AutoCloner

Multiple sequence alignment - TraesCS1D01G448900

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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	TraesCS1D01G448900	chr1D	100.000	3351	0	0	1335	4685	491042704	491046054	0.000000e+00	6189.0
1	TraesCS1D01G448900	chr1D	100.000	1013	0	0	1	1013	491041370	491042382	0.000000e+00	1871.0
2	TraesCS1D01G448900	chr1D	89.573	211	14	7	4111	4317	491041666	491041872	1.290000e-65	261.0
3	TraesCS1D01G448900	chr1D	89.573	211	14	7	297	503	491045480	491045686	1.290000e-65	261.0
4	TraesCS1D01G448900	chr1D	100.000	38	0	0	3691	3728	302256653	302256616	2.340000e-08	71.3
5	TraesCS1D01G448900	chr1B	91.374	2446	131	33	1335	3752	683473510	683475903	0.000000e+00	3275.0
6	TraesCS1D01G448900	chr1B	89.564	527	23	12	9	503	683472591	683473117	1.420000e-179	640.0
7	TraesCS1D01G448900	chr1B	90.182	275	20	5	723	990	683473153	683473427	7.460000e-93	351.0
8	TraesCS1D01G448900	chr1B	83.548	310	30	18	72	369	683476010	683476310	2.150000e-68	270.0
9	TraesCS1D01G448900	chr1B	93.605	172	7	2	4027	4194	683476147	683476318	2.160000e-63	254.0
10	TraesCS1D01G448900	chr1B	83.645	214	10	12	4491	4685	683476456	683476663	1.340000e-40	178.0
11	TraesCS1D01G448900	chr1B	80.851	235	15	16	4111	4319	683472889	683473119	1.750000e-34	158.0
12	TraesCS1D01G448900	chr1B	84.615	117	5	6	4263	4378	683476330	683476434	2.310000e-18	104.0
13	TraesCS1D01G448900	chr1A	90.389	1904	99	33	2503	4385	589041354	589043194	0.000000e+00	2425.0
14	TraesCS1D01G448900	chr1A	91.733	1137	65	10	1343	2471	589040243	589041358	0.000000e+00	1552.0
15	TraesCS1D01G448900	chr1A	91.228	399	21	7	598	990	589039764	589040154	8.930000e-147	531.0
16	TraesCS1D01G448900	chr1A	92.793	222	9	4	4423	4638	589043193	589043413	9.790000e-82	315.0
17	TraesCS1D01G448900	chr1A	80.942	446	36	23	53	474	589039301	589039721	1.640000e-79	307.0
18	TraesCS1D01G448900	chr1A	87.705	122	11	2	1685	1802	589054294	589054415	6.320000e-29	139.0
19	TraesCS1D01G448900	chr1A	97.368	38	1	0	3686	3723	47204539	47204576	1.090000e-06	65.8
20	TraesCS1D01G448900	chr1A	91.111	45	2	2	3694	3738	576371107	576371065	5.060000e-05	60.2
21	TraesCS1D01G448900	chr7B	85.714	154	10	3	13	157	604628009	604627859	8.120000e-33	152.0
22	TraesCS1D01G448900	chr6A	90.909	99	9	0	59	157	159242938	159242840	2.940000e-27	134.0
23	TraesCS1D01G448900	chr5D	100.000	49	0	0	4381	4429	438690580	438690532	1.800000e-14	91.6
24	TraesCS1D01G448900	chr5D	94.643	56	2	1	4371	4425	322388474	322388529	8.350000e-13	86.1
25	TraesCS1D01G448900	chr5D	88.235	68	6	2	4362	4429	52769266	52769201	3.890000e-11	80.5
26	TraesCS1D01G448900	chr5D	97.436	39	1	0	3691	3729	509426525	509426563	3.030000e-07	67.6
27	TraesCS1D01G448900	chr4D	96.364	55	1	1	4373	4426	66516183	66516237	6.460000e-14	89.8
28	TraesCS1D01G448900	chr4D	88.406	69	5	2	4364	4430	440018012	440018079	3.890000e-11	80.5
29	TraesCS1D01G448900	chr4D	95.556	45	1	1	3691	3734	426846092	426846048	2.340000e-08	71.3
30	TraesCS1D01G448900	chr4D	89.796	49	1	4	3691	3736	472879890	472879843	5.060000e-05	60.2
31	TraesCS1D01G448900	chr7D	91.045	67	3	3	4359	4424	226690454	226690390	2.320000e-13	87.9
32	TraesCS1D01G448900	chr5B	93.333	60	3	1	4371	4429	582975547	582975606	2.320000e-13	87.9
33	TraesCS1D01G448900	chr5B	89.796	49	3	2	3691	3738	581145060	581145013	1.410000e-05	62.1
34	TraesCS1D01G448900	chr2B	96.296	54	1	1	4374	4426	483458095	483458042	2.320000e-13	87.9
35	TraesCS1D01G448900	chr3B	100.000	46	0	0	4381	4426	443358137	443358092	8.350000e-13	86.1
36	TraesCS1D01G448900	chr5A	89.796	49	3	2	3691	3738	588845524	588845477	1.410000e-05	62.1
37	TraesCS1D01G448900	chrUn	97.222	36	0	1	3691	3726	46240401	46240435	5.060000e-05	60.2
38	TraesCS1D01G448900	chr3D	100.000	29	0	0	104	132	174821709	174821737	2.000000e-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	TraesCS1D01G448900	chr1D	491041370	491046054	4684	False	2145.50	6189	94.7865	1	4685	4	chr1D.!!$F1	4684
1	TraesCS1D01G448900	chr1B	683472591	683476663	4072	False	653.75	3275	87.1730	9	4685	8	chr1B.!!$F1	4676
2	TraesCS1D01G448900	chr1A	589039301	589043413	4112	False	1026.00	2425	89.4170	53	4638	5	chr1A.!!$F3	4585

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
573	735	0.109412	ATTCTTTGCAGCGAGCTTGC	60.109	50.0	18.89	18.89	45.94	4.01	F
778	940	0.251165	AAATACTTGCAGCCCGGTGT	60.251	50.0	0.00	0.00	0.00	4.16	F
1526	1714	0.515127	TACATCGGTTGCTGTTTGCG	59.485	50.0	0.00	0.00	46.63	4.85	F
2293	2499	0.167908	GGTGTGTGTGTGTGTGTGTG	59.832	55.0	0.00	0.00	0.00	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2285	2491	0.454285	GCACACACACACACACACAC	60.454	55.0	0.00	0.0	0.0	3.82	R
2293	2499	0.463654	TTCAGGGAGCACACACACAC	60.464	55.0	0.00	0.0	0.0	3.82	R
3324	3530	0.543174	ATACCTGCCCGATCTCTCCC	60.543	60.0	0.00	0.0	0.0	4.30	R
3960	4184	0.383949	CACAAAGTCCAAACACCGGG	59.616	55.0	6.32	0.0	0.0	5.73	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
227	228	1.323271	GGTGCTCTGAGACCGGATGA	61.323	60.000	9.46	0.00	0.00	2.92
228	229	0.532573	GTGCTCTGAGACCGGATGAA	59.467	55.000	9.46	0.00	0.00	2.57
232	241	0.465705	TCTGAGACCGGATGAATGGC	59.534	55.000	9.46	0.00	0.00	4.40
400	419	1.093159	AGTTAGTTCGACGCCGAGAT	58.907	50.000	0.00	0.00	46.39	2.75
434	473	6.634436	CGAGCTGCTTTATTTATGTGGATTTC	59.366	38.462	2.53	0.00	0.00	2.17
475	514	6.764308	TGCTTCTTCAAGATAAGGATTTGG	57.236	37.500	0.00	0.00	0.00	3.28
484	523	4.683832	AGATAAGGATTTGGTTCGTCTCG	58.316	43.478	0.00	0.00	0.00	4.04
503	542	6.237332	CGTCTCGAACAAGATATTCAACTGAC	60.237	42.308	0.00	0.00	0.00	3.51
504	543	6.809196	GTCTCGAACAAGATATTCAACTGACT	59.191	38.462	0.00	0.00	0.00	3.41
505	544	6.808704	TCTCGAACAAGATATTCAACTGACTG	59.191	38.462	0.00	0.00	0.00	3.51
506	545	6.687604	TCGAACAAGATATTCAACTGACTGA	58.312	36.000	0.00	0.00	0.00	3.41
507	546	7.323420	TCGAACAAGATATTCAACTGACTGAT	58.677	34.615	0.00	0.00	0.00	2.90
508	547	7.819415	TCGAACAAGATATTCAACTGACTGATT	59.181	33.333	0.00	0.00	0.00	2.57
509	548	8.113062	CGAACAAGATATTCAACTGACTGATTC	58.887	37.037	0.00	0.00	0.00	2.52
510	549	8.853077	AACAAGATATTCAACTGACTGATTCA	57.147	30.769	0.00	0.00	0.00	2.57
511	550	9.458727	AACAAGATATTCAACTGACTGATTCAT	57.541	29.630	0.00	0.00	32.17	2.57
512	551	8.890718	ACAAGATATTCAACTGACTGATTCATG	58.109	33.333	0.00	0.00	32.17	3.07
513	552	8.890718	CAAGATATTCAACTGACTGATTCATGT	58.109	33.333	0.00	0.00	32.17	3.21
514	553	8.434733	AGATATTCAACTGACTGATTCATGTG	57.565	34.615	0.00	0.00	32.17	3.21
515	554	8.045507	AGATATTCAACTGACTGATTCATGTGT	58.954	33.333	0.00	0.00	32.17	3.72
516	555	5.929697	TTCAACTGACTGATTCATGTGTC	57.070	39.130	0.00	0.00	32.17	3.67
517	556	4.959723	TCAACTGACTGATTCATGTGTCA	58.040	39.130	6.94	6.94	37.76	3.58
518	557	4.751600	TCAACTGACTGATTCATGTGTCAC	59.248	41.667	3.77	0.00	35.83	3.67
519	558	4.341366	ACTGACTGATTCATGTGTCACA	57.659	40.909	8.40	8.40	35.83	3.58
520	559	4.707105	ACTGACTGATTCATGTGTCACAA	58.293	39.130	10.28	0.00	35.83	3.33

Showing 1 to 25 of 312 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
227	228	0.610232	GGTGGTGAGCTTCAGCCATT	60.610	55.000	11.21	0.00	43.72	3.16
228	229	1.001641	GGTGGTGAGCTTCAGCCAT	60.002	57.895	11.21	0.00	43.72	4.40
232	241	2.082231	CAATCTGGTGGTGAGCTTCAG	58.918	52.381	0.00	0.00	0.00	3.02
322	333	8.283291	CACAATCAACTAACTAAAGAGTCCAAC	58.717	37.037	0.00	0.00	33.58	3.77
400	419	2.189191	AAAGCAGCTCGAGATGGGCA	62.189	55.000	30.05	0.00	31.02	5.36
434	473	2.860062	GCATAGAGCAACACAAGCAAG	58.140	47.619	0.00	0.00	44.79	4.01
484	523	8.939929	TGAATCAGTCAGTTGAATATCTTGTTC	58.060	33.333	0.00	0.00	0.00	3.18
488	527	8.890718	CACATGAATCAGTCAGTTGAATATCTT	58.109	33.333	0.00	0.00	40.43	2.40
503	542	6.753279	ACAAAAACTTGTGACACATGAATCAG	59.247	34.615	23.91	13.36	33.23	2.90
504	543	6.629128	ACAAAAACTTGTGACACATGAATCA	58.371	32.000	23.91	0.00	33.23	2.57
505	544	7.524294	AACAAAAACTTGTGACACATGAATC	57.476	32.000	23.91	0.00	34.99	2.52
506	545	7.903995	AAACAAAAACTTGTGACACATGAAT	57.096	28.000	23.91	11.88	34.99	2.57
507	546	7.655328	AGAAAACAAAAACTTGTGACACATGAA	59.345	29.630	23.91	3.59	34.99	2.57
508	547	7.116090	CAGAAAACAAAAACTTGTGACACATGA	59.884	33.333	23.91	4.29	34.99	3.07
509	548	7.095691	ACAGAAAACAAAAACTTGTGACACATG	60.096	33.333	17.43	17.43	34.99	3.21
510	549	6.928492	ACAGAAAACAAAAACTTGTGACACAT	59.072	30.769	9.55	0.00	34.99	3.21
511	550	6.199908	CACAGAAAACAAAAACTTGTGACACA	59.800	34.615	3.56	3.56	34.99	3.72
512	551	6.346518	CCACAGAAAACAAAAACTTGTGACAC	60.347	38.462	0.00	0.00	34.99	3.67
513	552	5.694006	CCACAGAAAACAAAAACTTGTGACA	59.306	36.000	3.51	0.00	34.99	3.58
514	553	5.694458	ACCACAGAAAACAAAAACTTGTGAC	59.306	36.000	3.51	0.00	34.99	3.67
515	554	5.848406	ACCACAGAAAACAAAAACTTGTGA	58.152	33.333	3.51	0.00	34.99	3.58
516	555	6.018343	ACAACCACAGAAAACAAAAACTTGTG	60.018	34.615	0.00	0.00	34.99	3.33
517	556	6.018343	CACAACCACAGAAAACAAAAACTTGT	60.018	34.615	0.00	0.00	36.59	3.16
518	557	6.361899	CACAACCACAGAAAACAAAAACTTG	58.638	36.000	0.00	0.00	0.00	3.16
519	558	5.468409	CCACAACCACAGAAAACAAAAACTT	59.532	36.000	0.00	0.00	0.00	2.66

Showing 1 to 25 of 319 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.