AutoCloner

Multiple sequence alignment - TraesCS3A01G203800

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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	TraesCS3A01G203800	chr3A	100.000	2675	0	0	1	2675	353166954	353169628	0.000000e+00	4940.0
1	TraesCS3A01G203800	chr3A	79.803	1015	162	29	905	1898	676220752	676219760	0.000000e+00	699.0
2	TraesCS3A01G203800	chr3A	84.561	421	51	4	1103	1510	199143646	199143227	3.210000e-109	405.0
3	TraesCS3A01G203800	chr3A	80.041	486	69	16	1914	2382	676219775	676219301	4.270000e-88	335.0
4	TraesCS3A01G203800	chr3A	80.377	265	31	9	1639	1898	199143087	199142839	5.880000e-42	182.0
5	TraesCS3A01G203800	chr3A	88.591	149	16	1	330	478	353184173	353184320	2.120000e-41	180.0
6	TraesCS3A01G203800	chr3B	95.608	1571	37	13	1108	2675	333455320	333453779	0.000000e+00	2490.0
7	TraesCS3A01G203800	chr3B	95.340	1030	33	8	1	1025	333456334	333455315	0.000000e+00	1622.0
8	TraesCS3A01G203800	chr3B	82.900	462	48	21	1914	2354	243782140	243782591	1.160000e-103	387.0
9	TraesCS3A01G203800	chr3B	80.377	265	31	9	1639	1898	243781907	243782155	5.880000e-42	182.0
10	TraesCS3A01G203800	chr6A	84.779	1084	129	24	845	1898	286332054	286330977	0.000000e+00	1055.0
11	TraesCS3A01G203800	chr6A	82.211	579	80	15	1323	1898	63026346	63026904	6.700000e-131	477.0
12	TraesCS3A01G203800	chr6A	80.080	502	57	11	1914	2382	286330992	286330501	1.530000e-87	333.0
13	TraesCS3A01G203800	chr6B	84.114	1089	130	33	845	1898	400347721	400346641	0.000000e+00	1013.0
14	TraesCS3A01G203800	chr6B	85.929	533	67	6	1370	1898	469295678	469296206	1.800000e-156	562.0
15	TraesCS3A01G203800	chr6B	91.111	270	24	0	2406	2675	75654613	75654344	1.510000e-97	366.0
16	TraesCS3A01G203800	chr4D	84.801	579	80	6	1323	1898	226567043	226567616	2.310000e-160	575.0
17	TraesCS3A01G203800	chr4D	84.906	477	45	12	1915	2370	226567602	226568072	8.730000e-125	457.0
18	TraesCS3A01G203800	chr4D	90.909	275	22	3	2401	2675	226568072	226568343	1.510000e-97	366.0
19	TraesCS3A01G203800	chr2A	82.241	580	95	6	1323	1898	701505085	701504510	6.650000e-136	494.0
20	TraesCS3A01G203800	chr2A	86.593	455	48	11	1027	1470	285618565	285619017	8.610000e-135	490.0
21	TraesCS3A01G203800	chr2A	84.536	485	46	11	1915	2379	459515073	459515548	1.130000e-123	453.0
22	TraesCS3A01G203800	chr2A	83.469	490	52	14	1915	2382	701504524	701504042	1.900000e-116	429.0
23	TraesCS3A01G203800	chr2A	92.164	268	21	0	2408	2675	459454311	459454578	1.940000e-101	379.0
24	TraesCS3A01G203800	chr2A	89.925	268	27	0	2408	2675	459515544	459515811	1.970000e-91	346.0
25	TraesCS3A01G203800	chr2A	89.925	268	27	0	2408	2675	701504049	701503782	1.970000e-91	346.0
26	TraesCS3A01G203800	chr2A	86.250	80	11	0	1024	1103	701505357	701505278	1.320000e-13	87.9
27	TraesCS3A01G203800	chr2A	86.250	80	11	0	1024	1103	701508046	701507967	1.320000e-13	87.9
28	TraesCS3A01G203800	chr4B	82.633	547	77	13	1360	1898	643279005	643279541	4.030000e-128	468.0
29	TraesCS3A01G203800	chr3D	81.897	580	80	12	1323	1898	135962172	135962730	1.450000e-127	466.0
30	TraesCS3A01G203800	chr3D	84.600	487	46	16	1915	2379	135962716	135963195	8.730000e-125	457.0
31	TraesCS3A01G203800	chr3D	87.248	149	18	1	330	478	272091434	272091287	4.580000e-38	169.0
32	TraesCS3A01G203800	chr5D	84.810	474	50	7	1915	2370	255066845	255067314	8.730000e-125	457.0
33	TraesCS3A01G203800	chr5D	88.806	268	30	0	2408	2675	95864964	95864697	1.990000e-86	329.0
34	TraesCS3A01G203800	chr6D	84.536	485	48	10	1915	2379	35692105	35692582	3.140000e-124	455.0
35	TraesCS3A01G203800	chr6D	84.342	479	47	7	1916	2374	303631655	303632125	6.800000e-121	444.0
36	TraesCS3A01G203800	chr6D	80.876	502	53	11	1914	2382	189761926	189761435	3.280000e-94	355.0
37	TraesCS3A01G203800	chr6D	87.687	268	33	0	2408	2675	36120328	36120061	2.000000e-81	313.0
38	TraesCS3A01G203800	chrUn	82.922	486	50	18	1919	2382	85312112	85311638	8.920000e-110	407.0
39	TraesCS3A01G203800	chrUn	90.672	268	22	1	2408	2675	85311645	85311381	1.180000e-93	353.0
40	TraesCS3A01G203800	chr1A	83.395	271	42	2	1103	1373	580950108	580950375	5.720000e-62	248.0

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	TraesCS3A01G203800	chr3A	353166954	353169628	2674	False	4940.00	4940	100.0000	1	2675	1	chr3A.!!$F1	2674
1	TraesCS3A01G203800	chr3A	676219301	676220752	1451	True	517.00	699	79.9220	905	2382	2	chr3A.!!$R2	1477
2	TraesCS3A01G203800	chr3A	199142839	199143646	807	True	293.50	405	82.4690	1103	1898	2	chr3A.!!$R1	795
3	TraesCS3A01G203800	chr3B	333453779	333456334	2555	True	2056.00	2490	95.4740	1	2675	2	chr3B.!!$R1	2674
4	TraesCS3A01G203800	chr3B	243781907	243782591	684	False	284.50	387	81.6385	1639	2354	2	chr3B.!!$F1	715
5	TraesCS3A01G203800	chr6A	286330501	286332054	1553	True	694.00	1055	82.4295	845	2382	2	chr6A.!!$R1	1537
6	TraesCS3A01G203800	chr6A	63026346	63026904	558	False	477.00	477	82.2110	1323	1898	1	chr6A.!!$F1	575
7	TraesCS3A01G203800	chr6B	400346641	400347721	1080	True	1013.00	1013	84.1140	845	1898	1	chr6B.!!$R2	1053
8	TraesCS3A01G203800	chr6B	469295678	469296206	528	False	562.00	562	85.9290	1370	1898	1	chr6B.!!$F1	528
9	TraesCS3A01G203800	chr4D	226567043	226568343	1300	False	466.00	575	86.8720	1323	2675	3	chr4D.!!$F1	1352
10	TraesCS3A01G203800	chr2A	459515073	459515811	738	False	399.50	453	87.2305	1915	2675	2	chr2A.!!$F3	760
11	TraesCS3A01G203800	chr2A	701503782	701508046	4264	True	288.96	494	85.6270	1024	2675	5	chr2A.!!$R1	1651
12	TraesCS3A01G203800	chr4B	643279005	643279541	536	False	468.00	468	82.6330	1360	1898	1	chr4B.!!$F1	538
13	TraesCS3A01G203800	chr3D	135962172	135963195	1023	False	461.50	466	83.2485	1323	2379	2	chr3D.!!$F1	1056
14	TraesCS3A01G203800	chrUn	85311381	85312112	731	True	380.00	407	86.7970	1919	2675	2	chrUn.!!$R1	756

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
507	510	0.676736	GAGAGGTTCATAGGCGGAGG	59.323	60.0	0.0	0.0	0.0	4.30	F
1065	1078	0.171007	CGGATGATGGGTGTTTGTGC	59.829	55.0	0.0	0.0	0.0	4.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1355	1463	1.110442	TGTGGCCTTTTCAGTGTTGG	58.890	50.0	3.32	0.0	0.0	3.77	R
2617	5572	2.104111	TCACTGCCCATAAGAATACCCG	59.896	50.0	0.00	0.0	0.0	5.28	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
107	109	7.156876	ACATATGTCAATGTTTTACCACTGG	57.843	36.000	1.41	0.00	36.71	4.00
180	182	3.426568	GCAAGACAGCACCGCCTC	61.427	66.667	0.00	0.00	0.00	4.70
181	183	2.031012	CAAGACAGCACCGCCTCA	59.969	61.111	0.00	0.00	0.00	3.86
187	189	1.008538	CAGCACCGCCTCAAAACAC	60.009	57.895	0.00	0.00	0.00	3.32
330	332	5.421374	TGATATGGAGAGGTATGCAGATCTG	59.579	44.000	18.84	18.84	39.25	2.90
350	352	4.127171	CTGTGGTATATGTGCCCAAGTAC	58.873	47.826	0.00	0.00	0.00	2.73
448	451	3.058570	GCACCACAACAACACATATCGAA	60.059	43.478	0.00	0.00	0.00	3.71
494	497	3.052566	TCCACATGGTATCAGAGAGAGGT	60.053	47.826	0.00	0.00	36.34	3.85
495	498	3.708631	CCACATGGTATCAGAGAGAGGTT	59.291	47.826	0.00	0.00	0.00	3.50
502	505	4.219725	GGTATCAGAGAGAGGTTCATAGGC	59.780	50.000	0.00	0.00	0.00	3.93
503	506	2.302260	TCAGAGAGAGGTTCATAGGCG	58.698	52.381	0.00	0.00	0.00	5.52
504	507	1.339610	CAGAGAGAGGTTCATAGGCGG	59.660	57.143	0.00	0.00	0.00	6.13
505	508	1.215673	AGAGAGAGGTTCATAGGCGGA	59.784	52.381	0.00	0.00	0.00	5.54
506	509	1.611491	GAGAGAGGTTCATAGGCGGAG	59.389	57.143	0.00	0.00	0.00	4.63
507	510	0.676736	GAGAGGTTCATAGGCGGAGG	59.323	60.000	0.00	0.00	0.00	4.30
537	540	2.123939	CAATGGCGGGGTATGGCA	60.124	61.111	0.00	0.00	46.52	4.92
633	636	3.761140	TGTGCGTTCGCCGGGATA	61.761	61.111	14.44	0.00	36.94	2.59
671	676	0.800631	CTGCTGTGTGGTATGTGCTG	59.199	55.000	0.00	0.00	0.00	4.41
674	679	0.800631	CTGTGTGGTATGTGCTGCTG	59.199	55.000	0.00	0.00	0.00	4.41
696	701	1.960763	TGTGGTACTTGCTGCTGCG	60.961	57.895	11.21	0.00	43.34	5.18
750	755	7.120432	ACAAAATAGTGGAGAAGAAGAGATTGC	59.880	37.037	0.00	0.00	0.00	3.56
835	840	1.462238	AAGAGGTGGTGCTGGAGGT	60.462	57.895	0.00	0.00	0.00	3.85
983	993	1.403814	CTGCCTGGGAAGATCGTAGA	58.596	55.000	0.00	0.00	45.75	2.59
986	996	1.964223	GCCTGGGAAGATCGTAGATGA	59.036	52.381	0.00	0.00	45.12	2.92
989	999	3.576118	CCTGGGAAGATCGTAGATGATGT	59.424	47.826	0.00	0.00	45.12	3.06
1039	1052	1.561542	AGACCAGGGTCATGGATTCAC	59.438	52.381	19.92	0.00	46.76	3.18
1042	1055	1.386533	CAGGGTCATGGATTCACTGC	58.613	55.000	0.00	0.00	0.00	4.40
1043	1056	0.994247	AGGGTCATGGATTCACTGCA	59.006	50.000	0.00	0.00	0.00	4.41
1056	1069	2.593725	CTGCAGCCGGATGATGGG	60.594	66.667	26.87	5.54	0.00	4.00
1065	1078	0.171007	CGGATGATGGGTGTTTGTGC	59.829	55.000	0.00	0.00	0.00	4.57
1069	1082	0.464554	TGATGGGTGTTTGTGCGACA	60.465	50.000	0.00	0.00	0.00	4.35
1106	1130	2.968574	GGCATGTAGGAGATGAAGGAGA	59.031	50.000	0.00	0.00	0.00	3.71
1182	1208	1.375523	GAAGGCGACGGTGAATGGT	60.376	57.895	0.00	0.00	0.00	3.55
1220	1246	1.135315	GTGCAGCAAGTATGTGGCG	59.865	57.895	0.00	0.00	32.59	5.69
1829	4736	2.604462	TCGATGATGAAACATCACTGCG	59.396	45.455	15.11	16.96	44.57	5.18
1893	4802	7.603180	TCCTGCTGTAATGAATGTAGTAGAT	57.397	36.000	0.00	0.00	0.00	1.98
1895	4804	9.143155	TCCTGCTGTAATGAATGTAGTAGATAA	57.857	33.333	0.00	0.00	0.00	1.75
1896	4805	9.416794	CCTGCTGTAATGAATGTAGTAGATAAG	57.583	37.037	0.00	0.00	0.00	1.73
1898	4807	9.967346	TGCTGTAATGAATGTAGTAGATAAGAC	57.033	33.333	0.00	0.00	0.00	3.01
1899	4808	9.413048	GCTGTAATGAATGTAGTAGATAAGACC	57.587	37.037	0.00	0.00	0.00	3.85
1900	4809	9.613957	CTGTAATGAATGTAGTAGATAAGACCG	57.386	37.037	0.00	0.00	0.00	4.79
1901	4810	9.128404	TGTAATGAATGTAGTAGATAAGACCGT	57.872	33.333	0.00	0.00	0.00	4.83
1902	4811	9.962783	GTAATGAATGTAGTAGATAAGACCGTT	57.037	33.333	0.00	0.00	0.00	4.44
1904	4813	9.530633	AATGAATGTAGTAGATAAGACCGTTTC	57.469	33.333	0.00	0.00	0.00	2.78
1905	4814	7.191551	TGAATGTAGTAGATAAGACCGTTTCG	58.808	38.462	0.00	0.00	0.00	3.46
1906	4815	6.932356	ATGTAGTAGATAAGACCGTTTCGA	57.068	37.500	0.00	0.00	0.00	3.71
1907	4816	6.741992	TGTAGTAGATAAGACCGTTTCGAA	57.258	37.500	0.00	0.00	0.00	3.71
1908	4817	7.144722	TGTAGTAGATAAGACCGTTTCGAAA	57.855	36.000	6.47	6.47	0.00	3.46
1909	4818	7.592938	TGTAGTAGATAAGACCGTTTCGAAAA	58.407	34.615	13.10	0.00	0.00	2.29
1910	4819	8.081633	TGTAGTAGATAAGACCGTTTCGAAAAA	58.918	33.333	13.10	0.00	0.00	1.94
2056	4981	0.537143	GGACAAGCCATGTGGTGTCA	60.537	55.000	18.74	0.00	44.12	3.58
2147	5089	9.260002	GAAACTTTCCAATGCTTCAAGAATTTA	57.740	29.630	0.00	0.00	0.00	1.40
2188	5130	8.458573	AATCACTACAATGTTCAGGTACAAAA	57.541	30.769	0.00	0.00	0.00	2.44
2189	5131	8.635765	ATCACTACAATGTTCAGGTACAAAAT	57.364	30.769	0.00	0.00	0.00	1.82
2382	5337	8.067751	ACTATGAATGTGCTGAAAGTCTAGTA	57.932	34.615	0.00	0.00	35.30	1.82
2617	5572	2.352960	GGCCGTCAAGTGAATCTTCATC	59.647	50.000	0.00	0.00	39.73	2.92
2657	5613	2.438021	TGAGGCTACAAGTGTTGGAGTT	59.562	45.455	0.95	0.00	43.78	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
107	109	9.750125	AAGTTCTGTATTGACATTTTTCCTTTC	57.250	29.630	0.00	0.00	34.24	2.62
180	182	4.670896	ATTTCTGTCCTTGGGTGTTTTG	57.329	40.909	0.00	0.00	0.00	2.44
181	183	5.692115	AAATTTCTGTCCTTGGGTGTTTT	57.308	34.783	0.00	0.00	0.00	2.43
187	189	4.576463	CGAGGATAAATTTCTGTCCTTGGG	59.424	45.833	18.31	10.32	41.03	4.12
282	284	9.303116	TCAGGTTTTATTGCAAGTTTATTAGGA	57.697	29.630	4.94	0.00	0.00	2.94
330	332	4.127171	CAGTACTTGGGCACATATACCAC	58.873	47.826	6.53	0.00	33.20	4.16
350	352	3.530067	GCCTTTATGGGCCAGCAG	58.470	61.111	13.78	7.41	45.92	4.24
431	434	4.385825	ACCTGTTCGATATGTGTTGTTGT	58.614	39.130	0.00	0.00	0.00	3.32
448	451	0.044855	AGGAGGGATGCCTAACCTGT	59.955	55.000	12.21	0.00	34.02	4.00
494	497	2.812499	GTCGCCTCCGCCTATGAA	59.188	61.111	0.00	0.00	0.00	2.57
495	498	3.592814	CGTCGCCTCCGCCTATGA	61.593	66.667	0.00	0.00	0.00	2.15
516	519	3.804329	ATACCCCGCCATTGCCGT	61.804	61.111	0.00	0.00	0.00	5.68
521	524	2.195683	CTGCCATACCCCGCCATT	59.804	61.111	0.00	0.00	0.00	3.16
553	556	2.737180	CCCGTATCCAGCTCGCAT	59.263	61.111	0.00	0.00	0.00	4.73
633	636	3.799366	CAGCAGCATTCTCTCAATCTCT	58.201	45.455	0.00	0.00	0.00	3.10
671	676	0.886490	AGCAAGTACCACACAGCAGC	60.886	55.000	0.00	0.00	34.08	5.25
674	679	0.886490	AGCAGCAAGTACCACACAGC	60.886	55.000	0.00	0.00	0.00	4.40
696	701	5.041940	CCCTACTCTAAAATCAGCACGTAC	58.958	45.833	0.00	0.00	0.00	3.67
725	730	7.470900	GCAATCTCTTCTTCTCCACTATTTTG	58.529	38.462	0.00	0.00	0.00	2.44
750	755	1.150567	GCAGCAGCTCCAGTCATACG	61.151	60.000	0.00	0.00	37.91	3.06
853	859	4.162509	GCTCCTACTTTACACTCCCAAGAT	59.837	45.833	0.00	0.00	0.00	2.40
858	864	2.168728	CCAGCTCCTACTTTACACTCCC	59.831	54.545	0.00	0.00	0.00	4.30
983	993	5.508567	TGAACATATCCACAACCACATCAT	58.491	37.500	0.00	0.00	0.00	2.45
986	996	4.155826	CGTTGAACATATCCACAACCACAT	59.844	41.667	0.00	0.00	39.22	3.21
989	999	3.749088	GTCGTTGAACATATCCACAACCA	59.251	43.478	0.00	0.00	39.22	3.67
1039	1052	2.593725	CCCATCATCCGGCTGCAG	60.594	66.667	10.11	10.11	0.00	4.41
1042	1055	0.680921	AAACACCCATCATCCGGCTG	60.681	55.000	0.00	0.00	0.00	4.85
1043	1056	0.680921	CAAACACCCATCATCCGGCT	60.681	55.000	0.00	0.00	0.00	5.52
1056	1069	0.304705	CCTCTGTGTCGCACAAACAC	59.695	55.000	12.53	5.87	44.08	3.32
1065	1078	1.203523	CTTCCTCCTTCCTCTGTGTCG	59.796	57.143	0.00	0.00	0.00	4.35
1069	1082	0.178891	TGCCTTCCTCCTTCCTCTGT	60.179	55.000	0.00	0.00	0.00	3.41
1106	1130	0.905357	CCTCTTCCGGTCATGGTCTT	59.095	55.000	0.00	0.00	0.00	3.01
1155	1181	2.973899	GTCGCCTTCTCTGCCTCA	59.026	61.111	0.00	0.00	0.00	3.86
1182	1208	1.408340	CATGTCCACAGCAAACCAACA	59.592	47.619	0.00	0.00	0.00	3.33
1355	1463	1.110442	TGTGGCCTTTTCAGTGTTGG	58.890	50.000	3.32	0.00	0.00	3.77
1731	4629	2.768527	CTCACAGTCCATGTACCTCCAT	59.231	50.000	0.00	0.00	41.41	3.41
1829	4736	2.629617	CAAAGGATACATGCCCCATTCC	59.370	50.000	0.00	0.00	41.41	3.01
2056	4981	5.009610	CACAAAATACCTTGCACCACTAACT	59.990	40.000	0.00	0.00	0.00	2.24
2147	5089	8.978874	TGTAGTGATTTTTCACATAGGCATAT	57.021	30.769	8.66	0.00	42.68	1.78
2188	5130	8.757982	ACTCAGTGCCATTATCAATTCTTTAT	57.242	30.769	0.00	0.00	0.00	1.40
2189	5131	9.851686	ATACTCAGTGCCATTATCAATTCTTTA	57.148	29.630	0.00	0.00	0.00	1.85
2196	5139	5.988287	TCACATACTCAGTGCCATTATCAA	58.012	37.500	0.00	0.00	36.93	2.57
2382	5337	3.541242	TGGTTTGTCAGGGATCCAATT	57.459	42.857	15.23	0.00	0.00	2.32
2617	5572	2.104111	TCACTGCCCATAAGAATACCCG	59.896	50.000	0.00	0.00	0.00	5.28

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.