AutoCloner

Multiple sequence alignment - TraesCS2D01G424700

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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	TraesCS2D01G424700	chr2D	100.000	4699	0	0	1	4699	537434895	537430197	0.000000e+00	8678.0
1	TraesCS2D01G424700	chr1D	95.435	2760	104	17	1	2750	454413678	454416425	0.000000e+00	4379.0
2	TraesCS2D01G424700	chr1D	96.759	2499	71	9	1	2496	478702792	478705283	0.000000e+00	4157.0
3	TraesCS2D01G424700	chr1D	94.043	1964	79	14	2763	4699	454416346	454418298	0.000000e+00	2944.0
4	TraesCS2D01G424700	chr1D	95.305	1427	61	6	2746	4171	478705259	478706680	0.000000e+00	2259.0
5	TraesCS2D01G424700	chr1D	96.085	613	20	3	4091	4699	478706645	478707257	0.000000e+00	996.0
6	TraesCS2D01G424700	chr1D	93.333	45	0	3	2685	2727	478705312	478705355	3.930000e-06	63.9
7	TraesCS2D01G424700	chr5A	94.583	2806	136	13	1	2796	702831248	702828449	0.000000e+00	4325.0
8	TraesCS2D01G424700	chr5A	94.798	865	43	2	2715	3579	702828576	702827714	0.000000e+00	1347.0
9	TraesCS2D01G424700	chr5A	90.193	673	38	12	3566	4238	702827693	702827049	0.000000e+00	852.0
10	TraesCS2D01G424700	chr5A	92.067	416	28	5	4288	4699	702827048	702826634	8.770000e-162	580.0
11	TraesCS2D01G424700	chr3B	91.396	2313	177	18	449	2750	42973782	42971481	0.000000e+00	3149.0
12	TraesCS2D01G424700	chr3B	87.802	1943	174	39	2763	4699	42971561	42969676	0.000000e+00	2217.0
13	TraesCS2D01G424700	chr3B	87.692	455	46	7	5	457	42974819	42974373	5.390000e-144	521.0
14	TraesCS2D01G424700	chr7D	90.822	2092	171	13	451	2529	572646890	572644807	0.000000e+00	2780.0
15	TraesCS2D01G424700	chr7D	89.793	676	59	9	2786	3459	572644730	572644063	0.000000e+00	857.0
16	TraesCS2D01G424700	chr7D	84.922	577	75	10	3450	4022	572636540	572635972	1.470000e-159	573.0
17	TraesCS2D01G424700	chr7D	85.909	440	57	5	2	440	572647941	572647506	9.210000e-127	464.0
18	TraesCS2D01G424700	chr3A	88.639	2086	212	16	451	2523	655204602	655206675	0.000000e+00	2516.0
19	TraesCS2D01G424700	chr3A	87.854	1095	119	11	2786	3876	655206760	655207844	0.000000e+00	1273.0
20	TraesCS2D01G424700	chr4B	80.267	1348	237	23	708	2042	672962039	672963370	0.000000e+00	989.0
21	TraesCS2D01G424700	chr4B	80.267	1348	237	23	708	2042	672966232	672967563	0.000000e+00	989.0
22	TraesCS2D01G424700	chr7B	78.547	1459	280	28	708	2150	583683792	583685233	0.000000e+00	929.0

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	TraesCS2D01G424700	chr2D	537430197	537434895	4698	True	8678.000000	8678	100.000000	1	4699	1	chr2D.!!$R1	4698
1	TraesCS2D01G424700	chr1D	454413678	454418298	4620	False	3661.500000	4379	94.739000	1	4699	2	chr1D.!!$F1	4698
2	TraesCS2D01G424700	chr1D	478702792	478707257	4465	False	1868.975000	4157	95.370500	1	4699	4	chr1D.!!$F2	4698
3	TraesCS2D01G424700	chr5A	702826634	702831248	4614	True	1776.000000	4325	92.910250	1	4699	4	chr5A.!!$R1	4698
4	TraesCS2D01G424700	chr3B	42969676	42974819	5143	True	1962.333333	3149	88.963333	5	4699	3	chr3B.!!$R1	4694
5	TraesCS2D01G424700	chr7D	572644063	572647941	3878	True	1367.000000	2780	88.841333	2	3459	3	chr7D.!!$R2	3457
6	TraesCS2D01G424700	chr7D	572635972	572636540	568	True	573.000000	573	84.922000	3450	4022	1	chr7D.!!$R1	572
7	TraesCS2D01G424700	chr3A	655204602	655207844	3242	False	1894.500000	2516	88.246500	451	3876	2	chr3A.!!$F1	3425
8	TraesCS2D01G424700	chr4B	672962039	672967563	5524	False	989.000000	989	80.267000	708	2042	2	chr4B.!!$F1	1334
9	TraesCS2D01G424700	chr7B	583683792	583685233	1441	False	929.000000	929	78.547000	708	2150	1	chr7B.!!$F1	1442

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	Hairpin	End Stability	Orientation
102	103	1.039856	GTTCCCAATGGCACTGTGTT	58.960	50.0	9.86	0.00	3.32	F
1533	2157	0.466543	ACAACCACAACCAGTCGCTA	59.533	50.0	0.00	0.00	4.26	F
1661	6478	0.107214	GACCAGGATTTCGGGATGCA	60.107	55.0	0.00	34.65	3.96	F
3272	8155	0.252375	AAGCACTTTGCCCCCATGAT	60.252	50.0	0.00	46.52	2.45	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1661	6478	0.107508	CACGTCCTCAATGCCTCCAT	60.108	55.0	0.00	0.00	3.41	R
3358	8241	0.038618	TGCGTCGTCTGCTATGTGTT	60.039	50.0	0.00	0.00	3.32	R
3521	8404	0.981183	AGTTATCTGTTGACGGCCCA	59.019	50.0	0.00	0.00	5.36	R
4095	9037	0.319297	GTTGACGCGAGGTGGTAACT	60.319	55.0	15.93	37.61	2.24	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	Hairpin	End Stability
102	103	1.039856	GTTCCCAATGGCACTGTGTT	58.960	50.000	9.86	0.00	3.32
264	267	2.473816	CATCATCGTACGCAGGTGAAT	58.526	47.619	11.24	0.00	2.57
272	275	3.004002	CGTACGCAGGTGAATGGTCTATA	59.996	47.826	0.52	0.00	1.31
553	1171	4.055360	CACACGAACAACAGACCTATCAA	58.945	43.478	0.00	0.00	2.57
671	1289	7.186570	TCTGATGATGGAAACTCTGATACAA	57.813	36.000	0.00	0.00	2.41
673	1291	8.102676	TCTGATGATGGAAACTCTGATACAAAA	58.897	33.333	0.00	0.00	2.44
994	1618	4.764050	TTGGTGAGAACAAACTGTCCTA	57.236	40.909	0.00	0.00	2.94
1533	2157	0.466543	ACAACCACAACCAGTCGCTA	59.533	50.000	0.00	0.00	4.26
1661	6478	0.107214	GACCAGGATTTCGGGATGCA	60.107	55.000	0.00	34.65	3.96
1816	6636	1.072266	TGACCACAGCTTAACCCCAT	58.928	50.000	0.00	0.00	4.00
2044	6864	3.499537	CAGATTTGTCAAGCAGTACAGCA	59.500	43.478	13.16	36.85	4.41
2104	6924	0.317020	GGCGAACACAGCACTCAAAC	60.317	55.000	0.00	36.08	2.93
2333	7157	2.821969	AGTGCTTGGCCTTGTAAATGAG	59.178	45.455	3.32	0.00	2.90
2364	7192	4.198530	TCTGAGATGCAAAACAGTTGACA	58.801	39.130	13.97	0.00	3.58
2458	7291	2.863740	CCGATGTCGCAAAGTGCTAATA	59.136	45.455	0.00	42.25	0.98
2551	7386	6.147492	TGAAAATAATGAACTTGCCATTGTGC	59.853	34.615	0.00	35.94	4.57
2558	7393	1.300003	TTGCCATTGTGCGTGCAAG	60.300	52.632	0.00	38.68	4.01
2622	7458	6.480320	GCTATATTTCAGAGTTGGTGTGGTAG	59.520	42.308	0.00	0.00	3.18
2683	7519	2.523015	CGTGAGCCAGAATGAATTTGC	58.477	47.619	0.00	39.69	3.68
2684	7520	2.733227	CGTGAGCCAGAATGAATTTGCC	60.733	50.000	0.00	39.69	4.52
2685	7521	2.231964	GTGAGCCAGAATGAATTTGCCA	59.768	45.455	0.00	39.69	4.92
2686	7522	3.101437	TGAGCCAGAATGAATTTGCCAT	58.899	40.909	0.00	39.69	4.40
2720	7602	5.595542	ACTTGCCATGCATAGTACAATGAAT	59.404	36.000	0.00	38.76	2.57
2721	7603	6.097270	ACTTGCCATGCATAGTACAATGAATT	59.903	34.615	0.00	38.76	2.17
2722	7604	6.468333	TGCCATGCATAGTACAATGAATTT	57.532	33.333	0.00	31.71	1.82

Showing 1 to 25 of 107 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
102	103	9.883142	ATTGTTCTTTAAAATTCCAAACTCACA	57.117	25.926	0.00	0.00	0.00	3.58
264	267	7.092802	TGGCAAGTTAGGTATGTTTATAGACCA	60.093	37.037	0.00	0.00	34.18	4.02
272	275	6.321821	TCCTATGGCAAGTTAGGTATGTTT	57.678	37.500	11.42	0.00	37.00	2.83
553	1171	0.598065	GCGGTCCTTGTTTGCTTGAT	59.402	50.000	0.00	0.00	0.00	2.57
671	1289	1.430992	TCAGGTTCGTCCCCTCTTTT	58.569	50.000	0.00	0.00	36.75	2.27
673	1291	0.905357	CATCAGGTTCGTCCCCTCTT	59.095	55.000	0.00	0.00	36.75	2.85
994	1618	0.034896	ACGTTCAGCTTCATTCGGGT	59.965	50.000	0.00	0.00	0.00	5.28
1533	2157	1.754226	ACAAAACCGCATCCAAACTGT	59.246	42.857	0.00	0.00	0.00	3.55
1661	6478	0.107508	CACGTCCTCAATGCCTCCAT	60.108	55.000	0.00	0.00	0.00	3.41
1816	6636	4.330944	TCCAGCTTGTTTCGAACTCTTA	57.669	40.909	0.00	0.00	0.00	2.10
2061	6881	2.782222	TTGTAGCTCCGCGCCTAGG	61.782	63.158	3.67	3.67	40.39	3.02
2364	7192	4.098349	CCATATGCATGGCAAGTTTAGTGT	59.902	41.667	10.16	0.00	45.29	3.55
2450	7283	7.709269	TGACATTTTCTCCGTATATTAGCAC	57.291	36.000	0.00	0.00	0.00	4.40
2458	7291	5.895636	TTTGCATGACATTTTCTCCGTAT	57.104	34.783	0.00	0.00	0.00	3.06
2584	7419	6.041979	TCTGAAATATAGCTGCCACATGACTA	59.958	38.462	0.00	0.00	0.00	2.59
2586	7421	5.059161	TCTGAAATATAGCTGCCACATGAC	58.941	41.667	0.00	0.00	0.00	3.06
2622	7458	2.084546	GCCTACATGTCACCACCTTTC	58.915	52.381	0.00	0.00	0.00	2.62
2673	7509	7.388437	AGTTCATTGTACATGGCAAATTCATT	58.612	30.769	0.00	0.00	0.00	2.57
2674	7510	6.938507	AGTTCATTGTACATGGCAAATTCAT	58.061	32.000	0.00	0.00	0.00	2.57
2675	7511	6.343716	AGTTCATTGTACATGGCAAATTCA	57.656	33.333	0.00	0.00	0.00	2.57
2676	7512	6.401367	GCAAGTTCATTGTACATGGCAAATTC	60.401	38.462	0.00	2.37	41.29	2.17
2677	7513	5.409214	GCAAGTTCATTGTACATGGCAAATT	59.591	36.000	0.00	0.00	41.29	1.82
2678	7514	4.931002	GCAAGTTCATTGTACATGGCAAAT	59.069	37.500	0.00	0.00	41.29	2.32
2679	7515	4.305769	GCAAGTTCATTGTACATGGCAAA	58.694	39.130	0.00	0.00	41.29	3.68
2680	7516	3.305950	GGCAAGTTCATTGTACATGGCAA	60.306	43.478	16.46	7.30	41.29	4.52

Showing 1 to 25 of 117 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.