AutoCloner

Multiple sequence alignment - TraesCS2A01G043900

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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	TraesCS2A01G043900	chr2A	100.000	2231	0	0	1	2231	17503112	17500882	0.000000e+00	4120
1	TraesCS2A01G043900	chr2A	93.032	1550	103	4	1	1548	17534176	17532630	0.000000e+00	2259
2	TraesCS2A01G043900	chr2A	89.666	1645	142	10	1	1626	17598697	17597062	0.000000e+00	2071
3	TraesCS2A01G043900	chr2A	90.316	1549	140	6	1	1548	17474955	17473416	0.000000e+00	2021
4	TraesCS2A01G043900	chr2A	89.533	1414	147	1	2	1415	17549508	17548096	0.000000e+00	1790
5	TraesCS2A01G043900	chr2A	90.024	822	79	3	1	821	17425298	17424479	0.000000e+00	1061
6	TraesCS2A01G043900	chr2A	87.772	597	48	4	1653	2231	17473263	17472674	0.000000e+00	675
7	TraesCS2A01G043900	chr2A	86.811	599	50	9	1653	2231	17547851	17547262	1.870000e-180	641
8	TraesCS2A01G043900	chr2A	86.622	598	55	7	1653	2231	17539847	17539256	2.420000e-179	638
9	TraesCS2A01G043900	chr2A	86.455	598	54	7	1653	2231	17532492	17531903	4.040000e-177	630
10	TraesCS2A01G043900	chr2A	79.585	867	92	32	1308	2157	17418556	17417758	1.950000e-150	542
11	TraesCS2A01G043900	chr2A	87.032	347	38	4	1287	1633	17559176	17558837	3.480000e-103	385
12	TraesCS2A01G043900	chr2A	91.597	119	10	0	1649	1767	17558767	17558649	4.930000e-37	165
13	TraesCS2A01G043900	chr2A	80.000	230	24	6	1762	1973	17558315	17558090	1.380000e-32	150
14	TraesCS2A01G043900	chr2A	81.507	146	16	7	1653	1797	17411473	17411338	2.340000e-20	110
15	TraesCS2A01G043900	chr2B	89.330	1790	176	6	1	1782	27544796	27543014	0.000000e+00	2233
16	TraesCS2A01G043900	chr2B	84.629	1646	190	34	1	1621	27617214	27615607	0.000000e+00	1580
17	TraesCS2A01G043900	chr2B	87.359	973	117	6	9	979	27582193	27581225	0.000000e+00	1110
18	TraesCS2A01G043900	chr2B	87.600	250	15	8	1853	2088	27543014	27542767	2.180000e-70	276
19	TraesCS2A01G043900	chr2B	89.241	158	11	4	2078	2231	27539597	27539442	2.260000e-45	193
20	TraesCS2A01G043900	chr2D	87.650	1247	146	3	1	1239	15506543	15505297	0.000000e+00	1443
21	TraesCS2A01G043900	chr2D	80.964	1660	259	37	1	1627	15472236	15470601	0.000000e+00	1262
22	TraesCS2A01G043900	chr2D	86.358	755	76	8	872	1606	15458327	15457580	0.000000e+00	798
23	TraesCS2A01G043900	chr2D	78.708	418	46	28	1653	2032	15470526	15470114	2.860000e-59	239
24	TraesCS2A01G043900	chr2D	80.282	213	29	9	1419	1621	15505169	15504960	4.960000e-32	148

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	TraesCS2A01G043900	chr2A	17500882	17503112	2230	True	4120.000000	4120	100.000000	1	2231	1	chr2A.!!$R4	2230
1	TraesCS2A01G043900	chr2A	17597062	17598697	1635	True	2071.000000	2071	89.666000	1	1626	1	chr2A.!!$R6	1625
2	TraesCS2A01G043900	chr2A	17531903	17534176	2273	True	1444.500000	2259	89.743500	1	2231	2	chr2A.!!$R8	2230
3	TraesCS2A01G043900	chr2A	17472674	17474955	2281	True	1348.000000	2021	89.044000	1	2231	2	chr2A.!!$R7	2230
4	TraesCS2A01G043900	chr2A	17547262	17549508	2246	True	1215.500000	1790	88.172000	2	2231	2	chr2A.!!$R9	2229
5	TraesCS2A01G043900	chr2A	17424479	17425298	819	True	1061.000000	1061	90.024000	1	821	1	chr2A.!!$R3	820
6	TraesCS2A01G043900	chr2A	17539256	17539847	591	True	638.000000	638	86.622000	1653	2231	1	chr2A.!!$R5	578
7	TraesCS2A01G043900	chr2A	17417758	17418556	798	True	542.000000	542	79.585000	1308	2157	1	chr2A.!!$R2	849
8	TraesCS2A01G043900	chr2A	17558090	17559176	1086	True	233.333333	385	86.209667	1287	1973	3	chr2A.!!$R10	686
9	TraesCS2A01G043900	chr2B	27615607	27617214	1607	True	1580.000000	1580	84.629000	1	1621	1	chr2B.!!$R2	1620
10	TraesCS2A01G043900	chr2B	27581225	27582193	968	True	1110.000000	1110	87.359000	9	979	1	chr2B.!!$R1	970
11	TraesCS2A01G043900	chr2B	27539442	27544796	5354	True	900.666667	2233	88.723667	1	2231	3	chr2B.!!$R3	2230
12	TraesCS2A01G043900	chr2D	15457580	15458327	747	True	798.000000	798	86.358000	872	1606	1	chr2D.!!$R1	734
13	TraesCS2A01G043900	chr2D	15504960	15506543	1583	True	795.500000	1443	83.966000	1	1621	2	chr2D.!!$R3	1620
14	TraesCS2A01G043900	chr2D	15470114	15472236	2122	True	750.500000	1262	79.836000	1	2032	2	chr2D.!!$R2	2031

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
617	630	0.54851	GAGAGGTGCCCCAAGCTATT	59.451	55.0	0.0	0.0	44.23	1.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2159	5906	0.324275	ACACTTGTTGGTGGTTGCCT	60.324	50.0	0.0	0.0	41.09	4.75	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
105	106	5.787953	TGCATCTTTTGACTTCAATTGGA	57.212	34.783	5.42	0.00	35.55	3.53
245	249	1.166531	GCCGTGAAGTTGCTCAAGGT	61.167	55.000	7.33	0.00	44.22	3.50
320	330	2.923121	AGAAGAACTGCAAGCTGTCAA	58.077	42.857	5.05	0.00	37.60	3.18
424	437	4.224594	TGCAAGATGAAGAGAAGATGGAGT	59.775	41.667	0.00	0.00	0.00	3.85
433	446	1.137872	AGAAGATGGAGTGTGGATCGC	59.862	52.381	0.00	0.00	0.00	4.58
468	481	3.128242	ACAACACTCGGAGGATTAGTACG	59.872	47.826	10.23	0.00	0.00	3.67
565	578	1.766494	CATTCCATGCCCACAAGCTA	58.234	50.000	0.00	0.00	0.00	3.32
617	630	0.548510	GAGAGGTGCCCCAAGCTATT	59.451	55.000	0.00	0.00	44.23	1.73
622	635	1.768870	GGTGCCCCAAGCTATTCTCTA	59.231	52.381	0.00	0.00	44.23	2.43
725	738	2.353704	CGTGCTACATCTGGAACTGGAA	60.354	50.000	0.00	0.00	0.00	3.53
867	880	1.326852	GAGACGCTCGAGATCGTGTAA	59.673	52.381	20.41	0.00	39.22	2.41
1245	1264	1.282157	AGGTGAGCTATGTTTGGTCCC	59.718	52.381	0.00	0.00	0.00	4.46
1276	1295	9.085645	TCCTTTCATCAGTAACTTACTTAGTGA	57.914	33.333	0.00	2.15	45.14	3.41
1311	1331	8.193438	ACTTACGTTTACCATTCTATCTGTACC	58.807	37.037	0.00	0.00	0.00	3.34
1518	1584	1.742761	TGCCTTACTTGATGCTGCTC	58.257	50.000	0.00	0.00	0.00	4.26
1519	1585	1.280133	TGCCTTACTTGATGCTGCTCT	59.720	47.619	0.00	0.00	0.00	4.09
1521	1589	2.869192	GCCTTACTTGATGCTGCTCTAC	59.131	50.000	0.00	0.00	0.00	2.59
1523	1591	4.202161	GCCTTACTTGATGCTGCTCTACTA	60.202	45.833	0.00	0.00	0.00	1.82
1537	1613	4.106197	GCTCTACTAGTCCGTGTGAAATG	58.894	47.826	0.00	0.00	0.00	2.32
1542	1618	0.944386	AGTCCGTGTGAAATGTGCAC	59.056	50.000	10.75	10.75	36.81	4.57
1561	1639	2.756207	CACCTGCAAATCCATGATGTGA	59.244	45.455	0.00	0.00	29.25	3.58
1606	1692	2.035530	TTTGCTTTGGTTTGGCTTGG	57.964	45.000	0.00	0.00	0.00	3.61
1607	1693	0.463474	TTGCTTTGGTTTGGCTTGGC	60.463	50.000	0.00	0.00	0.00	4.52
1608	1694	1.336632	TGCTTTGGTTTGGCTTGGCT	61.337	50.000	0.00	0.00	0.00	4.75
1609	1695	0.179048	GCTTTGGTTTGGCTTGGCTT	60.179	50.000	0.00	0.00	0.00	4.35
1610	1696	1.585297	CTTTGGTTTGGCTTGGCTTG	58.415	50.000	0.00	0.00	0.00	4.01
1611	1697	1.138661	CTTTGGTTTGGCTTGGCTTGA	59.861	47.619	0.00	0.00	0.00	3.02
1612	1698	1.422531	TTGGTTTGGCTTGGCTTGAT	58.577	45.000	0.00	0.00	0.00	2.57
1613	1699	1.422531	TGGTTTGGCTTGGCTTGATT	58.577	45.000	0.00	0.00	0.00	2.57
1614	1700	1.767681	TGGTTTGGCTTGGCTTGATTT	59.232	42.857	0.00	0.00	0.00	2.17
1615	1701	2.145536	GGTTTGGCTTGGCTTGATTTG	58.854	47.619	0.00	0.00	0.00	2.32
1616	1702	1.532437	GTTTGGCTTGGCTTGATTTGC	59.468	47.619	0.00	0.00	0.00	3.68
1617	1703	1.050204	TTGGCTTGGCTTGATTTGCT	58.950	45.000	0.00	0.00	0.00	3.91
1618	1704	1.050204	TGGCTTGGCTTGATTTGCTT	58.950	45.000	0.00	0.00	0.00	3.91
1619	1705	1.417145	TGGCTTGGCTTGATTTGCTTT	59.583	42.857	0.00	0.00	0.00	3.51
1620	1706	1.802365	GGCTTGGCTTGATTTGCTTTG	59.198	47.619	0.00	0.00	0.00	2.77
1621	1707	1.802365	GCTTGGCTTGATTTGCTTTGG	59.198	47.619	0.00	0.00	0.00	3.28
1622	1708	2.807837	GCTTGGCTTGATTTGCTTTGGT	60.808	45.455	0.00	0.00	0.00	3.67
1623	1709	3.469739	CTTGGCTTGATTTGCTTTGGTT	58.530	40.909	0.00	0.00	0.00	3.67
1732	1902	2.663075	CCTGCCTGCTCCTGCTGTA	61.663	63.158	0.00	0.00	40.48	2.74
1752	1922	0.317020	GCTCTCCGTTTGTGTGTTGC	60.317	55.000	0.00	0.00	0.00	4.17
1753	1923	1.013596	CTCTCCGTTTGTGTGTTGCA	58.986	50.000	0.00	0.00	0.00	4.08
1804	2313	6.561737	TTACTGTAATGCGAAACAATTCCA	57.438	33.333	0.00	0.00	31.52	3.53
1843	2358	5.625921	TGGTGATTTGTGTGTGTGATATG	57.374	39.130	0.00	0.00	0.00	1.78
1847	2362	7.392953	TGGTGATTTGTGTGTGTGATATGTAAT	59.607	33.333	0.00	0.00	0.00	1.89
1848	2363	8.888716	GGTGATTTGTGTGTGTGATATGTAATA	58.111	33.333	0.00	0.00	0.00	0.98
1857	2372	7.332182	TGTGTGTGATATGTAATAAACTGCGAA	59.668	33.333	0.00	0.00	29.06	4.70
1915	2448	7.883391	TTGTAAAATCCTTGACTGGTTGTTA	57.117	32.000	0.00	0.00	0.00	2.41
2045	2603	5.477607	TTTGGCTTACACTAGCAAGACTA	57.522	39.130	6.71	0.00	43.02	2.59
2091	5829	6.228616	AGTAAGTAGAAGCAGAATCCCTTC	57.771	41.667	3.86	3.86	38.14	3.46
2104	5846	6.376581	GCAGAATCCCTTCTATTTATCCATGG	59.623	42.308	4.97	4.97	39.78	3.66
2117	5859	2.885135	TCCATGGCACTGAAATGAGT	57.115	45.000	6.96	0.00	0.00	3.41
2159	5906	1.188871	TACCATGCGACACCTCCACA	61.189	55.000	0.00	0.00	0.00	4.17
2173	5920	1.756172	CCACAGGCAACCACCAACA	60.756	57.895	0.00	0.00	37.17	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
49	50	3.909732	CCTAATGGTGAAGCCCCAAATA	58.090	45.455	0.00	0.00	35.14	1.40
245	249	2.763710	TGCTGCTGGCTCCCGATA	60.764	61.111	0.00	0.00	42.39	2.92
264	268	8.955388	TCACTTGCATATAAGTATTGAGCAAAA	58.045	29.630	0.00	0.00	38.78	2.44
424	437	1.262417	TGTTCCTGTAGCGATCCACA	58.738	50.000	0.00	0.00	0.00	4.17
433	446	3.245284	CGAGTGTTGTGTTGTTCCTGTAG	59.755	47.826	0.00	0.00	0.00	2.74
468	481	1.168714	CAGGGGCTAAAGCAACACTC	58.831	55.000	4.07	0.00	44.36	3.51
565	578	2.437359	GAGCCAGCGCCAATCTGT	60.437	61.111	2.29	0.00	34.57	3.41
617	630	2.119495	GGGGAGTGGCAAAGATAGAGA	58.881	52.381	0.00	0.00	0.00	3.10
622	635	0.779997	AGTTGGGGAGTGGCAAAGAT	59.220	50.000	0.00	0.00	0.00	2.40
725	738	5.249780	TCCACTTGGTTGGTATGTTGTAT	57.750	39.130	0.00	0.00	37.93	2.29
867	880	3.843027	AGACTTCCTTCAGATCACCACAT	59.157	43.478	0.00	0.00	0.00	3.21
1157	1170	0.830648	TGGTTCATAGAGCGAAGGGG	59.169	55.000	0.00	0.00	0.00	4.79
1245	1264	7.607250	AGTAAGTTACTGATGAAAGGAGACAG	58.393	38.462	14.82	0.00	37.69	3.51
1518	1584	3.612860	GCACATTTCACACGGACTAGTAG	59.387	47.826	0.00	0.00	0.00	2.57
1519	1585	3.006003	TGCACATTTCACACGGACTAGTA	59.994	43.478	0.00	0.00	0.00	1.82
1521	1589	2.157668	GTGCACATTTCACACGGACTAG	59.842	50.000	13.17	0.00	34.73	2.57
1523	1591	0.944386	GTGCACATTTCACACGGACT	59.056	50.000	13.17	0.00	34.73	3.85
1542	1618	2.223409	CGTCACATCATGGATTTGCAGG	60.223	50.000	0.00	0.00	0.00	4.85
1548	1624	1.382522	GCACCGTCACATCATGGATT	58.617	50.000	0.00	0.00	0.00	3.01
1549	1625	0.811219	CGCACCGTCACATCATGGAT	60.811	55.000	0.00	0.00	0.00	3.41
1550	1626	1.447663	CGCACCGTCACATCATGGA	60.448	57.895	0.00	0.00	0.00	3.41
1561	1639	1.300697	GAACTGGAAGACGCACCGT	60.301	57.895	0.00	0.00	45.10	4.83
1606	1692	3.205338	ACCAAACCAAAGCAAATCAAGC	58.795	40.909	0.00	0.00	0.00	4.01
1607	1693	5.448904	CCAAACCAAACCAAAGCAAATCAAG	60.449	40.000	0.00	0.00	0.00	3.02
1608	1694	4.397417	CCAAACCAAACCAAAGCAAATCAA	59.603	37.500	0.00	0.00	0.00	2.57
1609	1695	3.944015	CCAAACCAAACCAAAGCAAATCA	59.056	39.130	0.00	0.00	0.00	2.57
1610	1696	3.243035	GCCAAACCAAACCAAAGCAAATC	60.243	43.478	0.00	0.00	0.00	2.17
1611	1697	2.687425	GCCAAACCAAACCAAAGCAAAT	59.313	40.909	0.00	0.00	0.00	2.32
1612	1698	2.087646	GCCAAACCAAACCAAAGCAAA	58.912	42.857	0.00	0.00	0.00	3.68
1613	1699	1.280421	AGCCAAACCAAACCAAAGCAA	59.720	42.857	0.00	0.00	0.00	3.91
1614	1700	0.908198	AGCCAAACCAAACCAAAGCA	59.092	45.000	0.00	0.00	0.00	3.91
1615	1701	1.670295	CAAGCCAAACCAAACCAAAGC	59.330	47.619	0.00	0.00	0.00	3.51
1616	1702	3.258971	TCAAGCCAAACCAAACCAAAG	57.741	42.857	0.00	0.00	0.00	2.77
1617	1703	3.922171	ATCAAGCCAAACCAAACCAAA	57.078	38.095	0.00	0.00	0.00	3.28
1618	1704	3.739519	CGAATCAAGCCAAACCAAACCAA	60.740	43.478	0.00	0.00	0.00	3.67
1619	1705	2.223923	CGAATCAAGCCAAACCAAACCA	60.224	45.455	0.00	0.00	0.00	3.67
1620	1706	2.403259	CGAATCAAGCCAAACCAAACC	58.597	47.619	0.00	0.00	0.00	3.27
1621	1707	2.223947	ACCGAATCAAGCCAAACCAAAC	60.224	45.455	0.00	0.00	0.00	2.93
1622	1708	2.035632	ACCGAATCAAGCCAAACCAAA	58.964	42.857	0.00	0.00	0.00	3.28
1623	1709	1.698506	ACCGAATCAAGCCAAACCAA	58.301	45.000	0.00	0.00	0.00	3.67
1732	1902	1.299541	CAACACACAAACGGAGAGCT	58.700	50.000	0.00	0.00	0.00	4.09
1752	1922	4.142752	CCATAGCTGACAAATCACACACTG	60.143	45.833	0.00	0.00	0.00	3.66
1753	1923	4.005650	CCATAGCTGACAAATCACACACT	58.994	43.478	0.00	0.00	0.00	3.55
1847	2362	9.907576	CAAAACAAAACATAAATTCGCAGTTTA	57.092	25.926	0.00	0.00	32.62	2.01
1848	2363	7.427895	GCAAAACAAAACATAAATTCGCAGTTT	59.572	29.630	0.00	0.00	34.19	2.66
1849	2364	6.904543	GCAAAACAAAACATAAATTCGCAGTT	59.095	30.769	0.00	0.00	0.00	3.16
1852	2367	5.427082	CGCAAAACAAAACATAAATTCGCA	58.573	33.333	0.00	0.00	0.00	5.10
1857	2372	6.423302	TGATCAGCGCAAAACAAAACATAAAT	59.577	30.769	11.47	0.00	0.00	1.40
2021	2579	5.316987	AGTCTTGCTAGTGTAAGCCAAATT	58.683	37.500	0.00	0.00	42.05	1.82
2091	5829	7.230108	ACTCATTTCAGTGCCATGGATAAATAG	59.770	37.037	18.40	11.86	0.00	1.73
2128	5871	4.094294	TGTCGCATGGTAGCTAATTGAAAC	59.906	41.667	0.00	0.00	0.00	2.78
2159	5906	0.324275	ACACTTGTTGGTGGTTGCCT	60.324	50.000	0.00	0.00	41.09	4.75
2173	5920	3.791973	TGAAATGCGGTGAAAACACTT	57.208	38.095	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.