AutoCloner

Multiple sequence alignment - TraesCS7D01G429100

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	TraesCS7D01G429100	chr7D	100.000	2360	0	0	1	2360	549122742	549125101	0.000000e+00	4359.0
1	TraesCS7D01G429100	chr7A	93.927	2371	100	19	1	2360	634438751	634441088	0.000000e+00	3541.0
2	TraesCS7D01G429100	chr6B	95.756	542	22	1	846	1387	695057498	695058038	0.000000e+00	872.0
3	TraesCS7D01G429100	chr5D	95.918	539	20	2	846	1383	399327366	399326829	0.000000e+00	872.0
4	TraesCS7D01G429100	chr5D	100.000	34	0	0	2272	2305	52250755	52250722	1.960000e-06	63.9
5	TraesCS7D01G429100	chr3D	95.725	538	23	0	846	1383	69661274	69661811	0.000000e+00	867.0
6	TraesCS7D01G429100	chr3D	73.391	233	48	12	2090	2315	588150508	588150283	9.050000e-10	75.0
7	TraesCS7D01G429100	chr3D	96.970	33	1	0	2276	2308	6434063	6434095	3.280000e-04	56.5
8	TraesCS7D01G429100	chr1A	95.572	542	23	1	846	1387	493004521	493005061	0.000000e+00	867.0
9	TraesCS7D01G429100	chr1A	95.362	539	23	1	846	1384	276801240	276800704	0.000000e+00	856.0
10	TraesCS7D01G429100	chr6A	95.539	538	21	1	846	1383	502340137	502340671	0.000000e+00	857.0
11	TraesCS7D01G429100	chr7B	95.362	539	24	1	846	1384	84528110	84528647	0.000000e+00	856.0
12	TraesCS7D01G429100	chr7B	95.766	496	16	3	256	750	592625489	592625980	0.000000e+00	795.0
13	TraesCS7D01G429100	chr7B	81.818	209	15	10	2	192	592625265	592625468	1.130000e-33	154.0
14	TraesCS7D01G429100	chr7B	91.753	97	8	0	730	826	592626003	592626099	4.090000e-28	135.0
15	TraesCS7D01G429100	chr5A	95.353	538	25	0	846	1383	671960041	671959504	0.000000e+00	856.0
16	TraesCS7D01G429100	chr4B	76.891	238	43	11	2090	2323	139331479	139331708	8.860000e-25	124.0
17	TraesCS7D01G429100	chr2B	79.545	132	21	5	1467	1596	52860890	52860763	3.230000e-14	89.8

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	TraesCS7D01G429100	chr7D	549122742	549125101	2359	False	4359.000000	4359	100.000	1	2360	1	chr7D.!!$F1	2359
1	TraesCS7D01G429100	chr7A	634438751	634441088	2337	False	3541.000000	3541	93.927	1	2360	1	chr7A.!!$F1	2359
2	TraesCS7D01G429100	chr6B	695057498	695058038	540	False	872.000000	872	95.756	846	1387	1	chr6B.!!$F1	541
3	TraesCS7D01G429100	chr5D	399326829	399327366	537	True	872.000000	872	95.918	846	1383	1	chr5D.!!$R2	537
4	TraesCS7D01G429100	chr3D	69661274	69661811	537	False	867.000000	867	95.725	846	1383	1	chr3D.!!$F2	537
5	TraesCS7D01G429100	chr1A	493004521	493005061	540	False	867.000000	867	95.572	846	1387	1	chr1A.!!$F1	541
6	TraesCS7D01G429100	chr1A	276800704	276801240	536	True	856.000000	856	95.362	846	1384	1	chr1A.!!$R1	538
7	TraesCS7D01G429100	chr6A	502340137	502340671	534	False	857.000000	857	95.539	846	1383	1	chr6A.!!$F1	537
8	TraesCS7D01G429100	chr7B	84528110	84528647	537	False	856.000000	856	95.362	846	1384	1	chr7B.!!$F1	538
9	TraesCS7D01G429100	chr7B	592625265	592626099	834	False	361.333333	795	89.779	2	826	3	chr7B.!!$F2	824
10	TraesCS7D01G429100	chr5A	671959504	671960041	537	True	856.000000	856	95.353	846	1383	1	chr5A.!!$R1	537

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
630	639	0.251922	TGCCGGAAGTAGTACACCCT	60.252	55.0	5.05	0.0	0.0	4.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1632	2256	1.072489	TGCTTATCCCGGAAACACACA	59.928	47.619	0.73	0.0	0.0	3.72	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
44	45	9.358123	CAAACATTATCTTAGCTTATTTCGACG	57.642	33.333	0.00	0.00	0.00	5.12
55	56	5.810587	AGCTTATTTCGACGAAGCAATCTTA	59.189	36.000	20.99	0.00	46.46	2.10
137	139	4.414182	AGAAGTCTCTCCTAGCTAGGCTAA	59.586	45.833	31.76	18.73	40.82	3.09
152	154	4.965200	AGGCTAAGCTACTTCCTATTGG	57.035	45.455	0.00	0.00	0.00	3.16
165	167	7.693969	ACTTCCTATTGGTTTTCTTGATCTG	57.306	36.000	0.00	0.00	34.23	2.90
176	178	6.239008	GGTTTTCTTGATCTGTTCATCAACCA	60.239	38.462	0.00	0.00	37.77	3.67
204	206	4.293494	TGAGAAGAGAGGAACCATGCTAT	58.707	43.478	0.00	0.00	0.00	2.97
250	254	4.207955	GGGTAAATAAGAAGGCAGGGAAG	58.792	47.826	0.00	0.00	0.00	3.46
275	279	3.161450	TACCTCGGAGGCCATGGC	61.161	66.667	29.47	29.47	39.63	4.40
297	301	0.459934	GCAGCTACAGCAGGAGTCAG	60.460	60.000	3.70	0.00	45.16	3.51
314	318	1.133637	TCAGGAGGAGAAGATCGGGAG	60.134	57.143	0.00	0.00	0.00	4.30
315	319	1.133637	CAGGAGGAGAAGATCGGGAGA	60.134	57.143	0.00	0.00	46.90	3.71
319	324	1.457009	GGAGAAGATCGGGAGACGGG	61.457	65.000	0.00	0.00	44.82	5.28
365	370	0.737219	GATGATGCCTGCACCTGTTC	59.263	55.000	0.00	0.00	0.00	3.18
381	386	3.119245	CCTGTTCTGGCTTCAATGATTGG	60.119	47.826	5.20	0.00	0.00	3.16
384	389	0.462789	CTGGCTTCAATGATTGGGGC	59.537	55.000	5.20	11.08	0.00	5.80
387	392	1.188863	GCTTCAATGATTGGGGCTGT	58.811	50.000	5.20	0.00	0.00	4.40
391	396	1.002017	AATGATTGGGGCTGTGGGG	59.998	57.895	0.00	0.00	0.00	4.96
435	440	4.530161	CAGGAGGAGGAAGAAGAAGAAGAA	59.470	45.833	0.00	0.00	0.00	2.52
436	441	4.777366	AGGAGGAGGAAGAAGAAGAAGAAG	59.223	45.833	0.00	0.00	0.00	2.85
437	442	4.775253	GGAGGAGGAAGAAGAAGAAGAAGA	59.225	45.833	0.00	0.00	0.00	2.87
537	546	3.052081	CATCCCCCTCGACCGATC	58.948	66.667	0.00	0.00	0.00	3.69
571	580	3.286407	CATTGTTCATGCCGGCCA	58.714	55.556	26.77	11.66	0.00	5.36
572	581	1.140161	CATTGTTCATGCCGGCCAG	59.860	57.895	26.77	16.96	0.00	4.85
573	582	2.713967	ATTGTTCATGCCGGCCAGC	61.714	57.895	26.77	3.21	0.00	4.85
630	639	0.251922	TGCCGGAAGTAGTACACCCT	60.252	55.000	5.05	0.00	0.00	4.34
683	692	1.197036	CTTTTCTTTTCGAGGGGTCGC	59.803	52.381	0.00	0.00	0.00	5.19
698	707	3.069729	GGGGTCGCTGTACATAGATTCTT	59.930	47.826	0.00	0.00	0.00	2.52
789	798	3.706594	CTCTAGGCCCACAACTATGAGAA	59.293	47.826	0.00	0.00	0.00	2.87
820	829	3.483558	CGCTTTGTTTGAGAGCAACTTTC	59.516	43.478	0.00	0.00	36.22	2.62
956	965	3.552684	GCAGCAACATTTGGAGCAGTTAA	60.553	43.478	0.00	0.00	0.00	2.01
1459	2082	0.228742	CACGTCAAGTGGTTCGTTCG	59.771	55.000	0.00	0.00	46.77	3.95
1465	2088	2.928642	AAGTGGTTCGTTCGGCCGTT	62.929	55.000	27.15	4.55	0.00	4.44
1543	2166	6.899114	ACATGTTTCCGAGTTTTAGATGTTC	58.101	36.000	0.00	0.00	0.00	3.18
1671	2295	2.032979	GCACAAATTTGCTTTTCGTGGG	60.033	45.455	18.12	0.00	39.59	4.61
1683	2307	1.996798	TTCGTGGGGGCACAAATTTA	58.003	45.000	0.00	0.00	0.00	1.40
1752	2376	9.971744	AAAAATCACATAATTATTCTTTTGCGC	57.028	25.926	0.00	0.00	0.00	6.09
1821	2445	0.729690	GATTTGCTCCCGTGAGAAGC	59.270	55.000	0.00	0.00	41.42	3.86
1822	2446	0.036732	ATTTGCTCCCGTGAGAAGCA	59.963	50.000	0.00	0.00	41.42	3.91
1823	2447	0.884704	TTTGCTCCCGTGAGAAGCAC	60.885	55.000	0.00	0.00	41.42	4.40
1852	2476	4.202673	TGTGCTTCTAGGGAAGGGAAAAAT	60.203	41.667	7.69	0.00	46.49	1.82
1919	2545	2.948979	TGCTTCTGCGAGAAAAGGAAAA	59.051	40.909	0.00	0.00	43.34	2.29
2039	2665	3.937706	AGAAGCACATACTTGCATCTCAC	59.062	43.478	0.00	0.00	45.12	3.51
2102	2728	5.976458	TGAAACTGGCATTAAAATGGGATC	58.024	37.500	4.93	0.00	36.90	3.36
2105	2731	7.564660	TGAAACTGGCATTAAAATGGGATCTAT	59.435	33.333	4.93	0.00	36.90	1.98
2110	2736	7.432869	TGGCATTAAAATGGGATCTATTTTCG	58.567	34.615	18.12	12.27	38.36	3.46
2149	2775	4.503741	AGTCCAATGGTGAAAACGATTG	57.496	40.909	0.00	6.61	36.17	2.67
2172	2798	1.614996	ATTTGGACACATGGTGCGAA	58.385	45.000	9.72	9.72	44.21	4.70
2174	2800	1.502990	TTGGACACATGGTGCGAACG	61.503	55.000	0.00	0.00	41.41	3.95
2268	2894	0.941542	GCAGTACGCCACTTGTCAAA	59.058	50.000	0.00	0.00	34.26	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
34	35	7.591006	AAGTAAGATTGCTTCGTCGAAATAA	57.409	32.000	9.30	7.48	35.56	1.40
43	44	5.675970	TCGTCAAAAAGTAAGATTGCTTCG	58.324	37.500	0.00	0.00	35.56	3.79
44	45	7.803189	TCATTCGTCAAAAAGTAAGATTGCTTC	59.197	33.333	0.00	0.00	35.56	3.86
55	56	8.237267	GGATTAGTTGATCATTCGTCAAAAAGT	58.763	33.333	0.00	0.00	37.34	2.66
137	139	6.779860	TCAAGAAAACCAATAGGAAGTAGCT	58.220	36.000	0.00	0.00	38.69	3.32
152	154	6.738114	TGGTTGATGAACAGATCAAGAAAAC	58.262	36.000	0.00	0.00	41.85	2.43
165	167	7.604164	TCTCTTCTCAGTTATTGGTTGATGAAC	59.396	37.037	0.00	0.00	0.00	3.18
176	178	6.648192	CATGGTTCCTCTCTTCTCAGTTATT	58.352	40.000	0.00	0.00	0.00	1.40
204	206	8.313292	CCCAACATCTCTTTTTATGATTTTCCA	58.687	33.333	0.00	0.00	0.00	3.53
250	254	1.465200	GCCTCCGAGGTACCATCTCC	61.465	65.000	15.94	0.00	37.80	3.71
275	279	1.153409	CTCCTGCTGTAGCTGCCAG	60.153	63.158	10.08	10.08	42.66	4.85
282	286	1.110442	CCTCCTGACTCCTGCTGTAG	58.890	60.000	0.00	0.00	0.00	2.74
284	288	0.614415	CTCCTCCTGACTCCTGCTGT	60.614	60.000	0.00	0.00	0.00	4.40
297	301	1.324383	GTCTCCCGATCTTCTCCTCC	58.676	60.000	0.00	0.00	0.00	4.30
314	318	1.008767	GACGACATCGATCCCCGTC	60.009	63.158	20.46	20.46	43.02	4.79
315	319	3.117372	GACGACATCGATCCCCGT	58.883	61.111	8.54	13.77	43.02	5.28
365	370	0.462789	GCCCCAATCATTGAAGCCAG	59.537	55.000	0.00	0.00	0.00	4.85
381	386	2.757980	TTTAAGTCGCCCCACAGCCC	62.758	60.000	0.00	0.00	0.00	5.19
384	389	3.195661	GTCTATTTAAGTCGCCCCACAG	58.804	50.000	0.00	0.00	0.00	3.66
387	392	2.589798	CGTCTATTTAAGTCGCCCCA	57.410	50.000	0.00	0.00	30.29	4.96
394	399	2.420129	CCTGGCAGGCGTCTATTTAAGT	60.420	50.000	22.68	0.00	0.00	2.24
435	440	1.141881	CCTTCCGTGCTACGCATCT	59.858	57.895	3.56	0.00	41.91	2.90
436	441	1.883084	CCCTTCCGTGCTACGCATC	60.883	63.158	3.56	0.00	41.91	3.91
437	442	1.895020	TTCCCTTCCGTGCTACGCAT	61.895	55.000	3.56	0.00	41.91	4.73
447	452	0.250727	TTCCTTGTGCTTCCCTTCCG	60.251	55.000	0.00	0.00	0.00	4.30
537	546	1.544825	ATGCCCATCCCTACCGATCG	61.545	60.000	8.51	8.51	0.00	3.69
581	590	3.058160	CTCCCAAGCCAACGCAGG	61.058	66.667	0.00	0.00	37.52	4.85
582	591	3.058160	CCTCCCAAGCCAACGCAG	61.058	66.667	0.00	0.00	37.52	5.18
698	707	2.202395	GCTGCTGGCCTTGGAAACA	61.202	57.895	3.32	0.00	34.39	2.83
789	798	2.193536	AAACAAAGCGCGCTTCCCT	61.194	52.632	42.82	27.36	34.84	4.20
820	829	1.202806	TGCTCTCAGACACCCCAAAAG	60.203	52.381	0.00	0.00	0.00	2.27
908	917	3.001228	TGTGTCATTATCAAATCTCGCGC	59.999	43.478	0.00	0.00	0.00	6.86
1527	2150	7.639945	ACTGAAAAAGAACATCTAAAACTCGG	58.360	34.615	0.00	0.00	0.00	4.63
1556	2180	5.648960	CCTAGGAAAACCAGGCGTAAATAAA	59.351	40.000	1.05	0.00	0.00	1.40
1558	2182	4.225717	ACCTAGGAAAACCAGGCGTAAATA	59.774	41.667	17.98	0.00	32.31	1.40
1560	2184	2.372837	ACCTAGGAAAACCAGGCGTAAA	59.627	45.455	17.98	0.00	32.31	2.01
1565	2189	2.299013	CCAAAACCTAGGAAAACCAGGC	59.701	50.000	17.98	0.00	32.31	4.85
1566	2190	3.826729	CTCCAAAACCTAGGAAAACCAGG	59.173	47.826	17.98	7.80	32.57	4.45
1630	2254	2.554893	GCTTATCCCGGAAACACACAAA	59.445	45.455	0.73	0.00	0.00	2.83
1631	2255	2.156098	GCTTATCCCGGAAACACACAA	58.844	47.619	0.73	0.00	0.00	3.33
1632	2256	1.072489	TGCTTATCCCGGAAACACACA	59.928	47.619	0.73	0.00	0.00	3.72
1633	2257	1.467342	GTGCTTATCCCGGAAACACAC	59.533	52.381	0.73	0.00	0.00	3.82
1638	2262	4.815269	CAAATTTGTGCTTATCCCGGAAA	58.185	39.130	0.73	0.00	0.00	3.13
1671	2295	4.095782	TCTCGCATAAGTAAATTTGTGCCC	59.904	41.667	0.00	0.00	40.69	5.36
1744	2368	1.522258	AGCAAAAACATCGCGCAAAAG	59.478	42.857	8.75	0.00	0.00	2.27
1752	2376	2.223144	TCTCGTGGAAGCAAAAACATCG	59.777	45.455	0.00	0.00	0.00	3.84
1822	2446	4.080863	CCTTCCCTAGAAGCACAACTATGT	60.081	45.833	0.00	0.00	46.97	2.29
1823	2447	4.446371	CCTTCCCTAGAAGCACAACTATG	58.554	47.826	0.00	0.00	46.97	2.23
1824	2448	3.456277	CCCTTCCCTAGAAGCACAACTAT	59.544	47.826	0.00	0.00	46.97	2.12
1825	2449	2.838202	CCCTTCCCTAGAAGCACAACTA	59.162	50.000	0.00	0.00	46.97	2.24
1826	2450	1.630878	CCCTTCCCTAGAAGCACAACT	59.369	52.381	0.00	0.00	46.97	3.16
1827	2451	1.628846	TCCCTTCCCTAGAAGCACAAC	59.371	52.381	0.00	0.00	46.97	3.32
1919	2545	5.984926	AGTTCACGCAAACAAATCATGATTT	59.015	32.000	24.83	24.83	41.33	2.17
2057	2683	9.771534	TTTCAACTTCTTTTCCTTTTCAAGAAA	57.228	25.926	0.00	0.00	36.37	2.52
2074	2700	6.147656	CCCATTTTAATGCCAGTTTCAACTTC	59.852	38.462	0.00	0.00	34.46	3.01
2102	2728	3.594467	CGCGTCGAGATCTACGAAAATAG	59.406	47.826	19.67	9.89	41.55	1.73
2105	2731	1.394572	TCGCGTCGAGATCTACGAAAA	59.605	47.619	19.67	3.49	41.55	2.29
2129	2755	4.497473	TCAATCGTTTTCACCATTGGAC	57.503	40.909	10.37	0.00	0.00	4.02
2131	2757	6.783892	ATTTTCAATCGTTTTCACCATTGG	57.216	33.333	0.00	0.00	0.00	3.16
2149	2775	2.730928	CGCACCATGTGTCCAAATTTTC	59.269	45.455	0.00	0.00	35.75	2.29
2268	2894	2.638363	GGTTACTCCCACCTTCTCAACT	59.362	50.000	0.00	0.00	0.00	3.16
2270	2896	2.986050	AGGTTACTCCCACCTTCTCAA	58.014	47.619	0.00	0.00	42.45	3.02
2302	2928	2.236395	CCGAAATCACTAGTTCAGGGGT	59.764	50.000	0.00	0.00	30.10	4.95

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.