AutoCloner

Multiple sequence alignment - TraesCS3B01G018700

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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	TraesCS3B01G018700	chr3B	100.000	2351	0	0	1	2351	8005912	8003562	0.000000e+00	4342.0
1	TraesCS3B01G018700	chr2B	89.701	2311	203	12	2	2292	424515227	424512932	0.000000e+00	2916.0
2	TraesCS3B01G018700	chr2B	86.354	2323	271	27	2	2292	243358821	243361129	0.000000e+00	2492.0
3	TraesCS3B01G018700	chr7B	89.860	2219	208	14	13	2219	654022233	654020020	0.000000e+00	2835.0
4	TraesCS3B01G018700	chr6B	88.605	2308	232	14	2	2288	365734850	365737147	0.000000e+00	2776.0
5	TraesCS3B01G018700	chr6B	91.842	1667	127	4	619	2279	484540856	484539193	0.000000e+00	2316.0
6	TraesCS3B01G018700	chr5D	87.669	2295	252	22	35	2313	35280717	35278438	0.000000e+00	2641.0
7	TraesCS3B01G018700	chr3D	87.802	2279	245	22	36	2293	126392446	126394712	0.000000e+00	2638.0
8	TraesCS3B01G018700	chr3D	83.639	1638	223	28	2	1612	492007104	492005485	0.000000e+00	1498.0
9	TraesCS3B01G018700	chr4A	87.671	2198	240	11	2	2181	666800217	666802401	0.000000e+00	2529.0
10	TraesCS3B01G018700	chr4A	90.909	55	4	1	2286	2340	366671408	366671461	3.240000e-09	73.1
11	TraesCS3B01G018700	chr2D	89.203	2019	205	8	230	2241	366494352	366496364	0.000000e+00	2508.0
12	TraesCS3B01G018700	chr2D	88.066	2120	223	21	190	2293	306627118	306625013	0.000000e+00	2486.0
13	TraesCS3B01G018700	chr1D	86.286	2348	266	33	2	2315	217012061	217009736	0.000000e+00	2501.0
14	TraesCS3B01G018700	chr1D	87.738	367	34	8	1921	2283	307359415	307359774	3.610000e-113	418.0
15	TraesCS3B01G018700	chr1A	82.030	2365	324	53	2	2315	442617699	442615385	0.000000e+00	1919.0
16	TraesCS3B01G018700	chr7A	79.310	1015	167	29	2	1000	265425945	265426932	0.000000e+00	671.0
17	TraesCS3B01G018700	chr6A	79.759	914	136	22	2	894	163245993	163245108	3.320000e-173	617.0
18	TraesCS3B01G018700	chr7D	81.962	632	80	20	2	610	576160437	576159817	2.700000e-139	505.0

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	TraesCS3B01G018700	chr3B	8003562	8005912	2350	True	4342	4342	100.000	1	2351	1	chr3B.!!$R1	2350
1	TraesCS3B01G018700	chr2B	424512932	424515227	2295	True	2916	2916	89.701	2	2292	1	chr2B.!!$R1	2290
2	TraesCS3B01G018700	chr2B	243358821	243361129	2308	False	2492	2492	86.354	2	2292	1	chr2B.!!$F1	2290
3	TraesCS3B01G018700	chr7B	654020020	654022233	2213	True	2835	2835	89.860	13	2219	1	chr7B.!!$R1	2206
4	TraesCS3B01G018700	chr6B	365734850	365737147	2297	False	2776	2776	88.605	2	2288	1	chr6B.!!$F1	2286
5	TraesCS3B01G018700	chr6B	484539193	484540856	1663	True	2316	2316	91.842	619	2279	1	chr6B.!!$R1	1660
6	TraesCS3B01G018700	chr5D	35278438	35280717	2279	True	2641	2641	87.669	35	2313	1	chr5D.!!$R1	2278
7	TraesCS3B01G018700	chr3D	126392446	126394712	2266	False	2638	2638	87.802	36	2293	1	chr3D.!!$F1	2257
8	TraesCS3B01G018700	chr3D	492005485	492007104	1619	True	1498	1498	83.639	2	1612	1	chr3D.!!$R1	1610
9	TraesCS3B01G018700	chr4A	666800217	666802401	2184	False	2529	2529	87.671	2	2181	1	chr4A.!!$F2	2179
10	TraesCS3B01G018700	chr2D	366494352	366496364	2012	False	2508	2508	89.203	230	2241	1	chr2D.!!$F1	2011
11	TraesCS3B01G018700	chr2D	306625013	306627118	2105	True	2486	2486	88.066	190	2293	1	chr2D.!!$R1	2103
12	TraesCS3B01G018700	chr1D	217009736	217012061	2325	True	2501	2501	86.286	2	2315	1	chr1D.!!$R1	2313
13	TraesCS3B01G018700	chr1A	442615385	442617699	2314	True	1919	1919	82.030	2	2315	1	chr1A.!!$R1	2313
14	TraesCS3B01G018700	chr7A	265425945	265426932	987	False	671	671	79.310	2	1000	1	chr7A.!!$F1	998
15	TraesCS3B01G018700	chr6A	163245108	163245993	885	True	617	617	79.759	2	894	1	chr6A.!!$R1	892
16	TraesCS3B01G018700	chr7D	576159817	576160437	620	True	505	505	81.962	2	610	1	chr7D.!!$R1	608

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
641	709	0.320946	ATACCCGGTTTCCACGTGTG	60.321	55.0	15.65	6.24	0.0	3.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2302	2427	0.035881	ACCATAGATCATGCCAGCGG	59.964	55.0	0.0	0.0	32.84	5.52	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
28	29	2.629763	GCGCGTCCACTTTTCGTT	59.370	55.556	8.43	0.00	0.00	3.85
31	32	1.814211	CGCGTCCACTTTTCGTTCGT	61.814	55.000	0.00	0.00	0.00	3.85
33	35	0.925466	CGTCCACTTTTCGTTCGTGT	59.075	50.000	0.00	0.00	0.00	4.49
52	54	1.118356	TGCGACCCATTTTTGGCCTT	61.118	50.000	3.32	0.00	0.00	4.35
118	122	2.202623	CGCGCGCCTACTTCTCTT	60.203	61.111	27.72	0.00	0.00	2.85
119	123	1.805945	CGCGCGCCTACTTCTCTTT	60.806	57.895	27.72	0.00	0.00	2.52
169	184	3.327464	CACCATTTTCCCACATTTTCCCT	59.673	43.478	0.00	0.00	0.00	4.20
174	189	6.429692	CCATTTTCCCACATTTTCCCTAAAAC	59.570	38.462	0.00	0.00	37.41	2.43
177	192	3.143168	TCCCACATTTTCCCTAAAACCCT	59.857	43.478	0.00	0.00	37.41	4.34
178	193	3.513912	CCCACATTTTCCCTAAAACCCTC	59.486	47.826	0.00	0.00	37.41	4.30
180	195	3.192633	CACATTTTCCCTAAAACCCTCCG	59.807	47.826	0.00	0.00	37.41	4.63
291	338	4.912395	AAAGGCAAGCCCCGTGCA	62.912	61.111	7.62	0.00	44.07	4.57
596	664	2.045926	GATGGTGCTGCCCGACTT	60.046	61.111	0.00	0.00	36.04	3.01
641	709	0.320946	ATACCCGGTTTCCACGTGTG	60.321	55.000	15.65	6.24	0.00	3.82
684	752	4.719369	GAGTGCTCGCCCGACGTT	62.719	66.667	0.00	0.00	44.19	3.99
737	817	1.164662	CCCATCAATCTCAGCGCCAG	61.165	60.000	2.29	0.00	0.00	4.85
870	953	3.525537	CGACAAGGACTACATGCAGAAT	58.474	45.455	0.00	0.00	0.00	2.40
879	962	6.054295	GGACTACATGCAGAATCTCATCTTT	58.946	40.000	0.00	0.00	0.00	2.52
913	996	2.919043	CCACTGGCTATGACCCCC	59.081	66.667	0.00	0.00	0.00	5.40
929	1013	1.763770	CCCAGGAGACACAAAGCCT	59.236	57.895	0.00	0.00	0.00	4.58
1049	1145	1.136252	CGAGTTTTCGGACGACTACGA	60.136	52.381	0.00	0.00	43.05	3.43
1074	1170	0.523966	AGGAAGAAGACGAGTGCGAG	59.476	55.000	0.00	0.00	41.64	5.03
1182	1278	3.379445	ACGGCGGTCGAGGACAAT	61.379	61.111	9.82	0.00	42.43	2.71
1300	1397	2.831685	TGAGCGCAAGAAGTTTCCTA	57.168	45.000	11.47	0.00	43.02	2.94
1344	1442	1.615919	GGGTGGGTGTCCATTTCGAAT	60.616	52.381	0.00	0.00	46.09	3.34
1454	1560	4.517285	CAAGACATGGTATGGTAGCAAGT	58.483	43.478	0.00	0.00	40.29	3.16
1465	1573	1.206371	GGTAGCAAGTCGCCCTCTTTA	59.794	52.381	0.00	0.00	44.04	1.85
1523	1633	2.496111	CCATTTGTGCCAACATGCTTT	58.504	42.857	0.00	0.00	35.83	3.51
1595	1707	0.381801	CAACGGCAAGTGCTTCAACT	59.618	50.000	2.85	0.00	41.70	3.16
1636	1749	6.887002	GGGTCATTAAAGATGAGGAGAAGTTT	59.113	38.462	0.00	0.00	0.00	2.66
1776	1889	3.093278	GGCATCGAACGCCTTGAG	58.907	61.111	19.20	0.00	46.56	3.02
1807	1920	4.766891	GTGGAGGGAATGATGAACAAGAAA	59.233	41.667	0.00	0.00	0.00	2.52
1865	1978	2.161855	AGCAAATGAACGCCTTCATGA	58.838	42.857	11.07	0.00	44.93	3.07
2012	2128	1.647629	GCTCTCGCAAGCATGATGG	59.352	57.895	0.00	0.00	42.05	3.51
2029	2145	1.841556	GGCCGGGGTGGAGATCATA	60.842	63.158	2.18	0.00	42.00	2.15
2226	2349	2.620242	CCACCCATTTTTATGTGCTGC	58.380	47.619	0.00	0.00	0.00	5.25
2229	2352	2.636893	ACCCATTTTTATGTGCTGCCAA	59.363	40.909	0.00	0.00	0.00	4.52
2298	2423	2.192664	TTTTAAGCCGGCATCAGACA	57.807	45.000	31.54	2.52	0.00	3.41
2300	2425	1.667236	TTAAGCCGGCATCAGACATG	58.333	50.000	31.54	0.00	0.00	3.21
2302	2427	3.589881	GCCGGCATCAGACATGGC	61.590	66.667	24.80	0.00	40.66	4.40
2320	2445	2.850439	CCGCTGGCATGATCTATGG	58.150	57.895	0.00	0.00	37.26	2.74
2321	2446	0.035881	CCGCTGGCATGATCTATGGT	59.964	55.000	0.00	0.00	37.26	3.55
2322	2447	1.544093	CCGCTGGCATGATCTATGGTT	60.544	52.381	0.00	0.00	37.26	3.67
2323	2448	2.224606	CGCTGGCATGATCTATGGTTT	58.775	47.619	0.00	0.00	37.26	3.27
2324	2449	2.225019	CGCTGGCATGATCTATGGTTTC	59.775	50.000	0.00	0.00	37.26	2.78
2325	2450	2.225019	GCTGGCATGATCTATGGTTTCG	59.775	50.000	0.00	0.00	37.26	3.46
2326	2451	2.810274	CTGGCATGATCTATGGTTTCGG	59.190	50.000	0.00	0.00	37.26	4.30
2327	2452	2.154462	GGCATGATCTATGGTTTCGGG	58.846	52.381	0.00	0.00	37.26	5.14
2328	2453	1.537202	GCATGATCTATGGTTTCGGGC	59.463	52.381	0.00	0.00	37.26	6.13
2329	2454	2.154462	CATGATCTATGGTTTCGGGCC	58.846	52.381	0.00	0.00	32.95	5.80
2330	2455	1.507140	TGATCTATGGTTTCGGGCCT	58.493	50.000	0.84	0.00	0.00	5.19
2331	2456	1.843851	TGATCTATGGTTTCGGGCCTT	59.156	47.619	0.84	0.00	0.00	4.35
2332	2457	2.158813	TGATCTATGGTTTCGGGCCTTC	60.159	50.000	0.84	0.00	0.00	3.46
2333	2458	1.580059	TCTATGGTTTCGGGCCTTCT	58.420	50.000	0.84	0.00	0.00	2.85
2334	2459	1.913419	TCTATGGTTTCGGGCCTTCTT	59.087	47.619	0.84	0.00	0.00	2.52
2335	2460	2.307686	TCTATGGTTTCGGGCCTTCTTT	59.692	45.455	0.84	0.00	0.00	2.52
2336	2461	2.891191	ATGGTTTCGGGCCTTCTTTA	57.109	45.000	0.84	0.00	0.00	1.85
2337	2462	2.660670	TGGTTTCGGGCCTTCTTTAA	57.339	45.000	0.84	0.00	0.00	1.52
2338	2463	2.946785	TGGTTTCGGGCCTTCTTTAAA	58.053	42.857	0.84	0.00	0.00	1.52
2339	2464	3.297736	TGGTTTCGGGCCTTCTTTAAAA	58.702	40.909	0.84	0.00	0.00	1.52
2340	2465	3.898741	TGGTTTCGGGCCTTCTTTAAAAT	59.101	39.130	0.84	0.00	0.00	1.82
2341	2466	4.345547	TGGTTTCGGGCCTTCTTTAAAATT	59.654	37.500	0.84	0.00	0.00	1.82
2342	2467	5.163290	TGGTTTCGGGCCTTCTTTAAAATTT	60.163	36.000	0.84	0.00	0.00	1.82
2343	2468	6.041751	TGGTTTCGGGCCTTCTTTAAAATTTA	59.958	34.615	0.84	0.00	0.00	1.40
2344	2469	6.930164	GGTTTCGGGCCTTCTTTAAAATTTAA	59.070	34.615	0.84	0.00	0.00	1.52
2345	2470	7.117236	GGTTTCGGGCCTTCTTTAAAATTTAAG	59.883	37.037	0.84	0.00	0.00	1.85
2346	2471	6.904463	TCGGGCCTTCTTTAAAATTTAAGT	57.096	33.333	0.84	0.00	0.00	2.24
2347	2472	7.999450	TCGGGCCTTCTTTAAAATTTAAGTA	57.001	32.000	0.84	0.00	0.00	2.24
2348	2473	8.584063	TCGGGCCTTCTTTAAAATTTAAGTAT	57.416	30.769	0.84	0.00	0.00	2.12
2349	2474	8.463607	TCGGGCCTTCTTTAAAATTTAAGTATG	58.536	33.333	0.84	0.00	0.00	2.39
2350	2475	7.704899	CGGGCCTTCTTTAAAATTTAAGTATGG	59.295	37.037	0.84	4.65	0.00	2.74

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.115892	GACGCGCGTCCATTTGGA	61.116	61.111	44.30	0.00	43.08	3.53
31	32	1.365633	GCCAAAAATGGGTCGCACA	59.634	52.632	0.00	0.00	0.00	4.57
33	35	1.118356	AAGGCCAAAAATGGGTCGCA	61.118	50.000	5.01	0.00	34.44	5.10
52	54	2.088423	ACGCAAATCCGGCTCAAAATA	58.912	42.857	0.00	0.00	0.00	1.40
100	102	3.701604	AAGAGAAGTAGGCGCGCGG	62.702	63.158	33.06	13.66	0.00	6.46
146	150	3.326297	GGGAAAATGTGGGAAAATGGTGA	59.674	43.478	0.00	0.00	0.00	4.02
169	184	3.638316	TGCGGGCGGAGGGTTTTA	61.638	61.111	0.00	0.00	0.00	1.52
610	678	1.153046	CGGGTATCGGGGTGCAAAT	60.153	57.895	0.00	0.00	34.75	2.32
611	679	2.269562	CGGGTATCGGGGTGCAAA	59.730	61.111	0.00	0.00	34.75	3.68
630	698	4.858680	TGCGGGCACACGTGGAAA	62.859	61.111	21.57	0.00	35.98	3.13
684	752	4.789075	GAAGACGCCGCCACGCTA	62.789	66.667	0.00	0.00	36.19	4.26
724	804	1.680522	ATCGGTCTGGCGCTGAGATT	61.681	55.000	7.64	0.00	0.00	2.40
726	806	1.448119	CTATCGGTCTGGCGCTGAGA	61.448	60.000	7.64	6.46	0.00	3.27
799	879	2.202703	GGCGTCCGATAGCACGTT	60.203	61.111	0.00	0.00	38.32	3.99
846	926	0.391130	GCATGTAGTCCTTGTCGCCA	60.391	55.000	0.00	0.00	0.00	5.69
913	996	0.397941	TCCAGGCTTTGTGTCTCCTG	59.602	55.000	0.00	0.00	44.25	3.86
958	1042	1.957177	GGTCGACTGATCATAGGCAGA	59.043	52.381	16.46	0.00	36.07	4.26
962	1046	4.554292	CATGAAGGTCGACTGATCATAGG	58.446	47.826	21.88	12.64	0.00	2.57
1049	1145	2.029470	CACTCGTCTTCTTCCTCTTGCT	60.029	50.000	0.00	0.00	0.00	3.91
1074	1170	2.100605	ACAAAGGCTCCACTTCGATC	57.899	50.000	0.00	0.00	0.00	3.69
1155	1251	1.743995	GACCGCCGTGTATGCCTTT	60.744	57.895	0.00	0.00	0.00	3.11
1182	1278	2.483876	CTCCAACACTCGCAAAGAAGA	58.516	47.619	0.00	0.00	0.00	2.87
1300	1397	2.031157	GCGTGCTCACAATTTGGTAAGT	60.031	45.455	0.78	0.00	0.00	2.24
1344	1442	4.220602	TCTTGTTGGATCACTCTTCATCGA	59.779	41.667	0.00	0.00	0.00	3.59
1454	1560	4.222145	ACTTAATGACACTAAAGAGGGCGA	59.778	41.667	0.00	0.00	0.00	5.54
1465	1573	4.378770	CGCAAGCATGAACTTAATGACACT	60.379	41.667	0.00	0.00	0.00	3.55
1595	1707	6.753913	AATGACCCTATAGCAATGAGAGAA	57.246	37.500	0.00	0.00	0.00	2.87
1652	1765	4.003788	CCCGTGCGACTTGAGGGT	62.004	66.667	0.00	0.00	37.36	4.34
1712	1825	1.254975	TTGGTCTTCTCCCGCGATCA	61.255	55.000	8.23	0.00	0.00	2.92
1715	1828	1.874345	GAGTTGGTCTTCTCCCGCGA	61.874	60.000	8.23	0.00	0.00	5.87
1722	1835	4.202409	CCTTCTTCTTGGAGTTGGTCTTCT	60.202	45.833	0.00	0.00	0.00	2.85
1792	1905	7.935755	TCTCTTGAGTCTTTCTTGTTCATCATT	59.064	33.333	0.00	0.00	0.00	2.57
1807	1920	1.681780	CGCTCCTCCTCTCTTGAGTCT	60.682	57.143	0.00	0.00	38.61	3.24
1865	1978	1.978361	AGCCTCCTCCTTTGGATCTT	58.022	50.000	0.00	0.00	35.30	2.40
2012	2128	0.472471	TTTATGATCTCCACCCCGGC	59.528	55.000	0.00	0.00	33.14	6.13
2029	2145	0.673644	CGGCGTTGAGATCCACCTTT	60.674	55.000	0.00	0.00	0.00	3.11
2194	2315	1.434513	ATGGGTGGGGCTTGAGTTCA	61.435	55.000	0.00	0.00	0.00	3.18
2204	2325	2.093553	CAGCACATAAAAATGGGTGGGG	60.094	50.000	0.00	0.00	0.00	4.96
2282	2407	0.179048	CCATGTCTGATGCCGGCTTA	60.179	55.000	29.70	8.87	0.00	3.09
2302	2427	0.035881	ACCATAGATCATGCCAGCGG	59.964	55.000	0.00	0.00	32.84	5.52
2315	2440	2.420058	AAGAAGGCCCGAAACCATAG	57.580	50.000	0.00	0.00	0.00	2.23
2316	2441	2.891191	AAAGAAGGCCCGAAACCATA	57.109	45.000	0.00	0.00	0.00	2.74
2317	2442	2.891191	TAAAGAAGGCCCGAAACCAT	57.109	45.000	0.00	0.00	0.00	3.55
2318	2443	2.660670	TTAAAGAAGGCCCGAAACCA	57.339	45.000	0.00	0.00	0.00	3.67
2319	2444	4.530710	ATTTTAAAGAAGGCCCGAAACC	57.469	40.909	0.00	0.00	0.00	3.27
2320	2445	7.654520	ACTTAAATTTTAAAGAAGGCCCGAAAC	59.345	33.333	0.00	0.00	0.00	2.78
2321	2446	7.728148	ACTTAAATTTTAAAGAAGGCCCGAAA	58.272	30.769	0.00	0.00	0.00	3.46
2322	2447	7.292713	ACTTAAATTTTAAAGAAGGCCCGAA	57.707	32.000	0.00	0.00	0.00	4.30
2323	2448	6.904463	ACTTAAATTTTAAAGAAGGCCCGA	57.096	33.333	0.00	0.00	0.00	5.14
2324	2449	7.704899	CCATACTTAAATTTTAAAGAAGGCCCG	59.295	37.037	0.00	0.00	0.00	6.13
2325	2450	8.942338	CCATACTTAAATTTTAAAGAAGGCCC	57.058	34.615	0.00	0.00	0.00	5.80

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.