AutoCloner

Multiple sequence alignment - TraesCS4D01G160900

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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	TraesCS4D01G160900	chr4D	100.000	2464	0	0	1	2464	240982006	240979543	0.000000e+00	4551
1	TraesCS4D01G160900	chr4D	97.049	1796	52	1	1	1795	123450063	123448268	0.000000e+00	3022
2	TraesCS4D01G160900	chr4D	96.868	479	15	0	1792	2270	123578269	123578747	0.000000e+00	802
3	TraesCS4D01G160900	chr4D	96.569	204	6	1	2261	2464	123579954	123580156	1.090000e-88	337
4	TraesCS4D01G160900	chrUn	97.044	1793	52	1	1	1792	217906591	217908383	0.000000e+00	3016
5	TraesCS4D01G160900	chrUn	96.660	479	16	0	1792	2270	273238474	273238952	0.000000e+00	797
6	TraesCS4D01G160900	chr3B	96.993	1796	53	1	1	1795	6011843	6010048	0.000000e+00	3016
7	TraesCS4D01G160900	chr3B	96.993	1796	50	3	1	1795	92297809	92296017	0.000000e+00	3014
8	TraesCS4D01G160900	chr3A	96.993	1796	53	1	1	1795	495105837	495104042	0.000000e+00	3016
9	TraesCS4D01G160900	chr7A	96.882	1796	55	1	1	1795	563523175	563521380	0.000000e+00	3005
10	TraesCS4D01G160900	chr7A	96.825	1795	56	1	2	1795	708281822	708280028	0.000000e+00	2998
11	TraesCS4D01G160900	chr7A	97.077	479	14	0	1792	2270	671960891	671960413	0.000000e+00	808
12	TraesCS4D01G160900	chr7A	97.059	204	5	1	2261	2464	734973234	734973032	2.350000e-90	342
13	TraesCS4D01G160900	chr2B	96.882	1796	55	1	1	1795	234542237	234540442	0.000000e+00	3005
14	TraesCS4D01G160900	chr6D	96.711	1794	56	3	1	1792	108484131	108485923	0.000000e+00	2983
15	TraesCS4D01G160900	chr3D	97.077	479	14	0	1792	2270	501827495	501827017	0.000000e+00	808
16	TraesCS4D01G160900	chr3D	96.868	479	15	0	1792	2270	202611623	202612101	0.000000e+00	802
17	TraesCS4D01G160900	chr7B	96.868	479	15	0	1792	2270	743065982	743066460	0.000000e+00	802
18	TraesCS4D01G160900	chr5A	96.868	479	15	0	1792	2270	16623598	16623120	0.000000e+00	802
19	TraesCS4D01G160900	chr5A	96.569	204	6	1	2261	2464	16621910	16621708	1.090000e-88	337
20	TraesCS4D01G160900	chr5A	96.569	204	6	1	2261	2464	300049929	300050131	1.090000e-88	337
21	TraesCS4D01G160900	chr5A	96.569	204	6	1	2261	2464	341687778	341687576	1.090000e-88	337
22	TraesCS4D01G160900	chr4A	96.868	479	15	0	1792	2270	67555240	67554762	0.000000e+00	802
23	TraesCS4D01G160900	chr2D	96.660	479	16	0	1792	2270	635036937	635037415	0.000000e+00	797
24	TraesCS4D01G160900	chr2D	96.569	204	6	1	2261	2464	17965825	17965623	1.090000e-88	337
25	TraesCS4D01G160900	chr2D	96.569	204	6	1	2261	2464	635038621	635038823	1.090000e-88	337
26	TraesCS4D01G160900	chr7D	96.078	204	7	1	2261	2464	382013509	382013307	5.080000e-87	331
27	TraesCS4D01G160900	chr1B	96.078	204	6	2	2261	2464	461453586	461453787	5.080000e-87	331

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	TraesCS4D01G160900	chr4D	240979543	240982006	2463	True	4551.0	4551	100.0000	1	2464	1	chr4D.!!$R2	2463
1	TraesCS4D01G160900	chr4D	123448268	123450063	1795	True	3022.0	3022	97.0490	1	1795	1	chr4D.!!$R1	1794
2	TraesCS4D01G160900	chr4D	123578269	123580156	1887	False	569.5	802	96.7185	1792	2464	2	chr4D.!!$F1	672
3	TraesCS4D01G160900	chrUn	217906591	217908383	1792	False	3016.0	3016	97.0440	1	1792	1	chrUn.!!$F1	1791
4	TraesCS4D01G160900	chr3B	6010048	6011843	1795	True	3016.0	3016	96.9930	1	1795	1	chr3B.!!$R1	1794
5	TraesCS4D01G160900	chr3B	92296017	92297809	1792	True	3014.0	3014	96.9930	1	1795	1	chr3B.!!$R2	1794
6	TraesCS4D01G160900	chr3A	495104042	495105837	1795	True	3016.0	3016	96.9930	1	1795	1	chr3A.!!$R1	1794
7	TraesCS4D01G160900	chr7A	563521380	563523175	1795	True	3005.0	3005	96.8820	1	1795	1	chr7A.!!$R1	1794
8	TraesCS4D01G160900	chr7A	708280028	708281822	1794	True	2998.0	2998	96.8250	2	1795	1	chr7A.!!$R3	1793
9	TraesCS4D01G160900	chr2B	234540442	234542237	1795	True	3005.0	3005	96.8820	1	1795	1	chr2B.!!$R1	1794
10	TraesCS4D01G160900	chr6D	108484131	108485923	1792	False	2983.0	2983	96.7110	1	1792	1	chr6D.!!$F1	1791
11	TraesCS4D01G160900	chr5A	16621708	16623598	1890	True	569.5	802	96.7185	1792	2464	2	chr5A.!!$R2	672
12	TraesCS4D01G160900	chr2D	635036937	635038823	1886	False	567.0	797	96.6145	1792	2464	2	chr2D.!!$F1	672

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
481	482	0.175302	CGCCAGTGATTCTCTGAGCT	59.825	55.0	15.54	0.0	35.2	4.09	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2413	3634	0.111639	GGGGGTTTACTGCACAAGGA	59.888	55.0	0.0	0.0	0.0	3.36	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
149	150	2.603473	TCGTGGTACCTGCTGCCT	60.603	61.111	14.36	0.00	0.00	4.75
180	181	4.647611	TCCACTTTGATAACCGTGTGAAT	58.352	39.130	0.00	0.00	0.00	2.57
251	252	2.159819	TTGAGCAGTGCGGGAGACTC	62.160	60.000	10.00	0.00	0.00	3.36
302	303	3.123804	CCGATTAAATCACAGACGAGGG	58.876	50.000	0.00	0.00	0.00	4.30
414	415	4.666907	AGGGATGGAATGGTCAATAGTCAT	59.333	41.667	0.00	0.00	0.00	3.06
448	449	2.214347	TCTTTGTTGGCGAAACGATGA	58.786	42.857	0.00	0.00	42.10	2.92
481	482	0.175302	CGCCAGTGATTCTCTGAGCT	59.825	55.000	15.54	0.00	35.20	4.09
555	557	5.104652	CCTTTTTATCCTCTTCCTTACCGGA	60.105	44.000	9.46	0.00	41.06	5.14
652	654	2.232941	CCATTCATTTCTGCAAGCAGGT	59.767	45.455	20.78	6.04	43.75	4.00
692	694	0.250081	CCTCCTAATCGAAGCCAGGC	60.250	60.000	1.84	1.84	0.00	4.85
739	741	1.600916	GTTTGGCTCCACGAAGGCT	60.601	57.895	10.80	0.00	42.10	4.58
776	778	3.011708	AGCCCCACTCATATTCAAAAGGT	59.988	43.478	0.00	0.00	0.00	3.50
879	881	2.092212	CCAGTGGGAGAGCCATGTTATT	60.092	50.000	0.00	0.00	35.59	1.40
908	910	0.322975	ATTGCACGGTTCAGAGAGCT	59.677	50.000	0.00	0.00	0.00	4.09
946	948	4.725737	GCAAGTGAACGTGTACGAAAAAGT	60.726	41.667	11.79	0.00	43.02	2.66
966	968	6.645700	AAGTTGTCGTAAAGTTTCGTTGTA	57.354	33.333	0.00	0.00	0.00	2.41
979	981	1.261885	TCGTTGTACGTTCCGTCGTTA	59.738	47.619	0.00	0.00	43.14	3.18
997	999	6.417044	CGTCGTTAACCCTATCTATGTTTCTG	59.583	42.308	0.00	0.00	0.00	3.02
1030	1032	0.035317	ACACGCTCATTCTTCAGCCA	59.965	50.000	0.00	0.00	31.37	4.75
1035	1037	3.118629	ACGCTCATTCTTCAGCCATAGAA	60.119	43.478	0.00	0.00	35.08	2.10
1159	1162	2.832643	ATGGATGTGGGAGCATCAAA	57.167	45.000	8.11	0.00	45.11	2.69
1228	1231	1.838073	GAAAGAGTCCCGGGAGCCAA	61.838	60.000	27.72	0.00	0.00	4.52
1320	1323	5.867903	TGATTCCTCCACACAACAATTTT	57.132	34.783	0.00	0.00	0.00	1.82
1404	1407	8.777578	ATTAGTGGATATTGGTACTGTCACTA	57.222	34.615	0.00	0.00	36.00	2.74
1457	1460	3.991773	GTGTAATGTTAAGAGGTCGTGCA	59.008	43.478	0.00	0.00	0.00	4.57
1462	1465	4.260139	TGTTAAGAGGTCGTGCAACATA	57.740	40.909	0.00	0.00	35.74	2.29
1465	1468	5.703592	TGTTAAGAGGTCGTGCAACATAAAT	59.296	36.000	0.00	0.00	35.74	1.40
1520	1523	1.021202	CAACAACGGTTCTGCCTGAA	58.979	50.000	0.00	0.00	34.21	3.02
1545	1548	6.101332	CCTACAAAAGCATGCATATGTTGTT	58.899	36.000	21.98	0.00	34.67	2.83
1579	1582	0.033504	GTGAAGCCTTGGAGACGACA	59.966	55.000	0.00	0.00	0.00	4.35
1585	1588	1.191535	CCTTGGAGACGACATACCCA	58.808	55.000	0.00	0.00	0.00	4.51
1638	1641	2.069273	GTGAGCGAATGTGTGTAAGCT	58.931	47.619	0.00	0.00	37.69	3.74
1641	1644	2.766313	AGCGAATGTGTGTAAGCTCAA	58.234	42.857	0.00	0.00	0.00	3.02
1804	1807	4.398549	TCGGCATAGTTTTTGAAGTTCG	57.601	40.909	0.00	0.00	0.00	3.95
1810	1813	3.145212	AGTTTTTGAAGTTCGGCACAC	57.855	42.857	0.00	0.00	0.00	3.82
1866	1869	2.416680	TCATGATTCGGCCATGTTCA	57.583	45.000	2.24	0.00	41.45	3.18
1872	1875	4.654915	TGATTCGGCCATGTTCATATCAT	58.345	39.130	2.24	0.00	0.00	2.45
1896	1899	1.471119	TCCTCGAGGACGTGCTATTT	58.529	50.000	30.49	0.00	39.78	1.40
1975	1978	2.234661	TGATCAAGTGTCGCCTTCATCT	59.765	45.455	0.00	0.00	0.00	2.90
2061	2064	5.839063	TCTCCTCGTGGATATTTGGTATCTT	59.161	40.000	6.68	0.00	42.29	2.40
2259	2262	5.478332	CCAGATGGCTTTTCCTAAGAAAGTT	59.522	40.000	0.00	0.00	42.78	2.66
2307	3528	1.207811	TGATCATCGTGTCCTGCATGT	59.792	47.619	0.00	0.00	35.64	3.21
2413	3634	0.480252	AAGCTTTTCCTCTGCAGGGT	59.520	50.000	13.79	0.00	40.80	4.34

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	1.537202	GGATGCTTCGCCATGGAATAC	59.463	52.381	18.40	0.10	0.00	1.89
149	150	1.075601	ATCAAAGTGGAGGAAGGGCA	58.924	50.000	0.00	0.00	0.00	5.36
180	181	1.418097	TTTGCTCTGCCCACTCTCCA	61.418	55.000	0.00	0.00	0.00	3.86
251	252	3.436496	GAGTTTACTCGACCCATTCTCG	58.564	50.000	0.00	0.00	32.78	4.04
321	322	8.869109	TGAGAACATACCCTTCAAATCAAAAAT	58.131	29.630	0.00	0.00	0.00	1.82
354	355	6.379133	TCTTCGAAGTATTTACCTCTGCCTTA	59.621	38.462	23.85	0.00	0.00	2.69
448	449	2.177594	CTGGCGTGCTTTCTCTCCCT	62.178	60.000	0.00	0.00	0.00	4.20
481	482	1.202879	AGGCGTTGGAAATGAAGACCA	60.203	47.619	0.00	0.00	33.73	4.02
555	557	2.147150	GAAGAAGAGAAGTGCGCCTTT	58.853	47.619	4.18	0.00	32.03	3.11
652	654	1.056700	GGGCTTAGCTCTGGATCCCA	61.057	60.000	9.90	0.00	32.68	4.37
739	741	1.150992	GGCTCCTAGTCTAGGCGGA	59.849	63.158	19.81	3.84	45.82	5.54
776	778	0.036732	ATCGTCTTGAAAGCTGGGCA	59.963	50.000	0.00	0.00	0.00	5.36
872	874	5.163663	CGTGCAATAAGGTCACCAATAACAT	60.164	40.000	0.00	0.00	0.00	2.71
879	881	0.398696	ACCGTGCAATAAGGTCACCA	59.601	50.000	0.00	0.00	36.30	4.17
908	910	4.640364	TCACTTGCATCACATACACAAGA	58.360	39.130	7.95	0.00	40.06	3.02
946	948	4.560819	ACGTACAACGAAACTTTACGACAA	59.439	37.500	6.44	0.00	46.05	3.18
979	981	5.300752	CATCGCAGAAACATAGATAGGGTT	58.699	41.667	0.00	0.00	43.58	4.11
997	999	2.877691	GTGTTCTTGGGCCATCGC	59.122	61.111	7.26	1.57	0.00	4.58
1030	1032	8.697507	ACCTCACAATTCAAAAGTCTTTCTAT	57.302	30.769	0.00	0.00	0.00	1.98
1035	1037	6.126409	TGGTACCTCACAATTCAAAAGTCTT	58.874	36.000	14.36	0.00	0.00	3.01
1159	1162	1.618343	CAAAAGCCCAAAGGAACGGAT	59.382	47.619	0.00	0.00	33.47	4.18
1228	1231	2.615447	CGTATGAAACTGGCATGCATCT	59.385	45.455	21.36	0.00	0.00	2.90
1404	1407	1.342174	CCAATCCTTTGCTTGCTGTGT	59.658	47.619	0.00	0.00	0.00	3.72
1462	1465	7.477864	TCCCCCATATTGCTATCAATGTATTT	58.522	34.615	2.03	0.00	42.50	1.40
1465	1468	6.045459	ACTTCCCCCATATTGCTATCAATGTA	59.955	38.462	2.03	0.00	42.50	2.29
1520	1523	5.185635	ACAACATATGCATGCTTTTGTAGGT	59.814	36.000	23.31	20.85	35.39	3.08
1558	1561	0.756294	TCGTCTCCAAGGCTTCACAA	59.244	50.000	0.00	0.00	0.00	3.33
1585	1588	1.382420	CTCAGCTCACCCTAGCCCT	60.382	63.158	0.00	0.00	43.86	5.19
1804	1807	3.616219	TGGATAACATAACCAGTGTGCC	58.384	45.455	0.00	0.00	0.00	5.01
1840	1843	1.764723	TGGCCGAATCATGATCACTCT	59.235	47.619	9.06	0.00	0.00	3.24
1975	1978	5.179368	GTCAGCGCCTTCATAGCAAATAATA	59.821	40.000	2.29	0.00	0.00	0.98
2073	2076	3.674410	GCTCGAGTGATCAAGTCATGACA	60.674	47.826	27.02	7.74	41.93	3.58
2116	2119	2.638480	CTCCAAGGGAGTGTCAACAA	57.362	50.000	4.08	0.00	44.25	2.83
2259	2262	8.506168	AGAAATTCACGAATTATGAAAGGCTA	57.494	30.769	5.48	0.00	39.88	3.93
2292	3513	0.324614	TCCAACATGCAGGACACGAT	59.675	50.000	4.84	0.00	0.00	3.73
2293	3514	0.324614	ATCCAACATGCAGGACACGA	59.675	50.000	4.84	0.00	36.60	4.35
2307	3528	9.661954	AAGAACATAGAATAGTAGAGGATCCAA	57.338	33.333	15.82	0.00	33.66	3.53
2413	3634	0.111639	GGGGGTTTACTGCACAAGGA	59.888	55.000	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.