AutoCloner

Multiple sequence alignment - TraesCS6B01G353000

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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	TraesCS6B01G353000	chr6B	100.000	2288	0	0	1	2288	618934448	618936735	0.000000e+00	4226.0
1	TraesCS6B01G353000	chr6B	95.122	41	2	0	1717	1757	618889245	618889285	5.280000e-07	65.8
2	TraesCS6B01G353000	chr7D	94.516	1714	77	8	1	1707	621162331	621164034	0.000000e+00	2628.0
3	TraesCS6B01G353000	chr3B	94.118	1717	88	9	1	1708	97752877	97751165	0.000000e+00	2599.0
4	TraesCS6B01G353000	chr3B	92.599	1716	114	8	1	1705	200855007	200856720	0.000000e+00	2453.0
5	TraesCS6B01G353000	chr4B	93.874	1714	89	6	2	1705	483940151	483941858	0.000000e+00	2569.0
6	TraesCS6B01G353000	chr7A	93.757	1714	94	9	1	1706	86218349	86216641	0.000000e+00	2560.0
7	TraesCS6B01G353000	chr7B	93.703	1715	96	8	1	1706	457414300	457416011	0.000000e+00	2558.0
8	TraesCS6B01G353000	chr7B	93.684	1710	97	9	2	1704	480272332	480270627	0.000000e+00	2549.0
9	TraesCS6B01G353000	chr1D	93.174	1714	106	7	1	1705	481925574	481927285	0.000000e+00	2507.0
10	TraesCS6B01G353000	chr5D	93.008	1702	104	9	13	1706	353957345	353959039	0.000000e+00	2470.0
11	TraesCS6B01G353000	chr6A	93.407	546	27	7	1750	2288	556526489	556527032	0.000000e+00	800.0
12	TraesCS6B01G353000	chr6D	91.758	546	29	11	1749	2288	411610270	411610805	0.000000e+00	745.0
13	TraesCS6B01G353000	chr2B	85.484	248	34	2	2028	2275	652620759	652620514	8.110000e-65	257.0
14	TraesCS6B01G353000	chr2D	84.411	263	38	3	2013	2275	545943806	545943547	2.920000e-64	255.0

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	TraesCS6B01G353000	chr6B	618934448	618936735	2287	False	4226	4226	100.000	1	2288	1	chr6B.!!$F2	2287
1	TraesCS6B01G353000	chr7D	621162331	621164034	1703	False	2628	2628	94.516	1	1707	1	chr7D.!!$F1	1706
2	TraesCS6B01G353000	chr3B	97751165	97752877	1712	True	2599	2599	94.118	1	1708	1	chr3B.!!$R1	1707
3	TraesCS6B01G353000	chr3B	200855007	200856720	1713	False	2453	2453	92.599	1	1705	1	chr3B.!!$F1	1704
4	TraesCS6B01G353000	chr4B	483940151	483941858	1707	False	2569	2569	93.874	2	1705	1	chr4B.!!$F1	1703
5	TraesCS6B01G353000	chr7A	86216641	86218349	1708	True	2560	2560	93.757	1	1706	1	chr7A.!!$R1	1705
6	TraesCS6B01G353000	chr7B	457414300	457416011	1711	False	2558	2558	93.703	1	1706	1	chr7B.!!$F1	1705
7	TraesCS6B01G353000	chr7B	480270627	480272332	1705	True	2549	2549	93.684	2	1704	1	chr7B.!!$R1	1702
8	TraesCS6B01G353000	chr1D	481925574	481927285	1711	False	2507	2507	93.174	1	1705	1	chr1D.!!$F1	1704
9	TraesCS6B01G353000	chr5D	353957345	353959039	1694	False	2470	2470	93.008	13	1706	1	chr5D.!!$F1	1693
10	TraesCS6B01G353000	chr6A	556526489	556527032	543	False	800	800	93.407	1750	2288	1	chr6A.!!$F1	538
11	TraesCS6B01G353000	chr6D	411610270	411610805	535	False	745	745	91.758	1749	2288	1	chr6D.!!$F1	539

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
671	680	0.671781	AAGAGTGACAGTCATGCCGC	60.672	55.0	6.51	0.0	0.0	6.53	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1481	1498	0.038599	ATGCAAGGCCTGATGTGTGA	59.961	50.0	5.69	0.0	0.0	3.58	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
106	108	0.757188	ATCTGCCAGGTAGGACGGAG	60.757	60.000	4.47	0.00	41.22	4.63
231	233	1.227556	GCACGGCGGTCATTAGGAT	60.228	57.895	13.24	0.00	0.00	3.24
253	255	4.931914	TCCTAGTAGGTCTTGTACTTGCT	58.068	43.478	16.02	0.00	36.53	3.91
359	361	1.363744	GGTCAGGAATCAGCGTCTTG	58.636	55.000	0.00	0.00	0.00	3.02
375	377	2.672381	GTCTTGAGCTCATCTTGAGTGC	59.328	50.000	19.04	5.72	45.94	4.40
578	582	1.004891	GGGGAGGAGGGAGGTTGAT	59.995	63.158	0.00	0.00	0.00	2.57
671	680	0.671781	AAGAGTGACAGTCATGCCGC	60.672	55.000	6.51	0.00	0.00	6.53
859	868	4.814294	CCGCCGAAGAAGACCCGG	62.814	72.222	0.00	0.00	45.51	5.73
1137	1152	0.627469	ATCAGGGTTGGGCCACCTAT	60.627	55.000	14.86	7.19	39.65	2.57
1374	1391	6.947644	TGAACTGTTATATCTGCGGTACTA	57.052	37.500	0.00	0.00	0.00	1.82
1416	1433	7.442364	TGCTAATTGATGCTCTGTTTATACTCC	59.558	37.037	0.00	0.00	0.00	3.85
1452	1469	2.280797	GCTGCCGAAGTGTGGTGA	60.281	61.111	0.00	0.00	0.00	4.02
1481	1498	4.288626	TCACCAACTAGCCAAAGAGGTTAT	59.711	41.667	0.00	0.00	40.61	1.89
1521	1538	2.672098	ACAACCAAACACCATGCCTTA	58.328	42.857	0.00	0.00	0.00	2.69
1536	1553	4.650972	TGCCTTAGGTTTGTGGACTAAT	57.349	40.909	0.00	0.00	0.00	1.73
1543	1560	5.435686	AGGTTTGTGGACTAATATGCAGA	57.564	39.130	0.00	0.00	0.00	4.26
1707	1727	1.579429	GCAACCAAACACGCCCTAG	59.421	57.895	0.00	0.00	0.00	3.02
1709	1729	0.250553	CAACCAAACACGCCCTAGGA	60.251	55.000	11.48	0.00	0.00	2.94
1710	1730	0.036306	AACCAAACACGCCCTAGGAG	59.964	55.000	11.48	6.50	0.00	3.69
1711	1731	1.125711	ACCAAACACGCCCTAGGAGT	61.126	55.000	11.48	7.23	35.79	3.85
1712	1732	0.899720	CCAAACACGCCCTAGGAGTA	59.100	55.000	11.48	0.00	33.08	2.59
1713	1733	1.134788	CCAAACACGCCCTAGGAGTAG	60.135	57.143	11.48	7.60	33.08	2.57
1714	1734	1.822990	CAAACACGCCCTAGGAGTAGA	59.177	52.381	11.48	0.00	33.08	2.59
1715	1735	1.765230	AACACGCCCTAGGAGTAGAG	58.235	55.000	11.48	0.00	33.08	2.43
1716	1736	0.917533	ACACGCCCTAGGAGTAGAGA	59.082	55.000	11.48	0.00	33.08	3.10
1717	1737	1.495574	ACACGCCCTAGGAGTAGAGAT	59.504	52.381	11.48	0.00	33.08	2.75
1718	1738	1.883275	CACGCCCTAGGAGTAGAGATG	59.117	57.143	11.48	0.00	33.08	2.90
1719	1739	1.775459	ACGCCCTAGGAGTAGAGATGA	59.225	52.381	11.48	0.00	33.08	2.92
1720	1740	2.175069	ACGCCCTAGGAGTAGAGATGAA	59.825	50.000	11.48	0.00	33.08	2.57
1721	1741	2.817258	CGCCCTAGGAGTAGAGATGAAG	59.183	54.545	11.48	0.00	0.00	3.02
1722	1742	3.497048	CGCCCTAGGAGTAGAGATGAAGA	60.497	52.174	11.48	0.00	0.00	2.87
1723	1743	3.824443	GCCCTAGGAGTAGAGATGAAGAC	59.176	52.174	11.48	0.00	0.00	3.01
1724	1744	4.069304	CCCTAGGAGTAGAGATGAAGACG	58.931	52.174	11.48	0.00	0.00	4.18
1725	1745	4.445162	CCCTAGGAGTAGAGATGAAGACGT	60.445	50.000	11.48	0.00	0.00	4.34
1726	1746	4.513692	CCTAGGAGTAGAGATGAAGACGTG	59.486	50.000	1.05	0.00	0.00	4.49
1727	1747	3.283751	AGGAGTAGAGATGAAGACGTGG	58.716	50.000	0.00	0.00	0.00	4.94
1728	1748	3.018149	GGAGTAGAGATGAAGACGTGGT	58.982	50.000	0.00	0.00	0.00	4.16
1729	1749	3.181495	GGAGTAGAGATGAAGACGTGGTG	60.181	52.174	0.00	0.00	0.00	4.17
1730	1750	2.755655	AGTAGAGATGAAGACGTGGTGG	59.244	50.000	0.00	0.00	0.00	4.61
1731	1751	1.924731	AGAGATGAAGACGTGGTGGA	58.075	50.000	0.00	0.00	0.00	4.02
1732	1752	2.461695	AGAGATGAAGACGTGGTGGAT	58.538	47.619	0.00	0.00	0.00	3.41
1733	1753	2.428890	AGAGATGAAGACGTGGTGGATC	59.571	50.000	0.00	0.00	0.00	3.36
1734	1754	1.482593	AGATGAAGACGTGGTGGATCC	59.517	52.381	4.20	4.20	0.00	3.36
1735	1755	0.541863	ATGAAGACGTGGTGGATCCC	59.458	55.000	9.90	0.00	34.77	3.85
1736	1756	1.153628	GAAGACGTGGTGGATCCCG	60.154	63.158	9.90	7.99	36.47	5.14
1737	1757	1.601419	GAAGACGTGGTGGATCCCGA	61.601	60.000	9.90	0.00	35.16	5.14
1738	1758	1.885163	AAGACGTGGTGGATCCCGAC	61.885	60.000	9.90	5.90	35.16	4.79
1739	1759	3.366739	GACGTGGTGGATCCCGACC	62.367	68.421	13.32	13.32	35.16	4.79
1740	1760	4.157120	CGTGGTGGATCCCGACCC	62.157	72.222	16.68	8.89	33.75	4.46
1741	1761	3.006728	GTGGTGGATCCCGACCCA	61.007	66.667	16.68	11.14	34.77	4.51
1742	1762	2.687200	TGGTGGATCCCGACCCAG	60.687	66.667	16.68	0.00	32.28	4.45
1743	1763	3.480133	GGTGGATCCCGACCCAGG	61.480	72.222	9.90	0.00	32.28	4.45
1757	1777	3.759618	CGACCCAGGGCTTGTAATAAAAA	59.240	43.478	4.91	0.00	0.00	1.94
1796	1816	3.436700	AACACACAAAGCCTTGCTAAC	57.563	42.857	0.00	0.00	38.25	2.34
1810	1830	4.319984	CCTTGCTAACGAAAACCCACTAAC	60.320	45.833	0.00	0.00	0.00	2.34
1815	1835	6.035217	GCTAACGAAAACCCACTAACAAAAA	58.965	36.000	0.00	0.00	0.00	1.94
1937	1961	3.365265	CCAACCTTGACCGCAGCC	61.365	66.667	0.00	0.00	0.00	4.85
1974	1998	3.408853	TCGCCGAGGAGGGAGAGA	61.409	66.667	0.00	0.00	41.48	3.10
2017	2043	3.438812	CCCCCAAATCCCTCCCCC	61.439	72.222	0.00	0.00	0.00	5.40
2019	2045	2.252898	CCCCAAATCCCTCCCCCAA	61.253	63.158	0.00	0.00	0.00	4.12
2039	2065	1.687297	CCTAGGGTTTCCGCCTCTCC	61.687	65.000	0.00	0.00	38.33	3.71
2094	2123	3.774959	GATGGACATCGACCGCGCT	62.775	63.158	5.56	0.00	37.46	5.92
2278	2308	1.313812	ATCACCACCTCGACGACTCC	61.314	60.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
231	233	4.931914	AGCAAGTACAAGACCTACTAGGA	58.068	43.478	9.28	0.00	37.67	2.94
253	255	3.583086	CCCTAAACAGAGGAAGAAGTGGA	59.417	47.826	0.00	0.00	39.15	4.02
335	337	1.452833	GCTGATTCCTGACCCAGCC	60.453	63.158	0.00	0.00	44.39	4.85
375	377	1.033746	AATGCCGTGCTCATGAAGGG	61.034	55.000	0.00	0.00	0.00	3.95
424	426	0.033504	GGAGGTGTGCTCGAACTTCA	59.966	55.000	0.38	0.00	0.00	3.02
570	574	5.299279	CCTCTCTTCTCTCACTATCAACCTC	59.701	48.000	0.00	0.00	0.00	3.85
578	582	2.024846	CACCCCCTCTCTTCTCTCACTA	60.025	54.545	0.00	0.00	0.00	2.74
671	680	8.178313	GGCTAATTCAAGAGCTTGTAGTTAAAG	58.822	37.037	9.79	0.00	41.16	1.85
808	817	0.907704	ACCTCGTCAGGCATTGGGTA	60.908	55.000	0.00	0.00	45.05	3.69
849	858	3.441290	CGCGTCTCCGGGTCTTCT	61.441	66.667	0.00	0.00	41.63	2.85
976	991	0.250467	ATGCACTCAAGCTTCGGTGT	60.250	50.000	21.75	7.63	34.99	4.16
1050	1065	1.207089	CAGCCGGTGTTATTCCTGAGA	59.793	52.381	1.90	0.00	0.00	3.27
1059	1074	2.662596	CAGGAGCAGCCGGTGTTA	59.337	61.111	1.90	0.00	43.43	2.41
1137	1152	0.249955	TGATCTGATGAACGGCTGCA	59.750	50.000	0.50	0.00	0.00	4.41
1176	1191	0.539051	CGGGAGTGAGGAGCTTGAAT	59.461	55.000	0.00	0.00	0.00	2.57
1395	1412	5.918608	ACGGAGTATAAACAGAGCATCAAT	58.081	37.500	0.00	0.00	41.94	2.57
1416	1433	2.160219	AGCACACATCATAAGCACAACG	59.840	45.455	0.00	0.00	0.00	4.10
1452	1469	4.288626	TCTTTGGCTAGTTGGTGAGGTTAT	59.711	41.667	0.00	0.00	0.00	1.89
1481	1498	0.038599	ATGCAAGGCCTGATGTGTGA	59.961	50.000	5.69	0.00	0.00	3.58
1521	1538	5.186198	GTCTGCATATTAGTCCACAAACCT	58.814	41.667	0.00	0.00	0.00	3.50
1536	1553	2.884012	CTGGTGTTTGGTTGTCTGCATA	59.116	45.455	0.00	0.00	0.00	3.14
1543	1560	0.324275	ACTGCCTGGTGTTTGGTTGT	60.324	50.000	0.00	0.00	0.00	3.32
1707	1727	3.018149	ACCACGTCTTCATCTCTACTCC	58.982	50.000	0.00	0.00	0.00	3.85
1709	1729	2.755655	CCACCACGTCTTCATCTCTACT	59.244	50.000	0.00	0.00	0.00	2.57
1710	1730	2.753452	TCCACCACGTCTTCATCTCTAC	59.247	50.000	0.00	0.00	0.00	2.59
1711	1731	3.081710	TCCACCACGTCTTCATCTCTA	57.918	47.619	0.00	0.00	0.00	2.43
1712	1732	1.924731	TCCACCACGTCTTCATCTCT	58.075	50.000	0.00	0.00	0.00	3.10
1713	1733	2.482142	GGATCCACCACGTCTTCATCTC	60.482	54.545	6.95	0.00	38.79	2.75
1714	1734	1.482593	GGATCCACCACGTCTTCATCT	59.517	52.381	6.95	0.00	38.79	2.90
1715	1735	1.473434	GGGATCCACCACGTCTTCATC	60.473	57.143	15.23	0.00	41.20	2.92
1716	1736	0.541863	GGGATCCACCACGTCTTCAT	59.458	55.000	15.23	0.00	41.20	2.57
1717	1737	1.884075	CGGGATCCACCACGTCTTCA	61.884	60.000	15.23	0.00	41.20	3.02
1718	1738	1.153628	CGGGATCCACCACGTCTTC	60.154	63.158	15.23	0.00	41.20	2.87
1719	1739	1.608336	TCGGGATCCACCACGTCTT	60.608	57.895	15.23	0.00	41.20	3.01
1720	1740	2.036731	TCGGGATCCACCACGTCT	59.963	61.111	15.23	0.00	41.20	4.18
1721	1741	2.183555	GTCGGGATCCACCACGTC	59.816	66.667	15.23	1.80	41.20	4.34
1722	1742	3.387947	GGTCGGGATCCACCACGT	61.388	66.667	15.23	0.00	41.20	4.49
1723	1743	4.157120	GGGTCGGGATCCACCACG	62.157	72.222	20.06	11.86	41.20	4.94
1724	1744	3.006728	TGGGTCGGGATCCACCAC	61.007	66.667	20.06	10.27	36.49	4.16
1725	1745	2.687200	CTGGGTCGGGATCCACCA	60.687	66.667	20.06	16.81	36.49	4.17
1726	1746	3.480133	CCTGGGTCGGGATCCACC	61.480	72.222	15.23	13.43	36.49	4.61
1730	1750	3.090532	AAGCCCTGGGTCGGGATC	61.091	66.667	15.56	0.00	43.42	3.36
1734	1754	0.834612	TATTACAAGCCCTGGGTCGG	59.165	55.000	15.56	6.36	0.00	4.79
1735	1755	2.702592	TTATTACAAGCCCTGGGTCG	57.297	50.000	15.56	5.62	0.00	4.79
1736	1756	4.159693	CCTTTTTATTACAAGCCCTGGGTC	59.840	45.833	15.56	6.83	0.00	4.46
1737	1757	4.093743	CCTTTTTATTACAAGCCCTGGGT	58.906	43.478	15.56	0.00	0.00	4.51
1738	1758	3.450817	CCCTTTTTATTACAAGCCCTGGG	59.549	47.826	8.86	8.86	0.00	4.45
1739	1759	3.118775	GCCCTTTTTATTACAAGCCCTGG	60.119	47.826	0.00	0.00	0.00	4.45
1740	1760	3.513515	TGCCCTTTTTATTACAAGCCCTG	59.486	43.478	0.00	0.00	0.00	4.45
1741	1761	3.785364	TGCCCTTTTTATTACAAGCCCT	58.215	40.909	0.00	0.00	0.00	5.19
1742	1762	4.020573	AGTTGCCCTTTTTATTACAAGCCC	60.021	41.667	0.00	0.00	0.00	5.19
1743	1763	5.147330	AGTTGCCCTTTTTATTACAAGCC	57.853	39.130	0.00	0.00	0.00	4.35
1744	1764	6.071560	AGGTAGTTGCCCTTTTTATTACAAGC	60.072	38.462	0.00	0.00	0.00	4.01
1745	1765	7.462571	AGGTAGTTGCCCTTTTTATTACAAG	57.537	36.000	0.00	0.00	0.00	3.16
1746	1766	7.726738	AGAAGGTAGTTGCCCTTTTTATTACAA	59.273	33.333	0.00	0.00	42.37	2.41
1747	1767	7.235804	AGAAGGTAGTTGCCCTTTTTATTACA	58.764	34.615	0.00	0.00	42.37	2.41
1757	1777	4.825634	GTGTTTTTAGAAGGTAGTTGCCCT	59.174	41.667	0.00	0.00	0.00	5.19
1873	1895	2.034221	GTCGCTTGAAGGGGGCTT	59.966	61.111	9.46	0.00	0.00	4.35
1903	1925	2.603776	GAGTGGGGACTGGTCGGT	60.604	66.667	0.00	0.00	0.00	4.69
1905	1927	2.214216	TTGGAGTGGGGACTGGTCG	61.214	63.158	0.00	0.00	0.00	4.79
1974	1998	1.118356	TTGGCGCCAATTCCAAACCT	61.118	50.000	37.30	0.00	39.22	3.50
2017	2043	0.392595	GAGGCGGAAACCCTAGGTTG	60.393	60.000	8.29	0.00	46.20	3.77
2019	2045	0.976590	GAGAGGCGGAAACCCTAGGT	60.977	60.000	8.29	0.00	37.65	3.08

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.