AutoCloner

Multiple sequence alignment - TraesCS2D01G043200

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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	TraesCS2D01G043200	chr2D	100.000	2632	0	0	1	2632	15582182	15584813	0.000000e+00	4861.0
1	TraesCS2D01G043200	chr2D	96.085	613	22	1	1	611	29016983	29016371	0.000000e+00	998.0
2	TraesCS2D01G043200	chr2D	77.009	809	139	33	853	1633	14976614	14977403	1.130000e-113	420.0
3	TraesCS2D01G043200	chr2B	90.505	1485	90	14	967	2442	27636175	27637617	0.000000e+00	1914.0
4	TraesCS2D01G043200	chr2B	89.589	365	21	4	617	970	27635793	27636151	5.170000e-122	448.0
5	TraesCS2D01G043200	chr2B	85.911	291	25	9	1361	1647	27017766	27018044	1.980000e-76	296.0
6	TraesCS2D01G043200	chr2B	85.502	269	27	7	1383	1647	27030447	27030707	1.200000e-68	270.0
7	TraesCS2D01G043200	chr2A	94.345	1061	43	9	967	2012	17610394	17611452	0.000000e+00	1611.0
8	TraesCS2D01G043200	chr2A	94.347	513	11	7	2132	2632	17612970	17613476	0.000000e+00	771.0
9	TraesCS2D01G043200	chr2A	93.132	364	9	3	618	970	17610012	17610370	1.080000e-143	520.0
10	TraesCS2D01G043200	chr2A	80.063	637	84	21	1015	1633	17133423	17134034	1.450000e-117	433.0
11	TraesCS2D01G043200	chr2A	96.491	57	2	0	2077	2133	17612810	17612866	7.760000e-16	95.3
12	TraesCS2D01G043200	chr7D	96.759	617	15	1	1	612	474520332	474520948	0.000000e+00	1024.0
13	TraesCS2D01G043200	chr7D	96.446	619	18	2	1	616	474023227	474022610	0.000000e+00	1018.0
14	TraesCS2D01G043200	chr7D	96.721	610	20	0	1	610	104281516	104280907	0.000000e+00	1016.0
15	TraesCS2D01G043200	chr7D	96.405	612	18	2	1	612	181032650	181032043	0.000000e+00	1005.0
16	TraesCS2D01G043200	chr7D	95.948	617	18	3	1	610	99838392	99837776	0.000000e+00	994.0
17	TraesCS2D01G043200	chr6D	96.563	611	16	2	1	607	17989316	17989925	0.000000e+00	1007.0
18	TraesCS2D01G043200	chr5D	96.540	607	20	1	1	607	52231867	52232472	0.000000e+00	1003.0
19	TraesCS2D01G043200	chr4D	96.382	608	16	3	1	607	12388182	12388784	0.000000e+00	996.0

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	TraesCS2D01G043200	chr2D	15582182	15584813	2631	False	4861.000	4861	100.00000	1	2632	1	chr2D.!!$F2	2631
1	TraesCS2D01G043200	chr2D	29016371	29016983	612	True	998.000	998	96.08500	1	611	1	chr2D.!!$R1	610
2	TraesCS2D01G043200	chr2D	14976614	14977403	789	False	420.000	420	77.00900	853	1633	1	chr2D.!!$F1	780
3	TraesCS2D01G043200	chr2B	27635793	27637617	1824	False	1181.000	1914	90.04700	617	2442	2	chr2B.!!$F3	1825
4	TraesCS2D01G043200	chr2A	17610012	17613476	3464	False	749.325	1611	94.57875	618	2632	4	chr2A.!!$F2	2014
5	TraesCS2D01G043200	chr2A	17133423	17134034	611	False	433.000	433	80.06300	1015	1633	1	chr2A.!!$F1	618
6	TraesCS2D01G043200	chr7D	474520332	474520948	616	False	1024.000	1024	96.75900	1	612	1	chr7D.!!$F1	611
7	TraesCS2D01G043200	chr7D	474022610	474023227	617	True	1018.000	1018	96.44600	1	616	1	chr7D.!!$R4	615
8	TraesCS2D01G043200	chr7D	104280907	104281516	609	True	1016.000	1016	96.72100	1	610	1	chr7D.!!$R2	609
9	TraesCS2D01G043200	chr7D	181032043	181032650	607	True	1005.000	1005	96.40500	1	612	1	chr7D.!!$R3	611
10	TraesCS2D01G043200	chr7D	99837776	99838392	616	True	994.000	994	95.94800	1	610	1	chr7D.!!$R1	609
11	TraesCS2D01G043200	chr6D	17989316	17989925	609	False	1007.000	1007	96.56300	1	607	1	chr6D.!!$F1	606
12	TraesCS2D01G043200	chr5D	52231867	52232472	605	False	1003.000	1003	96.54000	1	607	1	chr5D.!!$F1	606
13	TraesCS2D01G043200	chr4D	12388182	12388784	602	False	996.000	996	96.38200	1	607	1	chr4D.!!$F1	606

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
977	1061	1.135083	CCATCAAAGACTAGCGACCGT	60.135	52.381	0.0	0.0	0.0	4.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2473	4023	1.123077	CATCCGGGATCACTCTGGAA	58.877	55.0	6.55	0.0	32.27	3.53	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
156	157	2.839975	TGTGGTGCATGTCGAAAGTAA	58.160	42.857	0.00	0.00	0.00	2.24
166	167	7.438459	GTGCATGTCGAAAGTAATACTAATCCT	59.562	37.037	0.00	0.00	0.00	3.24
283	286	4.004982	GGTAAACCAAGCACGGAGATAAA	58.995	43.478	0.00	0.00	35.64	1.40
285	288	5.048573	GGTAAACCAAGCACGGAGATAAAAA	60.049	40.000	0.00	0.00	35.64	1.94
580	597	2.375146	GGACAAATGGGCCTTACGAAT	58.625	47.619	4.53	0.00	0.00	3.34
607	624	6.930731	GGACAAATGGCCATTTTTCTACTAA	58.069	36.000	37.66	5.28	44.76	2.24
647	664	5.006165	GTCAATCTTAAGATCTGCTGGTTCG	59.994	44.000	18.19	0.00	32.75	3.95
649	666	2.168521	TCTTAAGATCTGCTGGTTCGGG	59.831	50.000	0.00	0.00	0.00	5.14
738	755	3.097614	GGTCCCTAGTAGCAGAAGTGAA	58.902	50.000	0.00	0.00	0.00	3.18
766	783	2.155924	CGAACGAACCTCTGAAAGAAGC	59.844	50.000	0.00	0.00	46.34	3.86
769	786	3.134458	ACGAACCTCTGAAAGAAGCAAG	58.866	45.455	0.00	0.00	46.34	4.01
790	807	5.733620	AGTGGAGTAGGAAATTTCGTGTA	57.266	39.130	20.75	6.56	0.00	2.90
791	808	6.295719	AGTGGAGTAGGAAATTTCGTGTAT	57.704	37.500	20.75	8.40	0.00	2.29
792	809	6.106673	AGTGGAGTAGGAAATTTCGTGTATG	58.893	40.000	20.75	0.00	0.00	2.39
793	810	6.070995	AGTGGAGTAGGAAATTTCGTGTATGA	60.071	38.462	20.75	0.50	0.00	2.15
794	811	6.592607	GTGGAGTAGGAAATTTCGTGTATGAA	59.407	38.462	20.75	0.00	0.00	2.57
977	1061	1.135083	CCATCAAAGACTAGCGACCGT	60.135	52.381	0.00	0.00	0.00	4.83
1251	1335	2.410939	GTACTCCCTCCACGTCAAAAC	58.589	52.381	0.00	0.00	0.00	2.43
1252	1336	0.834612	ACTCCCTCCACGTCAAAACA	59.165	50.000	0.00	0.00	0.00	2.83
1253	1337	1.210967	ACTCCCTCCACGTCAAAACAA	59.789	47.619	0.00	0.00	0.00	2.83
1254	1338	2.294074	CTCCCTCCACGTCAAAACAAA	58.706	47.619	0.00	0.00	0.00	2.83
1255	1339	2.685897	CTCCCTCCACGTCAAAACAAAA	59.314	45.455	0.00	0.00	0.00	2.44
1256	1340	3.292460	TCCCTCCACGTCAAAACAAAAT	58.708	40.909	0.00	0.00	0.00	1.82
1257	1341	4.462133	TCCCTCCACGTCAAAACAAAATA	58.538	39.130	0.00	0.00	0.00	1.40
1357	1456	5.873179	TTCTCAATCCATGTTTAACCGTC	57.127	39.130	0.00	0.00	0.00	4.79
1378	1479	6.907212	CCGTCTGTTATTTCTTGTGATTATGC	59.093	38.462	0.00	0.00	0.00	3.14
1394	1495	3.616935	TGCGTACGTGCAGACTATC	57.383	52.632	17.90	0.00	40.62	2.08
1526	1627	1.768684	AAGTGAGGCCGAAAGCTGGA	61.769	55.000	0.00	0.00	43.05	3.86
1690	1791	1.001158	CGCTAGCTACCAAGACTAGCC	60.001	57.143	13.93	0.00	44.23	3.93
1719	1834	0.167908	CTTTGTGTGTGTGTGCGTGT	59.832	50.000	0.00	0.00	0.00	4.49
1737	1852	3.860125	GTGCGTGTGTGCGTGTGT	61.860	61.111	0.00	0.00	37.81	3.72
1738	1853	3.858989	TGCGTGTGTGCGTGTGTG	61.859	61.111	0.00	0.00	37.81	3.82
1740	1855	4.918060	CGTGTGTGCGTGTGTGCG	62.918	66.667	0.00	0.00	37.81	5.34
1741	1856	3.860125	GTGTGTGCGTGTGTGCGT	61.860	61.111	0.00	0.00	37.81	5.24
1742	1857	3.858989	TGTGTGCGTGTGTGCGTG	61.859	61.111	0.00	0.00	37.81	5.34
1743	1858	3.860125	GTGTGCGTGTGTGCGTGT	61.860	61.111	0.00	0.00	37.81	4.49
1754	1869	2.962786	TGCGTGTGTGCGTGTACC	60.963	61.111	0.00	0.00	37.81	3.34
1791	1906	2.107141	CAGCACGCTAGCTACCCC	59.893	66.667	13.93	0.00	44.54	4.95
1957	2075	0.884704	GAAACCCTGCTTGCGAGACA	60.885	55.000	4.70	1.41	0.00	3.41
1975	2093	5.292101	CGAGACACAGATTTAATCTTGGACC	59.708	44.000	4.51	0.00	37.58	4.46
1983	2101	5.707298	AGATTTAATCTTGGACCCGCATATG	59.293	40.000	0.99	0.00	35.76	1.78
1984	2102	2.276732	AATCTTGGACCCGCATATGG	57.723	50.000	4.56	0.00	0.00	2.74
1988	2106	2.976185	TCTTGGACCCGCATATGGATTA	59.024	45.455	4.56	0.00	0.00	1.75
2003	2121	5.901413	ATGGATTATCTTTCTCCTCTGCA	57.099	39.130	0.00	0.00	0.00	4.41
2012	2130	6.259550	TCTTTCTCCTCTGCAATTTTAAGC	57.740	37.500	0.00	0.00	0.00	3.09
2015	2133	6.655078	TTCTCCTCTGCAATTTTAAGCTTT	57.345	33.333	3.20	0.00	0.00	3.51
2018	2136	7.593825	TCTCCTCTGCAATTTTAAGCTTTTAC	58.406	34.615	3.20	0.00	0.00	2.01
2075	3513	4.048504	GCAAACAAGTAACCATGACCAAC	58.951	43.478	0.00	0.00	0.00	3.77
2205	3755	3.430042	AGTTCTGTGATGTGAAGCCAT	57.570	42.857	0.00	0.00	0.00	4.40
2260	3810	7.273381	CCGGATACAATGTTTGAAAATTCTGAC	59.727	37.037	0.00	0.00	0.00	3.51
2306	3856	7.867305	TGTTGTAAGAATTCCTTGTGTACAA	57.133	32.000	0.00	5.36	36.34	2.41
2307	3857	8.458573	TGTTGTAAGAATTCCTTGTGTACAAT	57.541	30.769	0.00	0.00	34.22	2.71
2378	3928	3.245016	TGCAAGAACAAGGATGGATGACT	60.245	43.478	0.00	0.00	0.00	3.41
2473	4023	2.032620	GTGGAGTATGTGATCCCGAGT	58.967	52.381	0.00	0.00	34.47	4.18
2477	4027	2.693591	GAGTATGTGATCCCGAGTTCCA	59.306	50.000	0.00	0.00	0.00	3.53
2478	4028	2.695666	AGTATGTGATCCCGAGTTCCAG	59.304	50.000	0.00	0.00	0.00	3.86
2509	4059	5.861787	CCCGGATGAACAGTAAAATTCAAAC	59.138	40.000	0.73	0.00	38.29	2.93
2595	4154	7.509050	TGCACATTTTCATGATGAAATTACG	57.491	32.000	20.04	11.62	44.75	3.18
2602	4161	9.689976	ATTTTCATGATGAAATTACGTTTGTGA	57.310	25.926	20.04	2.65	44.75	3.58
2612	4171	2.684001	ACGTTTGTGAAGGTGTGAGA	57.316	45.000	0.00	0.00	32.98	3.27

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
283	286	7.489239	AGCTAATAGAGAGAAGTGTCCTTTT	57.511	36.000	0.00	0.00	0.00	2.27
285	288	6.264518	GCTAGCTAATAGAGAGAAGTGTCCTT	59.735	42.308	7.70	0.00	32.76	3.36
478	495	1.125093	ACACCAACCGGGACAGATGA	61.125	55.000	6.32	0.00	41.15	2.92
580	597	1.638529	AAAATGGCCATTTGTCCCGA	58.361	45.000	37.84	0.00	40.57	5.14
613	630	9.140286	CAGATCTTAAGATTGACGAAGTTGTTA	57.860	33.333	18.88	0.00	36.08	2.41
647	664	1.112950	CCTAACTCTTCCGAGACCCC	58.887	60.000	0.00	0.00	39.74	4.95
649	666	0.460722	GGCCTAACTCTTCCGAGACC	59.539	60.000	0.00	0.00	39.74	3.85
662	679	4.568072	TCACTGCAATTTCTAGGCCTAA	57.432	40.909	14.85	0.51	0.00	2.69
728	745	0.880278	TCGTGGTGCTTCACTTCTGC	60.880	55.000	8.03	0.00	35.63	4.26
738	755	1.300697	GAGGTTCGTTCGTGGTGCT	60.301	57.895	0.00	0.00	0.00	4.40
766	783	4.755123	ACACGAAATTTCCTACTCCACTTG	59.245	41.667	12.54	0.00	0.00	3.16
769	786	6.103997	TCATACACGAAATTTCCTACTCCAC	58.896	40.000	12.54	0.00	0.00	4.02
790	807	5.753438	GCTGCATGTCATTGATTCATTTCAT	59.247	36.000	0.00	0.00	0.00	2.57
791	808	5.105513	AGCTGCATGTCATTGATTCATTTCA	60.106	36.000	1.02	0.00	0.00	2.69
792	809	5.348986	AGCTGCATGTCATTGATTCATTTC	58.651	37.500	1.02	0.00	0.00	2.17
793	810	5.339008	AGCTGCATGTCATTGATTCATTT	57.661	34.783	1.02	0.00	0.00	2.32
794	811	5.593095	ACTAGCTGCATGTCATTGATTCATT	59.407	36.000	1.02	0.00	0.00	2.57
977	1061	1.873591	GCCGCTTGTTTTGAGAGAGAA	59.126	47.619	0.00	0.00	0.00	2.87
1257	1341	9.605275	CAACCTGCTAATATGCACAGTATATAT	57.395	33.333	0.00	0.00	38.12	0.86
1264	1348	3.544684	TCCAACCTGCTAATATGCACAG	58.455	45.455	0.00	0.00	38.12	3.66
1357	1456	7.579093	CGTACGCATAATCACAAGAAATAACAG	59.421	37.037	0.52	0.00	0.00	3.16
1378	1479	1.823828	GTGGATAGTCTGCACGTACG	58.176	55.000	15.01	15.01	36.41	3.67
1394	1495	0.931702	TACGCACGTTTGTCAAGTGG	59.068	50.000	0.00	1.46	36.48	4.00
1526	1627	2.046314	CGGAAATGGGTGTCGGCT	60.046	61.111	0.00	0.00	0.00	5.52
1690	1791	4.394920	ACACACACACAAAGTAACCTTCTG	59.605	41.667	0.00	0.00	0.00	3.02
1719	1834	3.858989	CACACGCACACACGCACA	61.859	61.111	0.00	0.00	36.19	4.57
1737	1852	2.962786	GGTACACGCACACACGCA	60.963	61.111	0.00	0.00	36.19	5.24
1738	1853	2.654912	GAGGTACACGCACACACGC	61.655	63.158	0.00	0.00	36.19	5.34
1739	1854	2.362047	CGAGGTACACGCACACACG	61.362	63.158	0.00	0.00	34.76	4.49
1740	1855	3.534160	CGAGGTACACGCACACAC	58.466	61.111	0.00	0.00	34.76	3.82
1754	1869	1.202031	GCCGCCTTATTGAACAACGAG	60.202	52.381	0.00	0.00	0.00	4.18
1791	1906	1.739562	GAGAGCAACCTGCCAGTCG	60.740	63.158	0.00	0.00	46.52	4.18
1957	2075	3.279434	GCGGGTCCAAGATTAAATCTGT	58.721	45.455	0.00	0.00	40.13	3.41
1975	2093	5.738909	AGGAGAAAGATAATCCATATGCGG	58.261	41.667	0.00	0.00	35.45	5.69
1983	2101	7.579761	AAATTGCAGAGGAGAAAGATAATCC	57.420	36.000	0.00	0.00	0.00	3.01
1988	2106	6.662663	AGCTTAAAATTGCAGAGGAGAAAGAT	59.337	34.615	0.00	0.00	0.00	2.40
2003	2121	8.900983	TGCCATTTCTGTAAAAGCTTAAAATT	57.099	26.923	0.00	0.00	32.15	1.82
2075	3513	3.548818	GCTGGCTGTGTGTTTTAGTTCTG	60.549	47.826	0.00	0.00	0.00	3.02
2164	3714	2.427232	TCTAACAAGTTGTCCGGTCG	57.573	50.000	9.40	0.00	0.00	4.79
2235	3785	7.007367	CGTCAGAATTTTCAAACATTGTATCCG	59.993	37.037	0.00	0.00	0.00	4.18
2260	3810	4.910585	GGGCCGGGATGCACTACG	62.911	72.222	2.18	0.00	0.00	3.51
2378	3928	6.051717	GCTATATCTTCTCTTGTTCTTGCCA	58.948	40.000	0.00	0.00	0.00	4.92
2473	4023	1.123077	CATCCGGGATCACTCTGGAA	58.877	55.000	6.55	0.00	32.27	3.53
2477	4027	1.759445	CTGTTCATCCGGGATCACTCT	59.241	52.381	6.55	0.00	0.00	3.24
2478	4028	1.482593	ACTGTTCATCCGGGATCACTC	59.517	52.381	6.55	0.00	0.00	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.