AutoCloner

Multiple sequence alignment - TraesCS3A01G501200

Loading Multiple Alignment...

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	TraesCS3A01G501200	chr3A	100.000	2237	0	0	1	2237	725460567	725462803	0.000000e+00	4132
1	TraesCS3A01G501200	chr3A	84.908	1418	123	32	248	1609	725555803	725557185	0.000000e+00	1349
2	TraesCS3A01G501200	chr3A	84.908	1418	123	32	248	1609	725598351	725599733	0.000000e+00	1349
3	TraesCS3A01G501200	chr3A	88.924	641	38	14	1605	2237	41411474	41412089	0.000000e+00	760
4	TraesCS3A01G501200	chr3A	78.556	457	74	16	282	722	725476558	725477006	1.690000e-71	279
5	TraesCS3A01G501200	chr3B	84.577	1394	126	45	256	1609	798231579	798232923	0.000000e+00	1301
6	TraesCS3A01G501200	chr3B	86.349	630	30	13	1608	2237	69989676	69990249	8.710000e-179	636
7	TraesCS3A01G501200	chr3B	81.492	362	58	6	257	614	798251445	798251801	2.810000e-74	289
8	TraesCS3A01G501200	chr2A	95.404	631	5	1	1607	2237	89921404	89922010	0.000000e+00	983
9	TraesCS3A01G501200	chr2A	94.762	630	9	1	1608	2237	89797562	89796957	0.000000e+00	959
10	TraesCS3A01G501200	chr5B	93.968	630	14	12	1608	2237	9576798	9576193	0.000000e+00	931
11	TraesCS3A01G501200	chr4B	90.317	630	36	13	1608	2237	487298794	487298190	0.000000e+00	802
12	TraesCS3A01G501200	chr2D	90.063	634	30	15	1612	2237	339730467	339729859	0.000000e+00	791
13	TraesCS3A01G501200	chr1A	89.498	638	35	14	1608	2237	540662853	540662240	0.000000e+00	778
14	TraesCS3A01G501200	chr7B	89.382	631	43	13	1607	2237	704057858	704057252	0.000000e+00	773
15	TraesCS3A01G501200	chr3D	87.079	712	55	23	927	1609	594684636	594685339	0.000000e+00	771
16	TraesCS3A01G501200	chr3D	86.094	640	60	11	248	877	594771580	594772200	0.000000e+00	662
17	TraesCS3A01G501200	chr3D	84.006	669	68	21	223	877	594642706	594643349	6.830000e-170	606
18	TraesCS3A01G501200	chr3D	90.930	441	28	8	241	679	594683924	594684354	1.150000e-162	582
19	TraesCS3A01G501200	chr3D	84.095	591	57	22	1046	1609	594772952	594773532	9.090000e-149	536
20	TraesCS3A01G501200	chr3D	84.956	565	42	23	927	1463	594643370	594643919	1.180000e-147	532
21	TraesCS3A01G501200	chr3D	84.956	565	42	23	927	1463	594772221	594772770	1.180000e-147	532
22	TraesCS3A01G501200	chr3D	83.587	591	60	22	1046	1609	594644101	594644681	9.160000e-144	520
23	TraesCS3A01G501200	chr3D	90.726	248	20	2	631	877	594684370	594684615	5.960000e-86	327
24	TraesCS3A01G501200	chr3D	79.508	366	64	8	262	621	594800082	594800442	1.330000e-62	250
25	TraesCS3A01G501200	chr2B	88.050	636	44	12	1608	2235	49665238	49664627	0.000000e+00	725
26	TraesCS3A01G501200	chr1B	87.619	630	38	7	1608	2237	113092436	113091847	0.000000e+00	695
27	TraesCS3A01G501200	chr5D	86.882	465	35	6	1604	2067	313795108	313795547	4.290000e-137	497

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	TraesCS3A01G501200	chr3A	725460567	725462803	2236	False	4132.000000	4132	100.000000	1	2237	1	chr3A.!!$F2	2236
1	TraesCS3A01G501200	chr3A	725555803	725557185	1382	False	1349.000000	1349	84.908000	248	1609	1	chr3A.!!$F4	1361
2	TraesCS3A01G501200	chr3A	725598351	725599733	1382	False	1349.000000	1349	84.908000	248	1609	1	chr3A.!!$F5	1361
3	TraesCS3A01G501200	chr3A	41411474	41412089	615	False	760.000000	760	88.924000	1605	2237	1	chr3A.!!$F1	632
4	TraesCS3A01G501200	chr3B	798231579	798232923	1344	False	1301.000000	1301	84.577000	256	1609	1	chr3B.!!$F2	1353
5	TraesCS3A01G501200	chr3B	69989676	69990249	573	False	636.000000	636	86.349000	1608	2237	1	chr3B.!!$F1	629
6	TraesCS3A01G501200	chr2A	89921404	89922010	606	False	983.000000	983	95.404000	1607	2237	1	chr2A.!!$F1	630
7	TraesCS3A01G501200	chr2A	89796957	89797562	605	True	959.000000	959	94.762000	1608	2237	1	chr2A.!!$R1	629
8	TraesCS3A01G501200	chr5B	9576193	9576798	605	True	931.000000	931	93.968000	1608	2237	1	chr5B.!!$R1	629
9	TraesCS3A01G501200	chr4B	487298190	487298794	604	True	802.000000	802	90.317000	1608	2237	1	chr4B.!!$R1	629
10	TraesCS3A01G501200	chr2D	339729859	339730467	608	True	791.000000	791	90.063000	1612	2237	1	chr2D.!!$R1	625
11	TraesCS3A01G501200	chr1A	540662240	540662853	613	True	778.000000	778	89.498000	1608	2237	1	chr1A.!!$R1	629
12	TraesCS3A01G501200	chr7B	704057252	704057858	606	True	773.000000	773	89.382000	1607	2237	1	chr7B.!!$R1	630
13	TraesCS3A01G501200	chr3D	594771580	594773532	1952	False	576.666667	662	85.048333	248	1609	3	chr3D.!!$F4	1361
14	TraesCS3A01G501200	chr3D	594683924	594685339	1415	False	560.000000	771	89.578333	241	1609	3	chr3D.!!$F3	1368
15	TraesCS3A01G501200	chr3D	594642706	594644681	1975	False	552.666667	606	84.183000	223	1609	3	chr3D.!!$F2	1386
16	TraesCS3A01G501200	chr2B	49664627	49665238	611	True	725.000000	725	88.050000	1608	2235	1	chr2B.!!$R1	627
17	TraesCS3A01G501200	chr1B	113091847	113092436	589	True	695.000000	695	87.619000	1608	2237	1	chr1B.!!$R1	629

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
879	985	0.03563	GACACAGGATCAGCAGCCTT	60.036	55.0	0.0	0.0	30.41	4.35	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1874	3280	4.521062	GATGCAGCTCGCCTCCGT	62.521	66.667	0.0	0.0	41.33	4.69	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
30	31	8.902540	ATGTTGAATGTAGTTTGTACTTCTGA	57.097	30.769	0.00	0.00	35.78	3.27
31	32	8.902540	TGTTGAATGTAGTTTGTACTTCTGAT	57.097	30.769	0.00	0.00	35.78	2.90
32	33	8.773645	TGTTGAATGTAGTTTGTACTTCTGATG	58.226	33.333	0.00	0.00	35.78	3.07
33	34	8.988934	GTTGAATGTAGTTTGTACTTCTGATGA	58.011	33.333	0.00	0.00	35.78	2.92
34	35	9.554395	TTGAATGTAGTTTGTACTTCTGATGAA	57.446	29.630	0.00	0.00	35.78	2.57
35	36	8.988934	TGAATGTAGTTTGTACTTCTGATGAAC	58.011	33.333	0.00	0.00	35.78	3.18
36	37	7.582435	ATGTAGTTTGTACTTCTGATGAACG	57.418	36.000	0.00	0.00	35.78	3.95
37	38	6.509656	TGTAGTTTGTACTTCTGATGAACGT	58.490	36.000	0.00	0.00	35.78	3.99
38	39	6.982141	TGTAGTTTGTACTTCTGATGAACGTT	59.018	34.615	0.00	0.00	35.78	3.99
39	40	6.920569	AGTTTGTACTTCTGATGAACGTTT	57.079	33.333	0.46	0.00	0.00	3.60
40	41	8.971321	GTAGTTTGTACTTCTGATGAACGTTTA	58.029	33.333	0.46	0.00	35.78	2.01
41	42	8.603242	AGTTTGTACTTCTGATGAACGTTTAT	57.397	30.769	5.09	5.09	0.00	1.40
42	43	9.701098	AGTTTGTACTTCTGATGAACGTTTATA	57.299	29.630	5.44	0.00	0.00	0.98
70	71	6.806388	ATTTGGATTCCTTTCACAAAATGC	57.194	33.333	3.95	0.00	35.06	3.56
71	72	5.549742	TTGGATTCCTTTCACAAAATGCT	57.450	34.783	3.95	0.00	0.00	3.79
72	73	5.549742	TGGATTCCTTTCACAAAATGCTT	57.450	34.783	3.95	0.00	0.00	3.91
73	74	5.540911	TGGATTCCTTTCACAAAATGCTTC	58.459	37.500	3.95	0.00	0.00	3.86
74	75	4.622740	GGATTCCTTTCACAAAATGCTTCG	59.377	41.667	0.00	0.00	0.00	3.79
75	76	3.011949	TCCTTTCACAAAATGCTTCGC	57.988	42.857	0.00	0.00	0.00	4.70
76	77	2.360483	TCCTTTCACAAAATGCTTCGCA	59.640	40.909	0.00	0.00	44.86	5.10
77	78	2.727798	CCTTTCACAAAATGCTTCGCAG	59.272	45.455	0.00	0.00	43.65	5.18
78	79	3.550639	CCTTTCACAAAATGCTTCGCAGA	60.551	43.478	0.00	0.00	43.65	4.26
79	80	3.921119	TTCACAAAATGCTTCGCAGAT	57.079	38.095	0.00	0.00	43.65	2.90
80	81	3.476295	TCACAAAATGCTTCGCAGATC	57.524	42.857	0.00	0.00	43.65	2.75
81	82	2.813172	TCACAAAATGCTTCGCAGATCA	59.187	40.909	0.00	0.00	43.65	2.92

Showing 1 to 25 of 196 entries

Previous1 2 3 4 5…8Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
4	5	9.990360	TCAGAAGTACAAACTACATTCAACATA	57.010	29.630	0.00	0.00	33.75	2.29
5	6	8.902540	TCAGAAGTACAAACTACATTCAACAT	57.097	30.769	0.00	0.00	33.75	2.71
6	7	8.773645	CATCAGAAGTACAAACTACATTCAACA	58.226	33.333	0.00	0.00	33.75	3.33
7	8	8.988934	TCATCAGAAGTACAAACTACATTCAAC	58.011	33.333	0.00	0.00	33.75	3.18
8	9	9.554395	TTCATCAGAAGTACAAACTACATTCAA	57.446	29.630	0.00	0.00	33.75	2.69
9	10	8.988934	GTTCATCAGAAGTACAAACTACATTCA	58.011	33.333	0.00	0.00	33.75	2.57
10	11	8.162880	CGTTCATCAGAAGTACAAACTACATTC	58.837	37.037	0.00	0.00	33.75	2.67
11	12	7.656137	ACGTTCATCAGAAGTACAAACTACATT	59.344	33.333	0.00	0.00	33.75	2.71
12	13	7.152645	ACGTTCATCAGAAGTACAAACTACAT	58.847	34.615	0.00	0.00	33.75	2.29
13	14	6.509656	ACGTTCATCAGAAGTACAAACTACA	58.490	36.000	0.00	0.00	33.75	2.74
14	15	7.404139	AACGTTCATCAGAAGTACAAACTAC	57.596	36.000	0.00	0.00	33.75	2.73
15	16	9.701098	ATAAACGTTCATCAGAAGTACAAACTA	57.299	29.630	0.00	0.00	33.75	2.24
16	17	6.920569	AAACGTTCATCAGAAGTACAAACT	57.079	33.333	0.00	0.00	37.65	2.66
44	45	8.782144	GCATTTTGTGAAAGGAATCCAAATTTA	58.218	29.630	0.61	0.00	0.00	1.40
45	46	7.503230	AGCATTTTGTGAAAGGAATCCAAATTT	59.497	29.630	0.61	0.00	0.00	1.82
46	47	6.999871	AGCATTTTGTGAAAGGAATCCAAATT	59.000	30.769	0.61	0.00	0.00	1.82
47	48	6.536447	AGCATTTTGTGAAAGGAATCCAAAT	58.464	32.000	0.61	0.00	0.00	2.32
48	49	5.927819	AGCATTTTGTGAAAGGAATCCAAA	58.072	33.333	0.61	0.00	0.00	3.28
49	50	5.549742	AGCATTTTGTGAAAGGAATCCAA	57.450	34.783	0.61	0.00	0.00	3.53
50	51	5.540911	GAAGCATTTTGTGAAAGGAATCCA	58.459	37.500	0.61	0.00	0.00	3.41
51	52	4.622740	CGAAGCATTTTGTGAAAGGAATCC	59.377	41.667	0.00	0.00	0.00	3.01
52	53	5.752098	CGAAGCATTTTGTGAAAGGAATC	57.248	39.130	0.00	0.00	0.00	2.52
70	71	2.606725	GGAGATTGTGTGATCTGCGAAG	59.393	50.000	0.00	0.00	36.54	3.79
71	72	2.621338	GGAGATTGTGTGATCTGCGAA	58.379	47.619	0.00	0.00	36.54	4.70
72	73	1.134699	GGGAGATTGTGTGATCTGCGA	60.135	52.381	0.00	0.00	43.16	5.10

Showing 1 to 25 of 210 entries

Previous1 2 3 4 5…9Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.