AutoCloner

Multiple sequence alignment - TraesCS2A01G324000

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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	TraesCS2A01G324000	chr2A	100.000	3332	0	0	1	3332	554413948	554417279	0.000000e+00	6154.0
1	TraesCS2A01G324000	chr2D	92.812	1906	89	18	641	2513	432081452	432079562	0.000000e+00	2717.0
2	TraesCS2A01G324000	chr2D	84.375	672	88	11	2674	3332	432079382	432078715	0.000000e+00	643.0
3	TraesCS2A01G324000	chr2D	83.673	490	32	19	36	486	432082080	432081600	5.140000e-113	418.0
4	TraesCS2A01G324000	chr2D	90.608	181	16	1	1190	1369	461078665	461078485	4.300000e-59	239.0
5	TraesCS2A01G324000	chr2D	96.721	122	4	0	1608	1729	461078493	461078372	1.570000e-48	204.0
6	TraesCS2A01G324000	chr2D	95.200	125	6	0	1608	1732	352709821	352709945	7.290000e-47	198.0
7	TraesCS2A01G324000	chr2B	90.727	1898	90	29	685	2513	510898450	510896570	0.000000e+00	2451.0
8	TraesCS2A01G324000	chr2B	85.057	261	17	7	5	244	510901910	510901651	2.570000e-61	246.0
9	TraesCS2A01G324000	chr2B	87.047	193	17	5	301	492	510898615	510898430	9.370000e-51	211.0
10	TraesCS2A01G324000	chr6D	92.835	321	23	0	1488	1808	456305687	456305367	1.810000e-127	466.0
11	TraesCS2A01G324000	chr6D	95.690	116	5	0	1915	2030	456305370	456305255	1.580000e-43	187.0
12	TraesCS2A01G324000	chr7D	95.473	243	11	0	1488	1730	171027892	171028134	4.030000e-104	388.0
13	TraesCS2A01G324000	chr7D	95.683	139	6	0	1188	1326	171013670	171013808	1.200000e-54	224.0
14	TraesCS2A01G324000	chr7D	93.985	133	8	0	1317	1449	171027768	171027900	5.640000e-48	202.0
15	TraesCS2A01G324000	chr1D	92.655	177	13	0	1190	1366	307206149	307206325	4.270000e-64	255.0
16	TraesCS2A01G324000	chr1D	95.122	123	6	0	1608	1730	307206321	307206443	9.430000e-46	195.0
17	TraesCS2A01G324000	chr1B	95.082	122	6	0	1608	1729	646571821	646571700	3.390000e-45	193.0
18	TraesCS2A01G324000	chr1B	90.909	121	10	1	1610	1730	646571586	646571467	9.570000e-36	161.0
19	TraesCS2A01G324000	chr6B	87.500	80	7	2	2616	2693	699137716	699137794	4.580000e-14	89.8

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	TraesCS2A01G324000	chr2A	554413948	554417279	3331	False	6154.000000	6154	100.000000	1	3332	1	chr2A.!!$F1	3331
1	TraesCS2A01G324000	chr2D	432078715	432082080	3365	True	1259.333333	2717	86.953333	36	3332	3	chr2D.!!$R1	3296
2	TraesCS2A01G324000	chr2B	510896570	510901910	5340	True	969.333333	2451	87.610333	5	2513	3	chr2B.!!$R1	2508

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
496	3525	0.027194	CGAGATTGCTGCGTGATTGG	59.973	55.0	0.0	0.0	0.00	3.16	F
525	3554	0.037232	GTGGCTCTAACGCTGGTTCT	60.037	55.0	0.0	0.0	37.58	3.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1848	5004	0.108585	AAACCGGCTTCTTGCTCTGA	59.891	50.0	0.0	0.0	42.39	3.27	R
2502	5664	0.669625	GGCTAAAAGAGGCGACGTGT	60.670	55.0	0.0	0.0	41.55	4.49	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
25	26	6.199393	GCGGAATAAAGACATAAATGGACAC	58.801	40.000	0.00	0.00	0.00	3.67
68	69	7.814264	ATAATGAGAAACTTTATGGCAGAGG	57.186	36.000	0.00	0.00	30.91	3.69
72	73	3.523564	AGAAACTTTATGGCAGAGGGCTA	59.476	43.478	0.00	0.00	44.01	3.93
74	75	3.778954	ACTTTATGGCAGAGGGCTATC	57.221	47.619	0.00	0.00	43.38	2.08
125	147	1.743252	GTCCCTTTGAGAGGCTGCG	60.743	63.158	0.00	0.00	44.85	5.18
142	164	1.129624	TGCGCCGTGACATGTTTTATC	59.870	47.619	4.18	0.00	0.00	1.75
151	173	4.576463	GTGACATGTTTTATCCCTAGCCTG	59.424	45.833	0.00	0.00	0.00	4.85
168	190	0.755686	CTGGTAGGGCTAGGCAGAAG	59.244	60.000	19.14	4.16	0.00	2.85
206	228	1.615651	CCCGGTGATTTGACATGGGAA	60.616	52.381	0.00	0.00	39.23	3.97
238	287	0.179124	CAGAGCTTCCGTCTAGTGCC	60.179	60.000	0.00	0.00	0.00	5.01
268	317	2.292267	CCATACACACTGAAGCCATCC	58.708	52.381	0.00	0.00	0.00	3.51
271	320	2.119801	ACACACTGAAGCCATCCATC	57.880	50.000	0.00	0.00	0.00	3.51
272	321	1.012086	CACACTGAAGCCATCCATCG	58.988	55.000	0.00	0.00	0.00	3.84
273	322	0.904649	ACACTGAAGCCATCCATCGA	59.095	50.000	0.00	0.00	0.00	3.59
325	3352	3.324117	CGTATCAGGAATGCAGGATGAG	58.676	50.000	0.00	0.00	39.69	2.90
350	3377	1.410882	GAATCAGCTAGCGGTCCTTCT	59.589	52.381	14.70	0.00	0.00	2.85
351	3378	1.036707	ATCAGCTAGCGGTCCTTCTC	58.963	55.000	14.70	0.00	0.00	2.87
380	3407	2.668280	GCAACTCGCCAACCGTCTC	61.668	63.158	0.00	0.00	38.35	3.36
431	3458	1.668237	GAAAGAGAAGCGGAAGATGCC	59.332	52.381	0.00	0.00	0.00	4.40
438	3465	2.658593	CGGAAGATGCCGCCGTAG	60.659	66.667	0.00	0.00	45.38	3.51
439	3466	2.499685	GGAAGATGCCGCCGTAGT	59.500	61.111	0.00	0.00	0.00	2.73
440	3467	1.737816	GGAAGATGCCGCCGTAGTA	59.262	57.895	0.00	0.00	0.00	1.82
441	3468	0.596859	GGAAGATGCCGCCGTAGTAC	60.597	60.000	0.00	0.00	0.00	2.73
442	3469	0.101759	GAAGATGCCGCCGTAGTACA	59.898	55.000	0.38	0.00	0.00	2.90
443	3470	0.102481	AAGATGCCGCCGTAGTACAG	59.898	55.000	0.38	0.00	0.00	2.74

Showing 1 to 25 of 224 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	5.298276	TGTCCATTTATGTCTTTATTCCGCC	59.702	40.000	0.00	0.00	0.00	6.13
1	2	6.199393	GTGTCCATTTATGTCTTTATTCCGC	58.801	40.000	0.00	0.00	0.00	5.54
2	3	6.418956	CGTGTCCATTTATGTCTTTATTCCG	58.581	40.000	0.00	0.00	0.00	4.30
3	4	6.038271	AGCGTGTCCATTTATGTCTTTATTCC	59.962	38.462	0.00	0.00	0.00	3.01
15	16	5.010933	TGGGAATTTAAGCGTGTCCATTTA	58.989	37.500	0.00	0.00	0.00	1.40
68	69	6.993079	TGAAAAGAAAAAGAAAGGGATAGCC	58.007	36.000	0.00	0.00	0.00	3.93
72	73	6.546034	TCGTCTGAAAAGAAAAAGAAAGGGAT	59.454	34.615	0.00	0.00	0.00	3.85
74	75	6.131544	TCGTCTGAAAAGAAAAAGAAAGGG	57.868	37.500	0.00	0.00	0.00	3.95
80	81	5.453587	CACAGCTTCGTCTGAAAAGAAAAAG	59.546	40.000	8.57	0.00	37.51	2.27
125	147	2.365582	AGGGATAAAACATGTCACGGC	58.634	47.619	0.00	0.00	0.00	5.68
151	173	1.448069	GCTTCTGCCTAGCCCTACC	59.552	63.158	0.00	0.00	32.45	3.18
206	228	0.112025	AGCTCTGCTTTTTGGCTCCT	59.888	50.000	0.00	0.00	33.89	3.69
229	278	1.356938	GGTAAAGCGTGGCACTAGAC	58.643	55.000	16.72	6.30	0.00	2.59
232	281	0.616371	ATGGGTAAAGCGTGGCACTA	59.384	50.000	16.72	0.00	0.00	2.74
238	287	2.415168	CAGTGTGTATGGGTAAAGCGTG	59.585	50.000	0.00	0.00	0.00	5.34
268	317	4.909696	AGTAGAATCAGAGGTGTCGATG	57.090	45.455	0.00	0.00	0.00	3.84
271	320	4.035792	CCTGTAGTAGAATCAGAGGTGTCG	59.964	50.000	0.00	0.00	0.00	4.35
272	321	4.202070	GCCTGTAGTAGAATCAGAGGTGTC	60.202	50.000	0.00	0.00	0.00	3.67
273	322	3.702045	GCCTGTAGTAGAATCAGAGGTGT	59.298	47.826	0.00	0.00	0.00	4.16
325	3352	1.596477	CCGCTAGCTGATTCTGGCC	60.596	63.158	13.93	0.00	37.28	5.36
350	3377	1.587043	CGAGTTGCTCTCCGTCAGGA	61.587	60.000	4.44	0.00	46.11	3.86
351	3378	1.153939	CGAGTTGCTCTCCGTCAGG	60.154	63.158	4.44	0.00	39.84	3.86
431	3458	2.158959	GCAGCACTGTACTACGGCG	61.159	63.158	4.80	4.80	0.00	6.46
444	3471	4.322689	TGCATATGCAGTGCAGCA	57.677	50.000	26.32	23.21	46.76	4.41
474	3503	1.150567	ATCACGCAGCAATCTCGCTC	61.151	55.000	0.00	0.00	41.38	5.03

Showing 1 to 25 of 217 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.