AutoCloner

Multiple sequence alignment - TraesCS2A01G468000

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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	TraesCS2A01G468000	chr2A	100.000	2570	0	0	1	2570	712063872	712066441	0.000000e+00	4747
1	TraesCS2A01G468000	chr2D	93.265	2643	59	47	1	2565	572803861	572806462	0.000000e+00	3784
2	TraesCS2A01G468000	chr3A	87.819	1839	83	60	780	2539	336612616	336610840	0.000000e+00	2025
3	TraesCS2A01G468000	chr3A	82.444	843	58	29	1	771	336613851	336613027	0.000000e+00	654
4	TraesCS2A01G468000	chr3B	87.378	1846	80	54	780	2565	309409281	309411033	0.000000e+00	1977
5	TraesCS2A01G468000	chr3B	84.765	873	40	26	1	788	309408394	309409258	0.000000e+00	789
6	TraesCS2A01G468000	chr3D	84.207	1469	88	46	1	1355	253565253	253563815	0.000000e+00	1295
7	TraesCS2A01G468000	chr3D	88.827	537	22	19	1364	1885	253557034	253556521	2.170000e-175	625
8	TraesCS2A01G468000	chr3D	93.112	392	10	6	2179	2565	253554342	253553963	2.230000e-155	558
9	TraesCS2A01G468000	chr3D	92.466	292	8	4	1886	2173	253556414	253556133	3.080000e-109	405
10	TraesCS2A01G468000	chr1A	95.833	504	12	3	486	988	457343943	457344438	0.000000e+00	806
11	TraesCS2A01G468000	chr1A	92.174	115	7	2	467	579	457344643	457344529	7.360000e-36	161

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	TraesCS2A01G468000	chr2A	712063872	712066441	2569	False	4747.000000	4747	100.000000	1	2570	1	chr2A.!!$F1	2569
1	TraesCS2A01G468000	chr2D	572803861	572806462	2601	False	3784.000000	3784	93.265000	1	2565	1	chr2D.!!$F1	2564
2	TraesCS2A01G468000	chr3A	336610840	336613851	3011	True	1339.500000	2025	85.131500	1	2539	2	chr3A.!!$R1	2538
3	TraesCS2A01G468000	chr3B	309408394	309411033	2639	False	1383.000000	1977	86.071500	1	2565	2	chr3B.!!$F1	2564
4	TraesCS2A01G468000	chr3D	253563815	253565253	1438	True	1295.000000	1295	84.207000	1	1355	1	chr3D.!!$R1	1354
5	TraesCS2A01G468000	chr3D	253553963	253557034	3071	True	529.333333	625	91.468333	1364	2565	3	chr3D.!!$R2	1201

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
830	1357	0.036294	AAAAGACCGCTCCACCTAGC	60.036	55.0	0.0	0.0	39.21	3.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1648	2270	0.031585	CCATGCATCATCGCAAAGGG	59.968	55.0	0.0	0.0	46.87	3.95	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
206	214	0.465460	ACGTTTGCTTCTTCAGGGCA	60.465	50.000	0.00	0.00	0.00	5.36
220	228	2.158769	TCAGGGCATCGATTTGCTACAT	60.159	45.455	10.61	0.00	42.38	2.29
250	258	1.493311	GTCGGCGTCTTCTGCTTTG	59.507	57.895	6.85	0.00	0.00	2.77
336	344	1.467342	ACGGAAATTTAGAGGTTGCGC	59.533	47.619	0.00	0.00	39.36	6.09
500	557	0.903236	ACTAAGGAAAGAGGGGACGC	59.097	55.000	0.00	0.00	0.00	5.19
520	577	2.463876	CGAGATTGCGTGATGAAGCTA	58.536	47.619	0.00	0.00	0.00	3.32
655	733	4.518249	CATGATGCATGAGCCAGATAGAT	58.482	43.478	2.46	0.00	43.81	1.98
717	832	2.558359	GGTGGAGGTGGAAGAAACAATG	59.442	50.000	0.00	0.00	0.00	2.82
828	1355	5.048504	CGTATATAAAAGACCGCTCCACCTA	60.049	44.000	0.00	0.00	0.00	3.08
829	1356	3.821421	ATAAAAGACCGCTCCACCTAG	57.179	47.619	0.00	0.00	0.00	3.02
830	1357	0.036294	AAAAGACCGCTCCACCTAGC	60.036	55.000	0.00	0.00	39.21	3.42
831	1358	0.905337	AAAGACCGCTCCACCTAGCT	60.905	55.000	0.00	0.00	40.49	3.32
954	1485	0.735978	CACGCACGCCAGATTGACTA	60.736	55.000	0.00	0.00	0.00	2.59
955	1486	0.736325	ACGCACGCCAGATTGACTAC	60.736	55.000	0.00	0.00	0.00	2.73
957	1488	1.002366	GCACGCCAGATTGACTACTG	58.998	55.000	0.00	0.00	0.00	2.74
1363	1923	3.498334	CTCCGGCCCCTATATATCTACC	58.502	54.545	0.00	0.00	0.00	3.18
1364	1924	3.136896	TCCGGCCCCTATATATCTACCT	58.863	50.000	0.00	0.00	0.00	3.08
1365	1925	4.318633	TCCGGCCCCTATATATCTACCTA	58.681	47.826	0.00	0.00	0.00	3.08
1366	1926	4.353191	TCCGGCCCCTATATATCTACCTAG	59.647	50.000	0.00	0.00	0.00	3.02
1370	1930	6.486941	GGCCCCTATATATCTACCTAGCTAG	58.513	48.000	14.20	14.20	0.00	3.42
1421	1990	4.061596	CACTGCCTAGATTAAAGCTAGCC	58.938	47.826	12.13	0.00	35.19	3.93
1422	1991	3.970640	ACTGCCTAGATTAAAGCTAGCCT	59.029	43.478	12.13	2.37	35.19	4.58
1423	1992	5.011125	CACTGCCTAGATTAAAGCTAGCCTA	59.989	44.000	12.13	3.54	35.19	3.93
1424	1993	5.602978	ACTGCCTAGATTAAAGCTAGCCTAA	59.397	40.000	12.13	10.13	35.19	2.69
1456	2078	2.586425	TGTGAGGCCTGAAAAGAAAGG	58.414	47.619	12.00	0.00	36.58	3.11
1587	2209	5.189180	GGTTAGCTCATCTCCTGTGAATTT	58.811	41.667	0.00	0.00	0.00	1.82
1595	2217	5.887598	TCATCTCCTGTGAATTTAACCCATG	59.112	40.000	0.00	0.00	0.00	3.66
1597	2219	3.763360	CTCCTGTGAATTTAACCCATGCA	59.237	43.478	0.00	0.00	0.00	3.96
1598	2220	4.352009	TCCTGTGAATTTAACCCATGCAT	58.648	39.130	0.00	0.00	0.00	3.96
1600	2222	4.441913	CCTGTGAATTTAACCCATGCATCC	60.442	45.833	0.00	0.00	0.00	3.51
1601	2223	3.450457	TGTGAATTTAACCCATGCATCCC	59.550	43.478	0.00	0.00	0.00	3.85
1602	2224	3.450457	GTGAATTTAACCCATGCATCCCA	59.550	43.478	0.00	0.00	0.00	4.37
1603	2225	3.450457	TGAATTTAACCCATGCATCCCAC	59.550	43.478	0.00	0.00	0.00	4.61
1604	2226	1.468985	TTTAACCCATGCATCCCACG	58.531	50.000	0.00	0.00	0.00	4.94
1605	2227	1.034838	TTAACCCATGCATCCCACGC	61.035	55.000	0.00	0.00	0.00	5.34
1606	2228	2.902423	TAACCCATGCATCCCACGCC	62.902	60.000	0.00	0.00	0.00	5.68
1607	2229	4.818863	CCCATGCATCCCACGCCA	62.819	66.667	0.00	0.00	0.00	5.69
1608	2230	3.520862	CCATGCATCCCACGCCAC	61.521	66.667	0.00	0.00	0.00	5.01
1647	2269	3.257561	CGAGCGACGAGGGCATTG	61.258	66.667	0.00	0.00	45.77	2.82
1648	2270	3.567797	GAGCGACGAGGGCATTGC	61.568	66.667	0.00	0.00	0.00	3.56
1663	2304	0.103572	ATTGCCCTTTGCGATGATGC	59.896	50.000	0.00	0.00	42.76	3.91
1849	2503	5.565509	GAGTCCTCAAGGATTTTTCCTTCT	58.434	41.667	1.29	0.00	46.41	2.85
1993	2760	0.668535	GTGTTTGGCTGAGGACCAAC	59.331	55.000	0.00	0.00	46.66	3.77
1996	2763	1.963515	GTTTGGCTGAGGACCAACATT	59.036	47.619	0.00	0.00	46.66	2.71
2069	2841	2.423185	TGTGCACCAACTTTTGAGTGAG	59.577	45.455	15.69	0.00	35.32	3.51
2082	2860	0.948141	GAGTGAGCTCCTGTGTGTGC	60.948	60.000	12.15	0.00	35.76	4.57
2090	2874	2.106074	CCTGTGTGTGCGTGTGTGT	61.106	57.895	0.00	0.00	0.00	3.72

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
206	214	3.425525	CGCGTTCTATGTAGCAAATCGAT	59.574	43.478	0.00	0.00	0.00	3.59
250	258	1.398451	CGTCCGACAAGTTGTTGATGC	60.398	52.381	22.62	11.66	37.10	3.91
446	484	1.408969	TTGCCAAAAGGACCAAGGAC	58.591	50.000	0.00	0.00	0.00	3.85
447	485	1.760029	GTTTGCCAAAAGGACCAAGGA	59.240	47.619	0.00	0.00	0.00	3.36
448	486	1.484240	TGTTTGCCAAAAGGACCAAGG	59.516	47.619	0.00	0.00	0.00	3.61
500	557	1.284657	AGCTTCATCACGCAATCTCG	58.715	50.000	0.00	0.00	0.00	4.04
520	577	0.896019	CTGTGTGTCCTCCGGTCTCT	60.896	60.000	0.00	0.00	0.00	3.10
592	666	3.370840	TCTTGCAGCAACTGGGAATAT	57.629	42.857	2.83	0.00	31.21	1.28
593	667	2.877097	TCTTGCAGCAACTGGGAATA	57.123	45.000	2.83	0.00	31.21	1.75
594	668	1.999648	TTCTTGCAGCAACTGGGAAT	58.000	45.000	2.83	0.00	31.21	3.01
595	669	1.774110	TTTCTTGCAGCAACTGGGAA	58.226	45.000	2.83	3.50	31.21	3.97
596	670	1.614903	CATTTCTTGCAGCAACTGGGA	59.385	47.619	2.83	0.00	31.21	4.37
655	733	3.071602	CAGGGCAGGCTAGATTAAAGCTA	59.928	47.826	0.00	0.00	39.97	3.32
717	832	1.017387	GACGGAAAGGTGGATGCATC	58.983	55.000	18.81	18.81	0.00	3.91
828	1355	1.075601	TTGGTTTGGAGATGGGAGCT	58.924	50.000	0.00	0.00	0.00	4.09
829	1356	1.177401	GTTGGTTTGGAGATGGGAGC	58.823	55.000	0.00	0.00	0.00	4.70
830	1357	1.616994	GGGTTGGTTTGGAGATGGGAG	60.617	57.143	0.00	0.00	0.00	4.30
831	1358	0.407918	GGGTTGGTTTGGAGATGGGA	59.592	55.000	0.00	0.00	0.00	4.37
988	1545	6.925211	TCACCTTCTCCATCGCTATTAATAG	58.075	40.000	16.79	16.79	0.00	1.73
1142	1702	3.551496	TTGACTTCCCAGCTGCCGG	62.551	63.158	8.66	5.30	0.00	6.13
1318	1878	2.266055	GACGAACCTGGGGCAGAG	59.734	66.667	0.00	0.00	32.44	3.35
1421	1990	4.098501	GGCCTCACATTCCTTGGAAATTAG	59.901	45.833	6.16	2.66	0.00	1.73
1422	1991	4.023291	GGCCTCACATTCCTTGGAAATTA	58.977	43.478	6.16	0.00	0.00	1.40
1423	1992	2.833943	GGCCTCACATTCCTTGGAAATT	59.166	45.455	6.16	0.00	0.00	1.82
1424	1993	2.043526	AGGCCTCACATTCCTTGGAAAT	59.956	45.455	0.00	0.00	0.00	2.17
1587	2209	1.453015	GCGTGGGATGCATGGGTTA	60.453	57.895	2.46	0.00	0.00	2.85
1595	2217	0.100503	GTAAATGTGGCGTGGGATGC	59.899	55.000	0.00	0.00	0.00	3.91
1597	2219	1.004277	AGTGTAAATGTGGCGTGGGAT	59.996	47.619	0.00	0.00	0.00	3.85
1598	2220	0.398696	AGTGTAAATGTGGCGTGGGA	59.601	50.000	0.00	0.00	0.00	4.37
1600	2222	2.151202	AGAAGTGTAAATGTGGCGTGG	58.849	47.619	0.00	0.00	0.00	4.94
1601	2223	3.498397	AGAAGAAGTGTAAATGTGGCGTG	59.502	43.478	0.00	0.00	0.00	5.34
1602	2224	3.740115	AGAAGAAGTGTAAATGTGGCGT	58.260	40.909	0.00	0.00	0.00	5.68
1603	2225	4.024048	ACAAGAAGAAGTGTAAATGTGGCG	60.024	41.667	0.00	0.00	0.00	5.69
1604	2226	5.438761	ACAAGAAGAAGTGTAAATGTGGC	57.561	39.130	0.00	0.00	0.00	5.01
1605	2227	6.198966	GCAAACAAGAAGAAGTGTAAATGTGG	59.801	38.462	0.00	0.00	0.00	4.17
1606	2228	6.075415	CGCAAACAAGAAGAAGTGTAAATGTG	60.075	38.462	0.00	0.00	0.00	3.21
1607	2229	5.971202	CGCAAACAAGAAGAAGTGTAAATGT	59.029	36.000	0.00	0.00	0.00	2.71
1608	2230	6.198687	TCGCAAACAAGAAGAAGTGTAAATG	58.801	36.000	0.00	0.00	0.00	2.32
1645	2267	1.249469	TGCATCATCGCAAAGGGCAA	61.249	50.000	0.00	0.00	45.17	4.52
1646	2268	1.038681	ATGCATCATCGCAAAGGGCA	61.039	50.000	0.00	0.00	46.87	5.36
1647	2269	0.596600	CATGCATCATCGCAAAGGGC	60.597	55.000	0.00	0.00	46.87	5.19
1648	2270	0.031585	CCATGCATCATCGCAAAGGG	59.968	55.000	0.00	0.00	46.87	3.95
1649	2271	0.596600	GCCATGCATCATCGCAAAGG	60.597	55.000	0.00	0.00	46.87	3.11
1650	2272	0.101579	TGCCATGCATCATCGCAAAG	59.898	50.000	0.00	0.00	46.87	2.77
1660	2301	4.038282	CAGGTGTAAATATGTGCCATGCAT	59.962	41.667	0.00	0.00	41.91	3.96
1661	2302	3.380954	CAGGTGTAAATATGTGCCATGCA	59.619	43.478	0.00	0.00	35.60	3.96
1662	2303	3.631686	TCAGGTGTAAATATGTGCCATGC	59.368	43.478	0.00	0.00	0.00	4.06
1663	2304	4.639755	TGTCAGGTGTAAATATGTGCCATG	59.360	41.667	0.00	0.00	0.00	3.66
2069	2841	2.588877	ACACGCACACACAGGAGC	60.589	61.111	0.00	0.00	0.00	4.70
2082	2860	5.356882	AGGAACAATTAATCACACACACG	57.643	39.130	0.00	0.00	0.00	4.49

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.