AutoCloner

Multiple sequence alignment - TraesCS1B01G218700

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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	TraesCS1B01G218700	chr1B	100.000	3741	0	0	1	3741	396116006	396119746	0.000000e+00	6909
1	TraesCS1B01G218700	chr1B	96.667	330	10	1	284	613	114916024	114916352	7.060000e-152	547
2	TraesCS1B01G218700	chr1B	96.096	333	13	0	289	621	162352603	162352935	9.140000e-151	544
3	TraesCS1B01G218700	chr1D	91.959	2537	100	34	615	3089	294404970	294407464	0.000000e+00	3459
4	TraesCS1B01G218700	chr1D	83.130	492	73	6	3249	3731	463981768	463982258	1.230000e-119	440
5	TraesCS1B01G218700	chr1D	89.865	296	20	6	1	292	294404678	294404967	4.560000e-99	372
6	TraesCS1B01G218700	chr1A	92.521	1551	57	16	1570	3089	367381922	367383444	0.000000e+00	2167
7	TraesCS1B01G218700	chr1A	94.677	883	29	7	615	1485	367381053	367381929	0.000000e+00	1354
8	TraesCS1B01G218700	chr1A	91.525	295	22	1	1	292	367380756	367381050	1.620000e-108	403
9	TraesCS1B01G218700	chr5B	97.531	324	8	0	290	613	688021986	688022309	4.220000e-154	555
10	TraesCS1B01G218700	chr5B	81.047	554	89	8	3195	3733	118424200	118423648	9.600000e-116	427
11	TraesCS1B01G218700	chr4B	97.531	324	8	0	290	613	579401576	579401253	4.220000e-154	555
12	TraesCS1B01G218700	chr4B	97.516	322	8	0	292	613	653733487	653733808	5.460000e-153	551
13	TraesCS1B01G218700	chr2B	97.531	324	8	0	290	613	783866278	783865955	4.220000e-154	555
14	TraesCS1B01G218700	chr3A	97.239	326	9	0	288	613	580643691	580643366	1.520000e-153	553
15	TraesCS1B01G218700	chr3A	80.895	581	90	10	3172	3732	1646417	1646996	4.440000e-119	438
16	TraesCS1B01G218700	chr7A	97.231	325	9	0	289	613	726896108	726896432	5.460000e-153	551
17	TraesCS1B01G218700	chr4A	97.516	322	8	0	292	613	249545111	249545432	5.460000e-153	551
18	TraesCS1B01G218700	chr5D	81.753	559	95	7	3179	3732	523941398	523941954	9.470000e-126	460
19	TraesCS1B01G218700	chr5D	81.720	558	97	5	3179	3732	523995231	523995787	9.470000e-126	460
20	TraesCS1B01G218700	chr5D	82.731	498	81	5	3248	3741	515237624	515237128	4.440000e-119	438
21	TraesCS1B01G218700	chr2D	81.469	572	92	7	3183	3741	650470475	650469905	1.220000e-124	457
22	TraesCS1B01G218700	chr2D	75.532	282	59	8	1	274	136610083	136610362	3.030000e-26	130
23	TraesCS1B01G218700	chr2A	82.422	512	81	6	3233	3741	526281068	526281573	4.440000e-119	438
24	TraesCS1B01G218700	chr4D	82.677	508	71	9	3235	3741	312581807	312582298	5.740000e-118	435

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	TraesCS1B01G218700	chr1B	396116006	396119746	3740	False	6909.0	6909	100.000000	1	3741	1	chr1B.!!$F3	3740
1	TraesCS1B01G218700	chr1D	294404678	294407464	2786	False	1915.5	3459	90.912000	1	3089	2	chr1D.!!$F2	3088
2	TraesCS1B01G218700	chr1A	367380756	367383444	2688	False	1308.0	2167	92.907667	1	3089	3	chr1A.!!$F1	3088
3	TraesCS1B01G218700	chr5B	118423648	118424200	552	True	427.0	427	81.047000	3195	3733	1	chr5B.!!$R1	538
4	TraesCS1B01G218700	chr3A	1646417	1646996	579	False	438.0	438	80.895000	3172	3732	1	chr3A.!!$F1	560
5	TraesCS1B01G218700	chr5D	523941398	523941954	556	False	460.0	460	81.753000	3179	3732	1	chr5D.!!$F1	553
6	TraesCS1B01G218700	chr5D	523995231	523995787	556	False	460.0	460	81.720000	3179	3732	1	chr5D.!!$F2	553
7	TraesCS1B01G218700	chr2D	650469905	650470475	570	True	457.0	457	81.469000	3183	3741	1	chr2D.!!$R1	558
8	TraesCS1B01G218700	chr2A	526281068	526281573	505	False	438.0	438	82.422000	3233	3741	1	chr2A.!!$F1	508

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	Hairpin	End Stability	Orientation
332	336	0.034574	CGGTCATGAATGGGTTGGGA	60.035	55.0	0.00	4.37	F
493	497	0.035317	TGTGAGCATGACTGGTGGTC	59.965	55.0	44.70	4.02	F
1387	1419	0.040603	CGCCCGAGTCCGACTATAAC	60.041	60.0	38.22	1.89	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1800	1845	0.035152	GGATGATGTCCACCTGCACA	60.035	55.0	0.00	46.96	4.57	R
2223	2276	0.394192	TGAGCTCACCTCACCAAGTG	59.606	55.0	13.74	45.44	3.16	R
3159	3278	0.037605	CGTGCTTTAAGAGGTCCGGT	60.038	55.0	0.00	0.00	5.28	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
89	93	6.238320	GCAAAACAAATTACATGGCTTTGTCA	60.238	34.615	17.40	41.03	3.58
136	140	2.033049	GCTAGTAGCCGTCAGATCGAAA	59.967	50.000	11.33	34.48	3.46
164	168	2.093288	GGATGAGGACAGTCATTGCTGA	60.093	50.000	12.89	37.29	4.26
224	228	2.584391	AACGCCTCCTGTGACTCCC	61.584	63.158	0.00	0.00	4.30
225	229	2.997315	CGCCTCCTGTGACTCCCA	60.997	66.667	0.00	0.00	4.37
230	234	1.459348	TCCTGTGACTCCCAGCACA	60.459	57.895	0.00	42.25	4.57
232	236	1.302033	CTGTGACTCCCAGCACACC	60.302	63.158	0.00	39.86	4.16
235	239	4.394712	GACTCCCAGCACACCGGG	62.395	72.222	6.32	44.60	5.73
240	244	4.704833	CCAGCACACCGGGACAGG	62.705	72.222	6.32	37.30	4.00
276	280	8.378565	TCTAGTTCTTCAGAAATGATGGACTTT	58.621	33.333	9.56	34.73	2.66
292	296	3.274288	GACTTTGGGCCTGACATCTTAG	58.726	50.000	4.53	0.00	2.18
293	297	2.025887	ACTTTGGGCCTGACATCTTAGG	60.026	50.000	4.53	37.14	2.69
294	298	0.918983	TTGGGCCTGACATCTTAGGG	59.081	55.000	4.53	34.58	3.53
295	299	0.253160	TGGGCCTGACATCTTAGGGT	60.253	55.000	4.53	34.58	4.34
296	300	0.181350	GGGCCTGACATCTTAGGGTG	59.819	60.000	0.84	34.58	4.61
297	301	0.464554	GGCCTGACATCTTAGGGTGC	60.465	60.000	0.00	34.58	5.01
298	302	0.811616	GCCTGACATCTTAGGGTGCG	60.812	60.000	0.00	34.58	5.34
299	303	0.537188	CCTGACATCTTAGGGTGCGT	59.463	55.000	0.00	0.00	5.24
300	304	1.066143	CCTGACATCTTAGGGTGCGTT	60.066	52.381	0.00	0.00	4.84
301	305	2.615493	CCTGACATCTTAGGGTGCGTTT	60.615	50.000	0.00	0.00	3.60
302	306	2.416547	CTGACATCTTAGGGTGCGTTTG	59.583	50.000	0.00	0.00	2.93
303	307	1.737793	GACATCTTAGGGTGCGTTTGG	59.262	52.381	0.00	0.00	3.28
304	308	1.073284	ACATCTTAGGGTGCGTTTGGT	59.927	47.619	0.00	0.00	3.67
305	309	1.737793	CATCTTAGGGTGCGTTTGGTC	59.262	52.381	0.00	0.00	4.02
306	310	0.320073	TCTTAGGGTGCGTTTGGTCG	60.320	55.000	0.00	0.00	4.79

Showing 1 to 25 of 385 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
101	105	1.321074	ACTAGCTACCACCAGTCGCC	61.321	60.000	0.00	0.00	37.90	5.54
107	111	0.033796	ACGGCTACTAGCTACCACCA	60.034	55.000	7.99	0.00	41.99	4.17
136	140	2.035632	GACTGTCCTCATCCCTCGATT	58.964	52.381	0.00	0.00	0.00	3.34
164	168	1.206371	CCTTGGAAGATACCGGTTCGT	59.794	52.381	15.04	8.73	0.00	3.85
224	228	4.704833	CCCTGTCCCGGTGTGCTG	62.705	72.222	0.00	0.00	0.00	4.41
230	234	0.622136	GTTAATTCCCCTGTCCCGGT	59.378	55.000	0.00	0.00	0.00	5.28
232	236	1.838077	AGAGTTAATTCCCCTGTCCCG	59.162	52.381	0.00	0.00	0.00	5.14
235	239	6.547930	AGAACTAGAGTTAATTCCCCTGTC	57.452	41.667	0.00	0.00	38.56	3.51
240	244	9.674068	ATTTCTGAAGAACTAGAGTTAATTCCC	57.326	33.333	0.00	0.00	38.56	3.97
276	280	0.253160	ACCCTAAGATGTCAGGCCCA	60.253	55.000	0.00	0.00	0.00	5.36
306	310	1.434696	CATTCATGACCGCCCTTGC	59.565	57.895	0.00	0.00	0.00	4.01
307	311	1.386525	CCCATTCATGACCGCCCTTG	61.387	60.000	0.00	0.00	0.00	3.61
308	312	1.076777	CCCATTCATGACCGCCCTT	60.077	57.895	0.00	0.00	0.00	3.95
309	313	1.863155	AACCCATTCATGACCGCCCT	61.863	55.000	0.00	0.00	0.00	5.19
310	314	1.379843	AACCCATTCATGACCGCCC	60.380	57.895	0.00	0.00	0.00	6.13
311	315	1.666209	CCAACCCATTCATGACCGCC	61.666	60.000	0.00	0.00	0.00	6.13
312	316	1.666209	CCCAACCCATTCATGACCGC	61.666	60.000	0.00	0.00	0.00	5.68
313	317	0.034574	TCCCAACCCATTCATGACCG	60.035	55.000	0.00	0.00	0.00	4.79
314	318	2.310538	GATCCCAACCCATTCATGACC	58.689	52.381	0.00	0.00	0.00	4.02
315	319	1.949525	CGATCCCAACCCATTCATGAC	59.050	52.381	0.00	0.00	0.00	3.06
316	320	1.563879	ACGATCCCAACCCATTCATGA	59.436	47.619	0.00	0.00	0.00	3.07
317	321	2.057137	ACGATCCCAACCCATTCATG	57.943	50.000	0.00	0.00	0.00	3.07
318	322	2.025416	TGAACGATCCCAACCCATTCAT	60.025	45.455	0.00	0.00	0.00	2.57
319	323	1.352687	TGAACGATCCCAACCCATTCA	59.647	47.619	0.00	0.00	0.00	2.57
320	324	2.017049	CTGAACGATCCCAACCCATTC	58.983	52.381	0.00	0.00	0.00	2.67

Showing 1 to 25 of 376 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.