AutoCloner

Multiple sequence alignment - TraesCS3D01G233200

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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	TraesCS3D01G233200	chr3D	100.000	3659	0	0	1	3659	321870500	321874158	0.000000e+00	6758.0
1	TraesCS3D01G233200	chr3D	95.329	835	38	1	1	834	143153243	143154077	0.000000e+00	1325.0
2	TraesCS3D01G233200	chr3D	95.716	747	31	1	1	747	9070619	9069874	0.000000e+00	1201.0
3	TraesCS3D01G233200	chr3D	91.966	834	38	10	1	833	602822937	602823742	0.000000e+00	1142.0
4	TraesCS3D01G233200	chr3D	89.583	144	15	0	3077	3220	508465557	508465700	2.240000e-42	183.0
5	TraesCS3D01G233200	chr3D	83.240	179	15	7	3218	3383	508466470	508466646	2.280000e-32	150.0
6	TraesCS3D01G233200	chr3D	85.567	97	4	2	2919	3015	606777996	606777910	3.890000e-15	93.5
7	TraesCS3D01G233200	chr3A	95.198	2020	58	22	1665	3659	402135971	402133966	0.000000e+00	3157.0
8	TraesCS3D01G233200	chr3A	93.972	846	30	8	833	1667	402136887	402136052	0.000000e+00	1260.0
9	TraesCS3D01G233200	chr3B	91.811	1734	95	15	833	2540	397679309	397677597	0.000000e+00	2372.0
10	TraesCS3D01G233200	chr3B	93.773	1092	46	12	2580	3659	397677488	397676407	0.000000e+00	1620.0
11	TraesCS3D01G233200	chr1B	94.780	1092	38	11	2580	3659	637912904	637911820	0.000000e+00	1683.0
12	TraesCS3D01G233200	chr1B	86.303	898	80	19	1669	2543	637913886	637913009	0.000000e+00	937.0
13	TraesCS3D01G233200	chr2D	95.574	836	36	1	1	835	595505003	595504168	0.000000e+00	1338.0
14	TraesCS3D01G233200	chr2D	95.455	770	22	5	898	1665	634645040	634645798	0.000000e+00	1216.0
15	TraesCS3D01G233200	chr2D	94.423	789	29	9	2876	3659	634649448	634650226	0.000000e+00	1199.0
16	TraesCS3D01G233200	chr2D	87.542	899	72	15	1669	2543	634646754	634647636	0.000000e+00	1003.0
17	TraesCS3D01G233200	chr2D	96.117	309	11	1	2580	2888	634647741	634648048	1.520000e-138	503.0
18	TraesCS3D01G233200	chr7D	95.215	836	38	2	1	835	613373766	613374600	0.000000e+00	1321.0
19	TraesCS3D01G233200	chr7D	94.504	837	44	2	1	836	64068171	64067336	0.000000e+00	1290.0
20	TraesCS3D01G233200	chr7D	85.227	264	27	4	3131	3383	41303797	41303535	1.010000e-65	261.0
21	TraesCS3D01G233200	chr7D	87.442	215	16	3	2919	3133	41306360	41306157	1.700000e-58	237.0
22	TraesCS3D01G233200	chr5B	94.691	810	41	2	1	810	110043074	110043881	0.000000e+00	1256.0
23	TraesCS3D01G233200	chr6D	93.668	837	40	2	1	833	472322506	472323333	0.000000e+00	1240.0
24	TraesCS3D01G233200	chr6D	84.548	343	30	11	3239	3566	367749521	367749855	5.900000e-83	318.0
25	TraesCS3D01G233200	chr1D	93.653	835	40	8	2777	3604	462947671	462946843	0.000000e+00	1236.0
26	TraesCS3D01G233200	chr1D	95.579	769	23	4	897	1665	462968196	462967439	0.000000e+00	1221.0
27	TraesCS3D01G233200	chr1D	95.319	769	25	5	897	1665	462927762	462927005	0.000000e+00	1210.0
28	TraesCS3D01G233200	chr1D	95.065	770	25	5	897	1665	462890812	462890055	0.000000e+00	1199.0
29	TraesCS3D01G233200	chr1D	94.935	770	26	6	897	1665	462898498	462897741	0.000000e+00	1194.0
30	TraesCS3D01G233200	chr1D	94.928	769	28	5	897	1665	462913885	462913128	0.000000e+00	1194.0
31	TraesCS3D01G233200	chr1D	94.798	769	28	5	897	1665	462921112	462920356	0.000000e+00	1188.0
32	TraesCS3D01G233200	chr1D	87.528	898	71	17	1669	2543	462966492	462965613	0.000000e+00	1000.0
33	TraesCS3D01G233200	chr1D	92.566	417	24	3	1669	2083	462904471	462904060	3.150000e-165	592.0
34	TraesCS3D01G233200	chr1D	92.326	417	25	3	1669	2083	462909554	462909143	1.460000e-163	586.0
35	TraesCS3D01G233200	chr1D	92.326	417	25	3	1669	2083	462916782	462916371	1.460000e-163	586.0
36	TraesCS3D01G233200	chr1D	91.847	417	27	5	1669	2083	462924009	462923598	3.170000e-160	575.0
37	TraesCS3D01G233200	chr1D	97.115	208	6	0	2580	2787	462965508	462965301	5.810000e-93	351.0
38	TraesCS3D01G233200	chr5D	95.082	732	34	2	102	833	435680838	435680109	0.000000e+00	1151.0
39	TraesCS3D01G233200	chr6A	84.760	479	50	9	3054	3518	508249112	508249581	3.330000e-125	459.0

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	TraesCS3D01G233200	chr3D	321870500	321874158	3658	False	6758.000000	6758	100.000000	1	3659	1	chr3D.!!$F2	3658
1	TraesCS3D01G233200	chr3D	143153243	143154077	834	False	1325.000000	1325	95.329000	1	834	1	chr3D.!!$F1	833
2	TraesCS3D01G233200	chr3D	9069874	9070619	745	True	1201.000000	1201	95.716000	1	747	1	chr3D.!!$R1	746
3	TraesCS3D01G233200	chr3D	602822937	602823742	805	False	1142.000000	1142	91.966000	1	833	1	chr3D.!!$F3	832
4	TraesCS3D01G233200	chr3A	402133966	402136887	2921	True	2208.500000	3157	94.585000	833	3659	2	chr3A.!!$R1	2826
5	TraesCS3D01G233200	chr3B	397676407	397679309	2902	True	1996.000000	2372	92.792000	833	3659	2	chr3B.!!$R1	2826
6	TraesCS3D01G233200	chr1B	637911820	637913886	2066	True	1310.000000	1683	90.541500	1669	3659	2	chr1B.!!$R1	1990
7	TraesCS3D01G233200	chr2D	595504168	595505003	835	True	1338.000000	1338	95.574000	1	835	1	chr2D.!!$R1	834
8	TraesCS3D01G233200	chr2D	634645040	634650226	5186	False	980.250000	1216	93.384250	898	3659	4	chr2D.!!$F1	2761
9	TraesCS3D01G233200	chr7D	613373766	613374600	834	False	1321.000000	1321	95.215000	1	835	1	chr7D.!!$F1	834
10	TraesCS3D01G233200	chr7D	64067336	64068171	835	True	1290.000000	1290	94.504000	1	836	1	chr7D.!!$R1	835
11	TraesCS3D01G233200	chr7D	41303535	41306360	2825	True	249.000000	261	86.334500	2919	3383	2	chr7D.!!$R2	464
12	TraesCS3D01G233200	chr5B	110043074	110043881	807	False	1256.000000	1256	94.691000	1	810	1	chr5B.!!$F1	809
13	TraesCS3D01G233200	chr6D	472322506	472323333	827	False	1240.000000	1240	93.668000	1	833	1	chr6D.!!$F2	832
14	TraesCS3D01G233200	chr1D	462946843	462947671	828	True	1236.000000	1236	93.653000	2777	3604	1	chr1D.!!$R4	827
15	TraesCS3D01G233200	chr1D	462890055	462890812	757	True	1199.000000	1199	95.065000	897	1665	1	chr1D.!!$R1	768
16	TraesCS3D01G233200	chr1D	462897741	462898498	757	True	1194.000000	1194	94.935000	897	1665	1	chr1D.!!$R2	768
17	TraesCS3D01G233200	chr1D	462909143	462927762	18619	True	889.833333	1210	93.590667	897	2083	6	chr1D.!!$R5	1186
18	TraesCS3D01G233200	chr1D	462965301	462968196	2895	True	857.333333	1221	93.407333	897	2787	3	chr1D.!!$R6	1890
19	TraesCS3D01G233200	chr5D	435680109	435680838	729	True	1151.000000	1151	95.082000	102	833	1	chr5D.!!$R1	731

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
634	636	1.134753	CAGTTTGTTGAGCAGTTGCCA	59.865	47.619	0.0	0.0	43.38	4.92	F
1539	15441	0.095417	GATTTGCGGCTGTCTCGAAC	59.905	55.000	0.0	0.0	0.00	3.95	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1744	19222	0.250234	CCGCCAGATGTTCCTTCAGA	59.750	55.0	0.00	0.00	0.00	3.27	R
3211	24578	0.024238	CGACGAGGTAGTCACGTACG	59.976	60.0	15.01	15.01	40.98	3.67	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
63	64	5.046878	TCGGTCCATTGTAAGTGTATGTCTT	60.047	40.000	0.00	0.00	0.00	3.01
254	255	3.678289	TGATTTAGTCAGCACTGCATGT	58.322	40.909	3.30	0.00	33.62	3.21
413	414	4.319694	GGCAACCACAAGCATTTCATTTTC	60.320	41.667	0.00	0.00	0.00	2.29
420	421	6.645827	CCACAAGCATTTCATTTTCACACATA	59.354	34.615	0.00	0.00	0.00	2.29
467	468	8.673711	TGTATTGTAAGTATTCAGGTTTCATGC	58.326	33.333	0.00	0.00	0.00	4.06
600	602	4.998033	AGTTGAGTAGAGCTGGTTTTTAGC	59.002	41.667	0.00	0.00	41.43	3.09
634	636	1.134753	CAGTTTGTTGAGCAGTTGCCA	59.865	47.619	0.00	0.00	43.38	4.92
823	830	3.179888	TTGTAAGCGCCCCCGTTGA	62.180	57.895	2.29	0.00	36.67	3.18
924	931	1.637338	TGCATGGACTCTGTCTCTGT	58.363	50.000	0.00	0.00	32.47	3.41
927	934	1.898472	CATGGACTCTGTCTCTGTGGT	59.102	52.381	0.00	0.00	32.47	4.16
928	935	2.088104	TGGACTCTGTCTCTGTGGTT	57.912	50.000	0.00	0.00	32.47	3.67
931	938	3.964688	TGGACTCTGTCTCTGTGGTTTTA	59.035	43.478	0.00	0.00	32.47	1.52
933	940	4.932200	GGACTCTGTCTCTGTGGTTTTATG	59.068	45.833	0.00	0.00	32.47	1.90
961	968	2.637872	AGGACATCTTTGTTCCTCGGAA	59.362	45.455	0.00	0.00	35.79	4.30
1013	1022	1.310373	CTACCCCGTCTTCTCCCCT	59.690	63.158	0.00	0.00	0.00	4.79
1014	1023	0.756070	CTACCCCGTCTTCTCCCCTC	60.756	65.000	0.00	0.00	0.00	4.30
1015	1024	1.219824	TACCCCGTCTTCTCCCCTCT	61.220	60.000	0.00	0.00	0.00	3.69
1016	1025	2.060980	CCCCGTCTTCTCCCCTCTG	61.061	68.421	0.00	0.00	0.00	3.35
1017	1026	1.000486	CCCGTCTTCTCCCCTCTGA	60.000	63.158	0.00	0.00	0.00	3.27
1053	1062	1.525077	GGCCGCCATGGACGATTTA	60.525	57.895	24.22	0.00	42.00	1.40
1130	1139	2.104331	CCGCCGACGTGCTCTTAT	59.896	61.111	0.00	0.00	37.70	1.73
1356	1371	3.973516	GCAACAGCAGCAGCAGCA	61.974	61.111	12.92	0.00	45.49	4.41
1357	1372	2.255554	CAACAGCAGCAGCAGCAG	59.744	61.111	12.92	6.60	45.49	4.24
1503	10791	3.044059	GACTTCATGTGCTGCCGGC	62.044	63.158	22.73	22.73	42.22	6.13
1539	15441	0.095417	GATTTGCGGCTGTCTCGAAC	59.905	55.000	0.00	0.00	0.00	3.95
1700	19178	4.627467	ACATTTATGCTCAGTCGTGTTCTC	59.373	41.667	0.00	0.00	0.00	2.87
1714	19192	3.688272	GTGTTCTCGCATGATCAATTGG	58.312	45.455	5.42	0.00	0.00	3.16
1744	19222	4.450976	TCAACAAGCACATAGTGACAGTT	58.549	39.130	0.58	0.00	35.23	3.16
1807	19285	0.508641	GAATGGATCGTCCGCAATCG	59.491	55.000	0.59	0.00	40.17	3.34
1918	19400	0.482446	TGGTCCACCAAATCAAGCCT	59.518	50.000	0.00	0.00	44.35	4.58
1946	19428	6.094186	GGGTGAGTTCTATTTTCAACATCCTC	59.906	42.308	0.00	0.00	30.16	3.71
2006	19488	6.142817	CGAACGGAGTGAAATTTCAAAAGAT	58.857	36.000	22.07	9.06	45.00	2.40
2009	19491	9.118236	GAACGGAGTGAAATTTCAAAAGATAAG	57.882	33.333	22.07	10.68	45.00	1.73
2010	19492	8.391075	ACGGAGTGAAATTTCAAAAGATAAGA	57.609	30.769	22.07	0.00	42.51	2.10
2154	19658	3.360956	CGCAGCAAACTTTTTCATGAACG	60.361	43.478	7.89	2.40	0.00	3.95
2220	19724	3.192422	CCACGGCTTGGTTTATTTCATCA	59.808	43.478	1.04	0.00	41.10	3.07
2234	19738	4.933505	TTTCATCAGACCAACATGCAAA	57.066	36.364	0.00	0.00	0.00	3.68
2269	19775	6.014070	ACGGTATATGGGATGTGTTAGCATTA	60.014	38.462	0.00	0.00	0.00	1.90
2298	19804	1.295792	GTTCCTTTGTGCAGTGACGA	58.704	50.000	0.00	0.00	0.00	4.20
2338	19844	6.146184	TCGTCTTCAATCATTCAGACTTTCAC	59.854	38.462	5.16	0.00	34.62	3.18
2478	19987	0.809385	CTTGGCAGCCAGATCAACAG	59.191	55.000	15.50	3.15	33.81	3.16
2587	20165	9.646522	ATCTTCCAAATAGCCACAAATTAGTAT	57.353	29.630	0.00	0.00	0.00	2.12
2695	20273	5.406780	GTGAAAAGTCTACACTGGACTGATG	59.593	44.000	0.00	0.00	42.39	3.07
2727	20308	9.370126	GTAGAACACAAGCATATATTAAAAGCG	57.630	33.333	0.00	0.00	0.00	4.68
2797	20378	5.891198	TGGGGTACAACTCTTACTAGTACA	58.109	41.667	0.91	0.00	37.40	2.90
2928	21926	9.950496	ATAGTGTCAATACTTTTCTCTCATGTT	57.050	29.630	0.00	0.00	32.19	2.71
3021	22023	1.673033	CCACTTGGAGACATCGTCCAC	60.673	57.143	0.00	0.00	44.06	4.02
3211	24578	4.493747	CGACCTCTCGCCGTTCCC	62.494	72.222	0.00	0.00	31.91	3.97
3323	24711	2.030371	TCAGCACATGGACTGCAAAAA	58.970	42.857	11.32	0.00	37.08	1.94
3421	24810	0.620556	TCAATCTTGGTCCTCAGGGC	59.379	55.000	0.00	0.00	0.00	5.19
3545	24940	1.077787	CCAGCCGCTCAACCCAATA	60.078	57.895	0.00	0.00	0.00	1.90

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
5	6	4.789012	ATGCCTGGTAAGTCATTTGTTG	57.211	40.909	0.00	0.00	0.00	3.33
211	212	4.141233	TGCATGCAGTAAAGCTATCTCA	57.859	40.909	18.46	0.00	34.99	3.27
254	255	7.385752	CGGTTAAATCGGCCTAACTAAATCATA	59.614	37.037	11.24	0.00	0.00	2.15
442	443	8.673711	TGCATGAAACCTGAATACTTACAATAC	58.326	33.333	0.00	0.00	0.00	1.89
600	602	1.003545	CAAACTGAGCTGGTCGTTGTG	60.004	52.381	14.34	11.58	0.00	3.33
634	636	3.718815	GCTACCTAGAGCGCTACAAATT	58.281	45.455	11.50	0.00	31.57	1.82
663	665	0.535335	TTTCTCCGTTCGGATCTGGG	59.465	55.000	14.34	3.02	33.34	4.45
731	734	0.396139	ATTTGGGCTGGCATCGATGT	60.396	50.000	25.47	0.00	0.00	3.06
804	811	2.670592	AACGGGGGCGCTTACAAC	60.671	61.111	7.64	0.00	0.00	3.32
823	830	0.331616	GGGTCCTGTTAGGGCATGTT	59.668	55.000	1.50	0.00	43.30	2.71
924	931	9.747898	AAAGATGTCCTATACAACATAAAACCA	57.252	29.630	0.00	0.00	42.70	3.67
931	938	7.633789	AGGAACAAAGATGTCCTATACAACAT	58.366	34.615	0.00	0.00	42.70	2.71
933	940	6.255887	CGAGGAACAAAGATGTCCTATACAAC	59.744	42.308	0.00	0.00	42.70	3.32
961	968	0.109086	CGAGTCTGATGCACGGAGTT	60.109	55.000	0.00	0.00	41.61	3.01
1013	1022	3.481559	AGGAAGAAGGGTCAGATCAGA	57.518	47.619	0.00	0.00	0.00	3.27
1014	1023	3.370315	CCAAGGAAGAAGGGTCAGATCAG	60.370	52.174	0.00	0.00	0.00	2.90
1015	1024	2.573462	CCAAGGAAGAAGGGTCAGATCA	59.427	50.000	0.00	0.00	0.00	2.92
1016	1025	2.682269	GCCAAGGAAGAAGGGTCAGATC	60.682	54.545	0.00	0.00	0.00	2.75
1017	1026	1.283321	GCCAAGGAAGAAGGGTCAGAT	59.717	52.381	0.00	0.00	0.00	2.90
1130	1139	1.477685	GGTTTCGGTGAGGAGGACCA	61.478	60.000	0.00	0.00	38.94	4.02
1356	1371	4.982701	GCACCCCTGCCACTTGCT	62.983	66.667	0.00	0.00	42.00	3.91
1358	1373	3.297620	GTGCACCCCTGCCACTTG	61.298	66.667	5.22	0.00	43.51	3.16
1700	19178	0.933047	CGCTGCCAATTGATCATGCG	60.933	55.000	7.12	15.37	36.41	4.73
1744	19222	0.250234	CCGCCAGATGTTCCTTCAGA	59.750	55.000	0.00	0.00	0.00	3.27
1807	19285	0.438830	GAAGCCATGTCGTCGTTGAC	59.561	55.000	0.00	3.37	39.37	3.18
1918	19400	5.450453	TGTTGAAAATAGAACTCACCCCAA	58.550	37.500	0.00	0.00	0.00	4.12
1946	19428	2.868583	CAGGAGTAGATGGCATTTGACG	59.131	50.000	0.00	0.00	0.00	4.35
2090	19573	5.451798	GGATCATAATTTGGCAACGATTGGT	60.452	40.000	0.00	0.00	42.51	3.67
2154	19658	7.805071	CACAAAGAAGACTTATCACATCAAACC	59.195	37.037	0.00	0.00	35.05	3.27
2220	19724	3.225104	ACTGTCATTTGCATGTTGGTCT	58.775	40.909	0.00	0.00	0.00	3.85
2234	19738	6.042781	ACATCCCATATACCGTAAACTGTCAT	59.957	38.462	0.00	0.00	0.00	3.06
2269	19775	5.477984	ACTGCACAAAGGAACACATGATTAT	59.522	36.000	0.00	0.00	0.00	1.28
2315	19821	6.205464	TGGTGAAAGTCTGAATGATTGAAGAC	59.795	38.462	8.74	8.74	39.47	3.01
2338	19844	2.632028	TGTTTGGGGATCAACATTGTGG	59.368	45.455	0.00	0.00	34.67	4.17
2385	19891	0.935898	GTCATTGCTCAGCGATCCAG	59.064	55.000	0.00	0.00	28.96	3.86
2478	19987	4.253685	TCAAGATCAACTTCCACCGAATC	58.746	43.478	0.00	0.00	36.61	2.52
2727	20308	5.815740	ACCACACCAGTAATTTATGACGATC	59.184	40.000	0.00	0.00	0.00	3.69
3084	22086	9.731819	CCACATGATCATTATTTTTCTTCTGAG	57.268	33.333	5.16	0.00	0.00	3.35
3211	24578	0.024238	CGACGAGGTAGTCACGTACG	59.976	60.000	15.01	15.01	40.98	3.67
3323	24711	5.951747	TGGAAGAGGTTAGCATTGCTATTTT	59.048	36.000	18.62	6.27	41.01	1.82
3324	24712	5.509498	TGGAAGAGGTTAGCATTGCTATTT	58.491	37.500	18.62	7.81	41.01	1.40
3545	24940	2.567615	CCCTATTACCCTCAGCGCTATT	59.432	50.000	10.99	0.00	0.00	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.