AutoCloner

Multiple sequence alignment - TraesCS2D01G468000

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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	TraesCS2D01G468000	chr2D	100.000	2579	0	0	1	2579	572803859	572806437	0.000000e+00	4763
1	TraesCS2D01G468000	chr2A	93.359	2620	57	45	1	2579	712063870	712066413	0.000000e+00	3766
2	TraesCS2D01G468000	chr3A	88.655	1851	79	53	783	2576	336612616	336610840	0.000000e+00	2134
3	TraesCS2D01G468000	chr3A	84.323	842	49	21	1	774	336613853	336613027	0.000000e+00	747
4	TraesCS2D01G468000	chr3B	88.015	1844	60	57	783	2579	309409281	309411010	0.000000e+00	2032
5	TraesCS2D01G468000	chr3B	85.046	876	37	24	1	791	309408392	309409258	0.000000e+00	806
6	TraesCS2D01G468000	chr3D	85.753	1467	71	46	1	1355	253565255	253563815	0.000000e+00	1424
7	TraesCS2D01G468000	chr3D	89.735	565	13	12	1368	1929	253557026	253556504	0.000000e+00	680
8	TraesCS2D01G468000	chr3D	93.767	369	6	6	2216	2579	253554342	253553986	2.920000e-149	538
9	TraesCS2D01G468000	chr3D	85.099	302	13	9	1921	2210	253556414	253556133	1.950000e-71	279
10	TraesCS2D01G468000	chr1A	94.212	501	18	4	500	989	457343943	457344443	0.000000e+00	754
11	TraesCS2D01G468000	chr1A	93.913	115	5	2	481	593	457344643	457344529	3.410000e-39	172

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	TraesCS2D01G468000	chr2D	572803859	572806437	2578	False	4763.0	4763	100.000000	1	2579	1	chr2D.!!$F1	2578
1	TraesCS2D01G468000	chr2A	712063870	712066413	2543	False	3766.0	3766	93.359000	1	2579	1	chr2A.!!$F1	2578
2	TraesCS2D01G468000	chr3A	336610840	336613853	3013	True	1440.5	2134	86.489000	1	2576	2	chr3A.!!$R1	2575
3	TraesCS2D01G468000	chr3B	309408392	309411010	2618	False	1419.0	2032	86.530500	1	2579	2	chr3B.!!$F1	2578
4	TraesCS2D01G468000	chr3D	253563815	253565255	1440	True	1424.0	1424	85.753000	1	1355	1	chr3D.!!$R1	1354
5	TraesCS2D01G468000	chr3D	253553986	253557026	3040	True	499.0	680	89.533667	1368	2579	3	chr3D.!!$R2	1211
6	TraesCS2D01G468000	chr1A	457343943	457344443	500	False	754.0	754	94.212000	500	989	1	chr1A.!!$F1	489

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
713	838	0.916358	ATGGAGGTGGAGGTGGAAGG	60.916	60.0	0.0	0.0	0.0	3.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1628	2254	1.112459	CGTTGCTCGCAAACAAGAAC	58.888	50.0	5.83	0.0	37.7	3.01	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
143	148	5.645929	TGCGGAGTGTGTGATATTTGTATTT	59.354	36.000	0.00	0.00	0.00	1.40
146	151	6.509517	CGGAGTGTGTGATATTTGTATTTCCG	60.510	42.308	0.00	0.00	35.93	4.30
340	345	2.774687	ACGGAAATTTAGAGGTTGCGT	58.225	42.857	0.00	0.00	43.19	5.24
600	661	1.048601	GGAGAGGCCCATCAATCGTA	58.951	55.000	0.00	0.00	0.00	3.43
713	838	0.916358	ATGGAGGTGGAGGTGGAAGG	60.916	60.000	0.00	0.00	0.00	3.46
730	855	5.069516	GTGGAAGGAACAATAATGCATCCAT	59.930	40.000	0.00	0.00	37.98	3.41
917	1462	6.447084	ACCTTCTCCTTGGGTTAGATTGATAA	59.553	38.462	0.00	0.00	0.00	1.75
957	1506	1.470632	GCACGCTAGATTGACTGAGCT	60.471	52.381	0.00	0.00	32.60	4.09
960	1509	2.692557	ACGCTAGATTGACTGAGCTGAT	59.307	45.455	0.00	0.00	32.60	2.90
961	1510	3.885901	ACGCTAGATTGACTGAGCTGATA	59.114	43.478	0.00	0.00	32.60	2.15
1320	1901	3.682292	GAAGGCCGGCGACTGGATT	62.682	63.158	22.54	5.94	0.00	3.01
1366	1951	4.105377	TCCGGCCCCTATATATCTACCTAC	59.895	50.000	0.00	0.00	0.00	3.18
1617	2243	1.225983	CCCATCCCACGGCACATTA	59.774	57.895	0.00	0.00	0.00	1.90
1618	2244	0.395036	CCCATCCCACGGCACATTAA	60.395	55.000	0.00	0.00	0.00	1.40
1619	2245	1.691196	CCATCCCACGGCACATTAAT	58.309	50.000	0.00	0.00	0.00	1.40
1620	2246	2.031120	CCATCCCACGGCACATTAATT	58.969	47.619	0.00	0.00	0.00	1.40
1628	2254	4.856487	CCACGGCACATTAATTTACACTTG	59.144	41.667	0.00	0.00	0.00	3.16
1644	2270	1.742831	ACTTGTTCTTGTTTGCGAGCA	59.257	42.857	0.00	0.00	0.00	4.26
1659	2285	1.269569	CGAGCAACGAGGGCACATATA	60.270	52.381	0.00	0.00	45.77	0.86
1662	2288	3.141398	AGCAACGAGGGCACATATATTG	58.859	45.455	0.00	0.00	0.00	1.90
1665	2291	4.142816	GCAACGAGGGCACATATATTGATC	60.143	45.833	0.00	0.00	0.00	2.92
1734	2363	1.488812	ACAAACTGGTCTGGTGCTGTA	59.511	47.619	0.00	0.00	0.00	2.74
1735	2364	2.106511	ACAAACTGGTCTGGTGCTGTAT	59.893	45.455	0.00	0.00	0.00	2.29
1736	2365	2.479566	AACTGGTCTGGTGCTGTATG	57.520	50.000	0.00	0.00	0.00	2.39
1737	2366	0.036010	ACTGGTCTGGTGCTGTATGC	60.036	55.000	0.00	0.00	43.25	3.14
1976	2712	5.070313	GCTCAGACTCAGAAAAGGGAGATAT	59.930	44.000	0.00	0.00	35.17	1.63
1977	2713	6.266558	GCTCAGACTCAGAAAAGGGAGATATA	59.733	42.308	0.00	0.00	35.17	0.86
1978	2714	7.039082	GCTCAGACTCAGAAAAGGGAGATATAT	60.039	40.741	0.00	0.00	35.17	0.86
1979	2715	9.527157	CTCAGACTCAGAAAAGGGAGATATATA	57.473	37.037	0.00	0.00	35.17	0.86
2009	2745	5.448438	CACAAATTAACGTGTACATGTGCT	58.552	37.500	21.12	9.37	31.72	4.40
2011	2747	4.939509	AATTAACGTGTACATGTGCTCC	57.060	40.909	21.12	4.98	0.00	4.70
2012	2748	2.373540	TAACGTGTACATGTGCTCCC	57.626	50.000	21.12	2.61	0.00	4.30
2014	2750	1.214325	CGTGTACATGTGCTCCCGA	59.786	57.895	15.25	0.00	0.00	5.14
2017	2753	1.144057	GTACATGTGCTCCCGAGGG	59.856	63.158	9.11	0.65	0.00	4.30
2020	2756	1.002134	CATGTGCTCCCGAGGGTTT	60.002	57.895	8.20	0.00	36.47	3.27
2021	2757	0.251916	CATGTGCTCCCGAGGGTTTA	59.748	55.000	8.20	0.00	36.47	2.01
2022	2758	0.541863	ATGTGCTCCCGAGGGTTTAG	59.458	55.000	8.20	0.00	36.47	1.85
2024	2760	0.108281	GTGCTCCCGAGGGTTTAGTC	60.108	60.000	8.20	0.00	36.47	2.59
2025	2761	0.252103	TGCTCCCGAGGGTTTAGTCT	60.252	55.000	8.20	0.00	36.47	3.24
2026	2762	1.006281	TGCTCCCGAGGGTTTAGTCTA	59.994	52.381	8.20	0.00	36.47	2.59
2027	2763	2.105766	GCTCCCGAGGGTTTAGTCTAA	58.894	52.381	8.20	0.00	36.47	2.10
2028	2764	2.699321	GCTCCCGAGGGTTTAGTCTAAT	59.301	50.000	8.20	0.00	36.47	1.73
2033	2778	6.138263	TCCCGAGGGTTTAGTCTAATGATTA	58.862	40.000	8.20	0.00	36.47	1.75
2113	2869	1.831106	TGAGTGAACTCCTGTGTGTGT	59.169	47.619	7.96	0.00	42.20	3.72
2116	2872	1.665679	GTGAACTCCTGTGTGTGTGTG	59.334	52.381	0.00	0.00	0.00	3.82
2117	2873	1.277842	TGAACTCCTGTGTGTGTGTGT	59.722	47.619	0.00	0.00	0.00	3.72
2118	2874	1.665679	GAACTCCTGTGTGTGTGTGTG	59.334	52.381	0.00	0.00	0.00	3.82
2119	2875	0.107703	ACTCCTGTGTGTGTGTGTGG	60.108	55.000	0.00	0.00	0.00	4.17
2120	2876	0.815213	CTCCTGTGTGTGTGTGTGGG	60.815	60.000	0.00	0.00	0.00	4.61
2121	2877	1.823470	CCTGTGTGTGTGTGTGGGG	60.823	63.158	0.00	0.00	0.00	4.96
2363	4905	1.925285	TTCCGGGAGCAATCATGGCT	61.925	55.000	0.00	0.00	46.07	4.75

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
61	66	9.742552	GTCAAGCTATTAAAAGTTTAGTCTTCG	57.257	33.333	0.00	0.00	0.00	3.79
126	131	6.411376	AGTCCGGAAATACAAATATCACACA	58.589	36.000	5.23	0.00	0.00	3.72
239	244	3.319137	TGATGTAAAGCAGAAGACGCT	57.681	42.857	0.00	0.00	42.98	5.07
713	838	5.916883	CGGAAAGATGGATGCATTATTGTTC	59.083	40.000	0.00	6.76	0.00	3.18
730	855	0.971386	AGTAAAGCCGGACGGAAAGA	59.029	50.000	15.99	0.00	37.50	2.52
917	1462	1.463831	CGTGCGTGTGTCTAGTCTAGT	59.536	52.381	6.77	0.00	0.00	2.57
1320	1901	3.524648	GACGACGAACCTGGGGCAA	62.525	63.158	0.00	0.00	0.00	4.52
1389	1974	2.121948	TCTAGGCAGTGGAGCATGATT	58.878	47.619	0.00	0.00	35.83	2.57
1390	1975	1.798626	TCTAGGCAGTGGAGCATGAT	58.201	50.000	0.00	0.00	35.83	2.45
1391	1976	1.798626	ATCTAGGCAGTGGAGCATGA	58.201	50.000	0.00	0.00	35.83	3.07
1392	1977	2.634815	AATCTAGGCAGTGGAGCATG	57.365	50.000	0.00	0.00	35.83	4.06
1453	2075	9.546428	CAGGTGGTTAATTTTCTTTCTTTTCAT	57.454	29.630	0.00	0.00	0.00	2.57
1617	2243	6.326375	TCGCAAACAAGAACAAGTGTAAATT	58.674	32.000	0.00	0.00	0.00	1.82
1618	2244	5.885881	TCGCAAACAAGAACAAGTGTAAAT	58.114	33.333	0.00	0.00	0.00	1.40
1619	2245	5.298197	TCGCAAACAAGAACAAGTGTAAA	57.702	34.783	0.00	0.00	0.00	2.01
1620	2246	4.729458	GCTCGCAAACAAGAACAAGTGTAA	60.729	41.667	0.00	0.00	0.00	2.41
1628	2254	1.112459	CGTTGCTCGCAAACAAGAAC	58.888	50.000	5.83	0.00	37.70	3.01
1644	2270	4.021456	TCGATCAATATATGTGCCCTCGTT	60.021	41.667	0.00	0.00	0.00	3.85
1659	2285	5.691754	GCAAAAAGAAAAGGTGTCGATCAAT	59.308	36.000	0.00	0.00	0.00	2.57
1662	2288	3.664025	CGCAAAAAGAAAAGGTGTCGATC	59.336	43.478	0.00	0.00	0.00	3.69
1665	2291	3.059634	TCGCAAAAAGAAAAGGTGTCG	57.940	42.857	0.00	0.00	0.00	4.35
1734	2363	6.034161	TCGATTAGATGAGATCACATGCAT	57.966	37.500	10.58	0.00	0.00	3.96
1735	2364	5.458041	TCGATTAGATGAGATCACATGCA	57.542	39.130	10.58	0.00	0.00	3.96
1736	2365	6.964741	ATTCGATTAGATGAGATCACATGC	57.035	37.500	10.58	2.96	0.00	4.06
1737	2366	8.760103	AGAATTCGATTAGATGAGATCACATG	57.240	34.615	10.58	0.00	0.00	3.21
1976	2712	5.706369	ACACGTTAATTTGTGCCCACTTATA	59.294	36.000	0.00	0.00	39.71	0.98
1977	2713	4.521256	ACACGTTAATTTGTGCCCACTTAT	59.479	37.500	0.00	0.00	39.71	1.73
1978	2714	3.884091	ACACGTTAATTTGTGCCCACTTA	59.116	39.130	0.00	0.00	39.71	2.24
1979	2715	2.691011	ACACGTTAATTTGTGCCCACTT	59.309	40.909	0.00	0.00	39.71	3.16
2009	2745	3.985127	TCATTAGACTAAACCCTCGGGA	58.015	45.455	9.43	0.00	38.96	5.14
2011	2747	7.038941	AGGATAATCATTAGACTAAACCCTCGG	60.039	40.741	0.00	0.00	0.00	4.63
2012	2748	7.897864	AGGATAATCATTAGACTAAACCCTCG	58.102	38.462	0.00	0.00	0.00	4.63
2113	2869	1.735926	TAATCTCACACCCCCACACA	58.264	50.000	0.00	0.00	0.00	3.72
2116	2872	3.697166	ACAATTAATCTCACACCCCCAC	58.303	45.455	0.00	0.00	0.00	4.61
2117	2873	4.340617	GAACAATTAATCTCACACCCCCA	58.659	43.478	0.00	0.00	0.00	4.96
2118	2874	3.699538	GGAACAATTAATCTCACACCCCC	59.300	47.826	0.00	0.00	0.00	5.40
2119	2875	4.600062	AGGAACAATTAATCTCACACCCC	58.400	43.478	0.00	0.00	0.00	4.95
2120	2876	7.556275	TGATTAGGAACAATTAATCTCACACCC	59.444	37.037	5.99	0.00	37.25	4.61
2121	2877	8.506168	TGATTAGGAACAATTAATCTCACACC	57.494	34.615	5.99	0.00	37.25	4.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.