AutoCloner

Multiple sequence alignment - TraesCS2D01G462200

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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	TraesCS2D01G462200	chr2D	100.000	3455	0	0	1	3455	568233162	568229708	0.000000e+00	6381
1	TraesCS2D01G462200	chr2A	93.730	2791	124	25	445	3204	707751476	707748706	0.000000e+00	4137
2	TraesCS2D01G462200	chr2A	90.909	209	15	4	3234	3438	707748710	707748502	9.440000e-71	278
3	TraesCS2D01G462200	chr2B	95.612	2484	76	14	1000	3454	680769699	680767220	0.000000e+00	3952
4	TraesCS2D01G462200	chr2B	96.603	942	26	3	1	938	680771121	680770182	0.000000e+00	1557
5	TraesCS2D01G462200	chr6D	85.460	337	29	17	947	1276	67518566	67518243	1.990000e-87	333
6	TraesCS2D01G462200	chr6B	84.431	334	31	13	947	1271	142503406	142503085	3.350000e-80	309
7	TraesCS2D01G462200	chr6A	85.185	297	26	8	987	1276	85023391	85023106	4.360000e-74	289

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	TraesCS2D01G462200	chr2D	568229708	568233162	3454	True	6381.0	6381	100.0000	1	3455	1	chr2D.!!$R1	3454
1	TraesCS2D01G462200	chr2A	707748502	707751476	2974	True	2207.5	4137	92.3195	445	3438	2	chr2A.!!$R1	2993
2	TraesCS2D01G462200	chr2B	680767220	680771121	3901	True	2754.5	3952	96.1075	1	3454	2	chr2B.!!$R1	3453

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
398	402	2.516227	AGCTCCTTTAGGCTTTTCCC	57.484	50.0	0.0	0.0	34.96	3.97	F
1506	1945	0.314935	AGGAAAATGCCACTGTTGCG	59.685	50.0	0.0	0.0	0.00	4.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1853	2292	0.535797	GGTCCAACCTTCTCCCGTAG	59.464	60.0	0.0	0.0	34.73	3.51	R
3261	3716	1.576577	TCAGGACATCAGCCATGAGT	58.423	50.0	0.0	0.0	39.29	3.41	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
46	47	5.480642	TTGTTGGGATATGTGCATTTTGT	57.519	34.783	0.00	0.00	0.00	2.83
208	212	4.796830	CGTGTAGTGTTGTTATGTCGCTAT	59.203	41.667	0.00	0.00	0.00	2.97
231	235	5.178797	TCTAGTGACTTCTATTGGCTTTGC	58.821	41.667	0.00	0.00	0.00	3.68
235	239	4.333926	GTGACTTCTATTGGCTTTGCTAGG	59.666	45.833	0.00	0.00	0.00	3.02
280	284	8.073768	ACAAAACACACATTTTTACTAGATCCG	58.926	33.333	0.00	0.00	29.17	4.18
398	402	2.516227	AGCTCCTTTAGGCTTTTCCC	57.484	50.000	0.00	0.00	34.96	3.97
787	792	2.625790	CGGACCCAAACATTCCAGAAAA	59.374	45.455	0.00	0.00	0.00	2.29
876	885	2.731875	CCGCAATAAACGGCAAACC	58.268	52.632	0.00	0.00	44.90	3.27
1086	1525	2.360475	GTCTGCACCAAGCCCCTC	60.360	66.667	0.00	0.00	44.83	4.30
1323	1762	1.996191	GCAGACGGAGAAACTGATGTC	59.004	52.381	0.00	0.00	34.07	3.06
1350	1789	0.740737	CCCTTGCCGGAAATCATGAC	59.259	55.000	5.05	0.00	33.16	3.06
1378	1817	2.530151	TTCCTGGGCAGACTGGCT	60.530	61.111	26.27	0.00	43.20	4.75
1394	1833	3.264193	ACTGGCTTACAAGATGGTGATGA	59.736	43.478	0.00	0.00	0.00	2.92
1403	1842	2.477825	AGATGGTGATGATTTCGAGCG	58.522	47.619	0.00	0.00	0.00	5.03
1501	1940	0.890683	GGGTGAGGAAAATGCCACTG	59.109	55.000	0.00	0.00	0.00	3.66
1506	1945	0.314935	AGGAAAATGCCACTGTTGCG	59.685	50.000	0.00	0.00	0.00	4.85
1535	1974	1.457346	CAAGCTGGTGGTGAAGGATC	58.543	55.000	0.00	0.00	0.00	3.36
1558	1997	8.731591	ATCAGATAATGGGGAAATAAGCAATT	57.268	30.769	0.00	0.00	0.00	2.32
1565	2004	5.934781	TGGGGAAATAAGCAATTGTGTTTT	58.065	33.333	7.40	2.82	30.03	2.43
1619	2058	5.449588	GCATTGAATGTGACTCTAATGGTGG	60.450	44.000	7.05	0.00	0.00	4.61
1638	2077	3.184581	GTGGTGAGTGTTTCAGATTCGAC	59.815	47.826	0.00	0.00	36.21	4.20
1701	2140	0.321346	TCTCAGCCGCAAATCAGTCA	59.679	50.000	0.00	0.00	0.00	3.41
1713	2152	5.330295	GCAAATCAGTCAGAAAGCTATGTG	58.670	41.667	0.00	0.00	0.00	3.21
1743	2182	1.133790	GCTAATGCTGAAGGCCAACAG	59.866	52.381	20.18	20.18	40.92	3.16
1768	2207	5.237996	AGAAGTGAGACATGTGTGACAAATG	59.762	40.000	14.00	14.00	35.38	2.32

Showing 1 to 25 of 66 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	6.090129	CACATATCCCAACAAAAACCTAACG	58.910	40.000	0.00	0.00	0.00	3.18
208	212	5.046304	AGCAAAGCCAATAGAAGTCACTAGA	60.046	40.000	0.00	0.00	0.00	2.43
344	348	4.695455	CACTAAATCGGTTGGTTCATCAGT	59.305	41.667	0.00	0.00	0.00	3.41
765	770	0.768622	TCTGGAATGTTTGGGTCCGT	59.231	50.000	0.00	0.00	33.87	4.69
787	792	4.162888	CCCAATTAGGTTAGGTTAGTCCGT	59.837	45.833	0.00	0.00	37.14	4.69
876	885	1.137404	CGCTTTGGAGGCAAATCCG	59.863	57.895	0.00	0.00	42.77	4.18
986	1005	4.802051	CCATGGGTGGCGAGGTGG	62.802	72.222	2.85	0.00	39.01	4.61
1350	1789	1.964373	CCCAGGAACAACCGAACCG	60.964	63.158	0.00	0.00	44.74	4.44
1378	1817	5.294306	GCTCGAAATCATCACCATCTTGTAA	59.706	40.000	0.00	0.00	0.00	2.41
1394	1833	1.648467	GCCTTGGCTTCGCTCGAAAT	61.648	55.000	4.11	0.00	33.34	2.17
1403	1842	1.895131	TCAATCCTTTGCCTTGGCTTC	59.105	47.619	13.18	0.00	32.61	3.86
1501	1940	0.933796	GCTTGCCTAGAGATCGCAAC	59.066	55.000	0.00	0.00	37.58	4.17
1506	1945	1.202627	CCACCAGCTTGCCTAGAGATC	60.203	57.143	0.00	0.00	0.00	2.75
1535	1974	7.654520	CACAATTGCTTATTTCCCCATTATCTG	59.345	37.037	5.05	0.00	0.00	2.90
1558	1997	4.220602	TCGATCCAGATCAGAGAAAACACA	59.779	41.667	8.31	0.00	37.69	3.72
1565	2004	4.163441	ACTTCTCGATCCAGATCAGAGA	57.837	45.455	19.22	19.22	41.24	3.10
1619	2058	4.084328	CCTTGTCGAATCTGAAACACTCAC	60.084	45.833	0.00	0.00	0.00	3.51
1638	2077	2.741612	TGTTCATTGCTTTTCGCCTTG	58.258	42.857	0.00	0.00	38.05	3.61
1701	2140	1.753073	GCATTGGCCACATAGCTTTCT	59.247	47.619	3.88	0.00	0.00	2.52
1724	2163	2.681848	CTCTGTTGGCCTTCAGCATTAG	59.318	50.000	18.39	9.91	46.50	1.73
1743	2182	3.982475	TGTCACACATGTCTCACTTCTC	58.018	45.455	0.00	0.00	0.00	2.87
1768	2207	3.323115	TGAGGCAGATCATCATGTACCTC	59.677	47.826	0.00	0.00	42.26	3.85
1778	2217	3.118531	ACTAAAGGGTGAGGCAGATCAT	58.881	45.455	0.00	0.00	0.00	2.45
1853	2292	0.535797	GGTCCAACCTTCTCCCGTAG	59.464	60.000	0.00	0.00	34.73	3.51
1857	2296	1.003718	CACGGTCCAACCTTCTCCC	60.004	63.158	0.00	0.00	35.66	4.30

Showing 1 to 25 of 51 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.