AutoCloner

Multiple sequence alignment - TraesCS5D01G568200

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	TraesCS5D01G568200	chr5D	100.000	2599	0	0	1	2599	565348244	565350842	0.000000e+00	4800.0
1	TraesCS5D01G568200	chr5D	96.463	622	18	3	1	621	383320749	383320131	0.000000e+00	1024.0
2	TraesCS5D01G568200	chr5B	93.351	1549	72	11	612	2151	707876219	707874693	0.000000e+00	2261.0
3	TraesCS5D01G568200	chr5B	95.922	613	19	4	1	608	63252212	63251601	0.000000e+00	989.0
4	TraesCS5D01G568200	chr5B	87.419	310	21	3	2308	2599	707874594	707874285	8.910000e-90	340.0
5	TraesCS5D01G568200	chr5B	91.791	134	5	3	2169	2297	707874709	707874577	5.710000e-42	182.0
6	TraesCS5D01G568200	chr5B	72.269	238	51	14	1754	1984	243751581	243751810	2.790000e-05	60.2
7	TraesCS5D01G568200	chr4A	87.541	1517	117	28	645	2150	606811395	606812850	0.000000e+00	1688.0
8	TraesCS5D01G568200	chr3D	97.073	615	17	1	1	615	296182980	296182367	0.000000e+00	1035.0
9	TraesCS5D01G568200	chr3D	96.596	617	18	2	1	614	484120290	484119674	0.000000e+00	1020.0
10	TraesCS5D01G568200	chr3A	96.596	617	17	2	1	613	724701574	724702190	0.000000e+00	1020.0
11	TraesCS5D01G568200	chr4B	96.411	613	16	5	1	608	28682129	28681518	0.000000e+00	1005.0
12	TraesCS5D01G568200	chr1D	96.399	611	19	2	1	608	361400838	361400228	0.000000e+00	1003.0
13	TraesCS5D01G568200	chr1D	94.896	627	27	5	1	625	77899752	77899129	0.000000e+00	976.0
14	TraesCS5D01G568200	chr1D	72.574	237	52	12	1754	1984	32769626	32769855	6.000000e-07	65.8
15	TraesCS5D01G568200	chr2A	95.520	625	23	4	1	622	675581944	675581322	0.000000e+00	994.0
16	TraesCS5D01G568200	chr2A	77.348	181	36	3	1760	1936	209263880	209264059	4.580000e-18	102.0
17	TraesCS5D01G568200	chr6D	86.935	398	42	3	1754	2149	88482991	88482602	3.070000e-119	438.0
18	TraesCS5D01G568200	chr6D	94.872	39	0	2	1754	1791	287387995	287388032	2.790000e-05	60.2
19	TraesCS5D01G568200	chr1B	85.789	380	48	6	1754	2129	193463656	193464033	5.210000e-107	398.0
20	TraesCS5D01G568200	chr1B	100.000	32	0	0	2120	2151	193465116	193465147	2.790000e-05	60.2
21	TraesCS5D01G568200	chr7D	84.483	406	54	8	1754	2153	615575848	615575446	2.420000e-105	392.0
22	TraesCS5D01G568200	chr7B	83.696	368	55	5	1760	2123	708444800	708445166	2.480000e-90	342.0
23	TraesCS5D01G568200	chr7A	97.368	38	1	0	2169	2206	708318468	708318505	6.000000e-07	65.8

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	TraesCS5D01G568200	chr5D	565348244	565350842	2598	False	4800.000000	4800	100.000000	1	2599	1	chr5D.!!$F1	2598
1	TraesCS5D01G568200	chr5D	383320131	383320749	618	True	1024.000000	1024	96.463000	1	621	1	chr5D.!!$R1	620
2	TraesCS5D01G568200	chr5B	63251601	63252212	611	True	989.000000	989	95.922000	1	608	1	chr5B.!!$R1	607
3	TraesCS5D01G568200	chr5B	707874285	707876219	1934	True	927.666667	2261	90.853667	612	2599	3	chr5B.!!$R2	1987
4	TraesCS5D01G568200	chr4A	606811395	606812850	1455	False	1688.000000	1688	87.541000	645	2150	1	chr4A.!!$F1	1505
5	TraesCS5D01G568200	chr3D	296182367	296182980	613	True	1035.000000	1035	97.073000	1	615	1	chr3D.!!$R1	614
6	TraesCS5D01G568200	chr3D	484119674	484120290	616	True	1020.000000	1020	96.596000	1	614	1	chr3D.!!$R2	613
7	TraesCS5D01G568200	chr3A	724701574	724702190	616	False	1020.000000	1020	96.596000	1	613	1	chr3A.!!$F1	612
8	TraesCS5D01G568200	chr4B	28681518	28682129	611	True	1005.000000	1005	96.411000	1	608	1	chr4B.!!$R1	607
9	TraesCS5D01G568200	chr1D	361400228	361400838	610	True	1003.000000	1003	96.399000	1	608	1	chr1D.!!$R2	607
10	TraesCS5D01G568200	chr1D	77899129	77899752	623	True	976.000000	976	94.896000	1	625	1	chr1D.!!$R1	624
11	TraesCS5D01G568200	chr2A	675581322	675581944	622	True	994.000000	994	95.520000	1	622	1	chr2A.!!$R1	621
12	TraesCS5D01G568200	chr1B	193463656	193465147	1491	False	229.100000	398	92.894500	1754	2151	2	chr1B.!!$F1	397

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
778	791	0.324943	AATAAGTGCGCACCACCTCT	59.675	50.0	35.51	14.67	45.83	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2166	3284	0.535102	CCACACCGAGGCAAGTTCTT	60.535	55.0	0.0	0.0	0.0	2.52	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
81	85	4.338118	CCATGGTGTTTACACTGAAGTTGT	59.662	41.667	12.32	0.00	45.73	3.32
94	98	8.846943	ACACTGAAGTTGTCATGATATGTTTA	57.153	30.769	0.00	0.00	35.07	2.01
211	215	5.748152	GCCATGATACATGCACGTAAAATTT	59.252	36.000	0.00	0.00	0.00	1.82
552	560	3.669536	TCATACGTGGCAAAATGAGTGA	58.330	40.909	0.00	0.00	0.00	3.41
555	563	1.068333	ACGTGGCAAAATGAGTGATGC	60.068	47.619	0.00	0.00	38.06	3.91
632	641	9.883142	TTTCCAATAATAATTTTCATGTCCACC	57.117	29.630	0.00	0.00	0.00	4.61
645	654	3.820195	TGTCCACCTAGACACCTAGAA	57.180	47.619	0.00	0.00	44.00	2.10
646	655	4.332683	TGTCCACCTAGACACCTAGAAT	57.667	45.455	0.00	0.00	44.00	2.40
771	784	4.570772	TCTCCATCTTTAATAAGTGCGCAC	59.429	41.667	32.79	32.79	32.98	5.34
773	786	3.376859	CCATCTTTAATAAGTGCGCACCA	59.623	43.478	35.51	24.50	32.98	4.17
775	788	2.745281	TCTTTAATAAGTGCGCACCACC	59.255	45.455	35.51	12.65	45.83	4.61
776	789	2.483014	TTAATAAGTGCGCACCACCT	57.517	45.000	35.51	20.51	45.83	4.00
778	791	0.324943	AATAAGTGCGCACCACCTCT	59.675	50.000	35.51	14.67	45.83	3.69
779	792	0.391661	ATAAGTGCGCACCACCTCTG	60.392	55.000	35.51	0.00	45.83	3.35
780	793	1.468506	TAAGTGCGCACCACCTCTGA	61.469	55.000	35.51	7.61	45.83	3.27
806	820	7.856145	AGACCAATTGATTCTCTCATGTAAC	57.144	36.000	7.12	0.00	32.72	2.50
923	938	1.003696	CCTCTCCTTTCTTCCACCCAC	59.996	57.143	0.00	0.00	0.00	4.61
924	939	1.699634	CTCTCCTTTCTTCCACCCACA	59.300	52.381	0.00	0.00	0.00	4.17
925	940	2.106511	CTCTCCTTTCTTCCACCCACAA	59.893	50.000	0.00	0.00	0.00	3.33
926	941	2.716424	TCTCCTTTCTTCCACCCACAAT	59.284	45.455	0.00	0.00	0.00	2.71
927	942	3.140144	TCTCCTTTCTTCCACCCACAATT	59.860	43.478	0.00	0.00	0.00	2.32
928	943	3.230134	TCCTTTCTTCCACCCACAATTG	58.770	45.455	3.24	3.24	0.00	2.32
988	1003	4.640771	AATATATACCACCACCCTGCAG	57.359	45.455	6.78	6.78	0.00	4.41
1001	1016	4.765449	TGCAGGCGCCTACAGCTG	62.765	66.667	32.30	18.28	40.39	4.24
1006	1021	2.584694	GCGCCTACAGCTGAGCTC	60.585	66.667	23.35	6.82	36.40	4.09
1011	1026	0.528017	CCTACAGCTGAGCTCGACAA	59.472	55.000	23.35	0.00	36.40	3.18
1018	1033	2.261671	GAGCTCGACAAAGCCGGA	59.738	61.111	5.05	0.00	43.56	5.14
1175	1193	2.583441	CGTGGTCTCCTTCCTGGCA	61.583	63.158	0.00	0.00	35.26	4.92
1202	1220	1.817099	CTACGTCGACTACCGGGCT	60.817	63.158	14.70	0.00	39.14	5.19
1367	1385	3.573772	CTTGGCCTCGTCGCAGTCA	62.574	63.158	3.32	0.00	0.00	3.41
1379	1397	4.227134	CAGTCATCGGGGGCCTCG	62.227	72.222	22.64	22.64	0.00	4.63
1437	1455	1.002134	ATGGTGACTTTCCAGCCCG	60.002	57.895	0.00	0.00	38.42	6.13
1530	1548	3.757493	CTCCGTGTGTAGTACCTCTTCTT	59.243	47.826	0.00	0.00	0.00	2.52
1531	1549	4.147321	TCCGTGTGTAGTACCTCTTCTTT	58.853	43.478	0.00	0.00	0.00	2.52
1532	1550	4.586001	TCCGTGTGTAGTACCTCTTCTTTT	59.414	41.667	0.00	0.00	0.00	2.27
1533	1551	5.069516	TCCGTGTGTAGTACCTCTTCTTTTT	59.930	40.000	0.00	0.00	0.00	1.94
1534	1552	5.404667	CCGTGTGTAGTACCTCTTCTTTTTC	59.595	44.000	0.00	0.00	0.00	2.29
1794	1816	0.973632	TGTTGGGAGCATCGTGTACT	59.026	50.000	0.00	0.00	34.37	2.73
1827	1849	0.586319	AAGGTCATGTGTTGCGTTCG	59.414	50.000	0.00	0.00	0.00	3.95
1852	1875	0.107263	TGCTTGTTGCTGTCAGGTCA	60.107	50.000	1.14	0.00	43.37	4.02
2042	2067	0.675083	TTGGTCGAGACACGGCTTTA	59.325	50.000	5.55	0.00	46.52	1.85
2151	3269	1.594293	CGAACTTGCCTCGGTGTGT	60.594	57.895	0.00	0.00	32.62	3.72
2152	3270	1.557443	CGAACTTGCCTCGGTGTGTC	61.557	60.000	0.00	0.00	32.62	3.67
2153	3271	1.227853	AACTTGCCTCGGTGTGTCC	60.228	57.895	0.00	0.00	0.00	4.02
2154	3272	2.358737	CTTGCCTCGGTGTGTCCC	60.359	66.667	0.00	0.00	0.00	4.46
2155	3273	3.901797	CTTGCCTCGGTGTGTCCCC	62.902	68.421	0.00	0.00	0.00	4.81
2159	3277	4.308458	CTCGGTGTGTCCCCGCAA	62.308	66.667	0.00	0.00	45.09	4.85
2160	3278	3.818121	CTCGGTGTGTCCCCGCAAA	62.818	63.158	0.00	0.00	45.09	3.68
2161	3279	2.902846	CGGTGTGTCCCCGCAAAA	60.903	61.111	0.00	0.00	38.85	2.44
2162	3280	2.482333	CGGTGTGTCCCCGCAAAAA	61.482	57.895	0.00	0.00	38.85	1.94
2335	3457	5.277857	TCCACCTAAGCTAGCACTAATTC	57.722	43.478	18.83	0.00	0.00	2.17
2369	3491	9.319143	AGAATAACTAGCACTCACAAATGATAC	57.681	33.333	0.00	0.00	33.22	2.24
2372	3494	4.864806	ACTAGCACTCACAAATGATACGTG	59.135	41.667	0.00	0.00	33.66	4.49
2435	3557	2.253610	CCCATCGGGCTTGTATAGGTA	58.746	52.381	0.00	0.00	35.35	3.08
2459	3581	1.733526	AACAAACTGTTGCGCTCCC	59.266	52.632	9.73	0.00	39.45	4.30
2460	3582	2.058829	AACAAACTGTTGCGCTCCCG	62.059	55.000	9.73	0.00	39.45	5.14
2482	3604	0.930726	TTTTGAACCCTCCCCACAGT	59.069	50.000	0.00	0.00	0.00	3.55
2513	3647	6.873997	AGATTTTCCGGTTTTCTTTCTGTTT	58.126	32.000	0.00	0.00	0.00	2.83
2592	3732	7.908193	TTTATTCGTGAACTTTCTTGAAAGC	57.092	32.000	19.40	7.98	33.18	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
377	381	6.580791	CCATGTTGATATGTTTCGACGTTTTT	59.419	34.615	0.00	0.00	33.42	1.94
442	450	4.460505	AGCGAACTAAAAATCCGTTTTCG	58.539	39.130	0.00	0.00	40.07	3.46
552	560	4.415150	CCCACACGCCTCCAGCAT	62.415	66.667	0.00	0.00	44.04	3.79
625	634	3.820195	TTCTAGGTGTCTAGGTGGACA	57.180	47.619	0.00	0.00	42.42	4.02
632	641	7.235606	TGGATTATGGGAATTCTAGGTGTCTAG	59.764	40.741	5.23	0.00	43.27	2.43
637	646	5.770162	GGTTGGATTATGGGAATTCTAGGTG	59.230	44.000	5.23	0.00	0.00	4.00
638	647	5.162980	GGGTTGGATTATGGGAATTCTAGGT	60.163	44.000	5.23	0.00	0.00	3.08
640	649	5.952387	TGGGTTGGATTATGGGAATTCTAG	58.048	41.667	5.23	0.00	0.00	2.43
641	650	6.133356	GTTGGGTTGGATTATGGGAATTCTA	58.867	40.000	5.23	0.00	0.00	2.10
642	651	4.898014	TGGGTTGGATTATGGGAATTCT	57.102	40.909	5.23	0.00	0.00	2.40
643	652	4.714308	TGTTGGGTTGGATTATGGGAATTC	59.286	41.667	0.00	0.00	0.00	2.17
645	654	4.344938	TGTTGGGTTGGATTATGGGAAT	57.655	40.909	0.00	0.00	0.00	3.01
646	655	3.835478	TGTTGGGTTGGATTATGGGAA	57.165	42.857	0.00	0.00	0.00	3.97
692	701	0.464036	GAATCATTTTTCCCGCCCCC	59.536	55.000	0.00	0.00	0.00	5.40
694	703	2.099405	TCTGAATCATTTTTCCCGCCC	58.901	47.619	0.00	0.00	0.00	6.13
698	707	5.359292	AGCTAGCTTCTGAATCATTTTTCCC	59.641	40.000	12.68	0.00	0.00	3.97
699	708	6.318396	AGAGCTAGCTTCTGAATCATTTTTCC	59.682	38.462	20.42	0.00	0.00	3.13
762	775	2.116983	ATCAGAGGTGGTGCGCACTT	62.117	55.000	36.84	21.24	0.00	3.16
771	784	4.760530	TCAATTGGTCTATCAGAGGTGG	57.239	45.455	5.42	0.00	0.00	4.61
773	786	6.614906	AGAGAATCAATTGGTCTATCAGAGGT	59.385	38.462	5.42	0.00	37.82	3.85
775	788	7.724287	TGAGAGAATCAATTGGTCTATCAGAG	58.276	38.462	22.67	0.00	35.34	3.35
776	789	7.666063	TGAGAGAATCAATTGGTCTATCAGA	57.334	36.000	22.67	10.00	35.34	3.27
778	791	7.799081	ACATGAGAGAATCAATTGGTCTATCA	58.201	34.615	25.87	25.87	42.13	2.15
779	792	9.770097	TTACATGAGAGAATCAATTGGTCTATC	57.230	33.333	19.51	19.51	42.53	2.08
780	793	9.553064	GTTACATGAGAGAATCAATTGGTCTAT	57.447	33.333	5.42	6.27	42.53	1.98
806	820	5.012561	AGCTTAGCTATACATCAAAGGAGGG	59.987	44.000	4.30	0.00	36.99	4.30
906	921	2.656947	TTGTGGGTGGAAGAAAGGAG	57.343	50.000	0.00	0.00	0.00	3.69
923	938	3.006940	AGATGCCAAATGCTTGCAATTG	58.993	40.909	14.41	14.41	42.00	2.32
924	939	3.006940	CAGATGCCAAATGCTTGCAATT	58.993	40.909	0.00	0.00	42.00	2.32
925	940	2.627945	CAGATGCCAAATGCTTGCAAT	58.372	42.857	0.00	0.00	42.00	3.56
926	941	1.942127	GCAGATGCCAAATGCTTGCAA	60.942	47.619	0.00	0.00	40.11	4.08
927	942	0.390603	GCAGATGCCAAATGCTTGCA	60.391	50.000	0.00	0.00	40.11	4.08
928	943	2.380081	GCAGATGCCAAATGCTTGC	58.620	52.632	0.00	0.00	42.00	4.01
1001	1016	1.807573	CTCCGGCTTTGTCGAGCTC	60.808	63.158	2.73	2.73	42.32	4.09
1175	1193	0.327591	AGTCGACGTAGGAGGAGGTT	59.672	55.000	10.46	0.00	0.00	3.50
1350	1368	2.835701	GATGACTGCGACGAGGCCAA	62.836	60.000	5.01	0.00	0.00	4.52
1418	1436	1.308069	CGGGCTGGAAAGTCACCATG	61.308	60.000	0.00	0.00	36.79	3.66
1560	1578	4.760530	ATGCACACTGATAGTACCACAT	57.239	40.909	0.00	0.00	0.00	3.21
1794	1816	2.514803	TGACCTTCAGATCGTGTCTCA	58.485	47.619	0.00	0.00	34.00	3.27
1808	1830	0.586319	CGAACGCAACACATGACCTT	59.414	50.000	0.00	0.00	0.00	3.50
1852	1875	2.717639	ACATAGCGCCCTTGAAGATT	57.282	45.000	2.29	0.00	0.00	2.40
2042	2067	5.857845	AGGGGCCTATCCTAAACTGAAATAT	59.142	40.000	0.84	0.00	31.86	1.28
2163	3281	2.099098	CACACCGAGGCAAGTTCTTTTT	59.901	45.455	0.00	0.00	0.00	1.94
2164	3282	1.676006	CACACCGAGGCAAGTTCTTTT	59.324	47.619	0.00	0.00	0.00	2.27
2165	3283	1.308998	CACACCGAGGCAAGTTCTTT	58.691	50.000	0.00	0.00	0.00	2.52
2166	3284	0.535102	CCACACCGAGGCAAGTTCTT	60.535	55.000	0.00	0.00	0.00	2.52
2167	3285	1.071471	CCACACCGAGGCAAGTTCT	59.929	57.895	0.00	0.00	0.00	3.01
2168	3286	0.951040	CTCCACACCGAGGCAAGTTC	60.951	60.000	0.00	0.00	0.00	3.01
2169	3287	1.071471	CTCCACACCGAGGCAAGTT	59.929	57.895	0.00	0.00	0.00	2.66
2170	3288	2.140792	ACTCCACACCGAGGCAAGT	61.141	57.895	0.00	0.00	33.93	3.16
2171	3289	1.669115	CACTCCACACCGAGGCAAG	60.669	63.158	0.00	0.00	33.93	4.01
2172	3290	2.425592	CACTCCACACCGAGGCAA	59.574	61.111	0.00	0.00	33.93	4.52
2173	3291	3.625897	CCACTCCACACCGAGGCA	61.626	66.667	0.00	0.00	33.93	4.75
2202	3320	3.589988	AGACTATCCTTTGTTGCGAGTG	58.410	45.455	0.00	0.00	0.00	3.51
2402	3524	3.628646	GATGGGCCGGCTCACAACT	62.629	63.158	35.86	17.48	0.00	3.16
2426	3548	5.010922	ACAGTTTGTTGACCGTACCTATACA	59.989	40.000	0.00	0.00	0.00	2.29
2471	3593	1.071699	TCTTTCGAAACTGTGGGGAGG	59.928	52.381	6.47	0.00	0.00	4.30
2472	3594	2.543777	TCTTTCGAAACTGTGGGGAG	57.456	50.000	6.47	0.00	0.00	4.30
2479	3601	4.483476	ACCGGAAAATCTTTCGAAACTG	57.517	40.909	9.46	1.18	35.36	3.16
2480	3602	5.509716	AAACCGGAAAATCTTTCGAAACT	57.490	34.783	9.46	0.00	35.36	2.66
2482	3604	6.139048	AGAAAACCGGAAAATCTTTCGAAA	57.861	33.333	9.46	10.71	35.36	3.46
2564	3702	9.627395	TTTCAAGAAAGTTCACGAATAAAAACA	57.373	25.926	0.00	0.00	0.00	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.