AutoCloner

Multiple sequence alignment - TraesCS5B01G390000

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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	TraesCS5B01G390000	chr5B	100.000	2375	0	0	1	2375	569223487	569225861	0.000000e+00	4386.0
1	TraesCS5B01G390000	chr5B	97.692	1473	28	5	132	1603	569102983	569104450	0.000000e+00	2527.0
2	TraesCS5B01G390000	chr5B	96.118	644	8	1	1732	2375	569104447	569105073	0.000000e+00	1035.0
3	TraesCS5B01G390000	chr5B	94.650	486	12	9	742	1224	568845259	568845733	0.000000e+00	741.0
4	TraesCS5B01G390000	chr5B	86.517	534	41	12	193	722	569140113	569140619	2.060000e-155	558.0
5	TraesCS5B01G390000	chrUn	97.427	1516	33	5	89	1603	343569881	343571391	0.000000e+00	2579.0
6	TraesCS5B01G390000	chrUn	97.361	1516	33	5	89	1603	343623794	343625303	0.000000e+00	2571.0
7	TraesCS5B01G390000	chrUn	97.692	1473	28	5	132	1603	199466822	199465355	0.000000e+00	2527.0
8	TraesCS5B01G390000	chrUn	98.602	644	8	1	1732	2375	199465358	199464716	0.000000e+00	1138.0
9	TraesCS5B01G390000	chrUn	96.765	680	11	8	1	676	67088908	67088236	0.000000e+00	1123.0
10	TraesCS5B01G390000	chrUn	96.765	680	11	8	1	676	307430726	307431398	0.000000e+00	1123.0
11	TraesCS5B01G390000	chrUn	87.774	638	42	15	742	1354	67088215	67087589	0.000000e+00	713.0
12	TraesCS5B01G390000	chrUn	100.000	248	0	0	1732	1979	343571388	343571635	2.150000e-125	459.0
13	TraesCS5B01G390000	chrUn	100.000	248	0	0	1732	1979	343625300	343625547	2.150000e-125	459.0
14	TraesCS5B01G390000	chr5D	86.891	1335	101	39	43	1354	462745490	462746773	0.000000e+00	1428.0
15	TraesCS5B01G390000	chr5D	87.607	1170	75	37	104	1243	462668875	462670004	0.000000e+00	1293.0
16	TraesCS5B01G390000	chr5D	81.107	307	47	8	2071	2373	426979149	426979448	3.950000e-58	235.0
17	TraesCS5B01G390000	chr5D	83.459	266	26	12	1732	1989	462896313	462896568	5.110000e-57	231.0
18	TraesCS5B01G390000	chr5D	97.917	48	1	0	1	48	242855424	242855471	1.510000e-12	84.2
19	TraesCS5B01G390000	chr5A	85.638	1309	92	46	89	1354	582652077	582653332	0.000000e+00	1288.0
20	TraesCS5B01G390000	chr5A	86.965	1074	85	28	296	1354	582886567	582887600	0.000000e+00	1157.0
21	TraesCS5B01G390000	chr5A	97.222	144	3	1	1594	1736	53215175	53215032	2.360000e-60	243.0
22	TraesCS5B01G390000	chr5A	97.101	138	3	1	1597	1733	109342602	109342465	5.110000e-57	231.0
23	TraesCS5B01G390000	chr5A	83.571	140	16	3	1941	2074	582889619	582889757	8.910000e-25	124.0
24	TraesCS5B01G390000	chr6D	82.759	290	38	9	2077	2360	454925129	454925412	5.070000e-62	248.0
25	TraesCS5B01G390000	chr6D	98.148	54	1	0	1	54	472151111	472151058	6.990000e-16	95.3
26	TraesCS5B01G390000	chr3B	98.551	138	2	0	1600	1737	509999000	509998863	6.560000e-61	244.0
27	TraesCS5B01G390000	chr3B	80.731	301	46	10	2077	2372	782815695	782815988	8.540000e-55	224.0
28	TraesCS5B01G390000	chr3B	86.010	193	17	7	2086	2273	545667377	545667190	5.180000e-47	198.0
29	TraesCS5B01G390000	chr3B	86.207	174	21	3	2205	2375	34104675	34104502	4.030000e-43	185.0
30	TraesCS5B01G390000	chr7B	98.540	137	2	0	1599	1735	611967743	611967879	2.360000e-60	243.0
31	TraesCS5B01G390000	chr4B	96.575	146	4	1	1592	1737	27255651	27255795	8.480000e-60	241.0
32	TraesCS5B01G390000	chr4B	97.122	139	4	0	1599	1737	36001318	36001180	3.950000e-58	235.0
33	TraesCS5B01G390000	chr3A	97.794	136	2	1	1603	1738	215474228	215474094	1.420000e-57	233.0
34	TraesCS5B01G390000	chr1A	97.778	135	3	0	1599	1733	486680288	486680154	1.420000e-57	233.0
35	TraesCS5B01G390000	chr1A	78.894	199	20	14	662	854	559887472	559887290	5.360000e-22	115.0
36	TraesCS5B01G390000	chr2B	95.745	141	6	0	1595	1735	585193874	585193734	6.600000e-56	228.0
37	TraesCS5B01G390000	chr2B	91.803	61	5	0	1	61	164871766	164871826	4.210000e-13	86.1
38	TraesCS5B01G390000	chr1D	80.656	305	47	9	2077	2375	286646863	286646565	2.380000e-55	226.0
39	TraesCS5B01G390000	chr3D	80.233	258	42	8	2109	2363	589430869	589430618	4.030000e-43	185.0
40	TraesCS5B01G390000	chr6A	77.000	300	59	7	2077	2372	595992447	595992740	1.890000e-36	163.0
41	TraesCS5B01G390000	chr4A	97.917	48	1	0	1	48	743665453	743665406	1.510000e-12	84.2
42	TraesCS5B01G390000	chr7D	95.833	48	2	0	1	48	235479119	235479166	7.040000e-11	78.7

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	TraesCS5B01G390000	chr5B	569223487	569225861	2374	False	4386.0	4386	100.0000	1	2375	1	chr5B.!!$F3	2374
1	TraesCS5B01G390000	chr5B	569102983	569105073	2090	False	1781.0	2527	96.9050	132	2375	2	chr5B.!!$F4	2243
2	TraesCS5B01G390000	chr5B	569140113	569140619	506	False	558.0	558	86.5170	193	722	1	chr5B.!!$F2	529
3	TraesCS5B01G390000	chrUn	199464716	199466822	2106	True	1832.5	2527	98.1470	132	2375	2	chrUn.!!$R2	2243
4	TraesCS5B01G390000	chrUn	343569881	343571635	1754	False	1519.0	2579	98.7135	89	1979	2	chrUn.!!$F2	1890
5	TraesCS5B01G390000	chrUn	343623794	343625547	1753	False	1515.0	2571	98.6805	89	1979	2	chrUn.!!$F3	1890
6	TraesCS5B01G390000	chrUn	307430726	307431398	672	False	1123.0	1123	96.7650	1	676	1	chrUn.!!$F1	675
7	TraesCS5B01G390000	chrUn	67087589	67088908	1319	True	918.0	1123	92.2695	1	1354	2	chrUn.!!$R1	1353
8	TraesCS5B01G390000	chr5D	462745490	462746773	1283	False	1428.0	1428	86.8910	43	1354	1	chr5D.!!$F4	1311
9	TraesCS5B01G390000	chr5D	462668875	462670004	1129	False	1293.0	1293	87.6070	104	1243	1	chr5D.!!$F3	1139
10	TraesCS5B01G390000	chr5A	582652077	582653332	1255	False	1288.0	1288	85.6380	89	1354	1	chr5A.!!$F1	1265
11	TraesCS5B01G390000	chr5A	582886567	582889757	3190	False	640.5	1157	85.2680	296	2074	2	chr5A.!!$F2	1778

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
339	353	1.609061	CCAGCTGGTGTCGATCTTTGT	60.609	52.381	25.53	0.0	0.0	2.83	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1646	1753	0.753262	ATACCTAGCAAGCCACTCCG	59.247	55.0	0.0	0.0	0.0	4.63	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
339	353	1.609061	CCAGCTGGTGTCGATCTTTGT	60.609	52.381	25.53	0.00	0.00	2.83
1603	1710	4.613448	GTCGATCGATCCGATGAAACTTAG	59.387	45.833	22.50	1.09	47.00	2.18
1604	1711	3.914966	CGATCGATCCGATGAAACTTAGG	59.085	47.826	19.51	0.00	47.00	2.69
1605	1712	3.093717	TCGATCCGATGAAACTTAGGC	57.906	47.619	0.00	0.00	0.00	3.93
1606	1713	2.135933	CGATCCGATGAAACTTAGGCC	58.864	52.381	0.00	0.00	0.00	5.19
1607	1714	2.135933	GATCCGATGAAACTTAGGCCG	58.864	52.381	0.00	0.00	0.00	6.13
1608	1715	0.461339	TCCGATGAAACTTAGGCCGC	60.461	55.000	0.00	0.00	0.00	6.53
1609	1716	1.636340	CGATGAAACTTAGGCCGCG	59.364	57.895	0.00	0.00	0.00	6.46
1610	1717	1.082117	CGATGAAACTTAGGCCGCGT	61.082	55.000	4.92	0.00	0.00	6.01
1611	1718	1.084289	GATGAAACTTAGGCCGCGTT	58.916	50.000	4.92	0.00	0.00	4.84
1612	1719	1.062148	GATGAAACTTAGGCCGCGTTC	59.938	52.381	4.92	0.00	0.00	3.95
1613	1720	1.286354	TGAAACTTAGGCCGCGTTCG	61.286	55.000	4.92	0.00	0.00	3.95
1623	1730	4.493747	CGCGTTCGGACTCCCTCC	62.494	72.222	0.00	0.00	35.33	4.30
1659	1766	4.400961	GGAGCGGAGTGGCTTGCT	62.401	66.667	0.00	0.00	44.93	3.91
1660	1767	2.579201	GAGCGGAGTGGCTTGCTA	59.421	61.111	0.00	0.00	44.93	3.49
1661	1768	1.520342	GAGCGGAGTGGCTTGCTAG	60.520	63.158	0.00	0.00	44.93	3.42
1662	1769	2.512515	GCGGAGTGGCTTGCTAGG	60.513	66.667	0.00	0.00	0.00	3.02
1663	1770	2.982130	CGGAGTGGCTTGCTAGGT	59.018	61.111	0.00	0.00	0.00	3.08
1664	1771	1.956629	GCGGAGTGGCTTGCTAGGTA	61.957	60.000	0.00	0.00	0.00	3.08
1665	1772	0.753262	CGGAGTGGCTTGCTAGGTAT	59.247	55.000	0.00	0.00	0.00	2.73
1666	1773	1.961394	CGGAGTGGCTTGCTAGGTATA	59.039	52.381	0.00	0.00	0.00	1.47
1667	1774	2.364324	CGGAGTGGCTTGCTAGGTATAA	59.636	50.000	0.00	0.00	0.00	0.98
1668	1775	3.006967	CGGAGTGGCTTGCTAGGTATAAT	59.993	47.826	0.00	0.00	0.00	1.28
1669	1776	4.219944	CGGAGTGGCTTGCTAGGTATAATA	59.780	45.833	0.00	0.00	0.00	0.98
1670	1777	5.480205	GGAGTGGCTTGCTAGGTATAATAC	58.520	45.833	0.00	0.00	0.00	1.89
1671	1778	5.135508	AGTGGCTTGCTAGGTATAATACG	57.864	43.478	0.00	0.00	0.00	3.06
1672	1779	3.678548	GTGGCTTGCTAGGTATAATACGC	59.321	47.826	0.00	0.00	0.00	4.42
1673	1780	3.322541	TGGCTTGCTAGGTATAATACGCA	59.677	43.478	0.00	0.00	0.00	5.24
1674	1781	3.927142	GGCTTGCTAGGTATAATACGCAG	59.073	47.826	0.00	0.00	0.00	5.18
1675	1782	4.321750	GGCTTGCTAGGTATAATACGCAGA	60.322	45.833	0.00	0.00	0.00	4.26
1676	1783	4.859798	GCTTGCTAGGTATAATACGCAGAG	59.140	45.833	0.00	0.00	0.00	3.35
1677	1784	4.436242	TGCTAGGTATAATACGCAGAGC	57.564	45.455	0.00	0.00	0.00	4.09
1678	1785	4.079970	TGCTAGGTATAATACGCAGAGCT	58.920	43.478	0.00	0.00	0.00	4.09
1679	1786	4.082733	TGCTAGGTATAATACGCAGAGCTG	60.083	45.833	0.00	0.00	0.00	4.24
1690	1797	2.093216	CAGAGCTGCTAAAAGGGCG	58.907	57.895	0.15	0.00	0.00	6.13
1691	1798	1.746991	AGAGCTGCTAAAAGGGCGC	60.747	57.895	0.15	0.00	0.00	6.53
1692	1799	1.746991	GAGCTGCTAAAAGGGCGCT	60.747	57.895	7.64	0.00	40.19	5.92
1693	1800	1.710103	GAGCTGCTAAAAGGGCGCTC	61.710	60.000	7.64	1.48	43.03	5.03
1694	1801	2.765356	GCTGCTAAAAGGGCGCTCC	61.765	63.158	2.00	4.98	0.00	4.70
1695	1802	2.435938	TGCTAAAAGGGCGCTCCG	60.436	61.111	2.00	0.00	41.52	4.63
1728	1835	2.125350	GGAGAGCAGCCGAACAGG	60.125	66.667	0.00	0.00	44.97	4.00
2105	3794	1.663074	GGCGCACAAAAATTCCGCA	60.663	52.632	10.83	0.00	45.78	5.69
2126	3815	5.344884	GCACCCTAAAATAATTTTAGCGCA	58.655	37.500	11.47	0.00	46.75	6.09
2146	3835	5.094812	CGCATCATTTTAGCACTTTTAGCA	58.905	37.500	0.00	0.00	0.00	3.49
2225	3914	3.029074	CGCAGTGTAAATTATGAAGCGC	58.971	45.455	0.00	0.00	36.16	5.92
2227	3916	3.029074	CAGTGTAAATTATGAAGCGCGC	58.971	45.455	26.66	26.66	0.00	6.86

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
339	353	4.033009	TCATCTCTGCCCTAGATCACAAA	58.967	43.478	0.00	0.00	34.21	2.83
1522	1629	3.065786	TGCGTAGTTTCCGGAGTACTATG	59.934	47.826	27.52	27.52	0.00	2.23
1606	1713	4.493747	GGAGGGAGTCCGAACGCG	62.494	72.222	3.53	3.53	34.84	6.01
1642	1749	2.914777	CTAGCAAGCCACTCCGCTCC	62.915	65.000	0.00	0.00	38.44	4.70
1643	1750	1.520342	CTAGCAAGCCACTCCGCTC	60.520	63.158	0.00	0.00	38.44	5.03
1644	1751	2.581354	CTAGCAAGCCACTCCGCT	59.419	61.111	0.00	0.00	42.22	5.52
1645	1752	1.956629	TACCTAGCAAGCCACTCCGC	61.957	60.000	0.00	0.00	0.00	5.54
1646	1753	0.753262	ATACCTAGCAAGCCACTCCG	59.247	55.000	0.00	0.00	0.00	4.63
1647	1754	4.625607	ATTATACCTAGCAAGCCACTCC	57.374	45.455	0.00	0.00	0.00	3.85
1648	1755	5.162075	CGTATTATACCTAGCAAGCCACTC	58.838	45.833	0.00	0.00	0.00	3.51
1649	1756	4.560919	GCGTATTATACCTAGCAAGCCACT	60.561	45.833	0.00	0.00	0.00	4.00
1650	1757	3.678548	GCGTATTATACCTAGCAAGCCAC	59.321	47.826	0.00	0.00	0.00	5.01
1651	1758	3.322541	TGCGTATTATACCTAGCAAGCCA	59.677	43.478	1.92	0.00	0.00	4.75
1652	1759	3.921677	TGCGTATTATACCTAGCAAGCC	58.078	45.455	1.92	0.00	0.00	4.35
1653	1760	4.806330	TCTGCGTATTATACCTAGCAAGC	58.194	43.478	5.29	0.00	34.04	4.01
1654	1761	4.859798	GCTCTGCGTATTATACCTAGCAAG	59.140	45.833	5.29	6.68	34.04	4.01
1655	1762	4.523173	AGCTCTGCGTATTATACCTAGCAA	59.477	41.667	12.23	2.85	34.04	3.91
1656	1763	4.079970	AGCTCTGCGTATTATACCTAGCA	58.920	43.478	12.23	8.56	0.00	3.49
1657	1764	4.416620	CAGCTCTGCGTATTATACCTAGC	58.583	47.826	0.00	1.74	0.00	3.42
1672	1779	1.986575	GCGCCCTTTTAGCAGCTCTG	61.987	60.000	0.00	0.00	0.00	3.35
1673	1780	1.746991	GCGCCCTTTTAGCAGCTCT	60.747	57.895	0.00	0.00	0.00	4.09
1674	1781	1.710103	GAGCGCCCTTTTAGCAGCTC	61.710	60.000	2.29	11.59	43.78	4.09
1675	1782	1.746991	GAGCGCCCTTTTAGCAGCT	60.747	57.895	2.29	0.00	40.82	4.24
1676	1783	2.765356	GGAGCGCCCTTTTAGCAGC	61.765	63.158	2.29	0.00	0.00	5.25
1677	1784	2.464459	CGGAGCGCCCTTTTAGCAG	61.464	63.158	2.29	0.00	0.00	4.24
1678	1785	2.435938	CGGAGCGCCCTTTTAGCA	60.436	61.111	2.29	0.00	0.00	3.49
1709	1816	4.742201	TGTTCGGCTGCTCTCCGC	62.742	66.667	0.00	0.00	46.05	5.54
1711	1818	2.125350	CCTGTTCGGCTGCTCTCC	60.125	66.667	0.00	0.00	0.00	3.71
1720	1827	2.294979	GGTAATTAAGGGCCTGTTCGG	58.705	52.381	6.92	0.00	0.00	4.30
1721	1828	1.937899	CGGTAATTAAGGGCCTGTTCG	59.062	52.381	6.92	0.84	0.00	3.95
1722	1829	2.995283	ACGGTAATTAAGGGCCTGTTC	58.005	47.619	6.92	0.00	0.00	3.18
1723	1830	3.679639	CGTACGGTAATTAAGGGCCTGTT	60.680	47.826	6.92	5.50	0.00	3.16
1724	1831	2.159057	CGTACGGTAATTAAGGGCCTGT	60.159	50.000	6.92	0.00	0.00	4.00
1725	1832	2.101249	TCGTACGGTAATTAAGGGCCTG	59.899	50.000	16.52	0.00	0.00	4.85
1726	1833	2.363359	CTCGTACGGTAATTAAGGGCCT	59.637	50.000	16.52	0.00	0.00	5.19
1727	1834	2.546584	CCTCGTACGGTAATTAAGGGCC	60.547	54.545	16.52	0.00	0.00	5.80
1728	1835	2.101415	ACCTCGTACGGTAATTAAGGGC	59.899	50.000	16.52	0.00	34.94	5.19
1729	1836	4.391405	AACCTCGTACGGTAATTAAGGG	57.609	45.455	16.52	6.53	35.89	3.95
1730	1837	8.424274	AATTAAACCTCGTACGGTAATTAAGG	57.576	34.615	16.52	14.82	35.89	2.69
1731	1838	9.693157	CAAATTAAACCTCGTACGGTAATTAAG	57.307	33.333	16.52	3.04	35.89	1.85
1732	1839	9.213799	ACAAATTAAACCTCGTACGGTAATTAA	57.786	29.630	16.52	15.34	35.89	1.40
1733	1840	8.655092	CACAAATTAAACCTCGTACGGTAATTA	58.345	33.333	16.52	7.77	35.89	1.40
1734	1841	7.173047	ACACAAATTAAACCTCGTACGGTAATT	59.827	33.333	16.52	13.57	35.89	1.40
2126	3815	6.044682	GGCATGCTAAAAGTGCTAAAATGAT	58.955	36.000	18.92	0.00	38.83	2.45
2146	3835	1.140312	AGATATGTTGGGTCCGGCAT	58.860	50.000	0.00	0.00	0.00	4.40
2227	3916	3.033185	CAAATTTAAGCGCCGGATTACG	58.967	45.455	5.05	0.00	43.80	3.18
2344	4033	1.366494	CTCCGCGCGCTAAAATTCG	60.366	57.895	30.48	10.63	0.00	3.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.