AutoCloner

Multiple sequence alignment - TraesCS3D01G450100

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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	TraesCS3D01G450100	chr3D	100.000	2555	0	0	1	2555	558293570	558291016	0.000000e+00	4719.0
1	TraesCS3D01G450100	chr3D	78.626	262	56	0	1139	1400	558282305	558282044	9.400000e-40	174.0
2	TraesCS3D01G450100	chr3A	93.872	2252	83	13	335	2537	694534679	694532434	0.000000e+00	3343.0
3	TraesCS3D01G450100	chr3A	83.333	120	20	0	76	195	688304135	688304254	7.470000e-21	111.0
4	TraesCS3D01G450100	chrUn	95.685	1437	39	8	737	2162	40742523	40741099	0.000000e+00	2289.0
5	TraesCS3D01G450100	chrUn	95.685	1437	39	8	737	2162	40745382	40746806	0.000000e+00	2289.0
6	TraesCS3D01G450100	chrUn	95.685	1437	39	8	737	2162	303402077	303400653	0.000000e+00	2289.0
7	TraesCS3D01G450100	chrUn	91.207	762	46	6	3	745	40743725	40744484	0.000000e+00	1016.0
8	TraesCS3D01G450100	chrUn	92.000	350	25	3	2206	2555	40740894	40740548	2.950000e-134	488.0
9	TraesCS3D01G450100	chrUn	92.219	347	24	3	2206	2552	40747011	40747354	2.950000e-134	488.0
10	TraesCS3D01G450100	chrUn	92.000	350	25	3	2206	2555	303400448	303400102	2.950000e-134	488.0
11	TraesCS3D01G450100	chrUn	84.167	120	19	0	76	195	41472398	41472517	1.610000e-22	117.0
12	TraesCS3D01G450100	chr2A	84.192	291	34	10	1120	1404	603523788	603524072	3.240000e-69	272.0
13	TraesCS3D01G450100	chr2D	83.849	291	35	10	1120	1404	460648986	460649270	1.510000e-67	267.0
14	TraesCS3D01G450100	chr2D	81.533	287	51	2	2265	2549	214096467	214096753	4.250000e-58	235.0
15	TraesCS3D01G450100	chr2D	81.955	266	47	1	80	345	280644797	280645061	9.200000e-55	224.0
16	TraesCS3D01G450100	chr3B	83.406	229	36	2	2259	2485	788206860	788207088	7.160000e-51	211.0
17	TraesCS3D01G450100	chr3B	82.700	237	38	3	2258	2491	401817246	401817010	9.260000e-50	207.0
18	TraesCS3D01G450100	chr5A	83.051	236	35	4	2259	2491	315498018	315497785	2.580000e-50	209.0
19	TraesCS3D01G450100	chr1A	83.043	230	35	4	2258	2485	576791203	576791430	3.330000e-49	206.0
20	TraesCS3D01G450100	chr4B	82.479	234	39	2	2254	2485	648517865	648518098	1.200000e-48	204.0
21	TraesCS3D01G450100	chr7B	81.513	238	40	4	1123	1358	142283968	142283733	2.590000e-45	193.0
22	TraesCS3D01G450100	chr7B	81.328	241	35	9	1123	1358	143055669	143055434	1.210000e-43	187.0
23	TraesCS3D01G450100	chr1D	78.166	229	41	7	2259	2484	49924179	49924401	1.230000e-28	137.0
24	TraesCS3D01G450100	chr4A	84.034	119	19	0	77	195	563231916	563232034	5.780000e-22	115.0
25	TraesCS3D01G450100	chr6B	83.193	119	20	0	77	195	620654463	620654345	2.690000e-20	110.0
26	TraesCS3D01G450100	chr6B	82.353	119	21	0	77	195	574465874	574465992	1.250000e-18	104.0
27	TraesCS3D01G450100	chr2B	83.193	119	20	0	77	195	326674256	326674374	2.690000e-20	110.0
28	TraesCS3D01G450100	chr7D	81.818	88	15	1	2458	2545	53701816	53701902	3.530000e-09	73.1

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	TraesCS3D01G450100	chr3D	558291016	558293570	2554	True	4719.000000	4719	100.0000	1	2555	1	chr3D.!!$R2	2554
1	TraesCS3D01G450100	chr3A	694532434	694534679	2245	True	3343.000000	3343	93.8720	335	2537	1	chr3A.!!$R1	2202
2	TraesCS3D01G450100	chrUn	40740548	40742523	1975	True	1388.500000	2289	93.8425	737	2555	2	chrUn.!!$R1	1818
3	TraesCS3D01G450100	chrUn	303400102	303402077	1975	True	1388.500000	2289	93.8425	737	2555	2	chrUn.!!$R2	1818
4	TraesCS3D01G450100	chrUn	40743725	40747354	3629	False	1264.333333	2289	93.0370	3	2552	3	chrUn.!!$F2	2549

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
131	133	0.245266	TGGTGTCATGTACGTCGCAT	59.755	50.0	0.0	0.0	0.00	4.73	F
953	1887	0.817013	ACCGCCCGTATAAAAGACGA	59.183	50.0	0.0	0.0	42.98	4.20	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1116	2072	1.153289	CCGGTCCTGCTCCTTGATG	60.153	63.158	0.0	0.0	0.00	3.07	R
2432	3555	1.067846	CGATGTTCGTTCAGTGGGAGA	60.068	52.381	0.0	0.0	34.72	3.71	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)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
43	44	8.947115	AGAGTACAAAAACAACTATCTAATGCC	58.053	33.333	0.00	0.00	0.00	4.40
100	101	1.676006	GAATTGCATTGTAGGTCCCCG	59.324	52.381	0.00	0.00	0.00	5.73
128	130	2.601804	TCAATGGTGTCATGTACGTCG	58.398	47.619	0.00	0.00	33.18	5.12
131	133	0.245266	TGGTGTCATGTACGTCGCAT	59.755	50.000	0.00	0.00	0.00	4.73
144	146	7.157050	TGTACGTCGCATAACTATGAAAATC	57.843	36.000	0.00	0.00	35.75	2.17
145	147	6.752815	TGTACGTCGCATAACTATGAAAATCA	59.247	34.615	0.00	0.00	35.75	2.57
146	148	6.844696	ACGTCGCATAACTATGAAAATCAT	57.155	33.333	0.77	0.00	40.72	2.45
166	168	9.533831	AAATCATTATCCAAGTCCTTAAAGTGT	57.466	29.630	0.00	0.00	0.00	3.55
176	178	9.715121	CCAAGTCCTTAAAGTGTAATAAGTGTA	57.285	33.333	0.00	0.00	0.00	2.90
215	217	7.923414	AATCAGTTCAATACTAAAGTGGTCC	57.077	36.000	0.00	0.00	34.56	4.46
219	221	5.479375	AGTTCAATACTAAAGTGGTCCGAGA	59.521	40.000	0.00	0.00	34.56	4.04
228	230	7.887381	ACTAAAGTGGTCCGAGAATCTATATG	58.113	38.462	0.00	0.00	0.00	1.78
264	266	5.467705	ACACACTTATTGTACTTCGAGGAC	58.532	41.667	0.00	0.00	35.67	3.85
268	270	5.014858	ACTTATTGTACTTCGAGGACCTGA	58.985	41.667	0.00	0.00	0.00	3.86
278	280	4.286297	TCGAGGACCTGAATGACAATTT	57.714	40.909	0.00	0.00	0.00	1.82
279	281	4.651778	TCGAGGACCTGAATGACAATTTT	58.348	39.130	0.00	0.00	0.00	1.82
309	311	5.089970	TGAGAAACTATGTGACATCCCTG	57.910	43.478	0.00	0.00	0.00	4.45
324	326	7.337942	GTGACATCCCTGAAATAGTTCAAAGAT	59.662	37.037	7.08	8.88	43.18	2.40
333	335	9.208022	CTGAAATAGTTCAAAGATGTACTGTGA	57.792	33.333	7.08	0.00	43.18	3.58
353	355	6.981722	TGTGAATTTCCCTCTTTTTAGAAGC	58.018	36.000	0.00	0.00	0.00	3.86
364	366	6.350780	CCTCTTTTTAGAAGCATGCAATCCTT	60.351	38.462	21.98	4.39	0.00	3.36
371	373	3.587797	AGCATGCAATCCTTGAAACAG	57.412	42.857	21.98	0.00	0.00	3.16
413	415	2.839486	TGTGTCCTAGCAGTTCCAAG	57.161	50.000	0.00	0.00	0.00	3.61
418	420	1.902508	TCCTAGCAGTTCCAAGTCCTG	59.097	52.381	0.00	0.00	0.00	3.86
538	540	6.800543	TGAACAGACAATGGAAATCGAAAAA	58.199	32.000	0.00	0.00	0.00	1.94
774	1699	3.819652	AGCCACCAACACAGCCCA	61.820	61.111	0.00	0.00	0.00	5.36
792	1717	2.333069	CCAGCATATTCTCCCTCCTCA	58.667	52.381	0.00	0.00	0.00	3.86
877	1811	2.111999	AAAGTAGCCACGCTCCTGCA	62.112	55.000	0.00	0.00	40.44	4.41
879	1813	4.082523	TAGCCACGCTCCTGCACC	62.083	66.667	0.00	0.00	40.44	5.01
919	1853	2.167075	CAGTCCATTCAATTCCCAAGCC	59.833	50.000	0.00	0.00	0.00	4.35
953	1887	0.817013	ACCGCCCGTATAAAAGACGA	59.183	50.000	0.00	0.00	42.98	4.20
997	1935	1.606668	AGATCGAAGGAGCAGATCGAC	59.393	52.381	6.14	2.47	46.90	4.20
1530	2486	0.981277	ACAGGAGGGATAACACCGGG	60.981	60.000	6.32	0.00	0.00	5.73
1824	2785	2.095008	CACTAGGATCGATGGATGGACG	60.095	54.545	0.54	0.00	31.51	4.79
2040	3001	5.247507	TCAATTTATCGATGTGCCTTTGG	57.752	39.130	8.54	0.00	0.00	3.28
2045	3006	5.461032	TTATCGATGTGCCTTTGGTTTTT	57.539	34.783	8.54	0.00	0.00	1.94
2055	3016	3.612717	GCCTTTGGTTTTTCTGCTAGCTC	60.613	47.826	17.23	0.00	0.00	4.09
2152	3113	2.872245	CACGCTGAGGAAGTTTTCTGAA	59.128	45.455	0.00	0.00	0.00	3.02
2170	3131	5.324409	TCTGAATACTGACTTTTTGGGCAT	58.676	37.500	0.00	0.00	0.00	4.40
2177	3138	5.010282	ACTGACTTTTTGGGCATTAGTAGG	58.990	41.667	0.00	0.00	0.00	3.18
2178	3139	4.993028	TGACTTTTTGGGCATTAGTAGGT	58.007	39.130	0.00	0.00	0.00	3.08
2263	3386	4.023963	GGGAGTTCTGCACACTACTTTTTC	60.024	45.833	3.92	0.00	0.00	2.29
2265	3388	5.297029	GGAGTTCTGCACACTACTTTTTCTT	59.703	40.000	0.00	0.00	0.00	2.52
2267	3390	5.880332	AGTTCTGCACACTACTTTTTCTTGA	59.120	36.000	0.00	0.00	0.00	3.02
2271	3394	6.318648	TCTGCACACTACTTTTTCTTGAACAT	59.681	34.615	0.00	0.00	0.00	2.71
2292	3415	6.040247	ACATAGTACAATCGAAATCGCTCAA	58.960	36.000	0.00	0.00	39.60	3.02
2299	3422	5.121611	ACAATCGAAATCGCTCAAATACACA	59.878	36.000	0.00	0.00	39.60	3.72
2330	3453	0.464373	ACCCCTATGAACGCATGCAG	60.464	55.000	19.57	12.98	35.94	4.41
2360	3483	0.918983	CCCCTATGAGCACCTCCAAA	59.081	55.000	0.00	0.00	0.00	3.28
2366	3489	2.550830	TGAGCACCTCCAAAAGACTC	57.449	50.000	0.00	0.00	0.00	3.36
2386	3509	1.532868	CAGCCGGCATAGCATCTTAAC	59.467	52.381	31.54	0.00	0.00	2.01
2454	3577	0.670546	CCCACTGAACGAACATCGCT	60.671	55.000	0.00	0.00	45.12	4.93
2456	3579	0.179240	CACTGAACGAACATCGCTGC	60.179	55.000	0.00	0.00	45.12	5.25
2546	3669	5.459241	GGTTAGGGATATCACTGTCCTCCTA	60.459	48.000	18.14	6.85	33.34	2.94
2552	3675	6.726764	GGGATATCACTGTCCTCCTAACTATT	59.273	42.308	4.83	0.00	33.34	1.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	6.828785	AGTTGTTTTTGTACTCTCCAATGACT	59.171	34.615	0.00	0.00	0.00	3.41
9	10	7.027778	AGTTGTTTTTGTACTCTCCAATGAC	57.972	36.000	0.00	0.00	0.00	3.06
11	12	9.003658	AGATAGTTGTTTTTGTACTCTCCAATG	57.996	33.333	0.00	0.00	0.00	2.82
21	22	8.630054	ACTGGCATTAGATAGTTGTTTTTGTA	57.370	30.769	0.00	0.00	0.00	2.41
43	44	7.703058	AAAAATCCCATGTTACCTAGAACTG	57.297	36.000	0.00	0.00	0.00	3.16
70	71	7.168219	ACCTACAATGCAATTCACTCTTCTAA	58.832	34.615	0.00	0.00	31.22	2.10
71	72	6.711277	ACCTACAATGCAATTCACTCTTCTA	58.289	36.000	0.00	0.00	31.22	2.10
72	73	5.564550	ACCTACAATGCAATTCACTCTTCT	58.435	37.500	0.00	0.00	31.22	2.85
76	77	3.378427	GGGACCTACAATGCAATTCACTC	59.622	47.826	0.00	0.00	31.22	3.51
100	101	6.238103	CGTACATGACACCATTGAAATACCTC	60.238	42.308	0.00	0.00	0.00	3.85
166	168	9.967451	TTTTGGACCTGAATGATACACTTATTA	57.033	29.630	0.00	0.00	0.00	0.98
170	172	6.947733	TGATTTTGGACCTGAATGATACACTT	59.052	34.615	0.00	0.00	0.00	3.16
176	178	6.012113	TGAACTGATTTTGGACCTGAATGAT	58.988	36.000	0.00	0.00	0.00	2.45
184	186	8.793592	ACTTTAGTATTGAACTGATTTTGGACC	58.206	33.333	0.00	0.00	39.39	4.46
215	217	8.939201	AATGATAGGCAACATATAGATTCTCG	57.061	34.615	0.00	0.00	41.41	4.04
228	230	7.985476	ACAATAAGTGTGTAATGATAGGCAAC	58.015	34.615	0.00	0.00	39.72	4.17
264	266	9.350357	CTCAAACTATGAAAATTGTCATTCAGG	57.650	33.333	16.28	7.49	38.80	3.86
291	293	7.633789	ACTATTTCAGGGATGTCACATAGTTT	58.366	34.615	0.00	0.00	0.00	2.66
301	303	7.177878	ACATCTTTGAACTATTTCAGGGATGT	58.822	34.615	23.64	23.64	46.59	3.06
324	326	8.215050	TCTAAAAAGAGGGAAATTCACAGTACA	58.785	33.333	0.00	0.00	0.00	2.90
333	335	6.014327	TGCATGCTTCTAAAAAGAGGGAAATT	60.014	34.615	20.33	0.00	0.00	1.82
339	341	5.126707	AGGATTGCATGCTTCTAAAAAGAGG	59.873	40.000	20.33	0.00	0.00	3.69
371	373	5.929697	TGATCAGAGACAAACATGTTGTC	57.070	39.130	22.78	22.78	46.71	3.18
429	431	7.857734	TTTCGTCTTCAGAAATGGCATTATA	57.142	32.000	14.05	0.00	33.23	0.98
443	445	1.468565	CGCGAGGGTATTTCGTCTTCA	60.469	52.381	0.00	0.00	40.08	3.02
538	540	2.242043	CCTGCCTGACTGGTTGATTTT	58.758	47.619	0.00	0.00	38.35	1.82
774	1699	4.237843	TGAATGAGGAGGGAGAATATGCT	58.762	43.478	0.00	0.00	0.00	3.79
792	1717	6.984474	CGGAGCGGGTACATATATAAATGAAT	59.016	38.462	0.00	0.00	0.00	2.57
1116	2072	1.153289	CCGGTCCTGCTCCTTGATG	60.153	63.158	0.00	0.00	0.00	3.07
1912	2873	7.041440	TGCCACATAAATATTAATCTGGACACG	60.041	37.037	0.00	0.00	0.00	4.49
2040	3001	7.145932	TCCAAATTAGAGCTAGCAGAAAAAC	57.854	36.000	18.83	0.00	0.00	2.43
2045	3006	7.234371	AGTCATATCCAAATTAGAGCTAGCAGA	59.766	37.037	18.83	0.00	0.00	4.26
2152	3113	6.828785	CCTACTAATGCCCAAAAAGTCAGTAT	59.171	38.462	0.00	0.00	0.00	2.12
2263	3386	6.841286	GCGATTTCGATTGTACTATGTTCAAG	59.159	38.462	3.77	0.00	43.02	3.02
2265	3388	6.040247	AGCGATTTCGATTGTACTATGTTCA	58.960	36.000	3.77	0.00	43.02	3.18
2267	3390	6.040247	TGAGCGATTTCGATTGTACTATGTT	58.960	36.000	3.77	0.00	43.02	2.71
2271	3394	7.703197	TGTATTTGAGCGATTTCGATTGTACTA	59.297	33.333	3.77	0.00	43.02	1.82
2281	3404	4.722194	TGCTTGTGTATTTGAGCGATTTC	58.278	39.130	0.00	0.00	37.94	2.17
2292	3415	4.261801	GGGTGAGTGTATGCTTGTGTATT	58.738	43.478	0.00	0.00	0.00	1.89
2299	3422	3.384168	TCATAGGGGTGAGTGTATGCTT	58.616	45.455	0.00	0.00	0.00	3.91
2330	3453	1.625818	CTCATAGGGGTAGGATGTGCC	59.374	57.143	0.00	0.00	0.00	5.01
2360	3483	1.144936	GCTATGCCGGCTGAGTCTT	59.855	57.895	29.70	6.03	0.00	3.01
2366	3489	1.532868	GTTAAGATGCTATGCCGGCTG	59.467	52.381	29.70	18.36	0.00	4.85
2386	3509	2.476619	GTCTGTGGTGACTTCGTCAATG	59.523	50.000	0.00	0.00	44.49	2.82
2432	3555	1.067846	CGATGTTCGTTCAGTGGGAGA	60.068	52.381	0.00	0.00	34.72	3.71
2454	3577	7.523293	TTCTGGATTTATTTCAGACTTTGCA	57.477	32.000	0.00	0.00	37.28	4.08
2515	3638	5.070580	ACAGTGATATCCCTAACCTACTTGC	59.929	44.000	0.00	0.00	0.00	4.01

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.