AutoCloner

Multiple sequence alignment - TraesCS3A01G097800

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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	TraesCS3A01G097800	chr3A	100.000	4381	0	0	1	4381	63193257	63188877	0.000000e+00	8091.0
1	TraesCS3A01G097800	chr3A	87.683	341	33	5	3910	4249	443675837	443675505	5.310000e-104	388.0
2	TraesCS3A01G097800	chr3D	86.330	4016	246	130	1	3788	50012302	50008362	0.000000e+00	4095.0
3	TraesCS3A01G097800	chr3D	89.439	303	31	1	3941	4243	112101502	112101803	8.890000e-102	381.0
4	TraesCS3A01G097800	chr3D	90.391	281	9	6	1	267	50033036	50032760	1.940000e-93	353.0
5	TraesCS3A01G097800	chr3D	92.308	195	9	3	264	453	50014443	50014250	5.580000e-69	272.0
6	TraesCS3A01G097800	chr3D	90.141	142	14	0	3786	3927	449740281	449740422	7.480000e-43	185.0
7	TraesCS3A01G097800	chr3D	97.500	40	1	0	3402	3441	184661428	184661467	7.860000e-08	69.4
8	TraesCS3A01G097800	chr3B	84.460	3507	277	124	386	3704	79470598	79467172	0.000000e+00	3210.0
9	TraesCS3A01G097800	chr3B	86.471	510	36	20	3304	3788	79306415	79305914	3.000000e-146	529.0
10	TraesCS3A01G097800	chr3B	97.080	137	2	2	4247	4381	666404049	666404185	3.410000e-56	230.0
11	TraesCS3A01G097800	chr3B	97.059	136	4	0	4246	4381	715005782	715005917	3.410000e-56	230.0
12	TraesCS3A01G097800	chr3B	91.489	141	12	0	3787	3927	154663044	154663184	1.240000e-45	195.0
13	TraesCS3A01G097800	chr5A	87.608	347	35	5	3910	4256	435913635	435913973	3.180000e-106	396.0
14	TraesCS3A01G097800	chr5A	89.333	300	29	3	3943	4241	447872034	447872331	1.490000e-99	374.0
15	TraesCS3A01G097800	chr5A	95.652	138	6	0	4244	4381	36100341	36100204	5.700000e-54	222.0
16	TraesCS3A01G097800	chr5A	95.652	138	6	0	4244	4381	36129114	36128977	5.700000e-54	222.0
17	TraesCS3A01G097800	chr5A	95.652	138	6	0	4244	4381	36162732	36162595	5.700000e-54	222.0
18	TraesCS3A01G097800	chr5A	87.143	140	16	2	246	384	210626369	210626231	1.630000e-34	158.0
19	TraesCS3A01G097800	chr5A	93.333	60	4	0	1871	1930	290129402	290129461	6.030000e-14	89.8
20	TraesCS3A01G097800	chr1B	89.404	302	29	3	3941	4241	622367455	622367156	1.150000e-100	377.0
21	TraesCS3A01G097800	chrUn	89.333	300	29	3	3943	4241	335803092	335803389	1.490000e-99	374.0
22	TraesCS3A01G097800	chr7D	88.816	304	32	2	3941	4243	258232047	258231745	5.350000e-99	372.0
23	TraesCS3A01G097800	chr7D	97.037	135	4	0	4247	4381	383285017	383285151	1.230000e-55	228.0
24	TraesCS3A01G097800	chr7A	88.779	303	31	3	3941	4243	672082787	672082488	6.920000e-98	368.0
25	TraesCS3A01G097800	chr5B	88.704	301	32	2	3941	4241	69282647	69282945	2.490000e-97	366.0
26	TraesCS3A01G097800	chr5B	89.362	141	14	1	3787	3927	248390360	248390221	4.500000e-40	176.0
27	TraesCS3A01G097800	chr6B	97.037	135	4	0	4247	4381	87526285	87526151	1.230000e-55	228.0
28	TraesCS3A01G097800	chr6B	87.407	135	14	2	248	381	288414108	288414240	7.590000e-33	152.0
29	TraesCS3A01G097800	chr2A	97.037	135	4	0	4247	4381	723523029	723523163	1.230000e-55	228.0
30	TraesCS3A01G097800	chr2A	86.260	131	17	1	251	381	416014161	416014032	1.640000e-29	141.0
31	TraesCS3A01G097800	chr1A	95.652	138	6	0	4244	4381	570277336	570277473	5.700000e-54	222.0
32	TraesCS3A01G097800	chr5D	90.000	150	11	2	3781	3927	535865042	535865190	1.610000e-44	191.0
33	TraesCS3A01G097800	chr5D	90.210	143	12	1	3787	3927	393895829	393895687	7.480000e-43	185.0
34	TraesCS3A01G097800	chr5D	88.435	147	17	0	3781	3927	398108620	398108766	1.250000e-40	178.0
35	TraesCS3A01G097800	chr5D	89.286	140	15	0	3785	3924	487413547	487413686	4.500000e-40	176.0
36	TraesCS3A01G097800	chr2D	90.909	143	11	2	247	388	579962482	579962341	1.610000e-44	191.0
37	TraesCS3A01G097800	chr4B	88.889	144	15	1	3784	3927	532435165	532435023	4.500000e-40	176.0
38	TraesCS3A01G097800	chr1D	88.811	143	15	1	3785	3927	137636177	137636036	1.620000e-39	174.0
39	TraesCS3A01G097800	chr6A	92.174	115	5	4	1882	1995	123516433	123516322	4.540000e-35	159.0

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	TraesCS3A01G097800	chr3A	63188877	63193257	4380	True	8091.0	8091	100.000	1	4381	1	chr3A.!!$R1	4380
1	TraesCS3A01G097800	chr3D	50008362	50014443	6081	True	2183.5	4095	89.319	1	3788	2	chr3D.!!$R2	3787
2	TraesCS3A01G097800	chr3B	79467172	79470598	3426	True	3210.0	3210	84.460	386	3704	1	chr3B.!!$R2	3318
3	TraesCS3A01G097800	chr3B	79305914	79306415	501	True	529.0	529	86.471	3304	3788	1	chr3B.!!$R1	484

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
423	2579	0.255318	TCCTCCTCCGTCACTAGGTC	59.745	60.0	0.00	0.00	34.30	3.85	F
812	3009	0.463654	TGGTATCGCCAACATCAGGC	60.464	55.0	0.00	0.00	45.94	4.85	F
1624	3917	0.100325	CTGGCTAGCTCACTGTCGAG	59.900	60.0	15.72	3.77	36.02	4.04	F
1664	3964	0.108804	TCGAGCGAGGTGTCCAATTC	60.109	55.0	0.00	0.00	0.00	2.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1281	3545	0.035439	CCCCGCACAGGAACTTGTAT	60.035	55.000	0.00	0.0	45.00	2.29	R
2804	5164	0.246635	GGCGAACTGCTCTGAAGGTA	59.753	55.000	0.00	0.0	45.43	3.08	R
3259	5689	0.607489	CTGCAGGTGGGTCAAAGAGG	60.607	60.000	5.57	0.0	0.00	3.69	R
3390	5820	4.102649	CAGTTACAACATATGCGTCGAGA	58.897	43.478	1.58	0.0	0.00	4.04	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
213	2369	6.633668	TTTAACACACACCGAACAATTTTG	57.366	33.333	0.00	0.00	0.00	2.44
254	2410	5.514500	TTAATAGGTTTCTGAAGGCCTGT	57.486	39.130	5.69	13.18	32.90	4.00
256	2412	2.755952	AGGTTTCTGAAGGCCTGTTT	57.244	45.000	5.69	0.00	0.00	2.83
274	2430	1.913951	TTGGCATCACTCCGCTCCAT	61.914	55.000	0.00	0.00	0.00	3.41
279	2435	1.000283	CATCACTCCGCTCCATACTCC	60.000	57.143	0.00	0.00	0.00	3.85
286	2442	3.043419	CTCCATACTCCCGCTCCG	58.957	66.667	0.00	0.00	0.00	4.63
307	2463	0.603975	GAGCTGGCGGAGTTGAAGTT	60.604	55.000	0.00	0.00	0.00	2.66
311	2467	2.292292	GCTGGCGGAGTTGAAGTTAAAA	59.708	45.455	0.00	0.00	0.00	1.52
316	2472	7.222000	TGGCGGAGTTGAAGTTAAAAATTAT	57.778	32.000	0.00	0.00	0.00	1.28
355	2511	2.555199	CTCCGCAGATCCTCGAATTTT	58.445	47.619	5.86	0.00	0.00	1.82
357	2513	3.717707	TCCGCAGATCCTCGAATTTTAG	58.282	45.455	5.86	0.00	0.00	1.85
364	2520	3.543680	TCCTCGAATTTTAGGGAGCAG	57.456	47.619	7.07	0.00	33.40	4.24
365	2521	1.943340	CCTCGAATTTTAGGGAGCAGC	59.057	52.381	0.00	0.00	0.00	5.25
369	2525	2.680805	CGAATTTTAGGGAGCAGCTGGA	60.681	50.000	17.12	0.00	0.00	3.86
390	2546	3.829886	TTGCCGAACAGCTCTTAAATG	57.170	42.857	0.00	0.00	0.00	2.32
423	2579	0.255318	TCCTCCTCCGTCACTAGGTC	59.745	60.000	0.00	0.00	34.30	3.85
464	2620	7.147479	CCCAAAATATCTTAGAGAGACAGGGAA	60.147	40.741	0.00	0.00	37.17	3.97
471	2627	6.903534	ATCTTAGAGAGACAGGGAACCAATAA	59.096	38.462	0.00	0.00	45.65	1.40
472	2628	7.147637	ATCTTAGAGAGACAGGGAACCAATAAC	60.148	40.741	0.00	0.00	45.65	1.89
537	2700	4.257810	TCCCTCGGTCCCACCCAA	62.258	66.667	0.00	0.00	33.75	4.12
556	2719	3.710722	AGCCCAGCGGAGTGAAGG	61.711	66.667	0.00	0.00	0.00	3.46
614	2777	1.160329	ACTGCACGAGAACTTGCACC	61.160	55.000	0.00	0.00	44.21	5.01
653	2816	2.832838	TCCCTGCCTCTCAATCAACTA	58.167	47.619	0.00	0.00	0.00	2.24
654	2817	2.501723	TCCCTGCCTCTCAATCAACTAC	59.498	50.000	0.00	0.00	0.00	2.73
655	2818	2.503356	CCCTGCCTCTCAATCAACTACT	59.497	50.000	0.00	0.00	0.00	2.57

Showing 1 to 25 of 433 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	4.736793	CGCTAAAAGATTGCTTGCATTAGG	59.263	41.667	12.10	3.06	33.79	2.69
3	4	4.178545	ACGCTAAAAGATTGCTTGCATT	57.821	36.364	0.00	0.00	33.79	3.56
4	5	3.855689	ACGCTAAAAGATTGCTTGCAT	57.144	38.095	0.00	0.00	33.79	3.96
10	2152	4.875544	TCACCATACGCTAAAAGATTGC	57.124	40.909	0.00	0.00	0.00	3.56
122	2264	7.547697	TCGATCAATGGTCACCCTATTATTA	57.452	36.000	0.00	0.00	0.00	0.98
130	2272	2.691409	TCTTCGATCAATGGTCACCC	57.309	50.000	0.00	0.00	0.00	4.61
226	2382	9.541884	AGGCCTTCAGAAACCTATTAAAAATAA	57.458	29.630	0.00	0.00	0.00	1.40
228	2384	7.454694	ACAGGCCTTCAGAAACCTATTAAAAAT	59.545	33.333	0.00	0.00	0.00	1.82
231	2387	5.887754	ACAGGCCTTCAGAAACCTATTAAA	58.112	37.500	0.00	0.00	0.00	1.52
232	2388	5.514500	ACAGGCCTTCAGAAACCTATTAA	57.486	39.130	0.00	0.00	0.00	1.40
233	2389	5.514500	AACAGGCCTTCAGAAACCTATTA	57.486	39.130	0.00	0.00	0.00	0.98
254	2410	1.377202	GGAGCGGAGTGATGCCAAA	60.377	57.895	0.00	0.00	0.00	3.28
256	2412	1.048160	TATGGAGCGGAGTGATGCCA	61.048	55.000	0.00	0.00	0.00	4.92
286	2442	3.254024	TTCAACTCCGCCAGCTCCC	62.254	63.158	0.00	0.00	0.00	4.30
292	2448	5.523438	AATTTTTAACTTCAACTCCGCCA	57.477	34.783	0.00	0.00	0.00	5.69
298	2454	7.312899	CCGCTCCATAATTTTTAACTTCAACT	58.687	34.615	0.00	0.00	0.00	3.16
307	2463	3.955524	TCCCCCGCTCCATAATTTTTA	57.044	42.857	0.00	0.00	0.00	1.52
311	2467	0.923358	TGTTCCCCCGCTCCATAATT	59.077	50.000	0.00	0.00	0.00	1.40
316	2472	4.974438	ACCTGTTCCCCCGCTCCA	62.974	66.667	0.00	0.00	0.00	3.86
355	2511	1.528824	GCAATCCAGCTGCTCCCTA	59.471	57.895	8.66	0.00	36.84	3.53
357	2513	2.832201	GGCAATCCAGCTGCTCCC	60.832	66.667	8.66	0.00	39.82	4.30
364	2520	2.486966	GCTGTTCGGCAATCCAGC	59.513	61.111	0.00	0.00	42.94	4.85
365	2521	0.392193	AGAGCTGTTCGGCAATCCAG	60.392	55.000	0.00	0.00	34.17	3.86
369	2525	3.758554	ACATTTAAGAGCTGTTCGGCAAT	59.241	39.130	0.00	0.00	34.17	3.56
390	2546	1.751924	AGGAGGATGTCAACGCTAGAC	59.248	52.381	0.00	0.00	36.55	2.59

Showing 1 to 25 of 423 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.