AutoCloner

Multiple sequence alignment - TraesCS1B01G313000

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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	TraesCS1B01G313000	chr1B	100.000	1331	0	0	1	1331	536703842	536705172	0.000000e+00	2459.0
1	TraesCS1B01G313000	chr1B	100.000	548	0	0	1729	2276	536705570	536706117	0.000000e+00	1013.0
2	TraesCS1B01G313000	chr2B	97.389	1302	34	0	1	1302	104959965	104958664	0.000000e+00	2217.0
3	TraesCS1B01G313000	chr2B	94.216	536	31	0	1	536	726588518	726587983	0.000000e+00	819.0
4	TraesCS1B01G313000	chr7B	95.012	1303	60	2	1	1303	272716970	272718267	0.000000e+00	2041.0
5	TraesCS1B01G313000	chr7A	87.893	1305	143	7	1	1303	62033281	62031990	0.000000e+00	1520.0
6	TraesCS1B01G313000	chr5A	85.866	1316	165	8	1	1312	387391609	387390311	0.000000e+00	1380.0
7	TraesCS1B01G313000	chr6D	83.691	1306	208	5	2	1304	422296987	422298290	0.000000e+00	1227.0
8	TraesCS1B01G313000	chr6D	87.583	902	111	1	402	1302	73813927	73814828	0.000000e+00	1044.0
9	TraesCS1B01G313000	chr6A	83.129	1304	211	6	1	1302	496368960	496370256	0.000000e+00	1181.0
10	TraesCS1B01G313000	chr5B	83.361	1226	201	3	74	1298	482490134	482491357	0.000000e+00	1131.0
11	TraesCS1B01G313000	chr1D	93.034	445	22	7	1838	2276	400013116	400013557	1.910000e-180	641.0
12	TraesCS1B01G313000	chr1D	97.872	47	1	0	1791	1837	400013009	400013055	5.210000e-12	82.4
13	TraesCS1B01G313000	chr3B	75.658	1253	291	14	57	1303	544795954	544794710	1.490000e-171	612.0
14	TraesCS1B01G313000	chr1A	91.156	441	27	4	1838	2276	496439000	496439430	2.520000e-164	588.0

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	TraesCS1B01G313000	chr1B	536703842	536706117	2275	False	1736.0	2459	100.000	1	2276	2	chr1B.!!$F1	2275
1	TraesCS1B01G313000	chr2B	104958664	104959965	1301	True	2217.0	2217	97.389	1	1302	1	chr2B.!!$R1	1301
2	TraesCS1B01G313000	chr2B	726587983	726588518	535	True	819.0	819	94.216	1	536	1	chr2B.!!$R2	535
3	TraesCS1B01G313000	chr7B	272716970	272718267	1297	False	2041.0	2041	95.012	1	1303	1	chr7B.!!$F1	1302
4	TraesCS1B01G313000	chr7A	62031990	62033281	1291	True	1520.0	1520	87.893	1	1303	1	chr7A.!!$R1	1302
5	TraesCS1B01G313000	chr5A	387390311	387391609	1298	True	1380.0	1380	85.866	1	1312	1	chr5A.!!$R1	1311
6	TraesCS1B01G313000	chr6D	422296987	422298290	1303	False	1227.0	1227	83.691	2	1304	1	chr6D.!!$F2	1302
7	TraesCS1B01G313000	chr6D	73813927	73814828	901	False	1044.0	1044	87.583	402	1302	1	chr6D.!!$F1	900
8	TraesCS1B01G313000	chr6A	496368960	496370256	1296	False	1181.0	1181	83.129	1	1302	1	chr6A.!!$F1	1301
9	TraesCS1B01G313000	chr5B	482490134	482491357	1223	False	1131.0	1131	83.361	74	1298	1	chr5B.!!$F1	1224
10	TraesCS1B01G313000	chr1D	400013009	400013557	548	False	361.7	641	95.453	1791	2276	2	chr1D.!!$F1	485
11	TraesCS1B01G313000	chr3B	544794710	544795954	1244	True	612.0	612	75.658	57	1303	1	chr3B.!!$R1	1246

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
247	249	1.336332	CGGCTTATCGGACTCTCATGG	60.336	57.143	0.0	0.0	0.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1734	1743	0.241749	CCGCATAATCGCATTGGCAT	59.758	50.0	0.0	0.0	41.24	4.4	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
89	90	2.775960	TGATTGATGCAGAGACTGGGAT	59.224	45.455	0.00	0.00	31.21	3.85
129	131	4.683781	GTGCAAAACAATTTTATCGCTCCA	59.316	37.500	0.00	0.00	0.00	3.86
134	136	4.222124	ACAATTTTATCGCTCCAGAGGT	57.778	40.909	0.00	0.00	0.00	3.85
247	249	1.336332	CGGCTTATCGGACTCTCATGG	60.336	57.143	0.00	0.00	0.00	3.66
330	332	2.224281	ACAGATGTGGACGAAGCTTTGA	60.224	45.455	20.86	0.00	0.00	2.69
460	464	3.621268	GTGTAAAATATGCCTGTCAGCGA	59.379	43.478	0.00	0.00	34.65	4.93
586	591	2.982488	ACATGGTCCAGGGATATTCTCC	59.018	50.000	8.67	0.00	44.11	3.71
631	636	4.192317	GGACCAAGCTAAGATCATTTCGT	58.808	43.478	0.00	0.00	0.00	3.85
1077	1086	2.806818	CTCTCTGATAGCGCCGTTACTA	59.193	50.000	2.29	0.00	0.00	1.82
1320	1329	3.859061	AAACCCGGATATTCTCTTCCC	57.141	47.619	0.73	0.00	0.00	3.97
1321	1330	1.339097	ACCCGGATATTCTCTTCCCG	58.661	55.000	0.73	0.00	39.85	5.14
1322	1331	0.037232	CCCGGATATTCTCTTCCCGC	60.037	60.000	0.73	0.00	38.92	6.13
1323	1332	0.679505	CCGGATATTCTCTTCCCGCA	59.320	55.000	0.00	0.00	38.92	5.69
1324	1333	1.276421	CCGGATATTCTCTTCCCGCAT	59.724	52.381	0.00	0.00	38.92	4.73
1325	1334	2.289694	CCGGATATTCTCTTCCCGCATT	60.290	50.000	0.00	0.00	38.92	3.56
1326	1335	2.996621	CGGATATTCTCTTCCCGCATTC	59.003	50.000	0.00	0.00	33.47	2.67
1327	1336	3.339141	GGATATTCTCTTCCCGCATTCC	58.661	50.000	0.00	0.00	0.00	3.01
1328	1337	3.008485	GGATATTCTCTTCCCGCATTCCT	59.992	47.826	0.00	0.00	0.00	3.36
1329	1338	2.629336	ATTCTCTTCCCGCATTCCTC	57.371	50.000	0.00	0.00	0.00	3.71
1330	1339	1.275666	TTCTCTTCCCGCATTCCTCA	58.724	50.000	0.00	0.00	0.00	3.86
1749	1758	4.754372	CACAGTATGCCAATGCGATTAT	57.246	40.909	0.00	0.00	42.53	1.28
1750	1759	4.469552	CACAGTATGCCAATGCGATTATG	58.530	43.478	0.00	0.00	42.53	1.90
1751	1760	3.058016	ACAGTATGCCAATGCGATTATGC	60.058	43.478	0.00	0.00	42.53	3.14
1752	1761	2.160219	AGTATGCCAATGCGATTATGCG	59.840	45.455	0.00	0.00	41.78	4.73
1753	1762	0.241749	ATGCCAATGCGATTATGCGG	59.758	50.000	0.00	0.00	41.78	5.69
1754	1763	0.817229	TGCCAATGCGATTATGCGGA	60.817	50.000	0.00	0.00	41.78	5.54
1755	1764	0.523072	GCCAATGCGATTATGCGGAT	59.477	50.000	0.00	0.00	44.28	4.18
1756	1765	1.730121	GCCAATGCGATTATGCGGATG	60.730	52.381	0.00	0.00	41.52	3.51
1757	1766	1.609932	CAATGCGATTATGCGGATGC	58.390	50.000	0.00	0.00	41.52	3.91
1767	1776	2.512515	GCGGATGCAGTCTCCCAC	60.513	66.667	0.00	0.00	42.15	4.61
1768	1777	2.187946	CGGATGCAGTCTCCCACC	59.812	66.667	0.00	0.00	0.00	4.61
1769	1778	2.362369	CGGATGCAGTCTCCCACCT	61.362	63.158	0.00	0.00	0.00	4.00
1770	1779	1.524482	GGATGCAGTCTCCCACCTC	59.476	63.158	0.00	0.00	0.00	3.85
1771	1780	0.980231	GGATGCAGTCTCCCACCTCT	60.980	60.000	0.00	0.00	0.00	3.69
1772	1781	0.463620	GATGCAGTCTCCCACCTCTC	59.536	60.000	0.00	0.00	0.00	3.20
1773	1782	0.980231	ATGCAGTCTCCCACCTCTCC	60.980	60.000	0.00	0.00	0.00	3.71
1774	1783	2.716017	GCAGTCTCCCACCTCTCCG	61.716	68.421	0.00	0.00	0.00	4.63
1775	1784	2.055042	CAGTCTCCCACCTCTCCGG	61.055	68.421	0.00	0.00	39.35	5.14
1776	1785	3.462678	GTCTCCCACCTCTCCGGC	61.463	72.222	0.00	0.00	35.61	6.13
1795	1804	2.747855	GCTGCTGCCACCTACACC	60.748	66.667	3.85	0.00	0.00	4.16
1796	1805	2.434884	CTGCTGCCACCTACACCG	60.435	66.667	0.00	0.00	0.00	4.94
1890	1959	6.094186	GCAGTTGGGAGTTCTATTTTAGGAAG	59.906	42.308	0.00	0.00	0.00	3.46
1898	1967	6.860034	AGTTCTATTTTAGGAAGTTGGGGTT	58.140	36.000	0.00	0.00	0.00	4.11
1907	1976	2.562738	GGAAGTTGGGGTTTGATGAAGG	59.437	50.000	0.00	0.00	0.00	3.46
1912	1981	0.613012	GGGGTTTGATGAAGGCTGCT	60.613	55.000	0.00	0.00	0.00	4.24
1928	1998	1.812922	GCTGCTCGTGACCCTCATG	60.813	63.158	0.00	0.00	34.78	3.07
1954	2024	8.824756	AGATAGTCATCAAGTAGGTAAACTGA	57.175	34.615	0.00	0.00	33.21	3.41
1986	2056	5.978814	TCCTAGGTTTCTCTTGCAGAATAC	58.021	41.667	9.08	0.00	41.02	1.89
2016	2086	1.674962	CAGGAGAATTTAGCTGGCAGC	59.325	52.381	31.56	31.56	42.84	5.25
2033	2103	2.482374	CGCAAAGCAGCACTAGGC	59.518	61.111	0.00	0.00	45.30	3.93
2090	2163	1.833630	CTCCCATTGTGGCTCAGACTA	59.166	52.381	0.00	0.00	35.79	2.59
2091	2164	1.555075	TCCCATTGTGGCTCAGACTAC	59.445	52.381	0.00	0.00	35.79	2.73
2094	2167	1.204704	CATTGTGGCTCAGACTACGGA	59.795	52.381	0.00	0.00	0.00	4.69
2097	2170	1.899814	TGTGGCTCAGACTACGGAAAT	59.100	47.619	0.00	0.00	0.00	2.17
2102	2175	3.182967	GCTCAGACTACGGAAATGTCAG	58.817	50.000	0.00	0.00	33.56	3.51
2106	2179	3.935203	CAGACTACGGAAATGTCAGCAAT	59.065	43.478	0.00	0.00	33.56	3.56
2124	2197	4.339247	AGCAATGTCGGATAAAAATCCCAG	59.661	41.667	0.00	0.00	37.43	4.45
2135	2208	1.589414	AAATCCCAGCACTCTAGCCT	58.411	50.000	0.00	0.00	34.23	4.58
2170	2243	2.609427	TCTGCACAGTGCCATATCTC	57.391	50.000	23.06	0.00	44.23	2.75
2172	2245	2.159000	TCTGCACAGTGCCATATCTCAG	60.159	50.000	23.06	10.68	44.23	3.35
2173	2246	0.942962	GCACAGTGCCATATCTCAGC	59.057	55.000	15.27	0.00	37.42	4.26
2256	2329	5.365895	TGGATCATTCTCAGTCAGTCATCAT	59.634	40.000	0.00	0.00	0.00	2.45
2272	2345	6.018425	CAGTCATCATAGGCTAATGTCACAAC	60.018	42.308	0.00	0.00	0.00	3.32

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	3.814625	TGCACTATGTTGAGTTTCCACA	58.185	40.909	0.00	0.00	0.00	4.17
129	131	9.703677	GGGATATTTAGTATAGCTTCTACCTCT	57.296	37.037	0.00	0.00	0.00	3.69
330	332	0.537143	TGGGCACGACATTCAGCTTT	60.537	50.000	0.00	0.00	0.00	3.51
460	464	7.576861	TCAATGCATGATACATGTCTTCATT	57.423	32.000	17.29	10.44	31.50	2.57
586	591	2.057503	AGATCGAAATGAGGATCGCG	57.942	50.000	0.00	0.00	42.97	5.87
631	636	4.598807	AGATGTCCATATAGCCCACATCAA	59.401	41.667	11.77	0.00	43.88	2.57
815	822	4.992319	CCAAAAGAGAAATTGCAGCATCAA	59.008	37.500	0.00	0.00	0.00	2.57
850	857	0.537188	CGAGCCACTCCACCAATACT	59.463	55.000	0.00	0.00	0.00	2.12
852	859	0.907704	ACCGAGCCACTCCACCAATA	60.908	55.000	0.00	0.00	0.00	1.90
1002	1010	5.406780	CACTACATTCAAACAGTCAGTCTCC	59.593	44.000	0.00	0.00	0.00	3.71
1077	1086	5.976458	GCAGCTAGCTCCTCAATATCTAAT	58.024	41.667	16.15	0.00	41.15	1.73
1304	1313	0.679505	TGCGGGAAGAGAATATCCGG	59.320	55.000	0.00	0.00	40.88	5.14
1305	1314	2.751166	ATGCGGGAAGAGAATATCCG	57.249	50.000	0.00	0.00	43.13	4.18
1306	1315	3.008485	AGGAATGCGGGAAGAGAATATCC	59.992	47.826	0.00	0.00	34.85	2.59
1307	1316	4.249661	GAGGAATGCGGGAAGAGAATATC	58.750	47.826	0.00	0.00	0.00	1.63
1308	1317	3.648067	TGAGGAATGCGGGAAGAGAATAT	59.352	43.478	0.00	0.00	0.00	1.28
1309	1318	3.038280	TGAGGAATGCGGGAAGAGAATA	58.962	45.455	0.00	0.00	0.00	1.75
1311	1320	1.275666	TGAGGAATGCGGGAAGAGAA	58.724	50.000	0.00	0.00	0.00	2.87
1728	1737	4.469552	CATAATCGCATTGGCATACTGTG	58.530	43.478	0.00	0.00	41.24	3.66
1729	1738	3.058016	GCATAATCGCATTGGCATACTGT	60.058	43.478	0.00	0.00	41.24	3.55
1730	1739	3.495193	GCATAATCGCATTGGCATACTG	58.505	45.455	0.00	0.00	41.24	2.74
1731	1740	2.160219	CGCATAATCGCATTGGCATACT	59.840	45.455	0.00	0.00	41.24	2.12
1732	1741	2.508867	CGCATAATCGCATTGGCATAC	58.491	47.619	0.00	0.00	41.24	2.39
1733	1742	1.468127	CCGCATAATCGCATTGGCATA	59.532	47.619	0.00	0.00	41.24	3.14
1734	1743	0.241749	CCGCATAATCGCATTGGCAT	59.758	50.000	0.00	0.00	41.24	4.40
1735	1744	0.817229	TCCGCATAATCGCATTGGCA	60.817	50.000	0.00	0.00	41.24	4.92
1736	1745	0.523072	ATCCGCATAATCGCATTGGC	59.477	50.000	0.00	0.00	0.00	4.52
1737	1746	1.730121	GCATCCGCATAATCGCATTGG	60.730	52.381	0.00	0.00	38.36	3.16
1738	1747	1.069091	TGCATCCGCATAATCGCATTG	60.069	47.619	0.00	0.00	45.36	2.82
1739	1748	1.237533	TGCATCCGCATAATCGCATT	58.762	45.000	0.00	0.00	45.36	3.56
1740	1749	2.931246	TGCATCCGCATAATCGCAT	58.069	47.368	0.00	0.00	45.36	4.73
1741	1750	4.453093	TGCATCCGCATAATCGCA	57.547	50.000	0.00	0.00	45.36	5.10
1750	1759	2.512515	GTGGGAGACTGCATCCGC	60.513	66.667	0.00	0.00	37.75	5.54
1751	1760	2.187946	GGTGGGAGACTGCATCCG	59.812	66.667	0.00	0.00	37.75	4.18
1752	1761	0.980231	AGAGGTGGGAGACTGCATCC	60.980	60.000	0.00	0.00	35.99	3.51
1753	1762	0.463620	GAGAGGTGGGAGACTGCATC	59.536	60.000	0.00	0.00	0.00	3.91
1754	1763	0.980231	GGAGAGGTGGGAGACTGCAT	60.980	60.000	0.00	0.00	0.00	3.96
1755	1764	1.610673	GGAGAGGTGGGAGACTGCA	60.611	63.158	0.00	0.00	0.00	4.41
1756	1765	2.716017	CGGAGAGGTGGGAGACTGC	61.716	68.421	0.00	0.00	0.00	4.40
1757	1766	2.055042	CCGGAGAGGTGGGAGACTG	61.055	68.421	0.00	0.00	34.51	3.51
1758	1767	2.360980	CCGGAGAGGTGGGAGACT	59.639	66.667	0.00	0.00	34.51	3.24
1759	1768	3.462678	GCCGGAGAGGTGGGAGAC	61.463	72.222	5.05	0.00	43.70	3.36
1778	1787	2.747855	GGTGTAGGTGGCAGCAGC	60.748	66.667	20.04	11.20	41.10	5.25
1779	1788	2.434884	CGGTGTAGGTGGCAGCAG	60.435	66.667	20.04	0.00	34.37	4.24
1780	1789	4.697756	GCGGTGTAGGTGGCAGCA	62.698	66.667	20.04	1.95	34.37	4.41
1786	1795	4.467084	ATGGCGGCGGTGTAGGTG	62.467	66.667	9.78	0.00	0.00	4.00
1787	1796	4.157120	GATGGCGGCGGTGTAGGT	62.157	66.667	9.78	0.00	0.00	3.08
1788	1797	3.792053	GAGATGGCGGCGGTGTAGG	62.792	68.421	9.78	0.00	0.00	3.18
1789	1798	2.279517	GAGATGGCGGCGGTGTAG	60.280	66.667	9.78	0.00	0.00	2.74
1790	1799	3.845259	GGAGATGGCGGCGGTGTA	61.845	66.667	9.78	0.00	0.00	2.90
1792	1801	4.899239	GAGGAGATGGCGGCGGTG	62.899	72.222	9.78	0.00	0.00	4.94
1890	1959	1.273327	CAGCCTTCATCAAACCCCAAC	59.727	52.381	0.00	0.00	0.00	3.77
1898	1967	1.022982	CGAGCAGCAGCCTTCATCAA	61.023	55.000	0.00	0.00	43.56	2.57
1907	1976	4.385405	AGGGTCACGAGCAGCAGC	62.385	66.667	0.00	0.00	42.56	5.25
1912	1981	0.611896	TCTCATGAGGGTCACGAGCA	60.612	55.000	22.42	0.00	36.71	4.26
1928	1998	8.904834	TCAGTTTACCTACTTGATGACTATCTC	58.095	37.037	0.00	0.00	34.31	2.75
1954	2024	4.862371	AGAGAAACCTAGGAATCGAGACT	58.138	43.478	17.98	9.47	0.00	3.24
1986	2056	1.915141	AATTCTCCTGCAGTTGGTGG	58.085	50.000	13.81	0.00	0.00	4.61
2016	2086	2.482374	GCCTAGTGCTGCTTTGCG	59.518	61.111	0.00	0.00	36.87	4.85
2065	2138	1.555075	TGAGCCACAATGGGAGTAGTC	59.445	52.381	0.00	0.00	38.19	2.59
2090	2163	1.464608	CGACATTGCTGACATTTCCGT	59.535	47.619	0.00	0.00	0.00	4.69
2091	2164	1.202065	CCGACATTGCTGACATTTCCG	60.202	52.381	0.00	0.00	0.00	4.30
2094	2167	5.895636	TTTATCCGACATTGCTGACATTT	57.104	34.783	0.00	0.00	0.00	2.32
2097	2170	5.163663	GGATTTTTATCCGACATTGCTGACA	60.164	40.000	0.00	0.00	0.00	3.58
2102	2175	4.610945	CTGGGATTTTTATCCGACATTGC	58.389	43.478	0.00	0.00	41.63	3.56
2106	2179	3.013921	GTGCTGGGATTTTTATCCGACA	58.986	45.455	0.00	0.00	41.63	4.35
2124	2197	1.205893	AGTTGCTGTAGGCTAGAGTGC	59.794	52.381	18.70	8.07	42.39	4.40
2135	2208	3.748048	GTGCAGAATTCTGAGTTGCTGTA	59.252	43.478	34.43	6.69	46.59	2.74
2170	2243	6.812656	TGATTTATTTGTTGCTGGTAATGCTG	59.187	34.615	0.00	0.00	0.00	4.41
2172	2245	7.593875	TTGATTTATTTGTTGCTGGTAATGC	57.406	32.000	0.00	0.00	0.00	3.56
2173	2246	9.976255	CATTTGATTTATTTGTTGCTGGTAATG	57.024	29.630	0.00	0.00	0.00	1.90
2233	2306	5.273674	TGATGACTGACTGAGAATGATCC	57.726	43.478	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.