7D01G491800	chr6D	87.705	122	10	4	1368	1484	471276148	471276027	1.080000e-28	137.0
12	TraesCS7D01G491800	chr6D	79.762	168	18	9	89	249	459552417	459552259	8.450000e-20	108.0
13	TraesCS7D01G491800	chr2B	86.519	1261	101	29	521	1734	771415462	771416700	0.000000e+00	1323.0
14	TraesCS7D01G491800	chr2B	87.270	707	61	13	1049	1734	771480033	771480731	0.000000e+00	780.0
15	TraesCS7D01G491800	chr7A	93.234	872	31	8	1286	2142	692784895	692785753	0.000000e+00	1258.0
16	TraesCS7D01G491800	chr7A	97.568	329	8	0	914	1242	692784569	692784897	4.170000e-157	564.0
17	TraesCS7D01G491800	chr6A	82.415	1416	165	48	816	2153	616056291	616054882	0.000000e+00	1158.0
18	TraesCS7D01G491800	chr6A	87.712	472	47	4	355	822	616057206	616056742	7.030000e-150	540.0
19	TraesCS7D01G491800	chr6A	85.279	197	25	4	18	210	616094440	616094244	1.350000e-47	200.0
20	TraesCS7D01G491800	chr6B	87.933	895	91	7	355	1241	719307903	719308788	0.000000e+00	1038.0
21	TraesCS7D01G491800	chr6B	89.189	666	54	6	578	1236	719425313	719424659	0.000000e+00	815.0
22	TraesCS7D01G491800	chr3A	79.708	823	121	32	1371	2153	574280179	574279363	9.030000e-154	553.0
23	TraesCS7D01G491800	chr3A	91.791	268	18	4	708	971	574319003	574319270	9.760000e-99	370.0
24	TraesCS7D01G491800	chr3A	77.627	295	32	16	63	349	574318272	574318540	4.980000e-32	148.0
25	TraesCS7D01G491800	chr3A	76.068	234	21	11	1272	1488	574319277	574319492	3.060000e-14	89.8

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	TraesCS7D01G491800	chr7D	600863742	600865978	2236	False	4132.00	4132	100.000000	1	2237	1	chr7D.!!$F1	2236
1	TraesCS7D01G491800	chr7B	680073701	680075799	2098	False	1568.50	1982	93.657500	1	2155	2	chr7B.!!$F1	2154
2	TraesCS7D01G491800	chr7B	707879509	707883676	4167	False	867.25	1626	93.236000	1	2155	4	chr7B.!!$F2	2154
3	TraesCS7D01G491800	chr6D	471112251	471113078	827	False	998.00	998	88.571000	414	1241	1	chr6D.!!$F2	827
4	TraesCS7D01G491800	chr6D	459550778	459552417	1639	True	759.50	1411	83.645500	89	1734	2	chr6D.!!$R1	1645
5	TraesCS7D01G491800	chr6D	471276027	471277083	1056	True	566.50	996	87.132000	355	1484	2	chr6D.!!$R2	1129
6	TraesCS7D01G491800	chr2B	771415462	771416700	1238	False	1323.00	1323	86.519000	521	1734	1	chr2B.!!$F1	1213
7	TraesCS7D01G491800	chr2B	771480033	771480731	698	False	780.00	780	87.270000	1049	1734	1	chr2B.!!$F2	685
8	TraesCS7D01G491800	chr7A	692784569	692785753	1184	False	911.00	1258	95.401000	914	2142	2	chr7A.!!$F1	1228
9	TraesCS7D01G491800	chr6A	616054882	616057206	2324	True	849.00	1158	85.063500	355	2153	2	chr6A.!!$R2	1798
10	TraesCS7D01G491800	chr6B	719307903	719308788	885	False	1038.00	1038	87.933000	355	1241	1	chr6B.!!$F1	886
11	TraesCS7D01G491800	chr6B	719424659	719425313	654	True	815.00	815	89.189000	578	1236	1	chr6B.!!$R1	658
12	TraesCS7D01G491800	chr3A	574279363	574280179	816	True	553.00	553	79.708000	1371	2153	1	chr3A.!!$R1	782
13	TraesCS7D01G491800	chr3A	574318272	574319492	1220	False	202.60	370	81.828667	63	1488	3	chr3A.!!$F1	1425

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
661	894	0.107703	CCCTTCGATAACTGGCAGCA	60.108	55.0	15.89	2.65	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1598	2671	0.743097	GCTCCACCCAAGCAATCATC	59.257	55.0	0.0	0.0	39.61	2.92	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
172	178	4.906065	TGCATTTGCCAGAGATGATAAC	57.094	40.909	0.00	0.00	41.18	1.89
267	416	6.220930	TGAATAAGTATCTCATACCGCAACC	58.779	40.000	0.00	0.00	36.40	3.77
335	518	0.854218	TTGTTGGCTGTTAAGGGGGA	59.146	50.000	0.00	0.00	0.00	4.81
343	526	4.104102	TGGCTGTTAAGGGGGAATACTATG	59.896	45.833	0.00	0.00	0.00	2.23
349	532	6.674861	TGTTAAGGGGGAATACTATGTTCTGA	59.325	38.462	0.00	0.00	0.00	3.27
451	684	3.274288	GACTTGGCTGATTTGAGGGTAG	58.726	50.000	0.00	0.00	0.00	3.18
452	685	2.025887	ACTTGGCTGATTTGAGGGTAGG	60.026	50.000	0.00	0.00	0.00	3.18
471	704	4.432980	AGGGTACAACTTAGCAGTGTTT	57.567	40.909	0.00	0.00	31.60	2.83
661	894	0.107703	CCCTTCGATAACTGGCAGCA	60.108	55.000	15.89	2.65	0.00	4.41
973	1790	7.661968	ACAGTGCATATGTAGGTATCTTGTAG	58.338	38.462	4.29	0.00	0.00	2.74
1134	2123	1.261480	TCTCTCTGGCAGTTCCTCAC	58.739	55.000	15.27	0.00	35.26	3.51
1261	2255	0.385473	GGGTGAATTTGCGTGACACG	60.385	55.000	23.43	23.43	45.88	4.49
1590	2663	5.049336	GCTAAACACAGAGAGAAAAACCTCC	60.049	44.000	0.00	0.00	33.76	4.30
1598	2671	2.092323	GAGAAAAACCTCCCCATTCCG	58.908	52.381	0.00	0.00	0.00	4.30
1719	2797	0.032615	AACAAGGGACCAGGCAACAA	60.033	50.000	0.00	0.00	41.41	2.83
1829	2924	1.282738	ACATCAGCACCACCATCATCA	59.717	47.619	0.00	0.00	0.00	3.07
1857	2955	1.076438	TCCACCAGTCTGAGAGGAGA	58.924	55.000	0.00	0.00	0.00	3.71
1874	2984	3.316573	GACCACCAGCTTCCCCTCG	62.317	68.421	0.00	0.00	0.00	4.63
1953	3063	1.749334	GATCGGCATCTTCCCGTCCT	61.749	60.000	0.00	0.00	45.71	3.85
2155	5041	1.069765	GGATCACGGATGTGGCGAT	59.930	57.895	0.00	0.00	46.42	4.58
2156	5042	1.224069	GGATCACGGATGTGGCGATG	61.224	60.000	0.00	0.00	46.42	3.84
2157	5043	1.224069	GATCACGGATGTGGCGATGG	61.224	60.000	0.00	0.00	46.42	3.51
2158	5044	1.685355	ATCACGGATGTGGCGATGGA	61.685	55.000	0.00	0.00	46.42	3.41
2159	5045	1.227645	CACGGATGTGGCGATGGAT	60.228	57.895	0.00	0.00	42.59	3.41
2160	5046	0.033366	CACGGATGTGGCGATGGATA	59.967	55.000	0.00	0.00	42.59	2.59
2161	5047	0.756294	ACGGATGTGGCGATGGATAA	59.244	50.000	0.00	0.00	0.00	1.75
2162	5048	1.270305	ACGGATGTGGCGATGGATAAG	60.270	52.381	0.00	0.00	0.00	1.73
2163	5049	1.813513	GGATGTGGCGATGGATAAGG	58.186	55.000	0.00	0.00	0.00	2.69
2164	5050	1.347707	GGATGTGGCGATGGATAAGGA	59.652	52.381	0.00	0.00	0.00	3.36
2165	5051	2.417719	GATGTGGCGATGGATAAGGAC	58.582	52.381	0.00	0.00	0.00	3.85
2166	5052	0.104120	TGTGGCGATGGATAAGGACG	59.896	55.000	0.00	0.00	0.00	4.79
2167	5053	0.387929	GTGGCGATGGATAAGGACGA	59.612	55.000	0.00	0.00	0.00	4.20
2168	5054	1.000955	GTGGCGATGGATAAGGACGAT	59.999	52.381	0.00	0.00	0.00	3.73
2169	5055	1.000843	TGGCGATGGATAAGGACGATG	59.999	52.381	0.00	0.00	0.00	3.84
2170	5056	1.673033	GGCGATGGATAAGGACGATGG	60.673	57.143	0.00	0.00	0.00	3.51
2171	5057	1.272490	GCGATGGATAAGGACGATGGA	59.728	52.381	0.00	0.00	0.00	3.41
2172	5058	2.093973	GCGATGGATAAGGACGATGGAT	60.094	50.000	0.00	0.00	0.00	3.41
2173	5059	3.617531	GCGATGGATAAGGACGATGGATT	60.618	47.826	0.00	0.00	0.00	3.01
2174	5060	4.381612	GCGATGGATAAGGACGATGGATTA	60.382	45.833	0.00	0.00	0.00	1.75
2175	5061	5.682471	GCGATGGATAAGGACGATGGATTAT	60.682	44.000	0.00	0.00	0.00	1.28
2176	5062	6.341316	CGATGGATAAGGACGATGGATTATT	58.659	40.000	0.00	0.00	0.00	1.40
2177	5063	6.818644	CGATGGATAAGGACGATGGATTATTT	59.181	38.462	0.00	0.00	0.00	1.40
2178	5064	7.334421	CGATGGATAAGGACGATGGATTATTTT	59.666	37.037	0.00	0.00	0.00	1.82
2179	5065	9.667107	GATGGATAAGGACGATGGATTATTTTA	57.333	33.333	0.00	0.00	0.00	1.52
2181	5067	9.280174	TGGATAAGGACGATGGATTATTTTAAC	57.720	33.333	0.00	0.00	0.00	2.01
2182	5068	9.280174	GGATAAGGACGATGGATTATTTTAACA	57.720	33.333	0.00	0.00	0.00	2.41
2202	5088	9.483916	TTTAACATAAAAGAACAGACATCGAGA	57.516	29.630	0.00	0.00	0.00	4.04
2203	5089	7.588143	AACATAAAAGAACAGACATCGAGAG	57.412	36.000	0.00	0.00	0.00	3.20
2216	5102	2.573941	TCGAGAGATGATGCACAGTG	57.426	50.000	0.00	0.00	33.31	3.66
2217	5103	0.928922	CGAGAGATGATGCACAGTGC	59.071	55.000	19.37	19.37	45.29	4.40
2218	5104	1.471153	CGAGAGATGATGCACAGTGCT	60.471	52.381	25.83	11.80	45.31	4.40
2219	5105	2.630158	GAGAGATGATGCACAGTGCTT	58.370	47.619	25.83	19.88	45.31	3.91
2220	5106	2.352034	GAGAGATGATGCACAGTGCTTG	59.648	50.000	25.83	0.00	45.31	4.01
2221	5107	0.809385	AGATGATGCACAGTGCTTGC	59.191	50.000	25.83	14.98	45.31	4.01
2222	5108	0.179145	GATGATGCACAGTGCTTGCC	60.179	55.000	25.83	12.41	45.31	4.52
2223	5109	0.611062	ATGATGCACAGTGCTTGCCT	60.611	50.000	25.83	6.02	45.31	4.75
2224	5110	1.239296	TGATGCACAGTGCTTGCCTC	61.239	55.000	25.83	14.27	45.31	4.70
2225	5111	0.959372	GATGCACAGTGCTTGCCTCT	60.959	55.000	25.83	2.60	45.31	3.69
2226	5112	0.538977	ATGCACAGTGCTTGCCTCTT	60.539	50.000	25.83	0.00	45.31	2.85
2227	5113	1.285023	GCACAGTGCTTGCCTCTTG	59.715	57.895	18.92	0.00	40.96	3.02
2228	5114	1.954528	CACAGTGCTTGCCTCTTGG	59.045	57.895	0.00	0.00	0.00	3.61
2229	5115	1.228367	ACAGTGCTTGCCTCTTGGG	60.228	57.895	0.00	0.00	38.36	4.12
2230	5116	1.228367	CAGTGCTTGCCTCTTGGGT	60.228	57.895	0.00	0.00	37.43	4.51
2231	5117	1.228367	AGTGCTTGCCTCTTGGGTG	60.228	57.895	0.00	0.00	37.43	4.61
2232	5118	1.228245	GTGCTTGCCTCTTGGGTGA	60.228	57.895	0.00	0.00	37.43	4.02
2233	5119	1.073722	TGCTTGCCTCTTGGGTGAG	59.926	57.895	0.00	0.00	37.43	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
172	178	9.273016	TCACAATTACTAGAACCTTTCTTTCAG	57.727	33.333	0.00	0.00	41.14	3.02
267	416	7.254455	CCTTGCTAATAGAACCAAAGTACATCG	60.254	40.741	0.00	0.00	0.00	3.84
335	518	7.152645	AGTCAACAACGTCAGAACATAGTATT	58.847	34.615	0.00	0.00	0.00	1.89
343	526	4.859629	AAAGAGTCAACAACGTCAGAAC	57.140	40.909	0.00	0.00	0.00	3.01
349	532	6.249035	TCTTTCAAAAAGAGTCAACAACGT	57.751	33.333	0.00	0.00	0.00	3.99
451	684	5.163591	ACAAAAACACTGCTAAGTTGTACCC	60.164	40.000	0.00	0.00	32.98	3.69
452	685	5.886992	ACAAAAACACTGCTAAGTTGTACC	58.113	37.500	0.00	0.00	32.98	3.34
661	894	5.776173	ATATCTTCATCGTTCTCGTCCTT	57.224	39.130	0.00	0.00	38.33	3.36
973	1790	4.737855	TCCTAAAGACTATCACACAGGC	57.262	45.455	0.00	0.00	0.00	4.85
1134	2123	9.608617	GCAATACAGATGATAATCATGAACTTG	57.391	33.333	0.00	0.00	37.20	3.16
1261	2255	5.804979	ACACAGTTAATTTGACAAAGCACAC	59.195	36.000	6.77	1.27	0.00	3.82
1590	2663	1.338973	CCAAGCAATCATCGGAATGGG	59.661	52.381	0.00	0.00	33.42	4.00
1598	2671	0.743097	GCTCCACCCAAGCAATCATC	59.257	55.000	0.00	0.00	39.61	2.92
1719	2797	1.067295	TTCTGCAAGGTGGAGGTCAT	58.933	50.000	0.00	0.00	36.40	3.06
1808	2894	1.945394	GATGATGGTGGTGCTGATGTC	59.055	52.381	0.00	0.00	0.00	3.06
1812	2907	1.841919	AGATGATGATGGTGGTGCTGA	59.158	47.619	0.00	0.00	0.00	4.26
1815	2910	2.928334	AGAAGATGATGATGGTGGTGC	58.072	47.619	0.00	0.00	0.00	5.01
1829	2924	4.594920	TCTCAGACTGGTGGAAAAGAAGAT	59.405	41.667	1.81	0.00	0.00	2.40
1857	2955	3.322466	CGAGGGGAAGCTGGTGGT	61.322	66.667	0.00	0.00	0.00	4.16
1874	2984	3.319198	TCGGTGGACCTCAAGGGC	61.319	66.667	0.29	0.00	44.61	5.19
1930	3040	3.788672	GGGAAGATGCCGATCAACT	57.211	52.632	0.00	0.00	0.00	3.16
1953	3063	2.033141	GCTGCTGCTCAACTCCCA	59.967	61.111	8.53	0.00	36.03	4.37
1960	3070	1.004080	GGAGAGTTGCTGCTGCTCA	60.004	57.895	17.00	0.47	40.48	4.26
2155	5041	9.280174	GTTAAAATAATCCATCGTCCTTATCCA	57.720	33.333	0.00	0.00	0.00	3.41
2156	5042	9.280174	TGTTAAAATAATCCATCGTCCTTATCC	57.720	33.333	0.00	0.00	0.00	2.59
2176	5062	9.483916	TCTCGATGTCTGTTCTTTTATGTTAAA	57.516	29.630	0.00	0.00	0.00	1.52
2177	5063	9.140286	CTCTCGATGTCTGTTCTTTTATGTTAA	57.860	33.333	0.00	0.00	0.00	2.01
2178	5064	8.520351	TCTCTCGATGTCTGTTCTTTTATGTTA	58.480	33.333	0.00	0.00	0.00	2.41
2179	5065	7.378966	TCTCTCGATGTCTGTTCTTTTATGTT	58.621	34.615	0.00	0.00	0.00	2.71
2180	5066	6.925211	TCTCTCGATGTCTGTTCTTTTATGT	58.075	36.000	0.00	0.00	0.00	2.29
2181	5067	7.704047	TCATCTCTCGATGTCTGTTCTTTTATG	59.296	37.037	2.64	0.00	45.76	1.90
2182	5068	7.776107	TCATCTCTCGATGTCTGTTCTTTTAT	58.224	34.615	2.64	0.00	45.76	1.40
2183	5069	7.158099	TCATCTCTCGATGTCTGTTCTTTTA	57.842	36.000	2.64	0.00	45.76	1.52
2184	5070	6.030548	TCATCTCTCGATGTCTGTTCTTTT	57.969	37.500	2.64	0.00	45.76	2.27
2185	5071	5.651387	TCATCTCTCGATGTCTGTTCTTT	57.349	39.130	2.64	0.00	45.76	2.52
2186	5072	5.590145	CATCATCTCTCGATGTCTGTTCTT	58.410	41.667	2.64	0.00	45.76	2.52
2187	5073	4.499526	GCATCATCTCTCGATGTCTGTTCT	60.500	45.833	0.00	0.00	45.76	3.01
2188	5074	3.735240	GCATCATCTCTCGATGTCTGTTC	59.265	47.826	0.00	0.00	45.76	3.18
2189	5075	3.131755	TGCATCATCTCTCGATGTCTGTT	59.868	43.478	0.00	0.00	45.76	3.16
2190	5076	2.692041	TGCATCATCTCTCGATGTCTGT	59.308	45.455	0.00	0.00	45.76	3.41
2191	5077	3.051327	GTGCATCATCTCTCGATGTCTG	58.949	50.000	0.00	3.71	45.76	3.51
2192	5078	2.692041	TGTGCATCATCTCTCGATGTCT	59.308	45.455	0.00	0.00	45.76	3.41
2193	5079	3.051327	CTGTGCATCATCTCTCGATGTC	58.949	50.000	0.00	0.00	45.76	3.06
2194	5080	2.429971	ACTGTGCATCATCTCTCGATGT	59.570	45.455	0.00	0.00	45.76	3.06
2195	5081	2.795470	CACTGTGCATCATCTCTCGATG	59.205	50.000	0.00	0.00	46.73	3.84
2196	5082	2.802415	GCACTGTGCATCATCTCTCGAT	60.802	50.000	26.70	0.00	44.26	3.59
2197	5083	1.470458	GCACTGTGCATCATCTCTCGA	60.470	52.381	26.70	0.00	44.26	4.04
2198	5084	0.928922	GCACTGTGCATCATCTCTCG	59.071	55.000	26.70	0.00	44.26	4.04
2209	5095	1.285023	CAAGAGGCAAGCACTGTGC	59.715	57.895	24.59	24.59	45.46	4.57
2210	5096	1.521450	CCCAAGAGGCAAGCACTGTG	61.521	60.000	2.76	2.76	0.00	3.66
2211	5097	1.228367	CCCAAGAGGCAAGCACTGT	60.228	57.895	0.00	0.00	0.00	3.55
2212	5098	1.228367	ACCCAAGAGGCAAGCACTG	60.228	57.895	0.00	0.00	40.58	3.66
2213	5099	1.228367	CACCCAAGAGGCAAGCACT	60.228	57.895	0.00	0.00	40.58	4.40
2214	5100	1.228245	TCACCCAAGAGGCAAGCAC	60.228	57.895	0.00	0.00	40.58	4.40
2215	5101	1.073722	CTCACCCAAGAGGCAAGCA	59.926	57.895	0.00	0.00	40.58	3.91
2216	5102	3.993535	CTCACCCAAGAGGCAAGC	58.006	61.111	0.00	0.00	40.58	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.