AutoCloner

Multiple sequence alignment - TraesCS4A01G015900

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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	TraesCS4A01G015900	chr4A	100.000	4883	0	0	1	4883	9933449	9928567	0.000000e+00	9018
1	TraesCS4A01G015900	chr4A	96.751	708	23	0	4176	4883	9916689	9915982	0.000000e+00	1181
2	TraesCS4A01G015900	chr4D	95.408	1742	60	10	2445	4175	459026087	459027819	0.000000e+00	2756
3	TraesCS4A01G015900	chr4D	90.240	1834	80	33	655	2429	459024240	459026033	0.000000e+00	2303
4	TraesCS4A01G015900	chr4D	90.379	343	24	7	1	339	32722467	32722804	4.490000e-120	442
5	TraesCS4A01G015900	chr4D	95.652	138	6	0	428	565	459024108	459024245	6.360000e-54	222
6	TraesCS4A01G015900	chr4D	92.857	98	7	0	338	435	459009687	459009784	5.090000e-30	143
7	TraesCS4A01G015900	chr4B	92.466	1752	85	21	2445	4175	573274757	573276482	0.000000e+00	2460
8	TraesCS4A01G015900	chr4B	89.945	1810	86	38	676	2429	573272934	573274703	0.000000e+00	2246
9	TraesCS4A01G015900	chr4B	91.837	98	8	0	470	567	573272821	573272918	2.370000e-28	137
10	TraesCS4A01G015900	chr2A	97.599	708	17	0	4176	4883	262746761	262746054	0.000000e+00	1214
11	TraesCS4A01G015900	chr2A	90.265	339	26	3	1	339	39121841	39122172	2.090000e-118	436
12	TraesCS4A01G015900	chr6A	97.034	708	21	0	4176	4883	109951520	109950813	0.000000e+00	1192
13	TraesCS4A01G015900	chr6A	89.796	343	25	8	1	339	170538999	170539335	9.710000e-117	431
14	TraesCS4A01G015900	chr3A	97.034	708	21	0	4176	4883	81449132	81448425	0.000000e+00	1192
15	TraesCS4A01G015900	chr3A	97.159	704	20	0	4180	4883	68235238	68235941	0.000000e+00	1190
16	TraesCS4A01G015900	chr3A	96.751	708	23	0	4176	4883	238015619	238016326	0.000000e+00	1181
17	TraesCS4A01G015900	chr3A	96.615	709	24	0	4175	4883	446122149	446121441	0.000000e+00	1177
18	TraesCS4A01G015900	chr7A	96.761	710	22	1	4175	4883	143162938	143163647	0.000000e+00	1182
19	TraesCS4A01G015900	chr7A	96.751	708	22	1	4176	4883	143175532	143176238	0.000000e+00	1179
20	TraesCS4A01G015900	chr2D	91.471	340	24	5	1	339	71645461	71645126	3.440000e-126	462
21	TraesCS4A01G015900	chr2D	86.286	350	24	11	1	348	43331538	43331865	4.650000e-95	359
22	TraesCS4A01G015900	chr2D	94.624	93	5	0	568	660	99660914	99661006	1.420000e-30	145
23	TraesCS4A01G015900	chr1D	91.445	339	25	3	1	339	35857891	35858225	3.440000e-126	462
24	TraesCS4A01G015900	chr1D	96.774	93	3	0	568	660	250736884	250736976	6.540000e-34	156
25	TraesCS4A01G015900	chr5D	89.412	340	21	8	1	339	473036803	473037128	9.780000e-112	414
26	TraesCS4A01G015900	chr5D	96.774	93	3	0	568	660	8629796	8629888	6.540000e-34	156
27	TraesCS4A01G015900	chr6D	86.176	340	25	10	1	339	449233060	449232742	1.010000e-91	348
28	TraesCS4A01G015900	chr7D	85.714	301	21	11	40	339	440163023	440162744	1.030000e-76	298
29	TraesCS4A01G015900	chr3D	96.809	94	3	0	567	660	276578316	276578223	1.820000e-34	158
30	TraesCS4A01G015900	chr1A	96.774	93	3	0	568	660	371218960	371219052	6.540000e-34	156
31	TraesCS4A01G015900	chr6B	95.699	93	4	0	568	660	239325468	239325376	3.040000e-32	150
32	TraesCS4A01G015900	chr5A	95.699	93	4	0	568	660	523815088	523814996	3.040000e-32	150
33	TraesCS4A01G015900	chr5A	93.814	97	5	1	564	660	645471355	645471450	1.420000e-30	145
34	TraesCS4A01G015900	chr3B	94.624	93	5	0	568	660	30910529	30910437	1.420000e-30	145

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	TraesCS4A01G015900	chr4A	9928567	9933449	4882	True	9018.000000	9018	100.000000	1	4883	1	chr4A.!!$R2	4882
1	TraesCS4A01G015900	chr4A	9915982	9916689	707	True	1181.000000	1181	96.751000	4176	4883	1	chr4A.!!$R1	707
2	TraesCS4A01G015900	chr4D	459024108	459027819	3711	False	1760.333333	2756	93.766667	428	4175	3	chr4D.!!$F3	3747
3	TraesCS4A01G015900	chr4B	573272821	573276482	3661	False	1614.333333	2460	91.416000	470	4175	3	chr4B.!!$F1	3705
4	TraesCS4A01G015900	chr2A	262746054	262746761	707	True	1214.000000	1214	97.599000	4176	4883	1	chr2A.!!$R1	707
5	TraesCS4A01G015900	chr6A	109950813	109951520	707	True	1192.000000	1192	97.034000	4176	4883	1	chr6A.!!$R1	707
6	TraesCS4A01G015900	chr3A	81448425	81449132	707	True	1192.000000	1192	97.034000	4176	4883	1	chr3A.!!$R1	707
7	TraesCS4A01G015900	chr3A	68235238	68235941	703	False	1190.000000	1190	97.159000	4180	4883	1	chr3A.!!$F1	703
8	TraesCS4A01G015900	chr3A	238015619	238016326	707	False	1181.000000	1181	96.751000	4176	4883	1	chr3A.!!$F2	707
9	TraesCS4A01G015900	chr3A	446121441	446122149	708	True	1177.000000	1177	96.615000	4175	4883	1	chr3A.!!$R2	708
10	TraesCS4A01G015900	chr7A	143162938	143163647	709	False	1182.000000	1182	96.761000	4175	4883	1	chr7A.!!$F1	708
11	TraesCS4A01G015900	chr7A	143175532	143176238	706	False	1179.000000	1179	96.751000	4176	4883	1	chr7A.!!$F2	707

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
219	220	0.031585	GGCTTGGTTTGGTCGGTTTC	59.968	55.0	0.00	0.0	0.00	2.78	F
1324	1376	0.095417	GACGAGATTTGTGCCTTCGC	59.905	55.0	0.00	0.0	0.00	4.70	F
2408	2471	0.180406	GTCGGGGGTGCATTATGAGT	59.820	55.0	0.00	0.0	0.00	3.41	F
2808	2911	1.054406	GGGGGAATCCAGATGACCGA	61.054	60.0	0.09	0.0	37.22	4.69	F
3864	3974	0.980754	TGGTGGACGCCATGGACTAT	60.981	55.0	18.40	0.0	35.28	2.12	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1471	1523	0.034756	TTCACTGACATGTGGGTCCG	59.965	55.000	1.15	0.0	38.40	4.79	R
3208	3311	0.991355	AACAGACAGGGTTCCCACCA	60.991	55.000	10.73	0.0	46.43	4.17	R
3864	3974	0.247460	CTCAGAACCCTGACATCGCA	59.753	55.000	0.00	0.0	44.01	5.10	R
3867	3977	1.208293	GGTCCTCAGAACCCTGACATC	59.792	57.143	0.00	0.0	44.01	3.06	R
4669	4798	1.300233	GCTCTATCTTGGGCCGACG	60.300	63.158	0.00	0.0	0.00	5.12	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
21	22	4.078516	GGACCCGTGCGTAGGCTT	62.079	66.667	9.11	0.00	40.82	4.35
22	23	2.813908	GACCCGTGCGTAGGCTTG	60.814	66.667	9.11	0.93	40.82	4.01
23	24	3.584868	GACCCGTGCGTAGGCTTGT	62.585	63.158	9.11	0.62	40.82	3.16
24	25	2.813908	CCCGTGCGTAGGCTTGTC	60.814	66.667	9.11	0.00	40.82	3.18
25	26	2.813908	CCGTGCGTAGGCTTGTCC	60.814	66.667	9.11	0.00	40.82	4.02
27	28	1.374252	CGTGCGTAGGCTTGTCCTT	60.374	57.895	9.11	0.00	44.75	3.36
28	29	1.352156	CGTGCGTAGGCTTGTCCTTC	61.352	60.000	9.11	0.00	44.75	3.46
29	30	0.320421	GTGCGTAGGCTTGTCCTTCA	60.320	55.000	9.11	0.00	44.75	3.02
30	31	0.394938	TGCGTAGGCTTGTCCTTCAA	59.605	50.000	9.11	0.00	44.75	2.69
43	44	2.713595	TCCTTCAAGGAAAAGGGAGGA	58.286	47.619	2.63	0.00	42.51	3.71
44	45	2.644798	TCCTTCAAGGAAAAGGGAGGAG	59.355	50.000	2.63	0.00	42.51	3.69
45	46	2.291217	CCTTCAAGGAAAAGGGAGGAGG	60.291	54.545	0.00	0.00	39.75	4.30
46	47	1.372501	TCAAGGAAAAGGGAGGAGGG	58.627	55.000	0.00	0.00	0.00	4.30
47	48	0.332972	CAAGGAAAAGGGAGGAGGGG	59.667	60.000	0.00	0.00	0.00	4.79
48	49	0.851332	AAGGAAAAGGGAGGAGGGGG	60.851	60.000	0.00	0.00	0.00	5.40
49	50	1.544151	GGAAAAGGGAGGAGGGGGT	60.544	63.158	0.00	0.00	0.00	4.95
50	51	1.147190	GGAAAAGGGAGGAGGGGGTT	61.147	60.000	0.00	0.00	0.00	4.11
51	52	0.039764	GAAAAGGGAGGAGGGGGTTG	59.960	60.000	0.00	0.00	0.00	3.77
52	53	2.094170	AAAAGGGAGGAGGGGGTTGC	62.094	60.000	0.00	0.00	0.00	4.17
55	56	4.410400	GGAGGAGGGGGTTGCGTG	62.410	72.222	0.00	0.00	0.00	5.34
56	57	3.319198	GAGGAGGGGGTTGCGTGA	61.319	66.667	0.00	0.00	0.00	4.35
57	58	3.316573	GAGGAGGGGGTTGCGTGAG	62.317	68.421	0.00	0.00	0.00	3.51
58	59	4.410400	GGAGGGGGTTGCGTGAGG	62.410	72.222	0.00	0.00	0.00	3.86
101	102	4.447342	GGGTGCATGGAGGGGGTG	62.447	72.222	0.00	0.00	0.00	4.61
102	103	4.447342	GGTGCATGGAGGGGGTGG	62.447	72.222	0.00	0.00	0.00	4.61

Showing 1 to 25 of 347 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	3.387947	CTACGCACGGGTCCCCTT	61.388	66.667	1.00	0.00	0.00	3.95
4	5	4.078516	AAGCCTACGCACGGGTCC	62.079	66.667	0.00	0.00	37.52	4.46
5	6	2.813908	CAAGCCTACGCACGGGTC	60.814	66.667	0.00	0.00	37.52	4.46
6	7	3.584868	GACAAGCCTACGCACGGGT	62.585	63.158	0.00	0.00	37.52	5.28
7	8	2.813908	GACAAGCCTACGCACGGG	60.814	66.667	0.00	0.00	37.52	5.28
8	9	2.813908	GGACAAGCCTACGCACGG	60.814	66.667	0.00	0.00	37.52	4.94
17	18	2.297315	CCTTTTCCTTGAAGGACAAGCC	59.703	50.000	26.93	0.00	46.05	4.35
18	19	2.297315	CCCTTTTCCTTGAAGGACAAGC	59.703	50.000	26.93	0.00	46.05	4.01
19	20	3.823304	CTCCCTTTTCCTTGAAGGACAAG	59.177	47.826	25.88	25.88	45.78	3.16
20	21	3.436470	CCTCCCTTTTCCTTGAAGGACAA	60.436	47.826	14.62	13.07	45.78	3.18
21	22	2.108250	CCTCCCTTTTCCTTGAAGGACA	59.892	50.000	14.62	4.35	45.78	4.02
22	23	2.375509	TCCTCCCTTTTCCTTGAAGGAC	59.624	50.000	14.62	0.00	45.78	3.85
23	24	2.644798	CTCCTCCCTTTTCCTTGAAGGA	59.355	50.000	10.46	10.46	45.25	3.36
24	25	2.291217	CCTCCTCCCTTTTCCTTGAAGG	60.291	54.545	4.45	4.45	42.68	3.46
25	26	2.291217	CCCTCCTCCCTTTTCCTTGAAG	60.291	54.545	0.00	0.00	0.00	3.02
26	27	1.710809	CCCTCCTCCCTTTTCCTTGAA	59.289	52.381	0.00	0.00	0.00	2.69
27	28	1.372501	CCCTCCTCCCTTTTCCTTGA	58.627	55.000	0.00	0.00	0.00	3.02
28	29	0.332972	CCCCTCCTCCCTTTTCCTTG	59.667	60.000	0.00	0.00	0.00	3.61
29	30	0.851332	CCCCCTCCTCCCTTTTCCTT	60.851	60.000	0.00	0.00	0.00	3.36
30	31	1.230314	CCCCCTCCTCCCTTTTCCT	60.230	63.158	0.00	0.00	0.00	3.36
31	32	1.147190	AACCCCCTCCTCCCTTTTCC	61.147	60.000	0.00	0.00	0.00	3.13
32	33	0.039764	CAACCCCCTCCTCCCTTTTC	59.960	60.000	0.00	0.00	0.00	2.29
33	34	2.094170	GCAACCCCCTCCTCCCTTTT	62.094	60.000	0.00	0.00	0.00	2.27
34	35	2.548547	GCAACCCCCTCCTCCCTTT	61.549	63.158	0.00	0.00	0.00	3.11
35	36	2.941583	GCAACCCCCTCCTCCCTT	60.942	66.667	0.00	0.00	0.00	3.95

Showing 1 to 25 of 374 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.