AutoCloner

Multiple sequence alignment - TraesCS3A01G010500

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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	TraesCS3A01G010500	chr3A	100.000	2403	0	0	1	2403	8990462	8992864	0.000000e+00	4438.0
1	TraesCS3A01G010500	chr3A	96.301	1703	47	9	1	1699	8960947	8962637	0.000000e+00	2782.0
2	TraesCS3A01G010500	chr3A	95.890	1703	55	9	1	1699	8977775	8979466	0.000000e+00	2743.0
3	TraesCS3A01G010500	chr3A	93.304	1135	44	15	583	1699	8944873	8945993	0.000000e+00	1646.0
4	TraesCS3A01G010500	chr3A	84.073	1149	122	25	1269	2403	9007799	9008900	0.000000e+00	1051.0
5	TraesCS3A01G010500	chr3A	86.911	573	45	16	653	1209	9007241	9007799	1.220000e-172	616.0
6	TraesCS3A01G010500	chr3A	85.260	597	57	15	653	1230	9050766	9051350	9.570000e-164	586.0
7	TraesCS3A01G010500	chr3A	84.211	532	58	13	1701	2229	9051836	9052344	5.970000e-136	494.0
8	TraesCS3A01G010500	chr3A	94.371	302	17	0	1	302	43223590	43223891	4.680000e-127	464.0
9	TraesCS3A01G010500	chr3A	94.371	302	17	0	1	302	43813689	43813990	4.680000e-127	464.0
10	TraesCS3A01G010500	chr3A	80.274	583	83	14	1701	2280	8946059	8946612	6.180000e-111	411.0
11	TraesCS3A01G010500	chr3A	94.222	225	12	1	365	589	43813947	43814170	2.290000e-90	342.0
12	TraesCS3A01G010500	chr3A	93.778	225	13	1	365	589	43223848	43224071	1.060000e-88	337.0
13	TraesCS3A01G010500	chr3A	75.000	412	75	18	2001	2403	741622246	741621854	5.310000e-37	165.0
14	TraesCS3A01G010500	chr3A	96.250	80	3	0	298	377	8961169	8961248	5.390000e-27	132.0
15	TraesCS3A01G010500	chr3A	96.250	80	3	0	298	377	8977997	8978076	5.390000e-27	132.0
16	TraesCS3A01G010500	chr3A	95.000	80	4	0	298	377	8990684	8990763	2.510000e-25	126.0
17	TraesCS3A01G010500	chr3A	95.833	48	2	0	583	630	8906247	8906294	7.120000e-11	78.7
18	TraesCS3A01G010500	chr3D	88.184	1845	131	34	583	2403	687517	685736	0.000000e+00	2119.0
19	TraesCS3A01G010500	chr3D	86.558	1473	150	26	951	2403	587300	585856	0.000000e+00	1580.0
20	TraesCS3A01G010500	chr3D	83.257	657	84	12	1749	2401	622498	621864	4.450000e-162	580.0
21	TraesCS3A01G010500	chr3B	86.579	991	97	18	1254	2229	5773058	5772089	0.000000e+00	1061.0
22	TraesCS3A01G010500	chr3B	84.756	656	64	22	651	1283	5773622	5772980	2.030000e-175	625.0
23	TraesCS3A01G010500	chr3B	83.926	591	64	17	645	1230	5851498	5850934	9.780000e-149	536.0
24	TraesCS3A01G010500	chr3B	94.737	304	14	1	1	302	154178239	154178542	2.800000e-129	472.0
25	TraesCS3A01G010500	chr3B	93.981	216	13	0	365	580	154178499	154178714	6.410000e-86	327.0
26	TraesCS3A01G010500	chr3B	83.143	350	35	10	1338	1681	5850889	5850558	5.020000e-77	298.0
27	TraesCS3A01G010500	chr3B	86.897	145	15	1	1338	1478	6048521	6048665	2.470000e-35	159.0
28	TraesCS3A01G010500	chr3B	79.245	212	42	2	2171	2380	581653801	581654012	1.920000e-31	147.0
29	TraesCS3A01G010500	chr3B	93.023	86	4	1	298	381	154178461	154178546	9.020000e-25	124.0
30	TraesCS3A01G010500	chr4A	96.850	381	12	0	1	381	12725498	12725118	2.610000e-179	638.0
31	TraesCS3A01G010500	chr4A	96.911	259	8	0	123	381	519221793	519221535	3.670000e-118	435.0
32	TraesCS3A01G010500	chr4A	92.444	225	16	1	365	589	519221582	519221359	1.070000e-83	320.0
33	TraesCS3A01G010500	chr4A	90.667	225	10	2	365	589	12725165	12724952	3.020000e-74	289.0
34	TraesCS3A01G010500	chr4A	97.500	80	2	0	223	302	519221618	519221539	1.160000e-28	137.0
35	TraesCS3A01G010500	chr4A	95.349	86	4	0	1	86	519221987	519221902	1.160000e-28	137.0
36	TraesCS3A01G010500	chr4A	96.250	80	3	0	298	377	12725276	12725197	5.390000e-27	132.0
37	TraesCS3A01G010500	chrUn	84.946	558	49	20	651	1186	34334003	34333459	1.260000e-147	532.0
38	TraesCS3A01G010500	chrUn	83.427	531	62	15	1701	2229	243149310	243148804	1.010000e-128	470.0
39	TraesCS3A01G010500	chrUn	83.427	531	62	15	1701	2229	243162183	243161677	1.010000e-128	470.0
40	TraesCS3A01G010500	chrUn	83.619	525	60	13	1701	2223	270191338	270191838	1.010000e-128	470.0
41	TraesCS3A01G010500	chrUn	86.897	145	15	1	1338	1478	36067828	36067972	2.470000e-35	159.0
42	TraesCS3A01G010500	chr5B	96.689	302	10	0	1	302	696472065	696472366	9.920000e-139	503.0
43	TraesCS3A01G010500	chr5B	92.593	216	16	0	365	580	696472323	696472538	6.450000e-81	311.0
44	TraesCS3A01G010500	chr7D	79.373	383	66	12	2028	2403	557076960	557077336	8.520000e-65	257.0
45	TraesCS3A01G010500	chr2A	78.912	147	27	3	2258	2403	611349918	611350061	1.970000e-16	97.1
46	TraesCS3A01G010500	chr2A	84.375	96	12	3	2211	2305	10379901	10379808	9.150000e-15	91.6
47	TraesCS3A01G010500	chr2B	78.947	114	22	2	2183	2296	13478871	13478760	2.560000e-10	76.8

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	TraesCS3A01G010500	chr3A	8990462	8992864	2402	False	2282.00	4438	97.5000	1	2403	2	chr3A.!!$F5	2402
1	TraesCS3A01G010500	chr3A	8960947	8962637	1690	False	1457.00	2782	96.2755	1	1699	2	chr3A.!!$F3	1698
2	TraesCS3A01G010500	chr3A	8977775	8979466	1691	False	1437.50	2743	96.0700	1	1699	2	chr3A.!!$F4	1698
3	TraesCS3A01G010500	chr3A	8944873	8946612	1739	False	1028.50	1646	86.7890	583	2280	2	chr3A.!!$F2	1697
4	TraesCS3A01G010500	chr3A	9007241	9008900	1659	False	833.50	1051	85.4920	653	2403	2	chr3A.!!$F6	1750
5	TraesCS3A01G010500	chr3A	9050766	9052344	1578	False	540.00	586	84.7355	653	2229	2	chr3A.!!$F7	1576
6	TraesCS3A01G010500	chr3D	685736	687517	1781	True	2119.00	2119	88.1840	583	2403	1	chr3D.!!$R3	1820
7	TraesCS3A01G010500	chr3D	585856	587300	1444	True	1580.00	1580	86.5580	951	2403	1	chr3D.!!$R1	1452
8	TraesCS3A01G010500	chr3D	621864	622498	634	True	580.00	580	83.2570	1749	2401	1	chr3D.!!$R2	652
9	TraesCS3A01G010500	chr3B	5772089	5773622	1533	True	843.00	1061	85.6675	651	2229	2	chr3B.!!$R1	1578
10	TraesCS3A01G010500	chr3B	5850558	5851498	940	True	417.00	536	83.5345	645	1681	2	chr3B.!!$R2	1036
11	TraesCS3A01G010500	chr4A	12724952	12725498	546	True	353.00	638	94.5890	1	589	3	chr4A.!!$R1	588
12	TraesCS3A01G010500	chr4A	519221359	519221987	628	True	257.25	435	95.5510	1	589	4	chr4A.!!$R2	588
13	TraesCS3A01G010500	chrUn	34333459	34334003	544	True	532.00	532	84.9460	651	1186	1	chrUn.!!$R1	535
14	TraesCS3A01G010500	chrUn	243148804	243149310	506	True	470.00	470	83.4270	1701	2229	1	chrUn.!!$R2	528
15	TraesCS3A01G010500	chrUn	243161677	243162183	506	True	470.00	470	83.4270	1701	2229	1	chrUn.!!$R3	528
16	TraesCS3A01G010500	chrUn	270191338	270191838	500	False	470.00	470	83.6190	1701	2223	1	chrUn.!!$F2	522

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
468	553	2.987413	TTTGCAGATGCGAAATCGTT	57.013	40.0	4.99	0.0	45.83	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1538	1767	0.111253	AAAGAGTTGGGGACAGCAGG	59.889	55.0	0.0	0.0	45.11	4.85	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
115	200	3.660501	GGATGCAGATATCCGTACACA	57.339	47.619	0.00	0.00	37.48	3.72
468	553	2.987413	TTTGCAGATGCGAAATCGTT	57.013	40.000	4.99	0.00	45.83	3.85
857	975	6.348295	CGTTGCTGTCTGAGTACTTAACTAGA	60.348	42.308	0.00	0.00	39.07	2.43
1225	1417	4.450053	GAGGAGGAGACCAATTTGATCAG	58.550	47.826	0.00	0.00	0.00	2.90
1226	1418	3.201708	AGGAGGAGACCAATTTGATCAGG	59.798	47.826	0.00	0.00	0.00	3.86
1227	1419	3.549794	GAGGAGACCAATTTGATCAGGG	58.450	50.000	0.00	0.00	0.00	4.45
1228	1420	2.243221	AGGAGACCAATTTGATCAGGGG	59.757	50.000	0.00	0.00	0.00	4.79
1229	1421	2.659428	GAGACCAATTTGATCAGGGGG	58.341	52.381	0.00	0.00	0.00	5.40
1273	1478	5.259632	AGAGGAGGAAACCAATTTGATCAG	58.740	41.667	0.00	0.00	0.00	2.90
1466	1690	3.356290	GTTATTGGAAGGTGATGGCTGT	58.644	45.455	0.00	0.00	0.00	4.40
1474	1698	1.145738	AGGTGATGGCTGTTGGTCTTT	59.854	47.619	0.00	0.00	0.00	2.52
1515	1740	1.065782	TGCTTATCTTTGGCGCAGGTA	60.066	47.619	10.83	0.00	0.00	3.08
1538	1767	2.554893	TGCCCTTCGGTTGTAATTTGTC	59.445	45.455	0.00	0.00	0.00	3.18
1580	1809	9.262472	CTTTTAAACATTTGTATCTCGTGCTAC	57.738	33.333	0.00	0.00	0.00	3.58
1614	1848	5.607119	TTCATAGTTTTTGTTCGAGAGGC	57.393	39.130	0.00	0.00	0.00	4.70
1665	1899	4.457834	GCTCCAACTAGCAAGTCTCTTA	57.542	45.455	0.00	0.00	42.30	2.10
1670	1904	7.010645	GCTCCAACTAGCAAGTCTCTTAAATAC	59.989	40.741	0.00	0.00	42.30	1.89
1707	2068	4.458989	GTCTTAATGCAAATGGGTGACTCA	59.541	41.667	0.00	0.00	0.00	3.41
1771	2132	3.119101	TCTCCTTTCTACTGATCCAACGC	60.119	47.826	0.00	0.00	0.00	4.84
1785	2146	2.037251	TCCAACGCTATCTTATCCTGCC	59.963	50.000	0.00	0.00	0.00	4.85
1791	2154	4.816925	ACGCTATCTTATCCTGCCTTTTTC	59.183	41.667	0.00	0.00	0.00	2.29
1798	2162	5.940470	TCTTATCCTGCCTTTTTCTCTTCAC	59.060	40.000	0.00	0.00	0.00	3.18
1845	2210	2.359975	GCCCGCTGTAGTTGCCTT	60.360	61.111	0.00	0.00	0.00	4.35
1847	2212	1.090052	GCCCGCTGTAGTTGCCTTAG	61.090	60.000	0.00	0.00	0.00	2.18
1852	2217	3.120304	CCGCTGTAGTTGCCTTAGAAAAC	60.120	47.826	0.00	0.00	0.00	2.43
1906	2281	9.991388	CAAAATTTGAAGTTGAATTGTGTTCAT	57.009	25.926	0.00	0.00	29.74	2.57
1920	2295	5.638530	TGTGTTCATACTATAATGGGCCA	57.361	39.130	9.61	9.61	0.00	5.36
1921	2296	5.373222	TGTGTTCATACTATAATGGGCCAC	58.627	41.667	9.28	0.00	0.00	5.01
1922	2297	4.760204	GTGTTCATACTATAATGGGCCACC	59.240	45.833	9.28	0.00	37.24	4.61
1923	2298	3.973206	TCATACTATAATGGGCCACCG	57.027	47.619	9.28	0.00	40.75	4.94
1924	2299	3.512496	TCATACTATAATGGGCCACCGA	58.488	45.455	9.28	0.00	40.75	4.69
1925	2300	3.904965	TCATACTATAATGGGCCACCGAA	59.095	43.478	9.28	0.00	40.75	4.30
1926	2301	2.632987	ACTATAATGGGCCACCGAAC	57.367	50.000	9.28	0.00	40.75	3.95
1927	2302	2.124411	ACTATAATGGGCCACCGAACT	58.876	47.619	9.28	0.00	40.75	3.01
1928	2303	3.311091	ACTATAATGGGCCACCGAACTA	58.689	45.455	9.28	0.00	40.75	2.24
1929	2304	3.908103	ACTATAATGGGCCACCGAACTAT	59.092	43.478	9.28	1.98	40.75	2.12
1930	2305	5.088730	ACTATAATGGGCCACCGAACTATA	58.911	41.667	9.28	3.08	40.75	1.31
1931	2306	2.930826	AATGGGCCACCGAACTATAG	57.069	50.000	9.28	0.00	40.75	1.31
1932	2307	1.802553	ATGGGCCACCGAACTATAGT	58.197	50.000	9.28	0.00	40.75	2.12
1933	2308	0.828022	TGGGCCACCGAACTATAGTG	59.172	55.000	0.00	0.00	40.75	2.74
1934	2309	1.117150	GGGCCACCGAACTATAGTGA	58.883	55.000	6.06	0.00	33.21	3.41
1935	2310	1.202498	GGGCCACCGAACTATAGTGAC	60.202	57.143	6.06	3.36	33.21	3.67
2010	2386	8.854979	TTGTATGAAATATGATCTTTTTGCGG	57.145	30.769	0.00	0.00	0.00	5.69
2062	2439	4.261405	CGGATAACACAAAGCACCTCAAAA	60.261	41.667	0.00	0.00	0.00	2.44
2131	2514	1.591703	CTGCTACCAGAACGAGCCA	59.408	57.895	0.00	0.00	41.77	4.75
2136	2519	1.870055	TACCAGAACGAGCCACCGAC	61.870	60.000	0.00	0.00	0.00	4.79
2181	2571	8.303156	CCATACTGAAGTAGACCTGATCTTATG	58.697	40.741	0.00	0.00	39.04	1.90
2203	2593	2.795175	TGACAGTCGTGAAGTCTTCC	57.205	50.000	10.12	1.14	33.56	3.46
2223	2613	2.955881	GCACGTGCCCCTAAGGACT	61.956	63.158	30.12	0.00	38.24	3.85
2256	2646	0.315869	CGCAGTCGTTGGTGTTGAAC	60.316	55.000	0.00	0.00	0.00	3.18
2335	2730	4.408821	CCTAAGCCTGCCGTGCCA	62.409	66.667	0.00	0.00	0.00	4.92
2344	2739	4.043200	GCCGTGCCAAGGACTTGC	62.043	66.667	0.00	3.57	39.16	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
252	337	4.309933	CAACATGCTCTGTGTGACTTAGA	58.690	43.478	0.00	0.00	38.39	2.10
466	551	7.148641	TCTCTCTGCGATTTCATCCTATTAAC	58.851	38.462	0.00	0.00	0.00	2.01
468	553	6.901081	TCTCTCTGCGATTTCATCCTATTA	57.099	37.500	0.00	0.00	0.00	0.98
669	754	5.769662	TCTTTGGTGTTAGTGCATCTCAATT	59.230	36.000	0.00	0.00	0.00	2.32
857	975	3.075283	TGGTTGTGGATGGGTTACTCATT	59.925	43.478	0.00	0.00	0.00	2.57
1466	1690	2.127651	ACCACCCCTAGAAAGACCAA	57.872	50.000	0.00	0.00	0.00	3.67
1474	1698	0.549169	CCTCCCAAACCACCCCTAGA	60.549	60.000	0.00	0.00	0.00	2.43
1521	1746	3.502211	AGCAGGACAAATTACAACCGAAG	59.498	43.478	0.00	0.00	0.00	3.79
1538	1767	0.111253	AAAGAGTTGGGGACAGCAGG	59.889	55.000	0.00	0.00	45.11	4.85
1592	1826	4.151689	CGCCTCTCGAACAAAAACTATGAA	59.848	41.667	0.00	0.00	41.67	2.57
1670	1904	7.678194	TGCATTAAGACGAGAAAAACAAAAG	57.322	32.000	0.00	0.00	0.00	2.27
1707	2068	1.419387	AGAAGAAGTCACTGGCTTGCT	59.581	47.619	0.00	0.00	0.00	3.91
1771	2132	7.989741	TGAAGAGAAAAAGGCAGGATAAGATAG	59.010	37.037	0.00	0.00	0.00	2.08
1798	2162	9.218440	AGCCAACCTGAACATATTTTTATTTTG	57.782	29.630	0.00	0.00	0.00	2.44
1906	2281	3.311091	AGTTCGGTGGCCCATTATAGTA	58.689	45.455	0.00	0.00	0.00	1.82
1908	2283	2.930826	AGTTCGGTGGCCCATTATAG	57.069	50.000	0.00	0.00	0.00	1.31
1920	2295	6.837471	AAAGAAGAGTCACTATAGTTCGGT	57.163	37.500	1.56	0.00	0.00	4.69
1921	2296	6.035112	GCAAAAGAAGAGTCACTATAGTTCGG	59.965	42.308	1.56	0.00	0.00	4.30
1922	2297	6.586463	TGCAAAAGAAGAGTCACTATAGTTCG	59.414	38.462	1.56	0.00	0.00	3.95
1923	2298	7.891183	TGCAAAAGAAGAGTCACTATAGTTC	57.109	36.000	1.56	0.00	0.00	3.01
1924	2299	7.880195	ACATGCAAAAGAAGAGTCACTATAGTT	59.120	33.333	1.56	0.00	0.00	2.24
1925	2300	7.390027	ACATGCAAAAGAAGAGTCACTATAGT	58.610	34.615	0.00	0.00	0.00	2.12
1926	2301	7.547019	TGACATGCAAAAGAAGAGTCACTATAG	59.453	37.037	0.00	0.00	30.43	1.31
1927	2302	7.386059	TGACATGCAAAAGAAGAGTCACTATA	58.614	34.615	0.00	0.00	30.43	1.31
1928	2303	6.233434	TGACATGCAAAAGAAGAGTCACTAT	58.767	36.000	0.00	0.00	30.43	2.12
1929	2304	5.610398	TGACATGCAAAAGAAGAGTCACTA	58.390	37.500	0.00	0.00	30.43	2.74
1930	2305	4.454678	TGACATGCAAAAGAAGAGTCACT	58.545	39.130	0.00	0.00	30.43	3.41
1931	2306	4.818534	TGACATGCAAAAGAAGAGTCAC	57.181	40.909	0.00	0.00	30.43	3.67
1932	2307	4.260743	CGTTGACATGCAAAAGAAGAGTCA	60.261	41.667	0.00	0.00	38.44	3.41
1933	2308	4.214437	CGTTGACATGCAAAAGAAGAGTC	58.786	43.478	0.00	0.00	38.44	3.36
1934	2309	3.627577	ACGTTGACATGCAAAAGAAGAGT	59.372	39.130	0.00	0.00	38.44	3.24
1935	2310	3.970610	CACGTTGACATGCAAAAGAAGAG	59.029	43.478	0.00	0.00	38.44	2.85
1993	2369	6.530019	ACCTTTCCGCAAAAAGATCATATT	57.470	33.333	8.90	0.00	38.30	1.28
2001	2377	5.183014	AGTCTAAACCTTTCCGCAAAAAG	57.817	39.130	1.69	1.69	36.26	2.27
2131	2514	1.285023	GTGACAGTAGCACGTCGGT	59.715	57.895	0.00	0.00	34.78	4.69
2136	2519	1.801913	GAGCGGTGACAGTAGCACG	60.802	63.158	0.00	0.00	37.13	5.34
2141	2526	1.108776	GTATGGGAGCGGTGACAGTA	58.891	55.000	0.00	0.00	0.00	2.74
2181	2571	3.246619	GAAGACTTCACGACTGTCATCC	58.753	50.000	10.42	0.00	33.56	3.51
2203	2593	2.436646	CCTTAGGGGCACGTGCAG	60.437	66.667	38.60	26.71	44.36	4.41
2223	2613	2.283604	TGCGGCTCTGGGACACTA	60.284	61.111	0.00	0.00	0.00	2.74
2256	2646	5.007430	CAGGTTCTTCAGATCGATTCAATGG	59.993	44.000	0.00	0.00	0.00	3.16
2258	2648	5.814705	GTCAGGTTCTTCAGATCGATTCAAT	59.185	40.000	0.00	0.00	0.00	2.57
2335	2730	2.912956	TGTAGATTCCTGGCAAGTCCTT	59.087	45.455	0.00	0.00	35.26	3.36
2340	2735	4.802248	GCTCCTATGTAGATTCCTGGCAAG	60.802	50.000	0.00	0.00	0.00	4.01
2344	2739	4.415596	AGAGCTCCTATGTAGATTCCTGG	58.584	47.826	10.93	0.00	0.00	4.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.