AutoCloner

Multiple sequence alignment - TraesCS1A01G289100

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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	TraesCS1A01G289100	chr1A	100.000	2243	0	0	1	2243	486582326	486580084	0.000000e+00	4143.0
1	TraesCS1A01G289100	chr1A	79.756	1393	125	77	546	1886	486598891	486597604	0.000000e+00	865.0
2	TraesCS1A01G289100	chr1A	91.978	536	39	4	1	535	384293460	384292928	0.000000e+00	749.0
3	TraesCS1A01G289100	chr1A	91.589	535	45	0	1	535	564186765	564187299	0.000000e+00	739.0
4	TraesCS1A01G289100	chr1D	89.079	1575	101	29	537	2070	386750520	386748976	0.000000e+00	1890.0
5	TraesCS1A01G289100	chr1D	81.883	1264	111	64	647	1861	386787375	386786181	0.000000e+00	957.0
6	TraesCS1A01G289100	chr1D	90.503	179	8	2	2073	2242	386748940	386748762	6.230000e-56	228.0
7	TraesCS1A01G289100	chr1B	86.230	1467	111	43	585	1978	520145641	520144193	0.000000e+00	1506.0
8	TraesCS1A01G289100	chr1B	83.459	1330	82	58	994	2209	520243099	520241794	0.000000e+00	1110.0
9	TraesCS1A01G289100	chr1B	79.727	952	87	47	546	1425	520277618	520276701	1.920000e-165	592.0
10	TraesCS1A01G289100	chr1B	89.710	379	28	4	588	957	520243483	520243107	7.250000e-130	473.0
11	TraesCS1A01G289100	chr1B	95.906	171	5	2	2073	2242	520144098	520143929	2.190000e-70	276.0
12	TraesCS1A01G289100	chr1B	94.915	59	2	1	1483	1541	520276677	520276620	8.530000e-15	91.6
13	TraesCS1A01G289100	chr4A	93.458	535	34	1	1	535	591858462	591857929	0.000000e+00	793.0
14	TraesCS1A01G289100	chrUn	89.219	538	57	1	1	538	91648756	91648220	0.000000e+00	671.0
15	TraesCS1A01G289100	chrUn	89.346	535	56	1	1	535	239782950	239783483	0.000000e+00	671.0
16	TraesCS1A01G289100	chrUn	89.219	538	57	1	1	538	274317544	274317008	0.000000e+00	671.0
17	TraesCS1A01G289100	chr7D	89.219	538	55	3	1	538	547272739	547272205	0.000000e+00	669.0
18	TraesCS1A01G289100	chr5D	89.346	535	54	3	1	535	292705452	292705983	0.000000e+00	669.0
19	TraesCS1A01G289100	chr2A	89.326	534	56	1	2	535	209098503	209099035	0.000000e+00	669.0

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	TraesCS1A01G289100	chr1A	486580084	486582326	2242	True	4143.0	4143	100.0000	1	2243	1	chr1A.!!$R2	2242
1	TraesCS1A01G289100	chr1A	486597604	486598891	1287	True	865.0	865	79.7560	546	1886	1	chr1A.!!$R3	1340
2	TraesCS1A01G289100	chr1A	384292928	384293460	532	True	749.0	749	91.9780	1	535	1	chr1A.!!$R1	534
3	TraesCS1A01G289100	chr1A	564186765	564187299	534	False	739.0	739	91.5890	1	535	1	chr1A.!!$F1	534
4	TraesCS1A01G289100	chr1D	386748762	386750520	1758	True	1059.0	1890	89.7910	537	2242	2	chr1D.!!$R2	1705
5	TraesCS1A01G289100	chr1D	386786181	386787375	1194	True	957.0	957	81.8830	647	1861	1	chr1D.!!$R1	1214
6	TraesCS1A01G289100	chr1B	520143929	520145641	1712	True	891.0	1506	91.0680	585	2242	2	chr1B.!!$R1	1657
7	TraesCS1A01G289100	chr1B	520241794	520243483	1689	True	791.5	1110	86.5845	588	2209	2	chr1B.!!$R2	1621
8	TraesCS1A01G289100	chr1B	520276620	520277618	998	True	341.8	592	87.3210	546	1541	2	chr1B.!!$R3	995
9	TraesCS1A01G289100	chr4A	591857929	591858462	533	True	793.0	793	93.4580	1	535	1	chr4A.!!$R1	534
10	TraesCS1A01G289100	chrUn	91648220	91648756	536	True	671.0	671	89.2190	1	538	1	chrUn.!!$R1	537
11	TraesCS1A01G289100	chrUn	239782950	239783483	533	False	671.0	671	89.3460	1	535	1	chrUn.!!$F1	534
12	TraesCS1A01G289100	chrUn	274317008	274317544	536	True	671.0	671	89.2190	1	538	1	chrUn.!!$R2	537
13	TraesCS1A01G289100	chr7D	547272205	547272739	534	True	669.0	669	89.2190	1	538	1	chr7D.!!$R1	537
14	TraesCS1A01G289100	chr5D	292705452	292705983	531	False	669.0	669	89.3460	1	535	1	chr5D.!!$F1	534
15	TraesCS1A01G289100	chr2A	209098503	209099035	532	False	669.0	669	89.3260	2	535	1	chr2A.!!$F1	533

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
269	271	0.035739	GTGATACGTTGTGGGGTGGT	59.964	55.0	0.0	0.0	0.0	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2060	2336	0.161024	GCGACAACAGTGCTTCGTAC	59.839	55.0	9.56	0.0	0.0	3.67	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
26	27	5.182950	TGTGTATTTGCGAAGTTGAATGGAT	59.817	36.000	0.00	0.00	0.00	3.41
208	210	3.213506	CGAGAAATGTCCCATTATGGCA	58.786	45.455	5.57	0.00	35.79	4.92
232	234	2.011122	ACCGAGTGAGAAAGGAAGGA	57.989	50.000	0.00	0.00	0.00	3.36
269	271	0.035739	GTGATACGTTGTGGGGTGGT	59.964	55.000	0.00	0.00	0.00	4.16
340	343	0.804989	CAACCGCATTTCTCCCTCAC	59.195	55.000	0.00	0.00	0.00	3.51
390	393	8.723311	CCAGACTGTTCATACGGTTAAATTTTA	58.277	33.333	0.93	0.00	43.89	1.52
449	452	5.524646	ACGTTCGAACCTTTGAGAACAAATA	59.475	36.000	22.07	0.00	43.64	1.40
599	602	0.610687	CAGGCTCCTTCGAGAAACCT	59.389	55.000	0.00	0.00	38.52	3.50
710	722	1.199097	ACAATCGACCGTCCAAAATGC	59.801	47.619	0.00	0.00	0.00	3.56
891	945	1.745115	CTCTTTTCCGGCCATCGCA	60.745	57.895	2.24	0.00	37.59	5.10
1198	1305	2.355363	CCGACAAGAACGACGCCA	60.355	61.111	0.00	0.00	0.00	5.69
1203	1310	3.036084	AAGAACGACGCCAGCACG	61.036	61.111	0.00	5.02	39.50	5.34
1409	1592	4.095483	CAGTTGCCTTATTTGAGGTAGCAG	59.905	45.833	0.00	0.00	39.11	4.24
1453	1636	2.435059	GTCTTGAGCTGGGTCCGC	60.435	66.667	0.00	0.00	0.00	5.54
1469	1674	0.528684	CCGCCTCGGTGATCTTCTTC	60.529	60.000	0.00	0.00	42.73	2.87
1479	1684	1.065636	TGATCTTCTTCCTGCTGCTGG	60.066	52.381	18.44	18.44	0.00	4.85
1480	1685	1.209019	GATCTTCTTCCTGCTGCTGGA	59.791	52.381	22.44	22.44	0.00	3.86
1481	1686	0.612229	TCTTCTTCCTGCTGCTGGAG	59.388	55.000	24.37	18.79	33.24	3.86
1482	1687	0.324285	CTTCTTCCTGCTGCTGGAGT	59.676	55.000	24.37	0.00	33.24	3.85
1483	1688	0.035881	TTCTTCCTGCTGCTGGAGTG	59.964	55.000	24.37	20.69	33.24	3.51
1484	1689	2.033141	TTCCTGCTGCTGGAGTGC	59.967	61.111	24.37	0.00	33.24	4.40
1485	1690	2.466523	CTTCCTGCTGCTGGAGTGCT	62.467	60.000	24.37	0.00	33.24	4.40
1486	1691	2.743126	TTCCTGCTGCTGGAGTGCTG	62.743	60.000	24.37	0.09	33.24	4.41
1527	1734	1.604378	CTGGCATCTCGGGAGGTTT	59.396	57.895	0.00	0.00	0.00	3.27
1528	1735	0.745845	CTGGCATCTCGGGAGGTTTG	60.746	60.000	0.00	0.00	0.00	2.93
1529	1736	1.452108	GGCATCTCGGGAGGTTTGG	60.452	63.158	0.00	0.00	0.00	3.28
1587	1794	0.103937	CTGCGTCTTCATCTCCTCCC	59.896	60.000	0.00	0.00	0.00	4.30
1617	1824	2.355132	TCTGGTCGATCGTAGCTCTTTC	59.645	50.000	15.94	0.00	0.00	2.62
1618	1825	2.356382	CTGGTCGATCGTAGCTCTTTCT	59.644	50.000	15.94	0.00	0.00	2.52
1620	1827	3.181499	TGGTCGATCGTAGCTCTTTCTTC	60.181	47.826	15.94	0.00	0.00	2.87
1622	1829	2.358267	TCGATCGTAGCTCTTTCTTCCC	59.642	50.000	15.94	0.00	0.00	3.97
1643	1855	0.818852	TTGTGTGCTGCTGCTTGCTA	60.819	50.000	17.00	1.26	43.37	3.49
1660	1877	1.202348	GCTAGGGTTTGATTGTGTGCC	59.798	52.381	0.00	0.00	0.00	5.01
1671	1896	0.812014	TTGTGTGCCTGTGTACGGTG	60.812	55.000	0.00	0.00	0.00	4.94
1734	1963	0.319211	CGTCCGTCCTTGCTTGTGTA	60.319	55.000	0.00	0.00	0.00	2.90
1754	1987	2.691409	TGTGCTCCTAGTATTGTGGC	57.309	50.000	0.00	0.00	0.00	5.01
1791	2052	9.865321	TGAAATCAATACTACTGTACTGGTTAC	57.135	33.333	4.66	0.00	29.26	2.50
1802	2063	9.245962	CTACTGTACTGGTTACATATTAAGCAC	57.754	37.037	4.66	0.00	40.06	4.40
1805	2070	8.712285	TGTACTGGTTACATATTAAGCACTTC	57.288	34.615	0.00	2.48	35.64	3.01
1814	2079	6.403878	ACATATTAAGCACTTCCGTGTTACT	58.596	36.000	0.00	0.00	43.16	2.24
1826	2091	3.320541	TCCGTGTTACTTTAGAAACCCGA	59.679	43.478	0.00	0.00	29.57	5.14
1837	2102	2.807676	AGAAACCCGATTGATTTGGCT	58.192	42.857	0.00	0.00	0.00	4.75
1945	2221	3.135530	AGTGCATCCCTTTCTATGTCCTC	59.864	47.826	0.00	0.00	0.00	3.71
1990	2266	3.257469	AGCGCTCAGATTTGATTGAGA	57.743	42.857	2.64	0.00	42.67	3.27
1991	2267	2.935201	AGCGCTCAGATTTGATTGAGAC	59.065	45.455	2.64	0.00	42.67	3.36
1998	2274	4.925646	TCAGATTTGATTGAGACACGACAG	59.074	41.667	0.00	0.00	0.00	3.51
2017	2293	4.569943	ACAGTCGTCATAAGATTGCAAGT	58.430	39.130	4.94	0.00	0.00	3.16
2018	2294	4.997395	ACAGTCGTCATAAGATTGCAAGTT	59.003	37.500	4.94	3.59	0.00	2.66
2025	2301	6.955963	CGTCATAAGATTGCAAGTTAGAACAC	59.044	38.462	4.94	1.34	0.00	3.32
2076	2385	7.010183	GTGATATTATGTACGAAGCACTGTTGT	59.990	37.037	0.00	0.00	0.00	3.32
2092	2401	3.466836	TGTTGTCGCTCAAGTCTTGATT	58.533	40.909	15.60	0.00	39.30	2.57
2136	2446	2.574955	AAGTCAAGTCTCCGCCGCT	61.575	57.895	0.00	0.00	0.00	5.52
2242	2560	1.736645	CGTGACACGCAACCTAGGG	60.737	63.158	16.06	0.00	33.65	3.53

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
6	7	6.757897	AAGATCCATTCAACTTCGCAAATA	57.242	33.333	0.00	0.00	0.00	1.40
208	210	2.326428	TCCTTTCTCACTCGGTTTCCT	58.674	47.619	0.00	0.00	0.00	3.36
232	234	6.406400	CGTATCACCCTCTTTTTCTCTCAGAT	60.406	42.308	0.00	0.00	0.00	2.90
287	290	4.280819	CCCCATGTTATCTCCAACACATT	58.719	43.478	0.00	0.00	41.02	2.71
340	343	5.221126	GGCTGCCTCAAATTTAGACCTTATG	60.221	44.000	12.43	0.00	0.00	1.90
390	393	3.955650	TGAACGCTTAGTAGGCTCTTT	57.044	42.857	2.50	0.00	0.00	2.52
432	435	9.366216	GTCAAAACTTATTTGTTCTCAAAGGTT	57.634	29.630	1.35	0.00	45.01	3.50
578	581	0.391793	GTTTCTCGAAGGAGCCTGGG	60.392	60.000	0.00	0.00	40.26	4.45
599	602	0.179043	TGGCAAGTCGGTAGTGCAAA	60.179	50.000	0.00	0.00	40.12	3.68
710	722	0.301687	GCACAACGCGTCCATATCTG	59.698	55.000	14.44	7.91	0.00	2.90
818	862	1.530323	GGACCCAAAAGCGTACATGT	58.470	50.000	2.69	2.69	0.00	3.21
1373	1556	2.046314	AACTGAATCCGCCCACCG	60.046	61.111	0.00	0.00	0.00	4.94
1453	1636	1.472376	GCAGGAAGAAGATCACCGAGG	60.472	57.143	0.00	0.00	0.00	4.63
1469	1674	2.746671	CAGCACTCCAGCAGCAGG	60.747	66.667	0.00	0.00	36.85	4.85
1479	1684	0.465460	TTCACCACCAACCAGCACTC	60.465	55.000	0.00	0.00	0.00	3.51
1480	1685	0.466189	CTTCACCACCAACCAGCACT	60.466	55.000	0.00	0.00	0.00	4.40
1481	1686	2.032981	CTTCACCACCAACCAGCAC	58.967	57.895	0.00	0.00	0.00	4.40
1482	1687	1.827789	GCTTCACCACCAACCAGCA	60.828	57.895	0.00	0.00	0.00	4.41
1483	1688	2.564721	GGCTTCACCACCAACCAGC	61.565	63.158	0.00	0.00	38.86	4.85
1484	1689	0.890996	GAGGCTTCACCACCAACCAG	60.891	60.000	0.00	0.00	43.14	4.00
1485	1690	1.150536	GAGGCTTCACCACCAACCA	59.849	57.895	0.00	0.00	43.14	3.67
1486	1691	0.890996	CTGAGGCTTCACCACCAACC	60.891	60.000	0.00	0.00	43.14	3.77
1587	1794	2.343163	GATCGACCAGACCTGCTCGG	62.343	65.000	12.92	0.00	38.72	4.63
1617	1824	1.893808	AGCAGCACACAACGGGAAG	60.894	57.895	0.00	0.00	0.00	3.46
1618	1825	2.186160	CAGCAGCACACAACGGGAA	61.186	57.895	0.00	0.00	0.00	3.97
1620	1827	4.332637	GCAGCAGCACACAACGGG	62.333	66.667	0.00	0.00	41.58	5.28
1622	1829	1.656263	CAAGCAGCAGCACACAACG	60.656	57.895	3.17	0.00	45.49	4.10
1643	1855	1.331214	CAGGCACACAATCAAACCCT	58.669	50.000	0.00	0.00	0.00	4.34
1660	1877	3.805422	TCTTTTTACAGCACCGTACACAG	59.195	43.478	0.00	0.00	0.00	3.66
1671	1896	4.949856	TGATCCATCCCTTCTTTTTACAGC	59.050	41.667	0.00	0.00	0.00	4.40
1734	1963	2.774234	AGCCACAATACTAGGAGCACAT	59.226	45.455	0.00	0.00	0.00	3.21
1754	1987	8.043710	AGTAGTATTGATTTCACAAGAAGGGAG	58.956	37.037	0.00	0.00	34.71	4.30
1802	2063	4.151157	CGGGTTTCTAAAGTAACACGGAAG	59.849	45.833	14.16	0.00	44.68	3.46
1814	2079	4.770010	AGCCAAATCAATCGGGTTTCTAAA	59.230	37.500	0.00	0.00	0.00	1.85
1826	2091	1.843851	TCCTCCGGTAGCCAAATCAAT	59.156	47.619	0.00	0.00	0.00	2.57
1837	2102	0.744874	CGAAGCAGAATCCTCCGGTA	59.255	55.000	0.00	0.00	0.00	4.02
1856	2121	5.846473	GTCAAGCAAAAACGTGATAGAACTC	59.154	40.000	0.00	0.00	30.78	3.01
1971	2247	2.674852	TGTCTCAATCAAATCTGAGCGC	59.325	45.455	0.00	0.00	39.17	5.92
1979	2255	3.675225	CGACTGTCGTGTCTCAATCAAAT	59.325	43.478	21.30	0.00	34.72	2.32
1998	2274	6.887376	TCTAACTTGCAATCTTATGACGAC	57.113	37.500	0.00	0.00	0.00	4.34
2059	2335	1.483316	CGACAACAGTGCTTCGTACA	58.517	50.000	0.00	0.00	0.00	2.90
2060	2336	0.161024	GCGACAACAGTGCTTCGTAC	59.839	55.000	9.56	0.00	0.00	3.67
2076	2385	4.428209	GAGATGAATCAAGACTTGAGCGA	58.572	43.478	21.78	9.17	43.98	4.93
2092	2401	1.323271	GCGAGGTCTGTGGGAGATGA	61.323	60.000	0.00	0.00	31.63	2.92
2136	2446	1.016627	GCATCGGCAGCAAGTTGATA	58.983	50.000	7.16	0.00	40.72	2.15

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.