AutoCloner

Multiple sequence alignment - TraesCS2A01G422200

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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	TraesCS2A01G422200	chr2A	100.000	2549	0	0	1	2549	677414207	677411659	0.000000e+00	4708.0
1	TraesCS2A01G422200	chr2A	94.799	1961	91	10	592	2545	744582019	744583975	0.000000e+00	3046.0
2	TraesCS2A01G422200	chr2A	94.672	1952	90	11	602	2545	677958469	677956524	0.000000e+00	3016.0
3	TraesCS2A01G422200	chr2A	93.463	1958	106	16	602	2545	213959517	213957568	0.000000e+00	2887.0
4	TraesCS2A01G422200	chr2A	94.286	35	2	0	265	299	728813734	728813768	1.000000e-03	54.7
5	TraesCS2A01G422200	chr7A	95.077	1950	88	8	600	2545	36946198	36948143	0.000000e+00	3062.0
6	TraesCS2A01G422200	chr7D	94.944	1958	78	15	597	2545	63995386	63997331	0.000000e+00	3048.0
7	TraesCS2A01G422200	chr7D	94.667	1725	73	13	829	2545	577661198	577659485	0.000000e+00	2658.0
8	TraesCS2A01G422200	chr7D	94.444	36	2	0	264	299	123202111	123202146	3.540000e-04	56.5
9	TraesCS2A01G422200	chr3D	94.546	1962	87	14	592	2545	475106673	475108622	0.000000e+00	3013.0
10	TraesCS2A01G422200	chr5A	94.353	1948	98	10	602	2545	689446507	689444568	0.000000e+00	2977.0
11	TraesCS2A01G422200	chr5B	94.265	1953	99	9	602	2545	3450172	3448224	0.000000e+00	2974.0
12	TraesCS2A01G422200	chr2B	88.651	608	57	7	1	601	632605037	632604435	0.000000e+00	730.0
13	TraesCS2A01G422200	chr2B	90.909	440	31	6	596	1029	13181546	13181982	1.310000e-162	582.0
14	TraesCS2A01G422200	chr6A	92.308	39	3	0	261	299	23362602	23362640	3.540000e-04	56.5
15	TraesCS2A01G422200	chr6A	94.444	36	2	0	264	299	477135765	477135730	3.540000e-04	56.5
16	TraesCS2A01G422200	chr3B	94.444	36	2	0	264	299	700039637	700039672	3.540000e-04	56.5
17	TraesCS2A01G422200	chr3A	96.875	32	1	0	268	299	8229170	8229201	1.000000e-03	54.7
18	TraesCS2A01G422200	chr1D	100.000	29	0	0	271	299	470567449	470567421	1.000000e-03	54.7
19	TraesCS2A01G422200	chr1A	96.875	32	1	0	268	299	394238501	394238532	1.000000e-03	54.7

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	TraesCS2A01G422200	chr2A	677411659	677414207	2548	True	4708	4708	100.000	1	2549	1	chr2A.!!$R2	2548
1	TraesCS2A01G422200	chr2A	744582019	744583975	1956	False	3046	3046	94.799	592	2545	1	chr2A.!!$F2	1953
2	TraesCS2A01G422200	chr2A	677956524	677958469	1945	True	3016	3016	94.672	602	2545	1	chr2A.!!$R3	1943
3	TraesCS2A01G422200	chr2A	213957568	213959517	1949	True	2887	2887	93.463	602	2545	1	chr2A.!!$R1	1943
4	TraesCS2A01G422200	chr7A	36946198	36948143	1945	False	3062	3062	95.077	600	2545	1	chr7A.!!$F1	1945
5	TraesCS2A01G422200	chr7D	63995386	63997331	1945	False	3048	3048	94.944	597	2545	1	chr7D.!!$F1	1948
6	TraesCS2A01G422200	chr7D	577659485	577661198	1713	True	2658	2658	94.667	829	2545	1	chr7D.!!$R1	1716
7	TraesCS2A01G422200	chr3D	475106673	475108622	1949	False	3013	3013	94.546	592	2545	1	chr3D.!!$F1	1953
8	TraesCS2A01G422200	chr5A	689444568	689446507	1939	True	2977	2977	94.353	602	2545	1	chr5A.!!$R1	1943
9	TraesCS2A01G422200	chr5B	3448224	3450172	1948	True	2974	2974	94.265	602	2545	1	chr5B.!!$R1	1943
10	TraesCS2A01G422200	chr2B	632604435	632605037	602	True	730	730	88.651	1	601	1	chr2B.!!$R1	600

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
358	360	0.178995	TGTTCAGTGCATCCAGCCAA	60.179	50.0	0.0	0.0	44.83	4.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1769	1791	0.456221	GCACTTGGCTCTACGCTCTA	59.544	55.0	0.0	0.0	40.25	2.43	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
88	90	8.121305	AGTTCAATGTTTTATCTGGTAATGCA	57.879	30.769	0.00	0.00	0.00	3.96
89	91	8.028938	AGTTCAATGTTTTATCTGGTAATGCAC	58.971	33.333	0.00	0.00	0.00	4.57
100	102	2.752354	TGGTAATGCACTTTGGGAATCG	59.248	45.455	0.00	0.00	0.00	3.34
105	107	3.071874	TGCACTTTGGGAATCGAAGAT	57.928	42.857	0.00	0.00	45.12	2.40
106	108	3.420893	TGCACTTTGGGAATCGAAGATT	58.579	40.909	0.00	0.00	45.12	2.40
131	133	4.884164	ACTAAAGGATGGATTACTTGCTGC	59.116	41.667	0.00	0.00	0.00	5.25
173	175	1.002468	CGTCAAGGTTGAAGTTGGCTG	60.002	52.381	0.00	0.00	39.21	4.85
180	182	0.828762	TTGAAGTTGGCTGGCATGCT	60.829	50.000	18.92	3.85	0.00	3.79
185	187	1.017387	GTTGGCTGGCATGCTAGTAC	58.983	55.000	28.95	22.38	0.00	2.73
196	198	3.738281	GCATGCTAGTACCATCGTCAACT	60.738	47.826	11.37	0.00	0.00	3.16
197	199	3.777465	TGCTAGTACCATCGTCAACTC	57.223	47.619	0.00	0.00	0.00	3.01
198	200	2.096980	TGCTAGTACCATCGTCAACTCG	59.903	50.000	0.00	0.00	0.00	4.18
259	261	1.246649	GTCAACACCATGGACATGCA	58.753	50.000	21.47	0.00	37.49	3.96
273	275	5.754782	TGGACATGCAGTGGTTTCTATATT	58.245	37.500	0.00	0.00	0.00	1.28
285	287	8.434392	AGTGGTTTCTATATTTATAAAGCGGGA	58.566	33.333	3.94	0.00	33.25	5.14
317	319	6.258507	CCTATTTTTGAGTGCTTGTTTGCTTT	59.741	34.615	0.00	0.00	0.00	3.51
324	326	6.234920	TGAGTGCTTGTTTGCTTTACCTATA	58.765	36.000	0.00	0.00	0.00	1.31
326	328	7.088589	AGTGCTTGTTTGCTTTACCTATATG	57.911	36.000	0.00	0.00	0.00	1.78
334	336	5.303259	TGCTTTACCTATATGCATGTCCA	57.697	39.130	10.16	0.00	0.00	4.02
335	337	5.879763	TGCTTTACCTATATGCATGTCCAT	58.120	37.500	10.16	0.00	0.00	3.41
344	346	6.936335	CCTATATGCATGTCCATAAGTGTTCA	59.064	38.462	10.16	0.00	31.96	3.18
351	353	4.002982	TGTCCATAAGTGTTCAGTGCATC	58.997	43.478	0.00	0.00	0.00	3.91
358	360	0.178995	TGTTCAGTGCATCCAGCCAA	60.179	50.000	0.00	0.00	44.83	4.52
366	368	0.749454	GCATCCAGCCAAAGGACGAT	60.749	55.000	0.00	0.00	38.13	3.73
367	369	1.475034	GCATCCAGCCAAAGGACGATA	60.475	52.381	0.00	0.00	38.13	2.92

Showing 1 to 25 of 70 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	29	5.895636	TGGAGTGAAATGCGTCAATAATT	57.104	34.783	0.00	0.00	0.00	1.40
29	31	4.940654	TCATGGAGTGAAATGCGTCAATAA	59.059	37.500	0.00	0.00	32.78	1.40
30	32	4.512484	TCATGGAGTGAAATGCGTCAATA	58.488	39.130	0.00	0.00	32.78	1.90
32	34	2.777094	TCATGGAGTGAAATGCGTCAA	58.223	42.857	0.00	0.00	32.78	3.18
71	73	6.071616	TCCCAAAGTGCATTACCAGATAAAAC	60.072	38.462	0.00	0.00	0.00	2.43
76	78	3.737559	TCCCAAAGTGCATTACCAGAT	57.262	42.857	0.00	0.00	0.00	2.90
88	90	8.857694	TTTAGTTAATCTTCGATTCCCAAAGT	57.142	30.769	0.00	0.00	0.00	2.66
89	91	8.398665	CCTTTAGTTAATCTTCGATTCCCAAAG	58.601	37.037	0.00	0.00	0.00	2.77
105	107	7.067008	GCAGCAAGTAATCCATCCTTTAGTTAA	59.933	37.037	0.00	0.00	0.00	2.01
106	108	6.542370	GCAGCAAGTAATCCATCCTTTAGTTA	59.458	38.462	0.00	0.00	0.00	2.24
131	133	0.454600	GACCAATGATGCCTGCACTG	59.545	55.000	0.00	0.00	0.00	3.66
167	169	0.107214	GGTACTAGCATGCCAGCCAA	60.107	55.000	15.66	0.00	34.23	4.52
173	175	1.068588	TGACGATGGTACTAGCATGCC	59.931	52.381	15.66	0.00	36.31	4.40
180	182	3.603532	ACTCGAGTTGACGATGGTACTA	58.396	45.455	13.58	0.00	41.39	1.82
185	187	3.054276	GAGTACTCGAGTTGACGATGG	57.946	52.381	25.44	0.00	41.39	3.51
198	200	3.008330	TCAGTTAGGCAGTCGAGTACTC	58.992	50.000	13.18	13.18	35.76	2.59
259	261	8.434392	TCCCGCTTTATAAATATAGAAACCACT	58.566	33.333	0.00	0.00	0.00	4.00
273	275	2.093341	AGGCTTTCGTCCCGCTTTATAA	60.093	45.455	0.00	0.00	0.00	0.98
285	287	3.821033	AGCACTCAAAAATAGGCTTTCGT	59.179	39.130	0.00	0.00	0.00	3.85
287	289	5.532557	ACAAGCACTCAAAAATAGGCTTTC	58.467	37.500	0.00	0.00	39.36	2.62
291	293	4.084380	GCAAACAAGCACTCAAAAATAGGC	60.084	41.667	0.00	0.00	0.00	3.93
292	294	5.291971	AGCAAACAAGCACTCAAAAATAGG	58.708	37.500	0.00	0.00	36.85	2.57
300	302	3.287222	AGGTAAAGCAAACAAGCACTCA	58.713	40.909	0.00	0.00	36.85	3.41
317	319	7.553504	ACACTTATGGACATGCATATAGGTA	57.446	36.000	0.00	0.00	0.00	3.08
324	326	4.397103	CACTGAACACTTATGGACATGCAT	59.603	41.667	0.00	0.00	0.00	3.96

Showing 1 to 25 of 74 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.