AutoCloner

Multiple sequence alignment - TraesCS5A01G037800

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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	TraesCS5A01G037800	chr5A	100.000	7212	0	0	1	7212	34943376	34936165	0.000000e+00	13319
1	TraesCS5A01G037800	chr5A	97.147	7220	175	20	1	7212	465654119	465661315	0.000000e+00	12163
2	TraesCS5A01G037800	chr5A	96.759	7220	202	18	1	7212	541976899	541984094	0.000000e+00	12008
3	TraesCS5A01G037800	chr2A	97.272	7221	174	17	1	7212	685104325	685097119	0.000000e+00	12222
4	TraesCS5A01G037800	chr2A	96.981	7221	194	20	1	7212	284799907	284807112	0.000000e+00	12105
5	TraesCS5A01G037800	chr2A	96.816	7224	191	20	1	7212	572969922	572962726	0.000000e+00	12030
6	TraesCS5A01G037800	chr2A	96.691	7222	187	26	1	7212	80119629	80126808	0.000000e+00	11965
7	TraesCS5A01G037800	chr2A	96.469	7221	216	27	1	7212	716654164	716646974	0.000000e+00	11886
8	TraesCS5A01G037800	chr2A	96.983	4276	107	17	1	4269	384174893	384170633	0.000000e+00	7162
9	TraesCS5A01G037800	chr2A	88.688	2767	249	40	3	2756	160674569	160671854	0.000000e+00	3317
10	TraesCS5A01G037800	chr2A	88.542	2566	258	27	200	2750	369287157	369289701	0.000000e+00	3077
11	TraesCS5A01G037800	chr2A	88.806	1742	146	26	1013	2751	116996501	116994806	0.000000e+00	2091
12	TraesCS5A01G037800	chr2A	82.112	464	49	25	6761	7201	264101762	264101310	4.110000e-97	366
13	TraesCS5A01G037800	chr6A	97.007	7218	169	21	1	7212	158983448	158976272	0.000000e+00	12089
14	TraesCS5A01G037800	chr3A	96.801	7222	183	19	1	7212	662010411	662003228	0.000000e+00	12013
15	TraesCS5A01G037800	chr3A	96.469	7222	223	21	1	7212	554827438	554834637	0.000000e+00	11895
16	TraesCS5A01G037800	chr1A	97.388	6355	149	11	861	7212	70944910	70938570	0.000000e+00	10800
17	TraesCS5A01G037800	chr7B	90.450	2775	219	29	1	2756	665789672	665792419	0.000000e+00	3615

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	TraesCS5A01G037800	chr5A	34936165	34943376	7211	True	13319	13319	100.000	1	7212	1	chr5A.!!$R1	7211
1	TraesCS5A01G037800	chr5A	465654119	465661315	7196	False	12163	12163	97.147	1	7212	1	chr5A.!!$F1	7211
2	TraesCS5A01G037800	chr5A	541976899	541984094	7195	False	12008	12008	96.759	1	7212	1	chr5A.!!$F2	7211
3	TraesCS5A01G037800	chr2A	685097119	685104325	7206	True	12222	12222	97.272	1	7212	1	chr2A.!!$R6	7211
4	TraesCS5A01G037800	chr2A	284799907	284807112	7205	False	12105	12105	96.981	1	7212	1	chr2A.!!$F2	7211
5	TraesCS5A01G037800	chr2A	572962726	572969922	7196	True	12030	12030	96.816	1	7212	1	chr2A.!!$R5	7211
6	TraesCS5A01G037800	chr2A	80119629	80126808	7179	False	11965	11965	96.691	1	7212	1	chr2A.!!$F1	7211
7	TraesCS5A01G037800	chr2A	716646974	716654164	7190	True	11886	11886	96.469	1	7212	1	chr2A.!!$R7	7211
8	TraesCS5A01G037800	chr2A	384170633	384174893	4260	True	7162	7162	96.983	1	4269	1	chr2A.!!$R4	4268
9	TraesCS5A01G037800	chr2A	160671854	160674569	2715	True	3317	3317	88.688	3	2756	1	chr2A.!!$R2	2753
10	TraesCS5A01G037800	chr2A	369287157	369289701	2544	False	3077	3077	88.542	200	2750	1	chr2A.!!$F3	2550
11	TraesCS5A01G037800	chr2A	116994806	116996501	1695	True	2091	2091	88.806	1013	2751	1	chr2A.!!$R1	1738
12	TraesCS5A01G037800	chr6A	158976272	158983448	7176	True	12089	12089	97.007	1	7212	1	chr6A.!!$R1	7211
13	TraesCS5A01G037800	chr3A	662003228	662010411	7183	True	12013	12013	96.801	1	7212	1	chr3A.!!$R1	7211
14	TraesCS5A01G037800	chr3A	554827438	554834637	7199	False	11895	11895	96.469	1	7212	1	chr3A.!!$F1	7211
15	TraesCS5A01G037800	chr1A	70938570	70944910	6340	True	10800	10800	97.388	861	7212	1	chr1A.!!$R1	6351
16	TraesCS5A01G037800	chr7B	665789672	665792419	2747	False	3615	3615	90.450	1	2756	1	chr7B.!!$F1	2755

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	Hairpin	End Stability	Orientation
982	1014	0.390472	GTCTCTCTCCAAAGCCCACG	60.390	60.000	0.00	0.00	4.94	F
1473	1511	0.380378	TTGTGAAAAGTGGACGCAGC	59.620	50.000	0.00	0.00	5.25	F
2204	2249	1.072806	TCCTTGACTGATGTTGCAGCT	59.927	47.619	1.17	39.51	4.24	F
3139	3197	1.891150	GGCGAATCCCTAGTAATCCGA	59.109	52.381	0.00	0.00	4.55	F
4691	4759	1.003355	CCAGCGGCTCTCTCCAAAA	60.003	57.895	0.00	0.00	2.44	F
4893	4961	2.742372	CGAACCAGACAAGGCCGG	60.742	66.667	0.00	0.00	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2860	2913	2.667473	ATGGTACTTGCGTGTAGACC	57.333	50.000	0.0	0.00	0.00	3.85	R
3339	3403	0.980754	TTTCCGGCCCAGATAGCTCA	60.981	55.000	0.0	0.00	0.00	4.26	R
4092	4159	5.920273	ACTGAATTGTAATTTCAAACAGCGG	59.080	36.000	22.3	12.19	38.25	5.52	R
4856	4924	0.247460	CTGGTGCAGACGATCTCCAA	59.753	55.000	0.0	0.00	32.44	3.53	R
6096	6174	0.179225	CCATGACTTGTACGTTGCGC	60.179	55.000	0.0	0.00	0.00	6.09	R
6530	6608	3.507411	TGTCCTTAGTTAGTCTGCCACT	58.493	45.455	0.0	0.00	39.41	4.00	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
194	198	8.828644	ACTCTTGTATTACGTCAGTACTGATAG	58.171	37.037	27.54	24.34	42.18	2.08
522	544	6.381801	GTTCAATTACACTTCAATCACCAGG	58.618	40.000	0.00	0.00	0.00	4.45
631	653	1.268896	ACTATACGAATCGGTGCCACG	60.269	52.381	7.80	0.00	0.00	4.94
753	776	7.255346	CCATTTAACTTGGACGGTTAGTTCTTT	60.255	37.037	7.28	0.00	36.26	2.52
982	1014	0.390472	GTCTCTCTCCAAAGCCCACG	60.390	60.000	0.00	0.00	0.00	4.94
1214	1246	1.892819	CTCTGGAGGAAGCTTGGCGA	61.893	60.000	2.10	0.00	0.00	5.54
1225	1263	1.970917	GCTTGGCGACAGGATTCGTG	61.971	60.000	3.68	4.86	44.54	4.35
1372	1410	3.459598	AGCAATCCTACTCATTTGCCCTA	59.540	43.478	3.10	0.00	44.21	3.53
1468	1506	3.192633	AGTGTGGTTTGTGAAAAGTGGAC	59.807	43.478	0.00	0.00	0.00	4.02
1472	1510	2.450160	GTTTGTGAAAAGTGGACGCAG	58.550	47.619	0.00	0.00	0.00	5.18
1473	1511	0.380378	TTGTGAAAAGTGGACGCAGC	59.620	50.000	0.00	0.00	0.00	5.25
1474	1512	1.082756	GTGAAAAGTGGACGCAGCG	60.083	57.895	14.82	14.82	0.00	5.18
1475	1513	2.250939	TGAAAAGTGGACGCAGCGG	61.251	57.895	21.15	0.70	0.00	5.52
1476	1514	3.595108	GAAAAGTGGACGCAGCGGC	62.595	63.158	21.15	17.92	0.00	6.53
1501	1539	9.294030	GCCACAAAATTTTCTCAAGTAGATATG	57.706	33.333	0.00	0.00	33.05	1.78
1595	1634	7.431249	TGAAGTTGATCGACTAGTGTAGTTTT	58.569	34.615	16.19	0.00	39.59	2.43
2204	2249	1.072806	TCCTTGACTGATGTTGCAGCT	59.927	47.619	1.17	0.00	39.51	4.24
2216	2261	2.026915	TGTTGCAGCTAGTGTCATCCAT	60.027	45.455	1.17	0.00	0.00	3.41
2463	2510	5.070847	TGAAGATACATCAGAGCATGCCTTA	59.929	40.000	15.66	3.24	0.00	2.69
2474	2521	5.645497	CAGAGCATGCCTTAGTTTTACTTCT	59.355	40.000	15.66	2.53	0.00	2.85
2505	2552	5.752955	GCTTGCCTTTTATCTTGTTGTTTCA	59.247	36.000	0.00	0.00	0.00	2.69
2695	2748	5.401531	AGTAGCTTCTGAATGGAACGTTA	57.598	39.130	0.00	0.00	0.00	3.18
2714	2767	6.866179	CGTTATCGTTGCTCTAAAGTACTT	57.134	37.500	1.12	1.12	0.00	2.24
2860	2913	5.102313	TGAATGCACTATCAGTACAACTCG	58.898	41.667	0.00	0.00	0.00	4.18
2897	2950	7.680730	AGTACCATAGTTCTGAAAATGACACT	58.319	34.615	12.96	11.80	0.00	3.55
2941	2996	9.662545	AATCACAAAAACAAACACAAAAAGAAG	57.337	25.926	0.00	0.00	0.00	2.85
2943	2998	6.359352	CACAAAAACAAACACAAAAAGAAGGC	59.641	34.615	0.00	0.00	0.00	4.35
3020	3077	9.841295	AACAAAAAGTATGAGTCCAAGTTACTA	57.159	29.630	0.00	0.00	0.00	1.82
3030	3087	5.011586	AGTCCAAGTTACTAGAGGAGTCAC	58.988	45.833	0.00	0.00	39.81	3.67
3114	3172	5.667539	TGCTAGATACTTGAACTTGAGCT	57.332	39.130	0.00	0.00	0.00	4.09
3139	3197	1.891150	GGCGAATCCCTAGTAATCCGA	59.109	52.381	0.00	0.00	0.00	4.55
3194	3258	3.513438	GAGAGAGAGCGAGCGCCA	61.513	66.667	11.66	0.00	43.17	5.69
3223	3287	3.388024	AGCACTCAGGTAAGTGTTCAGAA	59.612	43.478	5.97	0.00	46.77	3.02
3452	3516	5.677852	GCGGGACAAAGAAATATAAACCACC	60.678	44.000	0.00	0.00	0.00	4.61
4092	4159	6.222389	TGTGACATCAAATTTCAAACCCATC	58.778	36.000	0.00	0.00	0.00	3.51
4312	4379	4.698304	ACAATACTTAAACATCCACACGGG	59.302	41.667	0.00	0.00	38.37	5.28
4427	4494	6.940739	AGTACAGCTTGACAAGACTAATCAT	58.059	36.000	19.51	3.23	0.00	2.45
4586	4653	3.936203	ACACACCACCATCGGCGT	61.936	61.111	6.85	0.00	0.00	5.68
4691	4759	1.003355	CCAGCGGCTCTCTCCAAAA	60.003	57.895	0.00	0.00	0.00	2.44
4856	4924	3.805928	TCCATGGCAAGGAGACGT	58.194	55.556	7.49	0.00	0.00	4.34
4893	4961	2.742372	CGAACCAGACAAGGCCGG	60.742	66.667	0.00	0.00	0.00	6.13
5386	5462	5.836024	TCTTTGGTGAAGTGGTATAGGTT	57.164	39.130	0.00	0.00	36.70	3.50
5568	5644	8.246180	TGATTCTCTAATTTGGTGAAGCATTTC	58.754	33.333	10.24	1.68	31.06	2.17
5837	5915	7.175990	GGGAGGAGAAATTGTACACATTTGTTA	59.824	37.037	15.92	0.00	37.15	2.41
6002	6080	4.450976	CGTCATCCACCCATTCTATGAAA	58.549	43.478	0.00	0.00	0.00	2.69
6679	6762	2.270352	TTCAGCCGAGGACAACATTT	57.730	45.000	0.00	0.00	0.00	2.32
6774	6858	5.125097	ACACCAGTACGTATTTCCTAGTCAG	59.875	44.000	0.00	0.00	0.00	3.51
6880	6964	4.398549	TCAGTTCGCATTCCTTAAAACG	57.601	40.909	0.00	0.00	0.00	3.60
7140	7227	6.552445	AGTACTAGCACAATTGGAATCTCT	57.448	37.500	10.83	0.24	0.00	3.10
7152	7239	7.119846	ACAATTGGAATCTCTGTACAACTAAGC	59.880	37.037	10.83	0.00	0.00	3.09

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	9.679661	TTAAATAATAATGTCACTCCTTCAGCA	57.320	29.630	0.00	0.00	0.00	4.41
194	198	0.243907	TTGTACTGCCGACTGAGAGC	59.756	55.000	0.00	0.00	0.00	4.09
335	348	8.835439	TGTATTATATTCGCATTTTGCTTGAGA	58.165	29.630	0.00	0.00	42.25	3.27
522	544	0.656785	CCTCTACTGTCGTACTCGGC	59.343	60.000	0.00	0.00	42.45	5.54
631	653	3.181476	GGTGGTGATGATGGCATTTTACC	60.181	47.826	14.55	14.55	34.11	2.85
1214	1246	1.069204	CGATGATCCCACGAATCCTGT	59.931	52.381	0.00	0.00	0.00	4.00
1225	1263	2.180204	CACCAACGCCGATGATCCC	61.180	63.158	0.00	0.00	0.00	3.85
1468	1506	1.220817	AAAATTTTGTGGCCGCTGCG	61.221	50.000	18.96	16.34	38.85	5.18
1472	1510	2.147436	TGAGAAAATTTTGTGGCCGC	57.853	45.000	10.11	10.11	0.00	6.53
1473	1511	3.716601	ACTTGAGAAAATTTTGTGGCCG	58.283	40.909	8.47	0.00	0.00	6.13
1474	1512	6.084326	TCTACTTGAGAAAATTTTGTGGCC	57.916	37.500	8.47	0.00	0.00	5.36
1475	1513	9.294030	CATATCTACTTGAGAAAATTTTGTGGC	57.706	33.333	8.47	0.00	37.85	5.01
1476	1514	9.294030	GCATATCTACTTGAGAAAATTTTGTGG	57.706	33.333	8.47	1.98	37.85	4.17
1595	1634	8.824756	AGACTACTCTATTGTATCAACTCCAA	57.175	34.615	0.00	0.00	0.00	3.53
1921	1963	8.805175	TGTTTTACAAGTGATGAATCCATGAAT	58.195	29.630	0.00	0.00	32.09	2.57
2170	2215	5.068723	TCAGTCAAGGAGTCGTACTCTTTTT	59.931	40.000	12.62	5.26	41.00	1.94
2204	2249	6.806668	TTGTAGAATGGATGGATGACACTA	57.193	37.500	0.00	0.00	0.00	2.74
2216	2261	5.178096	TCTTCATGCCTTTGTAGAATGGA	57.822	39.130	8.57	0.00	0.00	3.41
2463	2510	4.734695	GCAAGCACAAGCAGAAGTAAAACT	60.735	41.667	0.00	0.00	45.49	2.66
2474	2521	2.892852	AGATAAAAGGCAAGCACAAGCA	59.107	40.909	0.00	0.00	45.49	3.91
2505	2552	7.069455	ACCCAACAAGAGCAAACTACTAATTTT	59.931	33.333	0.00	0.00	0.00	1.82
2695	2748	6.307318	CGTAACAAGTACTTTAGAGCAACGAT	59.693	38.462	5.07	0.00	0.00	3.73
2714	2767	4.991687	TGTGTGATTAGTTGCATCGTAACA	59.008	37.500	0.00	0.00	0.00	2.41
2860	2913	2.667473	ATGGTACTTGCGTGTAGACC	57.333	50.000	0.00	0.00	0.00	3.85
2897	2950	9.996554	TTTGTGATTATTCTCAAGTGTCTTCTA	57.003	29.630	3.26	0.00	36.87	2.10
2938	2993	7.973601	TCTTTTTCATTTGAGTTTTTGCCTTC	58.026	30.769	0.00	0.00	0.00	3.46
2939	2994	7.920160	TCTTTTTCATTTGAGTTTTTGCCTT	57.080	28.000	0.00	0.00	0.00	4.35
2941	2996	9.650371	GTAATCTTTTTCATTTGAGTTTTTGCC	57.350	29.630	0.00	0.00	0.00	4.52
3020	3077	5.100344	TGAATCTAGTACGTGACTCCTCT	57.900	43.478	0.00	0.00	39.81	3.69
3139	3197	2.280592	GACGGGTCCTGCGTTGTT	60.281	61.111	0.00	0.00	0.00	2.83
3223	3287	1.173444	ACGCTCACCAGTCGAACTCT	61.173	55.000	0.00	0.00	0.00	3.24
3339	3403	0.980754	TTTCCGGCCCAGATAGCTCA	60.981	55.000	0.00	0.00	0.00	4.26
3452	3516	9.533253	AGAGGTTAATTGACAAACATTTTTCTG	57.467	29.630	2.50	0.00	0.00	3.02
4002	4069	9.230122	TGATGTTGTATGTATGTTTGAACTGAT	57.770	29.630	0.00	0.00	0.00	2.90
4092	4159	5.920273	ACTGAATTGTAATTTCAAACAGCGG	59.080	36.000	22.30	12.19	38.25	5.52
4312	4379	5.637810	TGACGTATGGATCTGTGAAGTTTTC	59.362	40.000	0.00	0.00	0.00	2.29
4318	4385	3.096852	AGGTGACGTATGGATCTGTGAA	58.903	45.455	0.00	0.00	0.00	3.18
4526	4593	1.251251	GTGTGTAGTAGTCGTGGGGT	58.749	55.000	0.00	0.00	0.00	4.95
4536	4603	2.638354	CGGGGGCGTGTGTGTAGTA	61.638	63.158	0.00	0.00	0.00	1.82
4856	4924	0.247460	CTGGTGCAGACGATCTCCAA	59.753	55.000	0.00	0.00	32.44	3.53
4893	4961	0.945265	GAGCCTGCTCATCATCTCGC	60.945	60.000	14.07	0.00	42.31	5.03
5011	5081	0.829333	AGCAGAGTTCCTCGATGCAT	59.171	50.000	0.00	0.00	39.34	3.96
5015	5085	1.066573	CACCAAGCAGAGTTCCTCGAT	60.067	52.381	0.00	0.00	35.36	3.59
5157	5230	8.367911	ACATGTAATCGTGTATCCACTTCATAT	58.632	33.333	0.00	0.00	41.37	1.78
5204	5277	6.096705	TGAAACAATCCACTTCACAGTTTCAT	59.903	34.615	12.20	0.00	44.60	2.57
5386	5462	6.824704	TGAGAAACATGTGCATCAAGATATGA	59.175	34.615	0.00	0.00	43.67	2.15
5568	5644	7.851822	TTTTTGCTATCTTCTTTGCTTTACG	57.148	32.000	0.00	0.00	0.00	3.18
5837	5915	2.158623	TGTCACCTCCAATGCTGAAACT	60.159	45.455	0.00	0.00	0.00	2.66
5871	5949	3.154827	TGATTTCCAAACCAGACTCCC	57.845	47.619	0.00	0.00	0.00	4.30
6002	6080	6.297582	CCCTATTCATCTTCTTCTTCATGCT	58.702	40.000	0.00	0.00	0.00	3.79
6058	6136	1.048601	ACGTGATGAGGTTGTCTGGT	58.951	50.000	0.00	0.00	0.00	4.00
6096	6174	0.179225	CCATGACTTGTACGTTGCGC	60.179	55.000	0.00	0.00	0.00	6.09
6530	6608	3.507411	TGTCCTTAGTTAGTCTGCCACT	58.493	45.455	0.00	0.00	39.41	4.00
6637	6720	8.938906	TGAAACTTAGTCTTTTTAGTGTTCGTT	58.061	29.630	0.00	0.00	0.00	3.85
6728	6812	4.669206	TTCTTTGCTTTTCCTGATGCAA	57.331	36.364	0.00	0.00	42.60	4.08
6774	6858	5.346181	ACTTTTCAGTCCTAGGATGCTAC	57.654	43.478	16.27	1.57	0.00	3.58
6880	6964	8.989980	GCCACTATTAATTCTTAGTATGTCACC	58.010	37.037	0.00	0.00	0.00	4.02
6900	6984	6.472016	TGAGATTTCAGTTGTATTGCCACTA	58.528	36.000	0.00	0.00	0.00	2.74
7140	7227	7.543172	CACTTACCGAATAAGCTTAGTTGTACA	59.457	37.037	17.58	0.00	43.76	2.90
7152	7239	9.077674	GTATCATCATAGCACTTACCGAATAAG	57.922	37.037	5.22	5.22	45.22	1.73

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.