AutoCloner

Multiple sequence alignment - TraesCS6A01G019900

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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	TraesCS6A01G019900	chr6A	100.000	2714	0	0	1	2714	9354625	9357338	0.000000e+00	5012
1	TraesCS6A01G019900	chr6A	88.528	1447	162	4	686	2132	9461583	9463025	0.000000e+00	1749
2	TraesCS6A01G019900	chr6B	89.995	2039	185	8	691	2714	15397818	15395784	0.000000e+00	2617
3	TraesCS6A01G019900	chr6B	87.996	2041	167	26	686	2714	670592571	670590597	0.000000e+00	2340
4	TraesCS6A01G019900	chr6B	81.803	610	77	15	2132	2714	16269016	16269618	5.260000e-132	481
5	TraesCS6A01G019900	chr6B	79.935	618	84	20	2132	2714	15233174	15232562	4.180000e-113	418
6	TraesCS6A01G019900	chr6B	78.723	611	75	13	1939	2504	90940906	90941506	9.240000e-95	357
7	TraesCS6A01G019900	chr6B	78.049	615	77	16	1939	2507	15215462	15214860	4.330000e-88	335
8	TraesCS6A01G019900	chr6B	80.864	324	46	11	2404	2714	16238726	16239046	9.710000e-60	241
9	TraesCS6A01G019900	chr2B	89.326	2033	203	7	691	2714	709569631	709567604	0.000000e+00	2540
10	TraesCS6A01G019900	chr2B	83.852	1381	190	22	686	2056	54016534	54015177	0.000000e+00	1284
11	TraesCS6A01G019900	chr2B	83.852	1381	186	23	686	2056	54043886	54042533	0.000000e+00	1280
12	TraesCS6A01G019900	chr2B	79.593	1279	192	29	1287	2522	89491345	89492597	0.000000e+00	852
13	TraesCS6A01G019900	chr5B	88.846	2062	178	25	686	2714	556795628	556793586	0.000000e+00	2486
14	TraesCS6A01G019900	chr5B	88.462	156	16	2	2560	2714	556624421	556624267	1.280000e-43	187
15	TraesCS6A01G019900	chr6D	86.835	1937	231	16	686	2607	33895167	33897094	0.000000e+00	2143
16	TraesCS6A01G019900	chr6D	91.915	804	44	6	1926	2714	8567307	8566510	0.000000e+00	1105
17	TraesCS6A01G019900	chr6D	80.209	1051	194	12	686	1728	8967708	8968752	0.000000e+00	776
18	TraesCS6A01G019900	chr6D	78.261	1035	212	10	686	1712	8899640	8900669	0.000000e+00	652
19	TraesCS6A01G019900	chr6D	77.895	1045	206	18	686	1722	7718999	7720026	6.380000e-176	627
20	TraesCS6A01G019900	chrUn	84.353	1259	190	5	749	2006	95438043	95439295	0.000000e+00	1227
21	TraesCS6A01G019900	chr1A	93.027	674	47	0	2	675	506297338	506296665	0.000000e+00	985
22	TraesCS6A01G019900	chr7D	90.222	675	64	2	2	675	51258155	51258828	0.000000e+00	880
23	TraesCS6A01G019900	chr7D	86.053	674	94	0	2	675	597126764	597126091	0.000000e+00	725
24	TraesCS6A01G019900	chr7A	85.757	674	96	0	2	675	721884233	721883560	0.000000e+00	713
25	TraesCS6A01G019900	chr5D	79.806	619	64	26	2132	2714	42077645	42078238	7.040000e-106	394
26	TraesCS6A01G019900	chr5D	82.207	444	46	13	2280	2693	499863241	499862801	4.300000e-93	351
27	TraesCS6A01G019900	chr7B	88.387	155	18	0	521	675	706221291	706221445	1.280000e-43	187

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	TraesCS6A01G019900	chr6A	9354625	9357338	2713	False	5012	5012	100.000	1	2714	1	chr6A.!!$F1	2713
1	TraesCS6A01G019900	chr6A	9461583	9463025	1442	False	1749	1749	88.528	686	2132	1	chr6A.!!$F2	1446
2	TraesCS6A01G019900	chr6B	15395784	15397818	2034	True	2617	2617	89.995	691	2714	1	chr6B.!!$R3	2023
3	TraesCS6A01G019900	chr6B	670590597	670592571	1974	True	2340	2340	87.996	686	2714	1	chr6B.!!$R4	2028
4	TraesCS6A01G019900	chr6B	16269016	16269618	602	False	481	481	81.803	2132	2714	1	chr6B.!!$F2	582
5	TraesCS6A01G019900	chr6B	15232562	15233174	612	True	418	418	79.935	2132	2714	1	chr6B.!!$R2	582
6	TraesCS6A01G019900	chr6B	90940906	90941506	600	False	357	357	78.723	1939	2504	1	chr6B.!!$F3	565
7	TraesCS6A01G019900	chr6B	15214860	15215462	602	True	335	335	78.049	1939	2507	1	chr6B.!!$R1	568
8	TraesCS6A01G019900	chr2B	709567604	709569631	2027	True	2540	2540	89.326	691	2714	1	chr2B.!!$R3	2023
9	TraesCS6A01G019900	chr2B	54015177	54016534	1357	True	1284	1284	83.852	686	2056	1	chr2B.!!$R1	1370
10	TraesCS6A01G019900	chr2B	54042533	54043886	1353	True	1280	1280	83.852	686	2056	1	chr2B.!!$R2	1370
11	TraesCS6A01G019900	chr2B	89491345	89492597	1252	False	852	852	79.593	1287	2522	1	chr2B.!!$F1	1235
12	TraesCS6A01G019900	chr5B	556793586	556795628	2042	True	2486	2486	88.846	686	2714	1	chr5B.!!$R2	2028
13	TraesCS6A01G019900	chr6D	33895167	33897094	1927	False	2143	2143	86.835	686	2607	1	chr6D.!!$F4	1921
14	TraesCS6A01G019900	chr6D	8566510	8567307	797	True	1105	1105	91.915	1926	2714	1	chr6D.!!$R1	788
15	TraesCS6A01G019900	chr6D	8967708	8968752	1044	False	776	776	80.209	686	1728	1	chr6D.!!$F3	1042
16	TraesCS6A01G019900	chr6D	8899640	8900669	1029	False	652	652	78.261	686	1712	1	chr6D.!!$F2	1026
17	TraesCS6A01G019900	chr6D	7718999	7720026	1027	False	627	627	77.895	686	1722	1	chr6D.!!$F1	1036
18	TraesCS6A01G019900	chrUn	95438043	95439295	1252	False	1227	1227	84.353	749	2006	1	chrUn.!!$F1	1257
19	TraesCS6A01G019900	chr1A	506296665	506297338	673	True	985	985	93.027	2	675	1	chr1A.!!$R1	673
20	TraesCS6A01G019900	chr7D	51258155	51258828	673	False	880	880	90.222	2	675	1	chr7D.!!$F1	673
21	TraesCS6A01G019900	chr7D	597126091	597126764	673	True	725	725	86.053	2	675	1	chr7D.!!$R1	673
22	TraesCS6A01G019900	chr7A	721883560	721884233	673	True	713	713	85.757	2	675	1	chr7A.!!$R1	673
23	TraesCS6A01G019900	chr5D	42077645	42078238	593	False	394	394	79.806	2132	2714	1	chr5D.!!$F1	582

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
291	292	0.323999	TCCTTACAGCGGACAGGCTA	60.324	55.0	0.0	0.0	42.53	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2018	2048	1.272147	GCCCACAAATGAAGGAGACCT	60.272	52.381	0.0	0.0	33.87	3.85	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
126	127	4.689062	AGGATGTCTTCTCCTGGAAACTA	58.311	43.478	0.00	0.00	41.66	2.24
141	142	3.335579	GAAACTAACGGAGTCAGGCATT	58.664	45.455	0.00	0.00	45.00	3.56
291	292	0.323999	TCCTTACAGCGGACAGGCTA	60.324	55.000	0.00	0.00	42.53	3.93
435	436	4.142182	CGTTTTCAATTACCCTCATGCCAT	60.142	41.667	0.00	0.00	0.00	4.40
501	502	2.548587	GATTGACGACCAACGCAGCG	62.549	60.000	14.82	14.82	46.94	5.18
558	560	2.238847	CTTGGACGATCTGGGGCGAA	62.239	60.000	0.00	0.00	0.00	4.70
573	575	1.135774	GGCGAAAGAAACAACCGGATC	60.136	52.381	9.46	0.00	0.00	3.36
594	596	0.537188	TCAGAGGCCAAGAACGATCC	59.463	55.000	5.01	0.00	0.00	3.36
675	677	4.115279	CACTTGATGCCGCGAGAT	57.885	55.556	8.23	0.00	0.00	2.75
676	678	1.930100	CACTTGATGCCGCGAGATC	59.070	57.895	8.23	9.14	0.00	2.75
677	679	0.807275	CACTTGATGCCGCGAGATCA	60.807	55.000	8.23	11.97	0.00	2.92
678	680	0.807667	ACTTGATGCCGCGAGATCAC	60.808	55.000	8.23	0.00	0.00	3.06
679	681	0.807275	CTTGATGCCGCGAGATCACA	60.807	55.000	8.23	5.11	0.00	3.58
680	682	0.390998	TTGATGCCGCGAGATCACAA	60.391	50.000	8.23	3.46	0.00	3.33
681	683	1.083806	TGATGCCGCGAGATCACAAC	61.084	55.000	8.23	0.00	0.00	3.32
682	684	1.766143	GATGCCGCGAGATCACAACC	61.766	60.000	8.23	0.00	0.00	3.77
683	685	2.125512	GCCGCGAGATCACAACCT	60.126	61.111	8.23	0.00	0.00	3.50
684	686	2.456119	GCCGCGAGATCACAACCTG	61.456	63.158	8.23	0.00	0.00	4.00
741	743	4.323477	CGACCCCAGGCCGTCAAA	62.323	66.667	8.90	0.00	0.00	2.69
952	954	4.862092	CTGACATCGCGCGCCTCT	62.862	66.667	27.95	7.27	0.00	3.69
979	981	2.478746	CCGTCCACAAATTCCGCG	59.521	61.111	0.00	0.00	0.00	6.46
1034	1040	4.547859	CCTCTTTGGCTCATCCGG	57.452	61.111	0.00	0.00	37.80	5.14
1184	1194	3.936203	ACCGAGGTTGCTCGCCAA	61.936	61.111	0.00	0.00	44.60	4.52
1266	1276	0.811616	CTAGGATGTTCAGGCACGCC	60.812	60.000	0.00	0.00	0.00	5.68
1530	1552	1.069258	GCCCCGGTACTATGCTGTC	59.931	63.158	0.00	0.00	0.00	3.51
1616	1638	3.198635	TCCGAGAAGGCATTCAAGAAGAT	59.801	43.478	14.34	0.00	40.77	2.40
1873	1895	4.461781	CAGCAGAGAAGAAACCATGGATTT	59.538	41.667	21.47	14.95	0.00	2.17
1875	1897	4.460382	GCAGAGAAGAAACCATGGATTTGA	59.540	41.667	21.47	0.00	0.00	2.69
1879	1901	8.566260	CAGAGAAGAAACCATGGATTTGATATC	58.434	37.037	21.47	9.85	0.00	1.63
1883	1905	8.599624	AAGAAACCATGGATTTGATATCAACT	57.400	30.769	21.47	12.72	35.28	3.16
2013	2043	4.096833	TGTGCATTGAGATAATGAGCCAAC	59.903	41.667	3.97	0.00	0.00	3.77
2018	2048	6.458206	GCATTGAGATAATGAGCCAACGTAAA	60.458	38.462	3.97	0.00	0.00	2.01
2038	2068	1.177401	GGTCTCCTTCATTTGTGGGC	58.823	55.000	0.00	0.00	0.00	5.36
2065	2095	7.418337	TGCATTCCTAATGTTCTACTACTGA	57.582	36.000	1.94	0.00	41.01	3.41
2072	2102	8.540388	TCCTAATGTTCTACTACTGATTTTGCT	58.460	33.333	0.00	0.00	0.00	3.91
2094	2124	8.023021	TGCTACTCATAGTGGATAATTTGAGT	57.977	34.615	9.44	9.44	42.73	3.41
2178	2234	9.619316	TTCAGTTATGGTTTGACATAAAAATCG	57.381	29.630	0.00	0.00	42.92	3.34
2531	2625	0.952984	AGAAGCACTTGCCGCTCTTC	60.953	55.000	0.00	0.00	43.38	2.87
2610	2767	5.590530	TTATGTGTTTATTGTGGATGGCC	57.409	39.130	0.00	0.00	0.00	5.36
2697	2854	3.516615	CAGAAGGTTCACTAGCAGCTAC	58.483	50.000	0.00	0.00	0.00	3.58
2700	2857	1.473278	AGGTTCACTAGCAGCTACGTC	59.527	52.381	0.00	0.00	0.00	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	2.041922	ACATCCCGCTCCCAGCTA	60.042	61.111	0.00	0.00	39.60	3.32
48	49	2.226437	CGTCCAGAGGTTGACAAATTGG	59.774	50.000	0.00	0.00	0.00	3.16
93	94	1.826024	GACATCCTGTCCTGCCGAT	59.174	57.895	0.00	0.00	41.37	4.18
126	127	2.427506	GAGAAAATGCCTGACTCCGTT	58.572	47.619	0.00	0.00	0.00	4.44
141	142	1.667830	CGCCGAGCTTGTGGAGAAA	60.668	57.895	0.00	0.00	0.00	2.52
291	292	3.939564	GGCCATTTCCTCGCCATT	58.060	55.556	0.00	0.00	42.52	3.16
390	391	2.830370	GCTCCCATCGCCCAAAGG	60.830	66.667	0.00	0.00	0.00	3.11
393	394	2.329539	GATCAGCTCCCATCGCCCAA	62.330	60.000	0.00	0.00	0.00	4.12
405	406	4.589908	AGGGTAATTGAAAACGATCAGCT	58.410	39.130	0.00	0.00	0.00	4.24
558	560	4.319177	CTCTGAAGATCCGGTTGTTTCTT	58.681	43.478	0.00	3.79	0.00	2.52
573	575	2.275318	GATCGTTCTTGGCCTCTGAAG	58.725	52.381	3.32	0.00	0.00	3.02
594	596	0.453793	AGTCCATTGCTCTCTCGACG	59.546	55.000	0.00	0.00	0.00	5.12
675	677	3.164977	TCCACGGCCAGGTTGTGA	61.165	61.111	13.20	0.00	35.66	3.58
676	678	2.669569	CTCCACGGCCAGGTTGTG	60.670	66.667	2.24	1.52	0.00	3.33
677	679	3.953775	CCTCCACGGCCAGGTTGT	61.954	66.667	2.24	0.00	0.00	3.32
678	680	3.612247	CTCCTCCACGGCCAGGTTG	62.612	68.421	2.24	2.02	0.00	3.77
679	681	2.741878	TACTCCTCCACGGCCAGGTT	62.742	60.000	2.24	0.00	0.00	3.50
680	682	3.233919	TACTCCTCCACGGCCAGGT	62.234	63.158	2.24	0.00	0.00	4.00
681	683	2.363795	TACTCCTCCACGGCCAGG	60.364	66.667	2.24	3.74	0.00	4.45
682	684	2.722201	GGTACTCCTCCACGGCCAG	61.722	68.421	2.24	0.00	0.00	4.85
683	685	2.682494	GGTACTCCTCCACGGCCA	60.682	66.667	2.24	0.00	0.00	5.36
684	686	2.363925	AGGTACTCCTCCACGGCC	60.364	66.667	0.00	0.00	40.58	6.13
741	743	2.668120	GGAGAGCTTGGCAGAGGCT	61.668	63.158	10.55	10.55	40.87	4.58
747	749	2.530151	AGGTGGGAGAGCTTGGCA	60.530	61.111	0.00	0.00	0.00	4.92
985	987	1.059098	TGCATCTTGGAGACCACAGT	58.941	50.000	0.00	0.00	30.78	3.55
1000	1003	1.144057	GGCGCAGGTAGTAGTGCAT	59.856	57.895	10.83	0.00	42.73	3.96
1029	1032	3.470888	CGGAGGAGGTTGCCGGAT	61.471	66.667	5.05	0.00	41.29	4.18
1128	1138	5.372343	TGGCAATATCACAATCACCTAGT	57.628	39.130	0.00	0.00	0.00	2.57
1184	1194	2.397413	CTGGAGACGCTTGGGGTTGT	62.397	60.000	0.00	0.00	0.00	3.32
1282	1292	3.573967	GCTATCTCCTCCTCTCTGAAAGG	59.426	52.174	0.00	0.00	35.05	3.11
1530	1552	6.146673	GCAATCCATTTTCCTTGAGAAACTTG	59.853	38.462	0.00	0.00	44.20	3.16
1616	1638	5.629133	GCTTCCTTATGAGGGTGTATGAACA	60.629	44.000	3.28	0.00	43.72	3.18
1919	1945	6.925211	TGATCTCACACTTACTTAGTTCCAG	58.075	40.000	0.00	0.00	33.85	3.86
2013	2043	4.154195	CCACAAATGAAGGAGACCTTTACG	59.846	45.833	4.51	0.00	44.82	3.18
2018	2048	1.272147	GCCCACAAATGAAGGAGACCT	60.272	52.381	0.00	0.00	33.87	3.85
2038	2068	8.554528	CAGTAGTAGAACATTAGGAATGCATTG	58.445	37.037	18.59	4.26	42.69	2.82
2094	2124	5.661503	TTGGGAAGGGCATCAGATTTATA	57.338	39.130	0.00	0.00	0.00	0.98
2250	2312	6.256757	GCAGACACCTTCTATAGTTGAATGAC	59.743	42.308	0.00	0.00	31.12	3.06
2466	2560	5.564550	AGCATAAGAATGGACAGACAAACT	58.435	37.500	0.00	0.00	33.38	2.66
2638	2795	4.034285	AGAATTACCCACAGGACCAAAG	57.966	45.455	0.00	0.00	36.73	2.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.